![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 2 years ago
Last modified 8 months ago
#9624 closed defect
ChimeraX bug report submission — at Initial Version
| Reported by: | Owned by: | ||
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Input/Output | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: Linux-4.18.0-425.19.2.el8_7.x86_64-x86_64-with-glibc2.28
ChimeraX Version: 1.6.1 (2023-05-09 17:57:07 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Segmentation fault
Thread 0x00007fd1c566f700 (most recent call first):
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/threading.py", line 316 in wait
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/threading.py", line 574 in wait
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/threading.py", line 1297 in run
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/threading.py", line 973 in _bootstrap_inner
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/threading.py", line 930 in _bootstrap
Current thread 0x00007fd239fd6740 (most recent call first):
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/chimerax/mmcif/__init__.py", line 43 in open
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/chimerax/open_command/cmd.py", line 435 in remember_data_format
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/chimerax/open_command/cmd.py", line 464 in collated_open
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/chimerax/open_command/cmd.py", line 194 in provider_open
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/chimerax/core/commands/cli.py", line 2897 in run
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/chimerax/open_command/cmd.py", line 119 in cmd_open
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/chimerax/core/commands/cli.py", line 2897 in run
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/chimerax/core/commands/run.py", line 38 in run
File "/scratch/cs-bioinfo/tngu/6k_data/fit_map.py", line 40 in main
File "/scratch/cs-bioinfo/tngu/6k_data/fit_map.py", line 51 in
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/chimerax/core/scripting.py", line 61 in _exec_python
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/chimerax/core/scripting.py", line 84 in open_python_script
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/chimerax/core/commands/runscript.py", line 38 in runscript
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/chimerax/core/commands/cli.py", line 2897 in run
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/chimerax/cmd_line/tool.py", line 319 in execute
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/chimerax/cmd_line/tool.py", line 146 in keyPressEvent
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/chimerax/ui/gui.py", line 275 in event_loop
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/chimerax/core/__main__.py", line 892 in init
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/chimerax/core/__main__.py", line 1043 in
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/runpy.py", line 87 in _run_code
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/runpy.py", line 197 in _run_module_as_main
===== Log before crash start =====
UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> runscript /scratch/cs-bioinfo/tngu/6k_data/fit_map.py --nogui
> wait
wait requires a frame count argument unless motion is in progress
> open /scratch/cs-
> bioinfo/tngu/6k_data/Box_Chains_new/0057_6gsm/0057_6gsm_G.cif
Summary of feedback from opening /scratch/cs-
bioinfo/tngu/6k_data/Box_Chains_new/0057_6gsm/0057_6gsm_G.cif
---
warnings | Invalid residue range for struct_conf "HELX1": invalid chain "C",
near line 52598
Invalid residue range for struct_conf "HELX2": invalid chain "C", near line
52599
Invalid residue range for struct_conf "HELX3": invalid chain "C", near line
52600
Invalid residue range for struct_conf "HELX4": invalid chain "C", near line
52601
Invalid residue range for struct_conf "HELX5": invalid chain "C", near line
52602
111 messages similar to the above omitted
Invalid sheet range for struct_sheet_range "? 1": invalid chain "C", near line
52851
Invalid sheet range for struct_sheet_range "? 2": invalid chain "C", near line
52852
Invalid sheet range for struct_sheet_range "? 3": invalid chain "C", near line
52853
Invalid sheet range for struct_sheet_range "? 4": invalid chain "C", near line
52854
Invalid sheet range for struct_sheet_range "? 5": invalid chain "C", near line
52855
139 messages similar to the above omitted
Atom OP2 has no neighbors to form bonds with according to residue template for
G /2:48
Atom C5' has no neighbors to form bonds with according to residue template for
G /2:48
Atom N6 has no neighbors to form bonds with according to residue template for
A /2:220
Atom OP2 has no neighbors to form bonds with according to residue template for
C /2:307
Atom O3' has no neighbors to form bonds with according to residue template for
G /2:376
Atom OP2 has no neighbors to form bonds with according to residue template for
C /2:410
Atom O5' has no neighbors to form bonds with according to residue template for
C /2:410
Atom N6 has no neighbors to form bonds with according to residue template for
A /2:469
Atom O2' has no neighbors to form bonds with according to residue template for
A /2:472
Atom OP1 has no neighbors to form bonds with according to residue template for
A /2:511
Atom C5' has no neighbors to form bonds with according to residue template for
A /2:511
Atom OP1 has no neighbors to form bonds with according to residue template for
U /2:637
Atom O6 has no neighbors to form bonds with according to residue template for
G /2:837
Atom OP1 has no neighbors to form bonds with according to residue template for
A /2:858
Atom O3' has no neighbors to form bonds with according to residue template for
C /2:1662
Atom ND1 has no neighbors to form bonds with according to residue template for
HIS /H:122
Atom N has no neighbors to form bonds with according to residue template for
LYS /H:124
Atom NZ has no neighbors to form bonds with according to residue template for
LYS /H:124
Atom O has no neighbors to form bonds with according to residue template for
ALA /J:55
Atom CB has no neighbors to form bonds with according to residue template for
ALA /J:55
Atom N has no neighbors to form bonds with according to residue template for
LYS /J:65
Atom O has no neighbors to form bonds with according to residue template for
ARG /J:107
Atom CG2 has no neighbors to form bonds with according to residue template for
ILE /J:129
Atom CD has no neighbors to form bonds with according to residue template for
LYS /J:175
Atom NZ has no neighbors to form bonds with according to residue template for
LYS /J:175
Atom N has no neighbors to form bonds with according to residue template for
ALA /J:177
Atom CB has no neighbors to form bonds with according to residue template for
ALA /J:177
Atom N has no neighbors to form bonds with according to residue template for
TYR /L:93
Atom CB has no neighbors to form bonds with according to residue template for
TYR /L:93
Atom CB has no neighbors to form bonds with according to residue template for
ARG /L:103
Atom CD has no neighbors to form bonds with according to residue template for
ARG /L:103
Atom CB has no neighbors to form bonds with according to residue template for
ASN /W:80
Atom ND2 has no neighbors to form bonds with according to residue template for
ASN /W:80
Atom OG1 has no neighbors to form bonds with according to residue template for
THR /W:105
Atom N has no neighbors to form bonds with according to residue template for
LYS /W:124
Atom CD has no neighbors to form bonds with according to residue template for
LYS /W:124
Atom O has no neighbors to form bonds with according to residue template for
LYS /p:711
Atom CB has no neighbors to form bonds with according to residue template for
LYS /p:711
Atom N has no neighbors to form bonds with according to residue template for
VAL /q:191
Atom O has no neighbors to form bonds with according to residue template for
LYS /q:203
Atom CB has no neighbors to form bonds with according to residue template for
LYS /q:203
Atom O has no neighbors to form bonds with according to residue template for
LYS /q:204
Chain information for 0057_6gsm_G.cif #1
---
Chain | Description
2 | 18S ribosomal RNA
E | 40S ribosomal protein S4
G | 40S ribosomal protein S6
H | 40S ribosomal protein S7
I | 40S ribosomal protein S8
J | KLLA0E23673p
L | KLLA0A10483p
N | KLLA0F18040p
W | 40S ribosomal protein S22
Y | 40S ribosomal protein S24
o | Eukaryotic translation initiation factor 3 subunit A,Eukaryotic
translation initiation factor 3 subunit A,eIF3a
p | Eukaryotic translation initiation factor 3 subunit B
q | Eukaryotic translation initiation factor 3 subunit C
s | Eukaryotic translation initiation factor 3 subunit I
> open /scratch/cs-
> bioinfo/tngu/6k_data/Box_Chains_new/0057_6gsm/0057_6gsm_G.mrc
Opened 0057_6gsm_G.mrc as #2, grid size 128,96,120, pixel 1, shown at level
0.137, step 1, values float32
> fitmap #1 inMap #2
Fit molecule 0057_6gsm_G.cif (#1) to map 0057_6gsm_G.mrc (#2) using 21277
atoms
average map value = 0.08241, steps = 52
shifted from previous position = 0.565
rotated from previous position = 0.0908 degrees
atoms outside contour = 19986, contour level = 0.13743
Position of 0057_6gsm_G.cif (#1) relative to 0057_6gsm_G.mrc (#2) coordinates:
Matrix rotation and translation
0.99999988 0.00036109 0.00033554 -0.46287238
-0.00036159 0.99999880 0.00150641 -0.65958073
-0.00033500 -0.00150654 0.99999881 0.32002281
Axis -0.95041723 0.21151699 -0.22796416
Axis point 0.00000000 246.46942257 469.98187871
Rotation angle (degrees) 0.09081766
Shift along axis 0.22745563
> save /scratch/cs-
> bioinfo/tngu/6k_data/Box_Chains_new/0057_6gsm/0057_6gsm_G_fitted.cif #1
> close #1
> close #2
> open /scratch/cs-
> bioinfo/tngu/6k_data/Box_Chains_new/0057_6gsm/0057_6gsm_E.cif
Summary of feedback from opening /scratch/cs-
bioinfo/tngu/6k_data/Box_Chains_new/0057_6gsm/0057_6gsm_E.cif
---
warnings | Invalid residue range for struct_conf "HELX1": invalid chain "C",
near line 52424
Invalid residue range for struct_conf "HELX2": invalid chain "C", near line
52425
Invalid residue range for struct_conf "HELX3": invalid chain "C", near line
52426
Invalid residue range for struct_conf "HELX4": invalid chain "C", near line
52427
Invalid residue range for struct_conf "HELX5": invalid chain "C", near line
52428
129 messages similar to the above omitted
Invalid sheet range for struct_sheet_range "? 1": invalid chain "C", near line
52677
Invalid sheet range for struct_sheet_range "? 2": invalid chain "C", near line
52678
Invalid sheet range for struct_sheet_range "? 3": invalid chain "C", near line
52679
Invalid sheet range for struct_sheet_range "? 4": invalid chain "C", near line
52680
Invalid sheet range for struct_sheet_range "? 5": invalid chain "C", near line
52681
151 messages similar to the above omitted
Atom OP1 has no neighbors to form bonds with according to residue template for
U /2:24
Atom O3' has no neighbors to form bonds with according to residue template for
A /2:135
Atom OP1 has no neighbors to form bonds with according to residue template for
U /2:157
Atom O2 has no neighbors to form bonds with according to residue template for
U /2:157
Atom C5 has no neighbors to form bonds with according to residue template for
U /2:160
Atom O2' has no neighbors to form bonds with according to residue template for
U /2:193
Atom O6 has no neighbors to form bonds with according to residue template for
G /2:280
Atom OP2 has no neighbors to form bonds with according to residue template for
A /2:368
Atom O2' has no neighbors to form bonds with according to residue template for
A /2:368
Atom O3' has no neighbors to form bonds with according to residue template for
A /2:369
Atom O2' has no neighbors to form bonds with according to residue template for
A /2:369
Atom OP2 has no neighbors to form bonds with according to residue template for
C /2:375
Atom O4' has no neighbors to form bonds with according to residue template for
C /2:413
Atom OP2 has no neighbors to form bonds with according to residue template for
A /2:517
Atom O4' has no neighbors to form bonds with according to residue template for
C /2:542
Atom OP1 has no neighbors to form bonds with according to residue template for
A /2:593
Atom C5' has no neighbors to form bonds with according to residue template for
A /2:593
Atom OP1 has no neighbors to form bonds with according to residue template for
G /2:594
Atom OP2 has no neighbors to form bonds with according to residue template for
G /2:594
Atom O2' has no neighbors to form bonds with according to residue template for
A /2:629
Atom OP2 has no neighbors to form bonds with according to residue template for
G /2:633
Atom N7 has no neighbors to form bonds with according to residue template for
G /2:633
Atom O6 has no neighbors to form bonds with according to residue template for
G /2:633
Atom O2' has no neighbors to form bonds with according to residue template for
C /2:717
Atom O2 has no neighbors to form bonds with according to residue template for
C /2:717
Atom N1 has no neighbors to form bonds with according to residue template for
G /2:720
Atom N2 has no neighbors to form bonds with according to residue template for
G /2:720
Atom O3' has no neighbors to form bonds with according to residue template for
C /2:826
Atom O2' has no neighbors to form bonds with according to residue template for
C /2:826
Atom OP1 has no neighbors to form bonds with according to residue template for
U /2:859
Atom O2' has no neighbors to form bonds with according to residue template for
A /2:962
Atom OP1 has no neighbors to form bonds with according to residue template for
U /2:1659
Atom O3' has no neighbors to form bonds with according to residue template for
A /2:1716
Atom O2' has no neighbors to form bonds with according to residue template for
A /2:1716
Atom OP1 has no neighbors to form bonds with according to residue template for
A /2:1717
Atom O3' has no neighbors to form bonds with according to residue template for
A /2:1717
Atom O2' has no neighbors to form bonds with according to residue template for
G /2:1735
Atom O has no neighbors to form bonds with according to residue template for
ARG /C:179
Atom NH2 has no neighbors to form bonds with according to residue template for
ARG /C:179
Atom N has no neighbors to form bonds with according to residue template for
HIS /G:81
Atom CE1 has no neighbors to form bonds with according to residue template for
HIS /G:81
Atom N has no neighbors to form bonds with according to residue template for
ARG /G:94
Atom NH1 has no neighbors to form bonds with according to residue template for
ARG /G:94
Atom O has no neighbors to form bonds with according to residue template for
LYS /G:131
Atom CD has no neighbors to form bonds with according to residue template for
LYS /G:131
Atom NZ has no neighbors to form bonds with according to residue template for
LYS /G:131
Atom N has no neighbors to form bonds with according to residue template for
GLY /G:146
Atom C has no neighbors to form bonds with according to residue template for
GLY /G:146
Atom N has no neighbors to form bonds with according to residue template for
PRO /H:113
Atom N has no neighbors to form bonds with according to residue template for
ARG /H:141
Atom N has no neighbors to form bonds with according to residue template for
ARG /I:59
Atom N has no neighbors to form bonds with according to residue template for
GLU /I:61
Atom N has no neighbors to form bonds with according to residue template for
GLU /I:89
Atom CB has no neighbors to form bonds with according to residue template for
GLU /I:89
Atom O has no neighbors to form bonds with according to residue template for
ARG /J:40
Atom N has no neighbors to form bonds with according to residue template for
SER /J:121
Atom O has no neighbors to form bonds with according to residue template for
SER /J:121
Atom OG has no neighbors to form bonds with according to residue template for
SER /J:121
Atom N has no neighbors to form bonds with according to residue template for
SER /N:133
Atom N has no neighbors to form bonds with according to residue template for
LEU /W:38
Atom N has no neighbors to form bonds with according to residue template for
ALA /W:91
Atom CB has no neighbors to form bonds with according to residue template for
