Changes between Initial Version and Version 1 of Ticket #9624


Ignore:
Timestamp:
Aug 23, 2023, 10:46:00 AM (2 years ago)
Author:
Eric Pettersen
Comment:

Reported by Thu Nguyen

Legend:

Unmodified
Added
Removed
Modified

  • Ticket #9624

    • Property Component Unassigned → Input/Output
    • Property Owner set to Greg Couch
    • Property Platform → all
    • Property Project → ChimeraX
    • Property Status new → assigned
    • Property Summary ChimeraX bug report submission → Crash opening mmCIF file

  • Ticket #9624 – Description

    initial v1  
    17461746 
    17471747
    1748 > open /scratch/cs-
    1749 > bioinfo/tngu/6k_data/Box_Chains_new/0057_6gsm/0057_6gsm_a.mrc
    1750 
    1751 Opened 0057_6gsm_a.mrc as #2, grid size 80,96,88, pixel 1, shown at level
    1752 0.149, step 1, values float32 
    1753 
    1754 > fitmap #1 inMap #2
    1755 
    1756 Fit molecule 0057_6gsm_a.cif (#1) to map 0057_6gsm_a.mrc (#2) using 18871
    1757 atoms 
    1758 average map value = 0.0811, steps = 56 
    1759 shifted from previous position = 0.485 
    1760 rotated from previous position = 0.143 degrees 
    1761 atoms outside contour = 18299, contour level = 0.14928 
    1762  
    1763 Position of 0057_6gsm_a.cif (#1) relative to 0057_6gsm_a.mrc (#2) coordinates: 
    1764 Matrix rotation and translation 
    1765 0.99999911 0.00018452 -0.00132388 0.02105214 
    1766 -0.00018729 0.99999778 -0.00209751 0.38372358 
    1767 0.00132349 0.00209776 0.99999692 -1.07470455 
    1768 Axis 0.84333037 -0.53217264 -0.07474067 
    1769 Axis point 0.00000000 516.31993276 155.46967396 
    1770 Rotation angle (degrees) 0.14251334 
    1771 Shift along axis -0.10612915 
    1772  
    1773 
    1774 > save /scratch/cs-
    1775 > bioinfo/tngu/6k_data/Box_Chains_new/0057_6gsm/0057_6gsm_a_fitted.cif #1
    1776 
    1777 > close #1
    1778 
    1779 > close #2
    1780 
    1781 > open /scratch/cs-
    1782 > bioinfo/tngu/6k_data/Box_Chains_new/0057_6gsm/0057_6gsm_U.cif
    1783 
    1784 Summary of feedback from opening /scratch/cs-
    1785 bioinfo/tngu/6k_data/Box_Chains_new/0057_6gsm/0057_6gsm_U.cif 
    1786 --- 
    1787 warnings | Invalid residue range for struct_conf "HELX1": invalid chain "C",
    1788 near line 44477 
    1789 Invalid residue range for struct_conf "HELX2": invalid chain "C", near line
    1790 44478 
    1791 Invalid residue range for struct_conf "HELX3": invalid chain "C", near line
    1792 44479 
    1793 Invalid residue range for struct_conf "HELX4": invalid chain "C", near line
    1794 44480 
    1795 Invalid residue range for struct_conf "HELX5": invalid chain "C", near line
    1796 44481 
    1797 174 messages similar to the above omitted 
    1798 Invalid sheet range for struct_sheet_range "? 1": invalid chain "C", near line
    1799 44730 
    1800 Invalid sheet range for struct_sheet_range "? 2": invalid chain "C", near line
    1801 44731 
    1802 Invalid sheet range for struct_sheet_range "? 3": invalid chain "C", near line
    1803 44732 
    1804 Invalid sheet range for struct_sheet_range "? 4": invalid chain "C", near line
    1805 44733 
    1806 Invalid sheet range for struct_sheet_range "? 5": invalid chain "C", near line
    1807 44734 
    1808 181 messages similar to the above omitted 
    1809 Atom O2' has no neighbors to form bonds with according to residue template for
    1810 C /1:39 
    1811 Atom O2 has no neighbors to form bonds with according to residue template for
    1812 C /1:39 
    1813 Atom O2' has no neighbors to form bonds with according to residue template for
    1814 C /1:40 
    1815 Atom O2 has no neighbors to form bonds with according to residue template for
    1816 C /1:40 
    1817 Atom O2' has no neighbors to form bonds with according to residue template for
    1818 C /1:41 
    1819 Atom C8 has no neighbors to form bonds with according to residue template for
    1820 A /2:1159 
    1821 Atom OP2 has no neighbors to form bonds with according to residue template for
    1822 C /2:1179 
    1823 Atom OP1 has no neighbors to form bonds with according to residue template for
    1824 A /2:1182 
    1825 Atom O5' has no neighbors to form bonds with according to residue template for
    1826 A /2:1182 
    1827 Atom OP2 has no neighbors to form bonds with according to residue template for
    1828 G /2:1262 
    1829 Atom O3' has no neighbors to form bonds with according to residue template for
    1830 U /2:1313 
    1831 Atom OP2 has no neighbors to form bonds with according to residue template for
    1832 A /2:1386 
    1833 Atom OP2 has no neighbors to form bonds with according to residue template for
    1834 A /2:1477 
    1835 Atom N3 has no neighbors to form bonds with according to residue template for
    1836 A /2:1581 
    1837 Atom N3 has no neighbors to form bonds with according to residue template for
    1838 A /3:28 
    1839 Atom OP2 has no neighbors to form bonds with according to residue template for
    1840 U /3:30 
    1841 Atom O5' has no neighbors to form bonds with according to residue template for
    1842 U /3:30 
    1843 Atom OE1 has no neighbors to form bonds with according to residue template for
    1844 GLN /D:101 
    1845 Atom O has no neighbors to form bonds with according to residue template for
    1846 ALA /D:147 
    1847 Atom CB has no neighbors to form bonds with according to residue template for
    1848 ALA /F:76 
    1849 Atom SD has no neighbors to form bonds with according to residue template for
    1850 MET /F:101 
    1851 Atom O has no neighbors to form bonds with according to residue template for
    1852 TYR /K:12 
    1853 Atom CD1 has no neighbors to form bonds with according to residue template for
    1854 PHE /K:16 
    1855 Atom N has no neighbors to form bonds with according to residue template for
    1856 VAL /K:74 
    1857 Atom N has no neighbors to form bonds with according to residue template for
    1858 LYS /P:24 
    1859 Atom O has no neighbors to form bonds with according to residue template for
    1860 SER /P:92 
    1861 Atom O has no neighbors to form bonds with according to residue template for
    1862 ASN /P:103 
    1863 Atom N has no neighbors to form bonds with according to residue template for
    1864 LYS /Q:26 
    1865 Atom C has no neighbors to form bonds with according to residue template for
    1866 LYS /Q:26 
    1867 Atom N has no neighbors to form bonds with according to residue template for
    1868 TYR /Q:92 
    1869 Atom O has no neighbors to form bonds with according to residue template for
    1870 LYS /R:32 
    1871 Atom CD has no neighbors to form bonds with according to residue template for
    1872 LYS /R:32 
    1873 Atom O has no neighbors to form bonds with according to residue template for
    1874 ARG /R:33 
    1875 Atom O has no neighbors to form bonds with according to residue template for
    1876 TRP /S:84 
    1877 Atom N has no neighbors to form bonds with according to residue template for
    1878 ASN /S:93 
    1879 Atom N has no neighbors to form bonds with according to residue template for
    1880 LEU /S:113 
    1881 Atom CD2 has no neighbors to form bonds with according to residue template for
    1882 LEU /S:131 
    1883 Atom O has no neighbors to form bonds with according to residue template for
    1884 LEU /T:45 
    1885 Atom N has no neighbors to form bonds with according to residue template for
    1886 ARG /f:92 
    1887 Atom N has no neighbors to form bonds with according to residue template for
    1888 TRP /g:93 
    1889 Atom CG2 has no neighbors to form bonds with according to residue template for
    1890 ILE /g:124 
    1891 Atom O has no neighbors to form bonds with according to residue template for
    1892 ASP /g:150 
    1893 Atom O has no neighbors to form bonds with according to residue template for
    1894 ILE /g:195 
    1895  
    1896 Chain information for 0057_6gsm_U.cif #1 
    1897 --- 
    1898 Chain | Description 
    1899 1 | Met-tRNAi 
    1900 2 | 18S ribosomal RNA 
    1901 3 | mRNA (5'-R(P*AP*AP*U)-3') 
    1902 C | KLLA0F09812p 
    1903 D | KLLA0D08305p 
    1904 F | KLLA0D10659p 
    1905 K | KLLA0B08173p 
    1906 P | KLLA0F07843p 
    1907 Q | 40S ribosomal protein S16 
    1908 R | KLLA0B01474p 
    1909 S | KLLA0B01562p 
    1910 T | KLLA0A07194p 
    1911 U | KLLA0F25542p 
    1912 Z | KLLA0B06182p 
    1913 d | 40S ribosomal protein S29 
    1914 f | Ubiquitin-40S ribosomal protein S27a 
    1915 g | KLLA0E12277p 
    1916 i | Eukaryotic translation initiation factor 1A 
    1917  
    1918 
    1919 > open /scratch/cs-
    1920 > bioinfo/tngu/6k_data/Box_Chains_new/0057_6gsm/0057_6gsm_U.mrc
    1921 
    1922 Opened 0057_6gsm_U.mrc as #2, grid size 112,72,72, pixel 1, shown at level
    1923 0.134, step 1, values float32 
    1924 
    1925 > fitmap #1 inMap #2
    1926 
    1927 Fit molecule 0057_6gsm_U.cif (#1) to map 0057_6gsm_U.mrc (#2) using 13328
    1928 atoms 
    1929 average map value = 0.07934, steps = 48 
    1930 shifted from previous position = 0.338 
    1931 rotated from previous position = 0.177 degrees 
    1932 atoms outside contour = 12826, contour level = 0.13392 
    1933  
    1934 Position of 0057_6gsm_U.cif (#1) relative to 0057_6gsm_U.mrc (#2) coordinates: 
    1935 Matrix rotation and translation 
    1936 0.99999647 0.00033916 0.00263397 -0.67215769 
    1937 -0.00034329 0.99999871 0.00156937 -0.49700188 
    1938 -0.00263344 -0.00157026 0.99999530 0.68166280 
    1939 Axis -0.50885627 0.85371602 -0.11060857 
    1940 Axis point 251.71663719 0.00000000 285.98413263 
    1941 Rotation angle (degrees) 0.17675705 
    1942 Shift along axis -0.15766456 
    1943  
    1944 
    1945 > save /scratch/cs-
    1946 > bioinfo/tngu/6k_data/Box_Chains_new/0057_6gsm/0057_6gsm_U_fitted.cif #1
    1947 
    1948 > close #1
    1949 
    1950 > close #2
    1951 
    1952 > open /scratch/cs-
    1953 > bioinfo/tngu/6k_data/Box_Chains_new/0057_6gsm/0057_6gsm_e.cif
    1954 
    1955 Summary of feedback from opening /scratch/cs-
    1956 bioinfo/tngu/6k_data/Box_Chains_new/0057_6gsm/0057_6gsm_e.cif 
    1957 --- 
    1958 warnings | Invalid residue range for struct_conf "HELX1": invalid chain "C",
    1959 near line 42816 
    1960 Invalid residue range for struct_conf "HELX2": invalid chain "C", near line
    1961 42817 
    1962 Invalid residue range for struct_conf "HELX3": invalid chain "C", near line
    1963 42818 
    1964 Invalid residue range for struct_conf "HELX4": invalid chain "C", near line
    1965 42819 
    1966 Invalid residue range for struct_conf "HELX5": invalid chain "C", near line
    1967 42820 
    1968 163 messages similar to the above omitted 
    1969 Invalid sheet range for struct_sheet_range "? 1": invalid chain "C", near line
    1970 43069 
    1971 Invalid sheet range for struct_sheet_range "? 2": invalid chain "C", near line
    1972 43070 
    1973 Invalid sheet range for struct_sheet_range "? 3": invalid chain "C", near line
    1974 43071 
    1975 Invalid sheet range for struct_sheet_range "? 4": invalid chain "C", near line
    1976 43072 
    1977 Invalid sheet range for struct_sheet_range "? 5": invalid chain "C", near line
    1978 43073 
    1979 166 messages similar to the above omitted 
    1980 Atom OP1 has no neighbors to form bonds with according to residue template for
    1981 C /2:18 
    1982 Atom OP1 has no neighbors to form bonds with according to residue template for
    1983 C /2:97 
    1984 Atom O3' has no neighbors to form bonds with according to residue template for
    1985 A /2:359 
    1986 Atom OP2 has no neighbors to form bonds with according to residue template for
    1987 G /2:389 
    1988 Atom O3' has no neighbors to form bonds with according to residue template for
    1989 A /2:411 
    1990 Atom O2' has no neighbors to form bonds with according to residue template for
    1991 A /2:411 
    1992 Atom O2' has no neighbors to form bonds with according to residue template for
    1993 G /2:421 
    1994 Atom O3' has no neighbors to form bonds with according to residue template for
    1995 G /2:425 
    1996 Atom OP2 has no neighbors to form bonds with according to residue template for
    1997 U /2:532 
    1998 Atom C3' has no neighbors to form bonds with according to residue template for
    1999 A /2:533 
    2000 Atom O3' has no neighbors to form bonds with according to residue template for
    2001 A /2:757 
    2002 Atom O4' has no neighbors to form bonds with according to residue template for
    2003 G /2:765 
    2004 Atom OP1 has no neighbors to form bonds with according to residue template for
    2005 U /2:767 
    2006 Atom O2' has no neighbors to form bonds with according to residue template for
    2007 A /2:1132 
    2008 Atom O3' has no neighbors to form bonds with according to residue template for
    2009 U /2:1256 
    2010 Atom C6 has no neighbors to form bonds with according to residue template for
    2011 U /2:1257 
    2012 Atom OP2 has no neighbors to form bonds with according to residue template for
    2013 U /2:1259 
    2014 Atom N7 has no neighbors to form bonds with according to residue template for
    2015 G /2:1266 
    2016 Atom O2 has no neighbors to form bonds with according to residue template for
    2017 U /2:1289 
    2018 Atom O2' has no neighbors to form bonds with according to residue template for
    2019 G /2:1291 
    2020 Atom O3' has no neighbors to form bonds with according to residue template for
    2021 A /2:1299 
    2022 Atom O2' has no neighbors to form bonds with according to residue template for
    2023 A /2:1299 
    2024 Atom OP1 has no neighbors to form bonds with according to residue template for
    2025 A /2:1325 
    2026 Atom N7 has no neighbors to form bonds with according to residue template for
    2027 G /2:1426 
    2028 Atom OP1 has no neighbors to form bonds with according to residue template for
    2029 A /2:1631 
    2030 Atom O2' has no neighbors to form bonds with according to residue template for
    2031 U /2:1659 
    2032 Atom C8 has no neighbors to form bonds with according to residue template for
    2033 G /2:1743 
    2034 Atom OP2 has no neighbors to form bonds with according to residue template for
    2035 G /2:1745 
    2036 Atom C5' has no neighbors to form bonds with according to residue template for
    2037 G /2:1745 
    2038 Atom O3' has no neighbors to form bonds with according to residue template for
    2039 U /2:1750 
    2040 Atom N has no neighbors to form bonds with according to residue template for
    2041 HIS /C:115 
    2042 Atom CB has no neighbors to form bonds with according to residue template for
    2043 HIS /C:115 
    2044 Atom N has no neighbors to form bonds with according to residue template for
    2045 GLY /C:117 
    2046 Atom CA has no neighbors to form bonds with according to residue template for
    2047 ILE /C:120 
    2048 Atom CG2 has no neighbors to form bonds with according to residue template for
    2049 ILE /C:120 
    2050 Atom CD1 has no neighbors to form bonds with according to residue template for
    2051 ILE /C:120 
    2052 Atom CB has no neighbors to form bonds with according to residue template for
    2053 PRO /C:178 
    2054 Atom N has no neighbors to form bonds with according to residue template for
    2055 VAL /C:201 
    2056 Atom O has no neighbors to form bonds with according to residue template for
    2057 VAL /C:201 
    2058 Atom OG1 has no neighbors to form bonds with according to residue template for
    2059 THR /C:209 
    2060 Atom O has no neighbors to form bonds with according to residue template for
    2061 GLY /D:36 
    2062 Atom CD1 has no neighbors to form bonds with according to residue template for
    2063 ILE /D:50 
    2064 Atom ND2 has no neighbors to form bonds with according to residue template for
    2065 ASN /D:62 
    2066 Atom CG has no neighbors to form bonds with according to residue template for
    2067 GLN /J:139 
    2068 Atom NE2 has no neighbors to form bonds with according to residue template for
    2069 GLN /J:139 
    2070 Atom OE1 has no neighbors to form bonds with according to residue template for
    2071 GLU /J:151 
    2072 Atom O has no neighbors to form bonds with according to residue template for
    2073 GLU /J:183 
    2074 Atom CE2 has no neighbors to form bonds with according to residue template for
    2075 TYR /K:12 
    2076 Atom OH has no neighbors to form bonds with according to residue template for
    2077 TYR /K:12 
    2078 Atom NE2 has no neighbors to form bonds with according to residue template for
    2079 GLN /K:47 
    2080 Atom N has no neighbors to form bonds with according to residue template for
    2081 GLN /K:58 
    2082 Atom CB has no neighbors to form bonds with according to residue template for
    2083 LYS /l:216 
    2084 Atom N has no neighbors to form bonds with according to residue template for
    2085 SER /l:219 
    2086 Atom OG has no neighbors to form bonds with according to residue template for
    2087 SER /l:219 
    2088 Atom N has no neighbors to form bonds with according to residue template for
    2089 GLN /m:31 
    2090 Atom C has no neighbors to form bonds with according to residue template for
    2091 GLN /m:31 
    2092 Atom N has no neighbors to form bonds with according to residue template for
    2093 CYS /m:89 
    2094 Atom SG has no neighbors to form bonds with according to residue template for
    2095 CYS /m:89 
    2096 Atom CD1 has no neighbors to form bonds with according to residue template for
    2097 LEU /p:390 
    2098 Atom CD2 has no neighbors to form bonds with according to residue template for
    2099 LEU /p:390 
    2100 Atom N has no neighbors to form bonds with according to residue template for
    2101 GLU /p:398 
    2102 Atom O has no neighbors to form bonds with according to residue template for
    2103 ASN /p:412 
    2104 Atom N has no neighbors to form bonds with according to residue template for
    2105 VAL /p:480 
    2106 Atom O has no neighbors to form bonds with according to residue template for
    2107 VAL /p:480 
    2108 Atom OE1 has no neighbors to form bonds with according to residue template for
    2109 GLU /p:530 
    2110 Atom OE2 has no neighbors to form bonds with according to residue template for
    2111 GLU /p:530 
    2112  
    2113 Chain information for 0057_6gsm_e.cif #1 
    2114 --- 
    2115 Chain | Description 
    2116 2 | 18S ribosomal RNA 
    2117 3 | mRNA (5'-R(P*AP*AP*U)-3') 
    2118 C | KLLA0F09812p 
    2119 D | KLLA0D08305p 
    2120 J | KLLA0E23673p 
    2121 K | KLLA0B08173p 
    2122 M | 40S ribosomal protein S12 
    2123 X | KLLA0B11231p 
    2124 e | 40S ribosomal protein S30 
    2125 i | Eukaryotic translation initiation factor 1A 
    2126 l | Eukaryotic translation initiation factor 2 subunit beta 
    2127 m | Eukaryotic translation initiation factor eIF-1 
    2128 p | Eukaryotic translation initiation factor 3 subunit B 
    2129  
    2130 
    2131 > open /scratch/cs-
    2132 > bioinfo/tngu/6k_data/Box_Chains_new/0057_6gsm/0057_6gsm_e.mrc
    2133 
    2134 Opened 0057_6gsm_e.mrc as #2, grid size 96,88,72, pixel 1, shown at level
    2135 0.14, step 1, values float32 
    2136 
    2137 > fitmap #1 inMap #2
    2138 
    2139 Fit molecule 0057_6gsm_e.cif (#1) to map 0057_6gsm_e.mrc (#2) using 11728
    2140 atoms 
    2141 average map value = 0.07883, steps = 48 
    2142 shifted from previous position = 0.345 
    2143 rotated from previous position = 0.156 degrees 
    2144 atoms outside contour = 11229, contour level = 0.14039 
    2145  
    2146 Position of 0057_6gsm_e.cif (#1) relative to 0057_6gsm_e.mrc (#2) coordinates: 
    2147 Matrix rotation and translation 
    2148 0.99999931 -0.00096213 -0.00066854 0.07989544 
    2149 0.00096378 0.99999650 0.00246569 -0.83572949 
    2150 0.00066616 -0.00246633 0.99999674 0.52309429 
    2151 Axis -0.90324313 -0.24443575 0.35270810 
    2152 Axis point 0.00000000 166.40782257 307.79255316 
    2153 Rotation angle (degrees) 0.15642749 
    2154 Shift along axis 0.31661676 
    2155  
    2156 
    2157 > save /scratch/cs-
    2158 > bioinfo/tngu/6k_data/Box_Chains_new/0057_6gsm/0057_6gsm_e_fitted.cif #1
    2159 
    2160 > close #1
    2161 
    2162 > close #2
    2163 
    2164 > open /scratch/cs-
    2165 > bioinfo/tngu/6k_data/Box_Chains_new/0057_6gsm/0057_6gsm_C.cif
    2166 
    2167 Summary of feedback from opening /scratch/cs-
    2168 bioinfo/tngu/6k_data/Box_Chains_new/0057_6gsm/0057_6gsm_C.cif 
    2169 --- 
    2170 warnings | Invalid residue range for struct_conf "HELX41": invalid chain "J",
    2171 near line 50359 
    2172 Invalid residue range for struct_conf "HELX42": invalid chain "J", near line
    2173 50360 
    2174 Invalid residue range for struct_conf "HELX43": invalid chain "J", near line
    2175 50361 
    2176 Invalid residue range for struct_conf "HELX51": invalid chain "L", near line
    2177 50369 
    2178 Invalid residue range for struct_conf "HELX52": invalid chain "L", near line
    2179 50370 
    2180 119 messages similar to the above omitted 
    2181 Invalid sheet range for struct_sheet_range "? 49": invalid chain "J", near
    2182 line 50620 
    2183 Invalid sheet range for struct_sheet_range "? 50": invalid chain "J", near
    2184 line 50621 
    2185 Invalid sheet range for struct_sheet_range "? 51": invalid chain "J", near
    2186 line 50622 
    2187 Invalid sheet range for struct_sheet_range "? 52": invalid chain "J", near
    2188 line 50623 
    2189 Invalid sheet range for struct_sheet_range "? 53": invalid chain "J", near
    2190 line 50624 
    2191 110 messages similar to the above omitted 
    2192 Atom O4' has no neighbors to form bonds with according to residue template for
    2193 U /1:36 
    2194 Atom OP2 has no neighbors to form bonds with according to residue template for
    2195 A /2:28 
    2196 Atom O2' has no neighbors to form bonds with according to residue template for
    2197 U /2:33 
    2198 Atom O4' has no neighbors to form bonds with according to residue template for
    2199 A /2:41 
    2200 Atom O3' has no neighbors to form bonds with according to residue template for
    2201 C /2:107 
    2202 Atom O2 has no neighbors to form bonds with according to residue template for
    2203 C /2:107 
    2204 Atom P has no neighbors to form bonds with according to residue template for U
    2205 /2:110 
    2206 Atom O3' has no neighbors to form bonds with according to residue template for
    2207 G /2:461 
    2208 Atom O5' has no neighbors to form bonds with according to residue template for
    2209 U /2:465 
    2210 Atom O3' has no neighbors to form bonds with according to residue template for
    2211 G /2:486 
    2212 Atom O2' has no neighbors to form bonds with according to residue template for
    2213 G /2:486 
    2214 Atom OP2 has no neighbors to form bonds with according to residue template for
    2215 C /2:565 
    2216 Atom O2 has no neighbors to form bonds with according to residue template for
    2217 U /2:587 
    2218 Atom N3 has no neighbors to form bonds with according to residue template for
    2219 U /2:587 
    2220 Atom O4 has no neighbors to form bonds with according to residue template for
    2221 U /2:587 
    2222 Atom OP2 has no neighbors to form bonds with according to residue template for
    2223 A /2:600 
    2224 Atom OP2 has no neighbors to form bonds with according to residue template for
    2225 C /2:644 
    2226 Atom N4 has no neighbors to form bonds with according to residue template for
    2227 C /2:644 
    2228 Atom C5 has no neighbors to form bonds with according to residue template for
    2229 C /2:644 
    2230 Atom OP2 has no neighbors to form bonds with according to residue template for
    2231 U /2:664 
    2232 Atom O4 has no neighbors to form bonds with according to residue template for
    2233 U /2:664 
    2234 Atom N4 has no neighbors to form bonds with according to residue template for
    2235 C /2:675 
    2236 Atom C5 has no neighbors to form bonds with according to residue template for
    2237 C /2:675 
    2238 Atom N7 has no neighbors to form bonds with according to residue template for
    2239 G /2:689 
    2240 Atom O6 has no neighbors to form bonds with according to residue template for
    2241 G /2:689 
    2242 Atom C3' has no neighbors to form bonds with according to residue template for
    2243 A /2:755 
    2244 Atom C5' has no neighbors to form bonds with according to residue template for
    2245 A /2:756 
    2246 Atom OP1 has no neighbors to form bonds with according to residue template for
    2247 A /2:864 
    2248 Atom O2' has no neighbors to form bonds with according to residue template for
    2249 A /2:864 
    2250 Atom N4 has no neighbors to form bonds with according to residue template for
    2251 C /2:942 
    2252 Atom C5 has no neighbors to form bonds with according to residue template for
    2253 C /2:942 
    2254 Atom O3' has no neighbors to form bonds with according to residue template for
    2255 A /2:1024 
    2256 Atom O2' has no neighbors to form bonds with according to residue template for
    2257 U /2:1186 
    2258 Atom N3 has no neighbors to form bonds with according to residue template for
    2259 A /2:1188 
    2260 Atom OP2 has no neighbors to form bonds with according to residue template for
    2261 C /2:1191 
    2262 Atom O5' has no neighbors to form bonds with according to residue template for
    2263 C /2:1191 
    2264 Atom OP1 has no neighbors to form bonds with according to residue template for
    2265 A /2:1192 
    2266 Atom O5' has no neighbors to form bonds with according to residue template for
    2267 A /2:1311 
    2268 Atom OP2 has no neighbors to form bonds with according to residue template for
    2269 U /2:1394 
    2270 Atom O3' has no neighbors to form bonds with according to residue template for
    2271 U /2:1394 
    2272 Atom O3' has no neighbors to form bonds with according to residue template for
    2273 G /2:1417 
    2274 Atom OP1 has no neighbors to form bonds with according to residue template for
    2275 U /2:1430 
    2276 Atom O3' has no neighbors to form bonds with according to residue template for
    2277 C /2:1618 
    2278 Atom O2' has no neighbors to form bonds with according to residue template for
    2279 C /2:1638 
    2280 Atom O2' has no neighbors to form bonds with according to residue template for
    2281 U /2:1767 
    2282 Atom OP1 has no neighbors to form bonds with according to residue template for
    2283 G /2:1787 
    2284 Atom OD1 has no neighbors to form bonds with according to residue template for
    2285 ASP /A:8 
    2286 Atom OP2 has no neighbors to form bonds with according to residue template for
    2287 A /3:29 
    2288 Atom CE2 has no neighbors to form bonds with according to residue template for
    2289 TYR /D:34 
    2290 Atom OH has no neighbors to form bonds with according to residue template for
    2291 TYR /D:34 
    2292 Atom N has no neighbors to form bonds with according to residue template for
    2293 VAL /D:39 
    2294 Atom O has no neighbors to form bonds with according to residue template for
    2295 VAL /D:39 
    2296 Atom CB has no neighbors to form bonds with according to residue template for
    2297 ARG /D:90 
    2298 Atom CG2 has no neighbors to form bonds with according to residue template for
    2299 ILE /E:248 
    2300 Atom CD1 has no neighbors to form bonds with according to residue template for
    2301 ILE /E:248 
    2302 Atom CE has no neighbors to form bonds with according to residue template for
    2303 LYS /H:105 
    2304 Atom CG2 has no neighbors to form bonds with according to residue template for
    2305 VAL /J:113 
    2306 Atom N has no neighbors to form bonds with according to residue template for
    2307 TYR /J:114 
    2308 Atom C has no neighbors to form bonds with according to residue template for
    2309 TYR /J:114 
    2310 Atom N has no neighbors to form bonds with according to residue template for
    2311 LYS /J:138 
    2312 Atom CE has no neighbors to form bonds with according to residue template for
    2313 LYS /J:138 
    2314 Atom O has no neighbors to form bonds with according to residue template for
    2315 GLN /J:139 
    2316 Atom N has no neighbors to form bonds with according to residue template for
    2317 ASN /J:142 
    2318 Atom O has no neighbors to form bonds with according to residue template for
    2319 LYS /L:105 
    2320 Atom N has no neighbors to form bonds with according to residue template for
    2321 SER /L:144 
    2322 Atom NZ has no neighbors to form bonds with according to residue template for
    2323 LYS /O:92 
    2324 Atom CB has no neighbors to form bonds with according to residue template for
    2325 LEU /O:137 
    2326 Atom CD1 has no neighbors to form bonds with according to residue template for
    2327 LEU /O:137 
    2328 Atom N has no neighbors to form bonds with according to residue template for
    2329 GLY /R:2 
    2330 Atom N has no neighbors to form bonds with according to residue template for
    2331 LYS /R:44 
    2332 Atom O has no neighbors to form bonds with according to residue template for
    2333 LYS /R:44 
    2334 Atom N has no neighbors to form bonds with according to residue template for
    2335 SER /X:66 
    2336 Atom OG has no neighbors to form bonds with according to residue template for
    2337 SER /X:66 
    2338 Atom NH1 has no neighbors to form bonds with according to residue template for
    2339 ARG /X:69 
    2340 Atom NH2 has no neighbors to form bonds with according to residue template for
    2341 ARG /X:69 
    2342 Atom N has no neighbors to form bonds with according to residue template for
    2343 SER /a:27 
    2344 Atom N has no neighbors to form bonds with according to residue template for
    2345 LEU /b:8 
