Changes between Initial Version and Version 1 of Ticket #8880


Ignore:
Timestamp:
Apr 20, 2023, 1:37:17 PM (3 years ago)
Author:
Eric Pettersen
Comment:

Reported by Leonardo Lima

Legend:

Unmodified
Added
Removed
Modified

  • Ticket #8880

    • Property Component Unassigned → Third Party
    • Property Owner set to Tristan Croll
    • Property Platform → all
    • Property Project → ChimeraX
    • Property Status new → assigned
    • Property Summary ChimeraX bug report submission → ResidueStepper referencing dead structure

  • Ticket #8880 – Description

    initial v1  
    12311231Done loading forcefield 
    12321232
    1233 > ui tool show "Ramachandran Plot"
    1234 
    1235 > isolde sim start sel
    1236 
    1237 ISOLDE: started sim 
    1238 
    1239 > isolde pepflip sel
    1240 
    1241 Flipping the peptide bond for 1 residues 
    1242 
    1243 > isolde pepflip sel
    1244 
    1245 Flipping the peptide bond for 1 residues 
    1246 
    1247 > isolde pepflip sel
    1248 
    1249 Flipping the peptide bond for 1 residues 
    1250 
    1251 > isolde pepflip sel
    1252 
    1253 Flipping the peptide bond for 1 residues 
    1254 
    1255 > isolde pepflip sel
    1256 
    1257 Flipping the peptide bond for 1 residues 
    1258 
    1259 > isolde sim stop discardTo start
    1260 
    1261 reverting to start 
    1262 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    1263 chains... 
    1264 ISOLDE: stopped sim 
    1265 
    1266 > isolde sim start sel
    1267 
    1268 ISOLDE: started sim 
    1269 
    1270 > isolde pepflip sel
    1271 
    1272 Flipping the peptide bond for 1 residues 
    1273 
    1274 > isolde pepflip sel
    1275 
    1276 Flipping the peptide bond for 1 residues 
    1277 
    1278 > isolde pepflip sel
    1279 
    1280 Flipping the peptide bond for 1 residues 
    1281 
    1282 > isolde pepflip sel
    1283 
    1284 Flipping the peptide bond for 1 residues 
    1285 
    1286 > isolde sim stop discardTo start
    1287 
    1288 reverting to start 
    1289 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    1290 chains... 
    1291 ISOLDE: stopped sim 
    1292 
    1293 > isolde sim start sel
    1294 
    1295 ISOLDE: started sim 
    1296 
    1297 > isolde sim stop
    1298 
    1299 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    1300 chains... 
    1301 ISOLDE: stopped sim 
    1302 
    1303 > volume #1.1.1.2 level 0.3144
    1304 
    1305 > volume #1.1.1.2
    1306 
    1307 > isolde sim start sel
    1308 
    1309 ISOLDE: started sim 
    1310 
    1311 > isolde pepflip sel
    1312 
    1313 Flipping the peptide bond for 1 residues 
    1314 
    1315 > isolde pepflip sel
    1316 
    1317 Flipping the peptide bond for 1 residues 
    1318 
    1319 > isolde pepflip sel
    1320 
    1321 Flipping the peptide bond for 1 residues 
    1322 
    1323 > isolde sim stop discardTo start
    1324 
    1325 reverting to start 
    1326 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    1327 chains... 
    1328 ISOLDE: stopped sim 
    1329 
    1330 > isolde sim start sel
    1331 
    1332 ISOLDE: started sim 
    1333 
    1334 > isolde sim stop discardTo start
    1335 
    1336 reverting to start 
    1337 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    1338 chains... 
    1339 ISOLDE: stopped sim 
    1340 
    1341 > isolde sim start sel
    1342 
    1343 ISOLDE: started sim 
    1344 
    1345 > isolde pepflip sel
    1346 
    1347 Flipping the peptide bond for 1 residues 
    1348 
    1349 > isolde pepflip sel
    1350 
    1351 Flipping the peptide bond for 1 residues 
    1352 
    1353 > isolde pepflip sel
    1354 
    1355 Flipping the peptide bond for 1 residues 
    1356 
    1357 > isolde pepflip sel
    1358 
    1359 Flipping the peptide bond for 1 residues 
    1360 
    1361 > isolde pepflip sel
    1362 
    1363 Flipping the peptide bond for 1 residues 
    1364 
    1365 > isolde pepflip sel
    1366 
    1367 Flipping the peptide bond for 1 residues 
    1368 
    1369 > isolde pepflip sel
    1370 
    1371 Flipping the peptide bond for 1 residues 
    1372 
    1373 > isolde sim stop
    1374 
    1375 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    1376 chains... 
    1377 ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
    1378 standards. 
    1379 ISOLDE: stopped sim 
    1380 
    1381 > isolde sim start sel
    1382 
    1383 ISOLDE: started sim 
    1384 
    1385 > isolde pepflip sel
    1386 
    1387 Flipping the peptide bond for 1 residues 
    1388 
    1389 > isolde pepflip sel
    1390 
    1391 Flipping the peptide bond for 1 residues 
    1392 
    1393 > isolde pepflip sel
    1394 
    1395 Flipping the peptide bond for 1 residues 
    1396 
    1397 > isolde pepflip sel
    1398 
    1399 Flipping the peptide bond for 1 residues 
    1400 
    1401 > isolde pepflip sel
    1402 
    1403 Flipping the peptide bond for 1 residues 
    1404 
    1405 > isolde sim stop
    1406 
    1407 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    1408 chains... 
    1409 ISOLDE: stopped sim 
    1410 
    1411 > isolde sim start sel
    1412 
    1413 ISOLDE: started sim 
    1414 
    1415 > isolde sim stop discardTo start
    1416 
    1417 reverting to start 
    1418 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    1419 chains... 
    1420 ISOLDE: stopped sim 
    1421 
    1422 > isolde sim start sel
    1423 
    1424 ISOLDE: started sim 
    1425 
    1426 > select clear
    1427 
    1428 [Repeated 3 time(s)]
    1429 
    1430 > isolde pepflip sel
    1431 
    1432 Flipping the peptide bond for 1 residues 
    1433 
    1434 > isolde sim stop
    1435 
    1436 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    1437 chains... 
    1438 ISOLDE: stopped sim 
    1439 
    1440 > isolde sim start sel
    1441 
    1442 ISOLDE: started sim 
    1443 
    1444 > isolde pepflip sel
    1445 
    1446 Flipping the peptide bond for 1 residues 
    1447 
    1448 > isolde sim pause
    1449 
    1450 > isolde sim resume
    1451 
    1452 > isolde sim stop
    1453 
    1454 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    1455 chains... 
    1456 ISOLDE: stopped sim 
    1457 
    1458 > isolde sim start sel
    1459 
    1460 ISOLDE: started sim 
    1461 
    1462 > isolde sim stop
    1463 
    1464 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    1465 chains... 
    1466 ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
    1467 standards. 
    1468 ISOLDE: stopped sim 
    1469 
    1470 > isolde sim start sel
    1471 
    1472 ISOLDE: started sim 
    1473 
    1474 > isolde pepflip sel
    1475 
    1476 Flipping the peptide bond for 1 residues 
    1477 
    1478 > isolde sim stop
    1479 
    1480 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    1481 chains... 
    1482 ISOLDE: stopped sim 
    1483 
    1484 > isolde sim start sel
    1485 
    1486 ISOLDE: started sim 
    1487 
    1488 > isolde pepflip sel
    1489 
    1490 Flipping the peptide bond for 1 residues 
    1491 
    1492 > isolde pepflip sel
    1493 
    1494 Flipping the peptide bond for 1 residues 
    1495 
    1496 > isolde pepflip sel
    1497 
    1498 Flipping the peptide bond for 1 residues 
    1499 
    1500 > isolde pepflip sel
    1501 
    1502 Flipping the peptide bond for 1 residues 
    1503 
    1504 > isolde pepflip sel
    1505 
    1506 Flipping the peptide bond for 1 residues 
    1507 
    1508 > isolde pepflip sel
    1509 
    1510 Flipping the peptide bond for 1 residues 
    1511 
    1512 > isolde sim stop
    1513 
    1514 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    1515 chains... 
    1516 ISOLDE: stopped sim 
    1517 
    1518 > isolde sim start sel
    1519 
    1520 ISOLDE: started sim 
    1521 
    1522 > isolde pepflip sel
    1523 
    1524 Flipping the peptide bond for 1 residues 
    1525 
    1526 > isolde pepflip sel
    1527 
    1528 Flipping the peptide bond for 1 residues 
    1529 
    1530 > isolde pepflip sel
    1531 
    1532 Flipping the peptide bond for 1 residues 
    1533 
    1534 > isolde pepflip sel
    1535 
    1536 Flipping the peptide bond for 1 residues 
    1537 
    1538 > select clear
    1539 
    1540 [Repeated 1 time(s)]
    1541 
    1542 > isolde pepflip sel
    1543 
    1544 Flipping the peptide bond for 1 residues 
    1545 
    1546 > isolde pepflip sel
    1547 
    1548 Flipping the peptide bond for 1 residues 
    1549 
    1550 > select clear
    1551 
    1552 > isolde pepflip sel
    1553 
    1554 Flipping the peptide bond for 1 residues 
    1555 
    1556 > isolde pepflip sel
    1557 
    1558 Flipping the peptide bond for 1 residues 
    1559 
    1560 > isolde pepflip sel
    1561 
    1562 Flipping the peptide bond for 1 residues 
    1563 
    1564 > isolde pepflip sel
    1565 
    1566 Flipping the peptide bond for 1 residues 
    1567 
    1568 > isolde pepflip sel
    1569 
    1570 Flipping the peptide bond for 1 residues 
    1571 
    1572 > isolde pepflip sel
    1573 
    1574 Flipping the peptide bond for 1 residues 
    1575 Peptide bond must be mobile in the simulation! 
    1576 
    1577 > isolde pepflip sel
    1578 
    1579 Flipping the peptide bond for 1 residues 
    1580 
    1581 > isolde sim stop
    1582 
    1583 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    1584 chains... 
    1585 ISOLDE: stopped sim 
    1586 
    1587 > isolde sim start sel
    1588 
    1589 ISOLDE: started sim 
    1590 
    1591 > isolde pepflip sel
    1592 
    1593 Flipping the peptide bond for 1 residues 
    1594 
    1595 > isolde sim stop
    1596 
    1597 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    1598 chains... 
    1599 ISOLDE: stopped sim 
    1600 
    1601 > isolde sim start sel
    1602 
    1603 ISOLDE: started sim 
    1604 
    1605 > isolde pepflip sel
    1606 
    1607 Flipping the peptide bond for 1 residues 
    1608 
    1609 > isolde pepflip sel
    1610 
    1611 Flipping the peptide bond for 1 residues 
    1612 
    1613 > isolde pepflip sel
    1614 
    1615 Flipping the peptide bond for 1 residues 
    1616 
    1617 > select clear
    1618 
    1619 > isolde pepflip sel
    1620 
    1621 Flipping the peptide bond for 1 residues 
    1622 
    1623 > isolde pepflip sel
    1624 
    1625 Flipping the peptide bond for 1 residues 
    1626 
    1627 > isolde pepflip sel
    1628 
    1629 Flipping the peptide bond for 1 residues 
    1630 
    1631 > isolde pepflip sel
    1632 
    1633 Flipping the peptide bond for 1 residues 
    1634 
    1635 > isolde pepflip sel
    1636 
    1637 Flipping the peptide bond for 1 residues 
    1638 
    1639 > isolde pepflip sel
    1640 
    1641 Flipping the peptide bond for 1 residues 
    1642 
    1643 > select clear
    1644 
    1645 > isolde pepflip sel
    1646 
    1647 Flipping the peptide bond for 1 residues 
    1648 
    1649 > isolde pepflip sel
    1650 
    1651 Flipping the peptide bond for 1 residues 
    1652 
    1653 > isolde pepflip sel
    1654 
    1655 Flipping the peptide bond for 1 residues 
    1656 
    1657 > isolde pepflip sel
    1658 
    1659 Flipping the peptide bond for 1 residues 
    1660 
    1661 > isolde sim stop
    1662 
    1663 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    1664 chains... 
    1665 ISOLDE: stopped sim 
    1666 
    1667 > select clear
    1668 
    1669 > isolde sim start sel
    1670 
    1671 ISOLDE: started sim 
    1672 
    1673 > select clear
    1674 
    1675 [Repeated 1 time(s)]
    1676 
    1677 > isolde pepflip sel
    1678 
    1679 Flipping the peptide bond for 1 residues 
    1680 
    1681 > isolde pepflip sel
    1682 
    1683 Flipping the peptide bond for 1 residues 
    1684 
    1685 > select clear
    1686 
    1687 [Repeated 1 time(s)]
    1688 
    1689 > isolde pepflip sel
    1690 
    1691 Flipping the peptide bond for 1 residues 
    1692 
    1693 > isolde sim stop
    1694 
    1695 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    1696 chains... 
    1697 ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
    1698 standards. 
    1699 ISOLDE: stopped sim 
    1700 
    1701 > isolde sim start sel
    1702 
    1703 ISOLDE: started sim 
    1704 
    1705 > isolde pepflip sel
    1706 
    1707 Flipping the peptide bond for 1 residues 
    1708 
    1709 > select clear
    1710 
    1711 > isolde pepflip sel
    1712 
    1713 Flipping the peptide bond for 1 residues 
    1714 
    1715 > isolde pepflip sel
    1716 
    1717 Flipping the peptide bond for 1 residues 
    1718 
    1719 > select clear
    1720 
    1721 > isolde pepflip sel
    1722 
    1723 Flipping the peptide bond for 1 residues 
    1724 
    1725 > isolde sim stop discardTo start
    1726 
    1727 reverting to start 
    1728 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    1729 chains... 
    1730 ISOLDE: stopped sim 
    1731 
    1732 > isolde sim start sel
    1733 
    1734 ISOLDE: started sim 
    1735 
    1736 > isolde pepflip sel
    1737 
    1738 Flipping the peptide bond for 1 residues 
    1739 
    1740 > isolde pepflip sel
    1741 
    1742 Flipping the peptide bond for 1 residues 
    1743 
    1744 > isolde pepflip sel
    1745 
    1746 Flipping the peptide bond for 1 residues 
    1747 
    1748 > isolde pepflip sel
    1749 
    1750 Flipping the peptide bond for 1 residues 
    1751 
    1752 > isolde pepflip sel
    1753 
    1754 Flipping the peptide bond for 1 residues 
    1755 
    1756 > isolde pepflip sel
    1757 
    1758 Flipping the peptide bond for 1 residues 
    1759 
    1760 > isolde sim stop
    1761 
    1762 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    1763 chains... 
    1764 ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
    1765 standards. 
    1766 ISOLDE: stopped sim 
    1767 
    1768 > isolde sim start sel
    1769 
    1770 ISOLDE: started sim 
    1771 
    1772 > isolde pepflip sel
    1773 
    1774 Flipping the peptide bond for 1 residues 
    1775 
    1776 > isolde pepflip sel
    1777 
    1778 Flipping the peptide bond for 1 residues 
    1779 
    1780 > isolde pepflip sel
    1781 
    1782 Flipping the peptide bond for 1 residues 
    1783 
    1784 > isolde pepflip sel
    1785 
    1786 Flipping the peptide bond for 1 residues 
    1787 
    1788 > isolde sim stop discardTo start
    1789 
    1790 reverting to start 
    1791 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    1792 chains... 
    1793 ISOLDE: stopped sim 
    1794 
    1795 > isolde sim start sel
    1796 
    1797 ISOLDE: started sim 
    1798 
    1799 > isolde pepflip sel
    1800 
    1801 Flipping the peptide bond for 1 residues 
    1802 
    1803 > isolde pepflip sel
    1804 
    1805 Flipping the peptide bond for 1 residues 
    1806 
    1807 > isolde pepflip sel
    1808 
    1809 Flipping the peptide bond for 1 residues 
    1810 
    1811 > isolde pepflip sel
    1812 
    1813 Flipping the peptide bond for 1 residues 
    1814 
    1815 > isolde pepflip sel
    1816 
    1817 Flipping the peptide bond for 1 residues 
    1818 
    1819 > select clear
    1820 
    1821 > isolde pepflip sel
    1822 
    1823 Flipping the peptide bond for 1 residues 
    1824 
    1825 > isolde sim stop
    1826 
    1827 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    1828 chains... 
    1829 ISOLDE: stopped sim 
    1830 
    1831 > isolde sim start sel
    1832 
    1833 ISOLDE: started sim 
    1834 
    1835 > isolde pepflip sel
    1836 
    1837 Flipping the peptide bond for 1 residues 
    1838 
    1839 > isolde sim stop
    1840 
    1841 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    1842 chains... 
    1843 ISOLDE: stopped sim 
    1844 
    1845 > isolde sim start sel
    1846 
    1847 ISOLDE: started sim 
    1848 
    1849 > isolde pepflip sel
    1850 
    1851 Flipping the peptide bond for 1 residues 
    1852 
    1853 > isolde sim stop
    1854 
    1855 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    1856 chains... 
    1857 ISOLDE: stopped sim 
    1858 
    1859 > isolde sim start sel
    1860 
    1861 ISOLDE: started sim 
    1862 
    1863 > isolde pepflip sel
    1864 
    1865 Flipping the peptide bond for 1 residues 
    1866 
    1867 > isolde pepflip sel
    1868 
    1869 Flipping the peptide bond for 1 residues 
    1870 
    1871 > isolde pepflip sel
    1872 
    1873 Flipping the peptide bond for 1 residues 
    1874 
    1875 > isolde sim stop discardTo start
    1876 
    1877 reverting to start 
    1878 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    1879 chains... 
    1880 ISOLDE: stopped sim 
    1881 
    1882 > isolde sim start sel
    1883 
    1884 ISOLDE: started sim 
    1885 
    1886 > isolde pepflip sel
    1887 
    1888 Flipping the peptide bond for 1 residues 
    1889 
    1890 > isolde pepflip sel
    1891 
    1892 Flipping the peptide bond for 1 residues 
    1893 
    1894 > isolde pepflip sel
    1895 
    1896 Flipping the peptide bond for 1 residues 
    1897 
    1898 > isolde pepflip sel
    1899 
    1900 Flipping the peptide bond for 1 residues 
    1901 
    1902 > isolde pepflip sel
    1903 
    1904 Flipping the peptide bond for 1 residues 
    1905 
    1906 > select clear
    1907 
    1908 > isolde pepflip sel
    1909 
    1910 Flipping the peptide bond for 1 residues 
    1911 
    1912 > isolde sim stop discardTo start
    1913 
    1914 reverting to start 
    1915 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    1916 chains... 
    1917 ISOLDE: stopped sim 
    1918 
    1919 > isolde sim start sel
    1920 
    1921 ISOLDE: started sim 
    1922 
    1923 > isolde pepflip sel
    1924 
    1925 Flipping the peptide bond for 1 residues 
    1926 
    1927 > isolde pepflip sel
    1928 
    1929 Flipping the peptide bond for 1 residues 
    1930 
    1931 > isolde pepflip sel
    1932 
    1933 Flipping the peptide bond for 1 residues 
    1934 
    1935 > isolde pepflip sel
    1936 
    1937 Flipping the peptide bond for 1 residues 
    1938 
    1939 > isolde pepflip sel
    1940 
    1941 Flipping the peptide bond for 1 residues 
    1942 
    1943 > isolde pepflip sel
    1944 
    1945 Flipping the peptide bond for 1 residues 
    1946 
    1947 > isolde pepflip sel
    1948 
    1949 Flipping the peptide bond for 1 residues 
    1950 
    1951 > isolde pepflip sel
    1952 
    1953 Flipping the peptide bond for 1 residues 
    1954 
    1955 > isolde pepflip sel
    1956 
    1957 Flipping the peptide bond for 1 residues 
    1958 
    1959 > isolde pepflip sel
    1960 
    1961 Flipping the peptide bond for 1 residues 
    1962 
    1963 > isolde pepflip sel
    1964 
    1965 Flipping the peptide bond for 1 residues 
    1966 
    1967 > isolde pepflip sel
    1968 
    1969 Flipping the peptide bond for 1 residues 
    1970 
    1971 > isolde pepflip sel
    1972 
    1973 Flipping the peptide bond for 1 residues 
    1974 
    1975 > isolde pepflip sel
    1976 
    1977 Flipping the peptide bond for 1 residues 
    1978 
    1979 > isolde pepflip sel
    1980 
    1981 Flipping the peptide bond for 1 residues 
    1982 
    1983 > isolde pepflip sel
    1984 
    1985 Flipping the peptide bond for 1 residues 
    1986 
    1987 > isolde pepflip sel
    1988 
    1989 Flipping the peptide bond for 1 residues 
    1990 
    1991 > isolde pepflip sel
    1992 
    1993 Flipping the peptide bond for 1 residues 
    1994 
    1995 > isolde pepflip sel
    1996 
    1997 Flipping the peptide bond for 1 residues 
    1998 
    1999 > isolde pepflip sel
    2000 
    2001 Flipping the peptide bond for 1 residues 
    2002 
    2003 > isolde pepflip sel
    2004 
    2005 Flipping the peptide bond for 1 residues 
    2006 Peptide bond must be mobile in the simulation! 
    2007 
    2008 > isolde sim stop discardTo start
    2009 
    2010 reverting to start 
    2011 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    2012 chains... 
    2013 ISOLDE: stopped sim 
    2014 
    2015 > isolde sim start sel
    2016 
    2017 ISOLDE: started sim 
    2018 
    2019 > isolde pepflip sel
    2020 
    2021 Flipping the peptide bond for 1 residues 
    2022 
    2023 > isolde pepflip sel
    2024 
    2025 Flipping the peptide bond for 1 residues 
    2026 
    2027 > isolde pepflip sel
    2028 
    2029 Flipping the peptide bond for 1 residues 
    2030 
    2031 > isolde pepflip sel
    2032 
    2033 Flipping the peptide bond for 1 residues 
    2034 
    2035 > isolde pepflip sel
    2036 
    2037 Flipping the peptide bond for 1 residues 
    2038 
    2039 > isolde pepflip sel
    2040 
    2041 Flipping the peptide bond for 1 residues 
    2042 
    2043 > isolde pepflip sel
    2044 
    2045 Flipping the peptide bond for 1 residues 
    2046 
    2047 > isolde pepflip sel
    2048 
    2049 Flipping the peptide bond for 1 residues 
    2050 
    2051 > isolde pepflip sel
    2052 
    2053 Flipping the peptide bond for 1 residues 
    2054 
    2055 > isolde sim stop
    2056 
    2057 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    2058 chains... 
    2059 ISOLDE: Corrected atom nomenclature of 3 residues in model #1.2 to IUPAC-IUB
    2060 standards. 
    2061 ISOLDE: stopped sim 
    2062 
    2063 > isolde sim start sel
    2064 
    2065 ISOLDE: started sim 
    2066 
    2067 > isolde pepflip sel
    2068 
    2069 Flipping the peptide bond for 1 residues 
    2070 
    2071 > isolde sim stop
    2072 
    2073 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    2074 chains... 
    2075 ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
    2076 standards. 
    2077 ISOLDE: stopped sim 
    2078 
    2079 > isolde sim start sel
    2080 
    2081 ISOLDE: started sim 
    2082 
    2083 > isolde pepflip sel
    2084 
    2085 Flipping the peptide bond for 1 residues 
    2086 
    2087 > select clear
    2088 
    2089 > isolde pepflip sel
    2090 
    2091 Flipping the peptide bond for 1 residues 
    2092 
    2093 > isolde pepflip sel
    2094 
    2095 Flipping the peptide bond for 1 residues 
    2096 
    2097 > select clear
    2098 
    2099 > isolde pepflip sel
    2100 
    2101 Flipping the peptide bond for 1 residues 
    2102 
    2103 > select clear
    2104 
    2105 > isolde pepflip sel
    2106 
    2107 Flipping the peptide bond for 1 residues 
    2108 
    2109 > select clear
    2110 
    2111 > isolde pepflip sel
    2112 
    2113 Flipping the peptide bond for 1 residues 
    2114 
    2115 > select clear
    2116 
    2117 > isolde pepflip sel
    2118 
    2119 Flipping the peptide bond for 1 residues 
    2120 
    2121 > isolde sim stop
    2122 
    2123 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    2124 chains... 
    2125 ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
    2126 standards. 
    2127 ISOLDE: stopped sim 
    2128 
    2129 > isolde sim start sel
    2130 
    2131 ISOLDE: started sim 
    2132 
    2133 > isolde pepflip sel
    2134 
    2135 Flipping the peptide bond for 1 residues 
    2136 
    2137 > isolde pepflip sel
    2138 
    2139 Flipping the peptide bond for 1 residues 
    2140 
    2141 > isolde pepflip sel
    2142 
    2143 Flipping the peptide bond for 1 residues 
    2144 
    2145 > isolde pepflip sel
    2146 
    2147 Flipping the peptide bond for 1 residues 
    2148 
    2149 > select clear
    2150 
    2151 [Repeated 1 time(s)]
    2152 
    2153 > isolde pepflip sel
    2154 
    2155 Flipping the peptide bond for 1 residues 
    2156 
    2157 > isolde pepflip sel
    2158 
    2159 Flipping the peptide bond for 1 residues 
    2160 
    2161 > isolde pepflip sel
    2162 
    2163 Flipping the peptide bond for 1 residues 
    2164 
    2165 > isolde pepflip sel
    2166 
    2167 Flipping the peptide bond for 1 residues 
    2168 
    2169 > isolde pepflip sel
    2170 
    2171 Flipping the peptide bond for 1 residues 
    2172 
    2173 > isolde pepflip sel
    2174 
    2175 Flipping the peptide bond for 1 residues 
    2176 
    2177 > isolde pepflip sel
    2178 
    2179 Flipping the peptide bond for 1 residues 
    2180 
    2181 > isolde pepflip sel
    2182 
    2183 Flipping the peptide bond for 1 residues 
    2184 
    2185 > isolde pepflip sel
    2186 
    2187 Flipping the peptide bond for 1 residues 
    2188 
    2189 > isolde pepflip sel
    2190 
    2191 Flipping the peptide bond for 1 residues 
    2192 
    2193 > isolde pepflip sel
    2194 
    2195 Flipping the peptide bond for 1 residues 
    2196 
    2197 > isolde pepflip sel
    2198 
    2199 Flipping the peptide bond for 1 residues 
    2200 
    2201 > isolde pepflip sel
    2202 
    2203 Flipping the peptide bond for 1 residues 
    2204 
    2205 > isolde pepflip sel
    2206 
    2207 Flipping the peptide bond for 1 residues 
    2208 
    2209 > isolde pepflip sel
    2210 
    2211 Flipping the peptide bond for 1 residues 
    2212 
    2213 > isolde pepflip sel
    2214 
    2215 Flipping the peptide bond for 1 residues 
    2216 
    2217 > isolde pepflip sel
    2218 
    2219 Flipping the peptide bond for 1 residues 
    2220 
    2221 > isolde pepflip sel
    2222 
    2223 Flipping the peptide bond for 1 residues 
    2224 
    2225 > isolde sim stop
    2226 
    2227 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    2228 chains... 
    2229 ISOLDE: stopped sim 
    2230 
    2231 > save D:/Rafa/OneDrive/Documentos/ubuntuStorage/krsp/5OPT-refinement/40S-wt-
    2232 > refinement/5-40S-KSRP-wt-Second-steps.cxs
    2233 
    2234 Taking snapshot of stepper: 40S-wt-concat.pdb 
    2235 
    2236 > save D:/Rafa/OneDrive/Documentos/ubuntuStorage/krsp/5OPT-refinement/40S-wt-
    2237 > refinement/5-40S-KSRP-wt-Second-steps.pdb models #1
    2238 
    2239 > cd "D:/Rafa/OneDrive/Documentos/ubuntuStorage/krsp/5OPT-refinement/40S-wt-
    2240 > refinement/New folder"
    2241 
    2242 Current working directory is:
    2243 D:\Rafa\OneDrive\Documentos\ubuntuStorage\krsp\5OPT-refinement\40S-wt-
    2244 refinement\New folder 
    2245 
    2246 > isolde sim start sel
    2247 
    2248 ISOLDE: started sim 
    2249 
    2250 > select clear
    2251 
    2252 > isolde pepflip sel
    2253 
    2254 Flipping the peptide bond for 1 residues 
    2255 
    2256 > isolde pepflip sel
    2257 
    2258 Flipping the peptide bond for 1 residues 
    2259 
    2260 > isolde pepflip sel
    2261 
    2262 Flipping the peptide bond for 1 residues 
    2263 
    2264 > isolde pepflip sel
    2265 
    2266 Flipping the peptide bond for 1 residues 
    2267 
    2268 > select clear
    2269 
    2270 > isolde pepflip sel
    2271 
    2272 Flipping the peptide bond for 1 residues 
    2273 
    2274 > select clear
    2275 
    2276 > isolde pepflip sel
    2277 
    2278 Flipping the peptide bond for 1 residues 
    2279 
    2280 > isolde sim stop
    2281 
    2282 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    2283 chains... 
    2284 ISOLDE: stopped sim 
    2285 
    2286 > isolde sim start sel
    2287 
    2288 ISOLDE: started sim 
    2289 
    2290 > select clear
    2291 
    2292 > isolde pepflip sel
    2293 
    2294 Flipping the peptide bond for 1 residues 
    2295 
    2296 > isolde pepflip sel
    2297 
    2298 Flipping the peptide bond for 1 residues 
    2299 
    2300 > isolde pepflip sel
    2301 
    2302 Flipping the peptide bond for 1 residues 
    2303 
    2304 > isolde pepflip sel
    2305 
    2306 Flipping the peptide bond for 1 residues 
    2307 
    2308 > isolde sim stop
    2309 
    2310 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    2311 chains... 
    2312 ISOLDE: stopped sim 
    2313 
    2314 > isolde sim start sel
    2315 
    2316 ISOLDE: started sim 
    2317 
    2318 > isolde pepflip sel
    2319 
    2320 Flipping the peptide bond for 1 residues 
    2321 
    2322 > isolde sim stop
    2323 
    2324 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    2325 chains... 
    2326 ISOLDE: Corrected atom nomenclature of 2 residues in model #1.2 to IUPAC-IUB
    2327 standards. 
    2328 ISOLDE: stopped sim 
    2329 
    2330 > isolde sim start sel
    2331 
    2332 ISOLDE: started sim 
    2333 
    2334 > isolde pepflip sel
    2335 
    2336 Flipping the peptide bond for 1 residues 
    2337 
    2338 > isolde pepflip sel
    2339 
    2340 Flipping the peptide bond for 1 residues 
    2341 
    2342 > isolde pepflip sel
    2343 
    2344 Flipping the peptide bond for 1 residues 
    2345 
    2346 > isolde pepflip sel
    2347 
    2348 Flipping the peptide bond for 1 residues 
    2349 
    2350 > isolde pepflip sel
    2351 
    2352 Flipping the peptide bond for 1 residues 
    2353 
    2354 > isolde pepflip sel
    2355 
    2356 Flipping the peptide bond for 1 residues 
    2357 
    2358 > isolde sim stop
    2359 
    2360 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    2361 chains... 
    2362 ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
    2363 standards. 
    2364 ISOLDE: stopped sim 
    2365 
    2366 > isolde sim start sel
    2367 
    2368 ISOLDE: started sim 
    2369 
    2370 > select clear
    2371 
    2372 > isolde pepflip sel
    2373 
    2374 Flipping the peptide bond for 1 residues 
    2375 
    2376 > isolde pepflip sel
    2377 
    2378 Flipping the peptide bond for 1 residues 
    2379 
    2380 > isolde pepflip sel
    2381 
    2382 Flipping the peptide bond for 1 residues 
    2383 
    2384 > isolde pepflip sel
    2385 
    2386 Flipping the peptide bond for 1 residues 
    2387 
    2388 > isolde pepflip sel
    2389 
    2390 Flipping the peptide bond for 1 residues 
    2391 
    2392 > isolde pepflip sel
    2393 
    2394 Flipping the peptide bond for 1 residues 
    2395 
    2396 > isolde pepflip sel
    2397 
    2398 Flipping the peptide bond for 1 residues 
    2399 
    2400 > isolde pepflip sel
    2401 
    2402 Flipping the peptide bond for 1 residues 
    2403 
    2404 > isolde pepflip sel
    2405 
    2406 Flipping the peptide bond for 1 residues 
    2407 
    2408 > isolde pepflip sel
    2409 
    2410 Flipping the peptide bond for 1 residues 
    2411 
    2412 > view #1/k:149
    2413 
    2414 > select #1/k:149
    2415 
    2416 10 atoms, 9 bonds, 1 residue, 1 model selected 
    2417 
    2418 > isolde sim stop discardTo start
    2419 
    2420 reverting to start 
    2421 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    2422 chains... 
    2423 ISOLDE: stopped sim 
    2424 
    2425 > isolde sim start sel
    2426 
    2427 ISOLDE: started sim 
    2428 
    2429 > isolde pepflip sel
    2430 
    2431 Flipping the peptide bond for 1 residues 
    2432 
    2433 > isolde pepflip sel
    2434 
    2435 Flipping the peptide bond for 1 residues 
    2436 
    2437 > isolde pepflip sel
    2438 
    2439 Flipping the peptide bond for 1 residues 
    2440 
    2441 > isolde pepflip sel
    2442 
    2443 Flipping the peptide bond for 1 residues 
    2444 
    2445 > isolde pepflip sel
    2446 
    2447 Flipping the peptide bond for 1 residues 
    2448 
    2449 > isolde sim stop
    2450 
    2451 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    2452 chains... 
    2453 ISOLDE: Corrected atom nomenclature of 3 residues in model #1.2 to IUPAC-IUB
    2454 standards. 
    2455 ISOLDE: stopped sim 
    2456 
    2457 > isolde sim start sel
    2458 
    2459 ISOLDE: started sim 
    2460 
    2461 > isolde sim stop discardTo start
    2462 
    2463 reverting to start 
    2464 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    2465 chains... 
    2466 ISOLDE: stopped sim 
    2467 
    2468 > isolde sim start sel
    2469 
    2470 ISOLDE: started sim 
    2471 
    2472 > isolde pepflip sel
    2473 
    2474 Flipping the peptide bond for 1 residues 
    2475 
    2476 > isolde pepflip sel
    2477 
    2478 Flipping the peptide bond for 1 residues 
    2479 
    2480 > isolde pepflip sel
    2481 
    2482 Flipping the peptide bond for 1 residues 
    2483 
    2484 > isolde sim stop
    2485 
    2486 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    2487 chains... 
    2488 ISOLDE: stopped sim 
    2489 
    2490 > isolde sim start sel
    2491 
    2492 ISOLDE: started sim 
    2493 
    2494 > isolde pepflip sel
    2495 
    2496 Flipping the peptide bond for 1 residues 
    2497 
    2498 > isolde pepflip sel
    2499 
    2500 Flipping the peptide bond for 1 residues 
    2501 
    2502 > isolde sim stop
    2503 
    2504 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    2505 chains... 
    2506 ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
    2507 standards. 
    2508 ISOLDE: stopped sim 
    2509 
    2510 > isolde sim start sel
    2511 
    2512 ISOLDE: started sim 
    2513 
    2514 > select clear
    2515 
    2516 > isolde pepflip sel
    2517 
    2518 Flipping the peptide bond for 1 residues 
    2519 
    2520 > isolde pepflip sel
    2521 
    2522 Flipping the peptide bond for 1 residues 
    2523 
    2524 > isolde pepflip sel
    2525 
    2526 Flipping the peptide bond for 1 residues 
    2527 
    2528 > isolde pepflip sel
    2529 
    2530 Flipping the peptide bond for 1 residues 
    2531 
    2532 > isolde pepflip sel
    2533 
    2534 Flipping the peptide bond for 1 residues 
    2535 
    2536 > isolde pepflip sel
    2537 
    2538 Flipping the peptide bond for 1 residues 
    2539 
    2540 > isolde pepflip sel
    2541 
    2542 Flipping the peptide bond for 1 residues 
    2543 
    2544 > isolde pepflip sel
    2545 
    2546 Flipping the peptide bond for 1 residues 
    2547 
    2548 > isolde pepflip sel
    2549 
    2550 Flipping the peptide bond for 1 residues 
    2551 
    2552 > isolde pepflip sel
    2553 
    2554 Flipping the peptide bond for 1 residues 
    2555 
    2556 > isolde pepflip sel
    2557 
    2558 Flipping the peptide bond for 1 residues 
    2559 
    2560 > isolde pepflip sel
    2561 
    2562 Flipping the peptide bond for 1 residues 
    2563 
    2564 > isolde sim stop
    2565 
    2566 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    2567 chains... 
    2568 ISOLDE: stopped sim 
    2569 
    2570 > isolde sim start sel
    2571 
    2572 ISOLDE: started sim 
    2573 
    2574 > isolde pepflip sel
    2575 
    2576 Flipping the peptide bond for 1 residues 
    2577 
    2578 > isolde pepflip sel
    2579 
    2580 Flipping the peptide bond for 1 residues 
    2581 
    2582 > isolde pepflip sel
    2583 
    2584 Flipping the peptide bond for 1 residues 
    2585 
    2586 > isolde pepflip sel
    2587 
    2588 Flipping the peptide bond for 1 residues 
    2589 
    2590 > isolde pepflip sel
    2591 
    2592 Flipping the peptide bond for 1 residues 
    2593 
    2594 > isolde pepflip sel
    2595 
    2596 Flipping the peptide bond for 1 residues 
    2597 
    2598 > isolde pepflip sel
    2599 
    2600 Flipping the peptide bond for 1 residues 
    2601 
    2602 > isolde pepflip sel
    2603 
    2604 Flipping the peptide bond for 1 residues 
    2605 
    2606 > isolde pepflip sel
    2607 
    2608 Flipping the peptide bond for 1 residues 
    2609 
    2610 > isolde pepflip sel
    2611 
    2612 Flipping the peptide bond for 1 residues 
    2613 
    2614 > isolde pepflip sel
    2615 
    2616 Flipping the peptide bond for 1 residues 
    2617 
    2618 > isolde pepflip sel
    2619 
    2620 Flipping the peptide bond for 1 residues 
    2621 
    2622 > select clear
    2623 
    2624 > isolde pepflip sel
    2625 
    2626 Flipping the peptide bond for 1 residues 
    2627 
    2628 > isolde pepflip sel
    2629 
    2630 Flipping the peptide bond for 1 residues 
    2631 
    2632 > isolde pepflip sel
    2633 
    2634 Flipping the peptide bond for 1 residues 
    2635 
    2636 > isolde sim stop
    2637 
    2638 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    2639 chains... 
    2640 ISOLDE: stopped sim 
    2641 
    2642 > isolde sim start sel
    2643 
    2644 ISOLDE: started sim 
    2645 
    2646 > isolde pepflip sel
    2647 
    2648 Flipping the peptide bond for 1 residues 
    2649 
    2650 > isolde pepflip sel
    2651 
    2652 Flipping the peptide bond for 1 residues 
    2653 
    2654 > select clear
    2655 
    2656 > isolde pepflip sel
    2657 
    2658 Flipping the peptide bond for 1 residues 
    2659 
    2660 > isolde pepflip sel
    2661 
    2662 Flipping the peptide bond for 1 residues 
    2663 
    2664 > isolde pepflip sel
    2665 
    2666 Flipping the peptide bond for 1 residues 
    2667 
    2668 > isolde pepflip sel
    2669 
    2670 Flipping the peptide bond for 1 residues 
    2671 
    2672 > isolde sim stop discardTo start
    2673 
    2674 reverting to start 
    2675 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    2676 chains... 
    2677 ISOLDE: stopped sim 
    2678 
    2679 > isolde sim start sel
    2680 
    2681 ISOLDE: started sim 
    2682 
    2683 > isolde pepflip sel
    2684 
    2685 Flipping the peptide bond for 1 residues 
    2686 
    2687 > isolde pepflip sel
    2688 
    2689 Flipping the peptide bond for 1 residues 
    2690 
    2691 > isolde pepflip sel
    2692 
    2693 Flipping the peptide bond for 1 residues 
    2694 
    2695 > isolde pepflip sel
    2696 
    2697 Flipping the peptide bond for 1 residues 
    2698 
    2699 > isolde pepflip sel
    2700 
    2701 Flipping the peptide bond for 1 residues 
    2702 
    2703 > isolde sim stop discardTo start
    2704 
    2705 reverting to start 
    2706 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    2707 chains... 
    2708 ISOLDE: stopped sim 
    2709 
    2710 > select #1/a:93
    2711 
    2712 22 atoms, 21 bonds, 1 residue, 1 model selected 
    2713 
    2714 > isolde sim start sel
    2715 
    2716 ISOLDE: started sim 
    2717 
    2718 > isolde sim stop discardTo start
    2719 
    2720 reverting to start 
    2721 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    2722 chains... 
    2723 ISOLDE: stopped sim 
    2724 
    2725 > isolde sim start sel
    2726 
    2727 ISOLDE: started sim 
    2728 
    2729 > select #1/a:93
    2730 
    2731 22 atoms, 21 bonds, 1 residue, 1 model selected 
    2732 
    2733 > isolde pepflip sel
    2734 
    2735 Flipping the peptide bond for 1 residues 
    2736 
    2737 > isolde pepflip sel
    2738 
    2739 Flipping the peptide bond for 1 residues 
    2740 
    2741 > isolde sim stop
    2742 
    2743 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    2744 chains... 
    2745 ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
    2746 standards. 
    2747 ISOLDE: stopped sim 
    2748 
    2749 > isolde sim start sel
    2750 
    2751 ISOLDE: started sim 
    2752 
    2753 > isolde pepflip sel
    2754 
    2755 Flipping the peptide bond for 1 residues 
    2756 
    2757 > isolde pepflip sel
    2758 
    2759 Flipping the peptide bond for 1 residues 
    2760 
    2761 > isolde pepflip sel
    2762 
    2763 Flipping the peptide bond for 1 residues 
    2764 
    2765 > isolde pepflip sel
    2766 
    2767 Flipping the peptide bond for 1 residues 
    2768 
    2769 > isolde pepflip sel
    2770 
    2771 Flipping the peptide bond for 1 residues 
    2772 
    2773 > select clear
    2774 
    2775 > isolde pepflip sel
    2776 
    2777 Flipping the peptide bond for 1 residues 
    2778 
    2779 > isolde pepflip sel
    2780 
    2781 Flipping the peptide bond for 1 residues 
    2782 
    2783 > isolde pepflip sel
    2784 
    2785 Flipping the peptide bond for 1 residues 
    2786 
    2787 > isolde pepflip sel
    2788 
    2789 Flipping the peptide bond for 1 residues 
    2790 
    2791 > isolde sim stop
    2792 
    2793 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    2794 chains... 
    2795 ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
    2796 standards. 
    2797 ISOLDE: stopped sim 
    2798 
    2799 > isolde sim start sel
    2800 
    2801 ISOLDE: started sim 
    2802 
    2803 > isolde pepflip sel
    2804 
    2805 Flipping the peptide bond for 1 residues 
    2806 
    2807 > isolde sim stop
    2808 
    2809 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    2810 chains... 
    2811 ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
    2812 standards. 
    2813 ISOLDE: stopped sim 
    2814 
    2815 > isolde sim start sel
    2816 
    2817 ISOLDE: started sim 
    2818 
    2819 > isolde pepflip sel
    2820 
    2821 Flipping the peptide bond for 1 residues 
    2822 
    2823 > select clear
    2824 
    2825 > isolde pepflip sel
    2826 
    2827 Flipping the peptide bond for 1 residues 
    2828 
    2829 > select clear
    2830 
    2831 > isolde pepflip sel
    2832 
    2833 Flipping the peptide bond for 1 residues 
    2834 
    2835 > isolde pepflip sel
    2836 
    2837 Flipping the peptide bond for 1 residues 
    2838 Unable to flip peptide bond after 50 rounds. Giving up. 
    2839 
    2840 > isolde pepflip sel
    2841 
    2842 Flipping the peptide bond for 1 residues 
    2843 
    2844 > isolde pepflip sel
    2845 
    2846 Flipping the peptide bond for 1 residues 
    2847 
    2848 > isolde pepflip sel
    2849 
    2850 Flipping the peptide bond for 1 residues 
    2851 
    2852 > isolde pepflip sel
    2853 
    2854 Flipping the peptide bond for 1 residues 
    2855 
    2856 > isolde pepflip sel
    2857 
    2858 Flipping the peptide bond for 1 residues 
    2859 
    2860 > isolde pepflip sel
    2861 
    2862 Flipping the peptide bond for 1 residues 
    2863 
    2864 > isolde pepflip sel
    2865 
    2866 Flipping the peptide bond for 1 residues 
    2867 
    2868 > select clear
    2869 
    2870 > isolde pepflip sel
    2871 
    2872 Flipping the peptide bond for 1 residues 
    2873 
    2874 > select clear
    2875 
    2876 > isolde pepflip sel
    2877 
    2878 Flipping the peptide bond for 1 residues 
    2879 
    2880 > isolde pepflip sel
    2881 
    2882 Flipping the peptide bond for 1 residues 
    2883 
    2884 > isolde pepflip sel
    2885 
    2886 Flipping the peptide bond for 1 residues 
    2887 
    2888 > isolde pepflip sel
    2889 
    2890 Flipping the peptide bond for 1 residues 
    2891 
    2892 > select clear
    2893 
    2894 [Repeated 1 time(s)]
    2895 
    2896 > isolde pepflip sel
    2897 
    2898 Flipping the peptide bond for 1 residues 
    2899 
    2900 > isolde pepflip sel
    2901 
    2902 Flipping the peptide bond for 1 residues 
    2903 
    2904 > select clear
    2905 
    2906 > isolde pepflip sel
    2907 
    2908 Flipping the peptide bond for 1 residues 
    2909 
    2910 > isolde sim stop
    2911 
    2912 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    2913 chains... 
    2914 ISOLDE: stopped sim 
    2915 
    2916 > isolde sim start sel
    2917 
    2918 ISOLDE: started sim 
    2919 
    2920 > isolde pepflip sel
    2921 
    2922 Flipping the peptide bond for 1 residues 
    2923 
    2924 > isolde pepflip sel
    2925 
    2926 Flipping the peptide bond for 1 residues 
    2927 
    2928 > isolde pepflip sel
    2929 
    2930 Flipping the peptide bond for 1 residues 
    2931 
    2932 > isolde pepflip sel
    2933 
    2934 Flipping the peptide bond for 1 residues 
    2935 
    2936 > isolde pepflip sel
    2937 
    2938 Flipping the peptide bond for 1 residues 
    2939 
    2940 > isolde pepflip sel
    2941 
    2942 Flipping the peptide bond for 1 residues 
    2943 
    2944 > select clear
    2945 
    2946 > isolde pepflip sel
    2947 
    2948 Flipping the peptide bond for 1 residues 
    2949 
    2950 > isolde pepflip sel
    2951 
    2952 Flipping the peptide bond for 1 residues 
    2953 
    2954 > isolde pepflip sel
    2955 
    2956 Flipping the peptide bond for 1 residues 
    2957 
    2958 > isolde sim stop
    2959 
    2960 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    2961 chains... 
    2962 ISOLDE: stopped sim 
    2963 
    2964 > isolde sim start sel
    2965 
    2966 ISOLDE: started sim 
    2967 
    2968 > isolde pepflip sel
    2969 
    2970 Flipping the peptide bond for 1 residues 
    2971 
    2972 > isolde sim stop
    2973 
    2974 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    2975 chains... 