ALA /W:91
Atom OE1 has no neighbors to form bonds with according to residue template for
GLN /W:98
Atom N has no neighbors to form bonds with according to residue template for
GLY /W:127
Atom O has no neighbors to form bonds with according to residue template for
GLY /W:127
Atom N has no neighbors to form bonds with according to residue template for
ASP /Y:3
Atom NH1 has no neighbors to form bonds with according to residue template for
ARG /p:472
Atom NH2 has no neighbors to form bonds with according to residue template for
ARG /p:472
Atom O has no neighbors to form bonds with according to residue template for
THR /p:474
Atom N has no neighbors to form bonds with according to residue template for
ASN /q:180
Atom C has no neighbors to form bonds with according to residue template for
ASN /q:180
Chain information for 0057_6gsm_E.cif #1
---
Chain | Description
2 | 18S ribosomal RNA
C | KLLA0F09812p
E | 40S ribosomal protein S4
G | 40S ribosomal protein S6
H | 40S ribosomal protein S7
I | 40S ribosomal protein S8
J | KLLA0E23673p
L | KLLA0A10483p
N | KLLA0F18040p
V | 40S ribosomal protein S21
W | 40S ribosomal protein S22
X | KLLA0B11231p
Y | 40S ribosomal protein S24
p | Eukaryotic translation initiation factor 3 subunit B
q | Eukaryotic translation initiation factor 3 subunit C
> open /scratch/cs-
> bioinfo/tngu/6k_data/Box_Chains_new/0057_6gsm/0057_6gsm_E.mrc
Opened 0057_6gsm_E.mrc as #2, grid size 104,88,104, pixel 1, shown at level
0.146, step 1, values float32
> fitmap #1 inMap #2
Fit molecule 0057_6gsm_E.cif (#1) to map 0057_6gsm_E.mrc (#2) using 21101
atoms
average map value = 0.08422, steps = 76
shifted from previous position = 0.485
rotated from previous position = 0.032 degrees
atoms outside contour = 20281, contour level = 0.14627
Position of 0057_6gsm_E.cif (#1) relative to 0057_6gsm_E.mrc (#2) coordinates:
Matrix rotation and translation
0.99999984 -0.00053731 -0.00015212 0.04774257
0.00053731 0.99999986 0.00001714 -0.54367070
0.00015211 -0.00001722 0.99999999 -0.22470372
Axis -0.03075560 -0.27226867 0.96172962
Axis point 1047.09390853 84.56971963 0.00000000
Rotation angle (degrees) 0.03201084
Shift along axis -0.06954807
> save /scratch/cs-
> bioinfo/tngu/6k_data/Box_Chains_new/0057_6gsm/0057_6gsm_E_fitted.cif #1
> close #1
> close #2
> open /scratch/cs-
> bioinfo/tngu/6k_data/Box_Chains_new/0057_6gsm/0057_6gsm_W.cif
Summary of feedback from opening /scratch/cs-
bioinfo/tngu/6k_data/Box_Chains_new/0057_6gsm/0057_6gsm_W.cif
---
warnings | Invalid residue range for struct_conf "HELX21": invalid chain "G",
near line 48617
Invalid residue range for struct_conf "HELX22": invalid chain "G", near line
48618
Invalid residue range for struct_conf "HELX23": invalid chain "G", near line
48619
Invalid residue range for struct_conf "HELX24": invalid chain "G", near line
48620
Invalid residue range for struct_conf "HELX25": invalid chain "G", near line
48621
131 messages similar to the above omitted
Invalid sheet range for struct_sheet_range "? 25": invalid chain "G", near
line 48874
Invalid sheet range for struct_sheet_range "? 26": invalid chain "G", near
line 48875
Invalid sheet range for struct_sheet_range "? 27": invalid chain "G", near
line 48876
Invalid sheet range for struct_sheet_range "? 28": invalid chain "G", near
line 48877
Invalid sheet range for struct_sheet_range "? 29": invalid chain "G", near
line 48878
179 messages similar to the above omitted
Atom O2' has no neighbors to form bonds with according to residue template for
C /2:297
Atom C8 has no neighbors to form bonds with according to residue template for
A /2:298
Atom OP1 has no neighbors to form bonds with according to residue template for
U /2:349
Atom O5' has no neighbors to form bonds with according to residue template for
U /2:349
Atom C3' has no neighbors to form bonds with according to residue template for
A /2:377
Atom OP1 has no neighbors to form bonds with according to residue template for
C /2:447
Atom O2' has no neighbors to form bonds with according to residue template for
A /2:569
Atom C8 has no neighbors to form bonds with according to residue template for
A /2:665
Atom OP2 has no neighbors to form bonds with according to residue template for
U /2:668
Atom OP2 has no neighbors to form bonds with according to residue template for
G /2:772
Atom C5' has no neighbors to form bonds with according to residue template for
C /2:773
Atom C5' has no neighbors to form bonds with according to residue template for
G /2:818
Atom OP1 has no neighbors to form bonds with according to residue template for
A /2:846
Atom N6 has no neighbors to form bonds with according to residue template for
A /2:880
Atom N1 has no neighbors to form bonds with according to residue template for
A /2:880
Atom OP2 has no neighbors to form bonds with according to residue template for
U /2:946
Atom O2' has no neighbors to form bonds with according to residue template for
C /2:974
Atom O4' has no neighbors to form bonds with according to residue template for
G /2:975
Atom O2' has no neighbors to form bonds with according to residue template for
G /2:975
Atom O2' has no neighbors to form bonds with according to residue template for
A /2:976
Atom N3 has no neighbors to form bonds with according to residue template for
A /2:976
Atom OP2 has no neighbors to form bonds with according to residue template for
U /2:1053
Atom O6 has no neighbors to form bonds with according to residue template for
G /2:1063
Atom OP2 has no neighbors to form bonds with according to residue template for
C /2:1065
Atom OP2 has no neighbors to form bonds with according to residue template for
C /2:1066
Atom C2' has no neighbors to form bonds with according to residue template for
C /2:1066
Atom OP2 has no neighbors to form bonds with according to residue template for
U /2:1078
Atom C8 has no neighbors to form bonds with according to residue template for
G /2:1294
Atom O2 has no neighbors to form bonds with according to residue template for
C /2:1770
Atom O3' has no neighbors to form bonds with according to residue template for
G /2:1786
Atom O5' has no neighbors to form bonds with according to residue template for
G /2:1787
Atom O3' has no neighbors to form bonds with according to residue template for
A /2:1789
Atom N has no neighbors to form bonds with according to residue template for
LEU /A:24
Atom O has no neighbors to form bonds with according to residue template for
LEU /A:24
Atom N has no neighbors to form bonds with according to residue template for
ASP /A:43
Atom C has no neighbors to form bonds with according to residue template for
ASP /A:43
Atom OD1 has no neighbors to form bonds with according to residue template for
ASP /A:43
Atom NH1 has no neighbors to form bonds with according to residue template for
ARG /A:127
Atom NH2 has no neighbors to form bonds with according to residue template for
ARG /A:127
Atom O has no neighbors to form bonds with according to residue template for
ILE /A:173
Atom CG has no neighbors to form bonds with according to residue template for
LEU /A:182
Atom N has no neighbors to form bonds with according to residue template for
ALA /C:123
Atom CB has no neighbors to form bonds with according to residue template for
ALA /C:123
Atom O has no neighbors to form bonds with according to residue template for
LYS /E:6
Atom CB has no neighbors to form bonds with according to residue template for
LYS /E:6
Atom OD1 has no neighbors to form bonds with according to residue template for
ASP /E:21
Atom N has no neighbors to form bonds with according to residue template for
GLU /E:202
Atom CG has no neighbors to form bonds with according to residue template for
GLU /E:202
Atom CB has no neighbors to form bonds with according to residue template for
LEU /E:214
Atom CD2 has no neighbors to form bonds with according to residue template for
LEU /E:214
Atom N has no neighbors to form bonds with according to residue template for
TYR /J:8
Atom OG1 has no neighbors to form bonds with according to residue template for
THR /J:14
Atom N has no neighbors to form bonds with according to residue template for
TYR /J:19
Atom N has no neighbors to form bonds with according to residue template for
ARG /J:82
Atom N has no neighbors to form bonds with according to residue template for
VAL /J:101
Atom CG1 has no neighbors to form bonds with according to residue template for
VAL /J:101
Atom N has no neighbors to form bonds with according to residue template for
PHE /L:60
Atom N has no neighbors to form bonds with according to residue template for
SER /L:65
Atom N has no neighbors to form bonds with according to residue template for
VAL /L:76
Atom CG2 has no neighbors to form bonds with according to residue template for
VAL /L:76
Atom O has no neighbors to form bonds with according to residue template for
VAL /L:107
Atom CB has no neighbors to form bonds with according to residue template for
ALA /L:114
Atom NE2 has no neighbors to form bonds with according to residue template for
GLN /L:118
Atom OD1 has no neighbors to form bonds with according to residue template for
ASN /L:138
Atom CE has no neighbors to form bonds with according to residue template for
LYS /N:27
Atom NE2 has no neighbors to form bonds with according to residue template for
GLN /N:36
Atom OD1 has no neighbors to form bonds with according to residue template for
ASP /N:108
Atom OD2 has no neighbors to form bonds with according to residue template for
ASP /N:108
Atom O has no neighbors to form bonds with according to residue template for
LYS /N:109
Atom NZ has no neighbors to form bonds with according to residue template for
LYS /N:109
Atom ND2 has no neighbors to form bonds with according to residue template for
ASN /N:138
Atom N has no neighbors to form bonds with according to residue template for
ASN /N:151
Atom O has no neighbors to form bonds with according to residue template for
ASN /X:65
Atom N has no neighbors to form bonds with according to residue template for
ILE /X:117
Atom CG1 has no neighbors to form bonds with according to residue template for
ILE /X:117
Atom N has no neighbors to form bonds with according to residue template for
ASN /a:8
Atom C has no neighbors to form bonds with according to residue template for
PHE /b:79
Chain information for 0057_6gsm_W.cif #1
---
Chain | Description
2 | 18S ribosomal RNA
A | 40S ribosomal protein S0
B | 40S ribosomal protein S1
C | KLLA0F09812p
E | 40S ribosomal protein S4
H | 40S ribosomal protein S7
J | KLLA0E23673p
L | KLLA0A10483p
N | KLLA0F18040p
R | KLLA0B01474p
V | 40S ribosomal protein S21
W | 40S ribosomal protein S22
X | KLLA0B11231p
a | 40S ribosomal protein S26
b | 40S ribosomal protein S27
q | Eukaryotic translation initiation factor 3 subunit C
> open /scratch/cs-
> bioinfo/tngu/6k_data/Box_Chains_new/0057_6gsm/0057_6gsm_W.mrc
Opened 0057_6gsm_W.mrc as #2, grid size 80,80,96, pixel 1, shown at level
0.151, step 1, values float32
> fitmap #1 inMap #2
Fit molecule 0057_6gsm_W.cif (#1) to map 0057_6gsm_W.mrc (#2) using 17398
atoms
average map value = 0.08231, steps = 44
shifted from previous position = 0.389
rotated from previous position = 0.0845 degrees
atoms outside contour = 16885, contour level = 0.15092
Position of 0057_6gsm_W.cif (#1) relative to 0057_6gsm_W.mrc (#2) coordinates:
Matrix rotation and translation
0.99999892 -0.00128029 -0.00071689 0.37524796
0.00128019 0.99999917 -0.00014574 -0.48830710
0.00071707 0.00014482 0.99999973 -0.43251942
Axis 0.09852578 -0.48624862 0.86824821
Axis point 420.03816705 300.52438078 0.00000000
Rotation angle (degrees) 0.08448321
Shift along axis -0.10112396
> save /scratch/cs-
> bioinfo/tngu/6k_data/Box_Chains_new/0057_6gsm/0057_6gsm_W_fitted.cif #1
> close #1
> close #2
> open /scratch/cs-
> bioinfo/tngu/6k_data/Box_Chains_new/0057_6gsm/0057_6gsm_Q.cif
Summary of feedback from opening /scratch/cs-
bioinfo/tngu/6k_data/Box_Chains_new/0057_6gsm/0057_6gsm_Q.cif
---
warnings | Invalid residue range for struct_conf "HELX7": invalid chain "E",
near line 50180
Invalid residue range for struct_conf "HELX8": invalid chain "E", near line
50181
Invalid residue range for struct_conf "HELX9": invalid chain "E", near line
50182
Invalid residue range for struct_conf "HELX10": invalid chain "E", near line
50183
Invalid residue range for struct_conf "HELX11": invalid chain "E", near line
50184
149 messages similar to the above omitted
Invalid sheet range for struct_sheet_range "? 8": invalid chain "E", near line
50434
Invalid sheet range for struct_sheet_range "? 9": invalid chain "E", near line
50435
Invalid sheet range for struct_sheet_range "? 10": invalid chain "E", near
line 50436
Invalid sheet range for struct_sheet_range "? 11": invalid chain "E", near
line 50437
Invalid sheet range for struct_sheet_range "? 12": invalid chain "E", near
line 50438
147 messages similar to the above omitted
Atom OP1 has no neighbors to form bonds with according to residue template for
G /1:24
Atom OP2 has no neighbors to form bonds with according to residue template for
G /1:24
Atom OP1 has no neighbors to form bonds with according to residue template for
C /1:25
Atom OP2 has no neighbors to form bonds with according to residue template for
C /1:25
Atom OP1 has no neighbors to form bonds with according to residue template for
M2G /1:26
Atom OP2 has no neighbors to form bonds with according to residue template for
M2G /1:26
Atom OP2 has no neighbors to form bonds with according to residue template for
A /2:906
Atom OP2 has no neighbors to form bonds with according to residue template for
C /2:1005
Atom O4 has no neighbors to form bonds with according to residue template for
U /2:1184
Atom OP2 has no neighbors to form bonds with according to residue template for
U /2:1186
Atom O4' has no neighbors to form bonds with according to residue template for
A /2:1201
Atom OP2 has no neighbors to form bonds with according to residue template for
A /2:1324
Atom O3' has no neighbors to form bonds with according to residue template for
A /2:1324
Atom OP1 has no neighbors to form bonds with according to residue template for
U /2:1430
Atom O2 has no neighbors to form bonds with according to residue template for
C /2:1454
Atom OP1 has no neighbors to form bonds with according to residue template for
C /2:1498
Atom OP2 has no neighbors to form bonds with according to residue template for
C /2:1498
Atom O2' has no neighbors to form bonds with according to residue template for
G /2:1510
Atom O2' has no neighbors to form bonds with according to residue template for
G /2:1511
Atom O2' has no neighbors to form bonds with according to residue template for
U /2:1558
Atom O2 has no neighbors to form bonds with according to residue template for
U /2:1796
Atom C has no neighbors to form bonds with according to residue template for
SER /D:6
Atom CB has no neighbors to form bonds with according to residue template for
SER /D:6
Atom N has no neighbors to form bonds with according to residue template for
LYS /D:10
Atom C has no neighbors to form bonds with according to residue template for
LYS /D:10
Atom C has no neighbors to form bonds with according to residue template for
ASP /D:14
Atom CE2 has no neighbors to form bonds with according to residue template for
TYR /D:34
Atom OH has no neighbors to form bonds with according to residue template for
TYR /D:34
Atom N has no neighbors to form bonds with according to residue template for
VAL /D:39
Atom O has no neighbors to form bonds with according to residue template for
VAL /D:39
Atom CB has no neighbors to form bonds with according to residue template for
ARG /D:90
Atom O has no neighbors to form bonds with according to residue template for
VAL /D:181
Atom N has no neighbors to form bonds with according to residue template for
PHE /O:27
Atom N has no neighbors to form bonds with according to residue template for
ALA /O:63
Atom CB has no neighbors to form bonds with according to residue template for
ALA /O:63
Atom NZ has no neighbors to form bonds with according to residue template for
LYS /O:92
Atom O has no neighbors to form bonds with according to residue template for
PRO /S:82
Atom N has no neighbors to form bonds with according to residue template for
ARG /S:88
Atom CE2 has no neighbors to form bonds with according to residue template for
TYR /S:98
Atom OH has no neighbors to form bonds with according to residue template for
TYR /S:98