    2346 Atom O has no neighbors to form bonds with according to residue template for
    2347 ARG /c:67 
    2348 Atom N has no neighbors to form bonds with according to residue template for
    2349 PHE /d:43 
    2350 Atom O has no neighbors to form bonds with according to residue template for
    2351 ARG /e:37 
    2352 Atom N has no neighbors to form bonds with according to residue template for
    2353 THR /g:131 
    2354 Atom CG2 has no neighbors to form bonds with according to residue template for
    2355 THR /g:131 
    2356 Atom CG2 has no neighbors to form bonds with according to residue template for
    2357 VAL /g:152 
    2358 Atom OG has no neighbors to form bonds with according to residue template for
    2359 SER /g:176 
    2360 Atom N has no neighbors to form bonds with according to residue template for
    2361 ASN /g:207 
    2362 Atom N has no neighbors to form bonds with according to residue template for
    2363 TRP /g:230 
    2364 Atom CE has no neighbors to form bonds with according to residue template for
    2365 MET /g:239 
    2366 Atom N has no neighbors to form bonds with according to residue template for
    2367 VAL /g:247 
    2368 Atom CD has no neighbors to form bonds with according to residue template for
    2369 LYS /i:23 
    2370 Atom NZ has no neighbors to form bonds with according to residue template for
    2371 LYS /i:23 
    2372 Atom O has no neighbors to form bonds with according to residue template for
    2373 LYS /i:67 
    2374  
    2375 Chain information for 0057_6gsm_C.cif #1 
    2376 --- 
    2377 Chain | Description 
    2378 1 | Met-tRNAi 
    2379 2 | 18S ribosomal RNA 
    2380 3 | mRNA (5'-R(P*AP*AP*U)-3') 
    2381 A | 40S ribosomal protein S0 
    2382 B | 40S ribosomal protein S1 
    2383 C | KLLA0F09812p 
    2384 D | KLLA0D08305p 
    2385 E | 40S ribosomal protein S4 
    2386 H | 40S ribosomal protein S7 
    2387 J | KLLA0E23673p 
    2388 L | KLLA0A10483p 
    2389 N | KLLA0F18040p 
    2390 O | 40S ribosomal protein S14 
    2391 R | KLLA0B01474p 
    2392 U | KLLA0F25542p 
    2393 V | 40S ribosomal protein S21 
    2394 W | 40S ribosomal protein S22 
    2395 X | KLLA0B11231p 
    2396 a | 40S ribosomal protein S26 
    2397 b | 40S ribosomal protein S27 
    2398 c | 40S ribosomal protein S28 
    2399 d | 40S ribosomal protein S29 
    2400 e | 40S ribosomal protein S30 
    2401 g | KLLA0E12277p 
    2402 i | Eukaryotic translation initiation factor 1A 
    2403  
    2404 
    2405 > open /scratch/cs-
    2406 > bioinfo/tngu/6k_data/Box_Chains_new/0057_6gsm/0057_6gsm_C.mrc
    2407 
    2408 Opened 0057_6gsm_C.mrc as #2, grid size 96,104,80, pixel 1, shown at level
    2409 0.146, step 1, values float32 
    2410 
    2411 > fitmap #1 inMap #2
    2412 
    2413 Fit molecule 0057_6gsm_C.cif (#1) to map 0057_6gsm_C.mrc (#2) using 19056
    2414 atoms 
    2415 average map value = 0.0813, steps = 60 
    2416 shifted from previous position = 0.29 
    2417 rotated from previous position = 0.049 degrees 
    2418 atoms outside contour = 18418, contour level = 0.14602 
    2419  
    2420 Position of 0057_6gsm_C.cif (#1) relative to 0057_6gsm_C.mrc (#2) coordinates: 
    2421 Matrix rotation and translation 
    2422 0.99999999 -0.00002143 0.00013169 -0.07370813 
    2423 0.00002132 0.99999964 0.00084431 -0.39245208 
    2424 -0.00013171 -0.00084430 0.99999963 0.02626946 
    2425 Axis -0.98774211 0.15407786 0.02501082 
    2426 Axis point 0.00000000 30.52682018 467.20587978 
    2427 Rotation angle (degrees) 0.04897546 
    2428 Shift along axis 0.01299346 
    2429  
    2430 
    2431 > save /scratch/cs-
    2432 > bioinfo/tngu/6k_data/Box_Chains_new/0057_6gsm/0057_6gsm_C_fitted.cif #1
    2433 
    2434 > close #1
    2435 
    2436 > close #2
    2437 
    2438 > open /scratch/cs-
    2439 > bioinfo/tngu/6k_data/Box_Chains_new/0057_6gsm/0057_6gsm_S.cif
    2440 
    2441 Summary of feedback from opening /scratch/cs-
    2442 bioinfo/tngu/6k_data/Box_Chains_new/0057_6gsm/0057_6gsm_S.cif 
    2443 --- 
    2444 warnings | Invalid residue range for struct_conf "HELX1": invalid chain "C",
    2445 near line 44865 
    2446 Invalid residue range for struct_conf "HELX2": invalid chain "C", near line
    2447 44866 
    2448 Invalid residue range for struct_conf "HELX3": invalid chain "C", near line
    2449 44867 
    2450 Invalid residue range for struct_conf "HELX4": invalid chain "C", near line
    2451 44868 
    2452 Invalid residue range for struct_conf "HELX5": invalid chain "C", near line
    2453 44869 
    2454 168 messages similar to the above omitted 
    2455 Invalid sheet range for struct_sheet_range "? 1": invalid chain "C", near line
    2456 45118 
    2457 Invalid sheet range for struct_sheet_range "? 2": invalid chain "C", near line
    2458 45119 
    2459 Invalid sheet range for struct_sheet_range "? 3": invalid chain "C", near line
    2460 45120 
    2461 Invalid sheet range for struct_sheet_range "? 4": invalid chain "C", near line
    2462 45121 
    2463 Invalid sheet range for struct_sheet_range "? 5": invalid chain "C", near line
    2464 45122 
    2465 203 messages similar to the above omitted 
    2466 Atom OP1 has no neighbors to form bonds with according to residue template for
    2467 C /1:6 
    2468 Atom O2' has no neighbors to form bonds with according to residue template for
    2469 C /1:6 
    2470 Atom O3' has no neighbors to form bonds with according to residue template for
    2471 U /1:50 
    2472 Atom C5' has no neighbors to form bonds with according to residue template for
    2473 G /2:1232 
    2474 Atom OP1 has no neighbors to form bonds with according to residue template for
    2475 U /2:1258 
    2476 Atom OP1 has no neighbors to form bonds with according to residue template for
    2477 G /2:1266 
    2478 Atom N2 has no neighbors to form bonds with according to residue template for
    2479 G /2:1266 
    2480 Atom N3 has no neighbors to form bonds with according to residue template for
    2481 G /2:1266 
    2482 Atom O4' has no neighbors to form bonds with according to residue template for
    2483 A /2:1286 
    2484 Atom O4' has no neighbors to form bonds with according to residue template for
    2485 G /2:1329 
    2486 Atom C5 has no neighbors to form bonds with according to residue template for
    2487 A /2:1398 
    2488 Atom N6 has no neighbors to form bonds with according to residue template for
    2489 A /2:1398 
    2490 Atom O3' has no neighbors to form bonds with according to residue template for
    2491 G /2:1426 
    2492 Atom OP1 has no neighbors to form bonds with according to residue template for
    2493 G /2:1484 
    2494 Atom O2' has no neighbors to form bonds with according to residue template for
    2495 U /2:1487 
    2496 Atom O2' has no neighbors to form bonds with according to residue template for
    2497 C /2:1489 
    2498 Atom OP2 has no neighbors to form bonds with according to residue template for
    2499 G /2:1496 
    2500 Atom OP2 has no neighbors to form bonds with according to residue template for
    2501 G /2:1497 
    2502 Atom OP2 has no neighbors to form bonds with according to residue template for
    2503 U /2:1508 
    2504 Atom O3' has no neighbors to form bonds with according to residue template for
    2505 U /2:1517 
    2506 Atom O2 has no neighbors to form bonds with according to residue template for
    2507 U /2:1517 
    2508 Atom CG2 has no neighbors to form bonds with according to residue template for
    2509 ILE /F:66 
    2510 Atom N has no neighbors to form bonds with according to residue template for
    2511 SER /F:67 
    2512 Atom C has no neighbors to form bonds with according to residue template for
    2513 SER /F:67 
    2514 Atom OD1 has no neighbors to form bonds with according to residue template for
    2515 ASP /F:128 
    2516 Atom CD1 has no neighbors to form bonds with according to residue template for
    2517 TYR /K:12 
    2518 Atom N has no neighbors to form bonds with according to residue template for
    2519 LEU /K:46 
    2520 Atom N has no neighbors to form bonds with according to residue template for
    2521 TYR /K:66 
    2522 Atom CD2 has no neighbors to form bonds with according to residue template for
    2523 LEU /Q:38 
    2524 Atom N has no neighbors to form bonds with according to residue template for
    2525 LYS /Q:47 
    2526 Atom N has no neighbors to form bonds with according to residue template for
    2527 ARG /T:63 
    2528 Atom CB has no neighbors to form bonds with according to residue template for
    2529 ARG /T:63 
    2530 Atom CD has no neighbors to form bonds with according to residue template for
    2531 ARG /T:63 
    2532 Atom N has no neighbors to form bonds with according to residue template for
    2533 THR /c:26 
    2534 Atom CG2 has no neighbors to form bonds with according to residue template for
    2535 THR /c:26 
    2536 Atom N has no neighbors to form bonds with according to residue template for
    2537 VAL /c:48 
    2538 Atom O has no neighbors to form bonds with according to residue template for
    2539 VAL /c:48 
    2540 Atom N has no neighbors to form bonds with according to residue template for
    2541 ASN /d:48 
    2542 Atom ND2 has no neighbors to form bonds with according to residue template for
    2543 ASN /d:48 
    2544 Atom O has no neighbors to form bonds with according to residue template for
    2545 ASN /j:41 
    2546 Atom ND2 has no neighbors to form bonds with according to residue template for
    2547 ASN /j:41 
    2548 Atom N has no neighbors to form bonds with according to residue template for
    2549 ALA /j:71 
    2550 Atom CB has no neighbors to form bonds with according to residue template for
    2551 ALA /j:71 
    2552 Atom O has no neighbors to form bonds with according to residue template for
    2553 ARG /j:88 
    2554 Atom CA has no neighbors to form bonds with according to residue template for
    2555 GLU /j:93 
    2556 Atom CG has no neighbors to form bonds with according to residue template for
    2557 GLU /j:93 
    2558 Atom N has no neighbors to form bonds with according to residue template for
    2559 ASP /j:94 
    2560 Atom N has no neighbors to form bonds with according to residue template for
    2561 ALA /j:116 
    2562 Atom C has no neighbors to form bonds with according to residue template for
    2563 ALA /j:116 
    2564 Atom O has no neighbors to form bonds with according to residue template for
    2565 GLN /j:120 
    2566 Atom N has no neighbors to form bonds with according to residue template for
    2567 ILE /j:173 
    2568 Atom CG1 has no neighbors to form bonds with according to residue template for
    2569 ILE /j:173 
    2570 Atom O has no neighbors to form bonds with according to residue template for
    2571 VAL /l:225 
    2572 Atom CG1 has no neighbors to form bonds with according to residue template for
    2573 VAL /l:225 
    2574 Atom CA has no neighbors to form bonds with according to residue template for
    2575 LEU /l:226 
    2576 Atom O has no neighbors to form bonds with according to residue template for
    2577 LEU /l:226 
    2578 Atom O has no neighbors to form bonds with according to residue template for
    2579 MET /m:74 
    2580  
    2581 Chain information for 0057_6gsm_S.cif #1 
    2582 --- 
    2583 Chain | Description 
    2584 1 | Met-tRNAi 
    2585 2 | 18S ribosomal RNA 
    2586 D | KLLA0D08305p 
    2587 F | KLLA0D10659p 
    2588 K | KLLA0B08173p 
    2589 P | KLLA0F07843p 
    2590 Q | 40S ribosomal protein S16 
    2591 R | KLLA0B01474p 
    2592 S | KLLA0B01562p 
    2593 T | KLLA0A07194p 
    2594 U | KLLA0F25542p 
    2595 Z | KLLA0B06182p 
    2596 c | 40S ribosomal protein S28 
    2597 d | 40S ribosomal protein S29 
    2598 f | Ubiquitin-40S ribosomal protein S27a 
    2599 j | Eukaryotic translation initiation factor 2 subunit alpha 
    2600 l | Eukaryotic translation initiation factor 2 subunit beta 
    2601 m | Eukaryotic translation initiation factor eIF-1 
    2602  
    2603 
    2604 > open /scratch/cs-
    2605 > bioinfo/tngu/6k_data/Box_Chains_new/0057_6gsm/0057_6gsm_S.mrc
    2606 
    2607 Opened 0057_6gsm_S.mrc as #2, grid size 80,104,96, pixel 1, shown at level
    2608 0.127, step 1, values float32 
    2609 
    2610 > fitmap #1 inMap #2
    2611 
    2612 Fit molecule 0057_6gsm_S.cif (#1) to map 0057_6gsm_S.mrc (#2) using 13752
    2613 atoms 
    2614 average map value = 0.07525, steps = 48 
    2615 shifted from previous position = 0.41 
    2616 rotated from previous position = 0.0854 degrees 
    2617 atoms outside contour = 13058, contour level = 0.12703 
    2618  
    2619 Position of 0057_6gsm_S.cif (#1) relative to 0057_6gsm_S.mrc (#2) coordinates: 
    2620 Matrix rotation and translation 
    2621 0.99999906 0.00133714 0.00031755 -0.63883129 
    2622 -0.00133696 0.99999894 -0.00057716 0.36463028 
    2623 -0.00031832 0.00057673 0.99999978 -0.16205439 
    2624 Axis 0.38707716 0.21330452 -0.89703537 
    2625 Axis point 276.20794680 470.96878257 0.00000000 
    2626 Rotation angle (degrees) 0.08540052 
    2627 Shift along axis -0.02413119 
    2628  
    2629 
    2630 > save /scratch/cs-
    2631 > bioinfo/tngu/6k_data/Box_Chains_new/0057_6gsm/0057_6gsm_S_fitted.cif #1
    2632 
    2633 > close #1
    2634 
    2635 > close #2
    2636 
    2637 > open /scratch/cs-
    2638 > bioinfo/tngu/6k_data/Box_Chains_new/0057_6gsm/0057_6gsm_h.cif
    2639 
    2640 Summary of feedback from opening /scratch/cs-
    2641 bioinfo/tngu/6k_data/Box_Chains_new/0057_6gsm/0057_6gsm_h.cif 
    2642 --- 
    2643 warnings | Invalid residue range for struct_conf "HELX1": invalid chain "C",
    2644 near line 39713 
    2645 Invalid residue range for struct_conf "HELX2": invalid chain "C", near line
    2646 39714 
    2647 Invalid residue range for struct_conf "HELX3": invalid chain "C", near line
    2648 39715 
    2649 Invalid residue range for struct_conf "HELX4": invalid chain "C", near line
    2650 39716 
    2651 Invalid residue range for struct_conf "HELX5": invalid chain "C", near line
    2652 39717 
    2653 114 messages similar to the above omitted 
    2654 Invalid sheet range for struct_sheet_range "? 1": invalid chain "C", near line
    2655 39966 
    2656 Invalid sheet range for struct_sheet_range "? 2": invalid chain "C", near line
    2657 39967 
    2658 Invalid sheet range for struct_sheet_range "? 3": invalid chain "C", near line
    2659 39968 
    2660 Invalid sheet range for struct_sheet_range "? 4": invalid chain "C", near line
    2661 39969 
    2662 Invalid sheet range for struct_sheet_range "? 5": invalid chain "C", near line
    2663 39970 
    2664 157 messages similar to the above omitted 
    2665 Atom N6 has no neighbors to form bonds with according to residue template for
    2666 A /2:11 
    2667 Atom OP2 has no neighbors to form bonds with according to residue template for
    2668 G /2:20 
    2669 Atom OP1 has no neighbors to form bonds with according to residue template for
    2670 C /2:309 
    2671 Atom OP1 has no neighbors to form bonds with according to residue template for
    2672 U /2:373 
    2673 Atom OP1 has no neighbors to form bonds with according to residue template for
    2674 A /2:605 
    2675 Atom OP2 has no neighbors to form bonds with according to residue template for
    2676 U /2:611 
    2677 Atom O2' has no neighbors to form bonds with according to residue template for
    2678 G /2:612 
    2679 Atom OP2 has no neighbors to form bonds with according to residue template for
    2680 C /2:613 
    2681 Atom O5' has no neighbors to form bonds with according to residue template for
    2682 C /2:613 
    2683 Atom P has no neighbors to form bonds with according to residue template for G
    2684 /2:633 
    2685 Atom N4 has no neighbors to form bonds with according to residue template for
    2686 C /2:942 
    2687 Atom C5 has no neighbors to form bonds with according to residue template for
    2688 C /2:942 
    2689 Atom N6 has no neighbors to form bonds with according to residue template for
    2690 A /2:997 
    2691 Atom N1 has no neighbors to form bonds with according to residue template for
    2692 A /2:997 
    2693 Atom O2' has no neighbors to form bonds with according to residue template for
    2694 A /2:1000 
    2695 Atom OP2 has no neighbors to form bonds with according to residue template for
    2696 U /2:1008 
    2697 Atom OP2 has no neighbors to form bonds with according to residue template for
    2698 C /2:1009 
    2699 Atom N6 has no neighbors to form bonds with according to residue template for
    2700 A /2:1018 
    2701 Atom N1 has no neighbors to form bonds with according to residue template for
    2702 A /2:1018 
    2703 Atom O2' has no neighbors to form bonds with according to residue template for
    2704 C /2:1074 
    2705 Atom OP2 has no neighbors to form bonds with according to residue template for
    2706 A /2:1142 
    2707 Atom O2' has no neighbors to form bonds with according to residue template for
    2708 G /2:1734 
    2709 Atom O3' has no neighbors to form bonds with according to residue template for
    2710 C /2:1794 
    2711 Atom C8 has no neighbors to form bonds with according to residue template for
    2712 A /3:29 
    2713 Atom CA has no neighbors to form bonds with according to residue template for
    2714 LYS /N:9 
    2715 Atom CB has no neighbors to form bonds with according to residue template for
    2716 LYS /O:92 
    2717 Atom NZ has no neighbors to form bonds with according to residue template for
    2718 LYS /O:92 
    2719 Atom O has no neighbors to form bonds with according to residue template for
    2720 ASN /X:79 
    2721 Atom O has no neighbors to form bonds with according to residue template for
    2722 ALA /X:113 
    2723 Atom C has no neighbors to form bonds with according to residue template for
    2724 LEU /i:42 
    2725 Atom CD2 has no neighbors to form bonds with according to residue template for
    2726 LEU /i:42 
    2727 Atom N has no neighbors to form bonds with according to residue template for
    2728 ASN /i:44 
    2729 Atom N has no neighbors to form bonds with according to residue template for
    2730 GLY /m:107 
    2731 Atom O has no neighbors to form bonds with according to residue template for
    2732 GLY /m:107 
    2733 Atom N has no neighbors to form bonds with according to residue template for
    2734 GLY /p:132 
    2735 Atom O has no neighbors to form bonds with according to residue template for
    2736 GLY /p:132 
    2737 Atom O has no neighbors to form bonds with according to residue template for
    2738 PRO /p:181 
    2739 Atom CB has no neighbors to form bonds with according to residue template for
    2740 LEU /p:189 
    2741 Atom CD2 has no neighbors to form bonds with according to residue template for
    2742 LEU /p:189 
    2743 Atom O has no neighbors to form bonds with according to residue template for
    2744 LYS /p:241 
    2745 Atom N has no neighbors to form bonds with according to residue template for
    2746 ARG /p:266 
    2747 Atom N has no neighbors to form bonds with according to residue template for
    2748 LEU /p:284 
    2749 Atom N has no neighbors to form bonds with according to residue template for
    2750 GLU /p:295 
    2751 Atom CB has no neighbors to form bonds with according to residue template for
    2752 GLU /p:295 
    2753 Atom OE2 has no neighbors to form bonds with according to residue template for
    2754 GLU /p:295 
    2755 Atom O has no neighbors to form bonds with according to residue template for
    2756 GLU /p:308 
    2757 Atom CA has no neighbors to form bonds with according to residue template for
    2758 ASP /p:397 
    2759 Atom O has no neighbors to form bonds with according to residue template for
    2760 THR /q:141 
    2761 Atom CB has no neighbors to form bonds with according to residue template for
    2762 THR /q:141 
    2763 Atom O has no neighbors to form bonds with according to residue template for
    2764 GLN /q:159 
    2765  
    2766 Chain information for 0057_6gsm_h.cif #1 
    2767 --- 
    2768 Chain | Description 
    2769 2 | 18S ribosomal RNA 
    2770 3 | mRNA (5'-R(P*AP*AP*U)-3') 
    2771 C | KLLA0F09812p 
    2772 L | KLLA0A10483p 
    2773 N | KLLA0F18040p 
    2774 O | 40S ribosomal protein S14 
    2775 X | KLLA0B11231p 
    2776 a | 40S ribosomal protein S26 
    2777 h | 60S ribosomal protein L41-A 
    2778 i | Eukaryotic translation initiation factor 1A 
    2779 k | Eukaryotic translation initiation factor 2 subunit gamma 
    2780 m | Eukaryotic translation initiation factor eIF-1 
    2781 o | Eukaryotic translation initiation factor 3 subunit A,Eukaryotic
    2782 translation initiation factor 3 subunit A,eIF3a 
    2783 p | Eukaryotic translation initiation factor 3 subunit B 
    2784 q | Eukaryotic translation initiation factor 3 subunit C 
    2785  
    2786 
    2787 > open /scratch/cs-
    2788 > bioinfo/tngu/6k_data/Box_Chains_new/0057_6gsm/0057_6gsm_h.mrc
    2789 
    2790 Opened 0057_6gsm_h.mrc as #2, grid size 80,64,56, pixel 1, shown at level
    2791 0.155, step 1, values float32 
    2792 
    2793 > fitmap #1 inMap #2
    2794 
    2795 Fit molecule 0057_6gsm_h.cif (#1) to map 0057_6gsm_h.mrc (#2) using 8610 atoms 
    2796 average map value = 0.08394, steps = 76 
    2797 shifted from previous position = 0.502 
    2798 rotated from previous position = 0.277 degrees 
    2799 atoms outside contour = 8377, contour level = 0.1553 
    2800  
    2801 Position of 0057_6gsm_h.cif (#1) relative to 0057_6gsm_h.mrc (#2) coordinates: 
    2802 Matrix rotation and translation 
    2803 0.99999390 0.00244455 0.00249314 -1.49360317 
    2804 -0.00245288 0.99999140 0.00334522 -0.36462362 
    2805 -0.00248494 -0.00335131 0.99999130 1.17721721 
    2806 Axis -0.69213279 0.51451966 -0.50618349 
    2807 Axis point 0.00000000 388.68717064 148.49285133 
    2808 Rotation angle (degrees) 0.27717525 
    2809 Shift along axis 0.25027779 
    2810  
    2811 
    2812 > save /scratch/cs-
    2813 > bioinfo/tngu/6k_data/Box_Chains_new/0057_6gsm/0057_6gsm_h_fitted.cif #1
    2814 
    2815 > close #1
    2816 
    2817 > close #2
    2818 
    2819 > open /scratch/cs-
    2820 > bioinfo/tngu/6k_data/Box_Chains_new/0057_6gsm/0057_6gsm_I.cif
    2821 
    2822 Summary of feedback from opening /scratch/cs-
    2823 bioinfo/tngu/6k_data/Box_Chains_new/0057_6gsm/0057_6gsm_I.cif 
    2824 --- 
    2825 warnings | Invalid residue range for struct_conf "HELX1": invalid chain "C",
    2826 near line 45675 
    2827 Invalid residue range for struct_conf "HELX2": invalid chain "C", near line
    2828 45676 
    2829 Invalid residue range for struct_conf "HELX3": invalid chain "C", near line
    2830 45677 
    2831 Invalid residue range for struct_conf "HELX4": invalid chain "C", near line
    2832 45678 
    2833 Invalid residue range for struct_conf "HELX5": invalid chain "C", near line
    2834 45679 
    2835 127 messages similar to the above omitted 
    2836 Invalid sheet range for struct_sheet_range "? 1": invalid chain "C", near line
    2837 45928 
    2838 Invalid sheet range for struct_sheet_range "? 2": invalid chain "C", near line
    2839 45929 
    2840 Invalid sheet range for struct_sheet_range "? 3": invalid chain "C", near line
    2841 45930 
    2842 Invalid sheet range for struct_sheet_range "? 4": invalid chain "C", near line
    2843 45931 
    2844 Invalid sheet range for struct_sheet_range "? 5": invalid chain "C", near line
    2845 45932 
    2846 179 messages similar to the above omitted 
    2847 Atom O2' has no neighbors to form bonds with according to residue template for
    2848 U /2:24 
    2849 Atom O2' has no neighbors to form bonds with according to residue template for
    2850 C /2:25 
    2851 Atom OP1 has no neighbors to form bonds with according to residue template for
    2852 A /2:40 
    2853 Atom O3' has no neighbors to form bonds with according to residue template for
    2854 A /2:41 
    2855 Atom O2' has no neighbors to form bonds with according to residue template for
    2856 U /2:64 
    2857 Atom OP2 has no neighbors to form bonds with according to residue template for
    2858 U /2:110 
    2859 Atom O5' has no neighbors to form bonds with according to residue template for
    2860 U /2:110 
    2861 Atom OP2 has no neighbors to form bonds with according to residue template for
    2862 U /2:111 
    2863 Atom O2' has no neighbors to form bonds with according to residue template for
    2864 A /2:146 
    2865 Atom O3' has no neighbors to form bonds with according to residue template for
    2866 G /2:162 
    2867 Atom N2 has no neighbors to form bonds with according to residue template for
    2868 G /2:162 
    2869 Atom OP2 has no neighbors to form bonds with according to residue template for
    2870 A /2:221 
    2871 Atom O5' has no neighbors to form bonds with according to residue template for
    2872 G /2:272 
    2873 Atom O2' has no neighbors to form bonds with according to residue template for
    2874 G /2:364 
    2875 Atom O2' has no neighbors to form bonds with according to residue template for
    2876 A /2:365 
    2877 Atom O2' has no neighbors to form bonds with according to residue template for
    2878 U /2:373 
    2879 Atom OP2 has no neighbors to form bonds with according to residue template for
    2880 G /2:417 
    2881 Atom C6 has no neighbors to form bonds with according to residue template for
    2882 C /2:423 
    2883 Atom N2 has no neighbors to form bonds with according to residue template for
    2884 G /2:433 
    2885 Atom N3 has no neighbors to form bonds with according to residue template for
    2886 G /2:433 
    2887 Atom O5' has no neighbors to form bonds with according to residue template for
    2888 A /2:459 
    2889 Atom O2' has no neighbors to form bonds with according to residue template for
    2890 C /2:468 
    2891 Atom O2 has no neighbors to form bonds with according to residue template for
    2892 C /2:468 
    2893 Atom OP1 has no neighbors to form bonds with according to residue template for
    2894 G /2:627 
    2895 Atom N2 has no neighbors to form bonds with according to residue template for
    2896 G /2:627 
    2897 Atom N3 has no neighbors to form bonds with according to residue template for
    2898 G /2:627 
    2899 Atom O4 has no neighbors to form bonds with according to residue template for
    2900 U /2:631 
    2901 Atom C5 has no neighbors to form bonds with according to residue template for
    2902 U /2:631 
    2903 Atom O2' has no neighbors to form bonds with according to residue template for
    2904 A /2:795 
    2905 Atom N3 has no neighbors to form bonds with according to residue template for
    2906 A /2:795 
    2907 Atom O4 has no neighbors to form bonds with according to residue template for
    2908 U /2:830 
    2909 Atom C5 has no neighbors to form bonds with according to residue template for
    2910 U /2:830 
    2911 Atom O2 has no neighbors to form bonds with according to residue template for
    2912 C /2:848 
    2913 Atom O3' has no neighbors to form bonds with according to residue template for
    2914 U /2:1103 
    2915 Atom O2' has no neighbors to form bonds with according to residue template for
    2916 G /2:1118 
    2917 Atom NH2 has no neighbors to form bonds with according to residue template for
    2918 ARG /E:11 
    2919 Atom CD1 has no neighbors to form bonds with according to residue template for
    2920 LEU /E:12 
    2921 Atom O has no neighbors to form bonds with according to residue template for
    2922 VAL /E:61 
    2923 Atom N has no neighbors to form bonds with according to residue template for
    2924 THR /E:141 
    2925 Atom O has no neighbors to form bonds with according to residue template for
    2926 THR /E:141 
    2927 Atom O has no neighbors to form bonds with according to residue template for
    2928 GLY /G:55 
    2929 Atom O has no neighbors to form bonds with according to residue template for
    2930 ILE /G:112 
    2931 Atom N has no neighbors to form bonds with according to residue template for
    2932 ILE /G:141 
    2933 Atom C has no neighbors to form bonds with according to residue template for
    2934 ILE /G:141 
    2935 Atom OD1 has no neighbors to form bonds with according to residue template for
    2936 ASP /G:152 
    2937 Atom N has no neighbors to form bonds with according to residue template for
    2938 GLU /N:86 
    2939 Atom O has no neighbors to form bonds with according to residue template for
    2940 GLU /N:86 
    2941 Atom N has no neighbors to form bonds with according to residue template for
    2942 VAL /N:132 
    2943 Atom N has no neighbors to form bonds with according to residue template for
    2944 ASN /X:22 
    2945 Atom OD1 has no neighbors to form bonds with according to residue template for
    2946 ASN /X:22 
    2947 Atom N has no neighbors to form bonds with according to residue template for
    2948 TRP /X:24 
    2949 Atom N has no neighbors to form bonds with according to residue template for
    2950 LYS /X:50 
    2951 Atom N has no neighbors to form bonds with according to residue template for
    2952 UNK /o:703 
    2953 Atom N has no neighbors to form bonds with according to residue template for
    2954 LEU /p:189 
    2955 Atom OG1 has no neighbors to form bonds with according to residue template for
    2956 THR /p:243 
    2957 Atom CG2 has no neighbors to form bonds with according to residue template for
    2958 THR /p:243 
    2959 Atom ND2 has no neighbors to form bonds with according to residue template for
    2960 ASN /p:445 
    2961  
    2962 Chain information for 0057_6gsm_I.cif #1 
    2963 --- 
    2964 Chain | Description 
    2965 2 | 18S ribosomal RNA 
    2966 E | 40S ribosomal protein S4 
    2967 G | 40S ribosomal protein S6 