    2976 ISOLDE: stopped sim 
    2977 
    2978 > isolde sim start sel
    2979 
    2980 ISOLDE: started sim 
    2981 
    2982 > isolde pepflip sel
    2983 
    2984 Flipping the peptide bond for 1 residues 
    2985 
    2986 > isolde pepflip sel
    2987 
    2988 Flipping the peptide bond for 1 residues 
    2989 
    2990 > isolde pepflip sel
    2991 
    2992 Flipping the peptide bond for 1 residues 
    2993 
    2994 > isolde pepflip sel
    2995 
    2996 Flipping the peptide bond for 1 residues 
    2997 
    2998 > isolde pepflip sel
    2999 
    3000 Flipping the peptide bond for 1 residues 
    3001 
    3002 > isolde pepflip sel
    3003 
    3004 Flipping the peptide bond for 1 residues 
    3005 
    3006 > isolde pepflip sel
    3007 
    3008 Flipping the peptide bond for 1 residues 
    3009 
    3010 > isolde pepflip sel
    3011 
    3012 Flipping the peptide bond for 1 residues 
    3013 
    3014 > isolde pepflip sel
    3015 
    3016 Flipping the peptide bond for 1 residues 
    3017 
    3018 > isolde pepflip sel
    3019 
    3020 Flipping the peptide bond for 1 residues 
    3021 
    3022 > isolde pepflip sel
    3023 
    3024 Flipping the peptide bond for 1 residues 
    3025 
    3026 > isolde pepflip sel
    3027 
    3028 Flipping the peptide bond for 1 residues 
    3029 
    3030 > isolde pepflip sel
    3031 
    3032 Flipping the peptide bond for 1 residues 
    3033 
    3034 > isolde pepflip sel
    3035 
    3036 Flipping the peptide bond for 1 residues 
    3037 
    3038 > isolde pepflip sel
    3039 
    3040 Flipping the peptide bond for 1 residues 
    3041 
    3042 > isolde pepflip sel
    3043 
    3044 Flipping the peptide bond for 1 residues 
    3045 
    3046 > isolde pepflip sel
    3047 
    3048 Flipping the peptide bond for 1 residues 
    3049 
    3050 > isolde pepflip sel
    3051 
    3052 Flipping the peptide bond for 1 residues 
    3053 
    3054 > isolde pepflip sel
    3055 
    3056 Flipping the peptide bond for 1 residues 
    3057 
    3058 > isolde pepflip sel
    3059 
    3060 Flipping the peptide bond for 1 residues 
    3061 
    3062 > select clear
    3063 
    3064 > isolde pepflip sel
    3065 
    3066 Flipping the peptide bond for 1 residues 
    3067 
    3068 > isolde pepflip sel
    3069 
    3070 Flipping the peptide bond for 1 residues 
    3071 
    3072 > isolde pepflip sel
    3073 
    3074 Flipping the peptide bond for 1 residues 
    3075 
    3076 > isolde pepflip sel
    3077 
    3078 Flipping the peptide bond for 1 residues 
    3079 
    3080 > isolde pepflip sel
    3081 
    3082 Flipping the peptide bond for 1 residues 
    3083 
    3084 > isolde pepflip sel
    3085 
    3086 Flipping the peptide bond for 1 residues 
    3087 
    3088 > isolde pepflip sel
    3089 
    3090 Flipping the peptide bond for 1 residues 
    3091 
    3092 > select clear
    3093 
    3094 > isolde pepflip sel
    3095 
    3096 Flipping the peptide bond for 1 residues 
    3097 
    3098 > isolde pepflip sel
    3099 
    3100 Flipping the peptide bond for 1 residues 
    3101 
    3102 > isolde pepflip sel
    3103 
    3104 Flipping the peptide bond for 1 residues 
    3105 
    3106 > isolde sim stop
    3107 
    3108 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    3109 chains... 
    3110 ISOLDE: stopped sim 
    3111 
    3112 > isolde sim start sel
    3113 
    3114 ISOLDE: started sim 
    3115 
    3116 > isolde sim stop
    3117 
    3118 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    3119 chains... 
    3120 ISOLDE: stopped sim 
    3121 
    3122 > isolde sim start sel
    3123 
    3124 ISOLDE: started sim 
    3125 
    3126 > isolde pepflip sel
    3127 
    3128 Flipping the peptide bond for 1 residues 
    3129 
    3130 > isolde pepflip sel
    3131 
    3132 Flipping the peptide bond for 1 residues 
    3133 
    3134 > isolde pepflip sel
    3135 
    3136 Flipping the peptide bond for 1 residues 
    3137 
    3138 > isolde sim stop
    3139 
    3140 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    3141 chains... 
    3142 ISOLDE: stopped sim 
    3143 
    3144 > isolde sim start sel
    3145 
    3146 ISOLDE: started sim 
    3147 
    3148 > isolde pepflip sel
    3149 
    3150 Flipping the peptide bond for 1 residues 
    3151 
    3152 > isolde pepflip sel
    3153 
    3154 Flipping the peptide bond for 1 residues 
    3155 
    3156 > isolde pepflip sel
    3157 
    3158 Flipping the peptide bond for 1 residues 
    3159 
    3160 > isolde pepflip sel
    3161 
    3162 Flipping the peptide bond for 1 residues 
    3163 
    3164 > isolde pepflip sel
    3165 
    3166 Flipping the peptide bond for 1 residues 
    3167 
    3168 > isolde pepflip sel
    3169 
    3170 Flipping the peptide bond for 1 residues 
    3171 
    3172 > isolde pepflip sel
    3173 
    3174 Flipping the peptide bond for 1 residues 
    3175 
    3176 > isolde sim stop
    3177 
    3178 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    3179 chains... 
    3180 ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
    3181 standards. 
    3182 ISOLDE: stopped sim 
    3183 
    3184 > isolde sim start sel
    3185 
    3186 ISOLDE: started sim 
    3187 
    3188 > isolde pepflip sel
    3189 
    3190 Flipping the peptide bond for 1 residues 
    3191 
    3192 > isolde pepflip sel
    3193 
    3194 Flipping the peptide bond for 1 residues 
    3195 
    3196 > isolde pepflip sel
    3197 
    3198 Flipping the peptide bond for 1 residues 
    3199 
    3200 > isolde pepflip sel
    3201 
    3202 Flipping the peptide bond for 1 residues 
    3203 
    3204 > isolde pepflip sel
    3205 
    3206 Flipping the peptide bond for 1 residues 
    3207 
    3208 > isolde pepflip sel
    3209 
    3210 Flipping the peptide bond for 1 residues 
    3211 
    3212 > isolde pepflip sel
    3213 
    3214 Flipping the peptide bond for 1 residues 
    3215 
    3216 > isolde pepflip sel
    3217 
    3218 Flipping the peptide bond for 1 residues 
    3219 
    3220 > isolde pepflip sel
    3221 
    3222 Flipping the peptide bond for 1 residues 
    3223 
    3224 > isolde pepflip sel
    3225 
    3226 Flipping the peptide bond for 1 residues 
    3227 
    3228 > isolde pepflip sel
    3229 
    3230 Flipping the peptide bond for 1 residues 
    3231 
    3232 > isolde pepflip sel
    3233 
    3234 Flipping the peptide bond for 1 residues 
    3235 
    3236 > isolde pepflip sel
    3237 
    3238 Flipping the peptide bond for 1 residues 
    3239 
    3240 > isolde pepflip sel
    3241 
    3242 Flipping the peptide bond for 1 residues 
    3243 
    3244 > isolde pepflip sel
    3245 
    3246 Flipping the peptide bond for 1 residues 
    3247 
    3248 > isolde pepflip sel
    3249 
    3250 Flipping the peptide bond for 1 residues 
    3251 
    3252 > isolde pepflip sel
    3253 
    3254 Flipping the peptide bond for 1 residues 
    3255 
    3256 > isolde pepflip sel
    3257 
    3258 Flipping the peptide bond for 1 residues 
    3259 
    3260 > isolde pepflip sel
    3261 
    3262 Flipping the peptide bond for 1 residues 
    3263 
    3264 > isolde sim stop discardTo start
    3265 
    3266 reverting to start 
    3267 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    3268 chains... 
    3269 ISOLDE: stopped sim 
    3270 
    3271 > isolde sim start sel
    3272 
    3273 ISOLDE: started sim 
    3274 
    3275 > isolde pepflip sel
    3276 
    3277 Flipping the peptide bond for 1 residues 
    3278 
    3279 > isolde sim stop discardTo start
    3280 
    3281 reverting to start 
    3282 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    3283 chains... 
    3284 ISOLDE: stopped sim 
    3285 
    3286 > isolde sim start sel
    3287 
    3288 ISOLDE: started sim 
    3289 
    3290 > isolde pepflip sel
    3291 
    3292 Flipping the peptide bond for 1 residues 
    3293 
    3294 > isolde pepflip sel
    3295 
    3296 Flipping the peptide bond for 1 residues 
    3297 
    3298 > isolde pepflip sel
    3299 
    3300 Flipping the peptide bond for 1 residues 
    3301 
    3302 > isolde pepflip sel
    3303 
    3304 Flipping the peptide bond for 1 residues 
    3305 
    3306 > select clear
    3307 
    3308 > isolde pepflip sel
    3309 
    3310 Flipping the peptide bond for 1 residues 
    3311 
    3312 > isolde pepflip sel
    3313 
    3314 Flipping the peptide bond for 1 residues 
    3315 
    3316 > isolde pepflip sel
    3317 
    3318 Flipping the peptide bond for 1 residues 
    3319 
    3320 > isolde sim stop
    3321 
    3322 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    3323 chains... 
    3324 ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
    3325 standards. 
    3326 ISOLDE: stopped sim 
    3327 
    3328 > isolde sim start sel
    3329 
    3330 ISOLDE: started sim 
    3331 
    3332 > isolde pepflip sel
    3333 
    3334 Flipping the peptide bond for 1 residues 
    3335 
    3336 > isolde pepflip sel
    3337 
    3338 Flipping the peptide bond for 1 residues 
    3339 
    3340 > select clear
    3341 
    3342 > isolde sim pause
    3343 
    3344 > isolde sim resume
    3345 
    3346 > isolde pepflip sel
    3347 
    3348 Flipping the peptide bond for 1 residues 
    3349 
    3350 > isolde pepflip sel
    3351 
    3352 Flipping the peptide bond for 1 residues 
    3353 
    3354 > isolde pepflip sel
    3355 
    3356 Flipping the peptide bond for 1 residues 
    3357 Unable to flip peptide bond after 50 rounds. Giving up. 
    3358 
    3359 > isolde pepflip sel
    3360 
    3361 Flipping the peptide bond for 1 residues 
    3362 
    3363 > select clear
    3364 
    3365 > isolde pepflip sel
    3366 
    3367 Flipping the peptide bond for 1 residues 
    3368 
    3369 > isolde sim stop
    3370 
    3371 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    3372 chains... 
    3373 ISOLDE: Corrected atom nomenclature of 4 residues in model #1.2 to IUPAC-IUB
    3374 standards. 
    3375 ISOLDE: stopped sim 
    3376 
    3377 > isolde sim start sel
    3378 
    3379 ISOLDE: started sim 
    3380 
    3381 > isolde pepflip sel
    3382 
    3383 Flipping the peptide bond for 1 residues 
    3384 
    3385 > isolde pepflip sel
    3386 
    3387 Flipping the peptide bond for 1 residues 
    3388 
    3389 > isolde pepflip sel
    3390 
    3391 Flipping the peptide bond for 1 residues 
    3392 
    3393 > isolde sim stop
    3394 
    3395 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    3396 chains... 
    3397 ISOLDE: stopped sim 
    3398 
    3399 > isolde sim start sel
    3400 
    3401 ISOLDE: started sim 
    3402 
    3403 > isolde pepflip sel
    3404 
    3405 Flipping the peptide bond for 1 residues 
    3406 
    3407 > isolde pepflip sel
    3408 
    3409 Flipping the peptide bond for 1 residues 
    3410 
    3411 > isolde pepflip sel
    3412 
    3413 Flipping the peptide bond for 1 residues 
    3414 
    3415 > isolde pepflip sel
    3416 
    3417 Flipping the peptide bond for 1 residues 
    3418 
    3419 > isolde pepflip sel
    3420 
    3421 Flipping the peptide bond for 1 residues 
    3422 
    3423 > isolde pepflip sel
    3424 
    3425 Flipping the peptide bond for 1 residues 
    3426 
    3427 > isolde pepflip sel
    3428 
    3429 Flipping the peptide bond for 1 residues 
    3430 
    3431 > isolde pepflip sel
    3432 
    3433 Flipping the peptide bond for 1 residues 
    3434 
    3435 > isolde pepflip sel
    3436 
    3437 Flipping the peptide bond for 1 residues 
    3438 
    3439 > isolde sim stop discardTo start
    3440 
    3441 reverting to start 
    3442 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    3443 chains... 
    3444 ISOLDE: stopped sim 
    3445 
    3446 > isolde sim start sel
    3447 
    3448 ISOLDE: started sim 
    3449 
    3450 > isolde pepflip sel
    3451 
    3452 Flipping the peptide bond for 1 residues 
    3453 
    3454 > isolde pepflip sel
    3455 
    3456 Flipping the peptide bond for 1 residues 
    3457 
    3458 > select clear
    3459 
    3460 > isolde pepflip sel
    3461 
    3462 Flipping the peptide bond for 1 residues 
    3463 
    3464 > isolde pepflip sel
    3465 
    3466 Flipping the peptide bond for 1 residues 
    3467 
    3468 > isolde pepflip sel
    3469 
    3470 Flipping the peptide bond for 1 residues 
    3471 
    3472 > isolde pepflip sel
    3473 
    3474 Flipping the peptide bond for 1 residues 
    3475 
    3476 > isolde pepflip sel
    3477 
    3478 Flipping the peptide bond for 1 residues 
    3479 
    3480 > isolde pepflip sel
    3481 
    3482 Flipping the peptide bond for 1 residues 
    3483 
    3484 > isolde pepflip sel
    3485 
    3486 Flipping the peptide bond for 1 residues 
    3487 
    3488 > isolde pepflip sel
    3489 
    3490 Flipping the peptide bond for 1 residues 
    3491 
    3492 > isolde pepflip sel
    3493 
    3494 Flipping the peptide bond for 1 residues 
    3495 
    3496 > isolde sim stop
    3497 
    3498 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    3499 chains... 
    3500 ISOLDE: stopped sim 
    3501 
    3502 > isolde sim start sel
    3503 
    3504 ISOLDE: started sim 
    3505 
    3506 > isolde sim stop discardTo start
    3507 
    3508 reverting to start 
    3509 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    3510 chains... 
    3511 ISOLDE: stopped sim 
    3512 
    3513 > isolde sim start sel
    3514 
    3515 ISOLDE: started sim 
    3516 
    3517 > isolde pepflip sel
    3518 
    3519 Flipping the peptide bond for 1 residues 
    3520 
    3521 > isolde pepflip sel
    3522 
    3523 Flipping the peptide bond for 1 residues 
    3524 
    3525 > isolde pepflip sel
    3526 
    3527 Flipping the peptide bond for 1 residues 
    3528 
    3529 > isolde pepflip sel
    3530 
    3531 Flipping the peptide bond for 1 residues 
    3532 
    3533 > isolde pepflip sel
    3534 
    3535 Flipping the peptide bond for 1 residues 
    3536 
    3537 > isolde sim stop discardTo start
    3538 
    3539 reverting to start 
    3540 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    3541 chains... 
    3542 ISOLDE: stopped sim 
    3543 
    3544 > isolde sim start sel
    3545 
    3546 ISOLDE: started sim 
    3547 
    3548 > isolde pepflip sel
    3549 
    3550 Flipping the peptide bond for 1 residues 
    3551 
    3552 > isolde pepflip sel
    3553 
    3554 Flipping the peptide bond for 1 residues 
    3555 
    3556 > isolde pepflip sel
    3557 
    3558 Flipping the peptide bond for 1 residues 
    3559 
    3560 > isolde pepflip sel
    3561 
    3562 Flipping the peptide bond for 1 residues 
    3563 
    3564 > isolde pepflip sel
    3565 
    3566 Flipping the peptide bond for 1 residues 
    3567 
    3568 > isolde pepflip sel
    3569 
    3570 Flipping the peptide bond for 1 residues 
    3571 
    3572 > isolde pepflip sel
    3573 
    3574 Flipping the peptide bond for 1 residues 
    3575 
    3576 > isolde pepflip sel
    3577 
    3578 Flipping the peptide bond for 1 residues 
    3579 
    3580 > isolde pepflip sel
    3581 
    3582 Flipping the peptide bond for 1 residues 
    3583 
    3584 > isolde pepflip sel
    3585 
    3586 Flipping the peptide bond for 1 residues 
    3587 
    3588 > isolde pepflip sel
    3589 
    3590 Flipping the peptide bond for 1 residues 
    3591 
    3592 > select clear
    3593 
    3594 > isolde pepflip sel
    3595 
    3596 Flipping the peptide bond for 1 residues 
    3597 
    3598 > select clear
    3599 
    3600 > isolde pepflip sel
    3601 
    3602 Flipping the peptide bond for 1 residues 
    3603 
    3604 > isolde pepflip sel
    3605 
    3606 Flipping the peptide bond for 1 residues 
    3607 
    3608 > isolde sim stop
    3609 
    3610 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    3611 chains... 
    3612 ISOLDE: stopped sim 
    3613 
    3614 > isolde sim start sel
    3615 
    3616 ISOLDE: started sim 
    3617 
    3618 > isolde pepflip sel
    3619 
    3620 Flipping the peptide bond for 1 residues 
    3621 
    3622 > isolde pepflip sel
    3623 
    3624 Flipping the peptide bond for 1 residues 
    3625 
    3626 > isolde pepflip sel
    3627 
    3628 Flipping the peptide bond for 1 residues 
    3629 
    3630 > isolde pepflip sel
    3631 
    3632 Flipping the peptide bond for 1 residues 
    3633 
    3634 > isolde sim stop
    3635 
    3636 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    3637 chains... 
    3638 ISOLDE: stopped sim 
    3639 
    3640 > isolde sim start sel
    3641 
    3642 ISOLDE: started sim 
    3643 
    3644 > isolde pepflip sel
    3645 
    3646 Flipping the peptide bond for 1 residues 
    3647 
    3648 > isolde pepflip sel
    3649 
    3650 Flipping the peptide bond for 1 residues 
    3651 
    3652 > isolde pepflip sel
    3653 
    3654 Flipping the peptide bond for 1 residues 
    3655 
    3656 > isolde pepflip sel
    3657 
    3658 Flipping the peptide bond for 1 residues 
    3659 
    3660 > isolde pepflip sel
    3661 
    3662 Flipping the peptide bond for 1 residues 
    3663 
    3664 > isolde pepflip sel
    3665 
    3666 Flipping the peptide bond for 1 residues 
    3667 
    3668 > isolde pepflip sel
    3669 
    3670 Flipping the peptide bond for 1 residues 
    3671 
    3672 > isolde pepflip sel
    3673 
    3674 Flipping the peptide bond for 1 residues 
    3675 
    3676 > isolde sim stop discardTo start
    3677 
    3678 reverting to start 
    3679 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    3680 chains... 
    3681 ISOLDE: stopped sim 
    3682 
    3683 > isolde sim start sel
    3684 
    3685 ISOLDE: started sim 
    3686 
    3687 > isolde pepflip sel
    3688 
    3689 Flipping the peptide bond for 1 residues 
    3690 
    3691 > isolde pepflip sel
    3692 
    3693 Flipping the peptide bond for 1 residues 
    3694 
    3695 > isolde pepflip sel
    3696 
    3697 Flipping the peptide bond for 1 residues 
    3698 
    3699 > isolde pepflip sel
    3700 
    3701 Flipping the peptide bond for 1 residues 
    3702 
    3703 > isolde sim stop discardTo start
    3704 
    3705 reverting to start 
    3706 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    3707 chains... 
    3708 ISOLDE: stopped sim 
    3709 
    3710 > isolde sim start sel
    3711 
    3712 ISOLDE: started sim 
    3713 
    3714 > isolde sim stop
    3715 
    3716 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    3717 chains... 
    3718 ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
    3719 standards. 
    3720 ISOLDE: stopped sim 
    3721 
    3722 > isolde sim start sel
    3723 
    3724 ISOLDE: started sim 
    3725 
    3726 > isolde pepflip sel
    3727 
    3728 Flipping the peptide bond for 1 residues 
    3729 
    3730 > select clear
    3731 
    3732 > isolde pepflip sel
    3733 
    3734 Flipping the peptide bond for 1 residues 
    3735 
    3736 > isolde pepflip sel
    3737 
    3738 Flipping the peptide bond for 1 residues 
    3739 
    3740 > isolde pepflip sel
    3741 
    3742 Flipping the peptide bond for 1 residues 
    3743 
    3744 > isolde pepflip sel
    3745 
    3746 Flipping the peptide bond for 1 residues 
    3747 
    3748 > isolde pepflip sel
    3749 
    3750 Flipping the peptide bond for 1 residues 
    3751 
    3752 > isolde pepflip sel
    3753 
    3754 Flipping the peptide bond for 1 residues 
    3755 
    3756 > isolde pepflip sel
    3757 
    3758 Flipping the peptide bond for 1 residues 
    3759 
    3760 > isolde pepflip sel
    3761 
    3762 Flipping the peptide bond for 1 residues 
    3763 
    3764 > isolde sim stop
    3765 
    3766 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    3767 chains... 
    3768 ISOLDE: Corrected atom nomenclature of 2 residues in model #1.2 to IUPAC-IUB
    3769 standards. 
    3770 ISOLDE: stopped sim 
    3771 
    3772 > isolde sim start sel
    3773 
    3774 ISOLDE: started sim 
    3775 
    3776 > isolde pepflip sel
    3777 
    3778 Flipping the peptide bond for 1 residues 
    3779 
    3780 > isolde pepflip sel
    3781 
    3782 Flipping the peptide bond for 1 residues 
    3783 
    3784 > isolde pepflip sel
    3785 
    3786 Flipping the peptide bond for 1 residues 
    3787 
    3788 > isolde pepflip sel
    3789 
    3790 Flipping the peptide bond for 1 residues 
    3791 
    3792 > isolde pepflip sel
    3793 
    3794 Flipping the peptide bond for 1 residues 
    3795 
    3796 > isolde pepflip sel
    3797 
    3798 Flipping the peptide bond for 1 residues 
    3799 
    3800 > isolde pepflip sel
    3801 
    3802 Flipping the peptide bond for 1 residues 
    3803 
    3804 > select clear
    3805 
    3806 > isolde pepflip sel
    3807 
    3808 Flipping the peptide bond for 1 residues 
    3809 
    3810 > isolde pepflip sel
    3811 
    3812 Flipping the peptide bond for 1 residues 
    3813 
    3814 > isolde pepflip sel
    3815 
    3816 Flipping the peptide bond for 1 residues 
    3817 
    3818 > isolde pepflip sel
    3819 
    3820 Flipping the peptide bond for 1 residues 
    3821 
    3822 > isolde pepflip sel
    3823 
    3824 Flipping the peptide bond for 1 residues 
    3825 Unable to flip peptide bond after 50 rounds. Giving up. 
    3826 
    3827 > isolde pepflip sel
    3828 
    3829 Flipping the peptide bond for 1 residues 
    3830 
    3831 > isolde pepflip sel
    3832 
    3833 Flipping the peptide bond for 1 residues 
    3834 
    3835 > isolde pepflip sel
    3836 
    3837 Flipping the peptide bond for 1 residues 
    3838 Unable to flip peptide bond after 50 rounds. Giving up. 
    3839 
    3840 > isolde pepflip sel
    3841 
    3842 Flipping the peptide bond for 1 residues 
    3843 
    3844 > isolde pepflip sel
    3845 
    3846 Flipping the peptide bond for 1 residues 
    3847 
    3848 > isolde pepflip sel
    3849 
    3850 Flipping the peptide bond for 1 residues 
    3851 Unable to flip peptide bond after 50 rounds. Giving up. 
    3852 
    3853 > isolde cisflip sel
    3854 
    3855 Performing cis<\-->trans flip for 1 residues 
    3856 
    3857 > isolde pepflip sel
    3858 
    3859 Flipping the peptide bond for 1 residues 
    3860 
    3861 > isolde pepflip sel
    3862 
    3863 Flipping the peptide bond for 1 residues 
    3864 
    3865 > isolde sim stop
    3866 
    3867 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    3868 chains... 
    3869 ISOLDE: stopped sim 
    3870 
    3871 > isolde sim start sel
    3872 
    3873 ISOLDE: started sim 
    3874 
    3875 > isolde pepflip sel
    3876 
    3877 Flipping the peptide bond for 1 residues 
    3878 
    3879 > isolde pepflip sel
    3880 
    3881 Flipping the peptide bond for 1 residues 
    3882 Unable to flip peptide bond after 50 rounds. Giving up. 
    3883 
    3884 > isolde sim stop
    3885 
    3886 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    3887 chains... 
    3888 ISOLDE: Corrected atom nomenclature of 3 residues in model #1.2 to IUPAC-IUB
    3889 standards. 
    3890 ISOLDE: stopped sim 
    3891 
    3892 > isolde sim start sel
    3893 
    3894 ISOLDE: started sim 
    3895 
    3896 > isolde pepflip sel
    3897 
    3898 Flipping the peptide bond for 1 residues 
    3899 
    3900 > isolde pepflip sel
    3901 
    3902 Flipping the peptide bond for 1 residues 
    3903 
    3904 > isolde pepflip sel
    3905 
    3906 Flipping the peptide bond for 1 residues 
    3907 
    3908 > select clear
    3909 
    3910 > isolde pepflip sel
    3911 
    3912 Flipping the peptide bond for 1 residues 
    3913 
    3914 > isolde pepflip sel
    3915 
    3916 Flipping the peptide bond for 1 residues 
    3917 
    3918 > isolde pepflip sel
    3919 
    3920 Flipping the peptide bond for 1 residues 
    3921 Unable to flip peptide bond after 50 rounds. Giving up. 
    3922 
    3923 > isolde pepflip sel
    3924 
    3925 Flipping the peptide bond for 1 residues 
    3926 
    3927 > isolde pepflip sel
    3928 
    3929 Flipping the peptide bond for 1 residues 
    3930 
    3931 > isolde sim stop discardTo start
    3932 
    3933 reverting to start 
    3934 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    3935 chains... 
    3936 ISOLDE: stopped sim 
    3937 
    3938 > isolde sim start sel
    3939 
    3940 ISOLDE: started sim 
    3941 
    3942 > isolde pepflip sel
    3943 
    3944 Flipping the peptide bond for 1 residues 
    3945 
    3946 > isolde pepflip sel
    3947 
    3948 Flipping the peptide bond for 1 residues 
    3949 
    3950 > isolde pepflip sel
    3951 
    3952 Flipping the peptide bond for 1 residues 
    3953 
    3954 > isolde pepflip sel
    3955 
    3956 Flipping the peptide bond for 1 residues 
    3957 
    3958 > isolde pepflip sel
    3959 
    3960 Flipping the peptide bond for 1 residues 
    3961 
    3962 > isolde pepflip sel
    3963 
    3964 Flipping the peptide bond for 1 residues 
    3965 
    3966 > isolde pepflip sel
    3967 
    3968 Flipping the peptide bond for 1 residues 
    3969 
    3970 > isolde pepflip sel
    3971 
    3972 Flipping the peptide bond for 1 residues 
    3973 
    3974 > isolde pepflip sel
    3975 
    3976 Flipping the peptide bond for 1 residues 
    3977 
    3978 > isolde pepflip sel
    3979 
    3980 Flipping the peptide bond for 1 residues 
    3981 
    3982 > isolde pepflip sel
    3983 
    3984 Flipping the peptide bond for 1 residues 
    3985 
    3986 > isolde pepflip sel
    3987 
    3988 Flipping the peptide bond for 1 residues 
    3989 
    3990 > isolde pepflip sel
    3991 
    3992 Flipping the peptide bond for 1 residues 
    3993 
    3994 > isolde pepflip sel
    3995 
    3996 Flipping the peptide bond for 1 residues 
    3997 
    3998 > isolde pepflip sel
    3999 
    4000 Flipping the peptide bond for 1 residues 
    4001 
    4002 > isolde pepflip sel
    4003 
    4004 Flipping the peptide bond for 1 residues 
    4005 Unable to flip peptide bond after 50 rounds. Giving up. 
    4006 
    4007 > isolde cisflip sel
    4008 
    4009 Performing cis<\-->trans flip for 1 residues 
    4010 
    4011 > isolde cisflip sel
    4012 
    4013 Performing cis<\-->trans flip for 1 residues 
    4014 
    4015 > select clear
    4016 
    4017 > isolde pepflip sel
    4018 
    4019 Flipping the peptide bond for 1 residues 
    4020 
    4021 > isolde pepflip sel
    4022 
    4023 Flipping the peptide bond for 1 residues 
    4024 
    4025 > isolde sim stop
    4026 
    4027 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    4028 chains... 
    4029 ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
    4030 standards. 
    4031 ISOLDE: stopped sim 
    4032 
    4033 > isolde sim start sel
    4034 
    4035 ISOLDE: started sim 
    4036 
    4037 > isolde pepflip sel
    4038 
    4039 Flipping the peptide bond for 1 residues 
    4040 
    4041 > isolde pepflip sel
    4042 
    4043 Flipping the peptide bond for 1 residues 
    4044 
    4045 > isolde pepflip sel
    4046 
    4047 Flipping the peptide bond for 1 residues 
    4048 
    4049 > isolde pepflip sel
    4050 
    4051 Flipping the peptide bond for 1 residues 
    4052 
    4053 > isolde pepflip sel
    4054 
    4055 Flipping the peptide bond for 1 residues 
    4056 
    4057 > isolde pepflip sel
    4058 
    4059 Flipping the peptide bond for 1 residues 
    4060 
    4061 > isolde pepflip sel
    4062 
    4063 Flipping the peptide bond for 1 residues 
    4064 
    4065 > isolde pepflip sel
    4066 
    4067 Flipping the peptide bond for 1 residues 
    4068 
    4069 > isolde pepflip sel
    4070 
    4071 Flipping the peptide bond for 1 residues 
    4072 
    4073 > isolde pepflip sel
    4074 
    4075 Flipping the peptide bond for 1 residues 
    4076 
    4077 > isolde pepflip sel
    4078 
    4079 Flipping the peptide bond for 1 residues 
    4080 
    4081 > isolde pepflip sel
    4082 
    4083 Flipping the peptide bond for 1 residues 
    4084 
    4085 > isolde pepflip sel
    4086 
    4087 Flipping the peptide bond for 1 residues 
    4088 
    4089 > isolde pepflip sel
    4090 
    4091 Flipping the peptide bond for 1 residues 
    4092 
    4093 > isolde pepflip sel
    4094 
    4095 Flipping the peptide bond for 1 residues 
    4096 Unable to flip peptide bond after 50 rounds. Giving up. 
    4097 
    4098 > isolde sim stop
    4099 
    4100 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    4101 chains... 
    4102 ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
    4103 standards. 
    4104 ISOLDE: stopped sim 
    4105 
    4106 > isolde sim start sel
    4107 
    4108 ISOLDE: started sim 
    4109 
    4110 > isolde pepflip sel
    4111 
    4112 Flipping the peptide bond for 1 residues 
    4113 
    4114 > isolde pepflip sel
    4115 
    4116 Flipping the peptide bond for 1 residues 
    4117 
    4118 > isolde sim stop
    4119 
    4120 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    4121 chains... 
    4122 ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
    4123 standards. 
    4124 ISOLDE: stopped sim 
    4125 
    4126 > isolde sim start sel
    4127 
    4128 ISOLDE: started sim 
    4129 
    4130 > isolde sim stop
    4131 
    4132 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    4133 chains... 
    4134 ISOLDE: Corrected atom nomenclature of 2 residues in model #1.2 to IUPAC-IUB
    4135 standards. 
    4136 ISOLDE: stopped sim 
    4137 
    4138 > isolde sim start sel
    4139 
    4140 ISOLDE: started sim 
    4141 
    4142 > isolde pepflip sel
    4143 
    4144 Flipping the peptide bond for 1 residues 
    4145 
    4146 > isolde pepflip sel
    4147 
    4148 Flipping the peptide bond for 1 residues 
    4149 
    4150 > isolde pepflip sel
    4151 
    4152 Flipping the peptide bond for 1 residues 
    4153 
    4154 > isolde sim stop
    4155 
    4156 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    4157 chains... 
    4158 ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
    4159 standards. 
    4160 ISOLDE: stopped sim 
    4161 
    4162 > isolde sim start sel
    4163 
    4164 ISOLDE: started sim 
    4165 
    4166 > isolde pepflip sel
    4167 
    4168 Flipping the peptide bond for 1 residues 
    4169 
    4170 > isolde pepflip sel
    4171 
    4172 Flipping the peptide bond for 1 residues 
    4173 
    4174 > isolde sim stop
    4175 
    4176 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    4177 chains... 
    4178 ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
    4179 standards. 
    4180 ISOLDE: stopped sim 
    4181 
    4182 > isolde sim start sel
    4183 
    4184 ISOLDE: started sim 
    4185 
    4186 > isolde pepflip sel
    4187 
    4188 Flipping the peptide bond for 1 residues 
    4189 
    4190 > isolde sim stop
    4191 
    4192 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    4193 chains... 
    4194 ISOLDE: stopped sim 
    4195 
    4196 > isolde pepflip sel
    4197 
    4198 Flipping the peptide bond for 1 residues 
    4199 ISOLDE: started sim 
    4200 
    4201 > isolde pepflip sel
    4202 
    4203 Flipping the peptide bond for 1 residues 
    4204 
    4205 > isolde sim stop
    4206 
    4207 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    4208 chains... 
    4209 ISOLDE: Corrected atom nomenclature of 2 residues in model #1.2 to IUPAC-IUB
    4210 standards. 
    4211 ISOLDE: stopped sim 
    4212 
    4213 > isolde sim start sel
    4214 
    4215 ISOLDE: started sim 
    4216 
    4217 > isolde pepflip sel
    4218 
    4219 Flipping the peptide bond for 1 residues 
    4220 
    4221 > isolde pepflip sel
    4222 
    4223 Flipping the peptide bond for 1 residues 
    4224 
    4225 > isolde pepflip sel
    4226 
    4227 Flipping the peptide bond for 1 residues 
    4228 
    4229 > isolde pepflip sel
    4230 
    4231 Flipping the peptide bond for 1 residues 
    4232 
    4233 > isolde sim stop
    4234 
    4235 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    4236 chains... 
    4237 ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
    4238 standards. 
    4239 ISOLDE: stopped sim 
    4240 
    4241 > isolde sim start sel
    4242 
    4243 ISOLDE: started sim 
    4244 
    4245 > isolde pepflip sel
    4246 
    4247 Flipping the peptide bond for 1 residues 
    4248 
    4249 > isolde sim stop
    4250 
    4251 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    4252 chains... 
    4253 ISOLDE: stopped sim 
    4254 
    4255 > isolde pepflip sel
    4256 
    4257 Flipping the peptide bond for 1 residues 
    4258 ISOLDE: started sim 
    4259 
    4260 > isolde pepflip sel
    4261 
    4262 Flipping the peptide bond for 1 residues 
    4263 
    4264 > isolde pepflip sel
    4265 
    4266 Flipping the peptide bond for 1 residues 
    4267 
    4268 > isolde pepflip sel
    4269 
    4270 Flipping the peptide bond for 1 residues 
    4271 
    4272 > isolde pepflip sel
    4273 
    4274 Flipping the peptide bond for 1 residues 
    4275 
    4276 > isolde pepflip sel
    4277 
    4278 Flipping the peptide bond for 1 residues 
    4279 
    4280 > isolde sim stop
    4281 
    4282 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    4283 chains... 
    4284 ISOLDE: stopped sim 
    4285 
    4286 > save D:/Rafa/OneDrive/Documentos/ubuntuStorage/krsp/5OPT-refinement/40S-wt-
    4287 > refinement/6-40S-KSRP-wt-Second-steps.pdb models #1
    4288 
    4289 > save D:/Rafa/OneDrive/Documentos/ubuntuStorage/krsp/5OPT-refinement/40S-wt-
    4290 > refinement/6-40S-KSRP-wt-Second-steps.cxs
    4291 
    4292 Taking snapshot of stepper: 40S-wt-concat.pdb 
    4293 
    4294 > isolde sim start sel
    4295 
    4296 ISOLDE: started sim 
    4297 
    4298 > isolde sim stop
    4299 
    4300 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    4301 chains... 
    4302 ISOLDE: stopped sim 
    4303 
    4304 > isolde sim start sel
    4305 
    4306 ISOLDE: started sim 
    4307 
    4308 > isolde pepflip sel
    4309 
    4310 Flipping the peptide bond for 1 residues 
    4311 
    4312 > isolde pepflip sel
    4313 
    4314 Flipping the peptide bond for 1 residues 
    4315 
    4316 > isolde pepflip sel
    4317 
    4318 Flipping the peptide bond for 1 residues 
    4319 
    4320 > isolde pepflip sel
    4321 
    4322 Flipping the peptide bond for 1 residues 
    4323 
    4324 > isolde pepflip sel
    4325 
    4326 Flipping the peptide bond for 1 residues 
    4327 
    4328 > isolde pepflip sel
    4329 
    4330 Flipping the peptide bond for 1 residues 
    4331 
    4332 > isolde pepflip sel
    4333 
    4334 Flipping the peptide bond for 1 residues 
    4335 
    4336 > isolde pepflip sel
    4337 
    4338 Flipping the peptide bond for 1 residues 
    4339 
    4340 > isolde pepflip sel
    4341 
    4342 Flipping the peptide bond for 1 residues 
    4343 
    4344 > isolde pepflip sel
    4345 
    4346 Flipping the peptide bond for 1 residues 
    4347 
    4348 > isolde pepflip sel
    4349 
    4350 Flipping the peptide bond for 1 residues 
    4351 
    4352 > isolde pepflip sel
    4353 
    4354 Flipping the peptide bond for 1 residues 
    4355 
    4356 > isolde pepflip sel
    4357 
    4358 Flipping the peptide bond for 1 residues 
    4359 
    4360 > isolde pepflip sel
    4361 
    4362 Flipping the peptide bond for 1 residues 
    4363 
    4364 > isolde pepflip sel
    4365 
    4366 Flipping the peptide bond for 1 residues 
    4367 
    4368 > isolde pepflip sel
    4369 
    4370 Flipping the peptide bond for 1 residues 
    4371 
    4372 > isolde pepflip sel
    4373 
    4374 Flipping the peptide bond for 1 residues 
    4375 
    4376 > isolde pepflip sel
    4377 
    4378 Flipping the peptide bond for 1 residues 
    4379 
    4380 > isolde sim stop
    4381 
    4382 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    4383 chains... 
    4384 ISOLDE: Corrected atom nomenclature of 2 residues in model #1.2 to IUPAC-IUB
    4385 standards. 
    4386 ISOLDE: stopped sim 
    4387 
    4388 > isolde sim start sel
    4389 
    4390 ISOLDE: started sim 
    4391 
    4392 > select clear
    4393 
    4394 > isolde pepflip sel
    4395 
    4396 Flipping the peptide bond for 1 residues 
    4397 
    4398 > isolde pepflip sel
    4399 
    4400 Flipping the peptide bond for 1 residues 
    4401 
    4402 > isolde pepflip sel
    4403 
    4404 Flipping the peptide bond for 1 residues 
    4405 
    4406 > select clear
    4407 
    4408 > isolde pepflip sel
    4409 
    4410 Flipping the peptide bond for 1 residues 
    4411 
    4412 > isolde pepflip sel
    4413 
    4414 Flipping the peptide bond for 1 residues 
    4415 
    4416 > isolde pepflip sel
    4417 
    4418 Flipping the peptide bond for 1 residues 
    4419 
    4420 > isolde pepflip sel
    4421 
    4422 Flipping the peptide bond for 1 residues 
    4423 
    4424 > isolde pepflip sel
    4425 
    4426 Flipping the peptide bond for 1 residues 
    4427 
    4428 > isolde pepflip sel
    4429 
    4430 Flipping the peptide bond for 1 residues 
    4431 
    4432 > isolde pepflip sel
    4433 
    4434 Flipping the peptide bond for 1 residues 
    4435 
    4436 > isolde pepflip sel
    4437 
    4438 Flipping the peptide bond for 1 residues 
    4439 
    4440 > isolde pepflip sel
    4441 
    4442 Flipping the peptide bond for 1 residues 
    4443 
    4444 > isolde pepflip sel
    4445 
    4446 Flipping the peptide bond for 1 residues 
    4447 
    4448 > isolde pepflip sel
    4449 
    4450 Flipping the peptide bond for 1 residues 
    4451 
    4452 > isolde pepflip sel
    4453 
    4454 Flipping the peptide bond for 1 residues 
    4455 
    4456 > isolde pepflip sel
    4457 
    4458 Flipping the peptide bond for 1 residues 
    4459 
    4460 > isolde sim stop
    4461 
    4462 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    4463 chains... 
    4464 ISOLDE: stopped sim 
    4465 
    4466 > isolde sim start sel
    4467 
    4468 ISOLDE: started sim 
    4469 
    4470 > isolde pepflip sel
    4471 
    4472 Flipping the peptide bond for 1 residues 
    4473 
    4474 > isolde sim stop
    4475 
    4476 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    4477 chains... 
    4478 ISOLDE: stopped sim 
    4479 
    4480 > isolde sim start sel
    4481 
    4482 ISOLDE: started sim 
    4483 
    4484 > select clear
    4485 
    4486 > isolde pepflip sel
    4487 
    4488 Flipping the peptide bond for 1 residues 
    4489 
    4490 > isolde pepflip sel
    4491 
    4492 Flipping the peptide bond for 1 residues 
    4493 
    4494 > isolde pepflip sel
    4495 
    4496 Flipping the peptide bond for 1 residues 
    4497 
    4498 > isolde sim stop
    4499 
    4500 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    4501 chains... 
    4502 ISOLDE: Corrected atom nomenclature of 3 residues in model #1.2 to IUPAC-IUB
    4503 standards. 
    4504 ISOLDE: stopped sim 
    4505 
    4506 > isolde sim start sel
    4507 
    4508 ISOLDE: started sim 
    4509 
    4510 > isolde pepflip sel
    4511 
    4512 Flipping the peptide bond for 1 residues 
    4513 
    4514 > isolde pepflip sel
    4515 
    4516 Flipping the peptide bond for 1 residues 
    4517 
    4518 > isolde pepflip sel
    4519 
    4520 Flipping the peptide bond for 1 residues 
    4521 
    4522 > isolde pepflip sel
    4523 
    4524 Flipping the peptide bond for 1 residues 
    4525 
    4526 > isolde sim stop
    4527 
    4528 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    4529 chains... 
    4530 ISOLDE: stopped sim 
    4531 
    4532 > isolde sim start sel
    4533 
    4534 ISOLDE: started sim 
    4535 
    4536 > isolde pepflip sel
    4537 
    4538 Flipping the peptide bond for 1 residues 
    4539 
    4540 > isolde pepflip sel
    4541 
    4542 Flipping the peptide bond for 1 residues 
    4543 
    4544 > isolde pepflip sel
    4545 
    4546 Flipping the peptide bond for 1 residues 
    4547 
    4548 > isolde pepflip sel
    4549 
    4550 Flipping the peptide bond for 1 residues 
    4551 
    4552 > isolde pepflip sel
    4553 
    4554 Flipping the peptide bond for 1 residues 
    4555 
    4556 > isolde pepflip sel
    4557 
    4558 Flipping the peptide bond for 1 residues 
    4559 
    4560 > isolde pepflip sel
    4561 
    4562 Flipping the peptide bond for 1 residues 
    4563 
    4564 > isolde pepflip sel
    4565 
    4566 Flipping the peptide bond for 1 residues 
    4567 
    4568 > isolde pepflip sel
    4569 
    4570 Flipping the peptide bond for 1 residues 
    4571 
    4572 > isolde pepflip sel
    4573 
    4574 Flipping the peptide bond for 1 residues 
    4575 
    4576 > isolde pepflip sel
    4577 
    4578 Flipping the peptide bond for 1 residues 
    4579 
    4580 > isolde pepflip sel
    4581 
    4582 Flipping the peptide bond for 1 residues 
    4583 
    4584 > isolde pepflip sel
    4585 
    4586 Flipping the peptide bond for 1 residues 
    4587 
    4588 > isolde pepflip sel
    4589 
    4590 Flipping the peptide bond for 1 residues 
    4591 
    4592 > isolde pepflip sel
    4593 
    4594 Flipping the peptide bond for 1 residues 
    4595 
    4596 > isolde pepflip sel
    4597 
    4598 Flipping the peptide bond for 1 residues 
    4599 
    4600 > isolde pepflip sel
    4601 
    4602 Flipping the peptide bond for 1 residues 
    4603 
    4604 > isolde pepflip sel
    4605 
    4606 Flipping the peptide bond for 1 residues 
    4607 
    4608 > isolde pepflip sel
    4609 
    4610 Flipping the peptide bond for 1 residues 
    4611 
    4612 > select clear
    4613 
    4614 > isolde pepflip sel
    4615 
    4616 Flipping the peptide bond for 1 residues 
    4617 
    4618 > isolde pepflip sel
    4619 
    4620 Flipping the peptide bond for 1 residues 
    4621 
    4622 > isolde pepflip sel
    4623 
    4624 Flipping the peptide bond for 1 residues 
    4625 
    4626 > isolde pepflip sel
    4627 
    4628 Flipping the peptide bond for 1 residues 
    4629 
    4630 > isolde pepflip sel
    4631 
    4632 Flipping the peptide bond for 1 residues 
    4633 
    4634 > isolde pepflip sel
    4635 
    4636 Flipping the peptide bond for 1 residues 
    4637 
    4638 > select clear
    4639 
    4640 > isolde pepflip sel
    4641 
    4642 Flipping the peptide bond for 1 residues 
    4643 
    4644 > isolde pepflip sel
    4645 
    4646 Flipping the peptide bond for 1 residues 
    4647 
    4648 > isolde pepflip sel
    4649 
    4650 Flipping the peptide bond for 1 residues 
    4651 
    4652 > isolde pepflip sel
    4653 
    4654 Flipping the peptide bond for 1 residues 
    4655 
    4656 > select clear
    4657 
    4658 > isolde pepflip sel
    4659 
    4660 Flipping the peptide bond for 1 residues 
    4661 
    4662 > isolde pepflip sel
    4663 
    4664 Flipping the peptide bond for 1 residues 
    4665 
    4666 > isolde pepflip sel
    4667 
    4668 Flipping the peptide bond for 1 residues 
    4669 
    4670 > isolde pepflip sel
    4671 
    4672 Flipping the peptide bond for 1 residues 
    4673 
    4674 > isolde pepflip sel
    4675 
    4676 Flipping the peptide bond for 1 residues 
    4677 
    4678 > isolde pepflip sel
    4679 
    4680 Flipping the peptide bond for 1 residues 
    4681 
    4682 > isolde pepflip sel
    4683 
    4684 Flipping the peptide bond for 1 residues 
    4685 
    4686 > isolde pepflip sel
    4687 
    4688 Flipping the peptide bond for 1 residues 
    4689 
    4690 > isolde pepflip sel
    4691 
    4692 Flipping the peptide bond for 1 residues 
    4693 
    4694 > isolde pepflip sel
    4695 
    4696 Flipping the peptide bond for 1 residues 
    4697 
    4698 > isolde sim stop
    4699 
    4700 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    4701 chains... 
    4702 ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
    4703 standards. 