Atom N has no neighbors to form bonds with according to residue template for
ARG /S:110
Atom N has no neighbors to form bonds with according to residue template for
PHE /S:128
Atom CE3 has no neighbors to form bonds with according to residue template for
TRP /S:129
Atom O has no neighbors to form bonds with according to residue template for
THR /U:104
Atom C has no neighbors to form bonds with according to residue template for
ILE /U:106
Atom NH1 has no neighbors to form bonds with according to residue template for
ARG /a:38
Atom N has no neighbors to form bonds with according to residue template for
SER /g:187
Atom O has no neighbors to form bonds with according to residue template for
LEU /g:188
Atom CB has no neighbors to form bonds with according to residue template for
LEU /g:232
Atom CD1 has no neighbors to form bonds with according to residue template for
LEU /g:232
Atom CD2 has no neighbors to form bonds with according to residue template for
LEU /g:232
Atom N has no neighbors to form bonds with according to residue template for
ASN /i:96
Atom OG has no neighbors to form bonds with according to residue template for
SER /j:4
Atom N has no neighbors to form bonds with according to residue template for
GLU /j:38
Atom CD2 has no neighbors to form bonds with according to residue template for
LEU /j:62
Atom OG1 has no neighbors to form bonds with according to residue template for
THR /l:172
Atom CD has no neighbors to form bonds with according to residue template for
LYS /l:214
Atom NZ has no neighbors to form bonds with according to residue template for
LYS /l:214
Chain information for 0057_6gsm_Q.cif #1
---
Chain | Description
1 | Met-tRNAi
2 | 18S ribosomal RNA
3 | mRNA (5'-R(P*AP*AP*U)-3')
A | 40S ribosomal protein S0
D | KLLA0D08305p
F | KLLA0D10659p
O | 40S ribosomal protein S14
P | KLLA0F07843p
Q | 40S ribosomal protein S16
R | KLLA0B01474p
S | KLLA0B01562p
T | KLLA0A07194p
U | KLLA0F25542p
Z | KLLA0B06182p
a | 40S ribosomal protein S26
c | 40S ribosomal protein S28
d | 40S ribosomal protein S29
g | KLLA0E12277p
i | Eukaryotic translation initiation factor 1A
j | Eukaryotic translation initiation factor 2 subunit alpha
l | Eukaryotic translation initiation factor 2 subunit beta
m | Eukaryotic translation initiation factor eIF-1
> open /scratch/cs-
> bioinfo/tngu/6k_data/Box_Chains_new/0057_6gsm/0057_6gsm_Q.mrc
Opened 0057_6gsm_Q.mrc as #2, grid size 112,96,80, pixel 1, shown at level
0.131, step 1, values float32
> fitmap #1 inMap #2
Fit molecule 0057_6gsm_Q.cif (#1) to map 0057_6gsm_Q.mrc (#2) using 19007
atoms
average map value = 0.07351, steps = 44
shifted from previous position = 0.452
rotated from previous position = 0.238 degrees
atoms outside contour = 18277, contour level = 0.13084
Position of 0057_6gsm_Q.cif (#1) relative to 0057_6gsm_Q.mrc (#2) coordinates:
Matrix rotation and translation
0.99999819 -0.00178385 0.00066254 -0.03363365
0.00178629 0.99999159 -0.00369093 0.32899231
-0.00065595 0.00369211 0.99999297 -0.85139789
Axis 0.88885447 0.15873590 0.42981467
Axis point 0.00000000 190.79468520 103.47866224
Rotation angle (degrees) 0.23795686
Shift along axis -0.34361583
> save /scratch/cs-
> bioinfo/tngu/6k_data/Box_Chains_new/0057_6gsm/0057_6gsm_Q_fitted.cif #1
> close #1
> close #2
> open /scratch/cs-
> bioinfo/tngu/6k_data/Box_Chains_new/0057_6gsm/0057_6gsm_2.cif
Summary of feedback from opening /scratch/cs-
bioinfo/tngu/6k_data/Box_Chains_new/0057_6gsm/0057_6gsm_2.cif
---
warnings | Invalid residue range for struct_conf "HELX72": invalid chain "P",
near line 72713
Invalid residue range for struct_conf "HELX73": invalid chain "P", near line
72714
Invalid residue range for struct_conf "HELX74": invalid chain "P", near line
72715
Invalid residue range for struct_conf "HELX75": invalid chain "P", near line
72716
Invalid residue range for struct_conf "HELX76": invalid chain "P", near line
72717
21 messages similar to the above omitted
Invalid sheet range for struct_sheet_range "? 79": invalid chain "P", near
line 72973
Invalid sheet range for struct_sheet_range "? 80": invalid chain "P", near
line 72974
Invalid sheet range for struct_sheet_range "? 95": invalid chain "W", near
line 72989
Invalid sheet range for struct_sheet_range "? 96": invalid chain "W", near
line 72990
Invalid sheet range for struct_sheet_range "? 97": invalid chain "W", near
line 72991
75 messages similar to the above omitted
Atom O2' has no neighbors to form bonds with according to residue template for
A /1:14
Atom N6 has no neighbors to form bonds with according to residue template for
A /1:44
Atom OP1 has no neighbors to form bonds with according to residue template for
A /2:84
Atom OP2 has no neighbors to form bonds with according to residue template for
U /2:88
Atom O4 has no neighbors to form bonds with according to residue template for
U /2:88
Atom OP2 has no neighbors to form bonds with according to residue template for
G /2:89
Atom O3' has no neighbors to form bonds with according to residue template for
U /2:147
Atom C5' has no neighbors to form bonds with according to residue template for
U /2:208
Atom O2' has no neighbors to form bonds with according to residue template for
A /2:243
Atom C6 has no neighbors to form bonds with according to residue template for
C /2:249
Atom OP2 has no neighbors to form bonds with according to residue template for
A /2:294
Atom O3' has no neighbors to form bonds with according to residue template for
A /2:294
Atom O2' has no neighbors to form bonds with according to residue template for
U /2:412
Atom N7 has no neighbors to form bonds with according to residue template for
A /2:451
Atom N6 has no neighbors to form bonds with according to residue template for
A /2:451
Atom O2 has no neighbors to form bonds with according to residue template for
U /2:453
Atom OP2 has no neighbors to form bonds with according to residue template for
C /2:535
Atom OP2 has no neighbors to form bonds with according to residue template for
G /2:642
Atom O5' has no neighbors to form bonds with according to residue template for
G /2:642
Atom N2 has no neighbors to form bonds with according to residue template for
G /2:703
Atom O3' has no neighbors to form bonds with according to residue template for
C /2:826
Atom O2' has no neighbors to form bonds with according to residue template for
C /2:826
Atom OP1 has no neighbors to form bonds with according to residue template for
U /2:859
Atom O3' has no neighbors to form bonds with according to residue template for
A /2:861
Atom O2' has no neighbors to form bonds with according to residue template for
G /2:866
Atom C8 has no neighbors to form bonds with according to residue template for
G /2:866
Atom O2' has no neighbors to form bonds with according to residue template for
G /2:877
Atom N3 has no neighbors to form bonds with according to residue template for
A /2:886
Atom O2' has no neighbors to form bonds with according to residue template for
U /2:895
Atom O2 has no neighbors to form bonds with according to residue template for
U /2:895
Atom C6 has no neighbors to form bonds with according to residue template for
U /2:927
Atom O3' has no neighbors to form bonds with according to residue template for
G /2:952
Atom O2' has no neighbors to form bonds with according to residue template for
A /2:962
Atom OP2 has no neighbors to form bonds with according to residue template for
G /2:985
Atom O5' has no neighbors to form bonds with according to residue template for
G /2:985
Atom O3' has no neighbors to form bonds with according to residue template for
A /2:1068
Atom O6 has no neighbors to form bonds with according to residue template for
G /2:1166
Atom O2' has no neighbors to form bonds with according to residue template for
G /2:1168
Atom N2 has no neighbors to form bonds with according to residue template for
G /2:1168
Atom O3' has no neighbors to form bonds with according to residue template for
U /2:1174
Atom OP2 has no neighbors to form bonds with according to residue template for
A /2:1201
Atom O5' has no neighbors to form bonds with according to residue template for
A /2:1201
Atom OP2 has no neighbors to form bonds with according to residue template for
G /2:1212
Atom O5' has no neighbors to form bonds with according to residue template for
G /2:1212
Atom O2' has no neighbors to form bonds with according to residue template for
G /2:1217
Atom OP2 has no neighbors to form bonds with according to residue template for
A /2:1324
Atom OP2 has no neighbors to form bonds with according to residue template for
C /2:1331
Atom C5' has no neighbors to form bonds with according to residue template for
U /2:1388
Atom OP1 has no neighbors to form bonds with according to residue template for
A /2:1398
Atom N1 has no neighbors to form bonds with according to residue template for
G /2:1407
Atom N2 has no neighbors to form bonds with according to residue template for
G /2:1407
Atom OP1 has no neighbors to form bonds with according to residue template for
G /2:1453
Atom O2 has no neighbors to form bonds with according to residue template for
C /2:1489
Atom O2 has no neighbors to form bonds with according to residue template for
U /2:1593
Atom O2 has no neighbors to form bonds with according to residue template for
C /2:1600
Atom N7 has no neighbors to form bonds with according to residue template for
A /2:1653
Atom O4' has no neighbors to form bonds with according to residue template for
U /2:1664
Atom C5 has no neighbors to form bonds with according to residue template for
U /2:1664
Atom O2 has no neighbors to form bonds with according to residue template for
C /2:1672
Atom O3' has no neighbors to form bonds with according to residue template for
C /2:1673
Atom O2' has no neighbors to form bonds with according to residue template for
C /2:1673
Atom OP1 has no neighbors to form bonds with according to residue template for
U /2:1726
Atom O2 has no neighbors to form bonds with according to residue template for
U /2:1726
Atom O3' has no neighbors to form bonds with according to residue template for
G /2:1735
Atom N has no neighbors to form bonds with according to residue template for
TYR /A:38
Atom CE1 has no neighbors to form bonds with according to residue template for
TYR /A:81
Atom OH has no neighbors to form bonds with according to residue template for
TYR /A:81
Atom N has no neighbors to form bonds with according to residue template for
PHE /A:102
Atom C has no neighbors to form bonds with according to residue template for
PHE /A:102
Atom N has no neighbors to form bonds with according to residue template for
SER /A:136
Atom C has no neighbors to form bonds with according to residue template for
SER /A:136
Atom OG has no neighbors to form bonds with according to residue template for
SER /A:136
Atom OD1 has no neighbors to form bonds with according to residue template for
ASN /A:140
Atom ND2 has no neighbors to form bonds with according to residue template for
ASN /A:140
Atom N has no neighbors to form bonds with according to residue template for
VAL /A:156
Atom C has no neighbors to form bonds with according to residue template for
ARG /B:115
Atom O has no neighbors to form bonds with according to residue template for
VAL /B:150
Atom CG1 has no neighbors to form bonds with according to residue template for
VAL /B:150
Atom CE1 has no neighbors to form bonds with according to residue template for
TYR /B:155
Atom OH has no neighbors to form bonds with according to residue template for
TYR /B:155
Atom O has no neighbors to form bonds with according to residue template for
VAL /C:68
Atom NE2 has no neighbors to form bonds with according to residue template for
GLN /C:155
Atom CD1 has no neighbors to form bonds with according to residue template for
LEU /D:11
Atom CG1 has no neighbors to form bonds with according to residue template for
ILE /D:73
Atom OG has no neighbors to form bonds with according to residue template for
SER /D:97
Atom N has no neighbors to form bonds with according to residue template for
ARG /E:113
Atom N has no neighbors to form bonds with according to residue template for
ILE /E:228
Atom OD1 has no neighbors to form bonds with according to residue template for
ASN /F:81
Atom O has no neighbors to form bonds with according to residue template for
ASP /F:147
Atom N has no neighbors to form bonds with according to residue template for
PRO /H:113
Atom N has no neighbors to form bonds with according to residue template for
VAL /H:182
Atom O has no neighbors to form bonds with according to residue template for
VAL /H:182
Atom N has no neighbors to form bonds with according to residue template for
ASN /I:88
Atom CD2 has no neighbors to form bonds with according to residue template for
LEU /I:190
Atom N has no neighbors to form bonds with according to residue template for
LEU /I:197
Atom N has no neighbors to form bonds with according to residue template for
ARG /J:174
Atom N has no neighbors to form bonds with according to residue template for
LYS /K:31
Atom N has no neighbors to form bonds with according to residue template for
HIS /L:18
Atom O has no neighbors to form bonds with according to residue template for
ILE /L:19
Atom O has no neighbors to form bonds with according to residue template for
ARG /L:29
Atom N has no neighbors to form bonds with according to residue template for
ALA /N:111
Atom CD1 has no neighbors to form bonds with according to residue template for
LEU /N:115
Atom N has no neighbors to form bonds with according to residue template for
SER /N:133
Atom CG has no neighbors to form bonds with according to residue template for
LYS /O:70
Atom NE has no neighbors to form bonds with according to residue template for
ARG /P:77
Atom NH2 has no neighbors to form bonds with according to residue template for
ARG /P:77
Atom OG1 has no neighbors to form bonds with according to residue template for
THR /P:124
Atom CG2 has no neighbors to form bonds with according to residue template for
THR /P:124
Atom N has no neighbors to form bonds with according to residue template for
THR /R:8
Atom CG2 has no neighbors to form bonds with according to residue template for
THR /R:8
Atom N has no neighbors to form bonds with according to residue template for
ILE /U:86
Atom C has no neighbors to form bonds with according to residue template for
ARG /Y:20
Atom OD1 has no neighbors to form bonds with according to residue template for
ASP /Y:53
Atom N has no neighbors to form bonds with according to residue template for
TYR /Y:76
Atom CB has no neighbors to form bonds with according to residue template for
ALA /Y:82
Atom O has no neighbors to form bonds with according to residue template for
LYS /Y:83
Atom NZ has no neighbors to form bonds with according to residue template for
LYS /Y:83
Atom N has no neighbors to form bonds with according to residue template for
SER /Y:124
Atom OG has no neighbors to form bonds with according to residue template for
SER /Y:124
Atom N has no neighbors to form bonds with according to residue template for
ALA /Y:126
Atom CB has no neighbors to form bonds with according to residue template for
ALA /Y:126
Atom N has no neighbors to form bonds with according to residue template for
SER /a:54
Atom OG has no neighbors to form bonds with according to residue template for
SER /a:54
Atom CG2 has no neighbors to form bonds with according to residue template for
VAL /b:25
Atom N has no neighbors to form bonds with according to residue template for
PHE /c:32
Atom O has no neighbors to form bonds with according to residue template for
GLU /c:58
Atom N has no neighbors to form bonds with according to residue template for
ARG /h:23
Atom CD1 has no neighbors to form bonds with according to residue template for
LEU /j:47
Atom N has no neighbors to form bonds with according to residue template for
GLN /j:60
Atom N has no neighbors to form bonds with according to residue template for
ILE /j:63
Atom N has no neighbors to form bonds with according to residue template for
ILE /j:96
Atom N has no neighbors to form bonds with according to residue template for
ILE /l:230
Atom NE has no neighbors to form bonds with according to residue template for
ARG /m:53
Atom CG has no neighbors to form bonds with according to residue template for
GLU /m:76
Atom OE2 has no neighbors to form bonds with according to residue template for
GLU /m:76
Atom CG has no neighbors to form bonds with according to residue template for
LEU /p:99