    2968 I | 40S ribosomal protein S8 
    2969 J | KLLA0E23673p 
    2970 L | KLLA0A10483p 
    2971 N | KLLA0F18040p 
    2972 X | KLLA0B11231p 
    2973 o | Eukaryotic translation initiation factor 3 subunit A,Eukaryotic
    2974 translation initiation factor 3 subunit A,eIF3a 
    2975 p | Eukaryotic translation initiation factor 3 subunit B 
    2976 q | Eukaryotic translation initiation factor 3 subunit C 
    2977  
    2978 
    2979 > open /scratch/cs-
    2980 > bioinfo/tngu/6k_data/Box_Chains_new/0057_6gsm/0057_6gsm_I.mrc
    2981 
    2982 Opened 0057_6gsm_I.mrc as #2, grid size 72,120,96, pixel 1, shown at level
    2983 0.144, step 1, values float32 
    2984 
    2985 > fitmap #1 inMap #2
    2986 
    2987 Fit molecule 0057_6gsm_I.cif (#1) to map 0057_6gsm_I.mrc (#2) using 14447
    2988 atoms 
    2989 average map value = 0.08325, steps = 64 
    2990 shifted from previous position = 0.639 
    2991 rotated from previous position = 0.171 degrees 
    2992 atoms outside contour = 13697, contour level = 0.14363 
    2993  
    2994 Position of 0057_6gsm_I.cif (#1) relative to 0057_6gsm_I.mrc (#2) coordinates: 
    2995 Matrix rotation and translation 
    2996 0.99999700 0.00094952 -0.00225603 -0.15605800 
    2997 -0.00094564 0.99999807 0.00172043 -0.49124166 
    2998 0.00225766 -0.00171829 0.99999598 -0.43873210 
    2999 Axis -0.57480111 -0.75448682 -0.31678593 
    3000 Axis point 110.38476831 0.00000000 83.37759510 
    3001 Rotation angle (degrees) 0.17138502 
    3002 Shift along axis 0.59932182 
    3003  
    3004 
    3005 > save /scratch/cs-
    3006 > bioinfo/tngu/6k_data/Box_Chains_new/0057_6gsm/0057_6gsm_I_fitted.cif #1
    3007 
    3008 > close #1
    3009 
    3010 > close #2
    3011 
    3012 > open /scratch/cs-
    3013 > bioinfo/tngu/6k_data/Box_Chains_new/0057_6gsm/0057_6gsm_j.cif
    3014 
    3015 Summary of feedback from opening /scratch/cs-
    3016 bioinfo/tngu/6k_data/Box_Chains_new/0057_6gsm/0057_6gsm_j.cif 
    3017 --- 
    3018 warnings | Invalid residue range for struct_conf "HELX1": invalid chain "C",
    3019 near line 45481 
    3020 Invalid residue range for struct_conf "HELX2": invalid chain "C", near line
    3021 45482 
    3022 Invalid residue range for struct_conf "HELX3": invalid chain "C", near line
    3023 45483 
    3024 Invalid residue range for struct_conf "HELX4": invalid chain "C", near line
    3025 45484 
    3026 Invalid residue range for struct_conf "HELX5": invalid chain "C", near line
    3027 45485 
    3028 121 messages similar to the above omitted 
    3029 Invalid sheet range for struct_sheet_range "? 1": invalid chain "C", near line
    3030 45734 
    3031 Invalid sheet range for struct_sheet_range "? 2": invalid chain "C", near line
    3032 45735 
    3033 Invalid sheet range for struct_sheet_range "? 3": invalid chain "C", near line
    3034 45736 
    3035 Invalid sheet range for struct_sheet_range "? 4": invalid chain "C", near line
    3036 45737 
    3037 Invalid sheet range for struct_sheet_range "? 5": invalid chain "C", near line
    3038 45738 
    3039 141 messages similar to the above omitted 
    3040 Atom O5' has no neighbors to form bonds with according to residue template for
    3041 U /2:920 
    3042 Atom OP2 has no neighbors to form bonds with according to residue template for
    3043 A /2:923 
    3044 Atom N3 has no neighbors to form bonds with according to residue template for
    3045 A /2:987 
    3046 Atom OP1 has no neighbors to form bonds with according to residue template for
    3047 G /2:1145 
    3048 Atom O2' has no neighbors to form bonds with according to residue template for
    3049 G /2:1145 
    3050 Atom N2 has no neighbors to form bonds with according to residue template for
    3051 G /2:1280 
    3052 Atom O3' has no neighbors to form bonds with according to residue template for
    3053 A /2:1286 
    3054 Atom O2' has no neighbors to form bonds with according to residue template for
    3055 A /2:1286 
    3056 Atom OP1 has no neighbors to form bonds with according to residue template for
    3057 G /2:1287 
    3058 Atom O2' has no neighbors to form bonds with according to residue template for
    3059 G /2:1287 
    3060 Atom O2' has no neighbors to form bonds with according to residue template for
    3061 U /2:1306 
    3062 Atom OP1 has no neighbors to form bonds with according to residue template for
    3063 C /2:1308 
    3064 Atom OP2 has no neighbors to form bonds with according to residue template for
    3065 C /2:1308 
    3066 Atom OP1 has no neighbors to form bonds with according to residue template for
    3067 G /2:1460 
    3068 Atom C8 has no neighbors to form bonds with according to residue template for
    3069 G /2:1462 
    3070 Atom C6 has no neighbors to form bonds with according to residue template for
    3071 C /2:1463 
    3072 Atom OP2 has no neighbors to form bonds with according to residue template for
    3073 U /2:1526 
    3074 Atom OP1 has no neighbors to form bonds with according to residue template for
    3075 U /2:1756 
    3076 Atom O3' has no neighbors to form bonds with according to residue template for
    3077 U /2:1756 
    3078 Atom OP1 has no neighbors to form bonds with according to residue template for
    3079 U /2:1783 
    3080 Atom C5' has no neighbors to form bonds with according to residue template for
    3081 U /2:1783 
    3082 Atom OP2 has no neighbors to form bonds with according to residue template for
    3083 U /2:1796 
    3084 Atom N has no neighbors to form bonds with according to residue template for
    3085 ARG /B:26 
    3086 Atom O has no neighbors to form bonds with according to residue template for
    3087 PHE /B:81 
    3088 Atom NZ has no neighbors to form bonds with according to residue template for
    3089 LYS /B:116 
    3090 Atom N has no neighbors to form bonds with according to residue template for
    3091 PHE /B:142 
    3092 Atom CG1 has no neighbors to form bonds with according to residue template for
    3093 VAL /F:55 
    3094 Atom CB has no neighbors to form bonds with according to residue template for
    3095 ARG /F:94 
    3096 Atom N has no neighbors to form bonds with according to residue template for
    3097 ASN /F:130 
    3098 Atom N has no neighbors to form bonds with according to residue template for
    3099 LEU /F:132 
    3100 Atom NE2 has no neighbors to form bonds with according to residue template for
    3101 GLN /F:133 
    3102 Atom OD1 has no neighbors to form bonds with according to residue template for
    3103 ASP /O:124 
    3104 Atom O has no neighbors to form bonds with according to residue template for
    3105 VAL /S:28 
    3106 Atom N has no neighbors to form bonds with according to residue template for
    3107 ALA /S:31 
    3108 Atom CB has no neighbors to form bonds with according to residue template for
    3109 ALA /S:31 
    3110 Atom CG has no neighbors to form bonds with according to residue template for
    3111 LEU /S:61 
    3112 Atom N has no neighbors to form bonds with according to residue template for
    3113 THR /S:62 
    3114 Atom CG2 has no neighbors to form bonds with according to residue template for
    3115 THR /S:62 
    3116 Atom N has no neighbors to form bonds with according to residue template for
    3117 VAL /Z:92 
    3118 Atom CG2 has no neighbors to form bonds with according to residue template for
    3119 VAL /Z:92 
    3120 Atom N has no neighbors to form bonds with according to residue template for
    3121 SER /a:88 
    3122 Atom CB has no neighbors to form bonds with according to residue template for
    3123 SER /a:88 
    3124 Atom OE2 has no neighbors to form bonds with according to residue template for
    3125 GLU /c:31 
    3126 Atom N has no neighbors to form bonds with according to residue template for
    3127 ASP /k:193 
    3128 Atom N has no neighbors to form bonds with according to residue template for
    3129 MET /k:211 
    3130 Atom SD has no neighbors to form bonds with according to residue template for
    3131 MET /k:211 
    3132 Atom CB has no neighbors to form bonds with according to residue template for
    3133 ALA /k:234 
    3134 Atom O has no neighbors to form bonds with according to residue template for
    3135 PHE /k:435 
    3136 Atom CD2 has no neighbors to form bonds with according to residue template for
    3137 PHE /k:435 
    3138 Atom NE has no neighbors to form bonds with according to residue template for
    3139 ARG /k:474 
    3140 Atom NH2 has no neighbors to form bonds with according to residue template for
    3141 ARG /k:474 
    3142 Atom C has no neighbors to form bonds with according to residue template for
    3143 ARG /l:167 
    3144 Atom CD has no neighbors to form bonds with according to residue template for
    3145 ARG /l:167 
    3146 Atom NH1 has no neighbors to form bonds with according to residue template for
    3147 ARG /l:167 
    3148 Atom N has no neighbors to form bonds with according to residue template for
    3149 ILE /p:116 
    3150 Atom OE1 has no neighbors to form bonds with according to residue template for
    3151 GLU /p:118 
    3152 Atom OE2 has no neighbors to form bonds with according to residue template for
    3153 GLU /p:118 
    3154 Atom C has no neighbors to form bonds with according to residue template for
    3155 LEU /p:127 
    3156  
    3157 Chain information for 0057_6gsm_j.cif #1 
    3158 --- 
    3159 Chain | Description 
    3160 1 | Met-tRNAi 
    3161 2 | 18S ribosomal RNA 
    3162 3 | mRNA (5'-R(P*AP*AP*U)-3') 
    3163 B | 40S ribosomal protein S1 
    3164 C | KLLA0F09812p 
    3165 F | KLLA0D10659p 
    3166 O | 40S ribosomal protein S14 
    3167 Q | 40S ribosomal protein S16 
    3168 S | KLLA0B01562p 
    3169 T | KLLA0A07194p 
    3170 U | KLLA0F25542p 
    3171 Z | KLLA0B06182p 
    3172 a | 40S ribosomal protein S26 
    3173 c | 40S ribosomal protein S28 
    3174 i | Eukaryotic translation initiation factor 1A 
    3175 j | Eukaryotic translation initiation factor 2 subunit alpha 
    3176 k | Eukaryotic translation initiation factor 2 subunit gamma 
    3177 l | Eukaryotic translation initiation factor 2 subunit beta 
    3178 m | Eukaryotic translation initiation factor eIF-1 
    3179 o | Eukaryotic translation initiation factor 3 subunit A,Eukaryotic
    3180 translation initiation factor 3 subunit A,eIF3a 
    3181 p | Eukaryotic translation initiation factor 3 subunit B 
    3182  
    3183 
    3184 > open /scratch/cs-
    3185 > bioinfo/tngu/6k_data/Box_Chains_new/0057_6gsm/0057_6gsm_j.mrc
    3186 
    3187 Opened 0057_6gsm_j.mrc as #2, grid size 136,104,80, pixel 1, shown at level
    3188 0.119, step 1, values float32 
    3189 
    3190 > fitmap #1 inMap #2
    3191 
    3192 Fit molecule 0057_6gsm_j.cif (#1) to map 0057_6gsm_j.mrc (#2) using 14398
    3193 atoms 
    3194 average map value = 0.06882, steps = 56 
    3195 shifted from previous position = 0.502 
    3196 rotated from previous position = 0.155 degrees 
    3197 atoms outside contour = 13409, contour level = 0.11916 
    3198  
    3199 Position of 0057_6gsm_j.cif (#1) relative to 0057_6gsm_j.mrc (#2) coordinates: 
    3200 Matrix rotation and translation 
    3201 0.99999853 0.00013427 0.00170961 -0.74251221 
    3202 -0.00013069 0.99999780 -0.00209394 0.48762654 
    3203 -0.00170989 0.00209372 0.99999635 -0.29123892 
    3204 Axis 0.77364167 0.63172986 -0.04894843 
    3205 Axis point 0.00000000 145.53493310 308.78942974 
    3206 Rotation angle (degrees) 0.15506880 
    3207 Shift along axis -0.25213445 
    3208  
    3209 
    3210 > save /scratch/cs-
    3211 > bioinfo/tngu/6k_data/Box_Chains_new/0057_6gsm/0057_6gsm_j_fitted.cif #1
    3212 
    3213 > close #1
    3214 
    3215 > close #2
    3216 
    3217 > open /scratch/cs-
    3218 > bioinfo/tngu/6k_data/Box_Chains_new/0057_6gsm/0057_6gsm_m.cif
    3219 
    3220 Summary of feedback from opening /scratch/cs-
    3221 bioinfo/tngu/6k_data/Box_Chains_new/0057_6gsm/0057_6gsm_m.cif 
    3222 --- 
    3223 warnings | Invalid residue range for struct_conf "HELX1": invalid chain "C",
    3224 near line 43790 
    3225 Invalid residue range for struct_conf "HELX2": invalid chain "C", near line
    3226 43791 
    3227 Invalid residue range for struct_conf "HELX3": invalid chain "C", near line
    3228 43792 
    3229 Invalid residue range for struct_conf "HELX4": invalid chain "C", near line
    3230 43793 
    3231 Invalid residue range for struct_conf "HELX5": invalid chain "C", near line
    3232 43794 
    3233 100 messages similar to the above omitted 
    3234 Invalid sheet range for struct_sheet_range "? 1": invalid chain "C", near line
    3235 44043 
    3236 Invalid sheet range for struct_sheet_range "? 2": invalid chain "C", near line
    3237 44044 
    3238 Invalid sheet range for struct_sheet_range "? 3": invalid chain "C", near line
    3239 44045 
    3240 Invalid sheet range for struct_sheet_range "? 4": invalid chain "C", near line
    3241 44046 
    3242 Invalid sheet range for struct_sheet_range "? 5": invalid chain "C", near line
    3243 44047 
    3244 153 messages similar to the above omitted 
    3245 Atom O6 has no neighbors to form bonds with according to residue template for
    3246 1MG /1:9 
    3247 Atom OP2 has no neighbors to form bonds with according to residue template for
    3248 2MG /1:10 
    3249 Atom O3' has no neighbors to form bonds with according to residue template for
    3250 G /1:22 
    3251 Atom OP1 has no neighbors to form bonds with according to residue template for
    3252 G /2:10 
    3253 Atom OP2 has no neighbors to form bonds with according to residue template for
    3254 G /2:10 
    3255 Atom O2' has no neighbors to form bonds with according to residue template for
    3256 U /2:15 
    3257 Atom O2 has no neighbors to form bonds with according to residue template for
    3258 U /2:15 
    3259 Atom OP1 has no neighbors to form bonds with according to residue template for
    3260 C /2:571 
    3261 Atom OP2 has no neighbors to form bonds with according to residue template for
    3262 C /2:571 
    3263 Atom O2 has no neighbors to form bonds with according to residue template for
    3264 U /2:617 
    3265 Atom N6 has no neighbors to form bonds with according to residue template for
    3266 A /2:620 
    3267 Atom OP1 has no neighbors to form bonds with according to residue template for
    3268 A /2:621 
    3269 Atom OP2 has no neighbors to form bonds with according to residue template for
    3270 A /2:621 
    3271 Atom OP2 has no neighbors to form bonds with according to residue template for
    3272 G /2:623 
    3273 Atom N2 has no neighbors to form bonds with according to residue template for
    3274 G /2:623 
    3275 Atom OP2 has no neighbors to form bonds with according to residue template for
    3276 A /2:899 
    3277 Atom O4' has no neighbors to form bonds with according to residue template for
    3278 C /2:909 
    3279 Atom OP2 has no neighbors to form bonds with according to residue template for
    3280 U /2:910 
    3281 Atom N3 has no neighbors to form bonds with according to residue template for
    3282 A /2:939 
    3283 Atom O3' has no neighbors to form bonds with according to residue template for
    3284 G /2:1108 
    3285 Atom O2' has no neighbors to form bonds with according to residue template for
    3286 C /2:1133 
    3287 Atom O2 has no neighbors to form bonds with according to residue template for
    3288 C /2:1133 
    3289 Atom C8 has no neighbors to form bonds with according to residue template for
    3290 G /2:1140 
    3291 Atom OP1 has no neighbors to form bonds with according to residue template for
    3292 A /2:1141 
    3293 Atom OP2 has no neighbors to form bonds with according to residue template for
    3294 A /2:1141 
    3295 Atom OP2 has no neighbors to form bonds with according to residue template for
    3296 C /2:1176 
    3297 Atom C5' has no neighbors to form bonds with according to residue template for
    3298 A /2:1188 
    3299 Atom O3' has no neighbors to form bonds with according to residue template for
    3300 C /2:1454 
    3301 Atom O2' has no neighbors to form bonds with according to residue template for
    3302 C /2:1454 
    3303 Atom OP2 has no neighbors to form bonds with according to residue template for
    3304 G /2:1456 
    3305 Atom OP2 has no neighbors to form bonds with according to residue template for
    3306 C /2:1463 
    3307 Atom N4 has no neighbors to form bonds with according to residue template for
    3308 C /2:1463 
    3309 Atom O3' has no neighbors to form bonds with according to residue template for
    3310 C /2:1617 
    3311 Atom O2' has no neighbors to form bonds with according to residue template for
    3312 C /2:1617 
    3313 Atom O3' has no neighbors to form bonds with according to residue template for
    3314 U /2:1619 
    3315 Atom OP1 has no neighbors to form bonds with according to residue template for
    3316 C /2:1632 
    3317 Atom O5' has no neighbors to form bonds with according to residue template for
    3318 A /2:1744 
    3319 Atom O4' has no neighbors to form bonds with according to residue template for
    3320 U /2:1793 
    3321 Atom N has no neighbors to form bonds with according to residue template for
    3322 ARG /B:8 
    3323 Atom O has no neighbors to form bonds with according to residue template for
    3324 ARG /B:8 
    3325 Atom CG1 has no neighbors to form bonds with according to residue template for
    3326 VAL /F:222 
    3327 Atom O has no neighbors to form bonds with according to residue template for
    3328 ARG /O:90 
    3329 Atom NH1 has no neighbors to form bonds with according to residue template for
    3330 ARG /O:103 
    3331 Atom NH2 has no neighbors to form bonds with according to residue template for
    3332 ARG /O:103 
    3333 Atom N has no neighbors to form bonds with according to residue template for
    3334 THR /S:140 
    3335 Atom CG2 has no neighbors to form bonds with according to residue template for
    3336 THR /S:140 
    3337 Atom O has no neighbors to form bonds with according to residue template for
    3338 CYS /X:71 
    3339 Atom N has no neighbors to form bonds with according to residue template for
    3340 VAL /X:120 
    3341 Atom CG2 has no neighbors to form bonds with according to residue template for
    3342 VAL /X:120 
    3343 Atom O has no neighbors to form bonds with according to residue template for
    3344 ASN /a:8 
    3345 Atom N has no neighbors to form bonds with according to residue template for
    3346 VAL /a:18 
    3347 Atom O has no neighbors to form bonds with according to residue template for
    3348 VAL /a:18 
    3349 Atom CG1 has no neighbors to form bonds with according to residue template for
    3350 VAL /a:21 
    3351 Atom O has no neighbors to form bonds with according to residue template for
    3352 LEU /a:71 
    3353 Atom CD1 has no neighbors to form bonds with according to residue template for
    3354 LEU /a:71 
    3355 Atom N has no neighbors to form bonds with according to residue template for
    3356 ILE /a:83 
    3357 Atom N has no neighbors to form bonds with according to residue template for
    3358 ARG /h:21 
    3359 Atom NH1 has no neighbors to form bonds with according to residue template for
    3360 ARG /h:21 
    3361 Atom CG has no neighbors to form bonds with according to residue template for
    3362 ARG /i:24 
    3363 Atom O has no neighbors to form bonds with according to residue template for
    3364 GLU /i:34 
    3365 Atom N has no neighbors to form bonds with according to residue template for
    3366 ASP /i:53 
    3367 Atom C has no neighbors to form bonds with according to residue template for
    3368 ASP /i:53 
    3369 Atom N has no neighbors to form bonds with according to residue template for
    3370 ASP /i:83 
    3371 Atom C has no neighbors to form bonds with according to residue template for
    3372 ASP /i:83 
    3373 Atom N has no neighbors to form bonds with according to residue template for
    3374 ARG /i:101 
    3375 Atom CD1 has no neighbors to form bonds with according to residue template for
    3376 LEU /i:109 
    3377 Atom CD2 has no neighbors to form bonds with according to residue template for
    3378 LEU /i:109 
    3379 Atom CG2 has no neighbors to form bonds with according to residue template for
    3380 ILE /j:19 
    3381 Atom CD1 has no neighbors to form bonds with according to residue template for
    3382 ILE /j:19 
    3383 Atom CG2 has no neighbors to form bonds with according to residue template for
    3384 ILE /j:46 
    3385 Atom OE1 has no neighbors to form bonds with according to residue template for
    3386 GLN /j:60 
    3387 Atom N has no neighbors to form bonds with according to residue template for
    3388 ARG /j:75 
    3389 Atom N has no neighbors to form bonds with according to residue template for
    3390 GLY /k:277 
    3391 Atom O has no neighbors to form bonds with according to residue template for
    3392 GLY /k:277 
    3393 Atom O has no neighbors to form bonds with according to residue template for
    3394 ILE /k:291 
    3395 Atom O has no neighbors to form bonds with according to residue template for
    3396 ASN /k:295 
    3397 Atom N has no neighbors to form bonds with according to residue template for
    3398 LYS /k:300 
    3399 Atom N has no neighbors to form bonds with according to residue template for
    3400 ILE /k:495 
    3401 Atom CD1 has no neighbors to form bonds with according to residue template for
    3402 TYR /p:248 
    3403 Atom OG has no neighbors to form bonds with according to residue template for
    3404 SER /p:275 
    3405 Atom CD2 has no neighbors to form bonds with according to residue template for
    3406 LEU /p:284 
    3407 Atom CD1 has no neighbors to form bonds with according to residue template for
    3408 TRP /p:336 
    3409 Atom N has no neighbors to form bonds with according to residue template for
    3410 ASP /p:360 
    3411 Atom O has no neighbors to form bonds with according to residue template for
    3412 ASP /p:360 
    3413 Atom N has no neighbors to form bonds with according to residue template for
    3414 ALA /p:370 
    3415 Atom O has no neighbors to form bonds with according to residue template for
    3416 ALA /p:370 
    3417 Atom N has no neighbors to form bonds with according to residue template for
    3418 VAL /q:112 
    3419  
    3420 Chain information for 0057_6gsm_m.cif #1 
    3421 --- 
    3422 Chain | Description 
    3423 1 | Met-tRNAi 
    3424 2 | 18S ribosomal RNA 
    3425 3 | mRNA (5'-R(P*AP*AP*U)-3') 
    3426 B | 40S ribosomal protein S1 
    3427 F | KLLA0D10659p 
    3428 O | 40S ribosomal protein S14 
    3429 P | KLLA0F07843p 
    3430 Q | 40S ribosomal protein S16 
    3431 S | KLLA0B01562p 
    3432 X | KLLA0B11231p 
    3433 a | 40S ribosomal protein S26 
    3434 c | 40S ribosomal protein S28 
    3435 e | 40S ribosomal protein S30 
    3436 h | 60S ribosomal protein L41-A 
    3437 i | Eukaryotic translation initiation factor 1A 
    3438 j | Eukaryotic translation initiation factor 2 subunit alpha 
    3439 k | Eukaryotic translation initiation factor 2 subunit gamma 
    3440 l | Eukaryotic translation initiation factor 2 subunit beta 
    3441 m | Eukaryotic translation initiation factor eIF-1 
    3442 o | Eukaryotic translation initiation factor 3 subunit A,Eukaryotic
    3443 translation initiation factor 3 subunit A,eIF3a 
    3444 p | Eukaryotic translation initiation factor 3 subunit B 
    3445 q | Eukaryotic translation initiation factor 3 subunit C 
    3446  
    3447 
    3448 > open /scratch/cs-
    3449 > bioinfo/tngu/6k_data/Box_Chains_new/0057_6gsm/0057_6gsm_m.mrc
    3450 
    3451 Opened 0057_6gsm_m.mrc as #2, grid size 104,72,72, pixel 1, shown at level
    3452 0.134, step 1, values float32 
    3453 
    3454 > fitmap #1 inMap #2
    3455 
    3456 Fit molecule 0057_6gsm_m.cif (#1) to map 0057_6gsm_m.mrc (#2) using 12721
    3457 atoms 
    3458 average map value = 0.0659, steps = 112 
    3459 shifted from previous position = 0.523 
    3460 rotated from previous position = 0.124 degrees 
    3461 atoms outside contour = 12229, contour level = 0.13429 
    3462  
    3463 Position of 0057_6gsm_m.cif (#1) relative to 0057_6gsm_m.mrc (#2) coordinates: 
    3464 Matrix rotation and translation 
    3465 0.99999779 0.00130994 0.00164375 -1.03339978 
    3466 -0.00130910 0.99999901 -0.00050917 0.23869542 
    3467 -0.00164441 0.00050701 0.99999852 0.15046608 
    3468 Axis 0.23496469 0.76030197 -0.60558444 
    3469 Axis point 34.81184266 0.00000000 606.93991431 
    3470 Rotation angle (degrees) 0.12389672 
    3471 Shift along axis -0.15245178 
    3472  
    3473 
    3474 > save /scratch/cs-
    3475 > bioinfo/tngu/6k_data/Box_Chains_new/0057_6gsm/0057_6gsm_m_fitted.cif #1
    3476 
    3477 > close #1
    3478 
    3479 > close #2
    3480 
    3481 > open /scratch/cs-
    3482 > bioinfo/tngu/6k_data/Box_Chains_new/0057_6gsm/0057_6gsm_T.cif
    3483 
    3484 Summary of feedback from opening /scratch/cs-
    3485 bioinfo/tngu/6k_data/Box_Chains_new/0057_6gsm/0057_6gsm_T.cif 
    3486 --- 
    3487 warnings | Invalid residue range for struct_conf "HELX1": invalid chain "C",
    3488 near line 44599 
    3489 Invalid residue range for struct_conf "HELX2": invalid chain "C", near line
    3490 44600 
    3491 Invalid residue range for struct_conf "HELX3": invalid chain "C", near line
    3492 44601 
    3493 Invalid residue range for struct_conf "HELX4": invalid chain "C", near line
    3494 44602 
    3495 Invalid residue range for struct_conf "HELX5": invalid chain "C", near line
    3496 44603 
    3497 174 messages similar to the above omitted 
    3498 Invalid sheet range for struct_sheet_range "? 1": invalid chain "C", near line
    3499 44852 
    3500 Invalid sheet range for struct_sheet_range "? 2": invalid chain "C", near line
    3501 44853 
    3502 Invalid sheet range for struct_sheet_range "? 3": invalid chain "C", near line
    3503 44854 
    3504 Invalid sheet range for struct_sheet_range "? 4": invalid chain "C", near line
    3505 44855 
    3506 Invalid sheet range for struct_sheet_range "? 5": invalid chain "C", near line
    3507 44856 
    3508 183 messages similar to the above omitted 
    3509 Atom O4' has no neighbors to form bonds with according to residue template for
    3510 G /1:43 
    3511 Atom O3' has no neighbors to form bonds with according to residue template for
    3512 C /2:1158 
    3513 Atom O2' has no neighbors to form bonds with according to residue template for
    3514 C /2:1158 
    3515 Atom OP2 has no neighbors to form bonds with according to residue template for
    3516 A /2:1159 
    3517 Atom O6 has no neighbors to form bonds with according to residue template for
    3518 G /2:1197 
    3519 Atom OP1 has no neighbors to form bonds with according to residue template for
    3520 U /2:1448 
    3521 Atom O2 has no neighbors to form bonds with according to residue template for
    3522 C /2:1617 
    3523 Atom N3 has no neighbors to form bonds with according to residue template for
    3524 C /2:1617 
    3525 Atom CG1 has no neighbors to form bonds with according to residue template for
    3526 VAL /D:41 
    3527 Atom CG2 has no neighbors to form bonds with according to residue template for
    3528 VAL /D:41 
    3529 Atom CD1 has no neighbors to form bonds with according to residue template for
    3530 ILE /F:42 
    3531 Atom CG2 has no neighbors to form bonds with according to residue template for
    3532 ILE /F:64 
    3533 Atom C has no neighbors to form bonds with according to residue template for
    3534 VAL /F:134 
    3535 Atom CB has no neighbors to form bonds with according to residue template for
    3536 ALA /F:138 
    3537 Atom O has no neighbors to form bonds with according to residue template for
    3538 SER /F:142 
    3539 Atom N has no neighbors to form bonds with according to residue template for
    3540 ARG /F:159 
    3541 Atom CG1 has no neighbors to form bonds with according to residue template for
    3542 VAL /F:222 
    3543 Atom CG2 has no neighbors to form bonds with according to residue template for
    3544 VAL /F:222 
    3545 Atom C has no neighbors to form bonds with according to residue template for
    3546 ASN /K:28 
    3547 Atom CB has no neighbors to form bonds with according to residue template for
    3548 ASN /K:28 
    3549 Atom OE1 has no neighbors to form bonds with according to residue template for
    3550 GLU /P:23 
    3551 Atom OE2 has no neighbors to form bonds with according to residue template for
    3552 GLU /P:23 
    3553 Atom O has no neighbors to form bonds with according to residue template for
    3554 GLY /P:48 
    3555 Atom O has no neighbors to form bonds with according to residue template for
    3556 ILE /P:85 
    3557 Atom O has no neighbors to form bonds with according to residue template for
    3558 VAL /P:94 
    3559 Atom CG2 has no neighbors to form bonds with according to residue template for
    3560 VAL /P:94 
    3561 Atom N has no neighbors to form bonds with according to residue template for
    3562 ARG /P:127 
    3563 Atom O has no neighbors to form bonds with according to residue template for
    3564 ARG /P:127 
    3565 Atom N has no neighbors to form bonds with according to residue template for
    3566 TRP /S:129 
    3567 Atom C has no neighbors to form bonds with according to residue template for
    3568 TRP /S:129 
    3569 Atom CB has no neighbors to form bonds with according to residue template for
    3570 TRP /S:129 
    3571 Atom CD1 has no neighbors to form bonds with according to residue template for
    3572 TRP /S:129 
    3573 Atom N has no neighbors to form bonds with according to residue template for
    3574 GLU /U:46 