    4704 ISOLDE: stopped sim 
    4705 
    4706 > isolde sim start sel
    4707 
    4708 ISOLDE: started sim 
    4709 
    4710 > isolde sim stop
    4711 
    4712 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    4713 chains... 
    4714 ISOLDE: stopped sim 
    4715 
    4716 > isolde sim start sel
    4717 
    4718 ISOLDE: started sim 
    4719 
    4720 > isolde pepflip sel
    4721 
    4722 Flipping the peptide bond for 1 residues 
    4723 
    4724 > isolde pepflip sel
    4725 
    4726 Flipping the peptide bond for 1 residues 
    4727 
    4728 > isolde pepflip sel
    4729 
    4730 Flipping the peptide bond for 1 residues 
    4731 
    4732 > select clear
    4733 
    4734 > isolde pepflip sel
    4735 
    4736 Flipping the peptide bond for 1 residues 
    4737 
    4738 > isolde pepflip sel
    4739 
    4740 Flipping the peptide bond for 1 residues 
    4741 
    4742 > isolde pepflip sel
    4743 
    4744 Flipping the peptide bond for 1 residues 
    4745 
    4746 > isolde pepflip sel
    4747 
    4748 Flipping the peptide bond for 1 residues 
    4749 
    4750 > isolde pepflip sel
    4751 
    4752 Flipping the peptide bond for 1 residues 
    4753 
    4754 > select clear
    4755 
    4756 > isolde sim stop
    4757 
    4758 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    4759 chains... 
    4760 ISOLDE: stopped sim 
    4761 
    4762 > isolde sim start sel
    4763 
    4764 ISOLDE: started sim 
    4765 
    4766 > isolde pepflip sel
    4767 
    4768 Flipping the peptide bond for 1 residues 
    4769 
    4770 > isolde pepflip sel
    4771 
    4772 Flipping the peptide bond for 1 residues 
    4773 
    4774 > select clear
    4775 
    4776 [Repeated 1 time(s)]
    4777 
    4778 > isolde pepflip sel
    4779 
    4780 Flipping the peptide bond for 1 residues 
    4781 
    4782 > isolde pepflip sel
    4783 
    4784 Flipping the peptide bond for 1 residues 
    4785 
    4786 > isolde sim stop
    4787 
    4788 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    4789 chains... 
    4790 ISOLDE: stopped sim 
    4791 
    4792 > isolde sim start sel
    4793 
    4794 ISOLDE: started sim 
    4795 
    4796 > isolde pepflip sel
    4797 
    4798 Flipping the peptide bond for 1 residues 
    4799 
    4800 > isolde sim stop
    4801 
    4802 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    4803 chains... 
    4804 ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
    4805 standards. 
    4806 ISOLDE: stopped sim 
    4807 
    4808 > isolde sim start sel
    4809 
    4810 ISOLDE: started sim 
    4811 
    4812 > isolde pepflip sel
    4813 
    4814 Flipping the peptide bond for 1 residues 
    4815 
    4816 > isolde sim stop
    4817 
    4818 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    4819 chains... 
    4820 ISOLDE: stopped sim 
    4821 
    4822 > isolde sim start sel
    4823 
    4824 ISOLDE: started sim 
    4825 
    4826 > isolde pepflip sel
    4827 
    4828 Flipping the peptide bond for 1 residues 
    4829 
    4830 > isolde pepflip sel
    4831 
    4832 Flipping the peptide bond for 1 residues 
    4833 
    4834 > isolde pepflip sel
    4835 
    4836 Flipping the peptide bond for 1 residues 
    4837 
    4838 > isolde pepflip sel
    4839 
    4840 Flipping the peptide bond for 1 residues 
    4841 
    4842 > isolde pepflip sel
    4843 
    4844 Flipping the peptide bond for 1 residues 
    4845 
    4846 > isolde sim stop
    4847 
    4848 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    4849 chains... 
    4850 ISOLDE: stopped sim 
    4851 
    4852 > isolde sim start sel
    4853 
    4854 ISOLDE: started sim 
    4855 
    4856 > isolde pepflip sel
    4857 
    4858 Flipping the peptide bond for 1 residues 
    4859 
    4860 > isolde pepflip sel
    4861 
    4862 Flipping the peptide bond for 1 residues 
    4863 
    4864 > isolde pepflip sel
    4865 
    4866 Flipping the peptide bond for 1 residues 
    4867 
    4868 > isolde pepflip sel
    4869 
    4870 Flipping the peptide bond for 1 residues 
    4871 
    4872 > isolde pepflip sel
    4873 
    4874 Flipping the peptide bond for 1 residues 
    4875 
    4876 > isolde pepflip sel
    4877 
    4878 Flipping the peptide bond for 1 residues 
    4879 
    4880 > isolde sim stop
    4881 
    4882 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    4883 chains... 
    4884 ISOLDE: stopped sim 
    4885 
    4886 > isolde sim start sel
    4887 
    4888 ISOLDE: started sim 
    4889 
    4890 > isolde pepflip sel
    4891 
    4892 Flipping the peptide bond for 1 residues 
    4893 
    4894 > isolde pepflip sel
    4895 
    4896 Flipping the peptide bond for 1 residues 
    4897 
    4898 > isolde pepflip sel
    4899 
    4900 Flipping the peptide bond for 1 residues 
    4901 
    4902 > isolde pepflip sel
    4903 
    4904 Flipping the peptide bond for 1 residues 
    4905 
    4906 > isolde pepflip sel
    4907 
    4908 Flipping the peptide bond for 1 residues 
    4909 
    4910 > isolde pepflip sel
    4911 
    4912 Flipping the peptide bond for 1 residues 
    4913 
    4914 > isolde pepflip sel
    4915 
    4916 Flipping the peptide bond for 1 residues 
    4917 
    4918 > isolde pepflip sel
    4919 
    4920 Flipping the peptide bond for 1 residues 
    4921 
    4922 > isolde pepflip sel
    4923 
    4924 Flipping the peptide bond for 1 residues 
    4925 
    4926 > isolde pepflip sel
    4927 
    4928 Flipping the peptide bond for 1 residues 
    4929 
    4930 > isolde pepflip sel
    4931 
    4932 Flipping the peptide bond for 1 residues 
    4933 Unable to flip peptide bond after 50 rounds. Giving up. 
    4934 
    4935 > isolde pepflip sel
    4936 
    4937 Flipping the peptide bond for 1 residues 
    4938 
    4939 > isolde pepflip sel
    4940 
    4941 Flipping the peptide bond for 1 residues 
    4942 
    4943 > isolde sim stop
    4944 
    4945 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    4946 chains... 
    4947 ISOLDE: stopped sim 
    4948 
    4949 > isolde sim start sel
    4950 
    4951 ISOLDE: started sim 
    4952 
    4953 > isolde pepflip sel
    4954 
    4955 Flipping the peptide bond for 1 residues 
    4956 
    4957 > isolde pepflip sel
    4958 
    4959 Flipping the peptide bond for 1 residues 
    4960 
    4961 > isolde pepflip sel
    4962 
    4963 Flipping the peptide bond for 1 residues 
    4964 
    4965 > select clear
    4966 
    4967 > isolde pepflip sel
    4968 
    4969 Flipping the peptide bond for 1 residues 
    4970 
    4971 > isolde pepflip sel
    4972 
    4973 Flipping the peptide bond for 1 residues 
    4974 
    4975 > isolde pepflip sel
    4976 
    4977 Flipping the peptide bond for 1 residues 
    4978 
    4979 > isolde sim stop
    4980 
    4981 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    4982 chains... 
    4983 ISOLDE: stopped sim 
    4984 
    4985 > isolde sim start sel
    4986 
    4987 ISOLDE: started sim 
    4988 
    4989 > isolde pepflip sel
    4990 
    4991 Flipping the peptide bond for 1 residues 
    4992 
    4993 > isolde pepflip sel
    4994 
    4995 Flipping the peptide bond for 1 residues 
    4996 
    4997 > isolde pepflip sel
    4998 
    4999 Flipping the peptide bond for 1 residues 
    5000 
    5001 > isolde sim stop
    5002 
    5003 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    5004 chains... 
    5005 ISOLDE: Corrected atom nomenclature of 3 residues in model #1.2 to IUPAC-IUB
    5006 standards. 
    5007 ISOLDE: stopped sim 
    5008 
    5009 > isolde sim start sel
    5010 
    5011 ISOLDE: started sim 
    5012 
    5013 > select clear
    5014 
    5015 > isolde pepflip sel
    5016 
    5017 Flipping the peptide bond for 1 residues 
    5018 
    5019 > isolde pepflip sel
    5020 
    5021 Flipping the peptide bond for 1 residues 
    5022 
    5023 > isolde pepflip sel
    5024 
    5025 Flipping the peptide bond for 1 residues 
    5026 
    5027 > isolde pepflip sel
    5028 
    5029 Flipping the peptide bond for 1 residues 
    5030 
    5031 > isolde pepflip sel
    5032 
    5033 Flipping the peptide bond for 1 residues 
    5034 
    5035 > isolde pepflip sel
    5036 
    5037 Flipping the peptide bond for 1 residues 
    5038 
    5039 > isolde pepflip sel
    5040 
    5041 Flipping the peptide bond for 1 residues 
    5042 
    5043 > isolde pepflip sel
    5044 
    5045 Flipping the peptide bond for 1 residues 
    5046 
    5047 > isolde pepflip sel
    5048 
    5049 Flipping the peptide bond for 1 residues 
    5050 
    5051 > isolde pepflip sel
    5052 
    5053 Flipping the peptide bond for 1 residues 
    5054 
    5055 > isolde pepflip sel
    5056 
    5057 Flipping the peptide bond for 1 residues 
    5058 
    5059 > isolde pepflip sel
    5060 
    5061 Flipping the peptide bond for 1 residues 
    5062 
    5063 > isolde pepflip sel
    5064 
    5065 Flipping the peptide bond for 1 residues 
    5066 
    5067 > isolde sim stop
    5068 
    5069 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    5070 chains... 
    5071 ISOLDE: Corrected atom nomenclature of 2 residues in model #1.2 to IUPAC-IUB
    5072 standards. 
    5073 ISOLDE: stopped sim 
    5074 
    5075 > isolde sim start sel
    5076 
    5077 ISOLDE: started sim 
    5078 
    5079 > isolde pepflip sel
    5080 
    5081 Flipping the peptide bond for 1 residues 
    5082 
    5083 > isolde pepflip sel
    5084 
    5085 Flipping the peptide bond for 1 residues 
    5086 
    5087 > isolde pepflip sel
    5088 
    5089 Flipping the peptide bond for 1 residues 
    5090 
    5091 > isolde pepflip sel
    5092 
    5093 Flipping the peptide bond for 1 residues 
    5094 
    5095 > isolde sim stop
    5096 
    5097 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    5098 chains... 
    5099 ISOLDE: Corrected atom nomenclature of 2 residues in model #1.2 to IUPAC-IUB
    5100 standards. 
    5101 ISOLDE: stopped sim 
    5102 
    5103 > isolde sim start sel
    5104 
    5105 ISOLDE: started sim 
    5106 
    5107 > isolde sim stop
    5108 
    5109 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    5110 chains... 
    5111 ISOLDE: stopped sim 
    5112 
    5113 > isolde sim start sel
    5114 
    5115 ISOLDE: started sim 
    5116 
    5117 > select clear
    5118 
    5119 > isolde pepflip sel
    5120 
    5121 Flipping the peptide bond for 1 residues 
    5122 
    5123 > isolde pepflip sel
    5124 
    5125 Flipping the peptide bond for 1 residues 
    5126 
    5127 > isolde sim stop
    5128 
    5129 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    5130 chains... 
    5131 ISOLDE: stopped sim 
    5132 
    5133 > isolde sim start sel
    5134 
    5135 ISOLDE: started sim 
    5136 
    5137 > isolde pepflip sel
    5138 
    5139 Flipping the peptide bond for 1 residues 
    5140 
    5141 > select clear
    5142 
    5143 > isolde pepflip sel
    5144 
    5145 Flipping the peptide bond for 1 residues 
    5146 
    5147 > isolde pepflip sel
    5148 
    5149 Flipping the peptide bond for 1 residues 
    5150 
    5151 > isolde pepflip sel
    5152 
    5153 Flipping the peptide bond for 1 residues 
    5154 
    5155 > isolde pepflip sel
    5156 
    5157 Flipping the peptide bond for 1 residues 
    5158 
    5159 > isolde pepflip sel
    5160 
    5161 Flipping the peptide bond for 1 residues 
    5162 
    5163 > isolde pepflip sel
    5164 
    5165 Flipping the peptide bond for 1 residues 
    5166 
    5167 > isolde pepflip sel
    5168 
    5169 Flipping the peptide bond for 1 residues 
    5170 
    5171 > isolde pepflip sel
    5172 
    5173 Flipping the peptide bond for 1 residues 
    5174 
    5175 > select clear
    5176 
    5177 > isolde pepflip sel
    5178 
    5179 Flipping the peptide bond for 1 residues 
    5180 
    5181 > isolde pepflip sel
    5182 
    5183 Flipping the peptide bond for 1 residues 
    5184 
    5185 > isolde pepflip sel
    5186 
    5187 Flipping the peptide bond for 1 residues 
    5188 
    5189 > isolde pepflip sel
    5190 
    5191 Flipping the peptide bond for 1 residues 
    5192 
    5193 > isolde pepflip sel
    5194 
    5195 Flipping the peptide bond for 1 residues 
    5196 
    5197 > isolde sim stop
    5198 
    5199 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    5200 chains... 
    5201 ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
    5202 standards. 
    5203 ISOLDE: stopped sim 
    5204 
    5205 > isolde sim start sel
    5206 
    5207 ISOLDE: started sim 
    5208 
    5209 > select clear
    5210 
    5211 [Repeated 1 time(s)]
    5212 
    5213 > isolde pepflip sel
    5214 
    5215 Flipping the peptide bond for 1 residues 
    5216 
    5217 > isolde pepflip sel
    5218 
    5219 Flipping the peptide bond for 1 residues 
    5220 
    5221 > isolde pepflip sel
    5222 
    5223 Flipping the peptide bond for 1 residues 
    5224 
    5225 > isolde pepflip sel
    5226 
    5227 Flipping the peptide bond for 1 residues 
    5228 
    5229 > isolde sim stop
    5230 
    5231 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    5232 chains... 
    5233 ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
    5234 standards. 
    5235 ISOLDE: stopped sim 
    5236 
    5237 > isolde sim start sel
    5238 
    5239 ISOLDE: started sim 
    5240 
    5241 > isolde pepflip sel
    5242 
    5243 Flipping the peptide bond for 1 residues 
    5244 
    5245 > isolde sim stop
    5246 
    5247 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    5248 chains... 
    5249 ISOLDE: Corrected atom nomenclature of 2 residues in model #1.2 to IUPAC-IUB
    5250 standards. 
    5251 ISOLDE: stopped sim 
    5252 
    5253 > isolde sim start sel
    5254 
    5255 ISOLDE: started sim 
    5256 
    5257 > isolde sim stop discardTo start
    5258 
    5259 reverting to start 
    5260 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    5261 chains... 
    5262 ISOLDE: stopped sim 
    5263 
    5264 > isolde sim start sel
    5265 
    5266 ISOLDE: started sim 
    5267 
    5268 > isolde pepflip sel
    5269 
    5270 Flipping the peptide bond for 1 residues 
    5271 
    5272 > isolde pepflip sel
    5273 
    5274 Flipping the peptide bond for 1 residues 
    5275 Unable to flip peptide bond after 50 rounds. Giving up. 
    5276 [Repeated 1 time(s)]
    5277 
    5278 > isolde pepflip sel
    5279 
    5280 Flipping the peptide bond for 1 residues 
    5281 
    5282 > isolde pepflip sel
    5283 
    5284 Flipping the peptide bond for 1 residues 
    5285 
    5286 > isolde pepflip sel
    5287 
    5288 Flipping the peptide bond for 1 residues 
    5289 
    5290 > isolde pepflip sel
    5291 
    5292 Flipping the peptide bond for 1 residues 
    5293 
    5294 > isolde pepflip sel
    5295 
    5296 Flipping the peptide bond for 1 residues 
    5297 
    5298 > select clear
    5299 
    5300 > isolde pepflip sel
    5301 
    5302 Flipping the peptide bond for 1 residues 
    5303 
    5304 > isolde pepflip sel
    5305 
    5306 Flipping the peptide bond for 1 residues 
    5307 
    5308 > select clear
    5309 
    5310 > isolde pepflip sel
    5311 
    5312 Flipping the peptide bond for 1 residues 
    5313 
    5314 > isolde pepflip sel
    5315 
    5316 Flipping the peptide bond for 1 residues 
    5317 
    5318 > isolde pepflip sel
    5319 
    5320 Flipping the peptide bond for 1 residues 
    5321 Unable to flip peptide bond after 50 rounds. Giving up. 
    5322 
    5323 > isolde pepflip sel
    5324 
    5325 Flipping the peptide bond for 1 residues 
    5326 
    5327 > isolde pepflip sel
    5328 
    5329 Flipping the peptide bond for 1 residues 
    5330 
    5331 > isolde pepflip sel
    5332 
    5333 Flipping the peptide bond for 1 residues 
    5334 Unable to flip peptide bond after 50 rounds. Giving up. 
    5335 
    5336 > isolde pepflip sel
    5337 
    5338 Flipping the peptide bond for 1 residues 
    5339 
    5340 > isolde pepflip sel
    5341 
    5342 Flipping the peptide bond for 1 residues 
    5343 
    5344 > isolde pepflip sel
    5345 
    5346 Flipping the peptide bond for 1 residues 
    5347 
    5348 > isolde pepflip sel
    5349 
    5350 Flipping the peptide bond for 1 residues 
    5351 
    5352 > isolde sim stop
    5353 
    5354 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    5355 chains... 
    5356 ISOLDE: Corrected atom nomenclature of 2 residues in model #1.2 to IUPAC-IUB
    5357 standards. 
    5358 ISOLDE: stopped sim 
    5359 
    5360 > isolde sim start sel
    5361 
    5362 ISOLDE: started sim 
    5363 
    5364 > isolde pepflip sel
    5365 
    5366 Flipping the peptide bond for 1 residues 
    5367 
    5368 > isolde pepflip sel
    5369 
    5370 Flipping the peptide bond for 1 residues 
    5371 
    5372 > isolde pepflip sel
    5373 
    5374 Flipping the peptide bond for 1 residues 
    5375 
    5376 > isolde sim stop
    5377 
    5378 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    5379 chains... 
    5380 ISOLDE: stopped sim 
    5381 
    5382 > isolde sim start sel
    5383 
    5384 ISOLDE: started sim 
    5385 
    5386 > isolde pepflip sel
    5387 
    5388 Flipping the peptide bond for 1 residues 
    5389 
    5390 > isolde sim stop
    5391 
    5392 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    5393 chains... 
    5394 ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
    5395 standards. 
    5396 ISOLDE: stopped sim 
    5397 
    5398 > isolde sim start sel
    5399 
    5400 ISOLDE: started sim 
    5401 
    5402 > isolde pepflip sel
    5403 
    5404 Flipping the peptide bond for 1 residues 
    5405 
    5406 > isolde pepflip sel
    5407 
    5408 Flipping the peptide bond for 1 residues 
    5409 
    5410 > isolde pepflip sel
    5411 
    5412 Flipping the peptide bond for 1 residues 
    5413 
    5414 > isolde pepflip sel
    5415 
    5416 Flipping the peptide bond for 1 residues 
    5417 
    5418 > isolde pepflip sel
    5419 
    5420 Flipping the peptide bond for 1 residues 
    5421 
    5422 > isolde pepflip sel
    5423 
    5424 Flipping the peptide bond for 1 residues 
    5425 
    5426 > isolde pepflip sel
    5427 
    5428 Flipping the peptide bond for 1 residues 
    5429 
    5430 > isolde pepflip sel
    5431 
    5432 Flipping the peptide bond for 1 residues 
    5433 
    5434 > isolde pepflip sel
    5435 
    5436 Flipping the peptide bond for 1 residues 
    5437 
    5438 > isolde pepflip sel
    5439 
    5440 Flipping the peptide bond for 1 residues 
    5441 
    5442 > isolde pepflip sel
    5443 
    5444 Flipping the peptide bond for 1 residues 
    5445 
    5446 > isolde sim stop
    5447 
    5448 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    5449 chains... 
    5450 ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
    5451 standards. 
    5452 ISOLDE: stopped sim 
    5453 
    5454 > isolde sim start sel
    5455 
    5456 ISOLDE: started sim 
    5457 
    5458 > isolde pepflip sel
    5459 
    5460 Flipping the peptide bond for 1 residues 
    5461 
    5462 > isolde pepflip sel
    5463 
    5464 Flipping the peptide bond for 1 residues 
    5465 
    5466 > isolde pepflip sel
    5467 
    5468 Flipping the peptide bond for 1 residues 
    5469 
    5470 > isolde sim stop
    5471 
    5472 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    5473 chains... 
    5474 ISOLDE: stopped sim 
    5475 
    5476 > isolde sim start sel
    5477 
    5478 ISOLDE: started sim 
    5479 
    5480 > isolde pepflip sel
    5481 
    5482 Flipping the peptide bond for 1 residues 
    5483 
    5484 > isolde pepflip sel
    5485 
    5486 Flipping the peptide bond for 1 residues 
    5487 
    5488 > isolde sim stop
    5489 
    5490 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    5491 chains... 
    5492 ISOLDE: stopped sim 
    5493 
    5494 > isolde sim start sel
    5495 
    5496 ISOLDE: started sim 
    5497 
    5498 > isolde pepflip sel
    5499 
    5500 Flipping the peptide bond for 1 residues 
    5501 
    5502 > isolde pepflip sel
    5503 
    5504 Flipping the peptide bond for 1 residues 
    5505 
    5506 > isolde pepflip sel
    5507 
    5508 Flipping the peptide bond for 1 residues 
    5509 
    5510 > isolde pepflip sel
    5511 
    5512 Flipping the peptide bond for 1 residues 
    5513 
    5514 > isolde pepflip sel
    5515 
    5516 Flipping the peptide bond for 1 residues 
    5517 
    5518 > isolde pepflip sel
    5519 
    5520 Flipping the peptide bond for 1 residues 
    5521 
    5522 > isolde pepflip sel
    5523 
    5524 Flipping the peptide bond for 1 residues 
    5525 
    5526 > isolde pepflip sel
    5527 
    5528 Flipping the peptide bond for 1 residues 
    5529 
    5530 > isolde pepflip sel
    5531 
    5532 Flipping the peptide bond for 1 residues 
    5533 
    5534 > isolde pepflip sel
    5535 
    5536 Flipping the peptide bond for 1 residues 
    5537 
    5538 > isolde pepflip sel
    5539 
    5540 Flipping the peptide bond for 1 residues 
    5541 
    5542 > isolde pepflip sel
    5543 
    5544 Flipping the peptide bond for 1 residues 
    5545 
    5546 > isolde sim stop
    5547 
    5548 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    5549 chains... 
    5550 ISOLDE: Corrected atom nomenclature of 4 residues in model #1.2 to IUPAC-IUB
    5551 standards. 
    5552 ISOLDE: stopped sim 
    5553 
    5554 > isolde sim start sel
    5555 
    5556 ISOLDE: started sim 
    5557 
    5558 > isolde pepflip sel
    5559 
    5560 Flipping the peptide bond for 1 residues 
    5561 
    5562 > isolde pepflip sel
    5563 
    5564 Flipping the peptide bond for 1 residues 
    5565 
    5566 > isolde pepflip sel
    5567 
    5568 Flipping the peptide bond for 1 residues 
    5569 
    5570 > isolde pepflip sel
    5571 
    5572 Flipping the peptide bond for 1 residues 
    5573 
    5574 > isolde pepflip sel
    5575 
    5576 Flipping the peptide bond for 1 residues 
    5577 
    5578 > isolde pepflip sel
    5579 
    5580 Flipping the peptide bond for 1 residues 
    5581 
    5582 > isolde pepflip sel
    5583 
    5584 Flipping the peptide bond for 1 residues 
    5585 
    5586 > isolde sim stop
    5587 
    5588 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    5589 chains... 
    5590 ISOLDE: stopped sim 
    5591 
    5592 > isolde sim start sel
    5593 
    5594 ISOLDE: started sim 
    5595 
    5596 > select clear
    5597 
    5598 > isolde pepflip sel
    5599 
    5600 Flipping the peptide bond for 1 residues 
    5601 
    5602 > isolde pepflip sel
    5603 
    5604 Flipping the peptide bond for 1 residues 
    5605 
    5606 > isolde pepflip sel
    5607 
    5608 Flipping the peptide bond for 1 residues 
    5609 
    5610 > isolde sim stop
    5611 
    5612 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    5613 chains... 
    5614 ISOLDE: stopped sim 
    5615 
    5616 > isolde sim start sel
    5617 
    5618 ISOLDE: started sim 
    5619 
    5620 > isolde pepflip sel
    5621 
    5622 Flipping the peptide bond for 1 residues 
    5623 
    5624 > isolde pepflip sel
    5625 
    5626 Flipping the peptide bond for 1 residues 
    5627 
    5628 > isolde pepflip sel
    5629 
    5630 Flipping the peptide bond for 1 residues 
    5631 
    5632 > isolde pepflip sel
    5633 
    5634 Flipping the peptide bond for 1 residues 
    5635 
    5636 > isolde pepflip sel
    5637 
    5638 Flipping the peptide bond for 1 residues 
    5639 
    5640 > isolde pepflip sel
    5641 
    5642 Flipping the peptide bond for 1 residues 
    5643 
    5644 > isolde pepflip sel
    5645 
    5646 Flipping the peptide bond for 1 residues 
    5647 
    5648 > isolde pepflip sel
    5649 
    5650 Flipping the peptide bond for 1 residues 
    5651 
    5652 > isolde pepflip sel
    5653 
    5654 Flipping the peptide bond for 1 residues 
    5655 
    5656 > isolde sim pause
    5657 
    5658 > isolde sim resume
    5659 
    5660 > isolde pepflip sel
    5661 
    5662 Flipping the peptide bond for 1 residues 
    5663 
    5664 > isolde pepflip sel
    5665 
    5666 Flipping the peptide bond for 1 residues 
    5667 
    5668 > isolde sim stop
    5669 
    5670 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    5671 chains... 
    5672 ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
    5673 standards. 
    5674 ISOLDE: stopped sim 
    5675 
    5676 > isolde sim start sel
    5677 
    5678 ISOLDE: started sim 
    5679 
    5680 > isolde sim stop
    5681 
    5682 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    5683 chains... 
    5684 ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
    5685 standards. 
    5686 ISOLDE: stopped sim 
    5687 
    5688 > isolde sim start sel
    5689 
    5690 ISOLDE: started sim 
    5691 
    5692 > isolde pepflip sel
    5693 
    5694 Flipping the peptide bond for 1 residues 
    5695 
    5696 > isolde pepflip sel
    5697 
    5698 Flipping the peptide bond for 1 residues 
    5699 
    5700 > isolde pepflip sel
    5701 
    5702 Flipping the peptide bond for 1 residues 
    5703 
    5704 > isolde pepflip sel
    5705 
    5706 Flipping the peptide bond for 1 residues 
    5707 
    5708 > isolde pepflip sel
    5709 
    5710 Flipping the peptide bond for 1 residues 
    5711 
    5712 > isolde sim stop
    5713 
    5714 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    5715 chains... 
    5716 ISOLDE: stopped sim 
    5717 
    5718 > isolde sim start sel
    5719 
    5720 ISOLDE: started sim 
    5721 
    5722 > isolde pepflip sel
    5723 
    5724 Flipping the peptide bond for 1 residues 
    5725 
    5726 > isolde pepflip sel
    5727 
    5728 Flipping the peptide bond for 1 residues 
    5729 
    5730 > isolde pepflip sel
    5731 
    5732 Flipping the peptide bond for 1 residues 
    5733 
    5734 > select clear
    5735 
    5736 > isolde pepflip sel
    5737 
    5738 Flipping the peptide bond for 1 residues 
    5739 
    5740 > isolde pepflip sel
    5741 
    5742 Flipping the peptide bond for 1 residues 
    5743 
    5744 > select clear
    5745 
    5746 > isolde pepflip sel
    5747 
    5748 Flipping the peptide bond for 1 residues 
    5749 
    5750 > isolde pepflip sel
    5751 
    5752 Flipping the peptide bond for 1 residues 
    5753 
    5754 > isolde pepflip sel
    5755 
    5756 Flipping the peptide bond for 1 residues 
    5757 
    5758 > isolde pepflip sel
    5759 
    5760 Flipping the peptide bond for 1 residues 
    5761 
    5762 > isolde pepflip sel
    5763 
    5764 Flipping the peptide bond for 1 residues 
    5765 
    5766 > isolde pepflip sel
    5767 
    5768 Flipping the peptide bond for 1 residues 
    5769 
    5770 > isolde pepflip sel
    5771 
    5772 Flipping the peptide bond for 1 residues 
    5773 
    5774 > select clear
    5775 
    5776 > isolde pepflip sel
    5777 
    5778 Flipping the peptide bond for 1 residues 
    5779 
    5780 > isolde pepflip sel
    5781 
    5782 Flipping the peptide bond for 1 residues 
    5783 
    5784 > select clear
    5785 
    5786 > isolde pepflip sel
    5787 
    5788 Flipping the peptide bond for 1 residues 
    5789 
    5790 > isolde pepflip sel
    5791 
    5792 Flipping the peptide bond for 1 residues 
    5793 
    5794 > isolde sim stop
    5795 
    5796 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    5797 chains... 
    5798 ISOLDE: stopped sim 
    5799 
    5800 > isolde sim start sel
    5801 
    5802 ISOLDE: started sim 
    5803 
    5804 > isolde pepflip sel
    5805 
    5806 Flipping the peptide bond for 1 residues 
    5807 
    5808 > isolde sim stop
    5809 
    5810 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    5811 chains... 
    5812 ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
    5813 standards. 
    5814 ISOLDE: stopped sim 
    5815 
    5816 > isolde sim start sel
    5817 
    5818 ISOLDE: started sim 
    5819 
    5820 > isolde pepflip sel
    5821 
    5822 Flipping the peptide bond for 1 residues 
    5823 
    5824 > isolde sim stop
    5825 
    5826 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    5827 chains... 
    5828 ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
    5829 standards. 
    5830 ISOLDE: stopped sim 
    5831 
    5832 > isolde sim start sel
    5833 
    5834 ISOLDE: started sim 
    5835 
    5836 > isolde pepflip sel
    5837 
    5838 Flipping the peptide bond for 1 residues 
    5839 
    5840 > isolde pepflip sel
    5841 
    5842 Flipping the peptide bond for 1 residues 
    5843 
    5844 > isolde sim stop
    5845 
    5846 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    5847 chains... 
    5848 ISOLDE: stopped sim 
    5849 
    5850 > isolde sim start sel
    5851 
    5852 ISOLDE: started sim 
    5853 
    5854 > isolde pepflip sel
    5855 
    5856 Flipping the peptide bond for 1 residues 
    5857 
    5858 > isolde pepflip sel
    5859 
    5860 Flipping the peptide bond for 1 residues 
    5861 
    5862 > isolde pepflip sel
    5863 
    5864 Flipping the peptide bond for 1 residues 
    5865 
    5866 > isolde pepflip sel
    5867 
    5868 Flipping the peptide bond for 1 residues 
    5869 
    5870 > isolde sim stop
    5871 
    5872 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    5873 chains... 
    5874 ISOLDE: Corrected atom nomenclature of 2 residues in model #1.2 to IUPAC-IUB
    5875 standards. 
    5876 ISOLDE: stopped sim 
    5877 
    5878 > isolde sim start sel
    5879 
    5880 ISOLDE: started sim 
    5881 
    5882 > isolde pepflip sel
    5883 
    5884 Flipping the peptide bond for 1 residues 
    5885 
    5886 > isolde pepflip sel
    5887 
    5888 Flipping the peptide bond for 1 residues 
    5889 
    5890 > isolde pepflip sel
    5891 
    5892 Flipping the peptide bond for 1 residues 
    5893 
    5894 > isolde pepflip sel
    5895 
    5896 Flipping the peptide bond for 1 residues 
    5897 
    5898 > isolde pepflip sel
    5899 
    5900 Flipping the peptide bond for 1 residues 
    5901 
    5902 > isolde pepflip sel
    5903 
    5904 Flipping the peptide bond for 1 residues 
    5905 
    5906 > isolde pepflip sel
    5907 
    5908 Flipping the peptide bond for 1 residues 
    5909 
    5910 > isolde pepflip sel
    5911 
    5912 Flipping the peptide bond for 1 residues 
    5913 
    5914 > isolde pepflip sel
    5915 
    5916 Flipping the peptide bond for 1 residues 
    5917 
    5918 > isolde pepflip sel
    5919 
    5920 Flipping the peptide bond for 1 residues 
    5921 
    5922 > isolde pepflip sel
    5923 
    5924 Flipping the peptide bond for 1 residues 
    5925 
    5926 > isolde pepflip sel
    5927 
    5928 Flipping the peptide bond for 1 residues 
    5929 
    5930 > isolde pepflip sel
    5931 
    5932 Flipping the peptide bond for 1 residues 
    5933 
    5934 > isolde pepflip sel
    5935 
    5936 Flipping the peptide bond for 1 residues 
    5937 
    5938 > isolde pepflip sel
    5939 
    5940 Flipping the peptide bond for 1 residues 
    5941 
    5942 > isolde pepflip sel
    5943 
    5944 Flipping the peptide bond for 1 residues 
    5945 
    5946 > isolde sim stop
    5947 
    5948 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    5949 chains... 
    5950 ISOLDE: Corrected atom nomenclature of 3 residues in model #1.2 to IUPAC-IUB
    5951 standards. 
    5952 ISOLDE: stopped sim 
    5953 
    5954 > isolde sim start sel
    5955 
    5956 ISOLDE: started sim 
    5957 
    5958 > isolde sim stop
    5959 
    5960 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    5961 chains... 
    5962 ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
    5963 standards. 
    5964 ISOLDE: stopped sim 
    5965 
    5966 > isolde sim start sel
    5967 
    5968 ISOLDE: started sim 
    5969 
    5970 > isolde sim stop
    5971 
    5972 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    5973 chains... 
    5974 ISOLDE: Corrected atom nomenclature of 2 residues in model #1.2 to IUPAC-IUB
    5975 standards. 
    5976 ISOLDE: stopped sim 
    5977 
    5978 > isolde sim start sel
    5979 
    5980 ISOLDE: started sim 
    5981 
    5982 > isolde pepflip sel
    5983 
    5984 Flipping the peptide bond for 1 residues 
    5985 
    5986 > isolde pepflip sel
    5987 
    5988 Flipping the peptide bond for 1 residues 
    5989 
    5990 > isolde pepflip sel
    5991 
    5992 Flipping the peptide bond for 1 residues 
    5993 
    5994 > isolde pepflip sel
    5995 
    5996 Flipping the peptide bond for 1 residues 
    5997 
    5998 > select clear
    5999 
    6000 > isolde pepflip sel
    6001 
    6002 Flipping the peptide bond for 1 residues 
    6003 
    6004 > isolde pepflip sel
    6005 
    6006 Flipping the peptide bond for 1 residues 
    6007 
    6008 > isolde sim stop
    6009 
    6010 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    6011 chains... 
    6012 ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
    6013 standards. 
    6014 ISOLDE: stopped sim 
    6015 
    6016 > isolde sim start sel
    6017 
    6018 ISOLDE: started sim 
    6019 
    6020 > isolde pepflip sel
    6021 
    6022 Flipping the peptide bond for 1 residues 
    6023 
    6024 > isolde pepflip sel
    6025 
    6026 Flipping the peptide bond for 1 residues 
    6027 
    6028 > isolde pepflip sel
    6029 
    6030 Flipping the peptide bond for 1 residues 
    6031 
    6032 > isolde pepflip sel
    6033 
    6034 Flipping the peptide bond for 1 residues 
    6035 
    6036 > isolde pepflip sel
    6037 
    6038 Flipping the peptide bond for 1 residues 
    6039 
    6040 > isolde pepflip sel
    6041 
    6042 Flipping the peptide bond for 1 residues 
    6043 
    6044 > isolde pepflip sel
    6045 
    6046 Flipping the peptide bond for 1 residues 
    6047 
    6048 > isolde pepflip sel
    6049 
    6050 Flipping the peptide bond for 1 residues 
    6051 
    6052 > isolde pepflip sel
    6053 
    6054 Flipping the peptide bond for 1 residues 
    6055 
    6056 > isolde pepflip sel
    6057 
    6058 Flipping the peptide bond for 1 residues 
    6059 
    6060 > isolde pepflip sel
    6061 
    6062 Flipping the peptide bond for 1 residues 
    6063 
    6064 > select clear
    6065 
    6066 > isolde pepflip sel
    6067 
    6068 Flipping the peptide bond for 1 residues 
    6069 
    6070 > isolde pepflip sel
    6071 
    6072 Flipping the peptide bond for 1 residues 
    6073 
    6074 > isolde pepflip sel
    6075 
    6076 Flipping the peptide bond for 1 residues 
    6077 
    6078 > isolde pepflip sel
    6079 
    6080 Flipping the peptide bond for 1 residues 
    6081 
    6082 > isolde pepflip sel
    6083 
    6084 Flipping the peptide bond for 1 residues 
    6085 
    6086 > isolde sim stop
    6087 
    6088 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    6089 chains... 
    6090 ISOLDE: stopped sim 
    6091 
    6092 > isolde sim start sel
    6093 
    6094 ISOLDE: started sim 
    6095 
    6096 > isolde pepflip sel
    6097 
    6098 Flipping the peptide bond for 1 residues 
    6099 
    6100 > isolde pepflip sel
    6101 
    6102 Flipping the peptide bond for 1 residues 
    6103 
    6104 > isolde pepflip sel
    6105 
    6106 Flipping the peptide bond for 1 residues 
    6107 
    6108 > isolde pepflip sel
    6109 
    6110 Flipping the peptide bond for 1 residues 
    6111 
    6112 > isolde pepflip sel
    6113 
    6114 Flipping the peptide bond for 1 residues 
    6115 
    6116 > isolde pepflip sel
    6117 
    6118 Flipping the peptide bond for 1 residues 
    6119 
    6120 > isolde pepflip sel
    6121 
    6122 Flipping the peptide bond for 1 residues 
    6123 
    6124 > isolde pepflip sel
    6125 
    6126 Flipping the peptide bond for 1 residues 
    6127 
    6128 > isolde pepflip sel
    6129 
    6130 Flipping the peptide bond for 1 residues 
    6131 
    6132 > isolde pepflip sel
    6133 
    6134 Flipping the peptide bond for 1 residues 
    6135 
    6136 > isolde pepflip sel
    6137 
    6138 Flipping the peptide bond for 1 residues 
    6139 
    6140 > isolde pepflip sel
    6141 
    6142 Flipping the peptide bond for 1 residues 
    6143 
    6144 > isolde pepflip sel
    6145 
    6146 Flipping the peptide bond for 1 residues 
    6147 
    6148 > isolde pepflip sel
    6149 
    6150 Flipping the peptide bond for 1 residues 
    6151 
    6152 > isolde pepflip sel
    6153 
    6154 Flipping the peptide bond for 1 residues 
    6155 
    6156 > isolde pepflip sel
    6157 
    6158 Flipping the peptide bond for 1 residues 
    6159 
    6160 > isolde pepflip sel
    6161 
    6162 Flipping the peptide bond for 1 residues 
    6163 
    6164 > isolde pepflip sel
    6165 
    6166 Flipping the peptide bond for 1 residues 
    6167 
    6168 > isolde pepflip sel
    6169 
    6170 Flipping the peptide bond for 1 residues 
    6171 
    6172 > isolde pepflip sel
    6173 
    6174 Flipping the peptide bond for 1 residues 
    6175 
    6176 > isolde pepflip sel
    6177 
    6178 Flipping the peptide bond for 1 residues 
    6179 
    6180 > isolde pepflip sel
    6181 
    6182 Flipping the peptide bond for 1 residues 
    6183 
    6184 > isolde pepflip sel
    6185 
    6186 Flipping the peptide bond for 1 residues 
    6187 
    6188 > isolde pepflip sel
    6189 
    6190 Flipping the peptide bond for 1 residues 
    6191 
    6192 > isolde sim pause
    6193 
    6194 > isolde sim resume
    6195 
    6196 > isolde pepflip sel
    6197 
    6198 Flipping the peptide bond for 1 residues 
    6199 
    6200 > isolde sim pause
    6201 
    6202 > isolde sim resume
    6203 
    6204 > isolde pepflip sel
    6205 
    6206 Flipping the peptide bond for 1 residues 
    6207 
    6208 > isolde pepflip sel
    6209 
    6210 Flipping the peptide bond for 1 residues 
    6211 Peptide bond must be mobile in the simulation! 
    6212 
    6213 > isolde pepflip sel
    6214 
    6215 Flipping the peptide bond for 1 residues 
    6216 Peptide bond must be mobile in the simulation! 
    6217 
    6218 > isolde pepflip sel
    6219 
    6220 Flipping the peptide bond for 1 residues 
    6221 
    6222 > isolde pepflip sel
    6223 
    6224 Flipping the peptide bond for 1 residues 
    6225 
    6226 > isolde pepflip sel
    6227 
    6228 Flipping the peptide bond for 1 residues 
    6229 
    6230 > isolde pepflip sel
    6231 
    6232 Flipping the peptide bond for 1 residues 
    6233 Peptide bond must be mobile in the simulation! 
    6234 
    6235 > isolde pepflip sel
    6236 
    6237 Flipping the peptide bond for 1 residues 
    6238 
    6239 > isolde pepflip sel
    6240 
    6241 Flipping the peptide bond for 1 residues 
    6242 
    6243 > isolde pepflip sel
    6244 
    6245 Flipping the peptide bond for 1 residues 
    6246 
    6247 > select clear
    6248 
    6249 > isolde pepflip sel
    6250 
    6251 Flipping the peptide bond for 1 residues 
    6252 
    6253 > isolde pepflip sel
    6254 
    6255 Flipping the peptide bond for 1 residues 
    6256 
    6257 > isolde sim stop
    6258 
    6259 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    6260 chains... 
    6261 ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
    6262 standards. 
    6263 ISOLDE: stopped sim 
    6264 
    6265 > isolde sim start sel
    6266 
    6267 ISOLDE: started sim 
    6268 
    6269 > isolde pepflip sel
    6270 
    6271 Flipping the peptide bond for 1 residues 
    6272 
    6273 > isolde sim stop
    6274 
    6275 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    6276 chains... 
    6277 ISOLDE: Corrected atom nomenclature of 2 residues in model #1.2 to IUPAC-IUB
    6278 standards. 
    6279 ISOLDE: stopped sim 
    6280 
    6281 > isolde sim start sel
    6282 
    6283 ISOLDE: started sim 
    6284 
    6285 > isolde pepflip sel
    6286 
    6287 Flipping the peptide bond for 1 residues 
    6288 
    6289 > isolde pepflip sel
    6290 
    6291 Flipping the peptide bond for 1 residues 
    6292 
    6293 > select clear
    6294 
    6295 > isolde pepflip sel
    6296 
    6297 Flipping the peptide bond for 1 residues 
    6298 
    6299 > isolde pepflip sel
    6300 
    6301 Flipping the peptide bond for 1 residues 
    6302 
    6303 > isolde pepflip sel
    6304 
    6305 Flipping the peptide bond for 1 residues 
    6306 
    6307 > select clear
    6308 
    6309 > isolde pepflip sel
    6310 
    6311 Flipping the peptide bond for 1 residues 
    6312 
    6313 > isolde pepflip sel
    6314 
    6315 Flipping the peptide bond for 1 residues 
    6316 
    6317 > isolde pepflip sel
    6318 
    6319 Flipping the peptide bond for 1 residues 
    6320 
    6321 > isolde pepflip sel
    6322 
    6323 Flipping the peptide bond for 1 residues 
    6324 
    6325 > select clear
    6326 
    6327 > isolde pepflip sel
    6328 
    6329 Flipping the peptide bond for 1 residues 
    6330 
    6331 > isolde sim stop
    6332 
    6333 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    6334 chains... 
    6335 ISOLDE: stopped sim 
    6336 
    6337 > isolde sim start sel
    6338 
    6339 ISOLDE: started sim 
    6340 
    6341 > isolde sim stop
    6342 
    6343 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    6344 chains... 
    6345 ISOLDE: stopped sim 
    6346 
    6347 > isolde sim start sel
    6348 
    6349 ISOLDE: started sim 
    6350 
    6351 > isolde pepflip sel
    6352 
    6353 Flipping the peptide bond for 1 residues 
    6354 
    6355 > isolde pepflip sel
    6356 
    6357 Flipping the peptide bond for 1 residues 
    6358 
    6359 > isolde pepflip sel
    6360 
    6361 Flipping the peptide bond for 1 residues 
    6362 
    6363 > isolde pepflip sel
    6364 
    6365 Flipping the peptide bond for 1 residues 
    6366 
    6367 > isolde pepflip sel
    6368 
    6369 Flipping the peptide bond for 1 residues 
    6370 
    6371 > isolde pepflip sel
    6372 
    6373 Flipping the peptide bond for 1 residues 
    6374 
    6375 > isolde pepflip sel
    6376 
    6377 Flipping the peptide bond for 1 residues 
    6378 
    6379 > isolde pepflip sel
    6380 
    6381 Flipping the peptide bond for 1 residues 
    6382 
    6383 > isolde pepflip sel
    6384 
    6385 Flipping the peptide bond for 1 residues 
    6386 
    6387 > isolde sim stop
    6388 
    6389 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    6390 chains... 
    6391 ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
    6392 standards. 
    6393 ISOLDE: stopped sim 
    6394 
    6395 > isolde sim start sel
    6396 
    6397 ISOLDE: started sim 
    6398 
    6399 > select clear
    6400 
    6401 > isolde pepflip sel
    6402 
    6403 Flipping the peptide bond for 1 residues 
    6404 
    6405 > isolde pepflip sel
    6406 
    6407 Flipping the peptide bond for 1 residues 
    6408 
    6409 > isolde pepflip sel
    6410 
    6411 Flipping the peptide bond for 1 residues 
    6412 
    6413 > isolde pepflip sel
    6414 
    6415 Flipping the peptide bond for 1 residues 
    6416 
    6417 > select clear
    6418 
    6419 [Repeated 1 time(s)]
    6420 
    6421 > isolde pepflip sel
    6422 
    6423 Flipping the peptide bond for 1 residues 
    6424 
    6425 > isolde pepflip sel
    6426 
    6427 Flipping the peptide bond for 1 residues 
    6428 
    6429 > isolde sim stop
    6430 
    6431 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    6432 chains... 
    6433 ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
    6434 standards. 