Atom N has no neighbors to form bonds with according to residue template for
THR /p:123
Atom O has no neighbors to form bonds with according to residue template for
THR /p:123
Atom N has no neighbors to form bonds with according to residue template for
HIS /p:153
Atom N has no neighbors to form bonds with according to residue template for
LYS /p:374
Atom CB has no neighbors to form bonds with according to residue template for
LYS /p:374
Atom N has no neighbors to form bonds with according to residue template for
VAL /p:422
Atom N has no neighbors to form bonds with according to residue template for
GLU /p:481
Atom OE1 has no neighbors to form bonds with according to residue template for
GLU /p:481
Atom CB has no neighbors to form bonds with according to residue template for
GLU /q:101
Atom N has no neighbors to form bonds with according to residue template for
ALA /q:177
Atom C has no neighbors to form bonds with according to residue template for
ALA /q:177
Atom N has no neighbors to form bonds with according to residue template for
LYS /q:189
Chain information for 0057_6gsm_2.cif #1
---
Chain | Description
1 | Met-tRNAi
2 | 18S ribosomal RNA
3 | mRNA (5'-R(P*AP*AP*U)-3')
A | 40S ribosomal protein S0
B | 40S ribosomal protein S1
C | KLLA0F09812p
D | KLLA0D08305p
E | 40S ribosomal protein S4
F | KLLA0D10659p
G | 40S ribosomal protein S6
H | 40S ribosomal protein S7
I | 40S ribosomal protein S8
J | KLLA0E23673p
K | KLLA0B08173p
L | KLLA0A10483p
N | KLLA0F18040p
O | 40S ribosomal protein S14
P | KLLA0F07843p
Q | 40S ribosomal protein S16
R | KLLA0B01474p
S | KLLA0B01562p
U | KLLA0F25542p
V | 40S ribosomal protein S21
W | 40S ribosomal protein S22
X | KLLA0B11231p
Y | 40S ribosomal protein S24
a | 40S ribosomal protein S26
b | 40S ribosomal protein S27
c | 40S ribosomal protein S28
d | 40S ribosomal protein S29
e | 40S ribosomal protein S30
f | Ubiquitin-40S ribosomal protein S27a
h | 60S ribosomal protein L41-A
i | Eukaryotic translation initiation factor 1A
j | Eukaryotic translation initiation factor 2 subunit alpha
l | Eukaryotic translation initiation factor 2 subunit beta
m | Eukaryotic translation initiation factor eIF-1
p | Eukaryotic translation initiation factor 3 subunit B
q | Eukaryotic translation initiation factor 3 subunit C
> open /scratch/cs-
> bioinfo/tngu/6k_data/Box_Chains_new/0057_6gsm/0057_6gsm_2.mrc
Opened 0057_6gsm_2.mrc as #2, grid size 88,144,112, pixel 1, shown at level
0.15, step 1, values float32
> fitmap #1 inMap #2
Fit molecule 0057_6gsm_2.cif (#1) to map 0057_6gsm_2.mrc (#2) using 40820
atoms
average map value = 0.08348, steps = 44
shifted from previous position = 0.372
rotated from previous position = 0.0986 degrees
atoms outside contour = 39641, contour level = 0.15035
Position of 0057_6gsm_2.cif (#1) relative to 0057_6gsm_2.mrc (#2) coordinates:
Matrix rotation and translation
0.99999880 0.00144453 -0.00056816 -0.47396073
-0.00144411 0.99999868 0.00074240 -0.07299325
0.00056923 -0.00074158 0.99999956 -0.08745279
Axis -0.43126971 -0.33054626 -0.83949128
Axis point 18.35108092 237.97475998 0.00000000
Rotation angle (degrees) 0.09857567
Shift along axis 0.30194841
> save /scratch/cs-
> bioinfo/tngu/6k_data/Box_Chains_new/0057_6gsm/0057_6gsm_2_fitted.cif #1
> close #1
> close #2
> open /scratch/cs-
> bioinfo/tngu/6k_data/Box_Chains_new/0057_6gsm/0057_6gsm_B.cif
Summary of feedback from opening /scratch/cs-
bioinfo/tngu/6k_data/Box_Chains_new/0057_6gsm/0057_6gsm_B.cif
---
warnings | Invalid residue range for struct_conf "HELX21": invalid chain "G",
near line 50029
Invalid residue range for struct_conf "HELX22": invalid chain "G", near line
50030
Invalid residue range for struct_conf "HELX23": invalid chain "G", near line
50031
Invalid residue range for struct_conf "HELX24": invalid chain "G", near line
50032
Invalid residue range for struct_conf "HELX25": invalid chain "G", near line
50033
83 messages similar to the above omitted
Invalid sheet range for struct_sheet_range "? 25": invalid chain "G", near
line 50286
Invalid sheet range for struct_sheet_range "? 26": invalid chain "G", near
line 50287
Invalid sheet range for struct_sheet_range "? 27": invalid chain "G", near
line 50288
Invalid sheet range for struct_sheet_range "? 28": invalid chain "G", near
line 50289
Invalid sheet range for struct_sheet_range "? 29": invalid chain "G", near
line 50290
123 messages similar to the above omitted
Atom OP1 has no neighbors to form bonds with according to residue template for
A /1:20
Atom OP2 has no neighbors to form bonds with according to residue template for
A /1:20
Atom N3 has no neighbors to form bonds with according to residue template for
A /1:54
Atom O2' has no neighbors to form bonds with according to residue template for
U /1:55
Atom O2' has no neighbors to form bonds with according to residue template for
C /1:61
Atom N6 has no neighbors to form bonds with according to residue template for
A /2:618
Atom O4' has no neighbors to form bonds with according to residue template for
C /2:626
Atom O2' has no neighbors to form bonds with according to residue template for
U /2:863
Atom O2 has no neighbors to form bonds with according to residue template for
U /2:863
Atom N7 has no neighbors to form bonds with according to residue template for
G /2:1034
Atom OP2 has no neighbors to form bonds with according to residue template for
G /2:1107
Atom OP2 has no neighbors to form bonds with according to residue template for
U /2:1116
Atom OP2 has no neighbors to form bonds with according to residue template for
C /2:1120
Atom O2' has no neighbors to form bonds with according to residue template for
G /2:1140
Atom OP1 has no neighbors to form bonds with according to residue template for
U /2:1143
Atom OP2 has no neighbors to form bonds with according to residue template for
U /2:1143
Atom O3' has no neighbors to form bonds with according to residue template for
G /2:1294
Atom O2' has no neighbors to form bonds with according to residue template for
G /2:1294
Atom O2' has no neighbors to form bonds with according to residue template for
A /2:1295
Atom O3' has no neighbors to form bonds with according to residue template for
G /2:1315
Atom O3' has no neighbors to form bonds with according to residue template for
A /2:1321
Atom N2 has no neighbors to form bonds with according to residue template for
G /2:1614
Atom OP1 has no neighbors to form bonds with according to residue template for
A /2:1779
Atom OP2 has no neighbors to form bonds with according to residue template for
A /2:1779
Atom OP2 has no neighbors to form bonds with according to residue template for
A /2:1780
Atom N6 has no neighbors to form bonds with according to residue template for
A /2:1780
Atom OP1 has no neighbors to form bonds with according to residue template for
C /2:1781
Atom CD1 has no neighbors to form bonds with according to residue template for
ILE /A:76
Atom N has no neighbors to form bonds with according to residue template for
PHE /A:107
Atom N has no neighbors to form bonds with according to residue template for
LYS /A:167
Atom O has no neighbors to form bonds with according to residue template for
PHE /F:50
Atom O has no neighbors to form bonds with according to residue template for
TYR /F:79
Atom N has no neighbors to form bonds with according to residue template for
ILE /F:201
Atom N has no neighbors to form bonds with according to residue template for
SER /N:13
Atom O has no neighbors to form bonds with according to residue template for
SER /N:13
Atom O has no neighbors to form bonds with according to residue template for
LYS /N:94
Atom N has no neighbors to form bonds with according to residue template for
ASP /Q:113
Atom CB has no neighbors to form bonds with according to residue template for
ASP /Q:113
Atom CG has no neighbors to form bonds with according to residue template for
LYS /R:14
Atom CD2 has no neighbors to form bonds with according to residue template for
LEU /V:69
Atom N has no neighbors to form bonds with according to residue template for
ASN /V:70
Atom N has no neighbors to form bonds with according to residue template for
ARG /W:23
Atom NH1 has no neighbors to form bonds with according to residue template for
ARG /W:23
Atom N has no neighbors to form bonds with according to residue template for
HIS /b:31
Atom O has no neighbors to form bonds with according to residue template for
HIS /b:31
Atom N has no neighbors to form bonds with according to residue template for
ASP /b:34
Atom CG2 has no neighbors to form bonds with according to residue template for
ILE /j:27
Atom N has no neighbors to form bonds with according to residue template for
ILE /j:56
Atom CG2 has no neighbors to form bonds with according to residue template for
ILE /j:63
Atom N has no neighbors to form bonds with according to residue template for
LEU /j:112
Atom CD1 has no neighbors to form bonds with according to residue template for
LEU /j:112
Atom O has no neighbors to form bonds with according to residue template for
TYR /j:127
Atom N has no neighbors to form bonds with according to residue template for
ILE /j:158
Atom CD1 has no neighbors to form bonds with according to residue template for
ILE /j:158
Atom CG1 has no neighbors to form bonds with according to residue template for
VAL /j:229
Atom CG2 has no neighbors to form bonds with according to residue template for
VAL /j:229
Atom O has no neighbors to form bonds with according to residue template for
ILE /m:68
Atom N has no neighbors to form bonds with according to residue template for
UNK /o:768
Atom C has no neighbors to form bonds with according to residue template for
UNK /o:768
Atom N has no neighbors to form bonds with according to residue template for
THR /p:159
Atom N has no neighbors to form bonds with according to residue template for
ASP /q:333
Atom CG2 has no neighbors to form bonds with according to residue template for
ILE /q:348
Atom N has no neighbors to form bonds with according to residue template for
SER /q:359
Atom OG has no neighbors to form bonds with according to residue template for
SER /q:359
Atom CD1 has no neighbors to form bonds with according to residue template for
LEU /q:366
Atom CB has no neighbors to form bonds with according to residue template for
ASP /q:400
Atom N has no neighbors to form bonds with according to residue template for
ASN /q:406
Atom CB has no neighbors to form bonds with according to residue template for
ARG /q:410
Atom O has no neighbors to form bonds with according to residue template for
GLN /q:529
Atom N has no neighbors to form bonds with according to residue template for
LEU /q:550
Atom CB has no neighbors to form bonds with according to residue template for
LEU /q:550
Atom CD2 has no neighbors to form bonds with according to residue template for
LEU /q:550
Atom C has no neighbors to form bonds with according to residue template for
HIS /q:575
Atom CD2 has no neighbors to form bonds with according to residue template for
HIS /q:575
Chain information for 0057_6gsm_B.cif #1
---
Chain | Description
1 | Met-tRNAi
2 | 18S ribosomal RNA
A | 40S ribosomal protein S0
B | 40S ribosomal protein S1
C | KLLA0F09812p
F | KLLA0D10659p
N | KLLA0F18040p
O | 40S ribosomal protein S14
Q | 40S ribosomal protein S16
R | KLLA0B01474p
V | 40S ribosomal protein S21
W | 40S ribosomal protein S22
a | 40S ribosomal protein S26
b | 40S ribosomal protein S27
c | 40S ribosomal protein S28
h | 60S ribosomal protein L41-A
j | Eukaryotic translation initiation factor 2 subunit alpha
m | Eukaryotic translation initiation factor eIF-1
o | Eukaryotic translation initiation factor 3 subunit A,Eukaryotic
translation initiation factor 3 subunit A,eIF3a
p | Eukaryotic translation initiation factor 3 subunit B
q | Eukaryotic translation initiation factor 3 subunit C
> open /scratch/cs-
> bioinfo/tngu/6k_data/Box_Chains_new/0057_6gsm/0057_6gsm_B.mrc
Opened 0057_6gsm_B.mrc as #2, grid size 112,104,96, pixel 1, shown at level
0.133, step 1, values float32
> fitmap #1 inMap #2
Fit molecule 0057_6gsm_B.cif (#1) to map 0057_6gsm_B.mrc (#2) using 18875
atoms
average map value = 0.06864, steps = 56
shifted from previous position = 0.533
rotated from previous position = 0.172 degrees
atoms outside contour = 17837, contour level = 0.13281
Position of 0057_6gsm_B.cif (#1) relative to 0057_6gsm_B.mrc (#2) coordinates:
Matrix rotation and translation
0.99999713 0.00094651 -0.00220125 0.08733287
-0.00095051 0.99999790 -0.00181705 0.52019808
0.00219953 0.00181914 0.99999593 -1.25779506
Axis 0.60446089 -0.73156077 -0.31535040
Axis point 562.00964176 0.00000000 20.02717774
Rotation angle (degrees) 0.17233460
Shift along axis 0.06887898
> save /scratch/cs-
> bioinfo/tngu/6k_data/Box_Chains_new/0057_6gsm/0057_6gsm_B_fitted.cif #1
> close #1
> close #2
> open /scratch/cs-
> bioinfo/tngu/6k_data/Box_Chains_new/0057_6gsm/0057_6gsm_a.cif
Summary of feedback from opening /scratch/cs-
bioinfo/tngu/6k_data/Box_Chains_new/0057_6gsm/0057_6gsm_a.cif
---
warnings | Invalid residue range for struct_conf "HELX21": invalid chain "G",
near line 50190
Invalid residue range for struct_conf "HELX22": invalid chain "G", near line
50191
Invalid residue range for struct_conf "HELX23": invalid chain "G", near line
50192
Invalid residue range for struct_conf "HELX24": invalid chain "G", near line
50193
Invalid residue range for struct_conf "HELX25": invalid chain "G", near line
50194
76 messages similar to the above omitted
Invalid sheet range for struct_sheet_range "? 25": invalid chain "G", near
line 50447
Invalid sheet range for struct_sheet_range "? 26": invalid chain "G", near
line 50448
Invalid sheet range for struct_sheet_range "? 27": invalid chain "G", near
line 50449
Invalid sheet range for struct_sheet_range "? 28": invalid chain "G", near
line 50450
Invalid sheet range for struct_sheet_range "? 29": invalid chain "G", near
line 50451
141 messages similar to the above omitted
Atom N4 has no neighbors to form bonds with according to residue template for
C /1:34
Atom C5 has no neighbors to form bonds with according to residue template for
C /1:34
Atom O2' has no neighbors to form bonds with according to residue template for
7MG /1:46
Atom C5' has no neighbors to form bonds with according to residue template for
A /1:59
Atom C5 has no neighbors to form bonds with according to residue template for
C /2:4
Atom OP1 has no neighbors to form bonds with according to residue template for
G /2:10
Atom N4 has no neighbors to form bonds with according to residue template for
C /2:18
Atom O3' has no neighbors to form bonds with according to residue template for
A /2:604
Atom O2' has no neighbors to form bonds with according to residue template for
A /2:604
Atom OP1 has no neighbors to form bonds with according to residue template for
G /2:866
Atom OP2 has no neighbors to form bonds with according to residue template for
G /2:866
Atom OP1 has no neighbors to form bonds with according to residue template for
G /2:867
Atom OP2 has no neighbors to form bonds with according to residue template for
G /2:867
Atom O3' has no neighbors to form bonds with according to residue template for
A /2:868
Atom N6 has no neighbors to form bonds with according to residue template for
A /2:868
Atom C5' has no neighbors to form bonds with according to residue template for
U /2:967
Atom O3' has no neighbors to form bonds with according to residue template for
U /2:967
Atom OP2 has no neighbors to form bonds with according to residue template for
A /2:972
Atom OP1 has no neighbors to form bonds with according to residue template for
U /2:1097
Atom O2' has no neighbors to form bonds with according to residue template for
U /2:1097
Atom OP2 has no neighbors to form bonds with according to residue template for
G /2:1118
Atom OP2 has no neighbors to form bonds with according to residue template for
C /2:1133
Atom C5' has no neighbors to form bonds with according to residue template for
G /2:1166
Atom O4' has no neighbors to form bonds with according to residue template for
G /2:1166
Atom OP1 has no neighbors to form bonds with according to residue template for
U /2:1284
Atom OP2 has no neighbors to form bonds with according to residue template for
G /2:1323
Atom O4' has no neighbors to form bonds with according to residue template for
A /2:1325
Atom C8 has no neighbors to form bonds with according to residue template for
A /2:1330
Atom N3 has no neighbors to form bonds with according to residue template for