    3575 Atom CD1 has no neighbors to form bonds with according to residue template for
    3576 ILE /U:99 
    3577 Atom CG2 has no neighbors to form bonds with according to residue template for
    3578 VAL /c:25 
    3579 Atom C has no neighbors to form bonds with according to residue template for
    3580 LYS /c:45 
    3581 Atom O has no neighbors to form bonds with according to residue template for
    3582 TYR /d:8 
    3583 Atom OH has no neighbors to form bonds with according to residue template for
    3584 TYR /d:8 
    3585 Atom O has no neighbors to form bonds with according to residue template for
    3586 ILE /d:38 
    3587 Atom CG1 has no neighbors to form bonds with according to residue template for
    3588 VAL /g:35 
    3589 Atom N has no neighbors to form bonds with according to residue template for
    3590 VAL /g:72 
    3591 Atom CD2 has no neighbors to form bonds with according to residue template for
    3592 LEU /g:112 
    3593 Atom N has no neighbors to form bonds with according to residue template for
    3594 ALA /g:249 
    3595 Atom CB has no neighbors to form bonds with according to residue template for
    3596 ALA /g:249 
    3597 Atom N has no neighbors to form bonds with according to residue template for
    3598 ARG /j:54 
    3599 Atom NZ has no neighbors to form bonds with according to residue template for
    3600 LYS /j:87 
    3601  
    3602 Chain information for 0057_6gsm_T.cif #1 
    3603 --- 
    3604 Chain | Description 
    3605 1 | Met-tRNAi 
    3606 2 | 18S ribosomal RNA 
    3607 D | KLLA0D08305p 
    3608 F | KLLA0D10659p 
    3609 K | KLLA0B08173p 
    3610 P | KLLA0F07843p 
    3611 Q | 40S ribosomal protein S16 
    3612 R | KLLA0B01474p 
    3613 S | KLLA0B01562p 
    3614 T | KLLA0A07194p 
    3615 U | KLLA0F25542p 
    3616 Z | KLLA0B06182p 
    3617 c | 40S ribosomal protein S28 
    3618 d | 40S ribosomal protein S29 
    3619 g | KLLA0E12277p 
    3620 j | Eukaryotic translation initiation factor 2 subunit alpha 
    3621  
    3622 
    3623 > open /scratch/cs-
    3624 > bioinfo/tngu/6k_data/Box_Chains_new/0057_6gsm/0057_6gsm_T.mrc
    3625 
    3626 Opened 0057_6gsm_T.mrc as #2, grid size 88,88,80, pixel 1, shown at level
    3627 0.133, step 1, values float32 
    3628 
    3629 > fitmap #1 inMap #2
    3630 
    3631 Fit molecule 0057_6gsm_T.cif (#1) to map 0057_6gsm_T.mrc (#2) using 13497
    3632 atoms 
    3633 average map value = 0.07745, steps = 60 
    3634 shifted from previous position = 0.338 
    3635 rotated from previous position = 0.083 degrees 
    3636 atoms outside contour = 12958, contour level = 0.13258 
    3637  
    3638 Position of 0057_6gsm_T.cif (#1) relative to 0057_6gsm_T.mrc (#2) coordinates: 
    3639 Matrix rotation and translation 
    3640 0.99999979 -0.00028336 0.00058636 -0.30702594 
    3641 0.00028412 0.99999912 -0.00129319 0.23254354 
    3642 -0.00058599 0.00129335 0.99999899 -0.30519742 
    3643 Axis 0.89315267 0.40482004 0.19595673 
    3644 Axis point -0.00000000 199.82647397 254.78106719 
    3645 Rotation angle (degrees) 0.08296346 
    3646 Shift along axis -0.23988825 
    3647  
    3648 
    3649 > save /scratch/cs-
    3650 > bioinfo/tngu/6k_data/Box_Chains_new/0057_6gsm/0057_6gsm_T_fitted.cif #1
    3651 
    3652 > close #1
    3653 
    3654 > close #2
    3655 
    3656 > open /scratch/cs-
    3657 > bioinfo/tngu/6k_data/Box_Chains_new/0057_6gsm/0057_6gsm_Y.cif
    3658 
    3659 Summary of feedback from opening /scratch/cs-
    3660 bioinfo/tngu/6k_data/Box_Chains_new/0057_6gsm/0057_6gsm_Y.cif 
    3661 --- 
    3662 warnings | Invalid residue range for struct_conf "HELX1": invalid chain "C",
    3663 near line 43436 
    3664 Invalid residue range for struct_conf "HELX2": invalid chain "C", near line
    3665 43437 
    3666 Invalid residue range for struct_conf "HELX3": invalid chain "C", near line
    3667 43438 
    3668 Invalid residue range for struct_conf "HELX4": invalid chain "C", near line
    3669 43439 
    3670 Invalid residue range for struct_conf "HELX5": invalid chain "C", near line
    3671 43440 
    3672 161 messages similar to the above omitted 
    3673 Invalid sheet range for struct_sheet_range "? 1": invalid chain "C", near line
    3674 43689 
    3675 Invalid sheet range for struct_sheet_range "? 2": invalid chain "C", near line
    3676 43690 
    3677 Invalid sheet range for struct_sheet_range "? 3": invalid chain "C", near line
    3678 43691 
    3679 Invalid sheet range for struct_sheet_range "? 4": invalid chain "C", near line
    3680 43692 
    3681 Invalid sheet range for struct_sheet_range "? 5": invalid chain "C", near line
    3682 43693 
    3683 187 messages similar to the above omitted 
    3684 Atom N2 has no neighbors to form bonds with according to residue template for
    3685 G /2:23 
    3686 Atom C8 has no neighbors to form bonds with according to residue template for
    3687 A /2:28 
    3688 Atom O4 has no neighbors to form bonds with according to residue template for
    3689 U /2:29 
    3690 Atom O3' has no neighbors to form bonds with according to residue template for
    3691 U /2:77 
    3692 Atom O2' has no neighbors to form bonds with according to residue template for
    3693 U /2:173 
    3694 Atom OP2 has no neighbors to form bonds with according to residue template for
    3695 U /2:271 
    3696 Atom N7 has no neighbors to form bonds with according to residue template for
    3697 G /2:290 
    3698 Atom O6 has no neighbors to form bonds with according to residue template for
    3699 G /2:290 
    3700 Atom C4' has no neighbors to form bonds with according to residue template for
    3701 C /2:297 
    3702 Atom O2' has no neighbors to form bonds with according to residue template for
    3703 C /2:297 
    3704 Atom O3' has no neighbors to form bonds with according to residue template for
    3705 A /2:359 
    3706 Atom OP2 has no neighbors to form bonds with according to residue template for
    3707 G /2:389 
    3708 Atom N4 has no neighbors to form bonds with according to residue template for
    3709 C /2:392 
    3710 Atom N3 has no neighbors to form bonds with according to residue template for
    3711 G /2:395 
    3712 Atom OP1 has no neighbors to form bonds with according to residue template for
    3713 A /2:396 
    3714 Atom O2' has no neighbors to form bonds with according to residue template for
    3715 A /2:398 
    3716 Atom O3' has no neighbors to form bonds with according to residue template for
    3717 G /2:508 
    3718 Atom OP1 has no neighbors to form bonds with according to residue template for
    3719 C /2:542 
    3720 Atom C5' has no neighbors to form bonds with according to residue template for
    3721 U /2:592 
    3722 Atom N6 has no neighbors to form bonds with according to residue template for
    3723 A /2:593 
    3724 Atom O2' has no neighbors to form bonds with according to residue template for
    3725 U /2:1659 
    3726 Atom N4 has no neighbors to form bonds with according to residue template for
    3727 C /2:1684 
    3728 Atom C8 has no neighbors to form bonds with according to residue template for
    3729 G /2:1711 
    3730 Atom N3 has no neighbors to form bonds with according to residue template for
    3731 A /2:1720 
    3732 Atom N has no neighbors to form bonds with according to residue template for
    3733 GLN /C:155 
    3734 Atom O has no neighbors to form bonds with according to residue template for
    3735 GLN /C:155 
    3736 Atom CB has no neighbors to form bonds with according to residue template for
    3737 PRO /C:178 
    3738 Atom O has no neighbors to form bonds with according to residue template for
    3739 ALA /E:2 
    3740 Atom CB has no neighbors to form bonds with according to residue template for
    3741 ALA /E:2 
    3742 Atom N has no neighbors to form bonds with according to residue template for
    3743 TYR /E:121 
    3744 Atom O has no neighbors to form bonds with according to residue template for
    3745 TYR /E:121 
    3746 Atom N has no neighbors to form bonds with according to residue template for
    3747 PHE /G:145 
    3748 Atom CG1 has no neighbors to form bonds with according to residue template for
    3749 VAL /G:153 
    3750 Atom CG2 has no neighbors to form bonds with according to residue template for
    3751 VAL /G:153 
    3752 Atom NH1 has no neighbors to form bonds with according to residue template for
    3753 ARG /G:159 
    3754 Atom O has no neighbors to form bonds with according to residue template for
    3755 GLU /J:183 
    3756 Atom O has no neighbors to form bonds with according to residue template for
    3757 ARG /p:663 
    3758 Atom N has no neighbors to form bonds with according to residue template for
    3759 ALA /p:692 
    3760 Atom CB has no neighbors to form bonds with according to residue template for
    3761 ALA /p:692 
    3762  
    3763 Chain information for 0057_6gsm_Y.cif #1 
    3764 --- 
    3765 Chain | Description 
    3766 2 | 18S ribosomal RNA 
    3767 C | KLLA0F09812p 
    3768 E | 40S ribosomal protein S4 
    3769 G | 40S ribosomal protein S6 
    3770 J | KLLA0E23673p 
    3771 Y | 40S ribosomal protein S24 
    3772 o | Eukaryotic translation initiation factor 3 subunit A,Eukaryotic
    3773 translation initiation factor 3 subunit A,eIF3a 
    3774 p | Eukaryotic translation initiation factor 3 subunit B 
    3775  
    3776 
    3777 > open /scratch/cs-
    3778 > bioinfo/tngu/6k_data/Box_Chains_new/0057_6gsm/0057_6gsm_Y.mrc
    3779 
    3780 Opened 0057_6gsm_Y.mrc as #2, grid size 128,80,72, pixel 1, shown at level
    3781 0.142, step 1, values float32 
    3782 
    3783 > fitmap #1 inMap #2
    3784 
    3785 Fit molecule 0057_6gsm_Y.cif (#1) to map 0057_6gsm_Y.mrc (#2) using 12319
    3786 atoms 
    3787 average map value = 0.08353, steps = 48 
    3788 shifted from previous position = 0.466 
    3789 rotated from previous position = 0.137 degrees 
    3790 atoms outside contour = 11679, contour level = 0.14216 
    3791  
    3792 Position of 0057_6gsm_Y.cif (#1) relative to 0057_6gsm_Y.mrc (#2) coordinates: 
    3793 Matrix rotation and translation 
    3794 0.99999809 -0.00071326 -0.00182141 0.23329565 
    3795 0.00071574 0.99999882 0.00136215 -0.76507248 
    3796 0.00182043 -0.00136345 0.99999741 0.02693523 
    3797 Axis -0.57164385 -0.76380649 0.29970477 
    3798 Axis point 61.17022831 0.00000000 272.10136371 
    3799 Rotation angle (degrees) 0.13659378 
    3800 Shift along axis 0.45907793 
    3801  
    3802 
    3803 > save /scratch/cs-
    3804 > bioinfo/tngu/6k_data/Box_Chains_new/0057_6gsm/0057_6gsm_Y_fitted.cif #1
    3805 
    3806 > close #1
    3807 
    3808 > close #2
    3809 
    3810 > open /scratch/cs-
    3811 > bioinfo/tngu/6k_data/Box_Chains_new/0057_6gsm/0057_6gsm_F.cif
    3812 
    3813 Summary of feedback from opening /scratch/cs-
    3814 bioinfo/tngu/6k_data/Box_Chains_new/0057_6gsm/0057_6gsm_F.cif 
    3815 --- 
    3816 warnings | Invalid residue range for struct_conf "HELX27": invalid chain "H",
    3817 near line 47739 
    3818 Invalid residue range for struct_conf "HELX28": invalid chain "H", near line
    3819 47740 
    3820 Invalid residue range for struct_conf "HELX29": invalid chain "H", near line
    3821 47741 
    3822 Invalid residue range for struct_conf "HELX30": invalid chain "H", near line
    3823 47742 
    3824 Invalid residue range for struct_conf "HELX31": invalid chain "H", near line
    3825 47743 
    3826 112 messages similar to the above omitted 
    3827 Invalid sheet range for struct_sheet_range "? 32": invalid chain "H", near
    3828 line 47997 
    3829 Invalid sheet range for struct_sheet_range "? 33": invalid chain "H", near
    3830 line 47998 
    3831 Invalid sheet range for struct_sheet_range "? 34": invalid chain "H", near
    3832 line 47999 
    3833 Invalid sheet range for struct_sheet_range "? 35": invalid chain "H", near
    3834 line 48000 
    3835 Invalid sheet range for struct_sheet_range "? 36": invalid chain "H", near
    3836 line 48001 
    3837 139 messages similar to the above omitted 
    3838 Atom OP1 has no neighbors to form bonds with according to residue template for
    3839 G /1:22 
    3840 Atom OP2 has no neighbors to form bonds with according to residue template for
    3841 G /1:22 
    3842 Atom C5' has no neighbors to form bonds with according to residue template for
    3843 G /1:22 
    3844 Atom O3' has no neighbors to form bonds with according to residue template for
    3845 G /1:22 
    3846 Atom O3' has no neighbors to form bonds with according to residue template for
    3847 C /1:23 
    3848 Atom O3' has no neighbors to form bonds with according to residue template for
    3849 G /1:24 
    3850 Atom O4 has no neighbors to form bonds with according to residue template for
    3851 U /1:45 
    3852 Atom C5 has no neighbors to form bonds with according to residue template for
    3853 U /1:45 
    3854 Atom C8 has no neighbors to form bonds with according to residue template for
    3855 A /2:899 
    3856 Atom O2' has no neighbors to form bonds with according to residue template for
    3857 A /2:987 
    3858 Atom N3 has no neighbors to form bonds with according to residue template for
    3859 A /2:987 
    3860 Atom O2 has no neighbors to form bonds with according to residue template for
    3861 C /2:999 
    3862 Atom OP1 has no neighbors to form bonds with according to residue template for
    3863 G /2:1145 
    3864 Atom O2' has no neighbors to form bonds with according to residue template for
    3865 G /2:1145 
    3866 Atom OP2 has no neighbors to form bonds with according to residue template for
    3867 C /2:1273 
    3868 Atom OP2 has no neighbors to form bonds with according to residue template for
    3869 C /2:1278 
    3870 Atom OP2 has no neighbors to form bonds with according to residue template for
    3871 A /2:1347 
    3872 Atom O4' has no neighbors to form bonds with according to residue template for
    3873 C /2:1354 
    3874 Atom OP2 has no neighbors to form bonds with according to residue template for
    3875 U /2:1355 
    3876 Atom C2' has no neighbors to form bonds with according to residue template for
    3877 A /2:1371 
    3878 Atom C6 has no neighbors to form bonds with according to residue template for
    3879 U /2:1520 
    3880 Atom O3' has no neighbors to form bonds with according to residue template for
    3881 A /2:1598 
    3882 Atom O2' has no neighbors to form bonds with according to residue template for
    3883 A /2:1598 
    3884 Atom OP1 has no neighbors to form bonds with according to residue template for
    3885 U /2:1783 
    3886 Atom C5' has no neighbors to form bonds with according to residue template for
    3887 U /2:1783 
    3888 Atom OP2 has no neighbors to form bonds with according to residue template for
    3889 U /2:1796 
    3890 Atom N has no neighbors to form bonds with according to residue template for
    3891 TYR /A:81 
    3892 Atom CB has no neighbors to form bonds with according to residue template for
    3893 GLN /A:83 
    3894 Atom N has no neighbors to form bonds with according to residue template for
    3895 VAL /B:3 
    3896 Atom OG1 has no neighbors to form bonds with according to residue template for
    3897 THR /B:107 
    3898 Atom NZ has no neighbors to form bonds with according to residue template for
    3899 LYS /B:116 
    3900 Atom CG1 has no neighbors to form bonds with according to residue template for
    3901 VAL /D:126 
    3902 Atom CG2 has no neighbors to form bonds with according to residue template for
    3903 VAL /D:126 
    3904 Atom N has no neighbors to form bonds with according to residue template for
    3905 ILE /D:138 
    3906 Atom N has no neighbors to form bonds with according to residue template for
    3907 MET /D:150 
    3908 Atom N has no neighbors to form bonds with according to residue template for
    3909 ASP /D:154 
    3910 Atom CG1 has no neighbors to form bonds with according to residue template for
    3911 VAL /D:186 
    3912 Atom N has no neighbors to form bonds with according to residue template for
    3913 GLU /D:214 
    3914 Atom N has no neighbors to form bonds with according to residue template for
    3915 LYS /O:72 
    3916 Atom OD1 has no neighbors to form bonds with according to residue template for
    3917 ASP /O:124 
    3918 Atom N has no neighbors to form bonds with according to residue template for
    3919 LEU /S:18 
    3920 Atom O has no neighbors to form bonds with according to residue template for
    3921 LEU /S:18 
    3922 Atom O has no neighbors to form bonds with according to residue template for
    3923 LYS /T:38 
    3924 Atom CG has no neighbors to form bonds with according to residue template for
    3925 LYS /T:38 
    3926 Atom N has no neighbors to form bonds with according to residue template for
    3927 ASN /U:36 
    3928 Atom OD1 has no neighbors to form bonds with according to residue template for
    3929 ASN /U:36 
    3930 Atom ND2 has no neighbors to form bonds with according to residue template for
    3931 ASN /U:36 
    3932 Atom N has no neighbors to form bonds with according to residue template for
    3933 LYS /U:61 
    3934 Atom OG1 has no neighbors to form bonds with according to residue template for
    3935 THR /U:67 
    3936 Atom N has no neighbors to form bonds with according to residue template for
    3937 SER /a:57 
    3938 Atom OG has no neighbors to form bonds with according to residue template for
    3939 SER /a:57 
    3940 Atom N has no neighbors to form bonds with according to residue template for
    3941 SER /a:88 
    3942 Atom CB has no neighbors to form bonds with according to residue template for
    3943 SER /a:88 
    3944 Atom OD1 has no neighbors to form bonds with according to residue template for
    3945 ASN /d:48 
    3946 Atom ND2 has no neighbors to form bonds with according to residue template for
    3947 ASN /d:48 
    3948 Atom CG1 has no neighbors to form bonds with according to residue template for
    3949 VAL /g:35 
    3950 Atom CD2 has no neighbors to form bonds with according to residue template for
    3951 LEU /g:48 
    3952 Atom N has no neighbors to form bonds with according to residue template for
    3953 VAL /g:72 
    3954 Atom N has no neighbors to form bonds with according to residue template for
    3955 ALA /g:249 
    3956 Atom CB has no neighbors to form bonds with according to residue template for
    3957 ALA /g:249 
    3958 Atom N has no neighbors to form bonds with according to residue template for
    3959 LYS /g:268 
    3960 Atom N has no neighbors to form bonds with according to residue template for
    3961 LEU /g:299 
    3962 Atom CD2 has no neighbors to form bonds with according to residue template for
    3963 LEU /g:299 
    3964 Atom CB has no neighbors to form bonds with according to residue template for
    3965 TYR /j:9 
    3966 Atom OG has no neighbors to form bonds with according to residue template for
    3967 SER /j:91 
    3968 Atom N has no neighbors to form bonds with according to residue template for
    3969 LEU /j:123 
    3970 Atom C has no neighbors to form bonds with according to residue template for
    3971 LEU /j:123 
    3972 Atom NE1 has no neighbors to form bonds with according to residue template for
    3973 TRP /j:132 
    3974 Atom O has no neighbors to form bonds with according to residue template for
    3975 ILE /l:173 
    3976 Atom NH1 has no neighbors to form bonds with according to residue template for
    3977 ARG /m:36 
    3978  
    3979 Chain information for 0057_6gsm_F.cif #1 
    3980 --- 
    3981 Chain | Description 
    3982 1 | Met-tRNAi 
    3983 2 | 18S ribosomal RNA 
    3984 3 | mRNA (5'-R(P*AP*AP*U)-3') 
    3985 A | 40S ribosomal protein S0 
    3986 B | 40S ribosomal protein S1 
    3987 C | KLLA0F09812p 
    3988 D | KLLA0D08305p 
    3989 F | KLLA0D10659p 
    3990 O | 40S ribosomal protein S14 
    3991 Q | 40S ribosomal protein S16 
    3992 R | KLLA0B01474p 
    3993 S | KLLA0B01562p 
    3994 T | KLLA0A07194p 
    3995 U | KLLA0F25542p 
    3996 Z | KLLA0B06182p 
    3997 a | 40S ribosomal protein S26 
    3998 c | 40S ribosomal protein S28 
    3999 d | 40S ribosomal protein S29 
    4000 g | KLLA0E12277p 
    4001 i | Eukaryotic translation initiation factor 1A 
    4002 j | Eukaryotic translation initiation factor 2 subunit alpha 
    4003 l | Eukaryotic translation initiation factor 2 subunit beta 
    4004 m | Eukaryotic translation initiation factor eIF-1 
    4005  
    4006 
    4007 > open /scratch/cs-
    4008 > bioinfo/tngu/6k_data/Box_Chains_new/0057_6gsm/0057_6gsm_F.mrc
    4009 
    4010 Opened 0057_6gsm_F.mrc as #2, grid size 96,104,80, pixel 1, shown at level
    4011 0.132, step 1, values float32 
    4012 
    4013 > fitmap #1 inMap #2
    4014 
    4015 Fit molecule 0057_6gsm_F.cif (#1) to map 0057_6gsm_F.mrc (#2) using 16573
    4016 atoms 
    4017 average map value = 0.07465, steps = 48 
    4018 shifted from previous position = 0.482 
    4019 rotated from previous position = 0.311 degrees 
    4020 atoms outside contour = 15915, contour level = 0.13241 
    4021  
    4022 Position of 0057_6gsm_F.cif (#1) relative to 0057_6gsm_F.mrc (#2) coordinates: 
    4023 Matrix rotation and translation 
    4024 0.99999869 -0.00155151 -0.00047107 0.19682187 
    4025 0.00154904 0.99998536 -0.00518424 0.71416720 
    4026 0.00047911 0.00518351 0.99998645 -1.35461568 
    4027 Axis 0.95440247 -0.08746900 0.28542090 
    4028 Axis point -0.00000000 247.29302550 132.65108473 
    4029 Rotation angle (degrees) 0.31120585 
    4030 Shift along axis -0.26125584 
    4031  
    4032 
    4033 > save /scratch/cs-
    4034 > bioinfo/tngu/6k_data/Box_Chains_new/0057_6gsm/0057_6gsm_F_fitted.cif #1
    4035 
    4036 > close #1
    4037 
    4038 > close #2
    4039 
    4040 > open /scratch/cs-
    4041 > bioinfo/tngu/6k_data/Box_Chains_new/0057_6gsm/0057_6gsm_L.cif
    4042 
    4043 Summary of feedback from opening /scratch/cs-
    4044 bioinfo/tngu/6k_data/Box_Chains_new/0057_6gsm/0057_6gsm_L.cif 
    4045 --- 
    4046 warnings | Invalid residue range for struct_conf "HELX1": invalid chain "C",
    4047 near line 51957 
    4048 Invalid residue range for struct_conf "HELX2": invalid chain "C", near line
    4049 51958 
    4050 Invalid residue range for struct_conf "HELX3": invalid chain "C", near line
    4051 51959 
    4052 Invalid residue range for struct_conf "HELX4": invalid chain "C", near line
    4053 51960 
    4054 Invalid residue range for struct_conf "HELX5": invalid chain "C", near line
    4055 51961 
    4056 107 messages similar to the above omitted 
    4057 Invalid sheet range for struct_sheet_range "? 1": invalid chain "C", near line
    4058 52210 
    4059 Invalid sheet range for struct_sheet_range "? 2": invalid chain "C", near line
    4060 52211 
    4061 Invalid sheet range for struct_sheet_range "? 3": invalid chain "C", near line
    4062 52212 
    4063 Invalid sheet range for struct_sheet_range "? 4": invalid chain "C", near line
    4064 52213 
    4065 Invalid sheet range for struct_sheet_range "? 5": invalid chain "C", near line
    4066 52214 
    4067 152 messages similar to the above omitted 
    4068 Atom OP2 has no neighbors to form bonds with according to residue template for
    4069 G /2:20 
    4070 Atom O2' has no neighbors to form bonds with according to residue template for
    4071 U /2:24 
    4072 Atom O2 has no neighbors to form bonds with according to residue template for
    4073 U /2:24 
    4074 Atom OP1 has no neighbors to form bonds with according to residue template for
    4075 A /2:26 
    4076 Atom O2' has no neighbors to form bonds with according to residue template for
    4077 A /2:43 
    4078 Atom OP1 has no neighbors to form bonds with according to residue template for
    4079 A /2:47 
    4080 Atom C6 has no neighbors to form bonds with according to residue template for
    4081 C /2:90 
    4082 Atom OP1 has no neighbors to form bonds with according to residue template for
    4083 A /2:135 
    4084 Atom O3' has no neighbors to form bonds with according to residue template for
    4085 A /2:135 
    4086 Atom OP2 has no neighbors to form bonds with according to residue template for
    4087 A /2:196 
    4088 Atom N7 has no neighbors to form bonds with according to residue template for
    4089 A /2:196 
    4090 Atom N6 has no neighbors to form bonds with according to residue template for
    4091 A /2:196 
    4092 Atom O4' has no neighbors to form bonds with according to residue template for
    4093 C /2:229 
    4094 Atom O2 has no neighbors to form bonds with according to residue template for
    4095 C /2:229 
    4096 Atom O2' has no neighbors to form bonds with according to residue template for
    4097 G /2:273 
    4098 Atom N2 has no neighbors to form bonds with according to residue template for
    4099 G /2:273 
    4100 Atom OP1 has no neighbors to form bonds with according to residue template for
    4101 C /2:281 
    4102 Atom OP2 has no neighbors to form bonds with according to residue template for
    4103 G /2:286 
    4104 Atom C5' has no neighbors to form bonds with according to residue template for
    4105 G /2:286 
    4106 Atom N7 has no neighbors to form bonds with according to residue template for
    4107 G /2:286 
    4108 Atom O6 has no neighbors to form bonds with according to residue template for
    4109 G /2:286 
    4110 Atom OP1 has no neighbors to form bonds with according to residue template for
    4111 A /2:287 
    4112 Atom OP2 has no neighbors to form bonds with according to residue template for
    4113 A /2:287 
    4114 Atom OP2 has no neighbors to form bonds with according to residue template for
    4115 U /2:288 
    4116 Atom OP1 has no neighbors to form bonds with according to residue template for
    4117 G /2:387 
    4118 Atom C5' has no neighbors to form bonds with according to residue template for
    4119 C /2:571 
    4120 Atom O4' has no neighbors to form bonds with according to residue template for
    4121 C /2:571 
    4122 Atom O2' has no neighbors to form bonds with according to residue template for
    4123 A /2:619 
    4124 Atom OP1 has no neighbors to form bonds with according to residue template for
    4125 U /2:695 
    4126 Atom OP2 has no neighbors to form bonds with according to residue template for
    4127 U /2:695 
    4128 Atom O3' has no neighbors to form bonds with according to residue template for
    4129 U /2:695 
    4130 Atom OP1 has no neighbors to form bonds with according to residue template for
    4131 G /2:729 
    4132 Atom O3' has no neighbors to form bonds with according to residue template for
    4133 G /2:729 
    4134 Atom O3' has no neighbors to form bonds with according to residue template for
    4135 C /2:731 
    4136 Atom O3' has no neighbors to form bonds with according to residue template for
    4137 G /2:786 
    4138 Atom O2' has no neighbors to form bonds with according to residue template for
    4139 C /2:949 
    4140 Atom OP1 has no neighbors to form bonds with according to residue template for
    4141 A /2:1019 
    4142 Atom O3' has no neighbors to form bonds with according to residue template for
    4143 A /2:1019 
    4144 Atom O3' has no neighbors to form bonds with according to residue template for
    4145 U /2:1048 
    4146 Atom O2' has no neighbors to form bonds with according to residue template for
    4147 U /2:1048 
    4148 Atom OP2 has no neighbors to form bonds with according to residue template for
    4149 G /2:1109 
    4150 Atom O6 has no neighbors to form bonds with according to residue template for
    4151 G /2:1109 
    4152 Atom N2 has no neighbors to form bonds with according to residue template for
    4153 G /2:1125 
    4154 Atom O2' has no neighbors to form bonds with according to residue template for
    4155 G /2:1647 
    4156 Atom O2' has no neighbors to form bonds with according to residue template for
    4157 G /2:1678 
    4158 Atom OP2 has no neighbors to form bonds with according to residue template for
    4159 U /2:1706 
    4160 Atom C5' has no neighbors to form bonds with according to residue template for
    4161 U /2:1706 
    4162 Atom N6 has no neighbors to form bonds with according to residue template for
    4163 A /2:1720 
    4164 Atom C5' has no neighbors to form bonds with according to residue template for
    4165 A /2:1744 
    4166 Atom O4' has no neighbors to form bonds with according to residue template for
    4167 A /2:1744 
    4168 Atom OG1 has no neighbors to form bonds with according to residue template for
    4169 THR /C:163 
    4170 Atom O has no neighbors to form bonds with according to residue template for
    4171 PRO /C:178 
    4172 Atom N has no neighbors to form bonds with according to residue template for
    4173 LEU /C:192 
    4174 Atom CB has no neighbors to form bonds with according to residue template for
    4175 LEU /C:192 
    4176 Atom N has no neighbors to form bonds with according to residue template for
    4177 ARG /C:210 
    4178 Atom CG has no neighbors to form bonds with according to residue template for
    4179 ARG /C:210 
    4180 Atom OG1 has no neighbors to form bonds with according to residue template for
    4181 THR /E:81 
    4182 Atom N has no neighbors to form bonds with according to residue template for
    4183 GLU /E:250 
    4184 Atom C has no neighbors to form bonds with according to residue template for
    4185 GLU /E:250 
    4186 Atom CB has no neighbors to form bonds with according to residue template for
    4187 GLU /E:250 
    4188 Atom O has no neighbors to form bonds with according to residue template for
    4189 ARG /G:88 
    4190 Atom O has no neighbors to form bonds with according to residue template for
    4191 ARG /G:183 
    4192 Atom NH2 has no neighbors to form bonds with according to residue template for