    6435 ISOLDE: stopped sim 
    6436 
    6437 > isolde sim start sel
    6438 
    6439 ISOLDE: started sim 
    6440 
    6441 > isolde pepflip sel
    6442 
    6443 Flipping the peptide bond for 1 residues 
    6444 
    6445 > isolde pepflip sel
    6446 
    6447 Flipping the peptide bond for 1 residues 
    6448 
    6449 > isolde pepflip sel
    6450 
    6451 Flipping the peptide bond for 1 residues 
    6452 
    6453 > isolde pepflip sel
    6454 
    6455 Flipping the peptide bond for 1 residues 
    6456 
    6457 > isolde pepflip sel
    6458 
    6459 Flipping the peptide bond for 1 residues 
    6460 
    6461 > isolde pepflip sel
    6462 
    6463 Flipping the peptide bond for 1 residues 
    6464 
    6465 > isolde pepflip sel
    6466 
    6467 Flipping the peptide bond for 1 residues 
    6468 
    6469 > isolde pepflip sel
    6470 
    6471 Flipping the peptide bond for 1 residues 
    6472 
    6473 > isolde pepflip sel
    6474 
    6475 Flipping the peptide bond for 1 residues 
    6476 
    6477 > isolde pepflip sel
    6478 
    6479 Flipping the peptide bond for 1 residues 
    6480 
    6481 > isolde pepflip sel
    6482 
    6483 Flipping the peptide bond for 1 residues 
    6484 
    6485 > isolde sim stop
    6486 
    6487 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    6488 chains... 
    6489 ISOLDE: stopped sim 
    6490 
    6491 > isolde sim start sel
    6492 
    6493 ISOLDE: started sim 
    6494 
    6495 > isolde pepflip sel
    6496 
    6497 Flipping the peptide bond for 1 residues 
    6498 
    6499 > isolde pepflip sel
    6500 
    6501 Flipping the peptide bond for 1 residues 
    6502 
    6503 > isolde pepflip sel
    6504 
    6505 Flipping the peptide bond for 1 residues 
    6506 
    6507 > isolde sim stop
    6508 
    6509 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    6510 chains... 
    6511 ISOLDE: Corrected atom nomenclature of 2 residues in model #1.2 to IUPAC-IUB
    6512 standards. 
    6513 ISOLDE: stopped sim 
    6514 
    6515 > isolde sim start sel
    6516 
    6517 ISOLDE: started sim 
    6518 
    6519 > isolde pepflip sel
    6520 
    6521 Flipping the peptide bond for 1 residues 
    6522 
    6523 > isolde pepflip sel
    6524 
    6525 Flipping the peptide bond for 1 residues 
    6526 
    6527 > select clear
    6528 
    6529 > isolde pepflip sel
    6530 
    6531 Flipping the peptide bond for 1 residues 
    6532 
    6533 > isolde pepflip sel
    6534 
    6535 Flipping the peptide bond for 1 residues 
    6536 
    6537 > select clear
    6538 
    6539 > isolde pepflip sel
    6540 
    6541 Flipping the peptide bond for 1 residues 
    6542 
    6543 > isolde pepflip sel
    6544 
    6545 Flipping the peptide bond for 1 residues 
    6546 
    6547 > isolde pepflip sel
    6548 
    6549 Flipping the peptide bond for 1 residues 
    6550 
    6551 > isolde pepflip sel
    6552 
    6553 Flipping the peptide bond for 1 residues 
    6554 
    6555 > isolde pepflip sel
    6556 
    6557 Flipping the peptide bond for 1 residues 
    6558 
    6559 > isolde pepflip sel
    6560 
    6561 Flipping the peptide bond for 1 residues 
    6562 
    6563 > isolde pepflip sel
    6564 
    6565 Flipping the peptide bond for 1 residues 
    6566 
    6567 > isolde pepflip sel
    6568 
    6569 Flipping the peptide bond for 1 residues 
    6570 
    6571 > isolde pepflip sel
    6572 
    6573 Flipping the peptide bond for 1 residues 
    6574 
    6575 > isolde pepflip sel
    6576 
    6577 Flipping the peptide bond for 1 residues 
    6578 
    6579 > isolde sim stop
    6580 
    6581 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    6582 chains... 
    6583 ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
    6584 standards. 
    6585 ISOLDE: stopped sim 
    6586 
    6587 > isolde sim start sel
    6588 
    6589 ISOLDE: started sim 
    6590 
    6591 > isolde sim stop
    6592 
    6593 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    6594 chains... 
    6595 ISOLDE: stopped sim 
    6596 
    6597 > isolde sim start sel
    6598 
    6599 ISOLDE: started sim 
    6600 
    6601 > select clear
    6602 
    6603 [Repeated 2 time(s)]
    6604 
    6605 > isolde pepflip sel
    6606 
    6607 Flipping the peptide bond for 1 residues 
    6608 
    6609 > isolde pepflip sel
    6610 
    6611 Flipping the peptide bond for 1 residues 
    6612 
    6613 > isolde sim stop
    6614 
    6615 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    6616 chains... 
    6617 ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
    6618 standards. 
    6619 ISOLDE: stopped sim 
    6620 
    6621 > isolde sim start sel
    6622 
    6623 ISOLDE: started sim 
    6624 
    6625 > isolde pepflip sel
    6626 
    6627 Flipping the peptide bond for 1 residues 
    6628 
    6629 > isolde pepflip sel
    6630 
    6631 Flipping the peptide bond for 1 residues 
    6632 
    6633 > isolde pepflip sel
    6634 
    6635 Flipping the peptide bond for 1 residues 
    6636 
    6637 > isolde pepflip sel
    6638 
    6639 Flipping the peptide bond for 1 residues 
    6640 
    6641 > isolde pepflip sel
    6642 
    6643 Flipping the peptide bond for 1 residues 
    6644 
    6645 > isolde sim stop
    6646 
    6647 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    6648 chains... 
    6649 ISOLDE: Corrected atom nomenclature of 2 residues in model #1.2 to IUPAC-IUB
    6650 standards. 
    6651 ISOLDE: stopped sim 
    6652 
    6653 > isolde sim start sel
    6654 
    6655 ISOLDE: started sim 
    6656 
    6657 > isolde pepflip sel
    6658 
    6659 Flipping the peptide bond for 1 residues 
    6660 
    6661 > isolde pepflip sel
    6662 
    6663 Flipping the peptide bond for 1 residues 
    6664 
    6665 > isolde sim stop
    6666 
    6667 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    6668 chains... 
    6669 ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
    6670 standards. 
    6671 ISOLDE: stopped sim 
    6672 
    6673 > isolde pepflip sel
    6674 
    6675 Flipping the peptide bond for 1 residues 
    6676 ISOLDE: started sim 
    6677 
    6678 > isolde pepflip sel
    6679 
    6680 Flipping the peptide bond for 1 residues 
    6681 
    6682 > isolde pepflip sel
    6683 
    6684 Flipping the peptide bond for 1 residues 
    6685 
    6686 > isolde pepflip sel
    6687 
    6688 Flipping the peptide bond for 1 residues 
    6689 
    6690 > isolde pepflip sel
    6691 
    6692 Flipping the peptide bond for 1 residues 
    6693 
    6694 > isolde pepflip sel
    6695 
    6696 Flipping the peptide bond for 1 residues 
    6697 
    6698 > isolde pepflip sel
    6699 
    6700 Flipping the peptide bond for 1 residues 
    6701 
    6702 > isolde pepflip sel
    6703 
    6704 Flipping the peptide bond for 1 residues 
    6705 
    6706 > isolde pepflip sel
    6707 
    6708 Flipping the peptide bond for 1 residues 
    6709 
    6710 > isolde pepflip sel
    6711 
    6712 Flipping the peptide bond for 1 residues 
    6713 
    6714 > isolde pepflip sel
    6715 
    6716 Flipping the peptide bond for 1 residues 
    6717 
    6718 > isolde pepflip sel
    6719 
    6720 Flipping the peptide bond for 1 residues 
    6721 
    6722 > isolde pepflip sel
    6723 
    6724 Flipping the peptide bond for 1 residues 
    6725 
    6726 > isolde pepflip sel
    6727 
    6728 Flipping the peptide bond for 1 residues 
    6729 
    6730 > isolde pepflip sel
    6731 
    6732 Flipping the peptide bond for 1 residues 
    6733 
    6734 > isolde sim stop
    6735 
    6736 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    6737 chains... 
    6738 ISOLDE: Corrected atom nomenclature of 2 residues in model #1.2 to IUPAC-IUB
    6739 standards. 
    6740 ISOLDE: stopped sim 
    6741 
    6742 > isolde pepflip sel
    6743 
    6744 Flipping the peptide bond for 1 residues 
    6745 ISOLDE: started sim 
    6746 
    6747 > isolde pepflip sel
    6748 
    6749 Flipping the peptide bond for 1 residues 
    6750 
    6751 > isolde sim stop
    6752 
    6753 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    6754 chains... 
    6755 ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
    6756 standards. 
    6757 ISOLDE: stopped sim 
    6758 
    6759 > isolde sim start sel
    6760 
    6761 ISOLDE: started sim 
    6762 
    6763 > isolde pepflip sel
    6764 
    6765 Flipping the peptide bond for 1 residues 
    6766 
    6767 > isolde pepflip sel
    6768 
    6769 Flipping the peptide bond for 1 residues 
    6770 
    6771 > select clear
    6772 
    6773 [Repeated 1 time(s)]
    6774 
    6775 > isolde pepflip sel
    6776 
    6777 Flipping the peptide bond for 1 residues 
    6778 
    6779 > isolde pepflip sel
    6780 
    6781 Flipping the peptide bond for 1 residues 
    6782 
    6783 > isolde sim stop
    6784 
    6785 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    6786 chains... 
    6787 ISOLDE: stopped sim 
    6788 
    6789 > isolde sim start sel
    6790 
    6791 ISOLDE: started sim 
    6792 
    6793 > isolde pepflip sel
    6794 
    6795 Flipping the peptide bond for 1 residues 
    6796 
    6797 > isolde pepflip sel
    6798 
    6799 Flipping the peptide bond for 1 residues 
    6800 
    6801 > select clear
    6802 
    6803 > isolde pepflip sel
    6804 
    6805 Flipping the peptide bond for 1 residues 
    6806 
    6807 > isolde pepflip sel
    6808 
    6809 Flipping the peptide bond for 1 residues 
    6810 
    6811 > isolde pepflip sel
    6812 
    6813 Flipping the peptide bond for 1 residues 
    6814 
    6815 > isolde pepflip sel
    6816 
    6817 Flipping the peptide bond for 1 residues 
    6818 
    6819 > isolde pepflip sel
    6820 
    6821 Flipping the peptide bond for 1 residues 
    6822 
    6823 > isolde pepflip sel
    6824 
    6825 Flipping the peptide bond for 1 residues 
    6826 
    6827 > isolde pepflip sel
    6828 
    6829 Flipping the peptide bond for 1 residues 
    6830 
    6831 > isolde pepflip sel
    6832 
    6833 Flipping the peptide bond for 1 residues 
    6834 
    6835 > isolde pepflip sel
    6836 
    6837 Flipping the peptide bond for 1 residues 
    6838 
    6839 > isolde pepflip sel
    6840 
    6841 Flipping the peptide bond for 1 residues 
    6842 
    6843 > isolde pepflip sel
    6844 
    6845 Flipping the peptide bond for 1 residues 
    6846 
    6847 > isolde sim stop
    6848 
    6849 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    6850 chains... 
    6851 ISOLDE: Corrected atom nomenclature of 2 residues in model #1.2 to IUPAC-IUB
    6852 standards. 
    6853 ISOLDE: stopped sim 
    6854 
    6855 > isolde sim start sel
    6856 
    6857 ISOLDE: started sim 
    6858 
    6859 > isolde pepflip sel
    6860 
    6861 Flipping the peptide bond for 1 residues 
    6862 
    6863 > isolde pepflip sel
    6864 
    6865 Flipping the peptide bond for 1 residues 
    6866 
    6867 > isolde pepflip sel
    6868 
    6869 Flipping the peptide bond for 1 residues 
    6870 
    6871 > isolde pepflip sel
    6872 
    6873 Flipping the peptide bond for 1 residues 
    6874 
    6875 > isolde cisflip sel
    6876 
    6877 Performing cis<\-->trans flip for 1 residues 
    6878 
    6879 > isolde cisflip sel
    6880 
    6881 Performing cis<\-->trans flip for 1 residues 
    6882 
    6883 > isolde pepflip sel
    6884 
    6885 Flipping the peptide bond for 1 residues 
    6886 
    6887 > isolde pepflip sel
    6888 
    6889 Flipping the peptide bond for 1 residues 
    6890 
    6891 > isolde pepflip sel
    6892 
    6893 Flipping the peptide bond for 1 residues 
    6894 
    6895 > isolde pepflip sel
    6896 
    6897 Flipping the peptide bond for 1 residues 
    6898 
    6899 > isolde pepflip sel
    6900 
    6901 Flipping the peptide bond for 1 residues 
    6902 
    6903 > isolde pepflip sel
    6904 
    6905 Flipping the peptide bond for 1 residues 
    6906 Unable to flip peptide bond after 50 rounds. Giving up. 
    6907 
    6908 > isolde pepflip sel
    6909 
    6910 Flipping the peptide bond for 1 residues 
    6911 
    6912 > isolde pepflip sel
    6913 
    6914 Flipping the peptide bond for 1 residues 
    6915 
    6916 > isolde pepflip sel
    6917 
    6918 Flipping the peptide bond for 1 residues 
    6919 
    6920 > isolde pepflip sel
    6921 
    6922 Flipping the peptide bond for 1 residues 
    6923 
    6924 > isolde cisflip sel
    6925 
    6926 Performing cis<\-->trans flip for 1 residues 
    6927 
    6928 > isolde pepflip sel
    6929 
    6930 Flipping the peptide bond for 1 residues 
    6931 
    6932 > isolde pepflip sel
    6933 
    6934 Flipping the peptide bond for 1 residues 
    6935 
    6936 > isolde pepflip sel
    6937 
    6938 Flipping the peptide bond for 1 residues 
    6939 
    6940 > isolde cisflip sel
    6941 
    6942 Performing cis<\-->trans flip for 1 residues 
    6943 
    6944 > isolde pepflip sel
    6945 
    6946 Flipping the peptide bond for 1 residues 
    6947 
    6948 > isolde pepflip sel
    6949 
    6950 Flipping the peptide bond for 1 residues 
    6951 
    6952 > isolde pepflip sel
    6953 
    6954 Flipping the peptide bond for 1 residues 
    6955 
    6956 > isolde pepflip sel
    6957 
    6958 Flipping the peptide bond for 1 residues 
    6959 
    6960 > isolde pepflip sel
    6961 
    6962 Flipping the peptide bond for 1 residues 
    6963 
    6964 > isolde pepflip sel
    6965 
    6966 Flipping the peptide bond for 1 residues 
    6967 
    6968 > isolde pepflip sel
    6969 
    6970 Flipping the peptide bond for 1 residues 
    6971 
    6972 > select clear
    6973 
    6974 [Repeated 2 time(s)]
    6975 
    6976 > isolde pepflip sel
    6977 
    6978 Flipping the peptide bond for 1 residues 
    6979 
    6980 > isolde cisflip sel
    6981 
    6982 Performing cis<\-->trans flip for 1 residues 
    6983 
    6984 > isolde pepflip sel
    6985 
    6986 Flipping the peptide bond for 1 residues 
    6987 Unable to flip peptide bond after 50 rounds. Giving up. 
    6988 
    6989 > isolde pepflip sel
    6990 
    6991 Flipping the peptide bond for 1 residues 
    6992 
    6993 > isolde sim stop
    6994 
    6995 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    6996 chains... 
    6997 ISOLDE: stopped sim 
    6998 
    6999 > isolde sim start sel
    7000 
    7001 ISOLDE: started sim 
    7002 
    7003 > isolde pepflip sel
    7004 
    7005 Flipping the peptide bond for 1 residues 
    7006 
    7007 > isolde pepflip sel
    7008 
    7009 Flipping the peptide bond for 1 residues 
    7010 
    7011 > isolde pepflip sel
    7012 
    7013 Flipping the peptide bond for 1 residues 
    7014 
    7015 > isolde pepflip sel
    7016 
    7017 Flipping the peptide bond for 1 residues 
    7018 
    7019 > isolde sim stop
    7020 
    7021 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    7022 chains... 
    7023 ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
    7024 standards. 
    7025 ISOLDE: stopped sim 
    7026 
    7027 > isolde sim start sel
    7028 
    7029 ISOLDE: started sim 
    7030 
    7031 > select clear
    7032 
    7033 > isolde sim stop
    7034 
    7035 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    7036 chains... 
    7037 ISOLDE: stopped sim 
    7038 
    7039 > isolde sim start sel
    7040 
    7041 ISOLDE: started sim 
    7042 
    7043 > isolde pepflip sel
    7044 
    7045 Flipping the peptide bond for 1 residues 
    7046 
    7047 > isolde pepflip sel
    7048 
    7049 Flipping the peptide bond for 1 residues 
    7050 
    7051 > isolde pepflip sel
    7052 
    7053 Flipping the peptide bond for 1 residues 
    7054 
    7055 > isolde pepflip sel
    7056 
    7057 Flipping the peptide bond for 1 residues 
    7058 
    7059 > isolde sim stop
    7060 
    7061 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    7062 chains... 
    7063 ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
    7064 standards. 
    7065 ISOLDE: stopped sim 
    7066 
    7067 > isolde sim start sel
    7068 
    7069 ISOLDE: started sim 
    7070 
    7071 > isolde pepflip sel
    7072 
    7073 Flipping the peptide bond for 1 residues 
    7074 
    7075 > select clear
    7076 
    7077 > isolde pepflip sel
    7078 
    7079 Flipping the peptide bond for 1 residues 
    7080 
    7081 > isolde pepflip sel
    7082 
    7083 Flipping the peptide bond for 1 residues 
    7084 
    7085 > isolde pepflip sel
    7086 
    7087 Flipping the peptide bond for 1 residues 
    7088 
    7089 > isolde pepflip sel
    7090 
    7091 Flipping the peptide bond for 1 residues 
    7092 
    7093 > isolde pepflip sel
    7094 
    7095 Flipping the peptide bond for 1 residues 
    7096 
    7097 > select clear
    7098 
    7099 > isolde pepflip sel
    7100 
    7101 Flipping the peptide bond for 1 residues 
    7102 
    7103 > isolde pepflip sel
    7104 
    7105 Flipping the peptide bond for 1 residues 
    7106 
    7107 > isolde pepflip sel
    7108 
    7109 Flipping the peptide bond for 1 residues 
    7110 
    7111 > isolde pepflip sel
    7112 
    7113 Flipping the peptide bond for 1 residues 
    7114 
    7115 > isolde cisflip sel
    7116 
    7117 Performing cis<\-->trans flip for 1 residues 
    7118 
    7119 > isolde cisflip sel
    7120 
    7121 Performing cis<\-->trans flip for 1 residues 
    7122 
    7123 > isolde pepflip sel
    7124 
    7125 Flipping the peptide bond for 1 residues 
    7126 
    7127 > isolde pepflip sel
    7128 
    7129 Flipping the peptide bond for 1 residues 
    7130 
    7131 > isolde pepflip sel
    7132 
    7133 Flipping the peptide bond for 1 residues 
    7134 
    7135 > isolde pepflip sel
    7136 
    7137 Flipping the peptide bond for 1 residues 
    7138 
    7139 > isolde pepflip sel
    7140 
    7141 Flipping the peptide bond for 1 residues 
    7142 
    7143 > isolde pepflip sel
    7144 
    7145 Flipping the peptide bond for 1 residues 
    7146 
    7147 > isolde pepflip sel
    7148 
    7149 Flipping the peptide bond for 1 residues 
    7150 
    7151 > isolde pepflip sel
    7152 
    7153 Flipping the peptide bond for 1 residues 
    7154 
    7155 > isolde pepflip sel
    7156 
    7157 Flipping the peptide bond for 1 residues 
    7158 
    7159 > isolde pepflip sel
    7160 
    7161 Flipping the peptide bond for 1 residues 
    7162 
    7163 > isolde sim stop
    7164 
    7165 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    7166 chains... 
    7167 ISOLDE: Corrected atom nomenclature of 2 residues in model #1.2 to IUPAC-IUB
    7168 standards. 
    7169 ISOLDE: stopped sim 
    7170 
    7171 > isolde sim start sel
    7172 
    7173 ISOLDE: started sim 
    7174 
    7175 > isolde pepflip sel
    7176 
    7177 Flipping the peptide bond for 1 residues 
    7178 
    7179 > isolde pepflip sel
    7180 
    7181 Flipping the peptide bond for 1 residues 
    7182 
    7183 > isolde sim stop
    7184 
    7185 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    7186 chains... 
    7187 ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
    7188 standards. 
    7189 ISOLDE: stopped sim 
    7190 
    7191 > isolde sim start sel
    7192 
    7193 ISOLDE: started sim 
    7194 
    7195 > isolde pepflip sel
    7196 
    7197 Flipping the peptide bond for 1 residues 
    7198 
    7199 > isolde pepflip sel
    7200 
    7201 Flipping the peptide bond for 1 residues 
    7202 
    7203 > isolde pepflip sel
    7204 
    7205 Flipping the peptide bond for 1 residues 
    7206 
    7207 > isolde sim stop
    7208 
    7209 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    7210 chains... 
    7211 ISOLDE: stopped sim 
    7212 
    7213 > isolde sim start sel
    7214 
    7215 ISOLDE: started sim 
    7216 
    7217 > isolde sim stop
    7218 
    7219 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    7220 chains... 
    7221 ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
    7222 standards. 
    7223 ISOLDE: stopped sim 
    7224 
    7225 > isolde sim start sel
    7226 
    7227 ISOLDE: started sim 
    7228 
    7229 > isolde pepflip sel
    7230 
    7231 Flipping the peptide bond for 1 residues 
    7232 
    7233 > isolde pepflip sel
    7234 
    7235 Flipping the peptide bond for 1 residues 
    7236 
    7237 > isolde pepflip sel
    7238 
    7239 Flipping the peptide bond for 1 residues 
    7240 
    7241 > isolde pepflip sel
    7242 
    7243 Flipping the peptide bond for 1 residues 
    7244 
    7245 > isolde pepflip sel
    7246 
    7247 Flipping the peptide bond for 1 residues 
    7248 
    7249 > isolde pepflip sel
    7250 
    7251 Flipping the peptide bond for 1 residues 
    7252 
    7253 > isolde pepflip sel
    7254 
    7255 Flipping the peptide bond for 1 residues 
    7256 
    7257 > isolde pepflip sel
    7258 
    7259 Flipping the peptide bond for 1 residues 
    7260 
    7261 > select clear
    7262 
    7263 > isolde pepflip sel
    7264 
    7265 Flipping the peptide bond for 1 residues 
    7266 
    7267 > isolde sim stop
    7268 
    7269 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    7270 chains... 
    7271 ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
    7272 standards. 
    7273 ISOLDE: stopped sim 
    7274 
    7275 > isolde sim start sel
    7276 
    7277 ISOLDE: started sim 
    7278 
    7279 > isolde pepflip sel
    7280 
    7281 Flipping the peptide bond for 1 residues 
    7282 
    7283 > isolde pepflip sel
    7284 
    7285 Flipping the peptide bond for 1 residues 
    7286 
    7287 > isolde sim stop discardTo start
    7288 
    7289 reverting to start 
    7290 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    7291 chains... 
    7292 ISOLDE: stopped sim 
    7293 
    7294 > isolde sim start sel
    7295 
    7296 ISOLDE: started sim 
    7297 
    7298 > select clear
    7299 
    7300 > isolde pepflip sel
    7301 
    7302 Flipping the peptide bond for 1 residues 
    7303 
    7304 > isolde pepflip sel
    7305 
    7306 Flipping the peptide bond for 1 residues 
    7307 
    7308 > isolde pepflip sel
    7309 
    7310 Flipping the peptide bond for 1 residues 
    7311 
    7312 > isolde pepflip sel
    7313 
    7314 Flipping the peptide bond for 1 residues 
    7315 
    7316 > select clear
    7317 
    7318 > isolde pepflip sel
    7319 
    7320 Flipping the peptide bond for 1 residues 
    7321 
    7322 > isolde pepflip sel
    7323 
    7324 Flipping the peptide bond for 1 residues 
    7325 
    7326 > isolde pepflip sel
    7327 
    7328 Flipping the peptide bond for 1 residues 
    7329 
    7330 > isolde pepflip sel
    7331 
    7332 Flipping the peptide bond for 1 residues 
    7333 
    7334 > isolde pepflip sel
    7335 
    7336 Flipping the peptide bond for 1 residues 
    7337 
    7338 > select clear
    7339 
    7340 [Repeated 1 time(s)]
    7341 
    7342 > isolde pepflip sel
    7343 
    7344 Flipping the peptide bond for 1 residues 
    7345 
    7346 > isolde pepflip sel
    7347 
    7348 Flipping the peptide bond for 1 residues 
    7349 
    7350 > isolde pepflip sel
    7351 
    7352 Flipping the peptide bond for 1 residues 
    7353 
    7354 > isolde pepflip sel
    7355 
    7356 Flipping the peptide bond for 1 residues 
    7357 
    7358 > isolde sim stop
    7359 
    7360 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    7361 chains... 
    7362 ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
    7363 standards. 
    7364 ISOLDE: stopped sim 
    7365 
    7366 > isolde sim start sel
    7367 
    7368 ISOLDE: started sim 
    7369 
    7370 > isolde sim stop
    7371 
    7372 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    7373 chains... 
    7374 ISOLDE: stopped sim 
    7375 
    7376 > isolde sim start sel
    7377 
    7378 ISOLDE: started sim 
    7379 
    7380 > isolde pepflip sel
    7381 
    7382 Flipping the peptide bond for 1 residues 
    7383 
    7384 > isolde pepflip sel
    7385 
    7386 Flipping the peptide bond for 1 residues 
    7387 
    7388 > isolde pepflip sel
    7389 
    7390 Flipping the peptide bond for 1 residues 
    7391 
    7392 > isolde pepflip sel
    7393 
    7394 Flipping the peptide bond for 1 residues 
    7395 
    7396 > isolde pepflip sel
    7397 
    7398 Flipping the peptide bond for 1 residues 
    7399 
    7400 > isolde pepflip sel
    7401 
    7402 Flipping the peptide bond for 1 residues 
    7403 
    7404 > isolde pepflip sel
    7405 
    7406 Flipping the peptide bond for 1 residues 
    7407 
    7408 > isolde pepflip sel
    7409 
    7410 Flipping the peptide bond for 1 residues 
    7411 
    7412 > isolde sim stop
    7413 
    7414 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    7415 chains... 
    7416 ISOLDE: stopped sim 
    7417 
    7418 > isolde sim start sel
    7419 
    7420 ISOLDE: started sim 
    7421 
    7422 > isolde pepflip sel
    7423 
    7424 Flipping the peptide bond for 1 residues 
    7425 
    7426 > isolde pepflip sel
    7427 
    7428 Flipping the peptide bond for 1 residues 
    7429 
    7430 > isolde pepflip sel
    7431 
    7432 Flipping the peptide bond for 1 residues 
    7433 
    7434 > isolde pepflip sel
    7435 
    7436 Flipping the peptide bond for 1 residues 
    7437 
    7438 > isolde pepflip sel
    7439 
    7440 Flipping the peptide bond for 1 residues 
    7441 
    7442 > isolde sim stop
    7443 
    7444 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    7445 chains... 
    7446 ISOLDE: Corrected atom nomenclature of 2 residues in model #1.2 to IUPAC-IUB
    7447 standards. 
    7448 ISOLDE: stopped sim 
    7449 
    7450 > isolde sim start sel
    7451 
    7452 ISOLDE: started sim 
    7453 
    7454 > isolde pepflip sel
    7455 
    7456 Flipping the peptide bond for 1 residues 
    7457 
    7458 > isolde pepflip sel
    7459 
    7460 Flipping the peptide bond for 1 residues 
    7461 
    7462 > isolde pepflip sel
    7463 
    7464 Flipping the peptide bond for 1 residues 
    7465 
    7466 > isolde pepflip sel
    7467 
    7468 Flipping the peptide bond for 1 residues 
    7469 
    7470 > isolde pepflip sel
    7471 
    7472 Flipping the peptide bond for 1 residues 
    7473 
    7474 > isolde pepflip sel
    7475 
    7476 Flipping the peptide bond for 1 residues 
    7477 
    7478 > isolde sim stop
    7479 
    7480 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    7481 chains... 
    7482 ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
    7483 standards. 
    7484 ISOLDE: stopped sim 
    7485 
    7486 > isolde sim start sel
    7487 
    7488 ISOLDE: started sim 
    7489 
    7490 > isolde pepflip sel
    7491 
    7492 Flipping the peptide bond for 1 residues 
    7493 
    7494 > isolde pepflip sel
    7495 
    7496 Flipping the peptide bond for 1 residues 
    7497 
    7498 > isolde pepflip sel
    7499 
    7500 Flipping the peptide bond for 1 residues 
    7501 
    7502 > isolde pepflip sel
    7503 
    7504 Flipping the peptide bond for 1 residues 
    7505 
    7506 > isolde pepflip sel
    7507 
    7508 Flipping the peptide bond for 1 residues 
    7509 
    7510 > isolde pepflip sel
    7511 
    7512 Flipping the peptide bond for 1 residues 
    7513 
    7514 > isolde pepflip sel
    7515 
    7516 Flipping the peptide bond for 1 residues 
    7517 
    7518 > isolde pepflip sel
    7519 
    7520 Flipping the peptide bond for 1 residues 
    7521 
    7522 > isolde pepflip sel
    7523 
    7524 Flipping the peptide bond for 1 residues 
    7525 
    7526 > isolde pepflip sel
    7527 
    7528 Flipping the peptide bond for 1 residues 
    7529 
    7530 > isolde pepflip sel
    7531 
    7532 Flipping the peptide bond for 1 residues 
    7533 
    7534 > isolde pepflip sel
    7535 
    7536 Flipping the peptide bond for 1 residues 
    7537 
    7538 > isolde pepflip sel
    7539 
    7540 Flipping the peptide bond for 1 residues 
    7541 
    7542 > isolde pepflip sel
    7543 
    7544 Flipping the peptide bond for 1 residues 
    7545 
    7546 > isolde pepflip sel
    7547 
    7548 Flipping the peptide bond for 1 residues 
    7549 
    7550 > select clear
    7551 
    7552 > isolde pepflip sel
    7553 
    7554 Flipping the peptide bond for 1 residues 
    7555 
    7556 > isolde pepflip sel
    7557 
    7558 Flipping the peptide bond for 1 residues 
    7559 
    7560 > isolde pepflip sel
    7561 
    7562 Flipping the peptide bond for 1 residues 
    7563 
    7564 > isolde pepflip sel
    7565 
    7566 Flipping the peptide bond for 1 residues 
    7567 
    7568 > isolde pepflip sel
    7569 
    7570 Flipping the peptide bond for 1 residues 
    7571 
    7572 > isolde sim stop
    7573 
    7574 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    7575 chains... 
    7576 ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
    7577 standards. 
    7578 ISOLDE: stopped sim 
    7579 
    7580 > isolde pepflip sel
    7581 
    7582 Flipping the peptide bond for 1 residues 
    7583 ISOLDE: started sim 
    7584 
    7585 > isolde pepflip sel
    7586 
    7587 Flipping the peptide bond for 1 residues 
    7588 
    7589 > isolde pepflip sel
    7590 
    7591 Flipping the peptide bond for 1 residues 
    7592 
    7593 > isolde sim stop
    7594 
    7595 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    7596 chains... 
    7597 ISOLDE: stopped sim 
    7598 
    7599 > isolde sim start sel
    7600 
    7601 ISOLDE: started sim 
    7602 
    7603 > isolde pepflip sel
    7604 
    7605 Flipping the peptide bond for 1 residues 
    7606 
    7607 > isolde pepflip sel
    7608 
    7609 Flipping the peptide bond for 1 residues 
    7610 
    7611 > select clear
    7612 
    7613 > isolde pepflip sel
    7614 
    7615 Flipping the peptide bond for 1 residues 
    7616 
    7617 > isolde sim stop
    7618 
    7619 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    7620 chains... 
    7621 ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
    7622 standards. 
    7623 ISOLDE: stopped sim 
    7624 
    7625 > isolde sim start sel
    7626 
    7627 ISOLDE: started sim 
    7628 
    7629 > isolde pepflip sel
    7630 
    7631 Flipping the peptide bond for 1 residues 
    7632 
    7633 > isolde pepflip sel
    7634 
    7635 Flipping the peptide bond for 1 residues 
    7636 
    7637 > isolde pepflip sel
    7638 
    7639 Flipping the peptide bond for 1 residues 
    7640 
    7641 > select clear
    7642 
    7643 [Repeated 1 time(s)]
    7644 
    7645 > isolde pepflip sel
    7646 
    7647 Flipping the peptide bond for 1 residues 
    7648 
    7649 > isolde pepflip sel
    7650 
    7651 Flipping the peptide bond for 1 residues 
    7652 
    7653 > isolde sim stop
    7654 
    7655 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    7656 chains... 
    7657 ISOLDE: Corrected atom nomenclature of 3 residues in model #1.2 to IUPAC-IUB
    7658 standards. 
    7659 ISOLDE: stopped sim 
    7660 
    7661 > save D:/Rafa/OneDrive/Documentos/ubuntuStorage/krsp/5OPT-refinement/40S-wt-
    7662 > refinement/7-40S-KSRP-wt-Second-steps.cxs
    7663 
    7664 Taking snapshot of stepper: 40S-wt-concat.pdb 
    7665 
    7666 > save D:/Rafa/OneDrive/Documentos/ubuntuStorage/krsp/5OPT-refinement/40S-wt-
    7667 > refinement/7-40S-KSRP-wt-Second-steps.pdb models #1
    7668 
    7669 > isolde sim start sel
    7670 
    7671 ISOLDE: started sim 
    7672 
    7673 > isolde pepflip sel
    7674 
    7675 Flipping the peptide bond for 1 residues 
    7676 
    7677 > isolde sim stop
    7678 
    7679 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    7680 chains... 
    7681 ISOLDE: stopped sim 
    7682 
    7683 > isolde sim start sel
    7684 
    7685 ISOLDE: started sim 
    7686 
    7687 > isolde pepflip sel
    7688 
    7689 Flipping the peptide bond for 1 residues 
    7690 
    7691 > isolde sim stop
    7692 
    7693 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    7694 chains... 
    7695 ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
    7696 standards. 
    7697 ISOLDE: stopped sim 
    7698 
    7699 > isolde sim start sel
    7700 
    7701 ISOLDE: started sim 
    7702 
    7703 > isolde pepflip sel
    7704 
    7705 Flipping the peptide bond for 1 residues 
    7706 
    7707 > isolde pepflip sel
    7708 
    7709 Flipping the peptide bond for 1 residues 
    7710 
    7711 > isolde pepflip sel
    7712 
    7713 Flipping the peptide bond for 1 residues 
    7714 
    7715 > isolde sim stop
    7716 
    7717 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    7718 chains... 
    7719 ISOLDE: stopped sim 
    7720 
    7721 > isolde sim start sel
    7722 
    7723 ISOLDE: started sim 
    7724 
    7725 > isolde pepflip sel
    7726 
    7727 Flipping the peptide bond for 1 residues 
    7728 
    7729 > isolde pepflip sel
    7730 
    7731 Flipping the peptide bond for 1 residues 
    7732 
    7733 > isolde pepflip sel
    7734 
    7735 Flipping the peptide bond for 1 residues 
    7736 
    7737 > isolde pepflip sel
    7738 
    7739 Flipping the peptide bond for 1 residues 
    7740 
    7741 > isolde pepflip sel
    7742 
    7743 Flipping the peptide bond for 1 residues 
    7744 
    7745 > isolde pepflip sel
    7746 
    7747 Flipping the peptide bond for 1 residues 
    7748 
    7749 > isolde pepflip sel
    7750 
    7751 Flipping the peptide bond for 1 residues 
    7752 
    7753 > isolde pepflip sel
    7754 
    7755 Flipping the peptide bond for 1 residues 
    7756 
    7757 > isolde sim stop
    7758 
    7759 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    7760 chains... 
    7761 ISOLDE: stopped sim 
    7762 
    7763 > isolde sim start sel
    7764 
    7765 ISOLDE: started sim 
    7766 
    7767 > isolde pepflip sel
    7768 
    7769 Flipping the peptide bond for 1 residues 
    7770 
    7771 > isolde pepflip sel
    7772 
    7773 Flipping the peptide bond for 1 residues 
    7774 
    7775 > isolde pepflip sel
    7776 
    7777 Flipping the peptide bond for 1 residues 
    7778 
    7779 > isolde pepflip sel
    7780 
    7781 Flipping the peptide bond for 1 residues 
    7782 Unable to flip peptide bond after 50 rounds. Giving up. 
    7783 
    7784 > isolde pepflip sel
    7785 
    7786 Flipping the peptide bond for 1 residues 
    7787 
    7788 > isolde pepflip sel
    7789 
    7790 Flipping the peptide bond for 1 residues 
    7791 
    7792 > isolde pepflip sel
    7793 
    7794 Flipping the peptide bond for 1 residues 
    7795 
    7796 > isolde pepflip sel
    7797 
    7798 Flipping the peptide bond for 1 residues 
    7799 
    7800 > isolde sim stop
    7801 
    7802 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    7803 chains... 
    7804 ISOLDE: Corrected atom nomenclature of 2 residues in model #1.2 to IUPAC-IUB
    7805 standards. 
    7806 ISOLDE: stopped sim 
    7807 
    7808 > select #1/H:
    7809 
    7810 Expected an objects specifier or a keyword 
    7811 
    7812 > select #1/h
    7813 
    7814 2780 atoms, 2803 bonds, 173 residues, 1 model selected 
    7815 
    7816 > view #1/h
    7817 
    7818 > isolde sim start sel
    7819 
    7820 ISOLDE: started sim 
    7821 
    7822 > isolde pepflip sel
    7823 
    7824 Flipping the peptide bond for 1 residues 
    7825 
    7826 > isolde pepflip sel
    7827 
    7828 Flipping the peptide bond for 1 residues 
    7829 
    7830 > isolde pepflip sel
    7831 
    7832 Flipping the peptide bond for 1 residues 
    7833 
    7834 > isolde cisflip sel
    7835 
    7836 Performing cis<\-->trans flip for 1 residues 
    7837 
    7838 > isolde pepflip sel
    7839 
    7840 Flipping the peptide bond for 1 residues 
    7841 
    7842 > isolde pepflip sel
    7843 
    7844 Flipping the peptide bond for 1 residues 
    7845 
    7846 > isolde sim stop discardTo start
    7847 
    7848 reverting to start 
    7849 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    7850 chains... 
    7851 ISOLDE: stopped sim 
    7852 
    7853 > isolde sim start sel
    7854 
    7855 ISOLDE: started sim 
    7856 
    7857 > isolde pepflip sel
    7858 
    7859 Flipping the peptide bond for 1 residues 
    7860 
    7861 > select clear
    7862 
    7863 > isolde pepflip sel
    7864 
    7865 Flipping the peptide bond for 1 residues 
    7866 
    7867 > isolde pepflip sel
    7868 
    7869 Flipping the peptide bond for 1 residues 
    7870 
    7871 > isolde pepflip sel
    7872 
    7873 Flipping the peptide bond for 1 residues 
    7874 
    7875 > isolde sim stop
    7876 
    7877 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    7878 chains... 
    7879 ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
    7880 standards. 
    7881 ISOLDE: stopped sim 
    7882 
    7883 > isolde sim start sel
    7884 
    7885 ISOLDE: started sim 
    7886 
    7887 > isolde sim stop
    7888 
    7889 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    7890 chains... 
    7891 ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
    7892 standards. 
    7893 ISOLDE: stopped sim 
    7894 
    7895 > isolde sim start sel
    7896 
    7897 ISOLDE: started sim 
    7898 
    7899 > isolde sim stop
    7900 
    7901 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    7902 chains... 
    7903 ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
    7904 standards. 
    7905 ISOLDE: stopped sim 
    7906 
    7907 > isolde sim start sel
    7908 
    7909 ISOLDE: started sim 
    7910 
    7911 > isolde sim stop
    7912 
    7913 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    7914 chains... 
    7915 ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
    7916 standards. 
    7917 ISOLDE: stopped sim 
    7918 
    7919 > isolde sim start sel
    7920 
    7921 ISOLDE: started sim 
    7922 
    7923 > isolde pepflip sel
    7924 
    7925 Flipping the peptide bond for 1 residues 
    7926 
    7927 > isolde sim stop
    7928 
    7929 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    7930 chains... 
    7931 ISOLDE: stopped sim 
    7932 
    7933 > isolde sim start sel
    7934 
    7935 ISOLDE: started sim 
    7936 
    7937 > isolde pepflip sel
    7938 
    7939 Flipping the peptide bond for 1 residues 
    7940 
    7941 > isolde pepflip sel
    7942 
    7943 Flipping the peptide bond for 1 residues 
    7944 
    7945 > isolde sim stop discardTo start
    7946 
    7947 reverting to start 
    7948 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    7949 chains... 
    7950 ISOLDE: stopped sim 
    7951 
    7952 > isolde sim start sel
    7953 
    7954 ISOLDE: started sim 
    7955 
    7956 > select clear
    7957 
    7958 > isolde pepflip sel
    7959 
    7960 Flipping the peptide bond for 1 residues 
    7961 
    7962 > isolde pepflip sel
    7963 
    7964 Flipping the peptide bond for 1 residues 
    7965 
    7966 > isolde pepflip sel
    7967 
    7968 Flipping the peptide bond for 1 residues 
    7969 
    7970 > isolde pepflip sel
    7971 
    7972 Flipping the peptide bond for 1 residues 
    7973 
    7974 > isolde pepflip sel
    7975 
    7976 Flipping the peptide bond for 1 residues 
    7977 
    7978 > isolde pepflip sel
    7979 
    7980 Flipping the peptide bond for 1 residues 
    7981 
    7982 > select clear
    7983 
    7984 > isolde pepflip sel
    7985 
    7986 Flipping the peptide bond for 1 residues 
    7987 
    7988 > isolde pepflip sel
    7989 
    7990 Flipping the peptide bond for 1 residues 
    7991 
    7992 > isolde pepflip sel
    7993 
    7994 Flipping the peptide bond for 1 residues 
    7995 
    7996 > isolde pepflip sel
    7997 
    7998 Flipping the peptide bond for 1 residues 
    7999 
    8000 > isolde pepflip sel
    8001 
    8002 Flipping the peptide bond for 1 residues 
    8003 
    8004 > isolde pepflip sel
    8005 
    8006 Flipping the peptide bond for 1 residues 
    8007 
    8008 > isolde pepflip sel
    8009 
    8010 Flipping the peptide bond for 1 residues 
    8011 
    8012 > isolde pepflip sel
    8013 
    8014 Flipping the peptide bond for 1 residues 
    8015 
    8016 > isolde pepflip sel
    8017 
    8018 Flipping the peptide bond for 1 residues 
    8019 
    8020 > isolde pepflip sel
    8021 
    8022 Flipping the peptide bond for 1 residues 
    8023 
    8024 > isolde pepflip sel
    8025 
    8026 Flipping the peptide bond for 1 residues 
    8027 
    8028 > isolde pepflip sel
    8029 
    8030 Flipping the peptide bond for 1 residues 
    8031 
    8032 > isolde pepflip sel
    8033 
    8034 Flipping the peptide bond for 1 residues 
    8035 
    8036 > isolde pepflip sel
    8037 
    8038 Flipping the peptide bond for 1 residues 
    8039 
    8040 > isolde pepflip sel
    8041 
    8042 Flipping the peptide bond for 1 residues 
    8043 
    8044 > isolde pepflip sel
    8045 
    8046 Flipping the peptide bond for 1 residues 
    8047 
    8048 > isolde pepflip sel
    8049 
    8050 Flipping the peptide bond for 1 residues 
    8051 
    8052 > isolde pepflip sel
    8053 
    8054 Flipping the peptide bond for 1 residues 
    8055 
    8056 > isolde pepflip sel
    8057 
    8058 Flipping the peptide bond for 1 residues 
    8059 
    8060 > isolde pepflip sel
    8061 
    8062 Flipping the peptide bond for 1 residues 
    8063 
    8064 > select clear
    8065 
    8066 > isolde pepflip sel
    8067 
    8068 Flipping the peptide bond for 1 residues 
    8069 
    8070 > isolde pepflip sel
    8071 
    8072 Flipping the peptide bond for 1 residues 
    8073 
    8074 > isolde pepflip sel
    8075 
    8076 Flipping the peptide bond for 1 residues 
    8077 
    8078 > isolde pepflip sel
    8079 
    8080 Flipping the peptide bond for 1 residues 
    8081 
    8082 > isolde pepflip sel
    8083 
    8084 Flipping the peptide bond for 1 residues 
    8085 
    8086 > isolde pepflip sel
    8087 
    8088 Flipping the peptide bond for 1 residues 
    8089 
    8090 > isolde pepflip sel
    8091 
    8092 Flipping the peptide bond for 1 residues 
    8093 
    8094 > isolde pepflip sel
    8095 
    8096 Flipping the peptide bond for 1 residues 
    8097 
    8098 > isolde pepflip sel
    8099 
    8100 Flipping the peptide bond for 1 residues 
    8101 
    8102 > isolde pepflip sel
    8103 
    8104 Flipping the peptide bond for 1 residues 
    8105 
    8106 > isolde pepflip sel
    8107 
    8108 Flipping the peptide bond for 1 residues 
    8109 
    8110 > isolde sim stop discardTo start
    8111 
    8112 reverting to start 
    8113 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    8114 chains... 
    8115 ISOLDE: stopped sim 
    8116 
    8117 > isolde sim start sel
    8118 
    8119 ISOLDE: started sim 
    8120 
    8121 > isolde sim stop
    8122 
    8123 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    8124 chains... 
    8125 ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
    8126 standards. 
    8127 ISOLDE: stopped sim 
    8128 
    8129 > save D:/Rafa/OneDrive/Documentos/ubuntuStorage/krsp/5OPT-refinement/40S-wt-
    8130 > refinement/7-40S-KSRP-wt-Second-steps.pdb
    8131 
    8132 > save D:/Rafa/OneDrive/Documentos/ubuntuStorage/krsp/5OPT-refinement/40S-wt-
    8133 > refinement/7-40S-KSRP-wt-Second-steps.cxs
    8134 
    8135 Taking snapshot of stepper: 40S-wt-concat.pdb 
    8136 Traceback (most recent call last): 
    8137 File "C:\Program Files\ChimeraX\bin\lib\site-
    8138 packages\chimerax\core\session.py", line 899, in save 
    8139 session.save(output, version=version, include_maps=include_maps) 
    8140 File "C:\Program Files\ChimeraX\bin\lib\site-
    8141 packages\chimerax\core\session.py", line 630, in save 
    8142 fserialize(stream, data) 
    8143 File "C:\Program Files\ChimeraX\bin\lib\site-
    8144 packages\chimerax\core\serialize.py", line 65, in msgpack_serialize 
    8145 stream.write(packer.pack(obj)) 
    8146 File "C:\Program Files\ChimeraX\bin\lib\site-
    8147 packages\chimerax\core\safesave.py", line 136, in write 
    8148 self._f.write(buf) 
    8149 File "C:\Program Files\ChimeraX\bin\lib\site-packages\lz4\frame\\__init__.py",
    8150 line 741, in write 
    8151 self._fp.write(compressed) 
    8152 OSError: [Errno 22] Invalid argument 
    8153  
    8154 OSError: [Errno 22] Invalid argument 
    8155  
    8156 File "C:\Program Files\ChimeraX\bin\lib\site-packages\lz4\frame\\__init__.py",
    8157 line 741, in write 
    8158 self._fp.write(compressed) 
    8159  
    8160 See log for complete Python traceback. 
    8161  
    8162 Cannot save 'D:/Rafa/OneDrive/Documentos/ubuntuStorage/krsp/5OPT-
    8163 refinement/40S-wt-refinement/7-40S-KSRP-wt-Second-steps.cxs': [Errno 22]
    8164 Invalid argument 
    8165 
    8166 > save D:/Rafa/OneDrive/Documentos/ubuntuStorage/krsp/5OPT-refinement/40S-wt-
    8167 > refinement/7-40S-KSRP-wt-Second-steps.cxs
    8168 
    8169 Taking snapshot of stepper: 40S-wt-concat.pdb 
    8170 
    8171 > isolde sim start sel
    8172 
    8173 ISOLDE: started sim 
    8174 
    8175 > isolde sim stop
    8176 
    8177 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    8178 chains... 