G /2:1410
Atom OP2 has no neighbors to form bonds with according to residue template for
C /2:1578
Atom OP2 has no neighbors to form bonds with according to residue template for
U /2:1607
Atom O5' has no neighbors to form bonds with according to residue template for
U /2:1607
Atom O4' has no neighbors to form bonds with according to residue template for
G /2:1643
Atom O3' has no neighbors to form bonds with according to residue template for
U /2:1648
Atom OP2 has no neighbors to form bonds with according to residue template for
G /2:1652
Atom N7 has no neighbors to form bonds with according to residue template for
G /2:1652
Atom O6 has no neighbors to form bonds with according to residue template for
G /2:1652
Atom C2' has no neighbors to form bonds with according to residue template for
G /2:1746
Atom N2 has no neighbors to form bonds with according to residue template for
G /2:1755
Atom NH1 has no neighbors to form bonds with according to residue template for
ARG /A:41
Atom O4 has no neighbors to form bonds with according to residue template for
U /3:30
Atom OD2 has no neighbors to form bonds with according to residue template for
ASP /B:131
Atom N has no neighbors to form bonds with according to residue template for
ASN /B:178
Atom O has no neighbors to form bonds with according to residue template for
ASN /B:178
Atom ND2 has no neighbors to form bonds with according to residue template for
ASN /B:178
Atom N has no neighbors to form bonds with according to residue template for
ASP /B:224
Atom N has no neighbors to form bonds with according to residue template for
THR /C:122
Atom CG2 has no neighbors to form bonds with according to residue template for
ILE /C:135
Atom N has no neighbors to form bonds with according to residue template for
LEU /C:174
Atom NH1 has no neighbors to form bonds with according to residue template for
ARG /C:210
Atom OD1 has no neighbors to form bonds with according to residue template for
ASN /F:102
Atom CG2 has no neighbors to form bonds with according to residue template for
ILE /F:139
Atom CG2 has no neighbors to form bonds with according to residue template for
ILE /F:140
Atom OG has no neighbors to form bonds with according to residue template for
SER /F:142
Atom O has no neighbors to form bonds with according to residue template for
TYR /F:211
Atom N has no neighbors to form bonds with according to residue template for
LYS /Q:14
Atom CG has no neighbors to form bonds with according to residue template for
LYS /Q:14
Atom CE has no neighbors to form bonds with according to residue template for
LYS /Q:14
Atom O has no neighbors to form bonds with according to residue template for
TYR /V:85
Atom OG has no neighbors to form bonds with according to residue template for
SER /V:86
Atom N has no neighbors to form bonds with according to residue template for
GLN /W:24
Atom O has no neighbors to form bonds with according to residue template for
GLN /W:24
Atom CG has no neighbors to form bonds with according to residue template for
LYS /X:3
Atom CG has no neighbors to form bonds with according to residue template for
GLU /X:26
Atom N has no neighbors to form bonds with according to residue template for
LEU /b:7
Atom N has no neighbors to form bonds with according to residue template for
GLY /j:81
Atom N has no neighbors to form bonds with according to residue template for
SER /j:105
Atom OG1 has no neighbors to form bonds with according to residue template for
THR /j:107
Atom CG2 has no neighbors to form bonds with according to residue template for
THR /j:107
Atom N has no neighbors to form bonds with according to residue template for
GLU /j:143
Atom CB has no neighbors to form bonds with according to residue template for
GLU /j:143
Atom O has no neighbors to form bonds with according to residue template for
LYS /m:56
Atom CG has no neighbors to form bonds with according to residue template for
LYS /m:56
Atom CB has no neighbors to form bonds with according to residue template for
LYS /o:64
Atom N has no neighbors to form bonds with according to residue template for
ILE /o:97
Atom N has no neighbors to form bonds with according to residue template for
ARG /o:170
Atom CG2 has no neighbors to form bonds with according to residue template for
ILE /o:177
Atom CD1 has no neighbors to form bonds with according to residue template for
TYR /o:179
Atom CG2 has no neighbors to form bonds with according to residue template for
THR /q:256
Atom O has no neighbors to form bonds with according to residue template for
ASP /q:305
Atom O has no neighbors to form bonds with according to residue template for
LYS /q:356
Atom CB has no neighbors to form bonds with according to residue template for
LYS /q:356
Atom CD has no neighbors to form bonds with according to residue template for
LYS /q:356
Atom N has no neighbors to form bonds with according to residue template for
GLU /q:600
Chain information for 0057_6gsm_a.cif #1
---
Chain | Description
1 | Met-tRNAi
2 | 18S ribosomal RNA
3 | mRNA (5'-R(P*AP*AP*U)-3')
A | 40S ribosomal protein S0
B | 40S ribosomal protein S1
C | KLLA0F09812p
F | KLLA0D10659p
N | KLLA0F18040p
O | 40S ribosomal protein S14
Q | 40S ribosomal protein S16
R | KLLA0B01474p
V | 40S ribosomal protein S21
W | 40S ribosomal protein S22
X | KLLA0B11231p
a | 40S ribosomal protein S26
b | 40S ribosomal protein S27
c | 40S ribosomal protein S28
h | 60S ribosomal protein L41-A
j | Eukaryotic translation initiation factor 2 subunit alpha
l | Eukaryotic translation initiation factor 2 subunit beta
m | Eukaryotic translation initiation factor eIF-1
o | Eukaryotic translation initiation factor 3 subunit A,Eukaryotic
translation initiation factor 3 subunit A,eIF3a
p | Eukaryotic translation initiation factor 3 subunit B
q | Eukaryotic translation initiation factor 3 subunit C
> open /scratch/cs-
> bioinfo/tngu/6k_data/Box_Chains_new/0057_6gsm/0057_6gsm_a.mrc
Opened 0057_6gsm_a.mrc as #2, grid size 80,96,88, pixel 1, shown at level
0.149, step 1, values float32
> fitmap #1 inMap #2
Fit molecule 0057_6gsm_a.cif (#1) to map 0057_6gsm_a.mrc (#2) using 18871
atoms
average map value = 0.0811, steps = 56
shifted from previous position = 0.485
rotated from previous position = 0.143 degrees
atoms outside contour = 18299, contour level = 0.14928
Position of 0057_6gsm_a.cif (#1) relative to 0057_6gsm_a.mrc (#2) coordinates:
Matrix rotation and translation
0.99999911 0.00018452 -0.00132388 0.02105214
-0.00018729 0.99999778 -0.00209751 0.38372358
0.00132349 0.00209776 0.99999692 -1.07470455
Axis 0.84333037 -0.53217264 -0.07474067
Axis point 0.00000000 516.31993276 155.46967396
Rotation angle (degrees) 0.14251334
Shift along axis -0.10612915
> save /scratch/cs-
> bioinfo/tngu/6k_data/Box_Chains_new/0057_6gsm/0057_6gsm_a_fitted.cif #1
> close #1
> close #2
> open /scratch/cs-
> bioinfo/tngu/6k_data/Box_Chains_new/0057_6gsm/0057_6gsm_U.cif
Summary of feedback from opening /scratch/cs-
bioinfo/tngu/6k_data/Box_Chains_new/0057_6gsm/0057_6gsm_U.cif
---
warnings | Invalid residue range for struct_conf "HELX1": invalid chain "C",
near line 44477
Invalid residue range for struct_conf "HELX2": invalid chain "C", near line
44478
Invalid residue range for struct_conf "HELX3": invalid chain "C", near line
44479
Invalid residue range for struct_conf "HELX4": invalid chain "C", near line
44480
Invalid residue range for struct_conf "HELX5": invalid chain "C", near line
44481
174 messages similar to the above omitted
Invalid sheet range for struct_sheet_range "? 1": invalid chain "C", near line
44730
Invalid sheet range for struct_sheet_range "? 2": invalid chain "C", near line
44731
Invalid sheet range for struct_sheet_range "? 3": invalid chain "C", near line
44732
Invalid sheet range for struct_sheet_range "? 4": invalid chain "C", near line
44733
Invalid sheet range for struct_sheet_range "? 5": invalid chain "C", near line
44734
181 messages similar to the above omitted
Atom O2' has no neighbors to form bonds with according to residue template for
C /1:39
Atom O2 has no neighbors to form bonds with according to residue template for
C /1:39
Atom O2' has no neighbors to form bonds with according to residue template for
C /1:40
Atom O2 has no neighbors to form bonds with according to residue template for
C /1:40
Atom O2' has no neighbors to form bonds with according to residue template for
C /1:41
Atom C8 has no neighbors to form bonds with according to residue template for
A /2:1159
Atom OP2 has no neighbors to form bonds with according to residue template for
C /2:1179
Atom OP1 has no neighbors to form bonds with according to residue template for
A /2:1182
Atom O5' has no neighbors to form bonds with according to residue template for
A /2:1182
Atom OP2 has no neighbors to form bonds with according to residue template for
G /2:1262
Atom O3' has no neighbors to form bonds with according to residue template for
U /2:1313
Atom OP2 has no neighbors to form bonds with according to residue template for
A /2:1386
Atom OP2 has no neighbors to form bonds with according to residue template for
A /2:1477
Atom N3 has no neighbors to form bonds with according to residue template for
A /2:1581
Atom N3 has no neighbors to form bonds with according to residue template for
A /3:28
Atom OP2 has no neighbors to form bonds with according to residue template for
U /3:30
Atom O5' has no neighbors to form bonds with according to residue template for
U /3:30
Atom OE1 has no neighbors to form bonds with according to residue template for
GLN /D:101
Atom O has no neighbors to form bonds with according to residue template for
ALA /D:147
Atom CB has no neighbors to form bonds with according to residue template for
ALA /F:76
Atom SD has no neighbors to form bonds with according to residue template for
MET /F:101
Atom O has no neighbors to form bonds with according to residue template for
TYR /K:12
Atom CD1 has no neighbors to form bonds with according to residue template for
PHE /K:16
Atom N has no neighbors to form bonds with according to residue template for
VAL /K:74
Atom N has no neighbors to form bonds with according to residue template for
LYS /P:24
Atom O has no neighbors to form bonds with according to residue template for
SER /P:92
Atom O has no neighbors to form bonds with according to residue template for
ASN /P:103
Atom N has no neighbors to form bonds with according to residue template for
LYS /Q:26
Atom C has no neighbors to form bonds with according to residue template for
LYS /Q:26
Atom N has no neighbors to form bonds with according to residue template for
TYR /Q:92
Atom O has no neighbors to form bonds with according to residue template for
LYS /R:32
Atom CD has no neighbors to form bonds with according to residue template for
LYS /R:32
Atom O has no neighbors to form bonds with according to residue template for
ARG /R:33
Atom O has no neighbors to form bonds with according to residue template for
TRP /S:84
Atom N has no neighbors to form bonds with according to residue template for
ASN /S:93
Atom N has no neighbors to form bonds with according to residue template for
LEU /S:113
Atom CD2 has no neighbors to form bonds with according to residue template for
LEU /S:131
Atom O has no neighbors to form bonds with according to residue template for
LEU /T:45
Atom N has no neighbors to form bonds with according to residue template for
ARG /f:92
Atom N has no neighbors to form bonds with according to residue template for
TRP /g:93
Atom CG2 has no neighbors to form bonds with according to residue template for
ILE /g:124
Atom O has no neighbors to form bonds with according to residue template for
ASP /g:150
Atom O has no neighbors to form bonds with according to residue template for
ILE /g:195
Chain information for 0057_6gsm_U.cif #1
---
Chain | Description
1 | Met-tRNAi
2 | 18S ribosomal RNA
3 | mRNA (5'-R(P*AP*AP*U)-3')
C | KLLA0F09812p
D | KLLA0D08305p
F | KLLA0D10659p
K | KLLA0B08173p
P | KLLA0F07843p
Q | 40S ribosomal protein S16
R | KLLA0B01474p
S | KLLA0B01562p
T | KLLA0A07194p
U | KLLA0F25542p
Z | KLLA0B06182p
d | 40S ribosomal protein S29
f | Ubiquitin-40S ribosomal protein S27a
g | KLLA0E12277p
i | Eukaryotic translation initiation factor 1A
> open /scratch/cs-
> bioinfo/tngu/6k_data/Box_Chains_new/0057_6gsm/0057_6gsm_U.mrc
Opened 0057_6gsm_U.mrc as #2, grid size 112,72,72, pixel 1, shown at level
0.134, step 1, values float32
> fitmap #1 inMap #2
Fit molecule 0057_6gsm_U.cif (#1) to map 0057_6gsm_U.mrc (#2) using 13328
atoms
average map value = 0.07934, steps = 48
shifted from previous position = 0.338
rotated from previous position = 0.177 degrees
atoms outside contour = 12826, contour level = 0.13392
Position of 0057_6gsm_U.cif (#1) relative to 0057_6gsm_U.mrc (#2) coordinates:
Matrix rotation and translation
0.99999647 0.00033916 0.00263397 -0.67215769
-0.00034329 0.99999871 0.00156937 -0.49700188
-0.00263344 -0.00157026 0.99999530 0.68166280
Axis -0.50885627 0.85371602 -0.11060857
Axis point 251.71663719 0.00000000 285.98413263
Rotation angle (degrees) 0.17675705
Shift along axis -0.15766456
> save /scratch/cs-
> bioinfo/tngu/6k_data/Box_Chains_new/0057_6gsm/0057_6gsm_U_fitted.cif #1
> close #1
> close #2
> open /scratch/cs-
> bioinfo/tngu/6k_data/Box_Chains_new/0057_6gsm/0057_6gsm_e.cif
Summary of feedback from opening /scratch/cs-
bioinfo/tngu/6k_data/Box_Chains_new/0057_6gsm/0057_6gsm_e.cif
---
warnings | Invalid residue range for struct_conf "HELX1": invalid chain "C",
near line 42816
Invalid residue range for struct_conf "HELX2": invalid chain "C", near line
42817
Invalid residue range for struct_conf "HELX3": invalid chain "C", near line
42818
Invalid residue range for struct_conf "HELX4": invalid chain "C", near line
42819
Invalid residue range for struct_conf "HELX5": invalid chain "C", near line
42820
163 messages similar to the above omitted
Invalid sheet range for struct_sheet_range "? 1": invalid chain "C", near line
43069
Invalid sheet range for struct_sheet_range "? 2": invalid chain "C", near line
43070
Invalid sheet range for struct_sheet_range "? 3": invalid chain "C", near line
43071
Invalid sheet range for struct_sheet_range "? 4": invalid chain "C", near line
43072
Invalid sheet range for struct_sheet_range "? 5": invalid chain "C", near line
43073
166 messages similar to the above omitted
Atom OP1 has no neighbors to form bonds with according to residue template for
C /2:18
Atom OP1 has no neighbors to form bonds with according to residue template for
C /2:97
Atom O3' has no neighbors to form bonds with according to residue template for
A /2:359
Atom OP2 has no neighbors to form bonds with according to residue template for
G /2:389
Atom O3' has no neighbors to form bonds with according to residue template for
A /2:411
Atom O2' has no neighbors to form bonds with according to residue template for
A /2:411
Atom O2' has no neighbors to form bonds with according to residue template for
G /2:421
Atom O3' has no neighbors to form bonds with according to residue template for
G /2:425
Atom OP2 has no neighbors to form bonds with according to residue template for
U /2:532
Atom C3' has no neighbors to form bonds with according to residue template for
A /2:533
Atom O3' has no neighbors to form bonds with according to residue template for
A /2:757
Atom O4' has no neighbors to form bonds with according to residue template for
G /2:765
Atom OP1 has no neighbors to form bonds with according to residue template for
U /2:767
Atom O2' has no neighbors to form bonds with according to residue template for
A /2:1132
Atom O3' has no neighbors to form bonds with according to residue template for
U /2:1256
Atom C6 has no neighbors to form bonds with according to residue template for
U /2:1257
Atom OP2 has no neighbors to form bonds with according to residue template for
U /2:1259
Atom N7 has no neighbors to form bonds with according to residue template for
G /2:1266
Atom O2 has no neighbors to form bonds with according to residue template for
U /2:1289
Atom O2' has no neighbors to form bonds with according to residue template for
G /2:1291
Atom O3' has no neighbors to form bonds with according to residue template for
A /2:1299
Atom O2' has no neighbors to form bonds with according to residue template for
A /2:1299
Atom OP1 has no neighbors to form bonds with according to residue template for
A /2:1325
Atom N7 has no neighbors to form bonds with according to residue template for