    4193 ARG /G:183 
    4194 Atom CD2 has no neighbors to form bonds with according to residue template for
    4195 LEU /G:184 
    4196 Atom C has no neighbors to form bonds with according to residue template for
    4197 ARG /H:96 
    4198 Atom CB has no neighbors to form bonds with according to residue template for
    4199 ARG /H:96 
    4200 Atom NH2 has no neighbors to form bonds with according to residue template for
    4201 ARG /H:96 
    4202 Atom N has no neighbors to form bonds with according to residue template for
    4203 VAL /H:121 
    4204 Atom CG2 has no neighbors to form bonds with according to residue template for
    4205 VAL /H:121 
    4206 Atom CG has no neighbors to form bonds with according to residue template for
    4207 LYS /I:138 
    4208 Atom O has no neighbors to form bonds with according to residue template for
    4209 LYS /J:16 
    4210 Atom NH1 has no neighbors to form bonds with according to residue template for
    4211 ARG /N:104 
    4212 Atom N has no neighbors to form bonds with according to residue template for
    4213 ASN /N:105 
    4214 Atom O has no neighbors to form bonds with according to residue template for
    4215 ASN /N:105 
    4216 Atom CD1 has no neighbors to form bonds with according to residue template for
    4217 ILE /W:14 
    4218 Atom CD1 has no neighbors to form bonds with according to residue template for
    4219 LEU /W:26 
    4220 Atom C has no neighbors to form bonds with according to residue template for
    4221 LYS /W:71 
    4222 Atom O has no neighbors to form bonds with according to residue template for
    4223 ASN /X:79 
    4224 Atom O has no neighbors to form bonds with according to residue template for
    4225 ALA /X:113 
    4226 Atom N has no neighbors to form bonds with according to residue template for
    4227 LYS /b:72 
    4228 Atom O has no neighbors to form bonds with according to residue template for
    4229 LYS /b:72 
    4230 Atom N has no neighbors to form bonds with according to residue template for
    4231 ARG /h:23 
    4232 Atom O has no neighbors to form bonds with according to residue template for
    4233 UNK /o:734 
    4234 Atom C has no neighbors to form bonds with according to residue template for
    4235 ASP /p:360 
    4236 Atom CA has no neighbors to form bonds with according to residue template for
    4237 ASP /p:397 
    4238 Atom N has no neighbors to form bonds with according to residue template for
    4239 ARG /p:677 
    4240 Atom CB has no neighbors to form bonds with according to residue template for
    4241 ARG /p:677 
    4242 Atom N has no neighbors to form bonds with according to residue template for
    4243 LYS /q:113 
    4244  
    4245 Chain information for 0057_6gsm_L.cif #1 
    4246 --- 
    4247 Chain | Description 
    4248 2 | 18S ribosomal RNA 
    4249 C | KLLA0F09812p 
    4250 E | 40S ribosomal protein S4 
    4251 G | 40S ribosomal protein S6 
    4252 H | 40S ribosomal protein S7 
    4253 I | 40S ribosomal protein S8 
    4254 J | KLLA0E23673p 
    4255 L | KLLA0A10483p 
    4256 N | KLLA0F18040p 
    4257 W | 40S ribosomal protein S22 
    4258 X | KLLA0B11231p 
    4259 b | 40S ribosomal protein S27 
    4260 h | 60S ribosomal protein L41-A 
    4261 o | Eukaryotic translation initiation factor 3 subunit A,Eukaryotic
    4262 translation initiation factor 3 subunit A,eIF3a 
    4263 p | Eukaryotic translation initiation factor 3 subunit B 
    4264 q | Eukaryotic translation initiation factor 3 subunit C 
    4265  
    4266 
    4267 > open /scratch/cs-
    4268 > bioinfo/tngu/6k_data/Box_Chains_new/0057_6gsm/0057_6gsm_L.mrc
    4269 
    4270 Opened 0057_6gsm_L.mrc as #2, grid size 88,112,104, pixel 1, shown at level
    4271 0.147, step 1, values float32 
    4272 
    4273 > fitmap #1 inMap #2
    4274 
    4275 Fit molecule 0057_6gsm_L.cif (#1) to map 0057_6gsm_L.mrc (#2) using 20625
    4276 atoms 
    4277 average map value = 0.0855, steps = 64 
    4278 shifted from previous position = 0.562 
    4279 rotated from previous position = 0.106 degrees 
    4280 atoms outside contour = 19726, contour level = 0.14692 
    4281  
    4282 Position of 0057_6gsm_L.cif (#1) relative to 0057_6gsm_L.mrc (#2) coordinates: 
    4283 Matrix rotation and translation 
    4284 0.99999903 0.00135370 -0.00033389 -0.56069105 
    4285 -0.00135329 0.99999833 0.00122632 -0.32874382 
    4286 0.00033555 -0.00122587 0.99999919 -0.08200758 
    4287 Axis -0.66036488 -0.18027934 -0.72898394 
    4288 Axis point -177.95394095 175.36755179 0.00000000 
    4289 Rotation angle (degrees) 0.10638074 
    4290 Shift along axis 0.48930860 
    4291  
    4292 
    4293 > save /scratch/cs-
    4294 > bioinfo/tngu/6k_data/Box_Chains_new/0057_6gsm/0057_6gsm_L_fitted.cif #1
    4295 
    4296 > close #1
    4297 
    4298 > close #2
    4299 
    4300 > open /scratch/cs-
    4301 > bioinfo/tngu/6k_data/Box_Chains_new/0057_6gsm/0057_6gsm_3.cif
    4302 
    4303 Summary of feedback from opening /scratch/cs-
    4304 bioinfo/tngu/6k_data/Box_Chains_new/0057_6gsm/0057_6gsm_3.cif 
    4305 --- 
    4306 warnings | Invalid residue range for struct_conf "HELX1": invalid chain "C",
    4307 near line 35563 
    4308 Invalid residue range for struct_conf "HELX2": invalid chain "C", near line
    4309 35564 
    4310 Invalid residue range for struct_conf "HELX3": invalid chain "C", near line
    4311 35565 
    4312 Invalid residue range for struct_conf "HELX4": invalid chain "C", near line
    4313 35566 
    4314 Invalid residue range for struct_conf "HELX5": invalid chain "C", near line
    4315 35567 
    4316 172 messages similar to the above omitted 
    4317 Invalid sheet range for struct_sheet_range "? 1": invalid chain "C", near line
    4318 35816 
    4319 Invalid sheet range for struct_sheet_range "? 2": invalid chain "C", near line
    4320 35817 
    4321 Invalid sheet range for struct_sheet_range "? 3": invalid chain "C", near line
    4322 35818 
    4323 Invalid sheet range for struct_sheet_range "? 4": invalid chain "C", near line
    4324 35819 
    4325 Invalid sheet range for struct_sheet_range "? 5": invalid chain "C", near line
    4326 35820 
    4327 187 messages similar to the above omitted 
    4328 Atom O5' has no neighbors to form bonds with according to residue template for
    4329 C /1:11 
    4330 Atom N6 has no neighbors to form bonds with according to residue template for
    4331 A /1:28 
    4332 Atom O4' has no neighbors to form bonds with according to residue template for
    4333 A /2:11 
    4334 Atom OP2 has no neighbors to form bonds with according to residue template for
    4335 U /2:12 
    4336 Atom O3' has no neighbors to form bonds with according to residue template for
    4337 A /2:579 
    4338 Atom C2' has no neighbors to form bonds with according to residue template for
    4339 U /2:580 
    4340 Atom O3' has no neighbors to form bonds with according to residue template for
    4341 A /2:906 
    4342 Atom O3' has no neighbors to form bonds with according to residue template for
    4343 A /2:991 
    4344 Atom C8 has no neighbors to form bonds with according to residue template for
    4345 G /2:993 
    4346 Atom OP1 has no neighbors to form bonds with according to residue template for
    4347 A /2:1029 
    4348 Atom O2' has no neighbors to form bonds with according to residue template for
    4349 A /2:1087 
    4350 Atom OP1 has no neighbors to form bonds with according to residue template for
    4351 A /2:1137 
    4352 Atom O5' has no neighbors to form bonds with according to residue template for
    4353 A /2:1137 
    4354 Atom O3' has no neighbors to form bonds with according to residue template for
    4355 A /2:1137 
    4356 Atom O6 has no neighbors to form bonds with according to residue template for
    4357 G /2:1152 
    4358 Atom N6 has no neighbors to form bonds with according to residue template for
    4359 A /2:1156 
    4360 Atom N1 has no neighbors to form bonds with according to residue template for
    4361 A /2:1156 
    4362 Atom N3 has no neighbors to form bonds with according to residue template for
    4363 A /2:1159 
    4364 Atom C2' has no neighbors to form bonds with according to residue template for
    4365 G /2:1187 
    4366 Atom C5' has no neighbors to form bonds with according to residue template for
    4367 C /2:1196 
    4368 Atom OP1 has no neighbors to form bonds with according to residue template for
    4369 G /2:1272 
    4370 Atom O3' has no neighbors to form bonds with according to residue template for
    4371 A /2:1274 
    4372 Atom OP1 has no neighbors to form bonds with according to residue template for
    4373 C /2:1424 
    4374 Atom OP1 has no neighbors to form bonds with according to residue template for
    4375 G /2:1462 
    4376 Atom C6 has no neighbors to form bonds with according to residue template for
    4377 U /2:1577 
    4378 Atom O4' has no neighbors to form bonds with according to residue template for
    4379 C /2:1578 
    4380 Atom OP1 has no neighbors to form bonds with according to residue template for
    4381 C /2:1749 
    4382 Atom OP2 has no neighbors to form bonds with according to residue template for
    4383 C /2:1749 
    4384 Atom OP2 has no neighbors to form bonds with according to residue template for
    4385 A /2:1751 
    4386 Atom O3' has no neighbors to form bonds with according to residue template for
    4387 A /2:1751 
    4388 Atom OP2 has no neighbors to form bonds with according to residue template for
    4389 U /2:1773 
    4390 Atom OP2 has no neighbors to form bonds with according to residue template for
    4391 G /2:1784 
    4392 Atom O6 has no neighbors to form bonds with according to residue template for
    4393 G /2:1784 
    4394 Atom O2' has no neighbors to form bonds with according to residue template for
    4395 A /2:1788 
    4396 Atom OP1 has no neighbors to form bonds with according to residue template for
    4397 C /2:1794 
    4398 Atom OP2 has no neighbors to form bonds with according to residue template for
    4399 C /2:1794 
    4400 Atom N has no neighbors to form bonds with according to residue template for
    4401 ILE /X:68 
    4402 Atom C has no neighbors to form bonds with according to residue template for
    4403 THR /c:19 
    4404 Atom CG2 has no neighbors to form bonds with according to residue template for
    4405 THR /c:19 
    4406 Atom N has no neighbors to form bonds with according to residue template for
    4407 GLY /c:23 
    4408 Atom O has no neighbors to form bonds with according to residue template for
    4409 GLY /c:23 
    4410 Atom CG1 has no neighbors to form bonds with according to residue template for
    4411 VAL /c:25 
    4412 Atom CG2 has no neighbors to form bonds with according to residue template for
    4413 VAL /c:25 
    4414 Atom N has no neighbors to form bonds with according to residue template for
    4415 LEU /h:13 
    4416 Atom O has no neighbors to form bonds with according to residue template for
    4417 ASN /i:55 
    4418 Atom N has no neighbors to form bonds with according to residue template for
    4419 LEU /i:78 
    4420 Atom N has no neighbors to form bonds with according to residue template for
    4421 VAL /j:90 
    4422 Atom N has no neighbors to form bonds with according to residue template for
    4423 ILE /l:180 
    4424 Atom N has no neighbors to form bonds with according to residue template for
    4425 THR /m:41 
    4426 Atom OG1 has no neighbors to form bonds with according to residue template for
    4427 THR /m:41 
    4428 Atom CG2 has no neighbors to form bonds with according to residue template for
    4429 THR /m:41 
    4430 Atom N has no neighbors to form bonds with according to residue template for
    4431 ASP /m:61 
    4432 Atom C has no neighbors to form bonds with according to residue template for
    4433 ASP /m:61 
    4434  
    4435 Chain information for 0057_6gsm_3.cif #1 
    4436 --- 
    4437 Chain | Description 
    4438 1 | Met-tRNAi 
    4439 2 | 18S ribosomal RNA 
    4440 3 | mRNA (5'-R(P*AP*AP*U)-3') 
    4441 C | KLLA0F09812p 
    4442 D | KLLA0D08305p 
    4443 F | KLLA0D10659p 
    4444 O | 40S ribosomal protein S14 
    4445 Q | 40S ribosomal protein S16 
    4446 U | KLLA0F25542p 
    4447 X | KLLA0B11231p 
    4448 a | 40S ribosomal protein S26 
    4449 c | 40S ribosomal protein S28 
    4450 h | 60S ribosomal protein L41-A 
    4451 i | Eukaryotic translation initiation factor 1A 
    4452 j | Eukaryotic translation initiation factor 2 subunit alpha 
    4453 l | Eukaryotic translation initiation factor 2 subunit beta 
    4454 m | Eukaryotic translation initiation factor eIF-1 
    4455  
    4456 
    4457 > open /scratch/cs-
    4458 > bioinfo/tngu/6k_data/Box_Chains_new/0057_6gsm/0057_6gsm_3.mrc
    4459 
    4460 Opened 0057_6gsm_3.mrc as #2, grid size 48,56,56, pixel 1, shown at level
    4461 0.147, step 1, values float32 
    4462 
    4463 > fitmap #1 inMap #2
    4464 
    4465 Fit molecule 0057_6gsm_3.cif (#1) to map 0057_6gsm_3.mrc (#2) using 4594 atoms 
    4466 average map value = 0.0782, steps = 56 
    4467 shifted from previous position = 0.482 
    4468 rotated from previous position = 0.264 degrees 
    4469 atoms outside contour = 4481, contour level = 0.14686 
    4470  
    4471 Position of 0057_6gsm_3.cif (#1) relative to 0057_6gsm_3.mrc (#2) coordinates: 
    4472 Matrix rotation and translation 
    4473 0.99999048 0.00086917 -0.00427518 0.27803584 
    4474 -0.00087555 0.99999851 -0.00149093 0.24639436 
    4475 0.00427388 0.00149466 0.99998975 -1.25590328 
    4476 Axis 0.32374789 -0.92703488 -0.18919205 
    4477 Axis point 289.60036558 0.00000000 56.87772451 
    4478 Rotation angle (degrees) 0.26419021 
    4479 Shift along axis 0.09920427 
    4480  
    4481 
    4482 > save /scratch/cs-
    4483 > bioinfo/tngu/6k_data/Box_Chains_new/0057_6gsm/0057_6gsm_3_fitted.cif #1
    4484 
    4485 > close #1
    4486 
    4487 > close #2
    4488 
    4489 > open /scratch/cs-
    4490 > bioinfo/tngu/6k_data/Box_Chains_new/0057_6gsm/0057_6gsm_J.cif
    4491 
    4492 Summary of feedback from opening /scratch/cs-
    4493 bioinfo/tngu/6k_data/Box_Chains_new/0057_6gsm/0057_6gsm_J.cif 
    4494 --- 
    4495 warnings | Invalid residue range for struct_conf "HELX7": invalid chain "E",
    4496 near line 51987 
    4497 Invalid residue range for struct_conf "HELX8": invalid chain "E", near line
    4498 51988 
    4499 Invalid residue range for struct_conf "HELX9": invalid chain "E", near line
    4500 51989 
    4501 Invalid residue range for struct_conf "HELX10": invalid chain "E", near line
    4502 51990 
    4503 Invalid residue range for struct_conf "HELX11": invalid chain "E", near line
    4504 51991 
    4505 147 messages similar to the above omitted 
    4506 Invalid sheet range for struct_sheet_range "? 8": invalid chain "E", near line
    4507 52241 
    4508 Invalid sheet range for struct_sheet_range "? 9": invalid chain "E", near line
    4509 52242 
    4510 Invalid sheet range for struct_sheet_range "? 10": invalid chain "E", near
    4511 line 52243 
    4512 Invalid sheet range for struct_sheet_range "? 11": invalid chain "E", near
    4513 line 52244 
    4514 Invalid sheet range for struct_sheet_range "? 12": invalid chain "E", near
    4515 line 52245 
    4516 130 messages similar to the above omitted 
    4517 Atom OP1 has no neighbors to form bonds with according to residue template for
    4518 A /2:11 
    4519 Atom OP2 has no neighbors to form bonds with according to residue template for
    4520 C /2:49 
    4521 Atom OP2 has no neighbors to form bonds with according to residue template for
    4522 U /2:295 
    4523 Atom O5' has no neighbors to form bonds with according to residue template for
    4524 U /2:295 
    4525 Atom OP2 has no neighbors to form bonds with according to residue template for
    4526 A /2:322 
    4527 Atom N7 has no neighbors to form bonds with according to residue template for
    4528 G /2:325 
    4529 Atom C4' has no neighbors to form bonds with according to residue template for
    4530 A /2:327 
    4531 Atom OP1 has no neighbors to form bonds with according to residue template for
    4532 G /2:328 
    4533 Atom OP2 has no neighbors to form bonds with according to residue template for
    4534 G /2:328 
    4535 Atom O4' has no neighbors to form bonds with according to residue template for
    4536 C /2:430 
    4537 Atom OP2 has no neighbors to form bonds with according to residue template for
    4538 G /2:431 
    4539 Atom OP2 has no neighbors to form bonds with according to residue template for
    4540 C /2:432 
    4541 Atom OP2 has no neighbors to form bonds with according to residue template for
    4542 C /2:565 
    4543 Atom O2' has no neighbors to form bonds with according to residue template for
    4544 A /2:629 
    4545 Atom O4 has no neighbors to form bonds with according to residue template for
    4546 U /2:666 
    4547 Atom OP1 has no neighbors to form bonds with according to residue template for
    4548 A /2:707 
    4549 Atom O3' has no neighbors to form bonds with according to residue template for
    4550 G /2:722 
    4551 Atom O2' has no neighbors to form bonds with according to residue template for
    4552 G /2:722 
    4553 Atom OP1 has no neighbors to form bonds with according to residue template for
    4554 U /2:745 
    4555 Atom O4' has no neighbors to form bonds with according to residue template for
    4556 A /2:805 
    4557 Atom O2' has no neighbors to form bonds with according to residue template for
    4558 A /2:978 
    4559 Atom N3 has no neighbors to form bonds with according to residue template for
    4560 A /2:978 
    4561 Atom C4' has no neighbors to form bonds with according to residue template for
    4562 G /2:979 
    4563 Atom O3' has no neighbors to form bonds with according to residue template for
    4564 G /2:979 
    4565 Atom O2' has no neighbors to form bonds with according to residue template for
    4566 G /2:979 
    4567 Atom O3' has no neighbors to form bonds with according to residue template for
    4568 C /2:1021 
    4569 Atom O2' has no neighbors to form bonds with according to residue template for
    4570 C /2:1021 
    4571 Atom OP2 has no neighbors to form bonds with according to residue template for
    4572 C /2:1032 
    4573 Atom C5' has no neighbors to form bonds with according to residue template for
    4574 A /2:1038 
    4575 Atom O4' has no neighbors to form bonds with according to residue template for
    4576 A /2:1038 
    4577 Atom OP2 has no neighbors to form bonds with according to residue template for
    4578 U /2:1088 
    4579 Atom O2' has no neighbors to form bonds with according to residue template for
    4580 A /2:1142 
    4581 Atom C5' has no neighbors to form bonds with according to residue template for
    4582 G /2:1294 
    4583 Atom O3' has no neighbors to form bonds with according to residue template for
    4584 G /2:1294 
    4585 Atom O4' has no neighbors to form bonds with according to residue template for
    4586 A /2:1299 
    4587 Atom OP1 has no neighbors to form bonds with according to residue template for
    4588 A /2:1738 
    4589 Atom O3' has no neighbors to form bonds with according to residue template for
    4590 A /2:1747 
    4591 Atom O2' has no neighbors to form bonds with according to residue template for
    4592 A /2:1747 
    4593 Atom C2 has no neighbors to form bonds with according to residue template for
    4594 A /2:1747 
    4595 Atom OP1 has no neighbors to form bonds with according to residue template for
    4596 A /2:1753 
    4597 Atom N6 has no neighbors to form bonds with according to residue template for
    4598 A /2:1753 
    4599 Atom O3' has no neighbors to form bonds with according to residue template for
    4600 C /2:1770 
    4601 Atom O2' has no neighbors to form bonds with according to residue template for
    4602 C /2:1770 
    4603 Atom O3' has no neighbors to form bonds with according to residue template for
    4604 A /2:1788 
    4605 Atom O2' has no neighbors to form bonds with according to residue template for
    4606 A /2:1788 
    4607 Atom O4' has no neighbors to form bonds with according to residue template for
    4608 G /2:1790 
    4609 Atom CD1 has no neighbors to form bonds with according to residue template for
    4610 LEU /A:59 
    4611 Atom OG1 has no neighbors to form bonds with according to residue template for
    4612 THR /A:108 
    4613 Atom CG2 has no neighbors to form bonds with according to residue template for
    4614 THR /A:108 
    4615 Atom O has no neighbors to form bonds with according to residue template for
    4616 LEU /A:177 
    4617 Atom NH1 has no neighbors to form bonds with according to residue template for
    4618 ARG /C:48 
    4619 Atom N has no neighbors to form bonds with according to residue template for
    4620 VAL /C:91 
    4621 Atom CD1 has no neighbors to form bonds with according to residue template for
    4622 PHE /C:103 
    4623 Atom OG1 has no neighbors to form bonds with according to residue template for
    4624 THR /C:122 
    4625 Atom N has no neighbors to form bonds with according to residue template for
    4626 GLY /C:128 
    4627 Atom OD1 has no neighbors to form bonds with according to residue template for
    4628 ASP /C:250 
    4629 Atom N has no neighbors to form bonds with according to residue template for
    4630 PRO /E:35 
    4631 Atom C has no neighbors to form bonds with according to residue template for
    4632 ASP /E:79 
    4633 Atom O has no neighbors to form bonds with according to residue template for
    4634 HIS /E:142 
    4635 Atom C has no neighbors to form bonds with according to residue template for
    4636 LEU /E:238 
    4637 Atom CA has no neighbors to form bonds with according to residue template for
    4638 GLY /H:145 
    4639 Atom O has no neighbors to form bonds with according to residue template for
    4640 GLY /H:145 
    4641 Atom N has no neighbors to form bonds with according to residue template for
    4642 THR /L:72 
    4643 Atom O has no neighbors to form bonds with according to residue template for
    4644 THR /L:72 
    4645 Atom C has no neighbors to form bonds with according to residue template for
    4646 ARG /L:87 
    4647 Atom OE2 has no neighbors to form bonds with according to residue template for
    4648 GLU /V:64 
    4649 Atom O has no neighbors to form bonds with according to residue template for
    4650 LEU /V:69 
    4651 Atom O has no neighbors to form bonds with according to residue template for
    4652 LYS /Y:52 
    4653 Atom N has no neighbors to form bonds with according to residue template for
    4654 VAL /Y:75 
    4655 Atom CG2 has no neighbors to form bonds with according to residue template for
    4656 VAL /Y:75 
    4657 Atom CE2 has no neighbors to form bonds with according to residue template for
    4658 TYR /Y:76 
    4659 Atom OH has no neighbors to form bonds with according to residue template for
    4660 TYR /Y:76 
    4661 Atom CD1 has no neighbors to form bonds with according to residue template for
    4662 LEU /Y:96 
    4663 Atom N has no neighbors to form bonds with according to residue template for
    4664 TRP /h:5 
    4665 Atom CD has no neighbors to form bonds with according to residue template for
    4666 ARG /i:57 
    4667 Atom NH1 has no neighbors to form bonds with according to residue template for
    4668 ARG /i:57 
    4669  
    4670 Chain information for 0057_6gsm_J.cif #1 
    4671 --- 
    4672 Chain | Description 
    4673 2 | 18S ribosomal RNA 
    4674 A | 40S ribosomal protein S0 
    4675 C | KLLA0F09812p 
    4676 E | 40S ribosomal protein S4 
    4677 H | 40S ribosomal protein S7 
    4678 I | 40S ribosomal protein S8 
    4679 J | KLLA0E23673p 
    4680 L | KLLA0A10483p 
    4681 V | 40S ribosomal protein S21 
    4682 W | 40S ribosomal protein S22 
    4683 X | KLLA0B11231p 
    4684 Y | 40S ribosomal protein S24 
    4685 a | 40S ribosomal protein S26 
    4686 e | 40S ribosomal protein S30 
    4687 h | 60S ribosomal protein L41-A 
    4688 i | Eukaryotic translation initiation factor 1A 
    4689  
    4690 
    4691 > open /scratch/cs-
    4692 > bioinfo/tngu/6k_data/Box_Chains_new/0057_6gsm/0057_6gsm_J.mrc
    4693 
    4694 Opened 0057_6gsm_J.mrc as #2, grid size 96,88,128, pixel 1, shown at level
    4695 0.146, step 1, values float32 
    4696 
    4697 > fitmap #1 inMap #2
    4698 
    4699 Fit molecule 0057_6gsm_J.cif (#1) to map 0057_6gsm_J.mrc (#2) using 20634
    4700 atoms 
    4701 average map value = 0.08539, steps = 48 
    4702 shifted from previous position = 0.283 
    4703 rotated from previous position = 0.0807 degrees 
    4704 atoms outside contour = 19712, contour level = 0.14584 
    4705  
    4706 Position of 0057_6gsm_J.cif (#1) relative to 0057_6gsm_J.mrc (#2) coordinates: 
    4707 Matrix rotation and translation 
    4708 0.99999926 0.00084597 0.00087723 -0.52834288 
    4709 -0.00084659 0.99999939 0.00070453 -0.19287997 
    4710 -0.00087663 -0.00070527 0.99999937 0.28359637 
    4711 Axis -0.50068506 0.62287955 -0.60111192 
    4712 Axis point 305.17755694 0.00000000 617.43129214 
    4713 Rotation angle (degrees) 0.08066466 
    4714 Shift along axis -0.02608076 
    4715  
    4716 
    4717 > save /scratch/cs-
    4718 > bioinfo/tngu/6k_data/Box_Chains_new/0057_6gsm/0057_6gsm_J_fitted.cif #1
    4719 
    4720 > close #1
    4721 
    4722 > close #2
    4723 
    4724 > open /scratch/cs-
    4725 > bioinfo/tngu/6k_data/Box_Chains_new/0057_6gsm/0057_6gsm_b.cif
    4726 
    4727 Summary of feedback from opening /scratch/cs-
    4728 bioinfo/tngu/6k_data/Box_Chains_new/0057_6gsm/0057_6gsm_b.cif 
    4729 --- 
    4730 warnings | Invalid residue range for struct_conf "HELX21": invalid chain "G",
    4731 near line 44712 
    4732 Invalid residue range for struct_conf "HELX22": invalid chain "G", near line
    4733 44713 
    4734 Invalid residue range for struct_conf "HELX23": invalid chain "G", near line
    4735 44714 
    4736 Invalid residue range for struct_conf "HELX24": invalid chain "G", near line
    4737 44715 
    4738 Invalid residue range for struct_conf "HELX25": invalid chain "G", near line
    4739 44716 
    4740 111 messages similar to the above omitted 
    4741 Invalid sheet range for struct_sheet_range "? 25": invalid chain "G", near
    4742 line 44969 
    4743 Invalid sheet range for struct_sheet_range "? 26": invalid chain "G", near
    4744 line 44970 
    4745 Invalid sheet range for struct_sheet_range "? 27": invalid chain "G", near
    4746 line 44971 
    4747 Invalid sheet range for struct_sheet_range "? 28": invalid chain "G", near
    4748 line 44972 
    4749 Invalid sheet range for struct_sheet_range "? 29": invalid chain "G", near
    4750 line 44973 
    4751 189 messages similar to the above omitted 
    4752 Atom OP1 has no neighbors to form bonds with according to residue template for
    4753 G /2:306 
    4754 Atom O2' has no neighbors to form bonds with according to residue template for
    4755 G /2:306 
    4756 Atom OP1 has no neighbors to form bonds with according to residue template for
    4757 C /2:308 
    4758 Atom OP2 has no neighbors to form bonds with according to residue template for
    4759 C /2:308 
    4760 Atom OP1 has no neighbors to form bonds with according to residue template for
    4761 U /2:348 
    4762 Atom O3' has no neighbors to form bonds with according to residue template for
    4763 U /2:348 
    4764 Atom O2 has no neighbors to form bonds with according to residue template for
    4765 U /2:349 
    4766 Atom O4 has no neighbors to form bonds with according to residue template for
    4767 U /2:637 
    4768 Atom O2' has no neighbors to form bonds with according to residue template for
    4769 U /2:639 
    4770 Atom O2' has no neighbors to form bonds with according to residue template for
    4771 U /2:794 
    4772 Atom O2 has no neighbors to form bonds with according to residue template for
    4773 U /2:794 
    4774 Atom OP2 has no neighbors to form bonds with according to residue template for
    4775 U /2:1023 
    4776 Atom C5 has no neighbors to form bonds with according to residue template for
    4777 U /2:1023 
    4778 Atom OP2 has no neighbors to form bonds with according to residue template for
    4779 G /2:1113 
    4780 Atom O3' has no neighbors to form bonds with according to residue template for
    4781 U /2:1302 
    4782 Atom O2' has no neighbors to form bonds with according to residue template for
    4783 U /2:1302 
    4784 Atom OP1 has no neighbors to form bonds with according to residue template for
    4785 U /2:1626 
    4786 Atom C5' has no neighbors to form bonds with according to residue template for
    4787 U /2:1626 
    4788 Atom O3' has no neighbors to form bonds with according to residue template for
    4789 U /2:1626 
    4790 Atom O4' has no neighbors to form bonds with according to residue template for
    4791 G /2:1772 
    4792 Atom OP2 has no neighbors to form bonds with according to residue template for
    4793 G /2:1786 
    4794 Atom N has no neighbors to form bonds with according to residue template for
    4795 THR /A:10 
    4796 Atom NZ has no neighbors to form bonds with according to residue template for
    4797 LYS /A:88 
    4798 Atom ND1 has no neighbors to form bonds with according to residue template for
    4799 HIS /A:92 
    4800 Atom N has no neighbors to form bonds with according to residue template for
    4801 GLY /A:100 
    4802 Atom NH2 has no neighbors to form bonds with according to residue template for
    4803 ARG /A:179 
    4804 Atom OE1 has no neighbors to form bonds with according to residue template for
    4805 GLU /B:122 
    4806 Atom CE has no neighbors to form bonds with according to residue template for