    8179 ISOLDE: stopped sim 
    8180 
    8181 > isolde sim start sel
    8182 
    8183 ISOLDE: started sim 
    8184 
    8185 > isolde pepflip sel
    8186 
    8187 Flipping the peptide bond for 1 residues 
    8188 
    8189 > isolde pepflip sel
    8190 
    8191 Flipping the peptide bond for 1 residues 
    8192 
    8193 > isolde pepflip sel
    8194 
    8195 Flipping the peptide bond for 1 residues 
    8196 
    8197 > select clear
    8198 
    8199 > isolde pepflip sel
    8200 
    8201 Flipping the peptide bond for 1 residues 
    8202 
    8203 > isolde pepflip sel
    8204 
    8205 Flipping the peptide bond for 1 residues 
    8206 
    8207 > isolde pepflip sel
    8208 
    8209 Flipping the peptide bond for 1 residues 
    8210 
    8211 > select clear
    8212 
    8213 [Repeated 1 time(s)]
    8214 
    8215 > isolde pepflip sel
    8216 
    8217 Flipping the peptide bond for 1 residues 
    8218 
    8219 > isolde pepflip sel
    8220 
    8221 Flipping the peptide bond for 1 residues 
    8222 
    8223 > isolde pepflip sel
    8224 
    8225 Flipping the peptide bond for 1 residues 
    8226 
    8227 > isolde pepflip sel
    8228 
    8229 Flipping the peptide bond for 1 residues 
    8230 
    8231 > isolde pepflip sel
    8232 
    8233 Flipping the peptide bond for 1 residues 
    8234 
    8235 > select clear
    8236 
    8237 > isolde pepflip sel
    8238 
    8239 Flipping the peptide bond for 1 residues 
    8240 
    8241 > isolde pepflip sel
    8242 
    8243 Flipping the peptide bond for 1 residues 
    8244 
    8245 > isolde sim stop
    8246 
    8247 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    8248 chains... 
    8249 ISOLDE: stopped sim 
    8250 
    8251 > isolde sim start sel
    8252 
    8253 ISOLDE: started sim 
    8254 
    8255 > select clear
    8256 
    8257 [Repeated 3 time(s)]
    8258 
    8259 > isolde pepflip sel
    8260 
    8261 Flipping the peptide bond for 1 residues 
    8262 
    8263 > isolde pepflip sel
    8264 
    8265 Flipping the peptide bond for 1 residues 
    8266 
    8267 > select clear
    8268 
    8269 > isolde pepflip sel
    8270 
    8271 Flipping the peptide bond for 1 residues 
    8272 
    8273 > isolde pepflip sel
    8274 
    8275 Flipping the peptide bond for 1 residues 
    8276 
    8277 > isolde pepflip sel
    8278 
    8279 Flipping the peptide bond for 1 residues 
    8280 
    8281 > isolde pepflip sel
    8282 
    8283 Flipping the peptide bond for 1 residues 
    8284 
    8285 > isolde pepflip sel
    8286 
    8287 Flipping the peptide bond for 1 residues 
    8288 
    8289 > isolde pepflip sel
    8290 
    8291 Flipping the peptide bond for 1 residues 
    8292 
    8293 > isolde pepflip sel
    8294 
    8295 Flipping the peptide bond for 1 residues 
    8296 
    8297 > isolde pepflip sel
    8298 
    8299 Flipping the peptide bond for 1 residues 
    8300 
    8301 > isolde pepflip sel
    8302 
    8303 Flipping the peptide bond for 1 residues 
    8304 
    8305 > isolde sim stop
    8306 
    8307 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    8308 chains... 
    8309 ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
    8310 standards. 
    8311 ISOLDE: stopped sim 
    8312 
    8313 > isolde sim start sel
    8314 
    8315 ISOLDE: started sim 
    8316 
    8317 > isolde pepflip sel
    8318 
    8319 Flipping the peptide bond for 1 residues 
    8320 
    8321 > isolde pepflip sel
    8322 
    8323 Flipping the peptide bond for 1 residues 
    8324 
    8325 > isolde pepflip sel
    8326 
    8327 Flipping the peptide bond for 1 residues 
    8328 
    8329 > isolde pepflip sel
    8330 
    8331 Flipping the peptide bond for 1 residues 
    8332 
    8333 > select clear
    8334 
    8335 > isolde pepflip sel
    8336 
    8337 Flipping the peptide bond for 1 residues 
    8338 
    8339 > isolde pepflip sel
    8340 
    8341 Flipping the peptide bond for 1 residues 
    8342 
    8343 > isolde pepflip sel
    8344 
    8345 Flipping the peptide bond for 1 residues 
    8346 
    8347 > isolde pepflip sel
    8348 
    8349 Flipping the peptide bond for 1 residues 
    8350 
    8351 > isolde pepflip sel
    8352 
    8353 Flipping the peptide bond for 1 residues 
    8354 
    8355 > isolde sim stop discardTo start
    8356 
    8357 reverting to start 
    8358 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    8359 chains... 
    8360 ISOLDE: stopped sim 
    8361 
    8362 > isolde sim start sel
    8363 
    8364 ISOLDE: started sim 
    8365 
    8366 > isolde pepflip sel
    8367 
    8368 Flipping the peptide bond for 1 residues 
    8369 
    8370 > select clear
    8371 
    8372 > isolde pepflip sel
    8373 
    8374 Flipping the peptide bond for 1 residues 
    8375 
    8376 > isolde pepflip sel
    8377 
    8378 Flipping the peptide bond for 1 residues 
    8379 
    8380 > isolde pepflip sel
    8381 
    8382 Flipping the peptide bond for 1 residues 
    8383 
    8384 > isolde pepflip sel
    8385 
    8386 Flipping the peptide bond for 1 residues 
    8387 
    8388 > isolde pepflip sel
    8389 
    8390 Flipping the peptide bond for 1 residues 
    8391 
    8392 > isolde pepflip sel
    8393 
    8394 Flipping the peptide bond for 1 residues 
    8395 
    8396 > isolde pepflip sel
    8397 
    8398 Flipping the peptide bond for 1 residues 
    8399 
    8400 > isolde pepflip sel
    8401 
    8402 Flipping the peptide bond for 1 residues 
    8403 
    8404 > isolde pepflip sel
    8405 
    8406 Flipping the peptide bond for 1 residues 
    8407 
    8408 > isolde pepflip sel
    8409 
    8410 Flipping the peptide bond for 1 residues 
    8411 
    8412 > isolde pepflip sel
    8413 
    8414 Flipping the peptide bond for 1 residues 
    8415 
    8416 > isolde pepflip sel
    8417 
    8418 Flipping the peptide bond for 1 residues 
    8419 
    8420 > isolde pepflip sel
    8421 
    8422 Flipping the peptide bond for 1 residues 
    8423 
    8424 > isolde pepflip sel
    8425 
    8426 Flipping the peptide bond for 1 residues 
    8427 
    8428 > isolde pepflip sel
    8429 
    8430 Flipping the peptide bond for 1 residues 
    8431 
    8432 > isolde pepflip sel
    8433 
    8434 Flipping the peptide bond for 1 residues 
    8435 
    8436 > isolde pepflip sel
    8437 
    8438 Flipping the peptide bond for 1 residues 
    8439 
    8440 > isolde sim stop
    8441 
    8442 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    8443 chains... 
    8444 ISOLDE: stopped sim 
    8445 
    8446 > isolde sim start sel
    8447 
    8448 ISOLDE: started sim 
    8449 
    8450 > isolde sim stop
    8451 
    8452 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    8453 chains... 
    8454 ISOLDE: stopped sim 
    8455 
    8456 > isolde sim start sel
    8457 
    8458 ISOLDE: started sim 
    8459 
    8460 > isolde pepflip sel
    8461 
    8462 Flipping the peptide bond for 1 residues 
    8463 
    8464 > isolde pepflip sel
    8465 
    8466 Flipping the peptide bond for 1 residues 
    8467 
    8468 > isolde sim stop
    8469 
    8470 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    8471 chains... 
    8472 ISOLDE: stopped sim 
    8473 
    8474 > isolde sim start sel
    8475 
    8476 ISOLDE: started sim 
    8477 
    8478 > isolde pepflip sel
    8479 
    8480 Flipping the peptide bond for 1 residues 
    8481 
    8482 > isolde pepflip sel
    8483 
    8484 Flipping the peptide bond for 1 residues 
    8485 
    8486 > isolde pepflip sel
    8487 
    8488 Flipping the peptide bond for 1 residues 
    8489 
    8490 > isolde pepflip sel
    8491 
    8492 Flipping the peptide bond for 1 residues 
    8493 
    8494 > isolde pepflip sel
    8495 
    8496 Flipping the peptide bond for 1 residues 
    8497 
    8498 > isolde pepflip sel
    8499 
    8500 Flipping the peptide bond for 1 residues 
    8501 
    8502 > isolde pepflip sel
    8503 
    8504 Flipping the peptide bond for 1 residues 
    8505 
    8506 > isolde pepflip sel
    8507 
    8508 Flipping the peptide bond for 1 residues 
    8509 
    8510 > isolde pepflip sel
    8511 
    8512 Flipping the peptide bond for 1 residues 
    8513 
    8514 > isolde pepflip sel
    8515 
    8516 Flipping the peptide bond for 1 residues 
    8517 
    8518 > isolde pepflip sel
    8519 
    8520 Flipping the peptide bond for 1 residues 
    8521 
    8522 > isolde pepflip sel
    8523 
    8524 Flipping the peptide bond for 1 residues 
    8525 
    8526 > select clear
    8527 
    8528 [Repeated 1 time(s)]
    8529 
    8530 > isolde pepflip sel
    8531 
    8532 Flipping the peptide bond for 1 residues 
    8533 
    8534 > isolde pepflip sel
    8535 
    8536 Flipping the peptide bond for 1 residues 
    8537 
    8538 > isolde pepflip sel
    8539 
    8540 Flipping the peptide bond for 1 residues 
    8541 
    8542 > isolde pepflip sel
    8543 
    8544 Flipping the peptide bond for 1 residues 
    8545 
    8546 > isolde pepflip sel
    8547 
    8548 Flipping the peptide bond for 1 residues 
    8549 
    8550 > isolde pepflip sel
    8551 
    8552 Flipping the peptide bond for 1 residues 
    8553 
    8554 > isolde pepflip sel
    8555 
    8556 Flipping the peptide bond for 1 residues 
    8557 
    8558 > isolde sim stop
    8559 
    8560 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    8561 chains... 
    8562 ISOLDE: stopped sim 
    8563 
    8564 > isolde sim start sel
    8565 
    8566 ISOLDE: started sim 
    8567 
    8568 > select clear
    8569 
    8570 > isolde pepflip sel
    8571 
    8572 Flipping the peptide bond for 1 residues 
    8573 
    8574 > isolde pepflip sel
    8575 
    8576 Flipping the peptide bond for 1 residues 
    8577 
    8578 > isolde pepflip sel
    8579 
    8580 Flipping the peptide bond for 1 residues 
    8581 
    8582 > isolde pepflip sel
    8583 
    8584 Flipping the peptide bond for 1 residues 
    8585 
    8586 > isolde pepflip sel
    8587 
    8588 Flipping the peptide bond for 1 residues 
    8589 
    8590 > isolde sim stop
    8591 
    8592 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    8593 chains... 
    8594 ISOLDE: stopped sim 
    8595 
    8596 > select clear
    8597 
    8598 > isolde sim start sel
    8599 
    8600 ISOLDE: started sim 
    8601 
    8602 > isolde sim stop
    8603 
    8604 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    8605 chains... 
    8606 ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
    8607 standards. 
    8608 ISOLDE: stopped sim 
    8609 
    8610 > isolde sim start sel
    8611 
    8612 ISOLDE: started sim 
    8613 
    8614 > isolde pepflip sel
    8615 
    8616 Flipping the peptide bond for 1 residues 
    8617 Peptide bond must be mobile in the simulation! 
    8618 
    8619 > isolde sim stop
    8620 
    8621 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    8622 chains... 
    8623 ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
    8624 standards. 
    8625 ISOLDE: stopped sim 
    8626 
    8627 > isolde sim start sel
    8628 
    8629 ISOLDE: started sim 
    8630 
    8631 > select clear
    8632 
    8633 > isolde sim stop
    8634 
    8635 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    8636 chains... 
    8637 ISOLDE: stopped sim 
    8638 
    8639 > isolde sim start sel
    8640 
    8641 ISOLDE: started sim 
    8642 
    8643 > select clear
    8644 
    8645 [Repeated 2 time(s)]
    8646 
    8647 > isolde sim stop
    8648 
    8649 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    8650 chains... 
    8651 ISOLDE: stopped sim 
    8652 
    8653 > isolde sim start sel
    8654 
    8655 ISOLDE: started sim 
    8656 
    8657 > isolde sim stop
    8658 
    8659 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    8660 chains... 
    8661 ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
    8662 standards. 
    8663 ISOLDE: stopped sim 
    8664 
    8665 > isolde sim start sel
    8666 
    8667 ISOLDE: started sim 
    8668 
    8669 > isolde sim stop
    8670 
    8671 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    8672 chains... 
    8673 ISOLDE: stopped sim 
    8674 
    8675 > isolde sim start sel
    8676 
    8677 ISOLDE: started sim 
    8678 
    8679 > isolde sim stop
    8680 
    8681 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    8682 chains... 
    8683 ISOLDE: stopped sim 
    8684 
    8685 > isolde sim start sel
    8686 
    8687 ISOLDE: started sim 
    8688 
    8689 > isolde sim stop
    8690 
    8691 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    8692 chains... 
    8693 ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
    8694 standards. 
    8695 ISOLDE: stopped sim 
    8696 
    8697 > isolde sim start sel
    8698 
    8699 ISOLDE: started sim 
    8700 
    8701 > isolde pepflip sel
    8702 
    8703 Flipping the peptide bond for 1 residues 
    8704 
    8705 > isolde pepflip sel
    8706 
    8707 Flipping the peptide bond for 1 residues 
    8708 Peptide bond must be mobile in the simulation! 
    8709 
    8710 > isolde sim stop
    8711 
    8712 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    8713 chains... 
    8714 ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
    8715 standards. 
    8716 ISOLDE: stopped sim 
    8717 
    8718 > isolde sim start sel
    8719 
    8720 ISOLDE: started sim 
    8721 
    8722 > isolde pepflip sel
    8723 
    8724 Flipping the peptide bond for 1 residues 
    8725 
    8726 > isolde pepflip sel
    8727 
    8728 Flipping the peptide bond for 1 residues 
    8729 
    8730 > isolde pepflip sel
    8731 
    8732 Flipping the peptide bond for 1 residues 
    8733 
    8734 > isolde sim stop
    8735 
    8736 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    8737 chains... 
    8738 ISOLDE: stopped sim 
    8739 
    8740 > isolde sim start sel
    8741 
    8742 ISOLDE: started sim 
    8743 
    8744 > select clear
    8745 
    8746 > isolde pepflip sel
    8747 
    8748 Flipping the peptide bond for 1 residues 
    8749 
    8750 > isolde pepflip sel
    8751 
    8752 Flipping the peptide bond for 1 residues 
    8753 Unable to flip peptide bond after 50 rounds. Giving up. 
    8754 
    8755 > isolde sim stop
    8756 
    8757 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    8758 chains... 
    8759 ISOLDE: stopped sim 
    8760 
    8761 > isolde sim start sel
    8762 
    8763 ISOLDE: started sim 
    8764 
    8765 > isolde pepflip sel
    8766 
    8767 Flipping the peptide bond for 1 residues 
    8768 
    8769 > isolde pepflip sel
    8770 
    8771 Flipping the peptide bond for 1 residues 
    8772 
    8773 > isolde pepflip sel
    8774 
    8775 Flipping the peptide bond for 1 residues 
    8776 
    8777 > isolde pepflip sel
    8778 
    8779 Flipping the peptide bond for 1 residues 
    8780 
    8781 > isolde pepflip sel
    8782 
    8783 Flipping the peptide bond for 1 residues 
    8784 
    8785 > isolde pepflip sel
    8786 
    8787 Flipping the peptide bond for 1 residues 
    8788 
    8789 > isolde pepflip sel
    8790 
    8791 Flipping the peptide bond for 1 residues 
    8792 
    8793 > isolde pepflip sel
    8794 
    8795 Flipping the peptide bond for 1 residues 
    8796 
    8797 > isolde pepflip sel
    8798 
    8799 Flipping the peptide bond for 1 residues 
    8800 
    8801 > isolde sim stop
    8802 
    8803 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    8804 chains... 
    8805 ISOLDE: Corrected atom nomenclature of 3 residues in model #1.2 to IUPAC-IUB
    8806 standards. 
    8807 ISOLDE: stopped sim 
    8808 
    8809 > isolde sim start sel
    8810 
    8811 ISOLDE: started sim 
    8812 
    8813 > isolde pepflip sel
    8814 
    8815 Flipping the peptide bond for 1 residues 
    8816 
    8817 > isolde sim stop
    8818 
    8819 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    8820 chains... 
    8821 ISOLDE: stopped sim 
    8822 
    8823 > isolde sim start sel
    8824 
    8825 ISOLDE: started sim 
    8826 
    8827 > isolde sim stop
    8828 
    8829 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    8830 chains... 
    8831 ISOLDE: stopped sim 
    8832 
    8833 > isolde sim start sel
    8834 
    8835 ISOLDE: started sim 
    8836 
    8837 > isolde sim stop
    8838 
    8839 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    8840 chains... 
    8841 ISOLDE: stopped sim 
    8842 
    8843 > isolde sim start sel
    8844 
    8845 ISOLDE: started sim 
    8846 
    8847 > isolde sim stop
    8848 
    8849 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    8850 chains... 
    8851 ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
    8852 standards. 
    8853 ISOLDE: stopped sim 
    8854 
    8855 > isolde sim start sel
    8856 
    8857 ISOLDE: started sim 
    8858 
    8859 > isolde pepflip sel
    8860 
    8861 Flipping the peptide bond for 1 residues 
    8862 
    8863 > isolde pepflip sel
    8864 
    8865 Flipping the peptide bond for 1 residues 
    8866 
    8867 > isolde pepflip sel
    8868 
    8869 Flipping the peptide bond for 1 residues 
    8870 
    8871 > isolde pepflip sel
    8872 
    8873 Flipping the peptide bond for 1 residues 
    8874 
    8875 > isolde pepflip sel
    8876 
    8877 Flipping the peptide bond for 1 residues 
    8878 
    8879 > isolde sim stop
    8880 
    8881 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    8882 chains... 
    8883 ISOLDE: stopped sim 
    8884 
    8885 > isolde sim start sel
    8886 
    8887 ISOLDE: started sim 
    8888 
    8889 > isolde sim stop
    8890 
    8891 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    8892 chains... 
    8893 ISOLDE: stopped sim 
    8894 
    8895 > isolde sim start sel
    8896 
    8897 ISOLDE: started sim 
    8898 
    8899 > isolde sim stop
    8900 
    8901 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    8902 chains... 
    8903 ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
    8904 standards. 
    8905 ISOLDE: stopped sim 
    8906 
    8907 > isolde sim start sel
    8908 
    8909 ISOLDE: started sim 
    8910 
    8911 > isolde sim stop
    8912 
    8913 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    8914 chains... 
    8915 ISOLDE: stopped sim 
    8916 
    8917 > isolde sim start sel
    8918 
    8919 ISOLDE: started sim 
    8920 
    8921 > isolde pepflip sel
    8922 
    8923 Flipping the peptide bond for 1 residues 
    8924 
    8925 > isolde pepflip sel
    8926 
    8927 Flipping the peptide bond for 1 residues 
    8928 
    8929 > isolde pepflip sel
    8930 
    8931 Flipping the peptide bond for 1 residues 
    8932 
    8933 > isolde pepflip sel
    8934 
    8935 Flipping the peptide bond for 1 residues 
    8936 
    8937 > isolde pepflip sel
    8938 
    8939 Flipping the peptide bond for 1 residues 
    8940 
    8941 > isolde pepflip sel
    8942 
    8943 Flipping the peptide bond for 1 residues 
    8944 
    8945 > isolde pepflip sel
    8946 
    8947 Flipping the peptide bond for 1 residues 
    8948 
    8949 > isolde pepflip sel
    8950 
    8951 Flipping the peptide bond for 1 residues 
    8952 
    8953 > isolde pepflip sel
    8954 
    8955 Flipping the peptide bond for 1 residues 
    8956 
    8957 > isolde pepflip sel
    8958 
    8959 Flipping the peptide bond for 1 residues 
    8960 
    8961 > isolde pepflip sel
    8962 
    8963 Flipping the peptide bond for 1 residues 
    8964 
    8965 > isolde pepflip sel
    8966 
    8967 Flipping the peptide bond for 1 residues 
    8968 
    8969 > isolde pepflip sel
    8970 
    8971 Flipping the peptide bond for 1 residues 
    8972 
    8973 > isolde pepflip sel
    8974 
    8975 Flipping the peptide bond for 1 residues 
    8976 
    8977 > isolde pepflip sel
    8978 
    8979 Flipping the peptide bond for 1 residues 
    8980 
    8981 > isolde sim stop
    8982 
    8983 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    8984 chains... 
    8985 ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
    8986 standards. 
    8987 ISOLDE: stopped sim 
    8988 
    8989 > isolde sim start sel
    8990 
    8991 ISOLDE: started sim 
    8992 
    8993 > isolde sim stop
    8994 
    8995 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    8996 chains... 
    8997 ISOLDE: stopped sim 
    8998 
    8999 > isolde sim start sel
    9000 
    9001 ISOLDE: started sim 
    9002 
    9003 > isolde pepflip sel
    9004 
    9005 Flipping the peptide bond for 1 residues 
    9006 
    9007 > isolde pepflip sel
    9008 
    9009 Flipping the peptide bond for 1 residues 
    9010 
    9011 > isolde pepflip sel
    9012 
    9013 Flipping the peptide bond for 1 residues 
    9014 
    9015 > isolde sim stop
    9016 
    9017 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    9018 chains... 
    9019 ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
    9020 standards. 
    9021 ISOLDE: stopped sim 
    9022 
    9023 > isolde sim start sel
    9024 
    9025 ISOLDE: started sim 
    9026 
    9027 > isolde sim stop
    9028 
    9029 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    9030 chains... 
    9031 ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
    9032 standards. 
    9033 ISOLDE: stopped sim 
    9034 
    9035 > isolde pepflip sel
    9036 
    9037 Flipping the peptide bond for 1 residues 
    9038 ISOLDE: started sim 
    9039 
    9040 > select clear
    9041 
    9042 > isolde sim stop
    9043 
    9044 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    9045 chains... 
    9046 ISOLDE: stopped sim 
    9047 
    9048 > isolde sim start sel
    9049 
    9050 ISOLDE: started sim 
    9051 
    9052 > isolde sim stop
    9053 
    9054 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    9055 chains... 
    9056 ISOLDE: stopped sim 
    9057 
    9058 > isolde sim start sel
    9059 
    9060 ISOLDE: started sim 
    9061 
    9062 > isolde sim stop
    9063 
    9064 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    9065 chains... 
    9066 ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
    9067 standards. 
    9068 ISOLDE: stopped sim 
    9069 
    9070 > isolde sim start sel
    9071 
    9072 ISOLDE: started sim 
    9073 
    9074 > isolde pepflip sel
    9075 
    9076 Flipping the peptide bond for 1 residues 
    9077 
    9078 > isolde pepflip sel
    9079 
    9080 Flipping the peptide bond for 1 residues 
    9081 
    9082 > isolde pepflip sel
    9083 
    9084 Flipping the peptide bond for 1 residues 
    9085 
    9086 > isolde pepflip sel
    9087 
    9088 Flipping the peptide bond for 1 residues 
    9089 
    9090 > isolde sim stop
    9091 
    9092 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    9093 chains... 
    9094 ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
    9095 standards. 
    9096 ISOLDE: stopped sim 
    9097 
    9098 > isolde sim start sel
    9099 
    9100 ISOLDE: started sim 
    9101 
    9102 > isolde pepflip sel
    9103 
    9104 Flipping the peptide bond for 1 residues 
    9105 
    9106 > isolde pepflip sel
    9107 
    9108 Flipping the peptide bond for 1 residues 
    9109 
    9110 > isolde pepflip sel
    9111 
    9112 Flipping the peptide bond for 1 residues 
    9113 
    9114 > isolde pepflip sel
    9115 
    9116 Flipping the peptide bond for 1 residues 
    9117 
    9118 > isolde pepflip sel
    9119 
    9120 Flipping the peptide bond for 1 residues 
    9121 
    9122 > isolde sim stop
    9123 
    9124 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    9125 chains... 
    9126 ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
    9127 standards. 
    9128 ISOLDE: stopped sim 
    9129 
    9130 > isolde sim start sel
    9131 
    9132 ISOLDE: started sim 
    9133 
    9134 > isolde sim stop
    9135 
    9136 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    9137 chains... 
    9138 ISOLDE: Corrected atom nomenclature of 3 residues in model #1.2 to IUPAC-IUB
    9139 standards. 
    9140 ISOLDE: stopped sim 
    9141 
    9142 > isolde sim start sel
    9143 
    9144 ISOLDE: started sim 
    9145 
    9146 > isolde pepflip sel
    9147 
    9148 Flipping the peptide bond for 1 residues 
    9149 
    9150 > isolde pepflip sel
    9151 
    9152 Flipping the peptide bond for 1 residues 
    9153 
    9154 > isolde pepflip sel
    9155 
    9156 Flipping the peptide bond for 1 residues 
    9157 
    9158 > isolde sim stop
    9159 
    9160 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    9161 chains... 
    9162 ISOLDE: stopped sim 
    9163 
    9164 > isolde sim start sel
    9165 
    9166 ISOLDE: started sim 
    9167 
    9168 > isolde sim stop
    9169 
    9170 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    9171 chains... 
    9172 ISOLDE: stopped sim 
    9173 
    9174 > isolde sim start sel
    9175 
    9176 ISOLDE: started sim 
    9177 
    9178 > isolde sim stop
    9179 
    9180 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    9181 chains... 
    9182 ISOLDE: stopped sim 
    9183 
    9184 > isolde sim start sel
    9185 
    9186 ISOLDE: started sim 
    9187 
    9188 > isolde sim stop
    9189 
    9190 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    9191 chains... 
    9192 ISOLDE: stopped sim 
    9193 
    9194 > isolde sim start sel
    9195 
    9196 ISOLDE: started sim 
    9197 
    9198 > isolde pepflip sel
    9199 
    9200 Flipping the peptide bond for 1 residues 
    9201 
    9202 > isolde pepflip sel
    9203 
    9204 Flipping the peptide bond for 1 residues 
    9205 
    9206 > isolde pepflip sel
    9207 
    9208 Flipping the peptide bond for 1 residues 
    9209 
    9210 > isolde pepflip sel
    9211 
    9212 Flipping the peptide bond for 1 residues 
    9213 
    9214 > isolde pepflip sel
    9215 
    9216 Flipping the peptide bond for 1 residues 
    9217 
    9218 > isolde pepflip sel
    9219 
    9220 Flipping the peptide bond for 1 residues 
    9221 
    9222 > isolde pepflip sel
    9223 
    9224 Flipping the peptide bond for 1 residues 
    9225 
    9226 > isolde pepflip sel
    9227 
    9228 Flipping the peptide bond for 1 residues 
    9229 
    9230 > isolde pepflip sel
    9231 
    9232 Flipping the peptide bond for 1 residues 
    9233 
    9234 > isolde sim stop
    9235 
    9236 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    9237 chains... 
    9238 ISOLDE: stopped sim 
    9239 
    9240 > isolde sim start sel
    9241 
    9242 ISOLDE: started sim 
    9243 
    9244 > isolde pepflip sel
    9245 
    9246 Flipping the peptide bond for 1 residues 
    9247 
    9248 > isolde pepflip sel
    9249 
    9250 Flipping the peptide bond for 1 residues 
    9251 
    9252 > isolde pepflip sel
    9253 
    9254 Flipping the peptide bond for 1 residues 
    9255 
    9256 > isolde pepflip sel
    9257 
    9258 Flipping the peptide bond for 1 residues 
    9259 
    9260 > isolde pepflip sel
    9261 
    9262 Flipping the peptide bond for 1 residues 
    9263 
    9264 > isolde pepflip sel
    9265 
    9266 Flipping the peptide bond for 1 residues 
    9267 
    9268 > isolde pepflip sel
    9269 
    9270 Flipping the peptide bond for 1 residues 
    9271 
    9272 > isolde pepflip sel
    9273 
    9274 Flipping the peptide bond for 1 residues 
    9275 
    9276 > isolde pepflip sel
    9277 
    9278 Flipping the peptide bond for 1 residues 
    9279 
    9280 > isolde pepflip sel
    9281 
    9282 Flipping the peptide bond for 1 residues 
    9283 
    9284 > isolde pepflip sel
    9285 
    9286 Flipping the peptide bond for 1 residues 
    9287 
    9288 > isolde pepflip sel
    9289 
    9290 Flipping the peptide bond for 1 residues 
    9291 
    9292 > isolde pepflip sel
    9293 
    9294 Flipping the peptide bond for 1 residues 
    9295 
    9296 > isolde pepflip sel
    9297 
    9298 Flipping the peptide bond for 1 residues 
    9299 
    9300 > isolde sim stop
    9301 
    9302 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    9303 chains... 
    9304 ISOLDE: Corrected atom nomenclature of 2 residues in model #1.2 to IUPAC-IUB
    9305 standards. 
    9306 ISOLDE: stopped sim 
    9307 
    9308 > isolde sim start sel
    9309 
    9310 ISOLDE: started sim 
    9311 
    9312 > isolde pepflip sel
    9313 
    9314 Flipping the peptide bond for 1 residues 
    9315 
    9316 > isolde pepflip sel
    9317 
    9318 Flipping the peptide bond for 1 residues 
    9319 
    9320 > isolde pepflip sel
    9321 
    9322 Flipping the peptide bond for 1 residues 
    9323 
    9324 > isolde sim stop
    9325 
    9326 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    9327 chains... 
    9328 ISOLDE: stopped sim 
    9329 
    9330 > isolde sim start sel
    9331 
    9332 ISOLDE: started sim 
    9333 
    9334 > isolde pepflip sel
    9335 
    9336 Flipping the peptide bond for 1 residues 
    9337 
    9338 > isolde pepflip sel
    9339 
    9340 Flipping the peptide bond for 1 residues 
    9341 
    9342 > isolde pepflip sel
    9343 
    9344 Flipping the peptide bond for 1 residues 
    9345 
    9346 > isolde pepflip sel
    9347 
    9348 Flipping the peptide bond for 1 residues 
    9349 
    9350 > isolde pepflip sel
    9351 
    9352 Flipping the peptide bond for 1 residues 
    9353 
    9354 > isolde pepflip sel
    9355 
    9356 Flipping the peptide bond for 1 residues 
    9357 
    9358 > isolde pepflip sel
    9359 
    9360 Flipping the peptide bond for 1 residues 
    9361 
    9362 > isolde pepflip sel
    9363 
    9364 Flipping the peptide bond for 1 residues 
    9365 
    9366 > isolde pepflip sel
    9367 
    9368 Flipping the peptide bond for 1 residues 
    9369 
    9370 > isolde pepflip sel
    9371 
    9372 Flipping the peptide bond for 1 residues 
    9373 
    9374 > isolde cisflip sel
    9375 
    9376 Performing cis<\-->trans flip for 1 residues 
    9377 
    9378 > isolde pepflip sel
    9379 
    9380 Flipping the peptide bond for 1 residues 
    9381 
    9382 > isolde pepflip sel
    9383 
    9384 Flipping the peptide bond for 1 residues 
    9385 
    9386 > isolde pepflip sel
    9387 
    9388 Flipping the peptide bond for 1 residues 
    9389 
    9390 > isolde pepflip sel
    9391 
    9392 Flipping the peptide bond for 1 residues 
    9393 
    9394 > isolde pepflip sel
    9395 
    9396 Flipping the peptide bond for 1 residues 
    9397 
    9398 > isolde pepflip sel
    9399 
    9400 Flipping the peptide bond for 1 residues 
    9401 
    9402 > isolde sim stop
    9403 
    9404 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    9405 chains... 
    9406 ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
    9407 standards. 
    9408 ISOLDE: stopped sim 
    9409 
    9410 > isolde sim start sel
    9411 
    9412 ISOLDE: started sim 
    9413 
    9414 > isolde pepflip sel
    9415 
    9416 Flipping the peptide bond for 1 residues 
    9417 
    9418 > select clear
    9419 
    9420 > isolde pepflip sel
    9421 
    9422 Flipping the peptide bond for 1 residues 
    9423 
    9424 > isolde pepflip sel
    9425 
    9426 Flipping the peptide bond for 1 residues 
    9427 
    9428 > isolde pepflip sel
    9429 
    9430 Flipping the peptide bond for 1 residues 
    9431 
    9432 > isolde pepflip sel
    9433 
    9434 Flipping the peptide bond for 1 residues 
    9435 
    9436 > isolde pepflip sel
    9437 
    9438 Flipping the peptide bond for 1 residues 
    9439 
    9440 > isolde pepflip sel
    9441 
    9442 Flipping the peptide bond for 1 residues 
    9443 
    9444 > isolde pepflip sel
    9445 
    9446 Flipping the peptide bond for 1 residues 
    9447 
    9448 > isolde sim stop
    9449 
    9450 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    9451 chains... 
    9452 ISOLDE: stopped sim 
    9453 
    9454 > isolde sim start sel
    9455 
    9456 ISOLDE: started sim 
    9457 
    9458 > isolde sim stop
    9459 
    9460 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    9461 chains... 
    9462 ISOLDE: stopped sim 
    9463 
    9464 > isolde sim start sel
    9465 
    9466 ISOLDE: started sim 
    9467 
    9468 > isolde sim stop
    9469 
    9470 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    9471 chains... 
    9472 ISOLDE: stopped sim 
    9473 
    9474 > isolde sim start sel
    9475 
    9476 ISOLDE: started sim 
    9477 
    9478 > select clear
    9479 
    9480 > isolde sim stop
    9481 
    9482 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    9483 chains... 
    9484 ISOLDE: Corrected atom nomenclature of 3 residues in model #1.2 to IUPAC-IUB
    9485 standards. 
    9486 ISOLDE: stopped sim 
    9487 
    9488 > isolde sim start sel
    9489 
    9490 ISOLDE: started sim 
    9491 
    9492 > isolde pepflip sel
    9493 
    9494 Flipping the peptide bond for 1 residues 
    9495 
    9496 > isolde pepflip sel
    9497 
    9498 Flipping the peptide bond for 1 residues 
    9499 
    9500 > isolde pepflip sel
    9501 
    9502 Flipping the peptide bond for 1 residues 
    9503 
    9504 > isolde cisflip sel
    9505 
    9506 Performing cis<\-->trans flip for 1 residues 
    9507 
    9508 > isolde cisflip sel
    9509 
    9510 Performing cis<\-->trans flip for 1 residues 
    9511 
    9512 > isolde pepflip sel
    9513 
    9514 Flipping the peptide bond for 1 residues 
    9515 
    9516 > isolde pepflip sel
    9517 
    9518 Flipping the peptide bond for 1 residues 
    9519 
    9520 > isolde sim stop
    9521 
    9522 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    9523 chains... 
    9524 ISOLDE: stopped sim 
    9525 
    9526 > isolde sim start sel
    9527 
    9528 ISOLDE: started sim 
    9529 
    9530 > isolde pepflip sel
    9531 
    9532 Flipping the peptide bond for 1 residues 
    9533 
    9534 > isolde pepflip sel
    9535 
    9536 Flipping the peptide bond for 1 residues 
    9537 
    9538 > isolde pepflip sel
    9539 
    9540 Flipping the peptide bond for 1 residues 
    9541 
    9542 > isolde pepflip sel
    9543 
    9544 Flipping the peptide bond for 1 residues 
    9545 
    9546 > isolde sim stop
    9547 
    9548 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    9549 chains... 
    9550 ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
    9551 standards. 
    9552 ISOLDE: stopped sim 
    9553 
    9554 > isolde sim start sel
    9555 
    9556 ISOLDE: started sim 
    9557 
    9558 > isolde pepflip sel
    9559 
    9560 Flipping the peptide bond for 1 residues 
    9561 
    9562 > isolde pepflip sel
    9563 
    9564 Flipping the peptide bond for 1 residues 
    9565 
    9566 > isolde pepflip sel
    9567 
    9568 Flipping the peptide bond for 1 residues 
    9569 
    9570 > isolde pepflip sel
    9571 
    9572 Flipping the peptide bond for 1 residues 
    9573 Unable to flip peptide bond after 50 rounds. Giving up. 
    9574 
    9575 > isolde pepflip sel
    9576 
    9577 Flipping the peptide bond for 1 residues 
    9578 
    9579 > isolde pepflip sel
    9580 
    9581 Flipping the peptide bond for 1 residues 
    9582 
    9583 > isolde pepflip sel
    9584 
    9585 Flipping the peptide bond for 1 residues 
    9586 
    9587 > isolde pepflip sel
    9588 
    9589 Flipping the peptide bond for 1 residues 
    9590 
    9591 > isolde pepflip sel
    9592 
    9593 Flipping the peptide bond for 1 residues 
    9594 
    9595 > isolde pepflip sel
    9596 
    9597 Flipping the peptide bond for 1 residues 
    9598 
    9599 > isolde pepflip sel
    9600 
    9601 Flipping the peptide bond for 1 residues 
    9602 
    9603 > isolde pepflip sel
    9604 
    9605 Flipping the peptide bond for 1 residues 
    9606 
    9607 > isolde pepflip sel
    9608 
    9609 Flipping the peptide bond for 1 residues 
    9610 
    9611 > isolde pepflip sel
    9612 
    9613 Flipping the peptide bond for 1 residues 
    9614 
    9615 > isolde pepflip sel
    9616 
    9617 Flipping the peptide bond for 1 residues 
    9618 
    9619 > isolde pepflip sel
    9620 
    9621 Flipping the peptide bond for 1 residues 
    9622 
    9623 > isolde pepflip sel
    9624 
    9625 Flipping the peptide bond for 1 residues 
    9626 
    9627 > isolde pepflip sel
    9628 
    9629 Flipping the peptide bond for 1 residues 
    9630 
    9631 > isolde sim stop
    9632 
    9633 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    9634 chains... 
    9635 ISOLDE: stopped sim 
    9636 
    9637 > isolde sim start sel
    9638 
    9639 ISOLDE: started sim 
    9640 
    9641 > isolde pepflip sel
    9642 
    9643 Flipping the peptide bond for 1 residues 
    9644 
    9645 > isolde pepflip sel
    9646 
    9647 Flipping the peptide bond for 1 residues 
    9648 
    9649 > isolde pepflip sel
    9650 
    9651 Flipping the peptide bond for 1 residues 
    9652 
    9653 > isolde cisflip sel
    9654 
    9655 Performing cis<\-->trans flip for 1 residues 
    9656 Unable to flip peptide bond after 50 rounds. Giving up. 
    9657 
    9658 > isolde cisflip sel
    9659 
    9660 Performing cis<\-->trans flip for 1 residues 
    9661 
    9662 > isolde pepflip sel
    9663 
    9664 Flipping the peptide bond for 1 residues 
    9665 
    9666 > isolde pepflip sel
    9667 
    9668 Flipping the peptide bond for 1 residues 
    9669 
    9670 > isolde pepflip sel
    9671 
    9672 Flipping the peptide bond for 1 residues 
    9673 
    9674 > isolde pepflip sel
    9675 
    9676 Flipping the peptide bond for 1 residues 
    9677 Unable to flip peptide bond after 50 rounds. Giving up. 
    9678 
    9679 > isolde pepflip sel
    9680 
    9681 Flipping the peptide bond for 1 residues 
    9682 
    9683 > isolde pepflip sel
    9684 
    9685 Flipping the peptide bond for 1 residues 
    9686 
    9687 > isolde pepflip sel
    9688 
    9689 Flipping the peptide bond for 1 residues 
    9690 
    9691 > isolde pepflip sel
    9692 
    9693 Flipping the peptide bond for 1 residues 
    9694 Unable to flip peptide bond after 50 rounds. Giving up. 
    9695 
    9696 > isolde pepflip sel
    9697 
    9698 Flipping the peptide bond for 1 residues 
    9699 
    9700 > isolde pepflip sel
    9701 
    9702 Flipping the peptide bond for 1 residues 
    9703 
    9704 > isolde pepflip sel
    9705 
    9706 Flipping the peptide bond for 1 residues 
    9707 
    9708 > isolde pepflip sel
    9709 
    9710 Flipping the peptide bond for 1 residues 
    9711 
    9712 > isolde pepflip sel
    9713 
    9714 Flipping the peptide bond for 1 residues 
    9715 
    9716 > isolde pepflip sel
    9717 
    9718 Flipping the peptide bond for 1 residues 
    9719 
    9720 > isolde pepflip sel
    9721 
    9722 Flipping the peptide bond for 1 residues 
    9723 
    9724 > select clear
    9725 
    9726 [Repeated 1 time(s)]
    9727 
    9728 > isolde pepflip sel
    9729 
    9730 Flipping the peptide bond for 1 residues 
    9731 
    9732 > isolde pepflip sel
    9733 
    9734 Flipping the peptide bond for 1 residues 
    9735 
    9736 > isolde sim stop
    9737 
    9738 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    9739 chains... 
    9740 ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
    9741 standards. 
    9742 ISOLDE: stopped sim 
    9743 
    9744 > isolde sim start sel
    9745 
    9746 ISOLDE: started sim 
    9747 
    9748 > isolde pepflip sel
    9749 
    9750 Flipping the peptide bond for 1 residues 
    9751 
    9752 > isolde pepflip sel
    9753 
    9754 Flipping the peptide bond for 1 residues 
    9755 
    9756 > isolde pepflip sel
    9757 
    9758 Flipping the peptide bond for 1 residues 
    9759 
    9760 > isolde sim stop
    9761 
    9762 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    9763 chains... 
    9764 ISOLDE: stopped sim 
    9765 
    9766 > isolde sim start sel
    9767 
    9768 ISOLDE: started sim 
    9769 
    9770 > isolde sim stop
    9771 
    9772 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    9773 chains... 
    9774 ISOLDE: stopped sim 
    9775 
    9776 > isolde sim start sel
    9777 
    9778 ISOLDE: started sim 
    9779 
    9780 > isolde pepflip sel
    9781 
    9782 Flipping the peptide bond for 1 residues 
    9783 
    9784 > isolde pepflip sel
    9785 
    9786 Flipping the peptide bond for 1 residues 
    9787 
    9788 > isolde pepflip sel
    9789 
    9790 Flipping the peptide bond for 1 residues 
    9791 
    9792 > isolde pepflip sel
    9793 
    9794 Flipping the peptide bond for 1 residues 
    9795 
    9796 > isolde pepflip sel
    9797 
    9798 Flipping the peptide bond for 1 residues 
    9799 
    9800 > isolde pepflip sel
    9801 
    9802 Flipping the peptide bond for 1 residues 
    9803 
    9804 > select clear
    9805 
    9806 > isolde pepflip sel
    9807 
    9808 Flipping the peptide bond for 1 residues 
    9809 
    9810 > isolde pepflip sel
    9811 
    9812 Flipping the peptide bond for 1 residues 
    9813 
    9814 > isolde pepflip sel
    9815 
    9816 Flipping the peptide bond for 1 residues 
    9817 
    9818 > isolde pepflip sel
    9819 
    9820 Flipping the peptide bond for 1 residues 
    9821 
    9822 > isolde pepflip sel
    9823 
    9824 Flipping the peptide bond for 1 residues 
    9825 
    9826 > isolde pepflip sel
    9827 
    9828 Flipping the peptide bond for 1 residues 
    9829 
    9830 > isolde pepflip sel
    9831 
    9832 Flipping the peptide bond for 1 residues 
    9833 
    9834 > isolde pepflip sel
    9835 
    9836 Flipping the peptide bond for 1 residues 
    9837 
    9838 > isolde pepflip sel
    9839 
    9840 Flipping the peptide bond for 1 residues 
    9841 
    9842 > isolde pepflip sel
    9843 
    9844 Flipping the peptide bond for 1 residues 
    9845 
    9846 > isolde pepflip sel
    9847 
    9848 Flipping the peptide bond for 1 residues 
    9849 
    9850 > isolde pepflip sel
    9851 
    9852 Flipping the peptide bond for 1 residues 
    9853 
    9854 > isolde pepflip sel
    9855 
    9856 Flipping the peptide bond for 1 residues 
    9857 
    9858 > isolde pepflip sel
    9859 
    9860 Flipping the peptide bond for 1 residues 
    9861 
    9862 > isolde pepflip sel
    9863 
    9864 Flipping the peptide bond for 1 residues 
    9865 
    9866 > isolde pepflip sel
    9867 
    9868 Flipping the peptide bond for 1 residues 
    9869 
    9870 > select clear
    9871 
    9872 [Repeated 1 time(s)]
    9873 
    9874 > isolde pepflip sel
    9875 
    9876 Flipping the peptide bond for 1 residues 
    9877 
    9878 > isolde pepflip sel
    9879 
    9880 Flipping the peptide bond for 1 residues 
    9881 
    9882 > isolde pepflip sel
    9883 
    9884 Flipping the peptide bond for 1 residues 
    9885 
    9886 > isolde pepflip sel
    9887 
    9888 Flipping the peptide bond for 1 residues 
    9889 
    9890 > isolde sim stop
    9891 
    9892 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    9893 chains... 
    9894 ISOLDE: stopped sim 
    9895 
    9896 > isolde sim start sel
    9897 
    9898 ISOLDE: started sim 
    9899 
    9900 > isolde sim stop
    9901 
    9902 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    9903 chains... 
    9904 ISOLDE: stopped sim 
    9905 
    9906 > isolde sim start sel
    9907 
    9908 ISOLDE: started sim 
    9909 
    9910 > isolde sim stop
    9911 
    9912 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    9913 chains... 
    9914 ISOLDE: stopped sim 
    9915 
    9916 > isolde sim start sel
    9917 
    9918 ISOLDE: started sim 
    9919 
    9920 > isolde pepflip sel
    9921 
    9922 Flipping the peptide bond for 1 residues 
    9923 
    9924 > isolde pepflip sel
    9925 
    9926 Flipping the peptide bond for 1 residues 
    9927 
    9928 > isolde pepflip sel
    9929 
    9930 Flipping the peptide bond for 1 residues 
    9931 
    9932 > isolde pepflip sel
    9933 
    9934 Flipping the peptide bond for 1 residues 
    9935 
    9936 > isolde pepflip sel
    9937 
    9938 Flipping the peptide bond for 1 residues 
    9939 
    9940 > isolde pepflip sel
    9941 
    9942 Flipping the peptide bond for 1 residues 
    9943 
    9944 > select clear
    9945 
    9946 [Repeated 1 time(s)]
    9947 
    9948 > isolde pepflip sel
    9949 
    9950 Flipping the peptide bond for 1 residues 
    9951 
    9952 > isolde pepflip sel
    9953 
    9954 Flipping the peptide bond for 1 residues 
    9955 
    9956 > isolde pepflip sel
    9957 
    9958 Flipping the peptide bond for 1 residues 
    9959 
    9960 > isolde pepflip sel
    9961 
    9962 Flipping the peptide bond for 1 residues 
    9963 
    9964 > isolde pepflip sel
    9965 
    9966 Flipping the peptide bond for 1 residues 
    9967 
    9968 > isolde pepflip sel
    9969 
    9970 Flipping the peptide bond for 1 residues 
    9971 
    9972 > isolde sim stop
    9973 
    9974 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    9975 chains... 