G /2:1426
Atom OP1 has no neighbors to form bonds with according to residue template for
A /2:1631
Atom O2' has no neighbors to form bonds with according to residue template for
U /2:1659
Atom C8 has no neighbors to form bonds with according to residue template for
G /2:1743
Atom OP2 has no neighbors to form bonds with according to residue template for
G /2:1745
Atom C5' has no neighbors to form bonds with according to residue template for
G /2:1745
Atom O3' has no neighbors to form bonds with according to residue template for
U /2:1750
Atom N has no neighbors to form bonds with according to residue template for
HIS /C:115
Atom CB has no neighbors to form bonds with according to residue template for
HIS /C:115
Atom N has no neighbors to form bonds with according to residue template for
GLY /C:117
Atom CA has no neighbors to form bonds with according to residue template for
ILE /C:120
Atom CG2 has no neighbors to form bonds with according to residue template for
ILE /C:120
Atom CD1 has no neighbors to form bonds with according to residue template for
ILE /C:120
Atom CB has no neighbors to form bonds with according to residue template for
PRO /C:178
Atom N has no neighbors to form bonds with according to residue template for
VAL /C:201
Atom O has no neighbors to form bonds with according to residue template for
VAL /C:201
Atom OG1 has no neighbors to form bonds with according to residue template for
THR /C:209
Atom O has no neighbors to form bonds with according to residue template for
GLY /D:36
Atom CD1 has no neighbors to form bonds with according to residue template for
ILE /D:50
Atom ND2 has no neighbors to form bonds with according to residue template for
ASN /D:62
Atom CG has no neighbors to form bonds with according to residue template for
GLN /J:139
Atom NE2 has no neighbors to form bonds with according to residue template for
GLN /J:139
Atom OE1 has no neighbors to form bonds with according to residue template for
GLU /J:151
Atom O has no neighbors to form bonds with according to residue template for
GLU /J:183
Atom CE2 has no neighbors to form bonds with according to residue template for
TYR /K:12
Atom OH has no neighbors to form bonds with according to residue template for
TYR /K:12
Atom NE2 has no neighbors to form bonds with according to residue template for
GLN /K:47
Atom N has no neighbors to form bonds with according to residue template for
GLN /K:58
Atom CB has no neighbors to form bonds with according to residue template for
LYS /l:216
Atom N has no neighbors to form bonds with according to residue template for
SER /l:219
Atom OG has no neighbors to form bonds with according to residue template for
SER /l:219
Atom N has no neighbors to form bonds with according to residue template for
GLN /m:31
Atom C has no neighbors to form bonds with according to residue template for
GLN /m:31
Atom N has no neighbors to form bonds with according to residue template for
CYS /m:89
Atom SG has no neighbors to form bonds with according to residue template for
CYS /m:89
Atom CD1 has no neighbors to form bonds with according to residue template for
LEU /p:390
Atom CD2 has no neighbors to form bonds with according to residue template for
LEU /p:390
Atom N has no neighbors to form bonds with according to residue template for
GLU /p:398
Atom O has no neighbors to form bonds with according to residue template for
ASN /p:412
Atom N has no neighbors to form bonds with according to residue template for
VAL /p:480
Atom O has no neighbors to form bonds with according to residue template for
VAL /p:480
Atom OE1 has no neighbors to form bonds with according to residue template for
GLU /p:530
Atom OE2 has no neighbors to form bonds with according to residue template for
GLU /p:530
Chain information for 0057_6gsm_e.cif #1
---
Chain | Description
2 | 18S ribosomal RNA
3 | mRNA (5'-R(P*AP*AP*U)-3')
C | KLLA0F09812p
D | KLLA0D08305p
J | KLLA0E23673p
K | KLLA0B08173p
M | 40S ribosomal protein S12
X | KLLA0B11231p
e | 40S ribosomal protein S30
i | Eukaryotic translation initiation factor 1A
l | Eukaryotic translation initiation factor 2 subunit beta
m | Eukaryotic translation initiation factor eIF-1
p | Eukaryotic translation initiation factor 3 subunit B
> open /scratch/cs-
> bioinfo/tngu/6k_data/Box_Chains_new/0057_6gsm/0057_6gsm_e.mrc
Opened 0057_6gsm_e.mrc as #2, grid size 96,88,72, pixel 1, shown at level
0.14, step 1, values float32
> fitmap #1 inMap #2
Fit molecule 0057_6gsm_e.cif (#1) to map 0057_6gsm_e.mrc (#2) using 11728
atoms
average map value = 0.07883, steps = 48
shifted from previous position = 0.345
rotated from previous position = 0.156 degrees
atoms outside contour = 11229, contour level = 0.14039
Position of 0057_6gsm_e.cif (#1) relative to 0057_6gsm_e.mrc (#2) coordinates:
Matrix rotation and translation
0.99999931 -0.00096213 -0.00066854 0.07989544
0.00096378 0.99999650 0.00246569 -0.83572949
0.00066616 -0.00246633 0.99999674 0.52309429
Axis -0.90324313 -0.24443575 0.35270810
Axis point 0.00000000 166.40782257 307.79255316
Rotation angle (degrees) 0.15642749
Shift along axis 0.31661676
> save /scratch/cs-
> bioinfo/tngu/6k_data/Box_Chains_new/0057_6gsm/0057_6gsm_e_fitted.cif #1
> close #1
> close #2
> open /scratch/cs-
> bioinfo/tngu/6k_data/Box_Chains_new/0057_6gsm/0057_6gsm_C.cif
Summary of feedback from opening /scratch/cs-
bioinfo/tngu/6k_data/Box_Chains_new/0057_6gsm/0057_6gsm_C.cif
---
warnings | Invalid residue range for struct_conf "HELX41": invalid chain "J",
near line 50359
Invalid residue range for struct_conf "HELX42": invalid chain "J", near line
50360
Invalid residue range for struct_conf "HELX43": invalid chain "J", near line
50361
Invalid residue range for struct_conf "HELX51": invalid chain "L", near line
50369
Invalid residue range for struct_conf "HELX52": invalid chain "L", near line
50370
119 messages similar to the above omitted
Invalid sheet range for struct_sheet_range "? 49": invalid chain "J", near
line 50620
Invalid sheet range for struct_sheet_range "? 50": invalid chain "J", near
line 50621
Invalid sheet range for struct_sheet_range "? 51": invalid chain "J", near
line 50622
Invalid sheet range for struct_sheet_range "? 52": invalid chain "J", near
line 50623
Invalid sheet range for struct_sheet_range "? 53": invalid chain "J", near
line 50624
110 messages similar to the above omitted
Atom O4' has no neighbors to form bonds with according to residue template for
U /1:36
Atom OP2 has no neighbors to form bonds with according to residue template for
A /2:28
Atom O2' has no neighbors to form bonds with according to residue template for
U /2:33
Atom O4' has no neighbors to form bonds with according to residue template for
A /2:41
Atom O3' has no neighbors to form bonds with according to residue template for
C /2:107
Atom O2 has no neighbors to form bonds with according to residue template for
C /2:107
Atom P has no neighbors to form bonds with according to residue template for U
/2:110
Atom O3' has no neighbors to form bonds with according to residue template for
G /2:461
Atom O5' has no neighbors to form bonds with according to residue template for
U /2:465
Atom O3' has no neighbors to form bonds with according to residue template for
G /2:486
Atom O2' has no neighbors to form bonds with according to residue template for
G /2:486
Atom OP2 has no neighbors to form bonds with according to residue template for
C /2:565
Atom O2 has no neighbors to form bonds with according to residue template for
U /2:587
Atom N3 has no neighbors to form bonds with according to residue template for
U /2:587
Atom O4 has no neighbors to form bonds with according to residue template for
U /2:587
Atom OP2 has no neighbors to form bonds with according to residue template for
A /2:600
Atom OP2 has no neighbors to form bonds with according to residue template for
C /2:644
Atom N4 has no neighbors to form bonds with according to residue template for
C /2:644
Atom C5 has no neighbors to form bonds with according to residue template for
C /2:644
Atom OP2 has no neighbors to form bonds with according to residue template for
U /2:664
Atom O4 has no neighbors to form bonds with according to residue template for
U /2:664
Atom N4 has no neighbors to form bonds with according to residue template for
C /2:675
Atom C5 has no neighbors to form bonds with according to residue template for
C /2:675
Atom N7 has no neighbors to form bonds with according to residue template for
G /2:689
Atom O6 has no neighbors to form bonds with according to residue template for
G /2:689
Atom C3' has no neighbors to form bonds with according to residue template for
A /2:755
Atom C5' has no neighbors to form bonds with according to residue template for
A /2:756
Atom OP1 has no neighbors to form bonds with according to residue template for
A /2:864
Atom O2' has no neighbors to form bonds with according to residue template for
A /2:864
Atom N4 has no neighbors to form bonds with according to residue template for
C /2:942
Atom C5 has no neighbors to form bonds with according to residue template for
C /2:942
Atom O3' has no neighbors to form bonds with according to residue template for
A /2:1024
Atom O2' has no neighbors to form bonds with according to residue template for
U /2:1186
Atom N3 has no neighbors to form bonds with according to residue template for
A /2:1188
Atom OP2 has no neighbors to form bonds with according to residue template for
C /2:1191
Atom O5' has no neighbors to form bonds with according to residue template for
C /2:1191
Atom OP1 has no neighbors to form bonds with according to residue template for
A /2:1192
Atom O5' has no neighbors to form bonds with according to residue template for
A /2:1311
Atom OP2 has no neighbors to form bonds with according to residue template for
U /2:1394
Atom O3' has no neighbors to form bonds with according to residue template for
U /2:1394
Atom O3' has no neighbors to form bonds with according to residue template for
G /2:1417
Atom OP1 has no neighbors to form bonds with according to residue template for
U /2:1430
Atom O3' has no neighbors to form bonds with according to residue template for
C /2:1618
Atom O2' has no neighbors to form bonds with according to residue template for
C /2:1638
Atom O2' has no neighbors to form bonds with according to residue template for
U /2:1767
Atom OP1 has no neighbors to form bonds with according to residue template for
G /2:1787
Atom OD1 has no neighbors to form bonds with according to residue template for
ASP /A:8
Atom OP2 has no neighbors to form bonds with according to residue template for
A /3:29
Atom CE2 has no neighbors to form bonds with according to residue template for
TYR /D:34
Atom OH has no neighbors to form bonds with according to residue template for
TYR /D:34
Atom N has no neighbors to form bonds with according to residue template for
VAL /D:39
Atom O has no neighbors to form bonds with according to residue template for
VAL /D:39
Atom CB has no neighbors to form bonds with according to residue template for
ARG /D:90
Atom CG2 has no neighbors to form bonds with according to residue template for
ILE /E:248
Atom CD1 has no neighbors to form bonds with according to residue template for
ILE /E:248
Atom CE has no neighbors to form bonds with according to residue template for
LYS /H:105
Atom CG2 has no neighbors to form bonds with according to residue template for
VAL /J:113
Atom N has no neighbors to form bonds with according to residue template for
TYR /J:114
Atom C has no neighbors to form bonds with according to residue template for
TYR /J:114
Atom N has no neighbors to form bonds with according to residue template for
LYS /J:138
Atom CE has no neighbors to form bonds with according to residue template for
LYS /J:138
Atom O has no neighbors to form bonds with according to residue template for
GLN /J:139
Atom N has no neighbors to form bonds with according to residue template for
ASN /J:142
Atom O has no neighbors to form bonds with according to residue template for
LYS /L:105
Atom N has no neighbors to form bonds with according to residue template for
SER /L:144
Atom NZ has no neighbors to form bonds with according to residue template for
LYS /O:92
Atom CB has no neighbors to form bonds with according to residue template for
LEU /O:137
Atom CD1 has no neighbors to form bonds with according to residue template for
LEU /O:137
Atom N has no neighbors to form bonds with according to residue template for
GLY /R:2
Atom N has no neighbors to form bonds with according to residue template for
LYS /R:44
Atom O has no neighbors to form bonds with according to residue template for
LYS /R:44
Atom N has no neighbors to form bonds with according to residue template for
SER /X:66
Atom OG has no neighbors to form bonds with according to residue template for
SER /X:66
Atom NH1 has no neighbors to form bonds with according to residue template for
ARG /X:69
Atom NH2 has no neighbors to form bonds with according to residue template for
ARG /X:69
Atom N has no neighbors to form bonds with according to residue template for
SER /a:27
Atom N has no neighbors to form bonds with according to residue template for
LEU /b:8
Atom O has no neighbors to form bonds with according to residue template for
ARG /c:67
Atom N has no neighbors to form bonds with according to residue template for
PHE /d:43
Atom O has no neighbors to form bonds with according to residue template for
ARG /e:37
Atom N has no neighbors to form bonds with according to residue template for
THR /g:131
Atom CG2 has no neighbors to form bonds with according to residue template for
THR /g:131
Atom CG2 has no neighbors to form bonds with according to residue template for
VAL /g:152
Atom OG has no neighbors to form bonds with according to residue template for
SER /g:176
Atom N has no neighbors to form bonds with according to residue template for
ASN /g:207
Atom N has no neighbors to form bonds with according to residue template for
TRP /g:230
Atom CE has no neighbors to form bonds with according to residue template for
MET /g:239
Atom N has no neighbors to form bonds with according to residue template for
VAL /g:247
Atom CD has no neighbors to form bonds with according to residue template for
LYS /i:23
Atom NZ has no neighbors to form bonds with according to residue template for
LYS /i:23
Atom O has no neighbors to form bonds with according to residue template for
LYS /i:67
Chain information for 0057_6gsm_C.cif #1
---
Chain | Description
1 | Met-tRNAi
2 | 18S ribosomal RNA
3 | mRNA (5'-R(P*AP*AP*U)-3')
A | 40S ribosomal protein S0
B | 40S ribosomal protein S1
C | KLLA0F09812p
D | KLLA0D08305p
E | 40S ribosomal protein S4
H | 40S ribosomal protein S7
J | KLLA0E23673p
L | KLLA0A10483p
N | KLLA0F18040p
O | 40S ribosomal protein S14
R | KLLA0B01474p
U | KLLA0F25542p
V | 40S ribosomal protein S21
W | 40S ribosomal protein S22
X | KLLA0B11231p
a | 40S ribosomal protein S26
b | 40S ribosomal protein S27
c | 40S ribosomal protein S28
d | 40S ribosomal protein S29
e | 40S ribosomal protein S30
g | KLLA0E12277p
i | Eukaryotic translation initiation factor 1A
> open /scratch/cs-
> bioinfo/tngu/6k_data/Box_Chains_new/0057_6gsm/0057_6gsm_C.mrc
Opened 0057_6gsm_C.mrc as #2, grid size 96,104,80, pixel 1, shown at level
0.146, step 1, values float32
> fitmap #1 inMap #2
Fit molecule 0057_6gsm_C.cif (#1) to map 0057_6gsm_C.mrc (#2) using 19056
atoms
average map value = 0.0813, steps = 60
shifted from previous position = 0.29
rotated from previous position = 0.049 degrees
atoms outside contour = 18418, contour level = 0.14602
Position of 0057_6gsm_C.cif (#1) relative to 0057_6gsm_C.mrc (#2) coordinates:
Matrix rotation and translation
0.99999999 -0.00002143 0.00013169 -0.07370813
0.00002132 0.99999964 0.00084431 -0.39245208
-0.00013171 -0.00084430 0.99999963 0.02626946
Axis -0.98774211 0.15407786 0.02501082
Axis point 0.00000000 30.52682018 467.20587978
Rotation angle (degrees) 0.04897546
Shift along axis 0.01299346
> save /scratch/cs-
> bioinfo/tngu/6k_data/Box_Chains_new/0057_6gsm/0057_6gsm_C_fitted.cif #1
> close #1
> close #2
> open /scratch/cs-
> bioinfo/tngu/6k_data/Box_Chains_new/0057_6gsm/0057_6gsm_S.cif
Summary of feedback from opening /scratch/cs-
bioinfo/tngu/6k_data/Box_Chains_new/0057_6gsm/0057_6gsm_S.cif
---
warnings | Invalid residue range for struct_conf "HELX1": invalid chain "C",
near line 44865
Invalid residue range for struct_conf "HELX2": invalid chain "C", near line