    4807 LYS /B:145 
    4808 Atom N has no neighbors to form bonds with according to residue template for
    4809 LEU /B:172 
    4810 Atom C has no neighbors to form bonds with according to residue template for
    4811 LEU /B:172 
    4812 Atom CB has no neighbors to form bonds with according to residue template for
    4813 LEU /B:172 
    4814 Atom CD1 has no neighbors to form bonds with according to residue template for
    4815 LEU /B:172 
    4816 Atom CE has no neighbors to form bonds with according to residue template for
    4817 MET /C:245 
    4818 Atom OD1 has no neighbors to form bonds with according to residue template for
    4819 ASP /H:87 
    4820 Atom OD2 has no neighbors to form bonds with according to residue template for
    4821 ASP /H:87 
    4822 Atom O has no neighbors to form bonds with according to residue template for
    4823 ARG /H:114 
    4824 Atom O has no neighbors to form bonds with according to residue template for
    4825 HIS /L:104 
    4826 Atom NH1 has no neighbors to form bonds with according to residue template for
    4827 ARG /N:99 
    4828 Atom NH2 has no neighbors to form bonds with according to residue template for
    4829 ARG /N:99 
    4830 Atom CB has no neighbors to form bonds with according to residue template for
    4831 LYS /N:100 
    4832 Atom CE has no neighbors to form bonds with according to residue template for
    4833 LYS /N:100 
    4834 Atom CG has no neighbors to form bonds with according to residue template for
    4835 LYS /N:140 
    4836 Atom N has no neighbors to form bonds with according to residue template for
    4837 ARG /O:133 
    4838 Atom N has no neighbors to form bonds with according to residue template for
    4839 SER /R:96 
    4840 Atom OG has no neighbors to form bonds with according to residue template for
    4841 SER /R:96 
    4842 Atom C has no neighbors to form bonds with according to residue template for
    4843 VAL /V:13 
    4844 Atom N has no neighbors to form bonds with according to residue template for
    4845 VAL /V:39 
    4846 Atom OD1 has no neighbors to form bonds with according to residue template for
    4847 ASP /q:393 
    4848 Atom CG2 has no neighbors to form bonds with according to residue template for
    4849 ILE /q:448 
    4850 Atom NE1 has no neighbors to form bonds with according to residue template for
    4851 TRP /q:456 
    4852 Atom CZ2 has no neighbors to form bonds with according to residue template for
    4853 TRP /q:456 
    4854 Atom OD1 has no neighbors to form bonds with according to residue template for
    4855 ASP /q:484 
    4856 Atom CA has no neighbors to form bonds with according to residue template for
    4857 GLN /q:517 
    4858 Atom CB has no neighbors to form bonds with according to residue template for
    4859 ARG /q:654 
    4860  
    4861 Chain information for 0057_6gsm_b.cif #1 
    4862 --- 
    4863 Chain | Description 
    4864 2 | 18S ribosomal RNA 
    4865 A | 40S ribosomal protein S0 
    4866 B | 40S ribosomal protein S1 
    4867 C | KLLA0F09812p 
    4868 H | 40S ribosomal protein S7 
    4869 L | KLLA0A10483p 
    4870 N | KLLA0F18040p 
    4871 O | 40S ribosomal protein S14 
    4872 R | KLLA0B01474p 
    4873 V | 40S ribosomal protein S21 
    4874 W | 40S ribosomal protein S22 
    4875 X | KLLA0B11231p 
    4876 a | 40S ribosomal protein S26 
    4877 b | 40S ribosomal protein S27 
    4878 h | 60S ribosomal protein L41-A 
    4879 o | Eukaryotic translation initiation factor 3 subunit A,Eukaryotic
    4880 translation initiation factor 3 subunit A,eIF3a 
    4881 q | Eukaryotic translation initiation factor 3 subunit C 
    4882  
    4883 
    4884 > open /scratch/cs-
    4885 > bioinfo/tngu/6k_data/Box_Chains_new/0057_6gsm/0057_6gsm_b.mrc
    4886 
    4887 Opened 0057_6gsm_b.mrc as #2, grid size 80,64,104, pixel 1, shown at level
    4888 0.145, step 1, values float32 
    4889 
    4890 > fitmap #1 inMap #2
    4891 
    4892 Fit molecule 0057_6gsm_b.cif (#1) to map 0057_6gsm_b.mrc (#2) using 13648
    4893 atoms 
    4894 average map value = 0.06975, steps = 120 
    4895 shifted from previous position = 0.477 
    4896 rotated from previous position = 0.155 degrees 
    4897 atoms outside contour = 13183, contour level = 0.1446 
    4898  
    4899 Position of 0057_6gsm_b.cif (#1) relative to 0057_6gsm_b.mrc (#2) coordinates: 
    4900 Matrix rotation and translation 
    4901 0.99999867 0.00068419 -0.00147724 0.10063725 
    4902 -0.00068737 0.99999744 -0.00215405 0.39911254 
    4903 0.00147576 0.00215506 0.99999659 -1.14122012 
    4904 Axis 0.79784835 -0.54676044 -0.25395084 
    4905 Axis point 0.00000000 512.00866074 223.23098321 
    4906 Rotation angle (degrees) 0.15472488 
    4907 Shift along axis 0.15188813 
    4908  
    4909 
    4910 > save /scratch/cs-
    4911 > bioinfo/tngu/6k_data/Box_Chains_new/0057_6gsm/0057_6gsm_b_fitted.cif #1
    4912 
    4913 > close #1
    4914 
    4915 > close #2
    4916 
    4917 > open /scratch/cs-
    4918 > bioinfo/tngu/6k_data/Box_Chains_new/0057_6gsm/0057_6gsm_c.cif
    4919 
    4920 Summary of feedback from opening /scratch/cs-
    4921 bioinfo/tngu/6k_data/Box_Chains_new/0057_6gsm/0057_6gsm_c.cif 
    4922 --- 
    4923 warnings | Invalid residue range for struct_conf "HELX27": invalid chain "H",
    4924 near line 40502 
    4925 Invalid residue range for struct_conf "HELX28": invalid chain "H", near line
    4926 40503 
    4927 Invalid residue range for struct_conf "HELX29": invalid chain "H", near line
    4928 40504 
    4929 Invalid residue range for struct_conf "HELX30": invalid chain "H", near line
    4930 40505 
    4931 Invalid residue range for struct_conf "HELX31": invalid chain "H", near line
    4932 40506 
    4933 134 messages similar to the above omitted 
    4934 Invalid sheet range for struct_sheet_range "? 32": invalid chain "H", near
    4935 line 40760 
    4936 Invalid sheet range for struct_sheet_range "? 33": invalid chain "H", near
    4937 line 40761 
    4938 Invalid sheet range for struct_sheet_range "? 34": invalid chain "H", near
    4939 line 40762 
    4940 Invalid sheet range for struct_sheet_range "? 35": invalid chain "H", near
    4941 line 40763 
    4942 Invalid sheet range for struct_sheet_range "? 36": invalid chain "H", near
    4943 line 40764 
    4944 163 messages similar to the above omitted 
    4945 Atom N4 has no neighbors to form bonds with according to residue template for
    4946 C /1:34 
    4947 Atom C5 has no neighbors to form bonds with according to residue template for
    4948 C /1:34 
    4949 Atom O2' has no neighbors to form bonds with according to residue template for
    4950 C /2:882 
    4951 Atom C5 has no neighbors to form bonds with according to residue template for
    4952 U /2:887 
    4953 Atom OP1 has no neighbors to form bonds with according to residue template for
    4954 G /2:900 
    4955 Atom OP2 has no neighbors to form bonds with according to residue template for
    4956 G /2:900 
    4957 Atom O4' has no neighbors to form bonds with according to residue template for
    4958 A /2:905 
    4959 Atom O2' has no neighbors to form bonds with according to residue template for
    4960 U /2:927 
    4961 Atom C5' has no neighbors to form bonds with according to residue template for
    4962 G /2:1166 
    4963 Atom O4' has no neighbors to form bonds with according to residue template for
    4964 G /2:1166 
    4965 Atom OP1 has no neighbors to form bonds with according to residue template for
    4966 U /2:1284 
    4967 Atom O3' has no neighbors to form bonds with according to residue template for
    4968 A /2:1320 
    4969 Atom O4' has no neighbors to form bonds with according to residue template for
    4970 A /2:1325 
    4971 Atom C8 has no neighbors to form bonds with according to residue template for
    4972 A /2:1330 
    4973 Atom O4' has no neighbors to form bonds with according to residue template for
    4974 C /2:1338 
    4975 Atom O3' has no neighbors to form bonds with according to residue template for
    4976 G /2:1532 
    4977 Atom O2' has no neighbors to form bonds with according to residue template for
    4978 G /2:1532 
    4979 Atom C1' has no neighbors to form bonds with according to residue template for
    4980 G /2:1532 
    4981 Atom OP2 has no neighbors to form bonds with according to residue template for
    4982 C /2:1578 
    4983 Atom OP1 has no neighbors to form bonds with according to residue template for
    4984 U /2:1607 
    4985 Atom OP2 has no neighbors to form bonds with according to residue template for
    4986 U /2:1607 
    4987 Atom O5' has no neighbors to form bonds with according to residue template for
    4988 U /2:1607 
    4989 Atom C4' has no neighbors to form bonds with according to residue template for
    4990 A /2:1631 
    4991 Atom O4' has no neighbors to form bonds with according to residue template for
    4992 U /2:1769 
    4993 Atom O3' has no neighbors to form bonds with according to residue template for
    4994 C /2:1782 
    4995 Atom O3' has no neighbors to form bonds with according to residue template for
    4996 G /2:1791 
    4997 Atom O2' has no neighbors to form bonds with according to residue template for
    4998 G /2:1791 
    4999 Atom O has no neighbors to form bonds with according to residue template for
    5000 ILE /A:111 
    5001 Atom CG2 has no neighbors to form bonds with according to residue template for
    5002 ILE /A:111 
    5003 Atom CD2 has no neighbors to form bonds with according to residue template for
    5004 HIS /A:168 
    5005 Atom O has no neighbors to form bonds with according to residue template for
    5006 TYR /A:204 
    5007 Atom O4 has no neighbors to form bonds with according to residue template for
    5008 U /3:30 
    5009 Atom OG1 has no neighbors to form bonds with according to residue template for
    5010 THR /B:46 
    5011 Atom N has no neighbors to form bonds with according to residue template for
    5012 VAL /B:84 
    5013 Atom O has no neighbors to form bonds with according to residue template for
    5014 VAL /B:84 
    5015 Atom SD has no neighbors to form bonds with according to residue template for
    5016 MET /B:103 
    5017 Atom OE1 has no neighbors to form bonds with according to residue template for
    5018 GLN /B:149 
    5019 Atom CA has no neighbors to form bonds with according to residue template for
    5020 VAL /B:150 
    5021 Atom O has no neighbors to form bonds with according to residue template for
    5022 VAL /B:150 
    5023 Atom CG1 has no neighbors to form bonds with according to residue template for
    5024 VAL /F:25 
    5025 Atom CG2 has no neighbors to form bonds with according to residue template for
    5026 VAL /F:25 
    5027 Atom O has no neighbors to form bonds with according to residue template for
    5028 GLU /F:34 
    5029 Atom CD has no neighbors to form bonds with according to residue template for
    5030 ARG /F:104 
    5031 Atom NH1 has no neighbors to form bonds with according to residue template for
    5032 ARG /F:104 
    5033 Atom N has no neighbors to form bonds with according to residue template for
    5034 ASP /F:128 
    5035 Atom C has no neighbors to form bonds with according to residue template for
    5036 ASP /F:128 
    5037 Atom N has no neighbors to form bonds with according to residue template for
    5038 MET /O:46 
    5039 Atom N has no neighbors to form bonds with according to residue template for
    5040 LYS /Q:14 
    5041 Atom CG has no neighbors to form bonds with according to residue template for
    5042 LYS /Q:14 
    5043 Atom CE has no neighbors to form bonds with according to residue template for
    5044 LYS /Q:14 
    5045 Atom C has no neighbors to form bonds with according to residue template for
    5046 ALA /Q:20 
    5047 Atom CB has no neighbors to form bonds with according to residue template for
    5048 ALA /Q:20 
    5049 Atom N has no neighbors to form bonds with according to residue template for
    5050 GLN /Q:40 
    5051 Atom N has no neighbors to form bonds with according to residue template for
    5052 GLN /Q:77 
    5053 Atom N has no neighbors to form bonds with according to residue template for
    5054 LEU /Q:89 
    5055 Atom CD1 has no neighbors to form bonds with according to residue template for
    5056 LEU /Q:105 
    5057 Atom OE1 has no neighbors to form bonds with according to residue template for
    5058 GLU /R:18 
    5059 Atom OE2 has no neighbors to form bonds with according to residue template for
    5060 GLU /R:18 
    5061 Atom OG1 has no neighbors to form bonds with according to residue template for
    5062 THR /R:54 
    5063 Atom OG1 has no neighbors to form bonds with according to residue template for
    5064 THR /R:55 
    5065 Atom CG1 has no neighbors to form bonds with according to residue template for
    5066 ILE /R:61 
    5067 Atom O has no neighbors to form bonds with according to residue template for
    5068 LYS /a:32 
    5069 Atom CG has no neighbors to form bonds with according to residue template for
    5070 LYS /a:32 
    5071 Atom CG has no neighbors to form bonds with according to residue template for
    5072 LYS /a:34 
    5073 Atom N has no neighbors to form bonds with according to residue template for
    5074 ASP /j:18 
    5075 Atom O has no neighbors to form bonds with according to residue template for
    5076 ASP /j:18 
    5077 Atom ND2 has no neighbors to form bonds with according to residue template for
    5078 ASN /j:23 
    5079 Atom CD1 has no neighbors to form bonds with according to residue template for
    5080 ILE /j:63 
    5081 Atom NH1 has no neighbors to form bonds with according to residue template for
    5082 ARG /j:64 
    5083 Atom N has no neighbors to form bonds with according to residue template for
    5084 VAL /o:48 
    5085 Atom NZ has no neighbors to form bonds with according to residue template for
    5086 LYS /o:76 
    5087  
    5088 Chain information for 0057_6gsm_c.cif #1 
    5089 --- 
    5090 Chain | Description 
    5091 1 | Met-tRNAi 
    5092 2 | 18S ribosomal RNA 
    5093 3 | mRNA (5'-R(P*AP*AP*U)-3') 
    5094 A | 40S ribosomal protein S0 
    5095 B | 40S ribosomal protein S1 
    5096 C | KLLA0F09812p 
    5097 D | KLLA0D08305p 
    5098 F | KLLA0D10659p 
    5099 O | 40S ribosomal protein S14 
    5100 Q | 40S ribosomal protein S16 
    5101 R | KLLA0B01474p 
    5102 Z | KLLA0B06182p 
    5103 a | 40S ribosomal protein S26 
    5104 c | 40S ribosomal protein S28 
    5105 g | KLLA0E12277p 
    5106 j | Eukaryotic translation initiation factor 2 subunit alpha 
    5107 o | Eukaryotic translation initiation factor 3 subunit A,Eukaryotic
    5108 translation initiation factor 3 subunit A,eIF3a 
    5109  
    5110 
    5111 > open /scratch/cs-
    5112 > bioinfo/tngu/6k_data/Box_Chains_new/0057_6gsm/0057_6gsm_c.mrc
    5113 
    5114 Opened 0057_6gsm_c.mrc as #2, grid size 72,80,72, pixel 1, shown at level
    5115 0.137, step 1, values float32 
    5116 
    5117 > fitmap #1 inMap #2
    5118 
    5119 Fit molecule 0057_6gsm_c.cif (#1) to map 0057_6gsm_c.mrc (#2) using 9480 atoms 
    5120 average map value = 0.07507, steps = 48 
    5121 shifted from previous position = 0.58 
    5122 rotated from previous position = 0.323 degrees 
    5123 atoms outside contour = 9159, contour level = 0.13696 
    5124  
    5125 Position of 0057_6gsm_c.cif (#1) relative to 0057_6gsm_c.mrc (#2) coordinates: 
    5126 Matrix rotation and translation 
    5127 0.99999841 -0.00143913 0.00105503 -0.05309246 
    5128 0.00144474 0.99998470 -0.00534025 0.88891144 
    5129 -0.00104733 0.00534177 0.99998518 -1.26219123 
    5130 Axis 0.94846552 0.18667082 0.25606087 
    5131 Axis point 0.00000000 226.81472737 173.06242894 
    5132 Rotation angle (degrees) 0.32264642 
    5133 Shift along axis -0.20762033 
    5134  
    5135 
    5136 > save /scratch/cs-
    5137 > bioinfo/tngu/6k_data/Box_Chains_new/0057_6gsm/0057_6gsm_c_fitted.cif #1
    5138 
    5139 > close #1
    5140 
    5141 > close #2
    5142 
    5143 > open /scratch/cs-
    5144 > bioinfo/tngu/6k_data/Box_Chains_new/0057_6gsm/0057_6gsm_i.cif
    5145 
    5146 Summary of feedback from opening /scratch/cs-
    5147 bioinfo/tngu/6k_data/Box_Chains_new/0057_6gsm/0057_6gsm_i.cif 
    5148 --- 
    5149 warnings | Invalid residue range for struct_conf "HELX1": invalid chain "C",
    5150 near line 41478 
    5151 Invalid residue range for struct_conf "HELX2": invalid chain "C", near line
    5152 41479 
    5153 Invalid residue range for struct_conf "HELX3": invalid chain "C", near line
    5154 41480 
    5155 Invalid residue range for struct_conf "HELX4": invalid chain "C", near line
    5156 41481 
    5157 Invalid residue range for struct_conf "HELX5": invalid chain "C", near line
    5158 41482 
    5159 130 messages similar to the above omitted 
    5160 Invalid sheet range for struct_sheet_range "? 1": invalid chain "C", near line
    5161 41731 
    5162 Invalid sheet range for struct_sheet_range "? 2": invalid chain "C", near line
    5163 41732 
    5164 Invalid sheet range for struct_sheet_range "? 3": invalid chain "C", near line
    5165 41733 
    5166 Invalid sheet range for struct_sheet_range "? 4": invalid chain "C", near line
    5167 41734 
    5168 Invalid sheet range for struct_sheet_range "? 5": invalid chain "C", near line
    5169 41735 
    5170 155 messages similar to the above omitted 
    5171 Atom O2 has no neighbors to form bonds with according to residue template for
    5172 C /1:11 
    5173 Atom OP1 has no neighbors to form bonds with according to residue template for
    5174 G /1:12 
    5175 Atom O3' has no neighbors to form bonds with according to residue template for
    5176 G /1:12 
    5177 Atom N2 has no neighbors to form bonds with according to residue template for
    5178 G /1:24 
    5179 Atom N3 has no neighbors to form bonds with according to residue template for
    5180 G /1:24 
    5181 Atom OP2 has no neighbors to form bonds with according to residue template for
    5182 G /1:29 
    5183 Atom O2 has no neighbors to form bonds with according to residue template for
    5184 C /1:69 
    5185 Atom O4' has no neighbors to form bonds with according to residue template for
    5186 U /1:72 
    5187 Atom OP2 has no neighbors to form bonds with according to residue template for
    5188 C /2:4 
    5189 Atom OP2 has no neighbors to form bonds with according to residue template for
    5190 C /2:13 
    5191 Atom N6 has no neighbors to form bonds with according to residue template for
    5192 A /2:540 
    5193 Atom O3' has no neighbors to form bonds with according to residue template for
    5194 A /2:544 
    5195 Atom O2' has no neighbors to form bonds with according to residue template for
    5196 A /2:544 
    5197 Atom OP2 has no neighbors to form bonds with according to residue template for
    5198 A /2:555 
    5199 Atom OP2 has no neighbors to form bonds with according to residue template for
    5200 G /2:556 
    5201 Atom OP2 has no neighbors to form bonds with according to residue template for
    5202 U /2:557 
    5203 Atom OP2 has no neighbors to form bonds with according to residue template for
    5204 C /2:588 
    5205 Atom O5' has no neighbors to form bonds with according to residue template for
    5206 C /2:588 
    5207 Atom OP2 has no neighbors to form bonds with according to residue template for
    5208 U /2:601 
    5209 Atom N7 has no neighbors to form bonds with according to residue template for
    5210 G /2:609 
    5211 Atom O6 has no neighbors to form bonds with according to residue template for
    5212 G /2:609 
    5213 Atom C8 has no neighbors to form bonds with according to residue template for
    5214 G /2:612 
    5215 Atom O4' has no neighbors to form bonds with according to residue template for
    5216 A /2:1085 
    5217 Atom O2' has no neighbors to form bonds with according to residue template for
    5218 A /2:1085 
    5219 Atom O2' has no neighbors to form bonds with according to residue template for
    5220 U /2:1114 
    5221 Atom O2' has no neighbors to form bonds with according to residue template for
    5222 A /2:1142 
    5223 Atom OP1 has no neighbors to form bonds with according to residue template for
    5224 G /2:1149 
    5225 Atom OP2 has no neighbors to form bonds with according to residue template for
    5226 G /2:1149 
    5227 Atom OP2 has no neighbors to form bonds with according to residue template for
    5228 C /2:1158 
    5229 Atom O3' has no neighbors to form bonds with according to residue template for
    5230 G /2:1175 
    5231 Atom O2' has no neighbors to form bonds with according to residue template for
    5232 G /2:1175 
    5233 Atom O2 has no neighbors to form bonds with according to residue template for
    5234 C /2:1176 
    5235 Atom O2 has no neighbors to form bonds with according to residue template for
    5236 U /2:1184 
    5237 Atom C5' has no neighbors to form bonds with according to residue template for
    5238 G /2:1199 
    5239 Atom OP2 has no neighbors to form bonds with according to residue template for
    5240 U /2:1213 
    5241 Atom O2' has no neighbors to form bonds with according to residue template for
    5242 C /2:1214 
    5243 Atom O3' has no neighbors to form bonds with according to residue template for
    5244 C /2:1215 
    5245 Atom N3 has no neighbors to form bonds with according to residue template for
    5246 A /2:1216 
    5247 Atom O4' has no neighbors to form bonds with according to residue template for
    5248 G /2:1264 
    5249 Atom O3' has no neighbors to form bonds with according to residue template for
    5250 G /2:1280 
    5251 Atom O5' has no neighbors to form bonds with according to residue template for
    5252 U /2:1281 
    5253 Atom O2 has no neighbors to form bonds with according to residue template for
    5254 U /2:1281 
    5255 Atom O2 has no neighbors to form bonds with according to residue template for
    5256 U /2:1282 
    5257 Atom N3 has no neighbors to form bonds with according to residue template for
    5258 A /2:1423 
    5259 Atom O4 has no neighbors to form bonds with according to residue template for
    5260 U /2:1435 
    5261 Atom OP2 has no neighbors to form bonds with according to residue template for
    5262 G /2:1436 
    5263 Atom O2' has no neighbors to form bonds with according to residue template for
    5264 G /2:1462 
    5265 Atom OP1 has no neighbors to form bonds with according to residue template for
    5266 A /2:1575 
    5267 Atom O5' has no neighbors to form bonds with according to residue template for
    5268 A /2:1575 
    5269 Atom O2' has no neighbors to form bonds with according to residue template for
    5270 A /2:1575 
    5271 Atom O4' has no neighbors to form bonds with according to residue template for
    5272 C /2:1622 
    5273 Atom OP2 has no neighbors to form bonds with according to residue template for
    5274 C /2:1623 
    5275 Atom O6 has no neighbors to form bonds with according to residue template for
    5276 G /2:1627 
    5277 Atom N1 has no neighbors to form bonds with according to residue template for
    5278 G /2:1627 
    5279 Atom N2 has no neighbors to form bonds with according to residue template for
    5280 G /2:1627 
    5281 Atom OP1 has no neighbors to form bonds with according to residue template for
    5282 U /2:1740 
    5283 Atom OP2 has no neighbors to form bonds with according to residue template for
    5284 U /2:1740 
    5285 Atom C5' has no neighbors to form bonds with according to residue template for
    5286 U /2:1740 
    5287 Atom N3 has no neighbors to form bonds with according to residue template for
    5288 A /2:1780 
    5289 Atom N has no neighbors to form bonds with according to residue template for
    5290 ALA /C:97 
    5291 Atom NH1 has no neighbors to form bonds with according to residue template for
    5292 ARG /J:23 
    5293 Atom NH2 has no neighbors to form bonds with according to residue template for
    5294 ARG /J:23 
    5295 Atom N has no neighbors to form bonds with according to residue template for
    5296 LYS /U:77 
    5297 Atom CD has no neighbors to form bonds with according to residue template for
    5298 LYS /X:39 
    5299 Atom N has no neighbors to form bonds with according to residue template for
    5300 LYS /X:78 
    5301 Atom C has no neighbors to form bonds with according to residue template for
    5302 LYS /X:78 
    5303 Atom N has no neighbors to form bonds with according to residue template for
    5304 LYS /f:90 
    5305 Atom O has no neighbors to form bonds with according to residue template for
    5306 LYS /f:90 
    5307 Atom O has no neighbors to form bonds with according to residue template for
    5308 ILE /l:141 
    5309 Atom CG2 has no neighbors to form bonds with according to residue template for
    5310 ILE /l:141 
    5311 Atom CD has no neighbors to form bonds with according to residue template for
    5312 ARG /l:253 
    5313 Atom CD1 has no neighbors to form bonds with according to residue template for
    5314 ILE /m:54 
    5315 Atom CA has no neighbors to form bonds with according to residue template for
    5316 LEU /m:55 
    5317 Atom O has no neighbors to form bonds with according to residue template for
    5318 LEU /m:55 
    5319 Atom N has no neighbors to form bonds with according to residue template for
    5320 ASN /m:67 
    5321 Atom O has no neighbors to form bonds with according to residue template for
    5322 ASN /m:67 
    5323 Atom N has no neighbors to form bonds with according to residue template for
    5324 TRP /p:315 
    5325 Atom N has no neighbors to form bonds with according to residue template for
    5326 GLY /p:320 
    5327 Atom CG1 has no neighbors to form bonds with according to residue template for
    5328 VAL /p:480 
    5329 Atom CG2 has no neighbors to form bonds with according to residue template for
    5330 VAL /p:480 
    5331  
    5332 Chain information for 0057_6gsm_i.cif #1 
    5333 --- 
    5334 Chain | Description 
    5335 1 | Met-tRNAi 
    5336 2 | 18S ribosomal RNA 
    5337 3 | mRNA (5'-R(P*AP*AP*U)-3') 
    5338 C | KLLA0F09812p 
    5339 D | KLLA0D08305p 
    5340 J | KLLA0E23673p 
    5341 Q | 40S ribosomal protein S16 
    5342 U | KLLA0F25542p 
    5343 X | KLLA0B11231p 
    5344 d | 40S ribosomal protein S29 
    5345 e | 40S ribosomal protein S30 
    5346 f | Ubiquitin-40S ribosomal protein S27a 
    5347 h | 60S ribosomal protein L41-A 
    5348 i | Eukaryotic translation initiation factor 1A 
    5349 j | Eukaryotic translation initiation factor 2 subunit alpha 
    5350 k | Eukaryotic translation initiation factor 2 subunit gamma 
    5351 l | Eukaryotic translation initiation factor 2 subunit beta 
    5352 m | Eukaryotic translation initiation factor eIF-1 
    5353 o | Eukaryotic translation initiation factor 3 subunit A,Eukaryotic
    5354 translation initiation factor 3 subunit A,eIF3a 
    5355 p | Eukaryotic translation initiation factor 3 subunit B 
    5356  
    5357 
    5358 > open /scratch/cs-
    5359 > bioinfo/tngu/6k_data/Box_Chains_new/0057_6gsm/0057_6gsm_i.mrc
    5360 
    5361 Opened 0057_6gsm_i.mrc as #2, grid size 80,80,72, pixel 1, shown at level
    5362 0.139, step 1, values float32 
    5363 
    5364 > fitmap #1 inMap #2
    5365 
    5366 Fit molecule 0057_6gsm_i.cif (#1) to map 0057_6gsm_i.mrc (#2) using 10393
    5367 atoms 
    5368 average map value = 0.07196, steps = 56 
    5369 shifted from previous position = 0.474 
    5370 rotated from previous position = 0.143 degrees 
    5371 atoms outside contour = 9995, contour level = 0.13898 
    5372  
    5373 Position of 0057_6gsm_i.cif (#1) relative to 0057_6gsm_i.mrc (#2) coordinates: 
    5374 Matrix rotation and translation 
    5375 0.99999692 0.00018283 0.00247368 -0.90601607 
    5376 -0.00018207 0.99999994 -0.00030762 -0.12008924 
    5377 -0.00247373 0.00030717 0.99999689 0.50653629 
    5378 Axis 0.12298613 0.98972007 -0.07299718 
    5379 Axis point 196.43577144 0.00000000 353.21954976 
    5380 Rotation angle (degrees) 0.14320519 
    5381 Shift along axis -0.26725786 
    5382  
    5383 
    5384 > save /scratch/cs-
    5385 > bioinfo/tngu/6k_data/Box_Chains_new/0057_6gsm/0057_6gsm_i_fitted.cif #1
    5386 
    5387 > close #1
    5388 
    5389 > close #2
    5390 
    5391 > open /scratch/cs-
    5392 > bioinfo/tngu/6k_data/Box_Chains_new/0057_6gsm/0057_6gsm_X.cif
    5393 
    5394 Summary of feedback from opening /scratch/cs-
    5395 bioinfo/tngu/6k_data/Box_Chains_new/0057_6gsm/0057_6gsm_X.cif 
    5396 --- 
    5397 warnings | Invalid residue range for struct_conf "HELX32": invalid chain "I",
    5398 near line 55763 
    5399 Invalid residue range for struct_conf "HELX33": invalid chain "I", near line
    5400 55764 
    5401 Invalid residue range for struct_conf "HELX34": invalid chain "I", near line
    5402 55765 
    5403 Invalid residue range for struct_conf "HELX35": invalid chain "I", near line
    5404 55766 
    5405 Invalid residue range for struct_conf "HELX36": invalid chain "I", near line
    5406 55767 
    5407 58 messages similar to the above omitted 
    5408 Invalid sheet range for struct_sheet_range "? 47": invalid chain "I", near
    5409 line 56031 
    5410 Invalid sheet range for struct_sheet_range "? 48": invalid chain "I", near
    5411 line 56032 
    5412 Invalid sheet range for struct_sheet_range "? 79": invalid chain "P", near
    5413 line 56063 
    5414 Invalid sheet range for struct_sheet_range "? 80": invalid chain "P", near
    5415 line 56064 
    5416 Invalid sheet range for struct_sheet_range "? 86": invalid chain "S", near
    5417 line 56070 
    5418 104 messages similar to the above omitted 
    5419 Atom N7 has no neighbors to form bonds with according to residue template for