    9976 ISOLDE: stopped sim 
    9977 
    9978 > isolde sim start sel
    9979 
    9980 ISOLDE: started sim 
    9981 
    9982 > isolde sim stop discardTo start
    9983 
    9984 reverting to start 
    9985 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    9986 chains... 
    9987 ISOLDE: stopped sim 
    9988 
    9989 > isolde sim start sel
    9990 
    9991 ISOLDE: started sim 
    9992 
    9993 > isolde sim stop
    9994 
    9995 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    9996 chains... 
    9997 ISOLDE: stopped sim 
    9998 
    9999 > isolde sim start sel
    10000 
    10001 ISOLDE: started sim 
    10002 
    10003 > isolde sim stop
    10004 
    10005 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    10006 chains... 
    10007 ISOLDE: stopped sim 
    10008 
    10009 > isolde sim start sel
    10010 
    10011 ISOLDE: started sim 
    10012 
    10013 > isolde pepflip sel
    10014 
    10015 Flipping the peptide bond for 1 residues 
    10016 
    10017 > isolde pepflip sel
    10018 
    10019 Flipping the peptide bond for 1 residues 
    10020 
    10021 > isolde pepflip sel
    10022 
    10023 Flipping the peptide bond for 1 residues 
    10024 
    10025 > isolde pepflip sel
    10026 
    10027 Flipping the peptide bond for 1 residues 
    10028 
    10029 > isolde pepflip sel
    10030 
    10031 Flipping the peptide bond for 1 residues 
    10032 
    10033 > isolde pepflip sel
    10034 
    10035 Flipping the peptide bond for 1 residues 
    10036 
    10037 > isolde pepflip sel
    10038 
    10039 Flipping the peptide bond for 1 residues 
    10040 
    10041 > isolde pepflip sel
    10042 
    10043 Flipping the peptide bond for 1 residues 
    10044 
    10045 > isolde pepflip sel
    10046 
    10047 Flipping the peptide bond for 1 residues 
    10048 
    10049 > isolde pepflip sel
    10050 
    10051 Flipping the peptide bond for 1 residues 
    10052 
    10053 > isolde pepflip sel
    10054 
    10055 Flipping the peptide bond for 1 residues 
    10056 Unable to flip peptide bond after 50 rounds. Giving up. 
    10057 
    10058 > isolde sim stop
    10059 
    10060 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    10061 chains... 
    10062 ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
    10063 standards. 
    10064 ISOLDE: stopped sim 
    10065 
    10066 > isolde sim start sel
    10067 
    10068 ISOLDE: started sim 
    10069 
    10070 > isolde sim stop
    10071 
    10072 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    10073 chains... 
    10074 ISOLDE: stopped sim 
    10075 
    10076 > isolde sim start sel
    10077 
    10078 ISOLDE: started sim 
    10079 
    10080 > select clear
    10081 
    10082 > isolde pepflip sel
    10083 
    10084 Flipping the peptide bond for 1 residues 
    10085 
    10086 > isolde pepflip sel
    10087 
    10088 Flipping the peptide bond for 1 residues 
    10089 
    10090 > isolde pepflip sel
    10091 
    10092 Flipping the peptide bond for 1 residues 
    10093 
    10094 > select clear
    10095 
    10096 > isolde pepflip sel
    10097 
    10098 Flipping the peptide bond for 1 residues 
    10099 
    10100 > isolde sim stop
    10101 
    10102 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    10103 chains... 
    10104 ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
    10105 standards. 
    10106 ISOLDE: stopped sim 
    10107 
    10108 > isolde sim start sel
    10109 
    10110 ISOLDE: started sim 
    10111 
    10112 > isolde pepflip sel
    10113 
    10114 Flipping the peptide bond for 1 residues 
    10115 
    10116 > isolde pepflip sel
    10117 
    10118 Flipping the peptide bond for 1 residues 
    10119 
    10120 > isolde pepflip sel
    10121 
    10122 Flipping the peptide bond for 1 residues 
    10123 
    10124 > isolde sim stop
    10125 
    10126 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    10127 chains... 
    10128 ISOLDE: stopped sim 
    10129 
    10130 > isolde sim start sel
    10131 
    10132 ISOLDE: started sim 
    10133 
    10134 > isolde pepflip sel
    10135 
    10136 Flipping the peptide bond for 1 residues 
    10137 
    10138 > isolde pepflip sel
    10139 
    10140 Flipping the peptide bond for 1 residues 
    10141 
    10142 > isolde pepflip sel
    10143 
    10144 Flipping the peptide bond for 1 residues 
    10145 
    10146 > isolde pepflip sel
    10147 
    10148 Flipping the peptide bond for 1 residues 
    10149 
    10150 > isolde pepflip sel
    10151 
    10152 Flipping the peptide bond for 1 residues 
    10153 
    10154 > select clear
    10155 
    10156 > isolde pepflip sel
    10157 
    10158 Flipping the peptide bond for 1 residues 
    10159 
    10160 > isolde pepflip sel
    10161 
    10162 Flipping the peptide bond for 1 residues 
    10163 
    10164 > select clear
    10165 
    10166 > isolde pepflip sel
    10167 
    10168 Flipping the peptide bond for 1 residues 
    10169 
    10170 > isolde pepflip sel
    10171 
    10172 Flipping the peptide bond for 1 residues 
    10173 
    10174 > isolde pepflip sel
    10175 
    10176 Flipping the peptide bond for 1 residues 
    10177 
    10178 > isolde pepflip sel
    10179 
    10180 Flipping the peptide bond for 1 residues 
    10181 
    10182 > isolde pepflip sel
    10183 
    10184 Flipping the peptide bond for 1 residues 
    10185 
    10186 > isolde pepflip sel
    10187 
    10188 Flipping the peptide bond for 1 residues 
    10189 
    10190 > isolde pepflip sel
    10191 
    10192 Flipping the peptide bond for 1 residues 
    10193 
    10194 > isolde pepflip sel
    10195 
    10196 Flipping the peptide bond for 1 residues 
    10197 
    10198 > isolde sim stop
    10199 
    10200 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    10201 chains... 
    10202 ISOLDE: stopped sim 
    10203 
    10204 > isolde sim start sel
    10205 
    10206 ISOLDE: started sim 
    10207 
    10208 > isolde pepflip sel
    10209 
    10210 Flipping the peptide bond for 1 residues 
    10211 
    10212 > isolde sim stop
    10213 
    10214 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    10215 chains... 
    10216 ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
    10217 standards. 
    10218 ISOLDE: stopped sim 
    10219 
    10220 > isolde sim start sel
    10221 
    10222 ISOLDE: started sim 
    10223 
    10224 > isolde pepflip sel
    10225 
    10226 Flipping the peptide bond for 1 residues 
    10227 
    10228 > isolde sim stop
    10229 
    10230 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    10231 chains... 
    10232 ISOLDE: stopped sim 
    10233 
    10234 > isolde sim start sel
    10235 
    10236 ISOLDE: started sim 
    10237 
    10238 > isolde pepflip sel
    10239 
    10240 Flipping the peptide bond for 1 residues 
    10241 
    10242 > isolde pepflip sel
    10243 
    10244 Flipping the peptide bond for 1 residues 
    10245 
    10246 > isolde pepflip sel
    10247 
    10248 Flipping the peptide bond for 1 residues 
    10249 
    10250 > isolde pepflip sel
    10251 
    10252 Flipping the peptide bond for 1 residues 
    10253 Unable to flip peptide bond after 50 rounds. Giving up. 
    10254 
    10255 > isolde pepflip sel
    10256 
    10257 Flipping the peptide bond for 1 residues 
    10258 
    10259 > isolde pepflip sel
    10260 
    10261 Flipping the peptide bond for 1 residues 
    10262 
    10263 > isolde pepflip sel
    10264 
    10265 Flipping the peptide bond for 1 residues 
    10266 
    10267 > isolde pepflip sel
    10268 
    10269 Flipping the peptide bond for 1 residues 
    10270 
    10271 > isolde pepflip sel
    10272 
    10273 Flipping the peptide bond for 1 residues 
    10274 
    10275 > isolde pepflip sel
    10276 
    10277 Flipping the peptide bond for 1 residues 
    10278 
    10279 > isolde pepflip sel
    10280 
    10281 Flipping the peptide bond for 1 residues 
    10282 
    10283 > isolde sim stop
    10284 
    10285 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    10286 chains... 
    10287 ISOLDE: Corrected atom nomenclature of 3 residues in model #1.2 to IUPAC-IUB
    10288 standards. 
    10289 ISOLDE: stopped sim 
    10290 
    10291 > isolde sim start sel
    10292 
    10293 ISOLDE: started sim 
    10294 
    10295 > select clear
    10296 
    10297 > isolde pepflip sel
    10298 
    10299 Flipping the peptide bond for 1 residues 
    10300 
    10301 > isolde pepflip sel
    10302 
    10303 Flipping the peptide bond for 1 residues 
    10304 
    10305 > isolde pepflip sel
    10306 
    10307 Flipping the peptide bond for 1 residues 
    10308 
    10309 > isolde pepflip sel
    10310 
    10311 Flipping the peptide bond for 1 residues 
    10312 
    10313 > isolde pepflip sel
    10314 
    10315 Flipping the peptide bond for 1 residues 
    10316 
    10317 > isolde pepflip sel
    10318 
    10319 Flipping the peptide bond for 1 residues 
    10320 
    10321 > select clear
    10322 
    10323 > isolde pepflip sel
    10324 
    10325 Flipping the peptide bond for 1 residues 
    10326 
    10327 > isolde pepflip sel
    10328 
    10329 Flipping the peptide bond for 1 residues 
    10330 
    10331 > isolde pepflip sel
    10332 
    10333 Flipping the peptide bond for 1 residues 
    10334 
    10335 > isolde pepflip sel
    10336 
    10337 Flipping the peptide bond for 1 residues 
    10338 
    10339 > isolde sim stop
    10340 
    10341 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    10342 chains... 
    10343 ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
    10344 standards. 
    10345 ISOLDE: stopped sim 
    10346 
    10347 > isolde sim start sel
    10348 
    10349 ISOLDE: started sim 
    10350 
    10351 > isolde pepflip sel
    10352 
    10353 Flipping the peptide bond for 1 residues 
    10354 
    10355 > isolde pepflip sel
    10356 
    10357 Flipping the peptide bond for 1 residues 
    10358 
    10359 > isolde pepflip sel
    10360 
    10361 Flipping the peptide bond for 1 residues 
    10362 
    10363 > isolde sim stop
    10364 
    10365 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    10366 chains... 
    10367 ISOLDE: Corrected atom nomenclature of 2 residues in model #1.2 to IUPAC-IUB
    10368 standards. 
    10369 ISOLDE: stopped sim 
    10370 
    10371 > isolde sim start sel
    10372 
    10373 ISOLDE: started sim 
    10374 
    10375 > isolde pepflip sel
    10376 
    10377 Flipping the peptide bond for 1 residues 
    10378 
    10379 > isolde pepflip sel
    10380 
    10381 Flipping the peptide bond for 1 residues 
    10382 
    10383 > isolde pepflip sel
    10384 
    10385 Flipping the peptide bond for 1 residues 
    10386 
    10387 > isolde pepflip sel
    10388 
    10389 Flipping the peptide bond for 1 residues 
    10390 
    10391 > isolde pepflip sel
    10392 
    10393 Flipping the peptide bond for 1 residues 
    10394 
    10395 > isolde pepflip sel
    10396 
    10397 Flipping the peptide bond for 1 residues 
    10398 
    10399 > isolde pepflip sel
    10400 
    10401 Flipping the peptide bond for 1 residues 
    10402 
    10403 > isolde pepflip sel
    10404 
    10405 Flipping the peptide bond for 1 residues 
    10406 
    10407 > isolde pepflip sel
    10408 
    10409 Flipping the peptide bond for 1 residues 
    10410 
    10411 > isolde pepflip sel
    10412 
    10413 Flipping the peptide bond for 1 residues 
    10414 
    10415 > isolde sim stop
    10416 
    10417 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    10418 chains... 
    10419 ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
    10420 standards. 
    10421 ISOLDE: stopped sim 
    10422 
    10423 > isolde sim start sel
    10424 
    10425 ISOLDE: started sim 
    10426 
    10427 > isolde sim stop
    10428 
    10429 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    10430 chains... 
    10431 ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
    10432 standards. 
    10433 ISOLDE: stopped sim 
    10434 
    10435 > isolde sim start sel
    10436 
    10437 ISOLDE: started sim 
    10438 
    10439 > isolde pepflip sel
    10440 
    10441 Flipping the peptide bond for 1 residues 
    10442 
    10443 > isolde pepflip sel
    10444 
    10445 Flipping the peptide bond for 1 residues 
    10446 
    10447 > isolde pepflip sel
    10448 
    10449 Flipping the peptide bond for 1 residues 
    10450 
    10451 > isolde pepflip sel
    10452 
    10453 Flipping the peptide bond for 1 residues 
    10454 
    10455 > select clear
    10456 
    10457 > isolde pepflip sel
    10458 
    10459 Flipping the peptide bond for 1 residues 
    10460 
    10461 > isolde pepflip sel
    10462 
    10463 Flipping the peptide bond for 1 residues 
    10464 
    10465 > isolde pepflip sel
    10466 
    10467 Flipping the peptide bond for 1 residues 
    10468 
    10469 > isolde pepflip sel
    10470 
    10471 Flipping the peptide bond for 1 residues 
    10472 
    10473 > isolde pepflip sel
    10474 
    10475 Flipping the peptide bond for 1 residues 
    10476 
    10477 > isolde pepflip sel
    10478 
    10479 Flipping the peptide bond for 1 residues 
    10480 
    10481 > isolde pepflip sel
    10482 
    10483 Flipping the peptide bond for 1 residues 
    10484 
    10485 > isolde pepflip sel
    10486 
    10487 Flipping the peptide bond for 1 residues 
    10488 
    10489 > isolde sim stop
    10490 
    10491 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    10492 chains... 
    10493 ISOLDE: Corrected atom nomenclature of 2 residues in model #1.2 to IUPAC-IUB
    10494 standards. 
    10495 ISOLDE: stopped sim 
    10496 
    10497 > isolde sim start sel
    10498 
    10499 ISOLDE: started sim 
    10500 
    10501 > isolde pepflip sel
    10502 
    10503 Flipping the peptide bond for 1 residues 
    10504 
    10505 > isolde pepflip sel
    10506 
    10507 Flipping the peptide bond for 1 residues 
    10508 
    10509 > isolde cisflip sel
    10510 
    10511 Performing cis<\-->trans flip for 1 residues 
    10512 
    10513 > isolde pepflip sel
    10514 
    10515 Flipping the peptide bond for 1 residues 
    10516 
    10517 > isolde pepflip sel
    10518 
    10519 Flipping the peptide bond for 1 residues 
    10520 
    10521 > isolde cisflip sel
    10522 
    10523 Performing cis<\-->trans flip for 1 residues 
    10524 
    10525 > isolde sim stop
    10526 
    10527 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    10528 chains... 
    10529 ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
    10530 standards. 
    10531 ISOLDE: stopped sim 
    10532 
    10533 > isolde sim start sel
    10534 
    10535 ISOLDE: started sim 
    10536 
    10537 > isolde pepflip sel
    10538 
    10539 Flipping the peptide bond for 1 residues 
    10540 
    10541 > isolde pepflip sel
    10542 
    10543 Flipping the peptide bond for 1 residues 
    10544 
    10545 > isolde pepflip sel
    10546 
    10547 Flipping the peptide bond for 1 residues 
    10548 
    10549 > isolde pepflip sel
    10550 
    10551 Flipping the peptide bond for 1 residues 
    10552 
    10553 > isolde pepflip sel
    10554 
    10555 Flipping the peptide bond for 1 residues 
    10556 
    10557 > isolde pepflip sel
    10558 
    10559 Flipping the peptide bond for 1 residues 
    10560 
    10561 > isolde pepflip sel
    10562 
    10563 Flipping the peptide bond for 1 residues 
    10564 
    10565 > isolde pepflip sel
    10566 
    10567 Flipping the peptide bond for 1 residues 
    10568 
    10569 > select clear
    10570 
    10571 > isolde pepflip sel
    10572 
    10573 Flipping the peptide bond for 1 residues 
    10574 
    10575 > select clear
    10576 
    10577 > isolde pepflip sel
    10578 
    10579 Flipping the peptide bond for 1 residues 
    10580 
    10581 > isolde sim stop
    10582 
    10583 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    10584 chains... 
    10585 ISOLDE: stopped sim 
    10586 
    10587 > isolde sim start sel
    10588 
    10589 ISOLDE: started sim 
    10590 
    10591 > isolde pepflip sel
    10592 
    10593 Flipping the peptide bond for 1 residues 
    10594 
    10595 > isolde sim stop
    10596 
    10597 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    10598 chains... 
    10599 ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
    10600 standards. 
    10601 ISOLDE: stopped sim 
    10602 
    10603 > isolde sim start sel
    10604 
    10605 ISOLDE: started sim 
    10606 
    10607 > isolde sim stop
    10608 
    10609 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    10610 chains... 
    10611 ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
    10612 standards. 
    10613 ISOLDE: stopped sim 
    10614 
    10615 > isolde sim start sel
    10616 
    10617 ISOLDE: started sim 
    10618 
    10619 > isolde pepflip sel
    10620 
    10621 Flipping the peptide bond for 1 residues 
    10622 
    10623 > isolde pepflip sel
    10624 
    10625 Flipping the peptide bond for 1 residues 
    10626 
    10627 > isolde pepflip sel
    10628 
    10629 Flipping the peptide bond for 1 residues 
    10630 Unable to flip peptide bond after 50 rounds. Giving up. 
    10631 
    10632 > isolde sim stop
    10633 
    10634 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    10635 chains... 
    10636 ISOLDE: stopped sim 
    10637 
    10638 > isolde sim start sel
    10639 
    10640 ISOLDE: started sim 
    10641 
    10642 > isolde pepflip sel
    10643 
    10644 Flipping the peptide bond for 1 residues 
    10645 
    10646 > isolde pepflip sel
    10647 
    10648 Flipping the peptide bond for 1 residues 
    10649 
    10650 > isolde pepflip sel
    10651 
    10652 Flipping the peptide bond for 1 residues 
    10653 
    10654 > isolde sim stop
    10655 
    10656 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    10657 chains... 
    10658 ISOLDE: stopped sim 
    10659 
    10660 > isolde sim start sel
    10661 
    10662 ISOLDE: started sim 
    10663 
    10664 > isolde pepflip sel
    10665 
    10666 Flipping the peptide bond for 1 residues 
    10667 
    10668 > isolde pepflip sel
    10669 
    10670 Flipping the peptide bond for 1 residues 
    10671 
    10672 > isolde sim stop
    10673 
    10674 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    10675 chains... 
    10676 ISOLDE: stopped sim 
    10677 
    10678 > isolde sim start sel
    10679 
    10680 ISOLDE: started sim 
    10681 
    10682 > isolde pepflip sel
    10683 
    10684 Flipping the peptide bond for 1 residues 
    10685 
    10686 > isolde pepflip sel
    10687 
    10688 Flipping the peptide bond for 1 residues 
    10689 
    10690 > isolde sim stop
    10691 
    10692 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    10693 chains... 
    10694 ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
    10695 standards. 
    10696 ISOLDE: stopped sim 
    10697 
    10698 > isolde sim start sel
    10699 
    10700 ISOLDE: started sim 
    10701 
    10702 > isolde pepflip sel
    10703 
    10704 Flipping the peptide bond for 1 residues 
    10705 
    10706 > isolde pepflip sel
    10707 
    10708 Flipping the peptide bond for 1 residues 
    10709 
    10710 > isolde pepflip sel
    10711 
    10712 Flipping the peptide bond for 1 residues 
    10713 
    10714 > isolde pepflip sel
    10715 
    10716 Flipping the peptide bond for 1 residues 
    10717 Unable to flip peptide bond after 50 rounds. Giving up. 
    10718 
    10719 > isolde sim stop
    10720 
    10721 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    10722 chains... 
    10723 ISOLDE: stopped sim 
    10724 
    10725 > isolde sim start sel
    10726 
    10727 ISOLDE: started sim 
    10728 
    10729 > isolde pepflip sel
    10730 
    10731 Flipping the peptide bond for 1 residues 
    10732 
    10733 > isolde pepflip sel
    10734 
    10735 Flipping the peptide bond for 1 residues 
    10736 
    10737 > isolde pepflip sel
    10738 
    10739 Flipping the peptide bond for 1 residues 
    10740 
    10741 > isolde pepflip sel
    10742 
    10743 Flipping the peptide bond for 1 residues 
    10744 
    10745 > isolde pepflip sel
    10746 
    10747 Flipping the peptide bond for 1 residues 
    10748 
    10749 > isolde pepflip sel
    10750 
    10751 Flipping the peptide bond for 1 residues 
    10752 
    10753 > isolde pepflip sel
    10754 
    10755 Flipping the peptide bond for 1 residues 
    10756 
    10757 > isolde pepflip sel
    10758 
    10759 Flipping the peptide bond for 1 residues 
    10760 
    10761 > isolde pepflip sel
    10762 
    10763 Flipping the peptide bond for 1 residues 
    10764 Unable to flip peptide bond after 50 rounds. Giving up. 
    10765 
    10766 > isolde pepflip sel
    10767 
    10768 Flipping the peptide bond for 1 residues 
    10769 
    10770 > isolde pepflip sel
    10771 
    10772 Flipping the peptide bond for 1 residues 
    10773 
    10774 > isolde pepflip sel
    10775 
    10776 Flipping the peptide bond for 1 residues 
    10777 
    10778 > isolde pepflip sel
    10779 
    10780 Flipping the peptide bond for 1 residues 
    10781 
    10782 > isolde pepflip sel
    10783 
    10784 Flipping the peptide bond for 1 residues 
    10785 
    10786 > isolde pepflip sel
    10787 
    10788 Flipping the peptide bond for 1 residues 
    10789 
    10790 > isolde pepflip sel
    10791 
    10792 Flipping the peptide bond for 1 residues 
    10793 
    10794 > isolde pepflip sel
    10795 
    10796 Flipping the peptide bond for 1 residues 
    10797 
    10798 > isolde pepflip sel
    10799 
    10800 Flipping the peptide bond for 1 residues 
    10801 
    10802 > isolde pepflip sel
    10803 
    10804 Flipping the peptide bond for 1 residues 
    10805 
    10806 > isolde pepflip sel
    10807 
    10808 Flipping the peptide bond for 1 residues 
    10809 
    10810 > isolde pepflip sel
    10811 
    10812 Flipping the peptide bond for 1 residues 
    10813 
    10814 > isolde sim stop
    10815 
    10816 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    10817 chains... 
    10818 ISOLDE: stopped sim 
    10819 
    10820 > isolde sim start sel
    10821 
    10822 ISOLDE: started sim 
    10823 
    10824 > isolde sim stop
    10825 
    10826 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    10827 chains... 
    10828 ISOLDE: stopped sim 
    10829 
    10830 > isolde sim start sel
    10831 
    10832 ISOLDE: started sim 
    10833 
    10834 > isolde sim stop
    10835 
    10836 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    10837 chains... 
    10838 ISOLDE: stopped sim 
    10839 
    10840 > isolde sim start sel
    10841 
    10842 ISOLDE: started sim 
    10843 
    10844 > isolde pepflip sel
    10845 
    10846 Flipping the peptide bond for 1 residues 
    10847 
    10848 > isolde pepflip sel
    10849 
    10850 Flipping the peptide bond for 1 residues 
    10851 
    10852 > isolde sim stop
    10853 
    10854 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    10855 chains... 
    10856 ISOLDE: stopped sim 
    10857 
    10858 > isolde sim start sel
    10859 
    10860 ISOLDE: started sim 
    10861 
    10862 > isolde sim stop
    10863 
    10864 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    10865 chains... 
    10866 ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
    10867 standards. 
    10868 ISOLDE: stopped sim 
    10869 
    10870 > isolde sim start sel
    10871 
    10872 ISOLDE: started sim 
    10873 
    10874 > isolde pepflip sel
    10875 
    10876 Flipping the peptide bond for 1 residues 
    10877 
    10878 > isolde pepflip sel
    10879 
    10880 Flipping the peptide bond for 1 residues 
    10881 
    10882 > isolde pepflip sel
    10883 
    10884 Flipping the peptide bond for 1 residues 
    10885 
    10886 > isolde pepflip sel
    10887 
    10888 Flipping the peptide bond for 1 residues 
    10889 
    10890 > isolde sim stop
    10891 
    10892 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    10893 chains... 
    10894 ISOLDE: stopped sim 
    10895 
    10896 > isolde sim start sel
    10897 
    10898 ISOLDE: started sim 
    10899 
    10900 > isolde sim stop
    10901 
    10902 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    10903 chains... 
    10904 ISOLDE: stopped sim 
    10905 
    10906 > isolde sim start sel
    10907 
    10908 ISOLDE: started sim 
    10909 
    10910 > isolde sim stop
    10911 
    10912 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    10913 chains... 
    10914 ISOLDE: stopped sim 
    10915 
    10916 > isolde sim start sel
    10917 
    10918 ISOLDE: started sim 
    10919 
    10920 > isolde sim stop
    10921 
    10922 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    10923 chains... 
    10924 ISOLDE: stopped sim 
    10925 
    10926 > isolde sim start sel
    10927 
    10928 ISOLDE: started sim 
    10929 
    10930 > isolde sim stop
    10931 
    10932 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    10933 chains... 
    10934 ISOLDE: stopped sim 
    10935 
    10936 > isolde sim start sel
    10937 
    10938 ISOLDE: started sim 
    10939 
    10940 > isolde sim stop
    10941 
    10942 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    10943 chains... 
    10944 ISOLDE: stopped sim 
    10945 
    10946 > isolde sim start sel
    10947 
    10948 ISOLDE: started sim 
    10949 
    10950 > isolde sim stop
    10951 
    10952 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    10953 chains... 
    10954 ISOLDE: stopped sim 
    10955 
    10956 > isolde sim start sel
    10957 
    10958 ISOLDE: started sim 
    10959 
    10960 > isolde pepflip sel
    10961 
    10962 Flipping the peptide bond for 1 residues 
    10963 
    10964 > isolde sim stop
    10965 
    10966 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    10967 chains... 
    10968 ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
    10969 standards. 
    10970 ISOLDE: stopped sim 
    10971 
    10972 > isolde sim start sel
    10973 
    10974 ISOLDE: started sim 
    10975 
    10976 > isolde sim stop
    10977 
    10978 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    10979 chains... 
    10980 ISOLDE: stopped sim 
    10981 
    10982 > isolde sim start sel
    10983 
    10984 ISOLDE: started sim 
    10985 
    10986 > isolde sim stop
    10987 
    10988 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    10989 chains... 
    10990 ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
    10991 standards. 
    10992 ISOLDE: stopped sim 
    10993 
    10994 > isolde sim start sel
    10995 
    10996 ISOLDE: started sim 
    10997 
    10998 > isolde sim stop
    10999 
    11000 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    11001 chains... 
    11002 ISOLDE: stopped sim 
    11003 
    11004 > isolde sim start sel
    11005 
    11006 ISOLDE: started sim 
    11007 
    11008 > isolde sim stop
    11009 
    11010 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    11011 chains... 
    11012 ISOLDE: stopped sim 
    11013 
    11014 > isolde sim start sel
    11015 
    11016 ISOLDE: started sim 
    11017 
    11018 > isolde sim stop
    11019 
    11020 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    11021 chains... 
    11022 ISOLDE: stopped sim 
    11023 
    11024 > isolde sim start sel
    11025 
    11026 ISOLDE: started sim 
    11027 
    11028 > isolde sim stop
    11029 
    11030 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    11031 chains... 
    11032 ISOLDE: stopped sim 
    11033 
    11034 > isolde sim start sel
    11035 
    11036 ISOLDE: started sim 
    11037 
    11038 > isolde sim stop
    11039 
    11040 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    11041 chains... 
    11042 ISOLDE: stopped sim 
    11043 
    11044 > isolde sim start sel
    11045 
    11046 ISOLDE: started sim 
    11047 
    11048 > isolde sim stop
    11049 
    11050 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    11051 chains... 
    11052 ISOLDE: stopped sim 
    11053 
    11054 > isolde sim start sel
    11055 
    11056 ISOLDE: started sim 
    11057 
    11058 > isolde sim stop
    11059 
    11060 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    11061 chains... 
    11062 ISOLDE: stopped sim 
    11063 
    11064 > isolde sim start sel
    11065 
    11066 ISOLDE: started sim 
    11067 
    11068 > isolde sim stop
    11069 
    11070 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    11071 chains... 
    11072 ISOLDE: stopped sim 
    11073 
    11074 > isolde sim start sel
    11075 
    11076 ISOLDE: started sim 
    11077 
    11078 > isolde sim stop
    11079 
    11080 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    11081 chains... 
    11082 ISOLDE: stopped sim 
    11083 
    11084 > isolde sim start sel
    11085 
    11086 ISOLDE: started sim 
    11087 
    11088 > isolde sim stop
    11089 
    11090 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    11091 chains... 
    11092 ISOLDE: stopped sim 
    11093 
    11094 > isolde sim start sel
    11095 
    11096 ISOLDE: started sim 
    11097 
    11098 > isolde sim stop
    11099 
    11100 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    11101 chains... 
    11102 ISOLDE: stopped sim 
    11103 
    11104 > ui windowfill toggle
    11105 
    11106 [Repeated 1 time(s)]
    11107 
    11108 > select :B@10
    11109 
    11110 Nothing selected 
    11111 
    11112 > select :I@52
    11113 
    11114 Nothing selected 
    11115 
    11116 > view :B@10
    11117 
    11118 No objects specified. 
    11119 
    11120 > view :B|10
    11121 
    11122 Expected an objects specifier or a view name or a keyword 
    11123 
    11124 > view :B@10
    11125 
    11126 No objects specified. 
    11127 
    11128 > view #B:10
    11129 
    11130 Expected an objects specifier or a view name or a keyword 
    11131 
    11132 > view #1/I:10
    11133 
    11134 No objects specified. 
    11135 
    11136 > view #1/I:52
    11137 
    11138 No objects specified. 
    11139 
    11140 > select #1/I:52
    11141 
    11142 Nothing selected 
    11143 
    11144 > select #1/o:52
    11145 
    11146 15 atoms, 14 bonds, 1 residue, 1 model selected 
    11147 
    11148 > select #1/o:60
    11149 
    11150 24 atoms, 23 bonds, 1 residue, 1 model selected 
    11151 
    11152 > view #1/o:60
    11153 
    11154 > view #1/l:52
    11155 
    11156 > select #1/l:52
    11157 
    11158 24 atoms, 23 bonds, 1 residue, 1 model selected 
    11159 
    11160 > view #1/l:52
    11161 
    11162 > isolde sim start sel
    11163 
    11164 ISOLDE: started sim 
    11165 
    11166 > isolde sim stop
    11167 
    11168 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    11169 chains... 
    11170 ISOLDE: stopped sim 
    11171 
    11172 > view #1/l:34
    11173 
    11174 > select #1/l:34
    11175 
    11176 14 atoms, 13 bonds, 1 residue, 1 model selected 
    11177 
    11178 > view #1/l:34,#1/l:52
    11179 
    11180 Expected an objects specifier or a view name or a keyword 
    11181 
    11182 > select #1/l:34,#1/l:52
    11183 
    11184 Expected an objects specifier or a keyword 
    11185 
    11186 > select #1/l:34,#1/l:52
    11187 
    11188 Expected an objects specifier or a keyword 
    11189 
    11190 > select #1/l:34.52
    11191 
    11192 Expected an objects specifier or a keyword 
    11193 
    11194 > select #1/l:34,#1/l:52
    11195 
    11196 Expected an objects specifier or a keyword 
    11197 
    11198 > select #1/l:34,#1/l:52
    11199 
    11200 Expected an objects specifier or a keyword 
    11201 
    11202 > select #1/l:34,#1/l:52
    11203 
    11204 Expected an objects specifier or a keyword 
    11205 
    11206 > select #1/l:34,52
    11207 
    11208 38 atoms, 36 bonds, 2 residues, 1 model selected 
    11209 
    11210 > view #1/l:34,52
    11211 
    11212 > isolde sim start sel
    11213 
    11214 ISOLDE: started sim 
    11215 
    11216 > isolde sim stop
    11217 
    11218 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    11219 chains... 
    11220 ISOLDE: stopped sim 
    11221 
    11222 > isolde sim start sel
    11223 
    11224 ISOLDE: started sim 
    11225 
    11226 > isolde pepflip sel
    11227 
    11228 Flipping the peptide bond for 1 residues 
    11229 
    11230 > isolde pepflip sel
    11231 
    11232 Flipping the peptide bond for 1 residues 
    11233 
    11234 > isolde pepflip sel
    11235 
    11236 Flipping the peptide bond for 1 residues 
    11237 
    11238 > isolde sim stop
    11239 
    11240 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    11241 chains... 
    11242 ISOLDE: stopped sim 
    11243 
    11244 > isolde sim start sel
    11245 
    11246 ISOLDE: started sim 
    11247 
    11248 > isolde pepflip sel
    11249 
    11250 Flipping the peptide bond for 1 residues 
    11251 
    11252 > isolde pepflip sel
    11253 
    11254 Flipping the peptide bond for 1 residues 
    11255 
    11256 > isolde pepflip sel
    11257 
    11258 Flipping the peptide bond for 1 residues 
    11259 
    11260 > isolde pepflip sel
    11261 
    11262 Flipping the peptide bond for 1 residues 
    11263 
    11264 > isolde pepflip sel
    11265 
    11266 Flipping the peptide bond for 1 residues 
    11267 
    11268 > isolde pepflip sel
    11269 
    11270 Flipping the peptide bond for 1 residues 
    11271 
    11272 > isolde pepflip sel
    11273 
    11274 Flipping the peptide bond for 1 residues 
    11275 
    11276 > isolde pepflip sel
    11277 
    11278 Flipping the peptide bond for 1 residues 
    11279 
    11280 > isolde pepflip sel
    11281 
    11282 Flipping the peptide bond for 1 residues 
    11283 
    11284 > isolde pepflip sel
    11285 
    11286 Flipping the peptide bond for 1 residues 
    11287 
    11288 > isolde sim stop
    11289 
    11290 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    11291 chains... 
    11292 ISOLDE: stopped sim 
    11293 
    11294 > isolde sim start sel
    11295 
    11296 ISOLDE: started sim 
    11297 
    11298 > isolde pepflip sel
    11299 
    11300 Flipping the peptide bond for 1 residues 
    11301 
    11302 > isolde sim stop
    11303 
    11304 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    11305 chains... 
    11306 ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
    11307 standards. 
    11308 ISOLDE: stopped sim 
    11309 
    11310 > isolde sim start sel
    11311 
    11312 ISOLDE: started sim 
    11313 
    11314 > select clear
    11315 
    11316 [Repeated 2 time(s)]
    11317 
    11318 > isolde pepflip sel
    11319 
    11320 Flipping the peptide bond for 1 residues 
    11321 
    11322 > isolde pepflip sel
    11323 
    11324 Flipping the peptide bond for 1 residues 
    11325 
    11326 > isolde pepflip sel
    11327 
    11328 Flipping the peptide bond for 1 residues 
    11329 
    11330 > isolde pepflip sel
    11331 
    11332 Flipping the peptide bond for 1 residues 
    11333 
    11334 > isolde pepflip sel
    11335 
    11336 Flipping the peptide bond for 1 residues 
    11337 
    11338 > isolde pepflip sel
    11339 
    11340 Flipping the peptide bond for 1 residues 
    11341 
    11342 > isolde pepflip sel
    11343 
    11344 Flipping the peptide bond for 1 residues 
    11345 
    11346 > isolde pepflip sel
    11347 
    11348 Flipping the peptide bond for 1 residues 
    11349 
    11350 > isolde sim stop
    11351 
    11352 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    11353 chains... 
    11354 ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
    11355 standards. 
    11356 ISOLDE: stopped sim 
    11357 
    11358 > isolde sim start sel
    11359 
    11360 ISOLDE: started sim 
    11361 
    11362 > isolde pepflip sel
    11363 
    11364 Flipping the peptide bond for 1 residues 
    11365 
    11366 > isolde sim stop
    11367 
    11368 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    11369 chains... 
    11370 ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
    11371 standards. 
    11372 ISOLDE: stopped sim 
    11373 
    11374 > isolde sim start sel
    11375 
    11376 ISOLDE: started sim 
    11377 
    11378 > isolde sim stop
    11379 
    11380 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    11381 chains... 
    11382 ISOLDE: stopped sim 
    11383 
    11384 > isolde sim start sel
    11385 
    11386 ISOLDE: started sim 
    11387 
    11388 > isolde pepflip sel
    11389 
    11390 Flipping the peptide bond for 1 residues 
    11391 
    11392 > select clear
    11393 
    11394 > isolde pepflip sel
    11395 
    11396 Flipping the peptide bond for 1 residues 
    11397 
    11398 > isolde pepflip sel
    11399 
    11400 Flipping the peptide bond for 1 residues 
    11401 
    11402 > isolde pepflip sel
    11403 
    11404 Flipping the peptide bond for 1 residues 
    11405 
    11406 > isolde pepflip sel
    11407 
    11408 Flipping the peptide bond for 1 residues 
    11409 
    11410 > isolde pepflip sel
    11411 
    11412 Flipping the peptide bond for 1 residues 
    11413 
    11414 > isolde pepflip sel
    11415 
    11416 Flipping the peptide bond for 1 residues 
    11417 
    11418 > isolde sim stop
    11419 
    11420 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    11421 chains... 
    11422 ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
    11423 standards. 
    11424 ISOLDE: stopped sim 
    11425 
    11426 > isolde sim start sel
    11427 
    11428 ISOLDE: started sim 
    11429 
    11430 > isolde pepflip sel
    11431 
    11432 Flipping the peptide bond for 1 residues 
    11433 
    11434 > isolde pepflip sel
    11435 
    11436 Flipping the peptide bond for 1 residues 
    11437 
    11438 > isolde pepflip sel
    11439 
    11440 Flipping the peptide bond for 1 residues 
    11441 
    11442 > select clear
    11443 
    11444 [Repeated 3 time(s)]
    11445 
    11446 > isolde pepflip sel
    11447 
    11448 Flipping the peptide bond for 1 residues 
    11449 
    11450 > isolde pepflip sel
    11451 
    11452 Flipping the peptide bond for 1 residues 
    11453 
    11454 > isolde pepflip sel
    11455 
    11456 Flipping the peptide bond for 1 residues 
    11457 
    11458 > isolde pepflip sel
    11459 
    11460 Flipping the peptide bond for 1 residues 
    11461 
    11462 > isolde pepflip sel
    11463 
    11464 Flipping the peptide bond for 1 residues 
    11465 
    11466 > isolde pepflip sel
    11467 
    11468 Flipping the peptide bond for 1 residues 
    11469 
    11470 > isolde pepflip sel
    11471 
    11472 Flipping the peptide bond for 1 residues 
    11473 Peptide bond must be mobile in the simulation! 
    11474 
    11475 > isolde pepflip sel
    11476 
    11477 Flipping the peptide bond for 1 residues 
    11478 
    11479 > isolde pepflip sel
    11480 
    11481 Flipping the peptide bond for 1 residues 
    11482 
    11483 > isolde sim stop
    11484 
    11485 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    11486 chains... 
    11487 ISOLDE: Corrected atom nomenclature of 3 residues in model #1.2 to IUPAC-IUB
    11488 standards. 
    11489 ISOLDE: stopped sim 
    11490 
    11491 > isolde sim start sel
    11492 
    11493 ISOLDE: started sim 
    11494 
    11495 > isolde sim stop
    11496 
    11497 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    11498 chains... 
    11499 ISOLDE: stopped sim 
    11500 
    11501 > isolde sim start sel
    11502 
    11503 ISOLDE: started sim 
    11504 
    11505 > isolde pepflip sel
    11506 
    11507 Flipping the peptide bond for 1 residues 
    11508 
    11509 > isolde pepflip sel
    11510 
    11511 Flipping the peptide bond for 1 residues 
    11512 
    11513 > isolde pepflip sel
    11514 
    11515 Flipping the peptide bond for 1 residues 
    11516 
    11517 > isolde sim stop
    11518 
    11519 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    11520 chains... 
    11521 ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
    11522 standards. 
    11523 ISOLDE: stopped sim 
    11524 
    11525 > isolde pepflip sel
    11526 
    11527 Flipping the peptide bond for 1 residues 
    11528 ISOLDE: started sim 
    11529 
    11530 > isolde sim stop discardTo start
    11531 
    11532 reverting to start 
    11533 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    11534 chains... 
    11535 ISOLDE: stopped sim 
    11536 
    11537 > isolde sim start sel
    11538 
    11539 ISOLDE: started sim 
    11540 
    11541 > isolde pepflip sel
    11542 
    11543 Flipping the peptide bond for 1 residues 
    11544 
    11545 > isolde pepflip sel
    11546 
    11547 Flipping the peptide bond for 1 residues 
    11548 
    11549 > isolde pepflip sel
    11550 
    11551 Flipping the peptide bond for 1 residues 
    11552 
    11553 > isolde pepflip sel
    11554 
    11555 Flipping the peptide bond for 1 residues 
    11556 
    11557 > isolde pepflip sel
    11558 
    11559 Flipping the peptide bond for 1 residues 
    11560 
    11561 > isolde sim stop
    11562 
    11563 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    11564 chains... 
    11565 ISOLDE: stopped sim 
    11566 
    11567 > isolde sim start sel
    11568 
    11569 ISOLDE: started sim 
    11570 
    11571 > isolde sim stop
    11572 
    11573 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    11574 chains... 
    11575 ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
    11576 standards. 
    11577 ISOLDE: stopped sim 
    11578 
    11579 > isolde sim start sel
    11580 
    11581 ISOLDE: started sim 
    11582 
    11583 > isolde sim stop
    11584 
    11585 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    11586 chains... 
    11587 ISOLDE: stopped sim 
    11588 
    11589 > isolde sim start sel
    11590 
    11591 ISOLDE: started sim 
    11592 
    11593 > isolde sim stop
    11594 
    11595 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    11596 chains... 
    11597 ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
    11598 standards. 
    11599 ISOLDE: stopped sim 
    11600 
    11601 > isolde sim start sel
    11602 
    11603 ISOLDE: started sim 
    11604 
    11605 > isolde pepflip sel
    11606 
    11607 Flipping the peptide bond for 1 residues 
    11608 
    11609 > isolde sim stop
    11610 
    11611 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    11612 chains... 
    11613 ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
    11614 standards. 
    11615 ISOLDE: stopped sim 
    11616 
    11617 > isolde sim start sel
    11618 
    11619 ISOLDE: started sim 
    11620 
    11621 > isolde sim stop
    11622 
    11623 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    11624 chains... 
    11625 ISOLDE: stopped sim 
    11626 
    11627 > isolde sim start sel
    11628 
    11629 ISOLDE: started sim 
    11630 
    11631 > isolde sim stop
    11632 
    11633 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    11634 chains... 
    11635 ISOLDE: stopped sim 
    11636 
    11637 > isolde sim start sel
    11638 
    11639 ISOLDE: started sim 
    11640 
    11641 > isolde sim stop
    11642 
    11643 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    11644 chains... 
    11645 ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
    11646 standards. 
    11647 ISOLDE: stopped sim 
    11648 
    11649 > isolde sim start sel
    11650 
    11651 ISOLDE: started sim 
    11652 
    11653 > isolde pepflip sel
    11654 
    11655 Flipping the peptide bond for 1 residues 
    11656 
    11657 > isolde pepflip sel
    11658 
    11659 Flipping the peptide bond for 1 residues 
    11660 
    11661 > isolde sim stop
    11662 
    11663 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    11664 chains... 
    11665 ISOLDE: stopped sim 
    11666 
    11667 > isolde sim start sel
    11668 
    11669 ISOLDE: started sim 
    11670 
    11671 > isolde sim stop
    11672 
    11673 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    11674 chains... 
    11675 ISOLDE: stopped sim 
    11676 
    11677 > isolde sim start sel
    11678 
    11679 ISOLDE: started sim 
    11680 
    11681 > isolde sim stop
    11682 
    11683 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    11684 chains... 
    11685 ISOLDE: stopped sim 
    11686 
    11687 > isolde sim start sel
    11688 
    11689 ISOLDE: started sim 
    11690 
    11691 > isolde sim stop
    11692 
    11693 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    11694 chains... 
    11695 ISOLDE: stopped sim 
    11696 
    11697 > isolde sim start sel
    11698 
    11699 ISOLDE: started sim 
    11700 
    11701 > isolde sim stop
    11702 
    11703 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    11704 chains... 
    11705 ISOLDE: stopped sim 
    11706 
    11707 > isolde sim start sel
    11708 
    11709 ISOLDE: started sim 
    11710 
    11711 > isolde sim stop
    11712 
    11713 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    11714 chains... 
    11715 ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
    11716 standards. 
    11717 ISOLDE: stopped sim 
    11718 
    11719 > isolde sim start sel
    11720 
    11721 ISOLDE: started sim 
    11722 
    11723 > isolde sim stop
    11724 
    11725 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    11726 chains... 
    11727 ISOLDE: stopped sim 
    11728 
    11729 > isolde sim start sel
    11730 
    11731 ISOLDE: started sim 
    11732 
    11733 > isolde sim stop
    11734 
    11735 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    11736 chains... 
    11737 ISOLDE: stopped sim 
    11738 
    11739 > isolde sim start sel
    11740 
    11741 ISOLDE: started sim 
    11742 
    11743 > isolde sim stop
    11744 
    11745 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    11746 chains... 
    11747 ISOLDE: stopped sim 
    11748 
    11749 > isolde sim start sel
    11750 
    11751 ISOLDE: started sim 
    11752 
    11753 > isolde sim stop
    11754 
    11755 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    11756 chains... 
    11757 ISOLDE: stopped sim 
    11758 
    11759 > isolde sim start sel
    11760 
    11761 ISOLDE: started sim 
    11762 
    11763 > isolde sim stop
    11764 
    11765 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    11766 chains... 
    11767 ISOLDE: stopped sim 
    11768 
    11769 > select #1/m:137
    11770 
    11771 16 atoms, 15 bonds, 1 residue, 1 model selected 
    11772 
    11773 > view #1/m:137
    11774 
    11775 > isolde sim start sel
    11776 
    11777 ISOLDE: started sim 
    11778 
    11779 > isolde sim stop
    11780 
    11781 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    11782 chains... 
    11783 ISOLDE: stopped sim 
    11784 
    11785 > view #1/m:137,104
    11786 
    11787 > select #1/m:137,104
    11788 
    11789 35 atoms, 33 bonds, 2 residues, 1 model selected 
    11790 
    11791 > isolde sim start sel
    11792 
    11793 ISOLDE: started sim 
    11794 
    11795 > select clear
    11796 
    11797 > isolde pepflip sel
    11798 
    11799 Flipping the peptide bond for 1 residues 
    11800 
    11801 > isolde sim stop
    11802 
    11803 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    11804 chains... 