44866
Invalid residue range for struct_conf "HELX3": invalid chain "C", near line
44867
Invalid residue range for struct_conf "HELX4": invalid chain "C", near line
44868
Invalid residue range for struct_conf "HELX5": invalid chain "C", near line
44869
168 messages similar to the above omitted
Invalid sheet range for struct_sheet_range "? 1": invalid chain "C", near line
45118
Invalid sheet range for struct_sheet_range "? 2": invalid chain "C", near line
45119
Invalid sheet range for struct_sheet_range "? 3": invalid chain "C", near line
45120
Invalid sheet range for struct_sheet_range "? 4": invalid chain "C", near line
45121
Invalid sheet range for struct_sheet_range "? 5": invalid chain "C", near line
45122
203 messages similar to the above omitted
Atom OP1 has no neighbors to form bonds with according to residue template for
C /1:6
Atom O2' has no neighbors to form bonds with according to residue template for
C /1:6
Atom O3' has no neighbors to form bonds with according to residue template for
U /1:50
Atom C5' has no neighbors to form bonds with according to residue template for
G /2:1232
Atom OP1 has no neighbors to form bonds with according to residue template for
U /2:1258
Atom OP1 has no neighbors to form bonds with according to residue template for
G /2:1266
Atom N2 has no neighbors to form bonds with according to residue template for
G /2:1266
Atom N3 has no neighbors to form bonds with according to residue template for
G /2:1266
Atom O4' has no neighbors to form bonds with according to residue template for
A /2:1286
Atom O4' has no neighbors to form bonds with according to residue template for
G /2:1329
Atom C5 has no neighbors to form bonds with according to residue template for
A /2:1398
Atom N6 has no neighbors to form bonds with according to residue template for
A /2:1398
Atom O3' has no neighbors to form bonds with according to residue template for
G /2:1426
Atom OP1 has no neighbors to form bonds with according to residue template for
G /2:1484
Atom O2' has no neighbors to form bonds with according to residue template for
U /2:1487
Atom O2' has no neighbors to form bonds with according to residue template for
C /2:1489
Atom OP2 has no neighbors to form bonds with according to residue template for
G /2:1496
Atom OP2 has no neighbors to form bonds with according to residue template for
G /2:1497
Atom OP2 has no neighbors to form bonds with according to residue template for
U /2:1508
Atom O3' has no neighbors to form bonds with according to residue template for
U /2:1517
Atom O2 has no neighbors to form bonds with according to residue template for
U /2:1517
Atom CG2 has no neighbors to form bonds with according to residue template for
ILE /F:66
Atom N has no neighbors to form bonds with according to residue template for
SER /F:67
Atom C has no neighbors to form bonds with according to residue template for
SER /F:67
Atom OD1 has no neighbors to form bonds with according to residue template for
ASP /F:128
Atom CD1 has no neighbors to form bonds with according to residue template for
TYR /K:12
Atom N has no neighbors to form bonds with according to residue template for
LEU /K:46
Atom N has no neighbors to form bonds with according to residue template for
TYR /K:66
Atom CD2 has no neighbors to form bonds with according to residue template for
LEU /Q:38
Atom N has no neighbors to form bonds with according to residue template for
LYS /Q:47
Atom N has no neighbors to form bonds with according to residue template for
ARG /T:63
Atom CB has no neighbors to form bonds with according to residue template for
ARG /T:63
Atom CD has no neighbors to form bonds with according to residue template for
ARG /T:63
Atom N has no neighbors to form bonds with according to residue template for
THR /c:26
Atom CG2 has no neighbors to form bonds with according to residue template for
THR /c:26
Atom N has no neighbors to form bonds with according to residue template for
VAL /c:48
Atom O has no neighbors to form bonds with according to residue template for
VAL /c:48
Atom N has no neighbors to form bonds with according to residue template for
ASN /d:48
Atom ND2 has no neighbors to form bonds with according to residue template for
ASN /d:48
Atom O has no neighbors to form bonds with according to residue template for
ASN /j:41
Atom ND2 has no neighbors to form bonds with according to residue template for
ASN /j:41
Atom N has no neighbors to form bonds with according to residue template for
ALA /j:71
Atom CB has no neighbors to form bonds with according to residue template for
ALA /j:71
Atom O has no neighbors to form bonds with according to residue template for
ARG /j:88
Atom CA has no neighbors to form bonds with according to residue template for
GLU /j:93
Atom CG has no neighbors to form bonds with according to residue template for
GLU /j:93
Atom N has no neighbors to form bonds with according to residue template for
ASP /j:94
Atom N has no neighbors to form bonds with according to residue template for
ALA /j:116
Atom C has no neighbors to form bonds with according to residue template for
ALA /j:116
Atom O has no neighbors to form bonds with according to residue template for
GLN /j:120
Atom N has no neighbors to form bonds with according to residue template for
ILE /j:173
Atom CG1 has no neighbors to form bonds with according to residue template for
ILE /j:173
Atom O has no neighbors to form bonds with according to residue template for
VAL /l:225
Atom CG1 has no neighbors to form bonds with according to residue template for
VAL /l:225
Atom CA has no neighbors to form bonds with according to residue template for
LEU /l:226
Atom O has no neighbors to form bonds with according to residue template for
LEU /l:226
Atom O has no neighbors to form bonds with according to residue template for
MET /m:74
Chain information for 0057_6gsm_S.cif #1
---
Chain | Description
1 | Met-tRNAi
2 | 18S ribosomal RNA
D | KLLA0D08305p
F | KLLA0D10659p
K | KLLA0B08173p
P | KLLA0F07843p
Q | 40S ribosomal protein S16
R | KLLA0B01474p
S | KLLA0B01562p
T | KLLA0A07194p
U | KLLA0F25542p
Z | KLLA0B06182p
c | 40S ribosomal protein S28
d | 40S ribosomal protein S29
f | Ubiquitin-40S ribosomal protein S27a
j | Eukaryotic translation initiation factor 2 subunit alpha
l | Eukaryotic translation initiation factor 2 subunit beta
m | Eukaryotic translation initiation factor eIF-1
> open /scratch/cs-
> bioinfo/tngu/6k_data/Box_Chains_new/0057_6gsm/0057_6gsm_S.mrc
Opened 0057_6gsm_S.mrc as #2, grid size 80,104,96, pixel 1, shown at level
0.127, step 1, values float32
> fitmap #1 inMap #2
Fit molecule 0057_6gsm_S.cif (#1) to map 0057_6gsm_S.mrc (#2) using 13752
atoms
average map value = 0.07525, steps = 48
shifted from previous position = 0.41
rotated from previous position = 0.0854 degrees
atoms outside contour = 13058, contour level = 0.12703
Position of 0057_6gsm_S.cif (#1) relative to 0057_6gsm_S.mrc (#2) coordinates:
Matrix rotation and translation
0.99999906 0.00133714 0.00031755 -0.63883129
-0.00133696 0.99999894 -0.00057716 0.36463028
-0.00031832 0.00057673 0.99999978 -0.16205439
Axis 0.38707716 0.21330452 -0.89703537
Axis point 276.20794680 470.96878257 0.00000000
Rotation angle (degrees) 0.08540052
Shift along axis -0.02413119
> save /scratch/cs-
> bioinfo/tngu/6k_data/Box_Chains_new/0057_6gsm/0057_6gsm_S_fitted.cif #1
> close #1
> close #2
> open /scratch/cs-
> bioinfo/tngu/6k_data/Box_Chains_new/0057_6gsm/0057_6gsm_h.cif
Summary of feedback from opening /scratch/cs-
bioinfo/tngu/6k_data/Box_Chains_new/0057_6gsm/0057_6gsm_h.cif
---
warnings | Invalid residue range for struct_conf "HELX1": invalid chain "C",
near line 39713
Invalid residue range for struct_conf "HELX2": invalid chain "C", near line
39714
Invalid residue range for struct_conf "HELX3": invalid chain "C", near line
39715
Invalid residue range for struct_conf "HELX4": invalid chain "C", near line
39716
Invalid residue range for struct_conf "HELX5": invalid chain "C", near line
39717
114 messages similar to the above omitted
Invalid sheet range for struct_sheet_range "? 1": invalid chain "C", near line
39966
Invalid sheet range for struct_sheet_range "? 2": invalid chain "C", near line
39967
Invalid sheet range for struct_sheet_range "? 3": invalid chain "C", near line
39968
Invalid sheet range for struct_sheet_range "? 4": invalid chain "C", near line
39969
Invalid sheet range for struct_sheet_range "? 5": invalid chain "C", near line
39970
157 messages similar to the above omitted
Atom N6 has no neighbors to form bonds with according to residue template for
A /2:11
Atom OP2 has no neighbors to form bonds with according to residue template for
G /2:20
Atom OP1 has no neighbors to form bonds with according to residue template for
C /2:309
Atom OP1 has no neighbors to form bonds with according to residue template for
U /2:373
Atom OP1 has no neighbors to form bonds with according to residue template for
A /2:605
Atom OP2 has no neighbors to form bonds with according to residue template for
U /2:611
Atom O2' has no neighbors to form bonds with according to residue template for
G /2:612
Atom OP2 has no neighbors to form bonds with according to residue template for
C /2:613
Atom O5' has no neighbors to form bonds with according to residue template for
C /2:613
Atom P has no neighbors to form bonds with according to residue template for G
/2:633
Atom N4 has no neighbors to form bonds with according to residue template for
C /2:942
Atom C5 has no neighbors to form bonds with according to residue template for
C /2:942
Atom N6 has no neighbors to form bonds with according to residue template for
A /2:997
Atom N1 has no neighbors to form bonds with according to residue template for
A /2:997
Atom O2' has no neighbors to form bonds with according to residue template for
A /2:1000
Atom OP2 has no neighbors to form bonds with according to residue template for
U /2:1008
Atom OP2 has no neighbors to form bonds with according to residue template for
C /2:1009
Atom N6 has no neighbors to form bonds with according to residue template for
A /2:1018
Atom N1 has no neighbors to form bonds with according to residue template for
A /2:1018
Atom O2' has no neighbors to form bonds with according to residue template for
C /2:1074
Atom OP2 has no neighbors to form bonds with according to residue template for
A /2:1142
Atom O2' has no neighbors to form bonds with according to residue template for
G /2:1734
Atom O3' has no neighbors to form bonds with according to residue template for
C /2:1794
Atom C8 has no neighbors to form bonds with according to residue template for
A /3:29
Atom CA has no neighbors to form bonds with according to residue template for
LYS /N:9
Atom CB has no neighbors to form bonds with according to residue template for
LYS /O:92
Atom NZ has no neighbors to form bonds with according to residue template for
LYS /O:92
Atom O has no neighbors to form bonds with according to residue template for
ASN /X:79
Atom O has no neighbors to form bonds with according to residue template for
ALA /X:113
Atom C has no neighbors to form bonds with according to residue template for
LEU /i:42
Atom CD2 has no neighbors to form bonds with according to residue template for
LEU /i:42
Atom N has no neighbors to form bonds with according to residue template for
ASN /i:44
Atom N has no neighbors to form bonds with according to residue template for
GLY /m:107
Atom O has no neighbors to form bonds with according to residue template for
GLY /m:107
Atom N has no neighbors to form bonds with according to residue template for
GLY /p:132
Atom O has no neighbors to form bonds with according to residue template for
GLY /p:132
Atom O has no neighbors to form bonds with according to residue template for
PRO /p:181
Atom CB has no neighbors to form bonds with according to residue template for
LEU /p:189
Atom CD2 has no neighbors to form bonds with according to residue template for
LEU /p:189
Atom O has no neighbors to form bonds with according to residue template for
LYS /p:241
Atom N has no neighbors to form bonds with according to residue template for
ARG /p:266
Atom N has no neighbors to form bonds with according to residue template for
LEU /p:284
Atom N has no neighbors to form bonds with according to residue template for
GLU /p:295
Atom CB has no neighbors to form bonds with according to residue template for
GLU /p:295
Atom OE2 has no neighbors to form bonds with according to residue template for
GLU /p:295
Atom O has no neighbors to form bonds with according to residue template for
GLU /p:308
Atom CA has no neighbors to form bonds with according to residue template for
ASP /p:397
Atom O has no neighbors to form bonds with according to residue template for
THR /q:141
Atom CB has no neighbors to form bonds with according to residue template for
THR /q:141
Atom O has no neighbors to form bonds with according to residue template for
GLN /q:159
Chain information for 0057_6gsm_h.cif #1
---
Chain | Description
2 | 18S ribosomal RNA
3 | mRNA (5'-R(P*AP*AP*U)-3')
C | KLLA0F09812p
L | KLLA0A10483p
N | KLLA0F18040p
O | 40S ribosomal protein S14
X | KLLA0B11231p
a | 40S ribosomal protein S26
h | 60S ribosomal protein L41-A
i | Eukaryotic translation initiation factor 1A
k | Eukaryotic translation initiation factor 2 subunit gamma
m | Eukaryotic translation initiation factor eIF-1
o | Eukaryotic translation initiation factor 3 subunit A,Eukaryotic
translation initiation factor 3 subunit A,eIF3a
p | Eukaryotic translation initiation factor 3 subunit B
q | Eukaryotic translation initiation factor 3 subunit C
> open /scratch/cs-
> bioinfo/tngu/6k_data/Box_Chains_new/0057_6gsm/0057_6gsm_h.mrc
Opened 0057_6gsm_h.mrc as #2, grid size 80,64,56, pixel 1, shown at level
0.155, step 1, values float32
> fitmap #1 inMap #2
Fit molecule 0057_6gsm_h.cif (#1) to map 0057_6gsm_h.mrc (#2) using 8610 atoms
average map value = 0.08394, steps = 76
shifted from previous position = 0.502
rotated from previous position = 0.277 degrees
atoms outside contour = 8377, contour level = 0.1553
Position of 0057_6gsm_h.cif (#1) relative to 0057_6gsm_h.mrc (#2) coordinates:
Matrix rotation and translation
0.99999390 0.00244455 0.00249314 -1.49360317
-0.00245288 0.99999140 0.00334522 -0.36462362
-0.00248494 -0.00335131 0.99999130 1.17721721
Axis -0.69213279 0.51451966 -0.50618349
Axis point 0.00000000 388.68717064 148.49285133
Rotation angle (degrees) 0.27717525
Shift along axis 0.25027779
> save /scratch/cs-
> bioinfo/tngu/6k_data/Box_Chains_new/0057_6gsm/0057_6gsm_h_fitted.cif #1
> close #1
> close #2
> open /scratch/cs-
> bioinfo/tngu/6k_data/Box_Chains_new/0057_6gsm/0057_6gsm_I.cif
Summary of feedback from opening /scratch/cs-
bioinfo/tngu/6k_data/Box_Chains_new/0057_6gsm/0057_6gsm_I.cif
---
warnings | Invalid residue range for struct_conf "HELX1": invalid chain "C",
near line 45675
Invalid residue range for struct_conf "HELX2": invalid chain "C", near line
45676
Invalid residue range for struct_conf "HELX3": invalid chain "C", near line
45677
Invalid residue range for struct_conf "HELX4": invalid chain "C", near line
45678
Invalid residue range for struct_conf "HELX5": invalid chain "C", near line
45679
127 messages similar to the above omitted
Invalid sheet range for struct_sheet_range "? 1": invalid chain "C", near line
45928
Invalid sheet range for struct_sheet_range "? 2": invalid chain "C", near line
45929
Invalid sheet range for struct_sheet_range "? 3": invalid chain "C", near line
45930
Invalid sheet range for struct_sheet_range "? 4": invalid chain "C", near line
45931
Invalid sheet range for struct_sheet_range "? 5": invalid chain "C", near line
45932
179 messages similar to the above omitted
Atom O2' has no neighbors to form bonds with according to residue template for
U /2:24
Atom O2' has no neighbors to form bonds with according to residue template for
C /2:25
Atom OP1 has no neighbors to form bonds with according to residue template for
A /2:40
Atom O3' has no neighbors to form bonds with according to residue template for
A /2:41
Atom O2' has no neighbors to form bonds with according to residue template for
U /2:64
Atom OP2 has no neighbors to form bonds with according to residue template for
U /2:110
Atom O5' has no neighbors to form bonds with according to residue template for
U /2:110
Atom OP2 has no neighbors to form bonds with according to residue template for
U /2:111