    5420 G /2:325 
    5421 Atom O6 has no neighbors to form bonds with according to residue template for
    5422 G /2:325 
    5423 Atom O3' has no neighbors to form bonds with according to residue template for
    5424 C /2:338 
    5425 Atom N4 has no neighbors to form bonds with according to residue template for
    5426 C /2:341 
    5427 Atom C5 has no neighbors to form bonds with according to residue template for
    5428 C /2:341 
    5429 Atom O4' has no neighbors to form bonds with according to residue template for
    5430 G /2:391 
    5431 Atom OP1 has no neighbors to form bonds with according to residue template for
    5432 A /2:415 
    5433 Atom O3' has no neighbors to form bonds with according to residue template for
    5434 A /2:459 
    5435 Atom OP2 has no neighbors to form bonds with according to residue template for
    5436 G /2:479 
    5437 Atom O2' has no neighbors to form bonds with according to residue template for
    5438 U /2:481 
    5439 Atom N6 has no neighbors to form bonds with according to residue template for
    5440 A /2:525 
    5441 Atom O2' has no neighbors to form bonds with according to residue template for
    5442 G /2:809 
    5443 Atom O2' has no neighbors to form bonds with according to residue template for
    5444 U /2:888 
    5445 Atom O3' has no neighbors to form bonds with according to residue template for
    5446 A /2:925 
    5447 Atom O2' has no neighbors to form bonds with according to residue template for
    5448 C /2:926 
    5449 Atom O2' has no neighbors to form bonds with according to residue template for
    5450 A /2:928 
    5451 Atom OP1 has no neighbors to form bonds with according to residue template for
    5452 C /2:930 
    5453 Atom OP2 has no neighbors to form bonds with according to residue template for
    5454 C /2:930 
    5455 Atom OP2 has no neighbors to form bonds with according to residue template for
    5456 C /2:936 
    5457 Atom OP2 has no neighbors to form bonds with according to residue template for
    5458 G /2:937 
    5459 Atom OP2 has no neighbors to form bonds with according to residue template for
    5460 A /2:943 
    5461 Atom N7 has no neighbors to form bonds with according to residue template for
    5462 A /2:943 
    5463 Atom C6 has no neighbors to form bonds with according to residue template for
    5464 U /2:964 
    5465 Atom O3' has no neighbors to form bonds with according to residue template for
    5466 G /2:1001 
    5467 Atom O2' has no neighbors to form bonds with according to residue template for
    5468 G /2:1001 
    5469 Atom OP1 has no neighbors to form bonds with according to residue template for
    5470 A /2:1002 
    5471 Atom O2' has no neighbors to form bonds with according to residue template for
    5472 A /2:1002 
    5473 Atom OP2 has no neighbors to form bonds with according to residue template for
    5474 U /2:1016 
    5475 Atom O2' has no neighbors to form bonds with according to residue template for
    5476 U /2:1043 
    5477 Atom O3' has no neighbors to form bonds with according to residue template for
    5478 C /2:1071 
    5479 Atom OP1 has no neighbors to form bonds with according to residue template for
    5480 A /2:1150 
    5481 Atom O6 has no neighbors to form bonds with according to residue template for
    5482 G /2:1290 
    5483 Atom O2' has no neighbors to form bonds with according to residue template for
    5484 A /2:1318 
    5485 Atom OP1 has no neighbors to form bonds with according to residue template for
    5486 U /2:1421 
    5487 Atom O3' has no neighbors to form bonds with according to residue template for
    5488 U /2:1435 
    5489 Atom O2' has no neighbors to form bonds with according to residue template for
    5490 U /2:1435 
    5491 Atom OP1 has no neighbors to form bonds with according to residue template for
    5492 C /2:1623 
    5493 Atom C5' has no neighbors to form bonds with according to residue template for
    5494 C /2:1623 
    5495 Atom O3' has no neighbors to form bonds with according to residue template for
    5496 C /2:1623 
    5497 Atom O2 has no neighbors to form bonds with according to residue template for
    5498 C /2:1635 
    5499 Atom OP2 has no neighbors to form bonds with according to residue template for
    5500 U /2:1667 
    5501 Atom OP1 has no neighbors to form bonds with according to residue template for
    5502 A /3:29 
    5503 Atom O has no neighbors to form bonds with according to residue template for
    5504 LEU /C:159 
    5505 Atom N has no neighbors to form bonds with according to residue template for
    5506 LEU /C:195 
    5507 Atom O has no neighbors to form bonds with according to residue template for
    5508 VAL /C:198 
    5509 Atom CG1 has no neighbors to form bonds with according to residue template for
    5510 VAL /C:198 
    5511 Atom CG2 has no neighbors to form bonds with according to residue template for
    5512 VAL /C:198 
    5513 Atom CE has no neighbors to form bonds with according to residue template for
    5514 MET /D:105 
    5515 Atom N has no neighbors to form bonds with according to residue template for
    5516 TYR /D:120 
    5517 Atom N has no neighbors to form bonds with according to residue template for
    5518 ALA /D:153 
    5519 Atom CB has no neighbors to form bonds with according to residue template for
    5520 ALA /D:153 
    5521 Atom NH1 has no neighbors to form bonds with according to residue template for
    5522 ARG /D:173 
    5523 Atom N has no neighbors to form bonds with according to residue template for
    5524 SER /H:106 
    5525 Atom N has no neighbors to form bonds with according to residue template for
    5526 GLN /H:110 
    5527 Atom O has no neighbors to form bonds with according to residue template for
    5528 GLN /H:110 
    5529 Atom N has no neighbors to form bonds with according to residue template for
    5530 LYS /J:65 
    5531 Atom O has no neighbors to form bonds with according to residue template for
    5532 LEU /J:93 
    5533 Atom N has no neighbors to form bonds with according to residue template for
    5534 ALA /J:177 
    5535 Atom CB has no neighbors to form bonds with according to residue template for
    5536 ALA /J:177 
    5537 Atom N has no neighbors to form bonds with according to residue template for
    5538 PHE /K:54 
    5539 Atom CE1 has no neighbors to form bonds with according to residue template for
    5540 PHE /K:54 
    5541 Atom NE has no neighbors to form bonds with according to residue template for
    5542 ARG /L:116 
    5543 Atom NH2 has no neighbors to form bonds with according to residue template for
    5544 ARG /L:116 
    5545 Atom O has no neighbors to form bonds with according to residue template for
    5546 VAL /L:125 
    5547 Atom C has no neighbors to form bonds with according to residue template for
    5548 SER /L:132 
    5549 Atom N has no neighbors to form bonds with according to residue template for
    5550 ARG /L:136 
    5551 Atom CA has no neighbors to form bonds with according to residue template for
    5552 GLY /L:147 
    5553 Atom O has no neighbors to form bonds with according to residue template for
    5554 GLY /L:147 
    5555 Atom O has no neighbors to form bonds with according to residue template for
    5556 ILE /N:116 
    5557 Atom O has no neighbors to form bonds with according to residue template for
    5558 THR /O:89 
    5559 Atom N has no neighbors to form bonds with according to residue template for
    5560 SER /O:125 
    5561 Atom OG has no neighbors to form bonds with according to residue template for
    5562 SER /O:125 
    5563 Atom N has no neighbors to form bonds with according to residue template for
    5564 GLN /W:39 
    5565 Atom N has no neighbors to form bonds with according to residue template for
    5566 MET /W:41 
    5567 Atom CD1 has no neighbors to form bonds with according to residue template for
    5568 LEU /W:69 
    5569 Atom CD2 has no neighbors to form bonds with according to residue template for
    5570 LEU /W:69 
    5571 Atom O has no neighbors to form bonds with according to residue template for
    5572 ASN /Y:31 
    5573 Atom N has no neighbors to form bonds with according to residue template for
    5574 ASN /a:25 
    5575 Atom C has no neighbors to form bonds with according to residue template for
    5576 ASN /a:25 
    5577 Atom CB has no neighbors to form bonds with according to residue template for
    5578 ASN /a:25 
    5579 Atom ND2 has no neighbors to form bonds with according to residue template for
    5580 ASN /a:25 
    5581 Atom N has no neighbors to form bonds with according to residue template for
    5582 MET /a:39 
    5583 Atom N has no neighbors to form bonds with according to residue template for
    5584 GLN /a:99 
    5585 Atom N has no neighbors to form bonds with according to residue template for
    5586 VAL /e:47 
    5587 Atom CG1 has no neighbors to form bonds with according to residue template for
    5588 VAL /e:47 
    5589 Atom O has no neighbors to form bonds with according to residue template for
    5590 ARG /m:36 
    5591 Atom O has no neighbors to form bonds with according to residue template for
    5592 THR /m:38 
    5593 Atom OG1 has no neighbors to form bonds with according to residue template for
    5594 THR /m:38 
    5595 Atom OE2 has no neighbors to form bonds with according to residue template for
    5596 GLU /m:47 
    5597 Atom OD1 has no neighbors to form bonds with according to residue template for
    5598 ASN /m:67 
    5599 Atom O has no neighbors to form bonds with according to residue template for
    5600 ILE /m:103 
    5601 Atom O has no neighbors to form bonds with according to residue template for
    5602 PRO /p:88 
    5603 Atom N has no neighbors to form bonds with according to residue template for
    5604 ILE /p:116 
    5605 Atom CD1 has no neighbors to form bonds with according to residue template for
    5606 ILE /p:116 
    5607 Atom N has no neighbors to form bonds with according to residue template for
    5608 ASP /p:380 
    5609 Atom N has no neighbors to form bonds with according to residue template for
    5610 GLN /p:444 
    5611 Atom O has no neighbors to form bonds with according to residue template for
    5612 GLN /p:444 
    5613 Atom N has no neighbors to form bonds with according to residue template for
    5614 GLU /p:455 
    5615 Atom CD2 has no neighbors to form bonds with according to residue template for
    5616 LEU /p:468 
    5617 Atom OD1 has no neighbors to form bonds with according to residue template for
    5618 ASN /p:592 
    5619 Atom ND2 has no neighbors to form bonds with according to residue template for
    5620 ASN /p:592 
    5621 Atom N has no neighbors to form bonds with according to residue template for
    5622 VAL /p:595 
    5623 Atom CG1 has no neighbors to form bonds with according to residue template for
    5624 VAL /p:595 
    5625  
    5626 Chain information for 0057_6gsm_X.cif #1 
    5627 --- 
    5628 Chain | Description 
    5629 2 | 18S ribosomal RNA 
    5630 3 | mRNA (5'-R(P*AP*AP*U)-3') 
    5631 B | 40S ribosomal protein S1 
    5632 C | KLLA0F09812p 
    5633 D | KLLA0D08305p 
    5634 E | 40S ribosomal protein S4 
    5635 H | 40S ribosomal protein S7 
    5636 I | 40S ribosomal protein S8 
    5637 J | KLLA0E23673p 
    5638 K | KLLA0B08173p 
    5639 L | KLLA0A10483p 
    5640 N | KLLA0F18040p 
    5641 O | 40S ribosomal protein S14 
    5642 V | 40S ribosomal protein S21 
    5643 W | 40S ribosomal protein S22 
    5644 X | KLLA0B11231p 
    5645 Y | 40S ribosomal protein S24 
    5646 a | 40S ribosomal protein S26 
    5647 b | 40S ribosomal protein S27 
    5648 e | 40S ribosomal protein S30 
    5649 h | 60S ribosomal protein L41-A 
    5650 i | Eukaryotic translation initiation factor 1A 
    5651 l | Eukaryotic translation initiation factor 2 subunit beta 
    5652 m | Eukaryotic translation initiation factor eIF-1 
    5653 o | Eukaryotic translation initiation factor 3 subunit A,Eukaryotic
    5654 translation initiation factor 3 subunit A,eIF3a 
    5655 p | Eukaryotic translation initiation factor 3 subunit B 
    5656 q | Eukaryotic translation initiation factor 3 subunit C 
    5657  
    5658 
    5659 > open /scratch/cs-
    5660 > bioinfo/tngu/6k_data/Box_Chains_new/0057_6gsm/0057_6gsm_X.mrc
    5661 
    5662 Opened 0057_6gsm_X.mrc as #2, grid size 88,88,112, pixel 1, shown at level
    5663 0.153, step 1, values float32 
    5664 
    5665 > fitmap #1 inMap #2
    5666 
    5667 Fit molecule 0057_6gsm_X.cif (#1) to map 0057_6gsm_X.mrc (#2) using 24244
    5668 atoms 
    5669 average map value = 0.08409, steps = 40 
    5670 shifted from previous position = 0.373 
    5671 rotated from previous position = 0.099 degrees 
    5672 atoms outside contour = 23533, contour level = 0.15287 
    5673  
    5674 Position of 0057_6gsm_X.cif (#1) relative to 0057_6gsm_X.mrc (#2) coordinates: 
    5675 Matrix rotation and translation 
    5676 0.99999908 0.00000025 0.00135501 -0.57857011 
    5677 -0.00000170 0.99999943 0.00107085 -0.40116203 
    5678 -0.00135501 -0.00107086 0.99999851 0.45634782 
    5679 Axis -0.62003964 0.78457028 -0.00056271 
    5680 Axis point 336.35507218 0.00000000 407.19792982 
    5681 Rotation angle (degrees) 0.09895421 
    5682 Shift along axis 0.04373981 
    5683  
    5684 
    5685 > save /scratch/cs-
    5686 > bioinfo/tngu/6k_data/Box_Chains_new/0057_6gsm/0057_6gsm_X_fitted.cif #1
    5687 
    5688 > close #1
    5689 
    5690 > close #2
    5691 
    5692 > open /scratch/cs-
    5693 > bioinfo/tngu/6k_data/Box_Chains_new/0057_6gsm/0057_6gsm_1.cif
    5694 
    5695 Summary of feedback from opening /scratch/cs-
    5696 bioinfo/tngu/6k_data/Box_Chains_new/0057_6gsm/0057_6gsm_1.cif 
    5697 --- 
    5698 warnings | Invalid residue range for struct_conf "HELX1": invalid chain "C",
    5699 near line 49791 
    5700 Invalid residue range for struct_conf "HELX2": invalid chain "C", near line
    5701 49792 
    5702 Invalid residue range for struct_conf "HELX3": invalid chain "C", near line
    5703 49793 
    5704 Invalid residue range for struct_conf "HELX4": invalid chain "C", near line
    5705 49794 
    5706 Invalid residue range for struct_conf "HELX5": invalid chain "C", near line
    5707 49795 
    5708 111 messages similar to the above omitted 
    5709 Invalid sheet range for struct_sheet_range "? 1": invalid chain "C", near line
    5710 50044 
    5711 Invalid sheet range for struct_sheet_range "? 2": invalid chain "C", near line
    5712 50045 
    5713 Invalid sheet range for struct_sheet_range "? 3": invalid chain "C", near line
    5714 50046 
    5715 Invalid sheet range for struct_sheet_range "? 4": invalid chain "C", near line
    5716 50047 
    5717 Invalid sheet range for struct_sheet_range "? 5": invalid chain "C", near line
    5718 50048 
    5719 131 messages similar to the above omitted 
    5720 Atom OP1 has no neighbors to form bonds with according to residue template for
    5721 U /2:577 
    5722 Atom OP2 has no neighbors to form bonds with according to residue template for
    5723 U /2:577 
    5724 Atom O2' has no neighbors to form bonds with according to residue template for
    5725 U /2:577 
    5726 Atom C5' has no neighbors to form bonds with according to residue template for
    5727 U /2:910 
    5728 Atom OP2 has no neighbors to form bonds with according to residue template for
    5729 A /2:1012 
    5730 Atom O4' has no neighbors to form bonds with according to residue template for
    5731 U /2:1181 
    5732 Atom OP1 has no neighbors to form bonds with according to residue template for
    5733 G /2:1270 
    5734 Atom C5' has no neighbors to form bonds with according to residue template for
    5735 G /2:1270 
    5736 Atom O3' has no neighbors to form bonds with according to residue template for
    5737 A /2:1286 
    5738 Atom O2' has no neighbors to form bonds with according to residue template for
    5739 A /2:1286 
    5740 Atom OP1 has no neighbors to form bonds with according to residue template for
    5741 G /2:1287 
    5742 Atom O2' has no neighbors to form bonds with according to residue template for
    5743 G /2:1287 
    5744 Atom O2' has no neighbors to form bonds with according to residue template for
    5745 U /2:1306 
    5746 Atom OP1 has no neighbors to form bonds with according to residue template for
    5747 C /2:1308 
    5748 Atom OP2 has no neighbors to form bonds with according to residue template for
    5749 C /2:1308 
    5750 Atom O2' has no neighbors to form bonds with according to residue template for
    5751 U /2:1435 
    5752 Atom O2' has no neighbors to form bonds with according to residue template for
    5753 G /2:1436 
    5754 Atom OP2 has no neighbors to form bonds with according to residue template for
    5755 U /2:1526 
    5756 Atom C4' has no neighbors to form bonds with according to residue template for
    5757 U /2:1556 
    5758 Atom O3' has no neighbors to form bonds with according to residue template for
    5759 U /2:1556 
    5760 Atom N4 has no neighbors to form bonds with according to residue template for
    5761 C /2:1589 
    5762 Atom O2' has no neighbors to form bonds with according to residue template for
    5763 G /2:1592 
    5764 Atom OP2 has no neighbors to form bonds with according to residue template for
    5765 U /2:1596 
    5766 Atom O5' has no neighbors to form bonds with according to residue template for
    5767 U /2:1596 
    5768 Atom O4' has no neighbors to form bonds with according to residue template for
    5769 U /2:1602 
    5770 Atom C8 has no neighbors to form bonds with according to residue template for
    5771 G /2:1784 
    5772 Atom CD has no neighbors to form bonds with according to residue template for
    5773 LYS /C:93 
    5774 Atom NZ has no neighbors to form bonds with according to residue template for
    5775 LYS /C:93 
    5776 Atom N has no neighbors to form bonds with according to residue template for
    5777 ARG /D:143 
    5778 Atom C has no neighbors to form bonds with according to residue template for
    5779 ARG /D:143 
    5780 Atom CG1 has no neighbors to form bonds with according to residue template for
    5781 VAL /F:55 
    5782 Atom CB has no neighbors to form bonds with according to residue template for
    5783 ARG /F:94 
    5784 Atom N has no neighbors to form bonds with according to residue template for
    5785 ASN /F:130 
    5786 Atom N has no neighbors to form bonds with according to residue template for
    5787 LEU /F:132 
    5788 Atom NE2 has no neighbors to form bonds with according to residue template for
    5789 GLN /F:133 
    5790 Atom N has no neighbors to form bonds with according to residue template for
    5791 LYS /O:92 
    5792 Atom O has no neighbors to form bonds with according to residue template for
    5793 THR /O:93 
    5794 Atom CB has no neighbors to form bonds with according to residue template for
    5795 VAL /S:52 
    5796 Atom O has no neighbors to form bonds with according to residue template for
    5797 LEU /S:66 
    5798 Atom N has no neighbors to form bonds with according to residue template for
    5799 ALA /S:83 
    5800 Atom CE3 has no neighbors to form bonds with according to residue template for
    5801 TRP /S:84 
    5802 Atom CD1 has no neighbors to form bonds with according to residue template for
    5803 PHE /S:128 
    5804 Atom CB has no neighbors to form bonds with according to residue template for
    5805 PRO /T:31 
    5806 Atom N has no neighbors to form bonds with according to residue template for
    5807 PHE /T:54 
    5808 Atom CB has no neighbors to form bonds with according to residue template for
    5809 ARG /Z:49 
    5810 Atom CD has no neighbors to form bonds with according to residue template for
    5811 ARG /Z:49 
    5812 Atom O has no neighbors to form bonds with according to residue template for
    5813 GLU /Z:84 
    5814 Atom N has no neighbors to form bonds with according to residue template for
    5815 VAL /Z:92 
    5816 Atom CG2 has no neighbors to form bonds with according to residue template for
    5817 VAL /Z:92 
    5818 Atom NH1 has no neighbors to form bonds with according to residue template for
    5819 ARG /a:89 
    5820 Atom OE2 has no neighbors to form bonds with according to residue template for
    5821 GLU /c:31 
    5822 Atom OE1 has no neighbors to form bonds with according to residue template for
    5823 GLU /c:34 
    5824 Atom OE2 has no neighbors to form bonds with according to residue template for
    5825 GLU /c:34 
    5826 Atom N has no neighbors to form bonds with according to residue template for
    5827 TYR /i:28 
    5828 Atom N has no neighbors to form bonds with according to residue template for
    5829 GLU /i:30 
    5830 Atom OE1 has no neighbors to form bonds with according to residue template for
    5831 GLU /i:30 
    5832 Atom O has no neighbors to form bonds with according to residue template for
    5833 SER /i:50 
    5834 Atom N has no neighbors to form bonds with according to residue template for
    5835 GLN /k:175 
    5836 Atom N has no neighbors to form bonds with according to residue template for
    5837 LEU /k:260 
    5838 Atom N has no neighbors to form bonds with according to residue template for
    5839 MET /k:310 
    5840 Atom N has no neighbors to form bonds with according to residue template for
    5841 GLU /k:457 
    5842 Atom N has no neighbors to form bonds with according to residue template for
    5843 ALA /k:477 
    5844 Atom OH has no neighbors to form bonds with according to residue template for
    5845 TYR /l:131 
    5846 Atom ND1 has no neighbors to form bonds with according to residue template for
    5847 HIS /p:145 
    5848 Atom O has no neighbors to form bonds with according to residue template for
    5849 LEU /p:149 
    5850 Atom O has no neighbors to form bonds with according to residue template for
    5851 ASP /q:97 
    5852  
    5853 Chain information for 0057_6gsm_1.cif #1 
    5854 --- 
    5855 Chain | Description 
    5856 1 | Met-tRNAi 
    5857 2 | 18S ribosomal RNA 
    5858 3 | mRNA (5'-R(P*AP*AP*U)-3') 
    5859 B | 40S ribosomal protein S1 
    5860 C | KLLA0F09812p 
    5861 D | KLLA0D08305p 
    5862 F | KLLA0D10659p 
    5863 O | 40S ribosomal protein S14 
    5864 P | KLLA0F07843p 
    5865 Q | 40S ribosomal protein S16 
    5866 S | KLLA0B01562p 
    5867 T | KLLA0A07194p 
    5868 U | KLLA0F25542p 
    5869 Z | KLLA0B06182p 
    5870 a | 40S ribosomal protein S26 
    5871 c | 40S ribosomal protein S28 
    5872 d | 40S ribosomal protein S29 
    5873 i | Eukaryotic translation initiation factor 1A 
    5874 j | Eukaryotic translation initiation factor 2 subunit alpha 
    5875 k | Eukaryotic translation initiation factor 2 subunit gamma 
    5876 l | Eukaryotic translation initiation factor 2 subunit beta 
    5877 m | Eukaryotic translation initiation factor eIF-1 
    5878 p | Eukaryotic translation initiation factor 3 subunit B 
    5879 q | Eukaryotic translation initiation factor 3 subunit C 
    5880  
    5881 
    5882 > open /scratch/cs-
    5883 > bioinfo/tngu/6k_data/Box_Chains_new/0057_6gsm/0057_6gsm_1.mrc
    5884 
    5885 Opened 0057_6gsm_1.mrc as #2, grid size 128,96,80, pixel 1, shown at level
    5886 0.126, step 1, values float32 
    5887 
    5888 > fitmap #1 inMap #2
    5889 
    5890 Fit molecule 0057_6gsm_1.cif (#1) to map 0057_6gsm_1.mrc (#2) using 18608
    5891 atoms 
    5892 average map value = 0.0684, steps = 64 
    5893 shifted from previous position = 0.53 
    5894 rotated from previous position = 0.158 degrees 
    5895 atoms outside contour = 17745, contour level = 0.126 
    5896  
    5897 Position of 0057_6gsm_1.cif (#1) relative to 0057_6gsm_1.mrc (#2) coordinates: 
    5898 Matrix rotation and translation 
    5899 0.99999827 0.00173579 0.00066214 -0.84382811 
    5900 -0.00173443 0.99999640 -0.00204519 0.72064419 
    5901 -0.00066568 0.00204403 0.99999769 -0.47427235 
    5902 Axis 0.74010988 0.24032262 -0.62807835 
    5903 Axis point 0.00000000 279.59960222 369.90215785 
    5904 Rotation angle (degrees) 0.15828409 
    5905 Shift along axis -0.15345823 
    5906  
    5907 
    5908 > save /scratch/cs-
    5909 > bioinfo/tngu/6k_data/Box_Chains_new/0057_6gsm/0057_6gsm_1_fitted.cif #1
    5910 
    5911 > close #1
    5912 
    5913 > close #2
    5914 
    5915 > open /scratch/cs-
    5916 > bioinfo/tngu/6k_data/Box_Chains_new/0057_6gsm/0057_6gsm_Z.cif
    5917 
    5918 Summary of feedback from opening /scratch/cs-
    5919 bioinfo/tngu/6k_data/Box_Chains_new/0057_6gsm/0057_6gsm_Z.cif 
    5920 --- 
    5921 warnings | Invalid residue range for struct_conf "HELX1": invalid chain "C",
    5922 near line 37310 
    5923 Invalid residue range for struct_conf "HELX2": invalid chain "C", near line
    5924 37311 
    5925 Invalid residue range for struct_conf "HELX3": invalid chain "C", near line
    5926 37312 
    5927 Invalid residue range for struct_conf "HELX4": invalid chain "C", near line
    5928 37313 
    5929 Invalid residue range for struct_conf "HELX5": invalid chain "C", near line
    5930 37314 
    5931 197 messages similar to the above omitted 
    5932 Invalid sheet range for struct_sheet_range "? 1": invalid chain "C", near line
    5933 37563 
    5934 Invalid sheet range for struct_sheet_range "? 2": invalid chain "C", near line
    5935 37564 
    5936 Invalid sheet range for struct_sheet_range "? 3": invalid chain "C", near line
    5937 37565 
    5938 Invalid sheet range for struct_sheet_range "? 4": invalid chain "C", near line
    5939 37566 
    5940 Invalid sheet range for struct_sheet_range "? 5": invalid chain "C", near line
    5941 37567 
    5942 227 messages similar to the above omitted 
    5943 Atom O3' has no neighbors to form bonds with according to residue template for
    5944 G /1:43 
    5945 Atom O3' has no neighbors to form bonds with according to residue template for
    5946 A /1:44 
    5947 Atom O3' has no neighbors to form bonds with according to residue template for
    5948 H2U /1:47 
    5949 Atom O3' has no neighbors to form bonds with according to residue template for
    5950 G /2:1166 
    5951 Atom O3' has no neighbors to form bonds with according to residue template for
    5952 G /2:1169 
    5953 Atom O2' has no neighbors to form bonds with according to residue template for
    5954 G /2:1348 
    5955 Atom N2 has no neighbors to form bonds with according to residue template for
    5956 G /2:1357 
    5957 Atom N3 has no neighbors to form bonds with according to residue template for
    5958 G /2:1357 
    5959 Atom O2 has no neighbors to form bonds with according to residue template for
    5960 C /2:1358 
    5961 Atom O3' has no neighbors to form bonds with according to residue template for
    5962 C /2:1364 
    5963 Atom O2 has no neighbors to form bonds with according to residue template for
    5964 C /2:1365 
    5965 Atom O2' has no neighbors to form bonds with according to residue template for
    5966 G /2:1367 
    5967 Atom O2 has no neighbors to form bonds with according to residue template for
    5968 C /2:1377 
    5969 Atom OP1 has no neighbors to form bonds with according to residue template for
    5970 C /2:1465 
    5971 Atom OP2 has no neighbors to form bonds with according to residue template for
    5972 C /2:1483 
    5973 Atom O4' has no neighbors to form bonds with according to residue template for
    5974 U /2:1542 
    5975 Atom O3' has no neighbors to form bonds with according to residue template for
    5976 U /2:1564 
    5977 Atom OD1 has no neighbors to form bonds with according to residue template for
    5978 ASP /F:62 
    5979 Atom N has no neighbors to form bonds with according to residue template for
    5980 ARG /F:145 
    5981 Atom CD2 has no neighbors to form bonds with according to residue template for
    5982 LEU /Q:28 
    5983 Atom O has no neighbors to form bonds with according to residue template for
    5984 ASP /Q:120 
    5985 Atom NH1 has no neighbors to form bonds with according to residue template for
    5986 ARG /S:41 
    5987 Atom N has no neighbors to form bonds with according to residue template for
    5988 ARG /S:68 
    5989 Atom N has no neighbors to form bonds with according to residue template for
    5990 VAL /S:70 
    5991 Atom N has no neighbors to form bonds with according to residue template for
    5992 ARG /S:143 
    5993 Atom CG1 has no neighbors to form bonds with according to residue template for
    5994 VAL /T:34 
    5995 Atom N has no neighbors to form bonds with according to residue template for
    5996 THR /T:39 
    5997 Atom N has no neighbors to form bonds with according to residue template for
    5998 GLN /T:70 
    5999 Atom O has no neighbors to form bonds with according to residue template for
    6000 GLN /T:70 
    6001 Atom CD2 has no neighbors to form bonds with according to residue template for
    6002 LEU /T:76 
    6003 Atom OD1 has no neighbors to form bonds with according to residue template for
    6004 ASP /T:95 
    6005 Atom N has no neighbors to form bonds with according to residue template for
    6006 VAL /T:114 
    6007 Atom OG has no neighbors to form bonds with according to residue template for
    6008 SER /T:125 
    6009 Atom CG2 has no neighbors to form bonds with according to residue template for
    6010 ILE /c:53 
    6011 Atom CD1 has no neighbors to form bonds with according to residue template for
    6012 ILE /c:53 
    6013 Atom N has no neighbors to form bonds with according to residue template for
    6014 ILE /j:27 
    6015 Atom O has no neighbors to form bonds with according to residue template for
    6016 ILE /j:27 
    6017 Atom CG has no neighbors to form bonds with according to residue template for
    6018 LYS /j:67 