    11805 ISOLDE: stopped sim 
    11806 
    11807 > save D:/Rafa/OneDrive/Documentos/ubuntuStorage/krsp/5OPT-refinement/40S-wt-
    11808 > refinement/8-40S-KSRP-wt-Second-steps.cxs
    11809 
    11810 Taking snapshot of stepper: 40S-wt-concat.pdb 
    11811 
    11812 ——— End of log from Mon Apr 17 16:03:12 2023 ———
    11813 
    11814 opened ChimeraX session 
    11815 
    11816 > isolde start
    11817 
    11818 > set selectionWidth 4
    11819 
    11820 > volume gaussian #1 bfactor 150
    11821 
    11822 Opened 40S-wt-concat.mrc gaussian as #3, grid size 400,400,400, pixel 1.16,
    11823 shown at step 1, values float32 
    11824 Opened 40S-wt-concat.mrc gaussian as #4, grid size 400,400,400, pixel 1.16,
    11825 shown at step 1, values float32 
    11826 
    11827 > close #1.1.1.2
    11828 
    11829 > close #4
    11830 
    11831 > volume #3 level 0.3
    11832 
    11833 > select #1/h
    11834 
    11835 2780 atoms, 2803 bonds, 173 residues, 1 model selected 
    11836 
    11837 > view #1/h
    11838 
    11839 > isolde sim start sel
    11840 
    11841 ISOLDE: started sim 
    11842 
    11843 > ui tool show "Ramachandran Plot"
    11844 
    11845 > isolde pepflip sel
    11846 
    11847 Flipping the peptide bond for 1 residues 
    11848 
    11849 > isolde cisflip sel
    11850 
    11851 Performing cis<\-->trans flip for 1 residues 
    11852 
    11853 > isolde cisflip sel
    11854 
    11855 Performing cis<\-->trans flip for 1 residues 
    11856 
    11857 > isolde pepflip sel
    11858 
    11859 Flipping the peptide bond for 1 residues 
    11860 
    11861 > isolde cisflip sel
    11862 
    11863 Performing cis<\-->trans flip for 1 residues 
    11864 
    11865 > isolde cisflip sel
    11866 
    11867 Performing cis<\-->trans flip for 1 residues 
    11868 
    11869 > isolde pepflip sel
    11870 
    11871 Flipping the peptide bond for 1 residues 
    11872 
    11873 > isolde sim stop
    11874 
    11875 Sim termination reason: None 
    11876 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    11877 chains... 
    11878 ISOLDE: Corrected atom nomenclature of 2 residues in model #1.2 to IUPAC-IUB
    11879 standards. 
    11880 ISOLDE: stopped sim 
    11881 
    11882 > isolde sim start sel
    11883 
    11884 ISOLDE: started sim 
    11885 
    11886 > isolde pepflip sel
    11887 
    11888 Flipping the peptide bond for 1 residues 
    11889 
    11890 > isolde pepflip sel
    11891 
    11892 Flipping the peptide bond for 1 residues 
    11893 
    11894 > isolde pepflip sel
    11895 
    11896 Flipping the peptide bond for 1 residues 
    11897 
    11898 > select clear
    11899 
    11900 > isolde pepflip sel
    11901 
    11902 Flipping the peptide bond for 1 residues 
    11903 Unable to flip peptide bond after 50 rounds. Giving up. 
    11904 
    11905 > isolde cisflip sel
    11906 
    11907 Performing cis<\-->trans flip for 1 residues 
    11908 
    11909 > isolde cisflip sel
    11910 
    11911 Performing cis<\-->trans flip for 1 residues 
    11912 
    11913 > isolde pepflip sel
    11914 
    11915 Flipping the peptide bond for 1 residues 
    11916 Unable to flip peptide bond after 50 rounds. Giving up. 
    11917 
    11918 > isolde sim stop
    11919 
    11920 Sim termination reason: None 
    11921 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    11922 chains... 
    11923 ISOLDE: stopped sim 
    11924 
    11925 > isolde sim start sel
    11926 
    11927 ISOLDE: started sim 
    11928 
    11929 > isolde sim stop
    11930 
    11931 Sim termination reason: None 
    11932 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    11933 chains... 
    11934 ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
    11935 standards. 
    11936 ISOLDE: stopped sim 
    11937 
    11938 > isolde sim start sel
    11939 
    11940 ISOLDE: started sim 
    11941 
    11942 > isolde pepflip sel
    11943 
    11944 Flipping the peptide bond for 1 residues 
    11945 
    11946 > isolde pepflip sel
    11947 
    11948 Flipping the peptide bond for 1 residues 
    11949 
    11950 > isolde sim stop
    11951 
    11952 Sim termination reason: None 
    11953 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    11954 chains... 
    11955 ISOLDE: stopped sim 
    11956 
    11957 > isolde sim start sel
    11958 
    11959 ISOLDE: started sim 
    11960 
    11961 > isolde pepflip sel
    11962 
    11963 Flipping the peptide bond for 1 residues 
    11964 
    11965 > isolde pepflip sel
    11966 
    11967 Flipping the peptide bond for 1 residues 
    11968 
    11969 > isolde pepflip sel
    11970 
    11971 Flipping the peptide bond for 1 residues 
    11972 
    11973 > isolde pepflip sel
    11974 
    11975 Flipping the peptide bond for 1 residues 
    11976 
    11977 > isolde pepflip sel
    11978 
    11979 Flipping the peptide bond for 1 residues 
    11980 
    11981 > isolde sim stop
    11982 
    11983 Sim termination reason: None 
    11984 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    11985 chains... 
    11986 ISOLDE: stopped sim 
    11987 
    11988 > select #1/h
    11989 
    11990 2780 atoms, 2803 bonds, 173 residues, 1 model selected 
    11991 
    11992 > isolde sim start sel
    11993 
    11994 ISOLDE: started sim 
    11995 
    11996 > isolde pepflip sel
    11997 
    11998 Flipping the peptide bond for 1 residues 
    11999 
    12000 > isolde pepflip sel
    12001 
    12002 Flipping the peptide bond for 1 residues 
    12003 
    12004 > isolde pepflip sel
    12005 
    12006 Flipping the peptide bond for 1 residues 
    12007 
    12008 > isolde pepflip sel
    12009 
    12010 Flipping the peptide bond for 1 residues 
    12011 
    12012 > isolde pepflip sel
    12013 
    12014 Flipping the peptide bond for 1 residues 
    12015 
    12016 > isolde pepflip sel
    12017 
    12018 Flipping the peptide bond for 1 residues 
    12019 
    12020 > isolde sim stop
    12021 
    12022 Sim termination reason: None 
    12023 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    12024 chains... 
    12025 ISOLDE: Corrected atom nomenclature of 2 residues in model #1.2 to IUPAC-IUB
    12026 standards. 
    12027 ISOLDE: stopped sim 
    12028 
    12029 > isolde sim start sel
    12030 
    12031 ISOLDE: started sim 
    12032 
    12033 > select clear
    12034 
    12035 [Repeated 1 time(s)]
    12036 
    12037 > isolde pepflip sel
    12038 
    12039 Flipping the peptide bond for 1 residues 
    12040 
    12041 > isolde cisflip sel
    12042 
    12043 Performing cis<\-->trans flip for 1 residues 
    12044 
    12045 > isolde cisflip sel
    12046 
    12047 Performing cis<\-->trans flip for 1 residues 
    12048 
    12049 > isolde pepflip sel
    12050 
    12051 Flipping the peptide bond for 1 residues 
    12052 
    12053 > isolde sim stop
    12054 
    12055 Sim termination reason: None 
    12056 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    12057 chains... 
    12058 ISOLDE: stopped sim 
    12059 
    12060 > isolde sim start sel
    12061 
    12062 ISOLDE: started sim 
    12063 
    12064 > isolde pepflip sel
    12065 
    12066 Flipping the peptide bond for 1 residues 
    12067 
    12068 > isolde pepflip sel
    12069 
    12070 Flipping the peptide bond for 1 residues 
    12071 
    12072 > isolde sim stop
    12073 
    12074 Sim termination reason: None 
    12075 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    12076 chains... 
    12077 ISOLDE: stopped sim 
    12078 
    12079 > select #1/P
    12080 
    12081 4114 atoms, 4139 bonds, 249 residues, 1 model selected 
    12082 
    12083 > view #1/P
    12084 
    12085 > isolde sim start sel
    12086 
    12087 ISOLDE: started sim 
    12088 
    12089 > isolde pepflip sel
    12090 
    12091 Flipping the peptide bond for 1 residues 
    12092 
    12093 > isolde sim stop
    12094 
    12095 Sim termination reason: None 
    12096 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    12097 chains... 
    12098 ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
    12099 standards. 
    12100 ISOLDE: stopped sim 
    12101 
    12102 > select #1/Z
    12103 
    12104 2911 atoms, 2931 bonds, 1 pseudobond, 175 residues, 2 models selected 
    12105 
    12106 > view #1/Z
    12107 
    12108 > isolde sim start sel
    12109 
    12110 ISOLDE: started sim 
    12111 
    12112 > isolde sim stop
    12113 
    12114 Sim termination reason: None 
    12115 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    12116 chains... 
    12117 ISOLDE: Corrected atom nomenclature of 2 residues in model #1.2 to IUPAC-IUB
    12118 standards. 
    12119 ISOLDE: stopped sim 
    12120 
    12121 > select #1/X
    12122 
    12123 2465 atoms, 2491 bonds, 148 residues, 1 model selected 
    12124 
    12125 > view #1/X
    12126 
    12127 > isolde sim start sel
    12128 
    12129 ISOLDE: started sim 
    12130 
    12131 > isolde pepflip sel
    12132 
    12133 Flipping the peptide bond for 1 residues 
    12134 
    12135 > isolde sim stop
    12136 
    12137 Sim termination reason: None 
    12138 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    12139 chains... 
    12140 ISOLDE: Corrected atom nomenclature of 5 residues in model #1.2 to IUPAC-IUB
    12141 standards. 
    12142 ISOLDE: stopped sim 
    12143 
    12144 > select #1/L
    12145 
    12146 4183 atoms, 4218 bonds, 258 residues, 1 model selected 
    12147 
    12148 > view #1/L
    12149 
    12150 > isolde sim start sel
    12151 
    12152 ISOLDE: started sim 
    12153 
    12154 > isolde pepflip sel
    12155 
    12156 Flipping the peptide bond for 1 residues 
    12157 
    12158 > isolde pepflip sel
    12159 
    12160 Flipping the peptide bond for 1 residues 
    12161 
    12162 > isolde pepflip sel
    12163 
    12164 Flipping the peptide bond for 1 residues 
    12165 
    12166 > isolde pepflip sel
    12167 
    12168 Flipping the peptide bond for 1 residues 
    12169 
    12170 > isolde sim stop
    12171 
    12172 Sim termination reason: None 
    12173 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    12174 chains... 
    12175 ISOLDE: Corrected atom nomenclature of 6 residues in model #1.2 to IUPAC-IUB
    12176 standards. 
    12177 ISOLDE: stopped sim 
    12178 
    12179 > select #1/Y
    12180 
    12181 2057 atoms, 2072 bonds, 123 residues, 1 model selected 
    12182 
    12183 > view #1/Y
    12184 
    12185 > isolde sim start sel
    12186 
    12187 ISOLDE: started sim 
    12188 
    12189 > isolde pepflip sel
    12190 
    12191 Flipping the peptide bond for 1 residues 
    12192 
    12193 > isolde sim stop
    12194 
    12195 Sim termination reason: None 
    12196 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    12197 chains... 
    12198 ISOLDE: Corrected atom nomenclature of 4 residues in model #1.2 to IUPAC-IUB
    12199 standards. 
    12200 ISOLDE: stopped sim 
    12201 
    12202 > save C:/Users/Rafa/OneDrive2/OneDrive/Documentos/ubuntuStorage/krsp/5OPT-
    12203 > refinement/40S-wt-refinement/9-40S-KSRP-wt-Second-steps.cxs
    12204 
    12205 Taking snapshot of stepper: 40S-wt-concat.pdb 
    12206 
    12207 ——— End of log from Wed Apr 19 10:10:38 2023 ———
    12208 
    12209 opened ChimeraX session 
    12210 
    12211 > isolde start
    12212 
    12213 > isolde sim start sel
    12214 
    12215 ISOLDE: started sim 
    12216 
    12217 > isolde sim stop discardTo start
    12218 
    12219 Sim termination reason: None 
    12220 reverting to start 
    12221 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    12222 chains... 
    12223 ISOLDE: stopped sim 
    12224 
    12225 > clipper associate #3 toModel #1
    12226 
    12227 Opened 40S-wt-concat.mrc gaussian as #1.1.1.2, grid size 400,400,400, pixel
    12228 1.16, shown at step 1, values float32 
    12229 
    12230 > color #1.1.1.2 #004c4cff models
    12231 
    12232 > volume #1.1.1.2 level 0.2598
    12233 
    12234 > volume #1.1.1.2 level 0.5645
    12235 
    12236 > select clear
    12237 
    12238 > volume #1.1.1.2 color #002323
    12239 
    12240 > volume #1.1.1.2 color #232323
    12241 
    12242 > volume #1.1.1.2 color #545454
    12243 
    12244 > view #1/h
    12245 
    12246 > volume #1.1.1.2 level 0.2919
    12247 
    12248 > save C:/Users/Rafa/OneDrive2/OneDrive/Documentos/ubuntuStorage/krsp/5OPT-
    12249 > refinement/40S-wt-refinement/9-40S-KSRP-wt-Second-steps.cxs
    12250 
    12251 Taking snapshot of stepper: 40S-wt-concat.pdb 
    12252 
    12253 ——— End of log from Wed Apr 19 16:46:00 2023 ———
    12254 
    12255 opened ChimeraX session 
    12256 
    12257 > hide #!1.2 models
    12258 
    12259 > show #!1.2 models
    12260 
    12261 > hide #1.3 models
    12262 
    12263 > show #1.3 models
    12264 
    12265 > hide #!1.1 models
    12266 
    12267 > show #!1.1 models
    12268 
    12269 > hide #!1.1 models
    12270 
    12271 > show #!1.1 models
    12272 
    12273 > hide #!1 models
    12274 
    12275 > show #!1 models
    12276 
    12277 > close
    12278 
    12279 > open /srv/home/leonardo/Documents/KSRP/Structures-maps-wt-mutants/40S-wt-
    12280 > refinement/Refinement-sent-fromRafael-in-Advance/Re-sent-
    12281 > byRafael-19-04-2023/9-40S-KSRP-wt-Second-steps-FINALoutliersRaf.pdb
    12282 
    12283 9-40S-KSRP-wt-Second-steps-FINALoutliersRaf.pdb title: 
    12284 Structure of KSRP In context of trypanosoma cruzi 40S [more info...] 
    12285  
    12286 Chain information for 9-40S-KSRP-wt-Second-steps-FINALoutliersRaf.pdb #1 
    12287 --- 
    12288 Chain | Description | UniProt 
    12289 E | 18S RRNA | 
    12290 L | 40S ribosomal protein S4 | Q4D5P4_TRYCC 
    12291 M | 40S ribosomal protein S23, putative | Q4DTQ1_TRYCC 
    12292 O | 40S ribosomal protein S5, putative | Q4E0Q3_TRYCC 
    12293 P | 40S ribosomal protein S6 | Q4DSU0_TRYCC 
    12294 Q | ribosomal protein S7, putative | Q4CUC7_TRYCC 
    12295 R | 40S ribosomal protein S13, putative | Q4DC38_TRYCC 
    12296 S | 40S ribosomal protein S27, putative | Q4DN73_TRYCC 
    12297 T | 40S ribosomal protein S26 | Q4CYE4_TRYCC 
    12298 U | 40S ribosomal protein S33, putative | Q4D7C8_TRYCC 
    12299 V | 40S ribosomal protein S14, putative | Q4D6I5_TRYCC 
    12300 W | 40S ribosomal protein S3A-2 | RS3A2_TRYCC 
    12301 X | 40S ribosomal protein S11, putative | Q4D0U7_TRYCC 
    12302 Y | 40S ribosomal protein S24 | Q4DW38_TRYCC 
    12303 Z | 40S ribosomal protein S8 | Q4DU83_TRYCC 
    12304 a | ribosomal protein S25, putative | Q4DTX6_TRYCC 
    12305 b | 40S ribosomal protein S9, putative | Q4D4S1_TRYCC 
    12306 c | 40S ribosomal protein S30 | Q4DA48_TRYCC 
    12307 d | 40S ribosomal protein S2, putative | Q4DIZ9_TRYCC 
    12308 e | 40S ribosomal protein S15A, putative | Q4E0N6_TRYCC 
    12309 f | 40S ribosomal protein sa | Q4CQ63_TRYCC 
    12310 g | 40S ribosomal protein S21, putative | Q4E3M0_TRYCC 
    12311 h | RNA-binding protein, putative | Q4DY32_TRYCC 
    12312 i | 40S ribosomal protein S12 | Q4CSL1_TRYCC 
    12313 j | ubiquitin/ribosomal protein S27A, putative | Q4D1T6_TRYCC 
    12314 k | 40S ribosomal protein S17, putative | Q4DK40_TRYCC 
    12315 l | ribosomal protein S20, putative | Q4D6H7_TRYCC 
    12316 m | 40S ribosomal protein S3, putative | Q4DMK9_TRYCC 
    12317 n | 40S ribosomal protein S10, putative | Q4E088_TRYCC 
    12318 o | ribosomal protein S19, putative | Q4DJY1_TRYCC 
    12319 p | activated protein kinase C receptor, putative | Q4DTN2_TRYCC 
    12320 q | ribosomal protein S29, putative | Q4CXR4_TRYCC 
    12321 r | 40S ribosomal protein S16, putative | Q4DEK4_TRYCC 
    12322 t | 40S ribosomal protein S15, putative | Q4DGZ5_TRYCC 
    12323 u | 40S ribosomal protein S18, putative | Q4E093_TRYCC 
    12324  
    12325 
    12326 > hide
    12327 
    12328 > ribbon
    12329 
    12330 > open /srv/home/leonardo/Documents/KSRP/Structures-maps-wt-mutants/40S-wt-
    12331 > refinement/40S-wt-concat.mrc
    12332 
    12333 Opened 40S-wt-concat.mrc as #2, grid size 400,400,400, pixel 1.16, shown at
    12334 level 0.185, step 2, values float32 
    12335 
    12336 > isolde start
    12337 
    12338 > set selectionWidth 4
    12339 
    12340 > clipper associate #2 toModel #1
    12341 
    12342 Opened 40S-wt-concat.mrc as #1.1.1.1, grid size 400,400,400, pixel 1.16, shown
    12343 at level 0.542, step 1, values float32 
    12344 9-40S-KSRP-wt-Second-steps-FINALoutliersRaf.pdb title: 
    12345 Structure of KSRP In context of trypanosoma cruzi 40S [more info...] 
    12346  
    12347 Chain information for 9-40S-KSRP-wt-Second-steps-FINALoutliersRaf.pdb 
    12348 --- 
    12349 Chain | Description | UniProt 
    12350 1.2/E | 18S RRNA | 
    12351 1.2/L | 40S ribosomal protein S4 | Q4D5P4_TRYCC 
    12352 1.2/M | 40S ribosomal protein S23, putative | Q4DTQ1_TRYCC 
    12353 1.2/O | 40S ribosomal protein S5, putative | Q4E0Q3_TRYCC 
    12354 1.2/P | 40S ribosomal protein S6 | Q4DSU0_TRYCC 
    12355 1.2/Q | ribosomal protein S7, putative | Q4CUC7_TRYCC 
    12356 1.2/R | 40S ribosomal protein S13, putative | Q4DC38_TRYCC 
    12357 1.2/S | 40S ribosomal protein S27, putative | Q4DN73_TRYCC 
    12358 1.2/T | 40S ribosomal protein S26 | Q4CYE4_TRYCC 
    12359 1.2/U | 40S ribosomal protein S33, putative | Q4D7C8_TRYCC 
    12360 1.2/V | 40S ribosomal protein S14, putative | Q4D6I5_TRYCC 
    12361 1.2/W | 40S ribosomal protein S3A-2 | RS3A2_TRYCC 
    12362 1.2/X | 40S ribosomal protein S11, putative | Q4D0U7_TRYCC 
    12363 1.2/Y | 40S ribosomal protein S24 | Q4DW38_TRYCC 
    12364 1.2/Z | 40S ribosomal protein S8 | Q4DU83_TRYCC 
    12365 1.2/a | ribosomal protein S25, putative | Q4DTX6_TRYCC 
    12366 1.2/b | 40S ribosomal protein S9, putative | Q4D4S1_TRYCC 
    12367 1.2/c | 40S ribosomal protein S30 | Q4DA48_TRYCC 
    12368 1.2/d | 40S ribosomal protein S2, putative | Q4DIZ9_TRYCC 
    12369 1.2/e | 40S ribosomal protein S15A, putative | Q4E0N6_TRYCC 
    12370 1.2/f | 40S ribosomal protein sa | Q4CQ63_TRYCC 
    12371 1.2/g | 40S ribosomal protein S21, putative | Q4E3M0_TRYCC 
    12372 1.2/h | RNA-binding protein, putative | Q4DY32_TRYCC 
    12373 1.2/i | 40S ribosomal protein S12 | Q4CSL1_TRYCC 
    12374 1.2/j | ubiquitin/ribosomal protein S27A, putative | Q4D1T6_TRYCC 
    12375 1.2/k | 40S ribosomal protein S17, putative | Q4DK40_TRYCC 
    12376 1.2/l | ribosomal protein S20, putative | Q4D6H7_TRYCC 
    12377 1.2/m | 40S ribosomal protein S3, putative | Q4DMK9_TRYCC 
    12378 1.2/n | 40S ribosomal protein S10, putative | Q4E088_TRYCC 
    12379 1.2/o | ribosomal protein S19, putative | Q4DJY1_TRYCC 
    12380 1.2/p | activated protein kinase C receptor, putative | Q4DTN2_TRYCC 
    12381 1.2/q | ribosomal protein S29, putative | Q4CXR4_TRYCC 
    12382 1.2/r | 40S ribosomal protein S16, putative | Q4DEK4_TRYCC 
    12383 1.2/t | 40S ribosomal protein S15, putative | Q4DGZ5_TRYCC 
    12384 1.2/u | 40S ribosomal protein S18, putative | Q4E093_TRYCC 
    12385  
    12386 
    12387 > view #1/P:240-249
    12388 
    12389 > volume gaussian #1 bfactor 150
    12390 
    12391 Opened 40S-wt-concat.mrc gaussian as #2, grid size 400,400,400, pixel 1.16,
    12392 shown at step 1, values float32 
    12393 
    12394 > clipper associate #2 toModel #1
    12395 
    12396 Opened 40S-wt-concat.mrc gaussian as #1.1.1.2, grid size 400,400,400, pixel
    12397 1.16, shown at step 1, values float32 
    12398 
    12399 > addh
    12400 
    12401 Summary of feedback from adding hydrogens to 9-40S-KSRP-wt-Second-steps-
    12402 FINALoutliersRaf.pdb #1.2 
    12403 --- 
    12404 notes | No usable SEQRES records for 9-40S-KSRP-wt-Second-steps-
    12405 FINALoutliersRaf.pdb (#1.2) chain E; guessing termini instead 
    12406 No usable SEQRES records for 9-40S-KSRP-wt-Second-steps-FINALoutliersRaf.pdb
    12407 (#1.2) chain L; guessing termini instead 
    12408 No usable SEQRES records for 9-40S-KSRP-wt-Second-steps-FINALoutliersRaf.pdb
    12409 (#1.2) chain M; guessing termini instead 
    12410 No usable SEQRES records for 9-40S-KSRP-wt-Second-steps-FINALoutliersRaf.pdb
    12411 (#1.2) chain O; guessing termini instead 
    12412 No usable SEQRES records for 9-40S-KSRP-wt-Second-steps-FINALoutliersRaf.pdb
    12413 (#1.2) chain P; guessing termini instead 
    12414 30 messages similar to the above omitted 
    12415 Chain-initial residues that are actual N termini: /L THR 2, /M THR 2, /O MET
    12416 1, /P MET 1, /Q VAL 3, /R VAL 2, /S ASP 5, /T MET 1, /U ASP 45, /V PHE 9, /W
    12417 GLU 22, /X HIS 11, /Y GLN 4, /Z GLY 2, /a ALA 41, /b MET 1, /c SER 7, /d LYS
    12418 37, /e THR 2, /f VAL 4, /g ILE 4, /h ASN 68, /i ALA 21, /j PRO 86, /k LYS 58,
    12419 /l GLN 15, /m LYS 6, /n LYS 7, /o ILE 12, /p TYR 5, /q ARG 20, /r LYS 10, /t
    12420 GLU 16, /u GLU 8 
    12421 Chain-initial residues that are not actual N termini: /Z ASP 157 
    12422 Chain-final residues that are actual C termini: /M ASN 143, /O ARG 190, /Q ARG
    12423 202, /S HIS 86, /U ARG 112, /a VAL 110, /c GLY 66, /e TYR 130, /i ARG 141, /q
    12424 ARG 57, /r ARG 149 
    12425 Chain-final residues that are not actual C termini: /L ALA 259, /P LYS 249, /R
    12426 GLU 142, /T VAL 104, /V ARG 143, /W PRO 238, /X VAL 158, /Y GLY 126, /Z LEU
    12427 216, /Z HIS 116, /b GLY 164, /d LYS 259, /f PRO 210, /g LYS 86, /h LYS 240, /j
    12428 ALA 149, /k VAL 175, /l ILE 113, /m THR 205, /n LYS 99, /o ILE 151, /p VAL
    12429 314, /t ILE 134, /u ALA 127 
    12430 7074 hydrogen bonds 
    12431 /L ALA 259 is not terminus, removing H atom from 'C' 
    12432 /P LYS 249 is not terminus, removing H atom from 'C' 
    12433 /R GLU 142 is not terminus, removing H atom from 'C' 
    12434 /T VAL 104 is not terminus, removing H atom from 'C' 
    12435 /V ARG 143 is not terminus, removing H atom from 'C' 
    12436 18 messages similar to the above omitted 
    12437 4 hydrogens added 
    12438  
    12439 
    12440 > isolde restrain ligands #1
    12441 
    12442 > select #1/P:240-249
    12443 
    12444 168 atoms, 168 bonds, 10 residues, 1 model selected 
    12445 
    12446 > isolde sim start sel
    12447 
    12448 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    12449 chains... 
    12450 
    12451 Launching using CUDA failed with the below message. Falling back to using
    12452 OpenCL. 
    12453  
    12454 Error compiling program: nvrtc: error: invalid value for --gpu-architecture
    12455 (-arch) 
    12456  
    12457 
    12458 ISOLDE: started sim 
    12459 
    12460 > isolde sim stop discardTo start
    12461 
    12462 reverting to start 
    12463 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    12464 chains... 
    12465 ISOLDE: stopped sim 
    12466 
    12467 > select #1/P:240-249
    12468 
    12469 168 atoms, 168 bonds, 10 residues, 1 model selected 
    12470 
    12471 > isolde sim start sel
    12472 
    12473 ISOLDE: started sim 
    12474 
    12475 > isolde sim stop discardTo start
    12476 
    12477 reverting to start 
    12478 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    12479 chains... 
    12480 ISOLDE: stopped sim 
    12481 
    12482 > select #1/P:240-249
    12483 
    12484 168 atoms, 168 bonds, 10 residues, 1 model selected 
    12485 
    12486 > isolde sim start sel
    12487 
    12488 ISOLDE: started sim 
    12489 
    12490 > isolde sim stop discardTo start
    12491 
    12492 reverting to start 
    12493 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    12494 chains... 
    12495 ISOLDE: stopped sim 
    12496 
    12497 > select #1/P:240-249
    12498 
    12499 168 atoms, 168 bonds, 10 residues, 1 model selected 
    12500 
    12501 > isolde sim start sel
    12502 
    12503 ISOLDE: started sim 
    12504 
    12505 > ui tool show "Ramachandran Plot"
    12506 
    12507 > isolde sim stop
    12508 
    12509 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    12510 chains... 
    12511 ISOLDE: stopped sim 
    12512 
    12513 > select #1/P:220-249
    12514 
    12515 503 atoms, 505 bonds, 30 residues, 1 model selected 
    12516 
    12517 > isolde sim start sel
    12518 
    12519 ISOLDE: started sim 
    12520 
    12521 > isolde sim stop
    12522 
    12523 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    12524 chains... 
    12525 ISOLDE: stopped sim 
    12526 
    12527 > select #1/P:220-249|/h
    12528 
    12529 3283 atoms, 3308 bonds, 203 residues, 1 model selected 
    12530 
    12531 > isolde sim start sel
    12532 
    12533 ISOLDE: started sim 
    12534 
    12535 > ui tool show "Ramachandran Plot"
    12536 
    12537 > select clear
    12538 
    12539 > ui tool show "Ramachandran Plot"
    12540 
    12541 > isolde sim pause
    12542 
    12543 > isolde sim stop
    12544 
    12545 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    12546 chains... 
    12547 ISOLDE: stopped sim 
    12548 
    12549 > select #1/P:220-249|/h:231-239
    12550 
    12551 653 atoms, 654 bonds, 39 residues, 1 model selected 
    12552 
    12553 > isolde sim start sel
    12554 
    12555 ISOLDE: started sim 
    12556 
    12557 > isolde pepflip sel
    12558 
    12559 Flipping the peptide bond for 1 residues 
    12560 
    12561 > isolde pepflip sel
    12562 
    12563 Flipping the peptide bond for 1 residues 
    12564 
    12565 > select clear
    12566 
    12567 > isolde pepflip sel
    12568 
    12569 Flipping the peptide bond for 1 residues 
    12570 
    12571 > ui tool show "Ramachandran Plot"
    12572 
    12573 > isolde sim stop
    12574 
    12575 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    12576 chains... 
    12577 ISOLDE: stopped sim 
    12578 
    12579 > select clear
    12580 
    12581 > select #1/P:220-249|/h
    12582 
    12583 3283 atoms, 3308 bonds, 203 residues, 1 model selected 
    12584 
    12585 > isolde sim start sel
    12586 
    12587 ISOLDE: started sim 
    12588 
    12589 > select clear
    12590 
    12591 > ui tool show "Ramachandran Plot"
    12592 
    12593 > isolde sim stop
    12594 
    12595 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    12596 chains... 
    12597 ISOLDE: stopped sim 
    12598 
    12599 > view #1/h:95-136
    12600 
    12601 > select #1/h:95-136
    12602 
    12603 685 atoms, 690 bonds, 42 residues, 1 model selected 
    12604 
    12605 > isolde sim start sel
    12606 
    12607 ISOLDE: started sim 
    12608 
    12609 > select clear
    12610 
    12611 > isolde sim pause
    12612 
    12613 > isolde sim resume
    12614 
    12615 > isolde pepflip sel
    12616 
    12617 Flipping the peptide bond for 1 residues 
    12618 
    12619 > select clear
    12620 
    12621 > ui tool show "Ramachandran Plot"
    12622 
    12623 > isolde pepflip sel
    12624 
    12625 Flipping the peptide bond for 1 residues 
    12626 
    12627 > isolde pepflip sel
    12628 
    12629 Flipping the peptide bond for 1 residues 
    12630 
    12631 > select clear
    12632 
    12633 > isolde sim pause
    12634 
    12635 > ui tool show "Ramachandran Plot"
    12636 
    12637 > isolde sim resume
    12638 
    12639 > ui tool show "Ramachandran Plot"
    12640 
    12641 > isolde sim pause
    12642 
    12643 > isolde sim resume
    12644 
    12645 > ui tool show "Ramachandran Plot"
    12646 
    12647 [Repeated 1 time(s)]Traceback (most recent call last): 
    12648 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    12649 packages/matplotlib/cbook/__init__.py", line 287, in process 
    12650 func(*args, **kwargs) 
    12651 File "/srv/home/leonardo/.local/share/ChimeraX/1.4/site-
    12652 packages/chimerax/isolde/validation/ramaplot/ramaplot.py", line 292, in
    12653 on_resize 
    12654 c.draw() 
    12655 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    12656 packages/matplotlib/backends/backend_agg.py", line 436, in draw 
    12657 self.figure.draw(self.renderer) 
    12658 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    12659 packages/matplotlib/artist.py", line 73, in draw_wrapper 
    12660 result = draw(artist, renderer, *args, **kwargs) 
    12661 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    12662 packages/matplotlib/artist.py", line 50, in draw_wrapper 
    12663 return draw(artist, renderer) 
    12664 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    12665 packages/matplotlib/figure.py", line 2796, in draw 
    12666 artists = self._get_draw_artists(renderer) 
    12667 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    12668 packages/matplotlib/figure.py", line 238, in _get_draw_artists 
    12669 ax.apply_aspect() 
    12670 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    12671 packages/matplotlib/axes/_base.py", line 1890, in apply_aspect 
    12672 pb1 = pb.shrunk_to_aspect(box_aspect, pb, fig_aspect) 
    12673 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    12674 packages/matplotlib/transforms.py", line 558, in shrunk_to_aspect 
    12675 raise ValueError("'box_aspect' and 'fig_aspect' must be positive") 
    12676 ValueError: 'box_aspect' and 'fig_aspect' must be positive 
    12677 
    12678 > select clear
    12679 
    12680 > isolde pepflip sel
    12681 
    12682 Flipping the peptide bond for 1 residues 
    12683 
    12684 > select clear
    12685 
    12686 > isolde sim pause
    12687 
    12688 > isolde sim resume
    12689 
    12690 > view h:135
    12691 
    12692 Expected an objects specifier or a view name or a keyword 
    12693 
    12694 > view #1/h:135
    12695 
    12696 > select clear
    12697 
    12698 [Repeated 1 time(s)]
    12699 
    12700 > isolde pepflip sel
    12701 
    12702 Flipping the peptide bond for 1 residues 
    12703 
    12704 > select clear
    12705 
    12706 > ui tool show "Ramachandran Plot"
    12707 
    12708 [Repeated 1 time(s)]
    12709 
    12710 > isolde sim pause
    12711 
    12712 > isolde sim stop
    12713 
    12714 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    12715 chains... 
    12716 ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
    12717 standards. 
    12718 ISOLDE: stopped sim 
    12719 
    12720 > select #1/h:95-136
    12721 
    12722 685 atoms, 690 bonds, 42 residues, 1 model selected 
    12723 
    12724 > isolde sim start sel
    12725 
    12726 ISOLDE: started sim 
    12727 
    12728 > isolde sim stop
    12729 
    12730 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    12731 chains... 
    12732 ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
    12733 standards. 
    12734 ISOLDE: stopped sim 
    12735 
    12736 > select #1/h:138-148
    12737 
    12738 156 atoms, 159 bonds, 11 residues, 1 model selected 
    12739 
    12740 > isolde sim start sel
    12741 
    12742 ISOLDE: started sim 
    12743 
    12744 > isolde pepflip sel
    12745 
    12746 Flipping the peptide bond for 1 residues 
    12747 
    12748 > isolde pepflip sel
    12749 
    12750 Flipping the peptide bond for 1 residues 
    12751 Unable to flip peptide bond after 50 rounds. Giving up. 
    12752 
    12753 > isolde pepflip sel
    12754 
    12755 Flipping the peptide bond for 1 residues 
    12756 
    12757 > isolde pepflip sel
    12758 
    12759 Flipping the peptide bond for 1 residues 
    12760 
    12761 > isolde pepflip sel
    12762 
    12763 Flipping the peptide bond for 1 residues 
    12764 
    12765 > isolde pepflip sel
    12766 
    12767 Flipping the peptide bond for 1 residues 
    12768 
    12769 > isolde pepflip sel
    12770 
    12771 Flipping the peptide bond for 1 residues 
    12772 Unable to flip peptide bond after 50 rounds. Giving up. 
    12773 
    12774 > ui tool show "Ramachandran Plot"
    12775 
    12776 > select clear
    12777 
    12778 > ui tool show "Ramachandran Plot"
    12779 
    12780 > select clear
    12781 
    12782 [Repeated 1 time(s)]
    12783 
    12784 > ui tool show "Ramachandran Plot"
    12785 
    12786 > view #1/h:138-148
    12787 
    12788 [Repeated 1 time(s)]
    12789 
    12790 > select #1/h:138-148
    12791 
    12792 156 atoms, 159 bonds, 11 residues, 1 model selected 
    12793 
    12794 > select clear
    12795 
    12796 > ui tool show "Ramachandran Plot"
    12797 
    12798 > isolde sim stop
    12799 
    12800 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    12801 chains... 
    12802 ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
    12803 standards. 
    12804 ISOLDE: stopped sim 
    12805 
    12806 > view #1/h:93-136
    12807 
    12808 > select #1/h:93-136
    12809 
    12810 717 atoms, 722 bonds, 44 residues, 1 model selected 
    12811 
    12812 > isolde sim start sel
    12813 
    12814 ISOLDE: started sim 
    12815 
    12816 > select clear
    12817 
    12818 > ui tool show "Ramachandran Plot"
    12819 
    12820 [Repeated 1 time(s)]
    12821 
    12822 > isolde sim pause
    12823 
    12824 > isolde sim resume
    12825 
    12826 > select clear
    12827 
    12828 > ui tool show "Ramachandran Plot"
    12829 
    12830 > select clear
    12831 
    12832 [Repeated 1 time(s)]
    12833 
    12834 > isolde sim pause
    12835 
    12836 > isolde sim resume
    12837 
    12838 > ui tool show "Ramachandran Plot"
    12839 
    12840 > isolde pepflip sel
    12841 
    12842 Flipping the peptide bond for 1 residues 
    12843 
    12844 > isolde pepflip sel
    12845 
    12846 Flipping the peptide bond for 1 residues 
    12847 
    12848 > isolde pepflip sel
    12849 
    12850 Flipping the peptide bond for 1 residues 
    12851 
    12852 > select clear
    12853 
    12854 > ui tool show "Ramachandran Plot"
    12855 
    12856 [Repeated 1 time(s)]
    12857 
    12858 > isolde sim stop
    12859 
    12860 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    12861 chains... 
    12862 ISOLDE: stopped sim 
    12863 
    12864 > view #1/h|/P:220-249
    12865 
    12866 > select #1/h|/P:220-249
    12867 
    12868 3283 atoms, 3308 bonds, 203 residues, 1 model selected 
    12869 
    12870 > isolde sim start sel
    12871 
    12872 ISOLDE: started sim 
    12873 
    12874 > ui tool show "Ramachandran Plot"
    12875 
    12876 > select clear
    12877 
    12878 > isolde sim stop
    12879 
    12880 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    12881 chains... 
    12882 ISOLDE: stopped sim 
    12883 
    12884 > ui tool show "Ramachandran Plot"
    12885 
    12886 > select #1/V:11-20
    12887 
    12888 133 atoms, 132 bonds, 10 residues, 1 model selected 
    12889 
    12890 > isolde sim start sel
    12891 
    12892 ISOLDE: started sim 
    12893 
    12894 > ui tool show "Ramachandran Plot"
    12895 
    12896 > isolde sim pause
    12897 
    12898 > select #1/V:21-26
    12899 
    12900 96 atoms, 97 bonds, 6 residues, 1 model selected 
    12901 
    12902 > isolde sim start sel
    12903 
    12904 Simulation already running! 
    12905 
    12906 > isolde sim stop
    12907 
    12908 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    12909 chains... 
    12910 ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
    12911 standards. 
    12912 ISOLDE: stopped sim 
    12913 
    12914 > select #1/V:21-26
    12915 
    12916 96 atoms, 97 bonds, 6 residues, 1 model selected 
    12917 
    12918 > isolde sim start sel
    12919 
    12920 ISOLDE: started sim 
    12921 
    12922 > ui tool show "Ramachandran Plot"
    12923 
    12924 > isolde sim stop
    12925 
    12926 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    12927 chains... 
    12928 ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
    12929 standards. 
    12930 ISOLDE: stopped sim 
    12931 
    12932 > view #1/V:11-20
    12933 
    12934 > select #1/V:11-20
    12935 
    12936 133 atoms, 132 bonds, 10 residues, 1 model selected 
    12937 
    12938 > isolde sim start sel
    12939 
    12940 ISOLDE: started sim 
    12941 
    12942 > ui tool show "Ramachandran Plot"
    12943 
    12944 > isolde sim stop
    12945 
    12946 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    12947 chains... 
    12948 ISOLDE: stopped sim 
    12949 
    12950 > save /srv/home/leonardo/Documents/KSRP/Structures-maps-wt-mutants/40S-wt-
    12951 > refinement/Refinement-sent-fromRafael-in-Advance/Re-sent-
    12952 > byRafael-19-04-2023/10-FINAL-outlierRefinement-40S-KSRPwt.pdb
    12953 
    12954 > save /srv/home/leonardo/Documents/KSRP/Structures-maps-wt-mutants/40S-wt-
    12955 > refinement/Refinement-sent-fromRafael-in-Advance/Re-sent-
    12956 > byRafael-19-04-2023/10-FINAL-outlierRefinement-40S-KSRPwt.cxs
    12957 
    12958 Taking snapshot of stepper: 9-40S-KSRP-wt-Second-steps-FINALoutliersRaf.pdb 
    12959 Taking snapshot of stepper: 40S-wt-concat.pdb 
    12960 Traceback (most recent call last): 
    12961 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    12962 packages/chimerax/core/session.py", line 285, in process 
    12963 data = sm.take_snapshot(obj, session, self.state_flags) 
    12964 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    12965 packages/chimerax/atomic/structure.py", line 1389, in take_snapshot 
    12966 'structure state': Structure.take_snapshot(self, session, flags), 
    12967 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    12968 packages/chimerax/atomic/structure.py", line 208, in take_snapshot 
    12969 data = {'model state': Model.take_snapshot(self, session, flags), 
    12970 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    12971 packages/chimerax/core/models.py", line 329, in take_snapshot 
    12972 'positions': self.positions.array(), 
    12973 AttributeError: 'NoneType' object has no attribute 'array' 
    12974  
    12975 The above exception was the direct cause of the following exception: 
    12976  
    12977 Traceback (most recent call last): 
    12978 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    12979 packages/chimerax/core/session.py", line 262, in discovery 
    12980 self.processed[key] = self.process(obj, parents) 
    12981 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    12982 packages/chimerax/core/session.py", line 290, in process 
    12983 raise RuntimeError(msg) from e 
    12984 RuntimeError: Error while saving session data for 'isolde residue stepper 3'
    12985 -> <chimerax.isolde.navigate.ResidueStepper object at 0x7ff3fb4ae490> ->
    12986 <chimerax.atomic.structure.AtomicStructure object at 0x7ff42425b760> '40S-wt-
    12987 concat.pdb' 
    12988  
    12989 During handling of the above exception, another exception occurred: 
    12990  
    12991 Traceback (most recent call last): 
    12992 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    12993 packages/chimerax/core/session.py", line 896, in save 
    12994 session.save(output, version=version, include_maps=include_maps) 
    12995 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    12996 packages/chimerax/core/session.py", line 625, in save 
    12997 mgr.discovery(self._state_containers) 
    12998 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    12999 packages/chimerax/core/session.py", line 266, in discovery 
    13000 raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e)) 
    13001 ValueError: error processing: 'isolde residue stepper 3' ->
    13002 <chimerax.isolde.navigate.ResidueStepper object at 0x7ff3fb4ae490> ->
    13003 <chimerax.atomic.structure.AtomicStructure object at 0x7ff42425b760> '40S-wt-
    13004 concat.pdb': Error while saving session data for 'isolde residue stepper 3' ->
    13005 <chimerax.isolde.navigate.ResidueStepper object at 0x7ff3fb4ae490> ->
    13006 <chimerax.atomic.structure.AtomicStructure object at 0x7ff42425b760> '40S-wt-
    13007 concat.pdb' 
    13008  
    13009 ValueError: error processing: 'isolde residue stepper 3' -> -> '40S-wt-
    13010 concat.pdb': Error while saving session data for 'isolde residue stepper 3' ->
    13011 -> '40S-wt-concat.pdb' 
    13012  
    13013 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    13014 packages/chimerax/core/session.py", line 266, in discovery 
    13015 raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e)) 
    13016  
    13017 See log for complete Python traceback. 
    13018  
    13019 Traceback (most recent call last): 
    13020 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    13021 packages/chimerax/core/session.py", line 285, in process 
    13022 data = sm.take_snapshot(obj, session, self.state_flags) 
    13023 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    13024 packages/chimerax/atomic/structure.py", line 1389, in take_snapshot 
    13025 'structure state': Structure.take_snapshot(self, session, flags), 
    13026 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    13027 packages/chimerax/atomic/structure.py", line 208, in take_snapshot 
    13028 data = {'model state': Model.take_snapshot(self, session, flags), 
    13029 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    13030 packages/chimerax/core/models.py", line 329, in take_snapshot 
    13031 'positions': self.positions.array(), 
    13032 AttributeError: 'NoneType' object has no attribute 'array' 
    13033  
    13034 The above exception was the direct cause of the following exception: 
    13035  
    13036 Traceback (most recent call last): 
    13037 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    13038 packages/chimerax/core/session.py", line 262, in discovery 
    13039 self.processed[key] = self.process(obj, parents) 
    13040 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    13041 packages/chimerax/core/session.py", line 290, in process 
    13042 raise RuntimeError(msg) from e 
    13043 RuntimeError: Error while saving session data for 'isolde residue stepper 3'
    13044 -> <chimerax.isolde.navigate.ResidueStepper object at 0x7ff3fb4ae490> ->
    13045 <chimerax.atomic.structure.AtomicStructure object at 0x7ff42425b760> '40S-wt-
    13046 concat.pdb' 
    13047  
    13048 During handling of the above exception, another exception occurred: 
    13049  
    13050 Traceback (most recent call last): 
    13051 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    13052 packages/chimerax/save_command/dialog.py", line 116, in <lambda> 
    13053 lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output
    13054 file", 
    13055 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    13056 packages/chimerax/save_command/dialog.py", line 127, in show_save_file_dialog 
    13057 _dlg.display(session, **kw) 
    13058 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    13059 packages/chimerax/save_command/dialog.py", line 51, in display 
    13060 run(session, cmd) 
    13061 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    13062 packages/chimerax/core/commands/run.py", line 38, in run 
    13063 results = command.run(text, log=log, return_json=return_json) 
    13064 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    13065 packages/chimerax/core/commands/cli.py", line 2897, in run 
    13066 result = ci.function(session, **kw_args) 
    13067 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    13068 packages/chimerax/save_command/cmd.py", line 75, in cmd_save 
    13069 Command(session, registry=registry).run(provider_cmd_text, log=log) 
    13070 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    13071 packages/chimerax/core/commands/cli.py", line 2897, in run 
    13072 result = ci.function(session, **kw_args) 
    13073 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    13074 packages/chimerax/save_command/cmd.py", line 90, in provider_save 
    13075 saver_info.save(session, path, **provider_kw) 
    13076 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    13077 packages/chimerax/core_formats/__init__.py", line 84, in save 
    13078 return cxs_save(session, path, **kw) 
    13079 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    13080 packages/chimerax/core/session.py", line 896, in save 
    13081 session.save(output, version=version, include_maps=include_maps) 
    13082 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    13083 packages/chimerax/core/session.py", line 625, in save 
    13084 mgr.discovery(self._state_containers) 
    13085 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    13086 packages/chimerax/core/session.py", line 266, in discovery 
    13087 raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e)) 
    13088 ValueError: error processing: 'isolde residue stepper 3' ->
    13089 <chimerax.isolde.navigate.ResidueStepper object at 0x7ff3fb4ae490> ->
    13090 <chimerax.atomic.structure.AtomicStructure object at 0x7ff42425b760> '40S-wt-
    13091 concat.pdb': Error while saving session data for 'isolde residue stepper 3' ->
    13092 <chimerax.isolde.navigate.ResidueStepper object at 0x7ff3fb4ae490> ->
    13093 <chimerax.atomic.structure.AtomicStructure object at 0x7ff42425b760> '40S-wt-
    13094 concat.pdb' 
    13095  
    13096 ValueError: error processing: 'isolde residue stepper 3' -> -> '40S-wt-
    13097 concat.pdb': Error while saving session data for 'isolde residue stepper 3' ->
    13098 -> '40S-wt-concat.pdb' 
    13099  
    13100 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    13101 packages/chimerax/core/session.py", line 266, in discovery 
    13102 raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e)) 
    13103  
    13104 See log for complete Python traceback. 
    13105  
    13106 
    13107 > save /srv/home/leonardo/Documents/KSRP/Structures-maps-wt-mutants/40S-wt-
    13108 > refinement/Refinement-sent-fromRafael-in-Advance/Re-sent-
    13109 > byRafael-19-04-2023/10-FINAL-outlierRefinement-40S-KSRPwt.cxs
    13110 
    13111 Taking snapshot of stepper: 9-40S-KSRP-wt-Second-steps-FINALoutliersRaf.pdb 
    13112 Taking snapshot of stepper: 40S-wt-concat.pdb 
    13113 Traceback (most recent call last): 
    13114 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    13115 packages/chimerax/core/session.py", line 285, in process 
    13116 data = sm.take_snapshot(obj, session, self.state_flags) 
    13117 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    13118 packages/chimerax/atomic/structure.py", line 1389, in take_snapshot 
    13119 'structure state': Structure.take_snapshot(self, session, flags), 
    13120 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    13121 packages/chimerax/atomic/structure.py", line 208, in take_snapshot 
    13122 data = {'model state': Model.take_snapshot(self, session, flags), 
    13123 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    13124 packages/chimerax/core/models.py", line 329, in take_snapshot 
    13125 'positions': self.positions.array(), 
    13126 AttributeError: 'NoneType' object has no attribute 'array' 
    13127  
    13128 The above exception was the direct cause of the following exception: 
    13129  
    13130 Traceback (most recent call last): 
    13131 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    13132 packages/chimerax/core/session.py", line 262, in discovery 
    13133 self.processed[key] = self.process(obj, parents) 
    13134 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    13135 packages/chimerax/core/session.py", line 290, in process 
    13136 raise RuntimeError(msg) from e 
    13137 RuntimeError: Error while saving session data for 'isolde residue stepper 3'
    13138 -> <chimerax.isolde.navigate.ResidueStepper object at 0x7ff3fb4ae490> ->
    13139 <chimerax.atomic.structure.AtomicStructure object at 0x7ff42425b760> '40S-wt-
    13140 concat.pdb' 
    13141  
    13142 During handling of the above exception, another exception occurred: 
    13143  
    13144 Traceback (most recent call last): 
    13145 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    13146 packages/chimerax/core/session.py", line 896, in save 
    13147 session.save(output, version=version, include_maps=include_maps) 
    13148 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    13149 packages/chimerax/core/session.py", line 625, in save 
    13150 mgr.discovery(self._state_containers) 
    13151 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    13152 packages/chimerax/core/session.py", line 266, in discovery 
    13153 raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e)) 
    13154 ValueError: error processing: 'isolde residue stepper 3' ->
    13155 <chimerax.isolde.navigate.ResidueStepper object at 0x7ff3fb4ae490> ->
    13156 <chimerax.atomic.structure.AtomicStructure object at 0x7ff42425b760> '40S-wt-
    13157 concat.pdb': Error while saving session data for 'isolde residue stepper 3' ->
    13158 <chimerax.isolde.navigate.ResidueStepper object at 0x7ff3fb4ae490> ->
    13159 <chimerax.atomic.structure.AtomicStructure object at 0x7ff42425b760> '40S-wt-
    13160 concat.pdb' 
    13161  
    13162 ValueError: error processing: 'isolde residue stepper 3' -> -> '40S-wt-
    13163 concat.pdb': Error while saving session data for 'isolde residue stepper 3' ->
    13164 -> '40S-wt-concat.pdb' 
    13165  
    13166 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    13167 packages/chimerax/core/session.py", line 266, in discovery 
    13168 raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e)) 
    13169  
    13170 See log for complete Python traceback. 
    13171  
    13172 Traceback (most recent call last): 
    13173 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    13174 packages/chimerax/core/session.py", line 285, in process 
    13175 data = sm.take_snapshot(obj, session, self.state_flags) 
    13176 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    13177 packages/chimerax/atomic/structure.py", line 1389, in take_snapshot 
    13178 'structure state': Structure.take_snapshot(self, session, flags), 
    13179 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    13180 packages/chimerax/atomic/structure.py", line 208, in take_snapshot 
    13181 data = {'model state': Model.take_snapshot(self, session, flags), 
    13182 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    13183 packages/chimerax/core/models.py", line 329, in take_snapshot 
    13184 'positions': self.positions.array(), 
    13185 AttributeError: 'NoneType' object has no attribute 'array' 
    13186  
    13187 The above exception was the direct cause of the following exception: 
    13188  
    13189 Traceback (most recent call last): 
    13190 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    13191 packages/chimerax/core/session.py", line 262, in discovery 
    13192 self.processed[key] = self.process(obj, parents) 
    13193 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    13194 packages/chimerax/core/session.py", line 290, in process 
    13195 raise RuntimeError(msg) from e 
    13196 RuntimeError: Error while saving session data for 'isolde residue stepper 3'
    13197 -> <chimerax.isolde.navigate.ResidueStepper object at 0x7ff3fb4ae490> ->
    13198 <chimerax.atomic.structure.AtomicStructure object at 0x7ff42425b760> '40S-wt-
    13199 concat.pdb' 
    13200  
    13201 During handling of the above exception, another exception occurred: 
    13202  
    13203 Traceback (most recent call last): 
    13204 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    13205 packages/chimerax/save_command/dialog.py", line 116, in <lambda> 
    13206 lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output
    13207 file", 
    13208 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    13209 packages/chimerax/save_command/dialog.py", line 127, in show_save_file_dialog 
    13210 _dlg.display(session, **kw) 
    13211 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    13212 packages/chimerax/save_command/dialog.py", line 51, in display 
    13213 run(session, cmd) 
    13214 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    13215 packages/chimerax/core/commands/run.py", line 38, in run 
    13216 results = command.run(text, log=log, return_json=return_json) 
    13217 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    13218 packages/chimerax/core/commands/cli.py", line 2897, in run 
    13219 result = ci.function(session, **kw_args) 
    13220 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    13221 packages/chimerax/save_command/cmd.py", line 75, in cmd_save 
    13222 Command(session, registry=registry).run(provider_cmd_text, log=log) 
    13223 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    13224 packages/chimerax/core/commands/cli.py", line 2897, in run 
    13225 result = ci.function(session, **kw_args) 
    13226 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    13227 packages/chimerax/save_command/cmd.py", line 90, in provider_save 
    13228 saver_info.save(session, path, **provider_kw) 
    13229 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    13230 packages/chimerax/core_formats/__init__.py", line 84, in save 
    13231 return cxs_save(session, path, **kw) 
    13232 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    13233 packages/chimerax/core/session.py", line 896, in save 
    13234 session.save(output, version=version, include_maps=include_maps) 
    13235 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    13236 packages/chimerax/core/session.py", line 625, in save 
    13237 mgr.discovery(self._state_containers) 
    13238 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    13239 packages/chimerax/core/session.py", line 266, in discovery 
    13240 raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e)) 
    13241 ValueError: error processing: 'isolde residue stepper 3' ->
    13242 <chimerax.isolde.navigate.ResidueStepper object at 0x7ff3fb4ae490> ->
    13243 <chimerax.atomic.structure.AtomicStructure object at 0x7ff42425b760> '40S-wt-
    13244 concat.pdb': Error while saving session data for 'isolde residue stepper 3' ->
    13245 <chimerax.isolde.navigate.ResidueStepper object at 0x7ff3fb4ae490> ->
    13246 <chimerax.atomic.structure.AtomicStructure object at 0x7ff42425b760> '40S-wt-
    13247 concat.pdb' 
    13248  
    13249 ValueError: error processing: 'isolde residue stepper 3' -> -> '40S-wt-
    13250 concat.pdb': Error while saving session data for 'isolde residue stepper 3' ->
    13251 -> '40S-wt-concat.pdb' 
    13252  
    13253 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    13254 packages/chimerax/core/session.py", line 266, in discovery 
    13255 raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e)) 
    13256  
    13257 See log for complete Python traceback. 
    13258  
    13259 
    13260 > save /srv/home/leonardo/Documents/KSRP/Structures-maps-wt-mutants/40S-wt-
    13261 > refinement/Refinement-sent-fromRafael-in-Advance/Re-sent-
    13262 > byRafael-19-04-2023/10-FINAL-outlierRefinement-40S-KSRPwt.cxs
    13263 
    13264 Taking snapshot of stepper: 9-40S-KSRP-wt-Second-steps-FINALoutliersRaf.pdb 
    13265 Taking snapshot of stepper: 40S-wt-concat.pdb 
    13266 Traceback (most recent call last): 
    13267 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    13268 packages/chimerax/core/session.py", line 285, in process 
    13269 data = sm.take_snapshot(obj, session, self.state_flags) 
    13270 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    13271 packages/chimerax/atomic/structure.py", line 1389, in take_snapshot 
    13272 'structure state': Structure.take_snapshot(self, session, flags), 
    13273 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    13274 packages/chimerax/atomic/structure.py", line 208, in take_snapshot 
    13275 data = {'model state': Model.take_snapshot(self, session, flags), 
    13276 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    13277 packages/chimerax/core/models.py", line 329, in take_snapshot 
    13278 'positions': self.positions.array(), 
    13279 AttributeError: 'NoneType' object has no attribute 'array' 
    13280  
    13281 The above exception was the direct cause of the following exception: 
    13282  
    13283 Traceback (most recent call last): 
    13284 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    13285 packages/chimerax/core/session.py", line 262, in discovery 
    13286 self.processed[key] = self.process(obj, parents) 
    13287 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    13288 packages/chimerax/core/session.py", line 290, in process 
    13289 raise RuntimeError(msg) from e 
    13290 RuntimeError: Error while saving session data for 'isolde residue stepper 3'
    13291 -> <chimerax.isolde.navigate.ResidueStepper object at 0x7ff3fb4ae490> ->
    13292 <chimerax.atomic.structure.AtomicStructure object at 0x7ff42425b760> '40S-wt-
    13293 concat.pdb' 
    13294  
    13295 During handling of the above exception, another exception occurred: 
    13296  
    13297 Traceback (most recent call last): 
    13298 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    13299 packages/chimerax/core/session.py", line 896, in save 
    13300 session.save(output, version=version, include_maps=include_maps) 
    13301 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    13302 packages/chimerax/core/session.py", line 625, in save 
    13303 mgr.discovery(self._state_containers) 
    13304 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    13305 packages/chimerax/core/session.py", line 266, in discovery 
    13306 raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e)) 
    13307 ValueError: error processing: 'isolde residue stepper 3' ->
    13308 <chimerax.isolde.navigate.ResidueStepper object at 0x7ff3fb4ae490> ->
    13309 <chimerax.atomic.structure.AtomicStructure object at 0x7ff42425b760> '40S-wt-
    13310 concat.pdb': Error while saving session data for 'isolde residue stepper 3' ->
    13311 <chimerax.isolde.navigate.ResidueStepper object at 0x7ff3fb4ae490> ->
    13312 <chimerax.atomic.structure.AtomicStructure object at 0x7ff42425b760> '40S-wt-
    13313 concat.pdb' 
    13314  
    13315 ValueError: error processing: 'isolde residue stepper 3' -> -> '40S-wt-
    13316 concat.pdb': Error while saving session data for 'isolde residue stepper 3' ->
    13317 -> '40S-wt-concat.pdb' 
    13318  
    13319 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    13320 packages/chimerax/core/session.py", line 266, in discovery 
    13321 raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e)) 
    13322  
    13323 See log for complete Python traceback. 
    13324  
    13325 Traceback (most recent call last): 
    13326 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    13327 packages/chimerax/core/session.py", line 285, in process 
    13328 data = sm.take_snapshot(obj, session, self.state_flags) 
    13329 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    13330 packages/chimerax/atomic/structure.py", line 1389, in take_snapshot 
    13331 'structure state': Structure.take_snapshot(self, session, flags), 
    13332 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    13333 packages/chimerax/atomic/structure.py", line 208, in take_snapshot 
    13334 data = {'model state': Model.take_snapshot(self, session, flags), 
    13335 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    13336 packages/chimerax/core/models.py", line 329, in take_snapshot 
    13337 'positions': self.positions.array(), 
    13338 AttributeError: 'NoneType' object has no attribute 'array' 
    13339  
    13340 The above exception was the direct cause of the following exception: 
    13341  
    13342 Traceback (most recent call last): 
    13343 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    13344 packages/chimerax/core/session.py", line 262, in discovery 
    13345 self.processed[key] = self.process(obj, parents) 
    13346 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    13347 packages/chimerax/core/session.py", line 290, in process 
    13348 raise RuntimeError(msg) from e 
    13349 RuntimeError: Error while saving session data for 'isolde residue stepper 3'
    13350 -> <chimerax.isolde.navigate.ResidueStepper object at 0x7ff3fb4ae490> ->
    13351 <chimerax.atomic.structure.AtomicStructure object at 0x7ff42425b760> '40S-wt-
    13352 concat.pdb' 
    13353  
    13354 During handling of the above exception, another exception occurred: 
    13355  
    13356 Traceback (most recent call last): 
    13357 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    13358 packages/chimerax/save_command/dialog.py", line 116, in <lambda> 
    13359 lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output
    13360 file", 
    13361 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    13362 packages/chimerax/save_command/dialog.py", line 127, in show_save_file_dialog 
    13363 _dlg.display(session, **kw) 
    13364 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    13365 packages/chimerax/save_command/dialog.py", line 51, in display 
    13366 run(session, cmd) 
    13367 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    13368 packages/chimerax/core/commands/run.py", line 38, in run 
    13369 results = command.run(text, log=log, return_json=return_json) 
    13370 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    13371 packages/chimerax/core/commands/cli.py", line 2897, in run 
    13372 result = ci.function(session, **kw_args) 
    13373 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    13374 packages/chimerax/save_command/cmd.py", line 75, in cmd_save 
    13375 Command(session, registry=registry).run(provider_cmd_text, log=log) 
    13376 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    13377 packages/chimerax/core/commands/cli.py", line 2897, in run 
    13378 result = ci.function(session, **kw_args) 
    13379 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    13380 packages/chimerax/save_command/cmd.py", line 90, in provider_save 
    13381 saver_info.save(session, path, **provider_kw) 
    13382 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    13383 packages/chimerax/core_formats/__init__.py", line 84, in save 
    13384 return cxs_save(session, path, **kw) 
    13385 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    13386 packages/chimerax/core/session.py", line 896, in save 
    13387 session.save(output, version=version, include_maps=include_maps) 
    13388 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    13389 packages/chimerax/core/session.py", line 625, in save 
    13390 mgr.discovery(self._state_containers) 
    13391 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    13392 packages/chimerax/core/session.py", line 266, in discovery 
    13393 raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e)) 
    13394 ValueError: error processing: 'isolde residue stepper 3' ->
    13395 <chimerax.isolde.navigate.ResidueStepper object at 0x7ff3fb4ae490> ->
    13396 <chimerax.atomic.structure.AtomicStructure object at 0x7ff42425b760> '40S-wt-
    13397 concat.pdb': Error while saving session data for 'isolde residue stepper 3' ->
    13398 <chimerax.isolde.navigate.ResidueStepper object at 0x7ff3fb4ae490> ->
    13399 <chimerax.atomic.structure.AtomicStructure object at 0x7ff42425b760> '40S-wt-
    13400 concat.pdb' 
    13401  
    13402 ValueError: error processing: 'isolde residue stepper 3' -> -> '40S-wt-
    13403 concat.pdb': Error while saving session data for 'isolde residue stepper 3' ->
    13404 -> '40S-wt-concat.pdb' 
    13405  
    13406 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
    13407 packages/chimerax/core/session.py", line 266, in discovery 
    13408 raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e)) 
    13409  
    13410 See log for complete Python traceback. 
    13411  
    13412 
    13413 > view #1
    13414 
    13415 > alphafold match #1 trim false
    13416 
    13417 Fetching AlphaFold database settings from
    13418 https://www.rbvi.ucsf.edu/chimerax/data/status/alphafold_database.json 
    13419 Fetching compressed AlphaFold Q4CXR4 from
    13420 https://alphafold.ebi.ac.uk/files/AF-Q4CXR4-F1-model_v2.cif 
    13421 Fetching compressed AlphaFold Q4D7C8 from
    13422 https://alphafold.ebi.ac.uk/files/AF-Q4D7C8-F1-model_v2.cif 
    13423 Fetching compressed AlphaFold Q4E3M0 from
    13424 https://alphafold.ebi.ac.uk/files/AF-Q4E3M0-F1-model_v2.cif 
    13425 Fetching compressed AlphaFold Q4D1T6 from
    13426 https://alphafold.ebi.ac.uk/files/AF-Q4D1T6-F1-model_v2.cif 
    13427 Fetching compressed AlphaFold Q4DK40 from
    13428 https://alphafold.ebi.ac.uk/files/AF-Q4DK40-F1-model_v2.cif 
    13429 Fetching compressed AlphaFold Q4DY32 from
    13430 https://alphafold.ebi.ac.uk/files/AF-Q4DY32-F1-model_v2.cif 
    13431 34 AlphaFold models found using UniProt identifiers: Q4DTN2 (chain p), Q4CXR4
    13432 (chain q), Q4DEK4 (chain r), Q4DGZ5 (chain t), Q4E093 (chain u), Q4D5P4 (chain
    13433 L), Q4DTQ1 (chain M), Q4E0Q3 (chain O), Q4CUC7 (chain Q), Q4DC38 (chain R),
    13434 Q4DN73 (chain S), Q4CYE4 (chain T), Q4D7C8 (chain U), Q4D6I5 (chain V), Q4DZ41
    13435 (chain W), Q4D0U7 (chain X), Q4DW38 (chain Y), Q4DU83 (chain Z), Q4D4S1 (chain
    13436 b), Q4CQ63 (chain f), Q4DIZ9 (chain d), Q4E0N6 (chain e), Q4E3M0 (chain g),
    13437 Q4DTX6 (chain a), Q4CSL1 (chain i), Q4D1T6 (chain j), Q4DSU0 (chain P), Q4DK40
    13438 (chain k), Q4D6H7 (chain l), Q4DMK9 (chain m), Q4E088 (chain n), Q4DJY1 (chain
    13439 o), Q4DA48 (chain c), Q4DY32 (chain h) 
    13440 AlphaFold chains matching 9-40S-KSRP-wt-Second-steps-FINALoutliersRaf.pdb 
    13441 --- 
    13442 Chain| UniProt Name| UniProt Id| RMSD| Length| Seen| % Id 
    13443 f | Q4CQ63_TRYCC | Q4CQ63 | 0.68 | 245 | 207 | 100 
    13444 i | Q4CSL1_TRYCC | Q4CSL1 | 3.63 | 141 | 121 | 100 
    13445 Q | Q4CUC7_TRYCC | Q4CUC7 | 1.58 | 211 | 200 | 100 
    13446 q | Q4CXR4_TRYCC | Q4CXR4 | 4.42 | 57 | 38 | 100 
    13447 T | Q4CYE4_TRYCC | Q4CYE4 | 1.46 | 112 | 104 | 100 
    13448 X | Q4D0U7_TRYCC | Q4D0U7 | 3.27 | 173 | 148 | 100 
    13449 j | Q4D1T6_TRYCC | Q4D1T6 | 9.31 | 150 | 64 | 100 
    13450 b | Q4D4S1_TRYCC | Q4D4S1 | 0.70 | 190 | 164 | 100 
    13451 L | Q4D5P4_TRYCC | Q4D5P4 | 0.60 | 273 | 258 | 100 
    13452 l | Q4D6H7_TRYCC | Q4D6H7 | 3.30 | 117 | 99 | 100 
    13453 V | Q4D6I5_TRYCC | Q4D6I5 | 1.02 | 144 | 135 | 100 
    13454 U | Q4D7C8_TRYCC | Q4D7C8 | 2.93 | 112 | 68 | 100 
    13455 c | Q4DA48_TRYCC | Q4DA48 | 2.56 | 66 | 60 | 100 
    13456 R | Q4DC38_TRYCC | Q4DC38 | 0.59 | 151 | 141 | 100 
    13457 r | Q4DEK4_TRYCC | Q4DEK4 | 2.36 | 149 | 140 | 100 
    13458 t | Q4DGZ5_TRYCC | Q4DGZ5 | 4.63 | 152 | 119 | 100 
    13459 d | Q4DIZ9_TRYCC | Q4DIZ9 | 0.81 | 263 | 223 | 100 
    13460 o | Q4DJY1_TRYCC | Q4DJY1 | 17.93 | 167 | 140 | 100 
    13461 k | Q4DK40_TRYCC | Q4DK40 | 5.23 | 196 | 118 | 100 
    13462 m | Q4DMK9_TRYCC | Q4DMK9 | 3.03 | 214 | 200 | 100 
    13463 S | Q4DN73_TRYCC | Q4DN73 | 1.27 | 86 | 82 | 100 
    13464 P | Q4DSU0_TRYCC | Q4DSU0 | 3.79 | 250 | 249 | 100 
    13465 p | Q4DTN2_TRYCC | Q4DTN2 | 3.23 | 318 | 310 | 100 
    13466 M | Q4DTQ1_TRYCC | Q4DTQ1 | 0.69 | 143 | 142 | 100 
    13467 a | Q4DTX6_TRYCC | Q4DTX6 | 3.69 | 110 | 70 | 100 
    13468 Z | Q4DU83_TRYCC | Q4DU83 | 0.67 | 221 | 175 | 100 
    13469 Y | Q4DW38_TRYCC | Q4DW38 | 0.91 | 137 | 123 | 100 
    13470 h | Q4DY32_TRYCC | Q4DY32 | 12.98 | 257 | 173 | 100 
    13471 n | Q4E088_TRYCC | Q4E088 | 3.25 | 161 | 93 | 100 
    13472 u | Q4E093_TRYCC | Q4E093 | 4.14 | 153 | 120 | 100 
    13473 e | Q4E0N6_TRYCC | Q4E0N6 | 0.48 | 130 | 129 | 100 
    13474 O | Q4E0Q3_TRYCC | Q4E0Q3 | 2.41 | 190 | 190 | 100 
    13475 g | Q4E3M0_TRYCC | Q4E3M0 | 0.80 | 236 | 83 | 100 
    13476 W | RS3A2_TRYCC | Q4DZ41 | 0.86 | 261 | 217 | 100 
    13477  
    13478 Opened 34 AlphaFold models 
    13479 
    13480 > combine #2
    13481 
    13482 > hide #!2 models
    13483 
    13484 > hide #3 models
    13485 
    13486 > show #3 models
    13487 
    13488 > matchmaker #3 to #1.2
    13489 
    13490 Parameters 
    13491 --- 
    13492 Chain pairing | bb 
    13493 Alignment algorithm | Needleman-Wunsch 
    13494 Similarity matrix | BLOSUM-62 
    13495 SS fraction | 0.3 
    13496 Gap open (HH/SS/other) | 18/18/6 
    13497 Gap extend | 1 
    13498 SS matrix |  |  | H | S | O 
    13499 ---|---|---|--- 
    13500 H | 6 | -9 | -6 
    13501 S |  | 6 | -6 
    13502 O |  |  | 4 
    13503 Iteration cutoff | 2 
    13504  
    13505 Matchmaker 9-40S-KSRP-wt-Second-steps-FINALoutliersRaf.pdb, chain L (#1.2)
    13506 with combination, chain L (#3), sequence alignment score = 1241.4 
    13507 RMSD between 257 pruned atom pairs is 0.567 angstroms; (across all 258 pairs:
    13508 0.599) 
    13509  
    13510 
    13511 > color #3 bychain
    13512 
    13513 > color #3 byhetero
    13514 
    13515 > color modify #3 hue + 50
    13516 
    13517 > view #1
    13518 
    13519 [Repeated 2 time(s)]
    13520 
    13521 "Adjust for PAE" is checked in the distance restraint options, but the
    13522 reference model has no PAE matrix assigned. This option has been ignored. 
    13523 
    13524 > isolde restrain distances
    13525 > "#1.2/L","#1.2/M","#1.2/O","#1.2/P","#1.2/Q","#1.2/R","#1.2/S","#1.2/T","#1.2/U","#1.2/V","#1.2/W","#1.2/X","#1.2/Y","#1.2/Z","#1.2/a","#1.2/b","#1.2/c","#1.2/d","#1.2/e","#1.2/f","#1.2/g","#1.2/h","#1.2/i","#1.2/j","#1.2/k","#1.2/l","#1.2/m","#1.2/n","#1.2/o","#1.2/p","#1.2/q","#1.2/r","#1.2/t","#1.2/u"
    13526 > templateAtoms
    13527 > "#3/L","#3/M","#3/O","#3/P","#3/Q","#3/R","#3/S","#3/T","#3/U","#3/V","#3/W","#3/X","#3/Y","#3/Z","#3/a","#3/b","#3/c","#3/d","#3/e","#3/f","#3/g","#3/h","#3/i","#3/j","#3/k","#3/l","#3/m","#3/n","#3/o","#3/p","#3/q","#3/r","#3/t","#3/u"
    13528 > perChain true adjustForConfidence false useCoordinateAlignment false kappa
    13529 > 4.40 fallOff 2.50 groupName "Reference Distance Restraints"
    13530 
    13531 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    13532 chains... 
    13533 [Repeated 1 time(s)]ISOLDE: Corrected atom nomenclature of 1038 residues in
    13534 model #3 to IUPAC-IUB standards. 
    13535 
    13536 > isolde restrain torsions #1.2/L templateResidues #3/L adjustForConfidence
    13537 > true sidechains true springConstant 250.00 alpha 0.20
    13538 
    13539 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    13540 chains... 
    13541 [Repeated 1 time(s)]
    13542 
    13543 > isolde restrain torsions #1.2/M templateResidues #3/M adjustForConfidence
    13544 > true sidechains true springConstant 250.00 alpha 0.20
    13545 
    13546 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    13547 chains... 
    13548 [Repeated 1 time(s)]
    13549 
    13550 > isolde restrain torsions #1.2/O templateResidues #3/O adjustForConfidence
    13551 > true sidechains true springConstant 250.00 alpha 0.20
    13552 
    13553 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    13554 chains... 
    13555 [Repeated 1 time(s)]
    13556 
    13557 > isolde restrain torsions #1.2/P templateResidues #3/P adjustForConfidence
    13558 > true sidechains true springConstant 250.00 alpha 0.20
    13559 
    13560 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    13561 chains... 
    13562 [Repeated 1 time(s)]
    13563 
    13564 > isolde restrain torsions #1.2/Q templateResidues #3/Q adjustForConfidence
    13565 > true sidechains true springConstant 250.00 alpha 0.20
    13566 
    13567 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    13568 chains... 
    13569 [Repeated 1 time(s)]
    13570 
    13571 > isolde restrain torsions #1.2/R templateResidues #3/R adjustForConfidence
    13572 > true sidechains true springConstant 250.00 alpha 0.20
    13573 
    13574 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    13575 chains... 
    13576 [Repeated 1 time(s)]
    13577 
    13578 > isolde restrain torsions #1.2/S templateResidues #3/S adjustForConfidence
    13579 > true sidechains true springConstant 250.00 alpha 0.20
    13580 
    13581 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    13582 chains... 
    13583 [Repeated 1 time(s)]
    13584 
    13585 > isolde restrain torsions #1.2/T templateResidues #3/T adjustForConfidence
    13586 > true sidechains true springConstant 250.00 alpha 0.20
    13587 
    13588 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    13589 chains... 
    13590 [Repeated 1 time(s)]
    13591 
    13592 > isolde restrain torsions #1.2/U templateResidues #3/U adjustForConfidence
    13593 > true sidechains true springConstant 250.00 alpha 0.20
    13594 
    13595 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    13596 chains... 
    13597 [Repeated 1 time(s)]
    13598 
    13599 > isolde restrain torsions #1.2/V templateResidues #3/V adjustForConfidence
    13600 > true sidechains true springConstant 250.00 alpha 0.20
    13601 
    13602 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    13603 chains... 
    13604 [Repeated 1 time(s)]
    13605 
    13606 > isolde restrain torsions #1.2/W templateResidues #3/W adjustForConfidence
    13607 > true sidechains true springConstant 250.00 alpha 0.20
    13608 
    13609 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    13610 chains... 
    13611 [Repeated 1 time(s)]
    13612 
    13613 > isolde restrain torsions #1.2/X templateResidues #3/X adjustForConfidence
    13614 > true sidechains true springConstant 250.00 alpha 0.20
    13615 
    13616 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    13617 chains... 
    13618 [Repeated 1 time(s)]
    13619 
    13620 > isolde restrain torsions #1.2/Y templateResidues #3/Y adjustForConfidence
    13621 > true sidechains true springConstant 250.00 alpha 0.20
    13622 
    13623 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    13624 chains... 
    13625 [Repeated 1 time(s)]
    13626 
    13627 > isolde restrain torsions #1.2/Z templateResidues #3/Z adjustForConfidence
    13628 > true sidechains true springConstant 250.00 alpha 0.20
    13629 
    13630 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    13631 chains... 
    13632 [Repeated 1 time(s)]
    13633 
    13634 > isolde restrain torsions #1.2/a templateResidues #3/a adjustForConfidence
    13635 > true sidechains true springConstant 250.00 alpha 0.20
    13636 
    13637 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    13638 chains... 
    13639 [Repeated 1 time(s)]
    13640 
    13641 > isolde restrain torsions #1.2/b templateResidues #3/b adjustForConfidence
    13642 > true sidechains true springConstant 250.00 alpha 0.20
    13643 
    13644 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    13645 chains... 
    13646 [Repeated 1 time(s)]
    13647 
    13648 > isolde restrain torsions #1.2/c templateResidues #3/c adjustForConfidence
    13649 > true sidechains true springConstant 250.00 alpha 0.20
    13650 
    13651 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    13652 chains... 
    13653 [Repeated 1 time(s)]
    13654 
    13655 > isolde restrain torsions #1.2/d templateResidues #3/d adjustForConfidence
    13656 > true sidechains true springConstant 250.00 alpha 0.20
    13657 
    13658 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    13659 chains... 
    13660 [Repeated 1 time(s)]
    13661 
    13662 > isolde restrain torsions #1.2/e templateResidues #3/e adjustForConfidence
    13663 > true sidechains true springConstant 250.00 alpha 0.20
    13664 
    13665 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    13666 chains... 
    13667 [Repeated 1 time(s)]
    13668 
    13669 > isolde restrain torsions #1.2/f templateResidues #3/f adjustForConfidence
    13670 > true sidechains true springConstant 250.00 alpha 0.20
    13671 
    13672 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    13673 chains... 
    13674 [Repeated 1 time(s)]
    13675 
    13676 > isolde restrain torsions #1.2/g templateResidues #3/g adjustForConfidence
    13677 > true sidechains true springConstant 250.00 alpha 0.20
    13678 
    13679 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    13680 chains... 
    13681 [Repeated 1 time(s)]
    13682 
    13683 > isolde restrain torsions #1.2/h templateResidues #3/h adjustForConfidence
    13684 > true sidechains true springConstant 250.00 alpha 0.20
    13685 
    13686 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    13687 chains... 
    13688 [Repeated 1 time(s)]
    13689 
    13690 > isolde restrain torsions #1.2/i templateResidues #3/i adjustForConfidence
    13691 > true sidechains true springConstant 250.00 alpha 0.20
    13692 
    13693 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    13694 chains... 
    13695 [Repeated 1 time(s)]
    13696 
    13697 > isolde restrain torsions #1.2/j templateResidues #3/j adjustForConfidence
    13698 > true sidechains true springConstant 250.00 alpha 0.20
    13699 
    13700 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    13701 chains... 
    13702 [Repeated 1 time(s)]
    13703 
    13704 > isolde restrain torsions #1.2/k templateResidues #3/k adjustForConfidence
    13705 > true sidechains true springConstant 250.00 alpha 0.20
    13706 
    13707 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    13708 chains... 
    13709 [Repeated 1 time(s)]
    13710 
    13711 > isolde restrain torsions #1.2/l templateResidues #3/l adjustForConfidence
    13712 > true sidechains true springConstant 250.00 alpha 0.20
    13713 
    13714 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    13715 chains... 
    13716 [Repeated 1 time(s)]
    13717 
    13718 > isolde restrain torsions #1.2/m templateResidues #3/m adjustForConfidence
    13719 > true sidechains true springConstant 250.00 alpha 0.20
    13720 
    13721 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    13722 chains... 
    13723 [Repeated 1 time(s)]
    13724 
    13725 > isolde restrain torsions #1.2/n templateResidues #3/n adjustForConfidence
    13726 > true sidechains true springConstant 250.00 alpha 0.20
    13727 
    13728 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    13729 chains... 
    13730 [Repeated 1 time(s)]
    13731 
    13732 > isolde restrain torsions #1.2/o templateResidues #3/o adjustForConfidence
    13733 > true sidechains true springConstant 250.00 alpha 0.20
    13734 
    13735 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    13736 chains... 
    13737 [Repeated 1 time(s)]
    13738 
    13739 > isolde restrain torsions #1.2/p templateResidues #3/p adjustForConfidence
    13740 > true sidechains true springConstant 250.00 alpha 0.20
    13741 
    13742 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    13743 chains... 
    13744 [Repeated 1 time(s)]
    13745 
    13746 > isolde restrain torsions #1.2/q templateResidues #3/q adjustForConfidence
    13747 > true sidechains true springConstant 250.00 alpha 0.20
    13748 
    13749 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    13750 chains... 
    13751 [Repeated 1 time(s)]
    13752 
    13753 > isolde restrain torsions #1.2/r templateResidues #3/r adjustForConfidence
    13754 > true sidechains true springConstant 250.00 alpha 0.20
    13755 
    13756 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    13757 chains... 
    13758 [Repeated 1 time(s)]
    13759 
    13760 > isolde restrain torsions #1.2/t templateResidues #3/t adjustForConfidence
    13761 > true sidechains true springConstant 250.00 alpha 0.20
    13762 
    13763 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    13764 chains... 
    13765 [Repeated 1 time(s)]
    13766 
    13767 > isolde restrain torsions #1.2/u templateResidues #3/u adjustForConfidence
    13768 > true sidechains true springConstant 250.00 alpha 0.20
    13769 
    13770 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    13771 chains... 
    13772 [Repeated 1 time(s)]
    13773 
    13774 > hide #!1.2 models
    13775 
    13776 > show #!1.2 models
    13777 
    13778 > isolde restrain distances
    13779 > "#1.2/L","#1.2/M","#1.2/O","#1.2/P","#1.2/Q","#1.2/R","#1.2/S","#1.2/T","#1.2/U","#1.2/V","#1.2/W","#1.2/X","#1.2/Y","#1.2/Z","#1.2/a","#1.2/b","#1.2/c","#1.2/d","#1.2/e","#1.2/f","#1.2/g","#1.2/h","#1.2/i","#1.2/j","#1.2/k","#1.2/l","#1.2/m","#1.2/n","#1.2/o","#1.2/p","#1.2/q","#1.2/r","#1.2/t","#1.2/u"
    13780 > templateAtoms
    13781 > "#3/L","#3/M","#3/O","#3/P","#3/Q","#3/R","#3/S","#3/T","#3/U","#3/V","#3/W","#3/X","#3/Y","#3/Z","#3/a","#3/b","#3/c","#3/d","#3/e","#3/f","#3/g","#3/h","#3/i","#3/j","#3/k","#3/l","#3/m","#3/n","#3/o","#3/p","#3/q","#3/r","#3/t","#3/u"
    13782 > perChain true adjustForConfidence true
    13783 
    13784 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
    13785 chains... 
    13786 [Repeated 1 time(s)]RMSD between 258 pruned atom pairs is 0.599 angstroms;
    13787 (across all 258 pairs: 0.599) 
    13788 RMSD between 142 pruned atom pairs is 0.689 angstroms; (across all 142 pairs:
    13789 0.689) 
    13790 RMSD between 180 pruned atom pairs is 1.868 angstroms; (across all 190 pairs:
    13791 2.411) 
    13792 RMSD between 3 pruned atom pairs is 3.639 angstroms; (across all 10 pairs:
    13793 20.579) 
    13794 RMSD between 3 pruned atom pairs is 2.894 angstroms; (across all 7 pairs:
    13795 23.001) 
    13796 RMSD between 241 pruned atom pairs is 1.848 angstroms; (across all 249 pairs:
    13797 2.212) 
    13798 RMSD between 8 pruned atom pairs is 2.160 angstroms; (across all 8 pairs:
    13799 2.160) 
    13800 RMSD between 200 pruned atom pairs is 1.538 angstroms; (across all 200 pairs:
    13801 1.538) 
    13802 RMSD between 141 pruned atom pairs is 0.586 angstroms; (across all 141 pairs:
    13803 0.586) 
    13804 RMSD between 82 pruned atom pairs is 1.246 angstroms; (across all 82 pairs:
    13805 1.246) 
    13806 RMSD between 102 pruned atom pairs is 0.975 angstroms; (across all 104 pairs:
    13807 1.456) 
    13808 RMSD between 63 pruned atom pairs is 1.692 angstroms; (across all 68 pairs:
    13809 2.920) 
    13810 RMSD between 4 pruned atom pairs is 2.704 angstroms; (across all 5 pairs:
    13811 7.281) 
    13812 RMSD between 135 pruned atom pairs is 1.009 angstroms; (across all 135 pairs:
    13813 1.009) 
    13814 RMSD between 217 pruned atom pairs is 0.860 angstroms; (across all 217 pairs:
    13815 0.860) 
    13816 RMSD between 139 pruned atom pairs is 0.725 angstroms; (across all 148 pairs:
    13817 3.236) 
    13818 RMSD between 9 pruned atom pairs is 2.465 angstroms; (across all 9 pairs:
    13819 2.465) 
    13820 RMSD between 123 pruned atom pairs is 0.906 angstroms; (across all 123 pairs:
    13821 0.906) 
    13822 RMSD between 175 pruned atom pairs is 0.667 angstroms; (across all 175 pairs:
    13823 0.667) 
    13824 RMSD between 63 pruned atom pairs is 2.398 angstroms; (across all 70 pairs:
    13825 3.506) 
    13826 RMSD between 4 pruned atom pairs is 2.868 angstroms; (across all 7 pairs:
    13827 16.045) 
    13828 RMSD between 164 pruned atom pairs is 0.701 angstroms; (across all 164 pairs:
    13829 0.701) 
    13830 RMSD between 56 pruned atom pairs is 1.556 angstroms; (across all 60 pairs:
    13831 2.589) 
    13832 RMSD between 4 pruned atom pairs is 3.151 angstroms; (across all 4 pairs:
    13833 3.151) 
    13834 RMSD between 223 pruned atom pairs is 0.810 angstroms; (across all 223 pairs:
    13835 0.810) 
    13836 RMSD between 129 pruned atom pairs is 0.483 angstroms; (across all 129 pairs:
    13837 0.483) 
    13838 RMSD between 207 pruned atom pairs is 0.677 angstroms; (across all 207 pairs:
    13839 0.677) 
    13840 RMSD between 83 pruned atom pairs is 0.793 angstroms; (across all 83 pairs:
    13841 0.793) 
    13842 RMSD between 90 pruned atom pairs is 1.992 angstroms; (across all 173 pairs:
    13843 12.868) 
    13844 RMSD between 48 pruned atom pairs is 2.616 angstroms; (across all 83 pairs:
    13845 23.923) 
    13846 RMSD between 10 pruned atom pairs is 2.772 angstroms; (across all 35 pairs:
    13847 16.593) 
    13848 RMSD between 10 pruned atom pairs is 2.897 angstroms; (across all 25 pairs:
    13849 17.922) 
    13850 RMSD between 5 pruned atom pairs is 3.334 angstroms; (across all 15 pairs:
    13851 16.191) 
    13852 RMSD between 3 pruned atom pairs is 2.426 angstroms; (across all 10 pairs:
    13853 20.550) 
    13854 RMSD between 3 pruned atom pairs is 0.594 angstroms; (across all 7 pairs:
    13855 40.773) 
    13856 RMSD between 3 pruned atom pairs is 0.712 angstroms; (across all 4 pairs:
    13857 36.874) 
    13858 RMSD between 102 pruned atom pairs is 2.089 angstroms; (across all 121 pairs:
    13859 3.339) 
    13860 RMSD between 9 pruned atom pairs is 2.431 angstroms; (across all 19 pairs:
    13861 13.634) 
    13862 RMSD between 7 pruned atom pairs is 1.791 angstroms; (across all 10 pairs:
    13863 14.348) 
    13864 RMSD between 35 pruned atom pairs is 1.742 angstroms; (across all 64 pairs:
    13865 9.033) 
    13866 RMSD between 9 pruned atom pairs is 3.563 angstroms; (across all 29 pairs:
    13867 16.417) 
    13868 RMSD between 6 pruned atom pairs is 2.214 angstroms; (across all 20 pairs:
    13869 30.051) 
    13870 RMSD between 4 pruned atom pairs is 2.233 angstroms; (across all 14 pairs:
    13871 17.266) 
    13872 RMSD between 4 pruned atom pairs is 2.512 angstroms; (across all 10 pairs:
    13873 26.405) 
    13874 RMSD between 3 pruned atom pairs is 1.792 angstroms; (across all 6 pairs:
    13875 17.667) 
    13876 RMSD between 103 pruned atom pairs is 2.396 angstroms; (across all 118 pairs:
    13877 3.200) 
    13878 RMSD between 10 pruned atom pairs is 3.061 angstroms; (across all 15 pairs:
    13879 5.580) 
    13880 RMSD between 4 pruned atom pairs is 3.752 angstroms; (across all 5 pairs:
    13881 7.655) 
    13882 RMSD between 87 pruned atom pairs is 1.913 angstroms; (across all 99 pairs:
    13883 2.995) 
    13884 RMSD between 6 pruned atom pairs is 3.529 angstroms; (across all 12 pairs:
    13885 11.064) 
    13886 RMSD between 4 pruned atom pairs is 2.023 angstroms; (across all 6 pairs:
    13887 9.957) 
    13888 RMSD between 188 pruned atom pairs is 1.661 angstroms; (across all 200 pairs:
    13889 2.771) 
    13890 RMSD between 8 pruned atom pairs is 2.821 angstroms; (across all 12 pairs:
    13891 5.566) 
    13892 RMSD between 3 pruned atom pairs is 2.054 angstroms; (across all 4 pairs:
    13893 5.146) 
    13894 RMSD between 85 pruned atom pairs is 2.340 angstroms; (across all 93 pairs:
    13895 2.858) 
    13896 RMSD between 6 pruned atom pairs is 3.294 angstroms; (across all 8 pairs:
    13897 5.900) 
    13898 RMSD between 15 pruned atom pairs is 3.062 angstroms; (across all 140 pairs:
    13899 18.668) 
    13900 RMSD between 13 pruned atom pairs is 3.301 angstroms; (across all 125 pairs:
    13901 21.299) 
    13902 RMSD between 12 pruned atom pairs is 3.349 angstroms; (across all 112 pairs:
    13903 19.745) 
    13904 RMSD between 17 pruned atom pairs is 3.611 angstroms; (across all 100 pairs:
    13905 21.723) 
    13906 RMSD between 6 pruned atom pairs is 2.867 angstroms; (across all 83 pairs:
    13907 24.042) 
    13908 RMSD between 7 pruned atom pairs is 2.920 angstroms; (across all 77 pairs:
    13909 20.579) 
    13910 RMSD between 4 pruned atom pairs is 0.894 angstroms; (across all 70 pairs:
    13911 27.506) 
    13912 RMSD between 8 pruned atom pairs is 3.136 angstroms; (across all 66 pairs:
    13913 24.308) 
    13914 RMSD between 7 pruned atom pairs is 2.956 angstroms; (across all 58 pairs:
    13915 24.244) 
    13916 RMSD between 4 pruned atom pairs is 2.438 angstroms; (across all 51 pairs:
    13917 23.583) 
    13918 RMSD between 9 pruned atom pairs is 3.476 angstroms; (across all 47 pairs:
    13919 37.550) 
    13920 RMSD between 8 pruned atom pairs is 3.356 angstroms; (across all 38 pairs:
    13921 26.741) 
    13922 RMSD between 5 pruned atom pairs is 3.390 angstroms; (across all 30 pairs:
    13923 22.470) 
    13924 RMSD between 5 pruned atom pairs is 2.674 angstroms; (across all 25 pairs:
    13925 27.614) 
    13926 RMSD between 3 pruned atom pairs is 3.654 angstroms; (across all 20 pairs:
    13927 23.133) 
    13928 RMSD between 3 pruned atom pairs is 1.332 angstroms; (across all 17 pairs:
    13929 33.111) 
    13930 RMSD between 4 pruned atom pairs is 2.460 angstroms; (across all 14 pairs:
    13931 26.636) 
    13932 RMSD between 3 pruned atom pairs is 1.606 angstroms; (across all 10 pairs:
    13933 34.125) 
    13934 RMSD between 280 pruned atom pairs is 2.350 angstroms; (across all 310 pairs:
    13935 3.184) 
    13936 RMSD between 6 pruned atom pairs is 3.836 angstroms; (across all 30 pairs:
    13937 25.777) 
    13938 RMSD between 3 pruned atom pairs is 2.431 angstroms; (across all 24 pairs:
    13939 35.002) 
    13940 RMSD between 3 pruned atom pairs is 1.495 angstroms; (across all 21 pairs:
    13941 37.257) 
    13942 RMSD between 4 pruned atom pairs is 2.902 angstroms; (across all 18 pairs:
    13943 32.028) 
    13944 RMSD between 3 pruned atom pairs is 2.970 angstroms; (across all 14 pairs:
    13945 31.208) 
    13946 RMSD between 28 pruned atom pairs is 3.018 angstroms; (across all 38 pairs:
    13947 4.226) 
    13948 RMSD between 5 pruned atom pairs is 2.929 angstroms; (across all 10 pairs:
    13949 8.508) 
    13950 RMSD between 4 pruned atom pairs is 3.822 angstroms; (across all 5 pairs:
    13951 8.113) 
    13952 RMSD between 137 pruned atom pairs is 2.192 angstroms; (across all 140 pairs:
    13953 2.319) 
    13954 RMSD between 107 pruned atom pairs is 2.519 angstroms; (across all 119 pairs:
    13955 4.496) 
    13956 RMSD between 4 pruned atom pairs is 3.524 angstroms; (across all 12 pairs:
    13957 18.255) 
    13958 RMSD between 99 pruned atom pairs is 2.675 angstroms; (across all 120 pairs:
    13959 3.947) 
    13960 RMSD between 8 pruned atom pairs is 3.667 angstroms; (across all 21 pairs:
    13961 18.291) 
    13962 RMSD between 4 pruned atom pairs is 3.515 angstroms; (across all 13 pairs:
    13963 22.863) 
    13964 
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