    6019 Atom CG1 has no neighbors to form bonds with according to residue template for
    6020 VAL /j:73 
    6021 Atom CG2 has no neighbors to form bonds with according to residue template for
    6022 VAL /j:73 
    6023 Atom O has no neighbors to form bonds with according to residue template for
    6024 ASP /j:84 
    6025  
    6026 Chain information for 0057_6gsm_Z.cif #1 
    6027 --- 
    6028 Chain | Description 
    6029 1 | Met-tRNAi 
    6030 2 | 18S ribosomal RNA 
    6031 F | KLLA0D10659p 
    6032 Q | 40S ribosomal protein S16 
    6033 S | KLLA0B01562p 
    6034 T | KLLA0A07194p 
    6035 Z | KLLA0B06182p 
    6036 c | 40S ribosomal protein S28 
    6037 j | Eukaryotic translation initiation factor 2 subunit alpha 
    6038  
    6039 
    6040 > open /scratch/cs-
    6041 > bioinfo/tngu/6k_data/Box_Chains_new/0057_6gsm/0057_6gsm_Z.mrc
    6042 
    6043 Opened 0057_6gsm_Z.mrc as #2, grid size 88,72,72, pixel 1, shown at level
    6044 0.12, step 1, values float32 
    6045 
    6046 > fitmap #1 inMap #2
    6047 
    6048 Fit molecule 0057_6gsm_Z.cif (#1) to map 0057_6gsm_Z.mrc (#2) using 6379 atoms 
    6049 average map value = 0.07059, steps = 52 
    6050 shifted from previous position = 0.758 
    6051 rotated from previous position = 0.382 degrees 
    6052 atoms outside contour = 6034, contour level = 0.1198 
    6053  
    6054 Position of 0057_6gsm_Z.cif (#1) relative to 0057_6gsm_Z.mrc (#2) coordinates: 
    6055 Matrix rotation and translation 
    6056 0.99999732 -0.00041871 0.00227831 -0.60321734 
    6057 0.00043294 0.99998038 -0.00624984 1.37470602 
    6058 -0.00227564 0.00625081 0.99997787 -1.05746611 
    6059 Axis 0.93767464 0.34159226 0.06388265 
    6060 Axis point 0.00000000 168.30919662 228.37113330 
    6061 Rotation angle (degrees) 0.38192337 
    6062 Shift along axis -0.16358642 
    6063  
    6064 
    6065 > save /scratch/cs-
    6066 > bioinfo/tngu/6k_data/Box_Chains_new/0057_6gsm/0057_6gsm_Z_fitted.cif #1
    6067 
    6068 > close #1
    6069 
    6070 > close #2
    6071 
    6072 > open /scratch/cs-
    6073 > bioinfo/tngu/6k_data/Box_Chains_new/0057_6gsm/0057_6gsm_H.cif
    6074 
    6075 Summary of feedback from opening /scratch/cs-
    6076 bioinfo/tngu/6k_data/Box_Chains_new/0057_6gsm/0057_6gsm_H.cif 
    6077 --- 
    6078 warnings | Invalid residue range for struct_conf "HELX21": invalid chain "G",
    6079 near line 46024 
    6080 Invalid residue range for struct_conf "HELX22": invalid chain "G", near line
    6081 46025 
    6082 Invalid residue range for struct_conf "HELX23": invalid chain "G", near line
    6083 46026 
    6084 Invalid residue range for struct_conf "HELX24": invalid chain "G", near line
    6085 46027 
    6086 Invalid residue range for struct_conf "HELX25": invalid chain "G", near line
    6087 46028 
    6088 132 messages similar to the above omitted 
    6089 Invalid sheet range for struct_sheet_range "? 25": invalid chain "G", near
    6090 line 46281 
    6091 Invalid sheet range for struct_sheet_range "? 26": invalid chain "G", near
    6092 line 46282 
    6093 Invalid sheet range for struct_sheet_range "? 27": invalid chain "G", near
    6094 line 46283 
    6095 Invalid sheet range for struct_sheet_range "? 28": invalid chain "G", near
    6096 line 46284 
    6097 Invalid sheet range for struct_sheet_range "? 29": invalid chain "G", near
    6098 line 46285 
    6099 179 messages similar to the above omitted 
    6100 Atom O3' has no neighbors to form bonds with according to residue template for
    6101 C /2:14 
    6102 Atom O2 has no neighbors to form bonds with according to residue template for
    6103 C /2:14 
    6104 Atom OP1 has no neighbors to form bonds with according to residue template for
    6105 U /2:15 
    6106 Atom O2' has no neighbors to form bonds with according to residue template for
    6107 G /2:213 
    6108 Atom O3' has no neighbors to form bonds with according to residue template for
    6109 C /2:307 
    6110 Atom O2' has no neighbors to form bonds with according to residue template for
    6111 G /2:370 
    6112 Atom N2 has no neighbors to form bonds with according to residue template for
    6113 G /2:370 
    6114 Atom OP1 has no neighbors to form bonds with according to residue template for
    6115 G /2:371 
    6116 Atom O3' has no neighbors to form bonds with according to residue template for
    6117 G /2:372 
    6118 Atom O3' has no neighbors to form bonds with according to residue template for
    6119 U /2:628 
    6120 Atom OP1 has no neighbors to form bonds with according to residue template for
    6121 U /2:718 
    6122 Atom N6 has no neighbors to form bonds with according to residue template for
    6123 A /2:728 
    6124 Atom OP1 has no neighbors to form bonds with according to residue template for
    6125 U /2:793 
    6126 Atom C6 has no neighbors to form bonds with according to residue template for
    6127 U /2:840 
    6128 Atom N4 has no neighbors to form bonds with according to residue template for
    6129 C /2:841 
    6130 Atom N7 has no neighbors to form bonds with according to residue template for
    6131 G /2:877 
    6132 Atom O6 has no neighbors to form bonds with according to residue template for
    6133 G /2:877 
    6134 Atom N2 has no neighbors to form bonds with according to residue template for
    6135 G /2:935 
    6136 Atom OP2 has no neighbors to form bonds with according to residue template for
    6137 G /2:941 
    6138 Atom C1' has no neighbors to form bonds with according to residue template for
    6139 C /2:942 
    6140 Atom OP2 has no neighbors to form bonds with according to residue template for
    6141 G /2:947 
    6142 Atom O5' has no neighbors to form bonds with according to residue template for
    6143 G /2:947 
    6144 Atom O3' has no neighbors to form bonds with according to residue template for
    6145 U /2:1060 
    6146 Atom C8 has no neighbors to form bonds with according to residue template for
    6147 G /2:1296 
    6148 Atom O has no neighbors to form bonds with according to residue template for
    6149 ILE /A:133 
    6150 Atom CG2 has no neighbors to form bonds with according to residue template for
    6151 ILE /A:133 
    6152 Atom N has no neighbors to form bonds with according to residue template for
    6153 ALA /A:145 
    6154 Atom O has no neighbors to form bonds with according to residue template for
    6155 ALA /A:145 
    6156 Atom CA has no neighbors to form bonds with according to residue template for
    6157 VAL /A:181 
    6158 Atom O has no neighbors to form bonds with according to residue template for
    6159 VAL /A:181 
    6160 Atom NE has no neighbors to form bonds with according to residue template for
    6161 ARG /A:185 
    6162 Atom CB has no neighbors to form bonds with according to residue template for
    6163 ARG /C:173 
    6164 Atom O has no neighbors to form bonds with according to residue template for
    6165 VAL /C:221 
    6166 Atom N has no neighbors to form bonds with according to residue template for
    6167 TYR /C:251 
    6168 Atom C has no neighbors to form bonds with according to residue template for
    6169 TYR /C:251 
    6170 Atom N has no neighbors to form bonds with according to residue template for
    6171 ARG /E:233 
    6172 Atom CB has no neighbors to form bonds with according to residue template for
    6173 ARG /E:233 
    6174 Atom N has no neighbors to form bonds with according to residue template for
    6175 LYS /L:46 
    6176 Atom CG1 has no neighbors to form bonds with according to residue template for
    6177 VAL /L:125 
    6178 Atom CG has no neighbors to form bonds with according to residue template for
    6179 GLU /V:2 
    6180 Atom OE1 has no neighbors to form bonds with according to residue template for
    6181 GLU /V:2 
    6182 Atom C has no neighbors to form bonds with according to residue template for
    6183 ALA /X:25 
    6184 Atom CB has no neighbors to form bonds with according to residue template for
    6185 ALA /X:25 
    6186 Atom NH1 has no neighbors to form bonds with according to residue template for
    6187 ARG /a:15 
    6188 Atom O has no neighbors to form bonds with according to residue template for
    6189 PHE /q:254 
    6190 Atom O has no neighbors to form bonds with according to residue template for
    6191 PHE /q:255 
    6192 Atom O has no neighbors to form bonds with according to residue template for
    6193 VAL /q:270 
    6194 Atom OE2 has no neighbors to form bonds with according to residue template for
    6195 GLU /q:281 
    6196 Atom OE2 has no neighbors to form bonds with according to residue template for
    6197 GLU /q:287 
    6198 Atom NH1 has no neighbors to form bonds with according to residue template for
    6199 ARG /q:303 
    6200 Atom N has no neighbors to form bonds with according to residue template for
    6201 GLN /q:334 
    6202 Atom CB has no neighbors to form bonds with according to residue template for
    6203 GLN /q:334 
    6204 Atom NE2 has no neighbors to form bonds with according to residue template for
    6205 GLN /q:334 
    6206 Atom N has no neighbors to form bonds with according to residue template for
    6207 THR /q:335 
    6208 Atom N has no neighbors to form bonds with according to residue template for
    6209 LYS /q:443 
    6210 Atom CG has no neighbors to form bonds with according to residue template for
    6211 LYS /q:443 
    6212 Atom CE has no neighbors to form bonds with according to residue template for
    6213 LYS /q:443 
    6214 Atom CD2 has no neighbors to form bonds with according to residue template for
    6215 LEU /q:486 
    6216 Atom CG2 has no neighbors to form bonds with according to residue template for
    6217 THR /q:488 
    6218 Atom CG2 has no neighbors to form bonds with according to residue template for
    6219 ILE /q:560 
    6220 Atom CD1 has no neighbors to form bonds with according to residue template for
    6221 LEU /q:576 
    6222 Atom N has no neighbors to form bonds with according to residue template for
    6223 GLN /q:583 
    6224 Atom O has no neighbors to form bonds with according to residue template for
    6225 SER /q:592 
    6226 Atom OG has no neighbors to form bonds with according to residue template for
    6227 SER /q:592 
    6228 Atom CA has no neighbors to form bonds with according to residue template for
    6229 SER /q:593 
    6230 Atom OG has no neighbors to form bonds with according to residue template for
    6231 SER /q:593 
    6232 Atom N has no neighbors to form bonds with according to residue template for
    6233 THR /q:634 
    6234 Atom C has no neighbors to form bonds with according to residue template for
    6235 THR /q:634 
    6236 Atom N has no neighbors to form bonds with according to residue template for
    6237 ARG /q:654 
    6238  
    6239 Chain information for 0057_6gsm_H.cif #1 
    6240 --- 
    6241 Chain | Description 
    6242 2 | 18S ribosomal RNA 
    6243 A | 40S ribosomal protein S0 
    6244 B | 40S ribosomal protein S1 
    6245 C | KLLA0F09812p 
    6246 E | 40S ribosomal protein S4 
    6247 H | 40S ribosomal protein S7 
    6248 L | KLLA0A10483p 
    6249 N | KLLA0F18040p 
    6250 R | KLLA0B01474p 
    6251 V | 40S ribosomal protein S21 
    6252 W | 40S ribosomal protein S22 
    6253 X | KLLA0B11231p 
    6254 a | 40S ribosomal protein S26 
    6255 b | 40S ribosomal protein S27 
    6256 q | Eukaryotic translation initiation factor 3 subunit C 
    6257  
    6258 
    6259 > open /scratch/cs-
    6260 > bioinfo/tngu/6k_data/Box_Chains_new/0057_6gsm/0057_6gsm_H.mrc
    6261 
    6262 Opened 0057_6gsm_H.mrc as #2, grid size 88,96,104, pixel 1, shown at level
    6263 0.137, step 1, values float32 
    6264 
    6265 > fitmap #1 inMap #2
    6266 
    6267 Fit molecule 0057_6gsm_H.cif (#1) to map 0057_6gsm_H.mrc (#2) using 14921
    6268 atoms 
    6269 average map value = 0.07261, steps = 80 
    6270 shifted from previous position = 0.499 
    6271 rotated from previous position = 0.179 degrees 
    6272 atoms outside contour = 14137, contour level = 0.1369 
    6273  
    6274 Position of 0057_6gsm_H.cif (#1) relative to 0057_6gsm_H.mrc (#2) coordinates: 
    6275 Matrix rotation and translation 
    6276 0.99999531 -0.00126111 -0.00279203 0.90794240 
    6277 0.00125934 0.99999900 -0.00063652 -0.43925796 
    6278 0.00279283 0.00063300 0.99999590 -1.02865610 
    6279 Axis 0.20288211 -0.89252153 0.40279544 
    6280 Axis point 392.13097233 0.00000000 312.76567637 
    6281 Rotation angle (degrees) 0.17926176 
    6282 Shift along axis 0.16191447 
    6283  
    6284 
    6285 > save /scratch/cs-
    6286 > bioinfo/tngu/6k_data/Box_Chains_new/0057_6gsm/0057_6gsm_H_fitted.cif #1
    6287 
    6288 > close #1
    6289 
    6290 > close #2
    6291 
    6292 > open /scratch/cs-
    6293 > bioinfo/tngu/6k_data/Box_Chains_new/0057_6gsm/0057_6gsm_l.cif
    6294 
    6295 Summary of feedback from opening /scratch/cs-
    6296 bioinfo/tngu/6k_data/Box_Chains_new/0057_6gsm/0057_6gsm_l.cif 
    6297 --- 
    6298 warnings | Invalid residue range for struct_conf "HELX1": invalid chain "C",
    6299 near line 42944 
    6300 Invalid residue range for struct_conf "HELX2": invalid chain "C", near line
    6301 42945 
    6302 Invalid residue range for struct_conf "HELX3": invalid chain "C", near line
    6303 42946 
    6304 Invalid residue range for struct_conf "HELX4": invalid chain "C", near line
    6305 42947 
    6306 Invalid residue range for struct_conf "HELX5": invalid chain "C", near line
    6307 42948 
    6308 140 messages similar to the above omitted 
    6309 Invalid sheet range for struct_sheet_range "? 1": invalid chain "C", near line
    6310 43197 
    6311 Invalid sheet range for struct_sheet_range "? 2": invalid chain "C", near line
    6312 43198 
    6313 Invalid sheet range for struct_sheet_range "? 3": invalid chain "C", near line
    6314 43199 
    6315 Invalid sheet range for struct_sheet_range "? 4": invalid chain "C", near line
    6316 43200 
    6317 Invalid sheet range for struct_sheet_range "? 5": invalid chain "C", near line
    6318 43201 
    6319 168 messages similar to the above omitted 
    6320 Atom O3' has no neighbors to form bonds with according to residue template for
    6321 G /1:19 
    6322 Atom OP1 has no neighbors to form bonds with according to residue template for
    6323 U /2:562 
    6324 Atom OP2 has no neighbors to form bonds with according to residue template for
    6325 U /2:562 
    6326 Atom C5' has no neighbors to form bonds with according to residue template for
    6327 U /2:1003 
    6328 Atom C8 has no neighbors to form bonds with according to residue template for
    6329 A /2:1151 
    6330 Atom O4' has no neighbors to form bonds with according to residue template for
    6331 C /2:1191 
    6332 Atom OP1 has no neighbors to form bonds with according to residue template for
    6333 A /2:1193 
    6334 Atom OP2 has no neighbors to form bonds with according to residue template for
    6335 A /2:1193 
    6336 Atom OP2 has no neighbors to form bonds with according to residue template for
    6337 A /2:1207 
    6338 Atom O6 has no neighbors to form bonds with according to residue template for
    6339 G /2:1217 
    6340 Atom N1 has no neighbors to form bonds with according to residue template for
    6341 G /2:1217 
    6342 Atom N2 has no neighbors to form bonds with according to residue template for
    6343 G /2:1217 
    6344 Atom OP1 has no neighbors to form bonds with according to residue template for
    6345 A /2:1243 
    6346 Atom OP2 has no neighbors to form bonds with according to residue template for
    6347 G /2:1269 
    6348 Atom OP1 has no neighbors to form bonds with according to residue template for
    6349 C /2:1273 
    6350 Atom O5' has no neighbors to form bonds with according to residue template for
    6351 C /2:1273 
    6352 Atom OP1 has no neighbors to form bonds with according to residue template for
    6353 A /2:1425 
    6354 Atom N7 has no neighbors to form bonds with according to residue template for
    6355 G /2:1446 
    6356 Atom O2' has no neighbors to form bonds with according to residue template for
    6357 G /2:1540 
    6358 Atom C6 has no neighbors to form bonds with according to residue template for
    6359 U /2:1542 
    6360 Atom O3' has no neighbors to form bonds with according to residue template for
    6361 A /2:1553 
    6362 Atom O2' has no neighbors to form bonds with according to residue template for
    6363 A /2:1553 
    6364 Atom OP1 has no neighbors to form bonds with according to residue template for
    6365 A /2:1554 
    6366 Atom O2' has no neighbors to form bonds with according to residue template for
    6367 A /2:1554 
    6368 Atom O2' has no neighbors to form bonds with according to residue template for
    6369 A /2:1567 
    6370 Atom O4' has no neighbors to form bonds with according to residue template for
    6371 U /2:1577 
    6372 Atom O2 has no neighbors to form bonds with according to residue template for
    6373 C /2:1617 
    6374 Atom O2' has no neighbors to form bonds with according to residue template for
    6375 U /2:1626 
    6376 Atom O2 has no neighbors to form bonds with according to residue template for
    6377 U /2:1626 
    6378 Atom O3' has no neighbors to form bonds with according to residue template for
    6379 U /2:1768 
    6380 Atom O3' has no neighbors to form bonds with according to residue template for
    6381 G /2:1776 
    6382 Atom O3' has no neighbors to form bonds with according to residue template for
    6383 G /2:1790 
    6384 Atom O2' has no neighbors to form bonds with according to residue template for
    6385 G /2:1790 
    6386 Atom C1' has no neighbors to form bonds with according to residue template for
    6387 G /2:1790 
    6388 Atom N has no neighbors to form bonds with according to residue template for
    6389 GLU /F:183 
    6390 Atom OE1 has no neighbors to form bonds with according to residue template for
    6391 GLU /F:218 
    6392 Atom OE2 has no neighbors to form bonds with according to residue template for
    6393 GLU /F:218 
    6394 Atom C has no neighbors to form bonds with according to residue template for
    6395 LYS /P:59 
    6396 Atom CG has no neighbors to form bonds with according to residue template for
    6397 LYS /P:64 
    6398 Atom CE has no neighbors to form bonds with according to residue template for
    6399 LYS /P:64 
    6400 Atom N has no neighbors to form bonds with according to residue template for
    6401 VAL /P:86 
    6402 Atom CG2 has no neighbors to form bonds with according to residue template for
    6403 VAL /P:86 
    6404 Atom O has no neighbors to form bonds with according to residue template for
    6405 PRO /a:2 
    6406 Atom OD1 has no neighbors to form bonds with according to residue template for
    6407 ASP /i:90 
    6408 Atom O has no neighbors to form bonds with according to residue template for
    6409 LYS /j:35 
    6410 Atom O has no neighbors to form bonds with according to residue template for
    6411 ILE /j:46 
    6412 Atom CD1 has no neighbors to form bonds with according to residue template for
    6413 ILE /j:46 
    6414 Atom O has no neighbors to form bonds with according to residue template for
    6415 ILE /j:95 
    6416 Atom CG2 has no neighbors to form bonds with according to residue template for
    6417 ILE /j:96 
    6418 Atom O has no neighbors to form bonds with according to residue template for
    6419 LYS /j:106 
    6420 Atom SG has no neighbors to form bonds with according to residue template for
    6421 CYS /j:262 
    6422 Atom N has no neighbors to form bonds with according to residue template for
    6423 ASN /j:263 
    6424 Atom O has no neighbors to form bonds with according to residue template for
    6425 LYS /p:142 
    6426 Atom CG has no neighbors to form bonds with according to residue template for
    6427 GLU /p:290 
    6428 Atom OE1 has no neighbors to form bonds with according to residue template for
    6429 GLU /p:290 
    6430 Atom N has no neighbors to form bonds with according to residue template for
    6431 ILE /p:292 
    6432 Atom N has no neighbors to form bonds with according to residue template for
    6433 HIS /p:310 
    6434 Atom CE1 has no neighbors to form bonds with according to residue template for
    6435 HIS /p:310 
    6436  
    6437 Chain information for 0057_6gsm_l.cif #1 
    6438 --- 
    6439 Chain | Description 
    6440 1 | Met-tRNAi 
    6441 2 | 18S ribosomal RNA 
    6442 3 | mRNA (5'-R(P*AP*AP*U)-3') 
    6443 F | KLLA0D10659p 
    6444 P | KLLA0F07843p 
    6445 Q | 40S ribosomal protein S16 
    6446 S | KLLA0B01562p 
    6447 c | 40S ribosomal protein S28 
    6448 e | 40S ribosomal protein S30 
    6449 f | Ubiquitin-40S ribosomal protein S27a 
    6450 h | 60S ribosomal protein L41-A 
    6451 i | Eukaryotic translation initiation factor 1A 
    6452 j | Eukaryotic translation initiation factor 2 subunit alpha 
    6453 k | Eukaryotic translation initiation factor 2 subunit gamma 
    6454 l | Eukaryotic translation initiation factor 2 subunit beta 
    6455 m | Eukaryotic translation initiation factor eIF-1 
    6456 p | Eukaryotic translation initiation factor 3 subunit B 
    6457 q | Eukaryotic translation initiation factor 3 subunit C 
    6458  
    6459 
    6460 > open /scratch/cs-
    6461 > bioinfo/tngu/6k_data/Box_Chains_new/0057_6gsm/0057_6gsm_l.mrc
    6462 
    6463 Opened 0057_6gsm_l.mrc as #2, grid size 120,72,88, pixel 1, shown at level
    6464 0.117, step 1, values float32 
    6465 
    6466 > fitmap #1 inMap #2
    6467 
    6468 Fit molecule 0057_6gsm_l.cif (#1) to map 0057_6gsm_l.mrc (#2) using 11892
    6469 atoms 
    6470 average map value = 0.06384, steps = 72 
    6471 shifted from previous position = 0.608 
    6472 rotated from previous position = 0.153 degrees 
    6473 atoms outside contour = 11222, contour level = 0.11707 
    6474  
    6475 Position of 0057_6gsm_l.cif (#1) relative to 0057_6gsm_l.mrc (#2) coordinates: 
    6476 Matrix rotation and translation 
    6477 0.99999771 0.00015409 0.00213271 -0.96507720 
    6478 -0.00015068 0.99999871 -0.00159690 0.08959189 
    6479 -0.00213295 0.00159657 0.99999645 0.13446134 
    6480 Axis 0.59832829 0.79921371 -0.05710259 
    6481 Axis point 48.77929787 0.00000000 308.50125021 
    6482 Rotation angle (degrees) 0.15290296 
    6483 Shift along axis -0.51350801 
    6484  
    6485 
    6486 > save /scratch/cs-
    6487 > bioinfo/tngu/6k_data/Box_Chains_new/0057_6gsm/0057_6gsm_l_fitted.cif #1
    6488 
    6489 > close #1
    6490 
    6491 > close #2
    6492 
    6493 > open /scratch/cs-
    6494 > bioinfo/tngu/6k_data/Box_Chains_new/0057_6gsm/0057_6gsm_f.cif
    6495 
    6496 Summary of feedback from opening /scratch/cs-
    6497 bioinfo/tngu/6k_data/Box_Chains_new/0057_6gsm/0057_6gsm_f.cif 
    6498 --- 
    6499 warnings | Invalid residue range for struct_conf "HELX1": invalid chain "C",
    6500 near line 41078 
    6501 Invalid residue range for struct_conf "HELX2": invalid chain "C", near line
    6502 41079 
    6503 Invalid residue range for struct_conf "HELX3": invalid chain "C", near line
    6504 41080 
    6505 Invalid residue range for struct_conf "HELX4": invalid chain "C", near line
    6506 41081 
    6507 Invalid residue range for struct_conf "HELX5": invalid chain "C", near line
    6508 41082 
    6509 193 messages similar to the above omitted 
    6510 Invalid sheet range for struct_sheet_range "? 1": invalid chain "C", near line
    6511 41331 
    6512 Invalid sheet range for struct_sheet_range "? 2": invalid chain "C", near line
    6513 41332 
    6514 Invalid sheet range for struct_sheet_range "? 3": invalid chain "C", near line
    6515 41333 
    6516 Invalid sheet range for struct_sheet_range "? 4": invalid chain "C", near line
    6517 41334 
    6518 Invalid sheet range for struct_sheet_range "? 5": invalid chain "C", near line
    6519 41335 
    6520 220 messages similar to the above omitted 
    6521 Atom OP2 has no neighbors to form bonds with according to residue template for
    6522 A /2:1193 
    6523 Atom O2' has no neighbors to form bonds with according to residue template for
    6524 G /2:1280 
    6525 Atom OP2 has no neighbors to form bonds with according to residue template for
    6526 C /2:1424 
    6527 Atom O2' has no neighbors to form bonds with according to residue template for
    6528 G /2:1464 
    6529 Atom O2 has no neighbors to form bonds with according to residue template for
    6530 C /2:1465 
    6531 Atom OP2 has no neighbors to form bonds with according to residue template for
    6532 C /2:1483 
    6533 Atom O4' has no neighbors to form bonds with according to residue template for
    6534 G /2:1496 
    6535 Atom O3' has no neighbors to form bonds with according to residue template for
    6536 G /2:1502 
    6537 Atom OP1 has no neighbors to form bonds with according to residue template for
    6538 G /2:1588 
    6539 Atom O5' has no neighbors to form bonds with according to residue template for
    6540 G /2:1603 
    6541 Atom O has no neighbors to form bonds with according to residue template for
    6542 VAL /D:37 
    6543 Atom O has no neighbors to form bonds with according to residue template for
    6544 ASP /D:57 
    6545 Atom O has no neighbors to form bonds with according to residue template for
    6546 ARG /D:64 
    6547 Atom N has no neighbors to form bonds with according to residue template for
    6548 SER /D:129 
    6549 Atom CB has no neighbors to form bonds with according to residue template for
    6550 SER /D:129 
    6551 Atom O has no neighbors to form bonds with according to residue template for
    6552 LYS /D:190 
    6553 Atom CG has no neighbors to form bonds with according to residue template for
    6554 LYS /D:190 
    6555 Atom N has no neighbors to form bonds with according to residue template for
    6556 GLN /M:122 
    6557 Atom C has no neighbors to form bonds with according to residue template for
    6558 GLN /M:122 
    6559 Atom CB has no neighbors to form bonds with according to residue template for
    6560 GLN /M:122 
    6561 Atom N has no neighbors to form bonds with according to residue template for
    6562 MET /P:28 
    6563 Atom NH2 has no neighbors to form bonds with according to residue template for
    6564 ARG /S:110 
    6565 Atom CB has no neighbors to form bonds with according to residue template for
    6566 ALA /T:41 
    6567 Atom N has no neighbors to form bonds with according to residue template for
    6568 TYR /T:80 
    6569 Atom N has no neighbors to form bonds with according to residue template for
    6570 ALA /T:96 
    6571 Atom O has no neighbors to form bonds with according to residue template for
    6572 ALA /T:96 
    6573 Atom O has no neighbors to form bonds with according to residue template for
    6574 THR /U:29 
    6575 Atom N has no neighbors to form bonds with according to residue template for
    6576 ARG /d:56 
    6577 Atom CD2 has no neighbors to form bonds with according to residue template for
    6578 LEU /i:65 
    6579 Atom N has no neighbors to form bonds with according to residue template for
    6580 LEU /i:78 
    6581 Atom CB has no neighbors to form bonds with according to residue template for
    6582 LEU /i:78 
    6583 Atom N has no neighbors to form bonds with according to residue template for
    6584 LEU /i:109 
    6585 Atom O has no neighbors to form bonds with according to residue template for
    6586 ARG /l:167 
    6587 Atom N has no neighbors to form bonds with according to residue template for
    6588 GLN /l:178 
    6589 Atom CB has no neighbors to form bonds with according to residue template for
    6590 GLN /l:178 
    6591 Atom N has no neighbors to form bonds with according to residue template for
    6592 ASP /l:179 
    6593  
    6594 Chain information for 0057_6gsm_f.cif #1 
    6595 --- 
    6596 Chain | Description 
    6597 1 | Met-tRNAi 
    6598 2 | 18S ribosomal RNA 
    6599 D | KLLA0D08305p 
    6600 K | KLLA0B08173p 
    6601 M | 40S ribosomal protein S12 
    6602 P | KLLA0F07843p 
    6603 S | KLLA0B01562p 
    6604 T | KLLA0A07194p 
    6605 U | KLLA0F25542p 
    6606 d | 40S ribosomal protein S29 
    6607 f | Ubiquitin-40S ribosomal protein S27a 
    6608 i | Eukaryotic translation initiation factor 1A 
    6609 l | Eukaryotic translation initiation factor 2 subunit beta 
    6610  
    6611 
    6612 > open /scratch/cs-
    6613 > bioinfo/tngu/6k_data/Box_Chains_new/0057_6gsm/0057_6gsm_f.mrc
    6614 
    6615 Opened 0057_6gsm_f.mrc as #2, grid size 80,72,120, pixel 1, shown at level
    6616 0.121, step 1, values float32 
    6617 
    6618 > fitmap #1 inMap #2
    6619 
    6620 Fit molecule 0057_6gsm_f.cif (#1) to map 0057_6gsm_f.mrc (#2) using 10038
    6621 atoms 
    6622 average map value = 0.07064, steps = 48 
    6623 shifted from previous position = 0.453 
    6624 rotated from previous position = 0.191 degrees 
    6625 atoms outside contour = 9477, contour level = 0.12053 
    6626  
    6627 Position of 0057_6gsm_f.cif (#1) relative to 0057_6gsm_f.mrc (#2) coordinates: 
    6628 Matrix rotation and translation 
    6629 0.99999742 0.00017353 -0.00226392 0.00548192 
    6630 -0.00016801 0.99999701 0.00243768 -0.65676907 
    6631 0.00226434 -0.00243729 0.99999447 0.03413541 
    6632 Axis -0.73171784 -0.67967718 -0.05126334 
    6633 Axis point 0.00000000 22.94036133 146.59506449 
    6634 Rotation angle (degrees) 0.19086294 
    6635 Shift along axis 0.44062983 
    6636  
    6637 
    6638 > save /scratch/cs-
    6639 > bioinfo/tngu/6k_data/Box_Chains_new/0057_6gsm/0057_6gsm_f_fitted.cif #1
    6640 
    6641 > close #1
    6642 
    6643 > close #2
     1748
     1749[deleted to fit within ticket limits]
    66441750
    66451751> open /scratch/cs-