Atom O2' has no neighbors to form bonds with according to residue template for
A /2:146
Atom O3' has no neighbors to form bonds with according to residue template for
G /2:162
Atom N2 has no neighbors to form bonds with according to residue template for
G /2:162
Atom OP2 has no neighbors to form bonds with according to residue template for
A /2:221
Atom O5' has no neighbors to form bonds with according to residue template for
G /2:272
Atom O2' has no neighbors to form bonds with according to residue template for
G /2:364
Atom O2' has no neighbors to form bonds with according to residue template for
A /2:365
Atom O2' has no neighbors to form bonds with according to residue template for
U /2:373
Atom OP2 has no neighbors to form bonds with according to residue template for
G /2:417
Atom C6 has no neighbors to form bonds with according to residue template for
C /2:423
Atom N2 has no neighbors to form bonds with according to residue template for
G /2:433
Atom N3 has no neighbors to form bonds with according to residue template for
G /2:433
Atom O5' has no neighbors to form bonds with according to residue template for
A /2:459
Atom O2' has no neighbors to form bonds with according to residue template for
C /2:468
Atom O2 has no neighbors to form bonds with according to residue template for
C /2:468
Atom OP1 has no neighbors to form bonds with according to residue template for
G /2:627
Atom N2 has no neighbors to form bonds with according to residue template for
G /2:627
Atom N3 has no neighbors to form bonds with according to residue template for
G /2:627
Atom O4 has no neighbors to form bonds with according to residue template for
U /2:631
Atom C5 has no neighbors to form bonds with according to residue template for
U /2:631
Atom O2' has no neighbors to form bonds with according to residue template for
A /2:795
Atom N3 has no neighbors to form bonds with according to residue template for
A /2:795
Atom O4 has no neighbors to form bonds with according to residue template for
U /2:830
Atom C5 has no neighbors to form bonds with according to residue template for
U /2:830
Atom O2 has no neighbors to form bonds with according to residue template for
C /2:848
Atom O3' has no neighbors to form bonds with according to residue template for
U /2:1103
Atom O2' has no neighbors to form bonds with according to residue template for
G /2:1118
Atom NH2 has no neighbors to form bonds with according to residue template for
ARG /E:11
Atom CD1 has no neighbors to form bonds with according to residue template for
LEU /E:12
Atom O has no neighbors to form bonds with according to residue template for
VAL /E:61
Atom N has no neighbors to form bonds with according to residue template for
THR /E:141
Atom O has no neighbors to form bonds with according to residue template for
THR /E:141
Atom O has no neighbors to form bonds with according to residue template for
GLY /G:55
Atom O has no neighbors to form bonds with according to residue template for
ILE /G:112
Atom N has no neighbors to form bonds with according to residue template for
ILE /G:141
Atom C has no neighbors to form bonds with according to residue template for
ILE /G:141
Atom OD1 has no neighbors to form bonds with according to residue template for
ASP /G:152
Atom N has no neighbors to form bonds with according to residue template for
GLU /N:86
Atom O has no neighbors to form bonds with according to residue template for
GLU /N:86
Atom N has no neighbors to form bonds with according to residue template for
VAL /N:132
Atom N has no neighbors to form bonds with according to residue template for
ASN /X:22
Atom OD1 has no neighbors to form bonds with according to residue template for
ASN /X:22
Atom N has no neighbors to form bonds with according to residue template for
TRP /X:24
Atom N has no neighbors to form bonds with according to residue template for
LYS /X:50
Atom N has no neighbors to form bonds with according to residue template for
UNK /o:703
Atom N has no neighbors to form bonds with according to residue template for
LEU /p:189
Atom OG1 has no neighbors to form bonds with according to residue template for
THR /p:243
Atom CG2 has no neighbors to form bonds with according to residue template for
THR /p:243
Atom ND2 has no neighbors to form bonds with according to residue template for
ASN /p:445
Chain information for 0057_6gsm_I.cif #1
---
Chain | Description
2 | 18S ribosomal RNA
E | 40S ribosomal protein S4
G | 40S ribosomal protein S6
I | 40S ribosomal protein S8
J | KLLA0E23673p
L | KLLA0A10483p
N | KLLA0F18040p
X | KLLA0B11231p
o | Eukaryotic translation initiation factor 3 subunit A,Eukaryotic
translation initiation factor 3 subunit A,eIF3a
p | Eukaryotic translation initiation factor 3 subunit B
q | Eukaryotic translation initiation factor 3 subunit C
> open /scratch/cs-
> bioinfo/tngu/6k_data/Box_Chains_new/0057_6gsm/0057_6gsm_I.mrc
Opened 0057_6gsm_I.mrc as #2, grid size 72,120,96, pixel 1, shown at level
0.144, step 1, values float32
> fitmap #1 inMap #2
Fit molecule 0057_6gsm_I.cif (#1) to map 0057_6gsm_I.mrc (#2) using 14447
atoms
average map value = 0.08325, steps = 64
shifted from previous position = 0.639
rotated from previous position = 0.171 degrees
atoms outside contour = 13697, contour level = 0.14363
Position of 0057_6gsm_I.cif (#1) relative to 0057_6gsm_I.mrc (#2) coordinates:
Matrix rotation and translation
0.99999700 0.00094952 -0.00225603 -0.15605800
-0.00094564 0.99999807 0.00172043 -0.49124166
0.00225766 -0.00171829 0.99999598 -0.43873210
Axis -0.57480111 -0.75448682 -0.31678593
Axis point 110.38476831 0.00000000 83.37759510
Rotation angle (degrees) 0.17138502
Shift along axis 0.59932182
> save /scratch/cs-
> bioinfo/tngu/6k_data/Box_Chains_new/0057_6gsm/0057_6gsm_I_fitted.cif #1
> close #1
> close #2
> open /scratch/cs-
> bioinfo/tngu/6k_data/Box_Chains_new/0057_6gsm/0057_6gsm_j.cif
Summary of feedback from opening /scratch/cs-
bioinfo/tngu/6k_data/Box_Chains_new/0057_6gsm/0057_6gsm_j.cif
---
warnings | Invalid residue range for struct_conf "HELX1": invalid chain "C",
near line 45481
Invalid residue range for struct_conf "HELX2": invalid chain "C", near line
45482
Invalid residue range for struct_conf "HELX3": invalid chain "C", near line
45483
Invalid residue range for struct_conf "HELX4": invalid chain "C", near line
45484
Invalid residue range for struct_conf "HELX5": invalid chain "C", near line
45485
121 messages similar to the above omitted
Invalid sheet range for struct_sheet_range "? 1": invalid chain "C", near line
45734
Invalid sheet range for struct_sheet_range "? 2": invalid chain "C", near line
45735
Invalid sheet range for struct_sheet_range "? 3": invalid chain "C", near line
45736
Invalid sheet range for struct_sheet_range "? 4": invalid chain "C", near line
45737
Invalid sheet range for struct_sheet_range "? 5": invalid chain "C", near line
45738
141 messages similar to the above omitted
Atom O5' has no neighbors to form bonds with according to residue template for
U /2:920
Atom OP2 has no neighbors to form bonds with according to residue template for
A /2:923
Atom N3 has no neighbors to form bonds with according to residue template for
A /2:987
Atom OP1 has no neighbors to form bonds with according to residue template for
G /2:1145
Atom O2' has no neighbors to form bonds with according to residue template for
G /2:1145
Atom N2 has no neighbors to form bonds with according to residue template for
G /2:1280
Atom O3' has no neighbors to form bonds with according to residue template for
A /2:1286
Atom O2' has no neighbors to form bonds with according to residue template for
A /2:1286
Atom OP1 has no neighbors to form bonds with according to residue template for
G /2:1287
Atom O2' has no neighbors to form bonds with according to residue template for
G /2:1287
Atom O2' has no neighbors to form bonds with according to residue template for
U /2:1306
Atom OP1 has no neighbors to form bonds with according to residue template for
C /2:1308
Atom OP2 has no neighbors to form bonds with according to residue template for
C /2:1308
Atom OP1 has no neighbors to form bonds with according to residue template for
G /2:1460
Atom C8 has no neighbors to form bonds with according to residue template for
G /2:1462
Atom C6 has no neighbors to form bonds with according to residue template for
C /2:1463
Atom OP2 has no neighbors to form bonds with according to residue template for
U /2:1526
Atom OP1 has no neighbors to form bonds with according to residue template for
U /2:1756
Atom O3' has no neighbors to form bonds with according to residue template for
U /2:1756
Atom OP1 has no neighbors to form bonds with according to residue template for
U /2:1783
Atom C5' has no neighbors to form bonds with according to residue template for
U /2:1783
Atom OP2 has no neighbors to form bonds with according to residue template for
U /2:1796
Atom N has no neighbors to form bonds with according to residue template for
ARG /B:26
Atom O has no neighbors to form bonds with according to residue template for
PHE /B:81
Atom NZ has no neighbors to form bonds with according to residue template for
LYS /B:116
Atom N has no neighbors to form bonds with according to residue template for
PHE /B:142
Atom CG1 has no neighbors to form bonds with according to residue template for
VAL /F:55
Atom CB has no neighbors to form bonds with according to residue template for
ARG /F:94
Atom N has no neighbors to form bonds with according to residue template for
ASN /F:130
Atom N has no neighbors to form bonds with according to residue template for
LEU /F:132
Atom NE2 has no neighbors to form bonds with according to residue template for
GLN /F:133
Atom OD1 has no neighbors to form bonds with according to residue template for
ASP /O:124
Atom O has no neighbors to form bonds with according to residue template for
VAL /S:28
Atom N has no neighbors to form bonds with according to residue template for
ALA /S:31
Atom CB has no neighbors to form bonds with according to residue template for
ALA /S:31
Atom CG has no neighbors to form bonds with according to residue template for
LEU /S:61
Atom N has no neighbors to form bonds with according to residue template for
THR /S:62
Atom CG2 has no neighbors to form bonds with according to residue template for
THR /S:62
Atom N has no neighbors to form bonds with according to residue template for
VAL /Z:92
Atom CG2 has no neighbors to form bonds with according to residue template for
VAL /Z:92
Atom N has no neighbors to form bonds with according to residue template for
SER /a:88
Atom CB has no neighbors to form bonds with according to residue template for
SER /a:88
Atom OE2 has no neighbors to form bonds with according to residue template for
GLU /c:31
Atom N has no neighbors to form bonds with according to residue template for
ASP /k:193
Atom N has no neighbors to form bonds with according to residue template for
MET /k:211
Atom SD has no neighbors to form bonds with according to residue template for
MET /k:211
Atom CB has no neighbors to form bonds with according to residue template for
ALA /k:234
Atom O has no neighbors to form bonds with according to residue template for
PHE /k:435
Atom CD2 has no neighbors to form bonds with according to residue template for
PHE /k:435
Atom NE has no neighbors to form bonds with according to residue template for
ARG /k:474
Atom NH2 has no neighbors to form bonds with according to residue template for
ARG /k:474
Atom C has no neighbors to form bonds with according to residue template for
ARG /l:167
Atom CD has no neighbors to form bonds with according to residue template for
ARG /l:167
Atom NH1 has no neighbors to form bonds with according to residue template for
ARG /l:167
Atom N has no neighbors to form bonds with according to residue template for
ILE /p:116
Atom OE1 has no neighbors to form bonds with according to residue template for
GLU /p:118
Atom OE2 has no neighbors to form bonds with according to residue template for
GLU /p:118
Atom C has no neighbors to form bonds with according to residue template for
LEU /p:127
Chain information for 0057_6gsm_j.cif #1
---
Chain | Description
1 | Met-tRNAi
2 | 18S ribosomal RNA
3 | mRNA (5'-R(P*AP*AP*U)-3')
B | 40S ribosomal protein S1
C | KLLA0F09812p
F | KLLA0D10659p
O | 40S ribosomal protein S14
Q | 40S ribosomal protein S16
S | KLLA0B01562p
T | KLLA0A07194p
U | KLLA0F25542p
Z | KLLA0B06182p
a | 40S ribosomal protein S26
c | 40S ribosomal protein S28
i | Eukaryotic translation initiation factor 1A
j | Eukaryotic translation initiation factor 2 subunit alpha
k | Eukaryotic translation initiation factor 2 subunit gamma
l | Eukaryotic translation initiation factor 2 subunit beta
m | Eukaryotic translation initiation factor eIF-1
o | Eukaryotic translation initiation factor 3 subunit A,Eukaryotic
translation initiation factor 3 subunit A,eIF3a
p | Eukaryotic translation initiation factor 3 subunit B
> open /scratch/cs-
> bioinfo/tngu/6k_data/Box_Chains_new/0057_6gsm/0057_6gsm_j.mrc
Opened 0057_6gsm_j.mrc as #2, grid size 136,104,80, pixel 1, shown at level
0.119, step 1, values float32
> fitmap #1 inMap #2
Fit molecule 0057_6gsm_j.cif (#1) to map 0057_6gsm_j.mrc (#2) using 14398
atoms
average map value = 0.06882, steps = 56
shifted from previous position = 0.502
rotated from previous position = 0.155 degrees
atoms outside contour = 13409, contour level = 0.11916
Position of 0057_6gsm_j.cif (#1) relative to 0057_6gsm_j.mrc (#2) coordinates:
Matrix rotation and translation
0.99999853 0.00013427 0.00170961 -0.74251221
-0.00013069 0.99999780 -0.00209394 0.48762654
-0.00170989 0.00209372 0.99999635 -0.29123892
Axis 0.77364167 0.63172986 -0.04894843
Axis point 0.00000000 145.53493310 308.78942974
Rotation angle (degrees) 0.15506880
Shift along axis -0.25213445
> save /scratch/cs-
> bioinfo/tngu/6k_data/Box_Chains_new/0057_6gsm/0057_6gsm_j_fitted.cif #1
> close #1
> close #2
> open /scratch/cs-
> bioinfo/tngu/6k_data/Box_Chains_new/0057_6gsm/0057_6gsm_m.cif
Summary of feedback from opening /scratch/cs-
bioinfo/tngu/6k_data/Box_Chains_new/0057_6gsm/0057_6gsm_m.cif
---
warnings | Invalid residue range for struct_conf "HELX1": invalid chain "C",
near line 43790
Invalid residue range for struct_conf "HELX2": invalid chain "C", near line
43791
Invalid residue range for struct_conf "HELX3": invalid chain "C", near line
43792
Invalid residue range for struct_conf "HELX4": invalid chain "C", near line
43793
Invalid residue range for struct_conf "HELX5": invalid chain "C", near line
43794
100 messages similar to the above omitted
Invalid sheet range for struct_sheet_range "? 1": invalid chain "C", near line
44043
Invalid sheet range for struct_sheet_range "? 2": invalid chain "C", near line
44044
Invalid sheet range for struct_sheet_range "? 3": invalid chain "C", near line
44045
Invalid sheet range for struct_sheet_range "? 4": invalid chain "C", near line
44046
Invalid sheet range for struct_sheet_range "? 5": invalid chain "C", near line
44047
153 messages similar to the above omitted
Atom O6 has no neighbors to form bonds with according to residue template for
1MG /1:9
Atom OP2 has no neighbors to form bonds with according to residue template for
2MG /1:10
Atom O3' has no neighbors to form bonds with according to residue template for
G /1:22
Atom OP1 has no neighbors to form bonds with according to residue template for
G /2:10
Atom OP2 has no neighbors to form bonds with according to residue template for
G /2:10
Atom O2' has no neighbors to form bonds with according to residue template for
U /2:15
Atom O2 has no neighbors to form bonds with according to residue template for
U /2:15
Atom OP1 has no neighbors to form bonds with according to residue template for
C /2:571
Atom OP2 has no neighbors to form bonds with according to residue template for
C /2:571
Atom O2 has no neighbors to form bonds with according to residue template for
U /2:617
Atom N6 has no neighbors to form bonds with according to residue template for
A /2:620
Atom OP1 has no neighbors to form bonds with according to residue template for
A /2:621
Atom OP2 has no neighbors to form bonds with according to residue template for
A /2:621
Atom OP2 has no neighbors to form bonds with according to residue template for
G /2:623
Atom N2 has no neighbors to form bonds with according to residue template for
G /2:623
Atom OP2 has no neighbors to form bonds with according to residue template for
A /2:899
Atom O4' has no neighbors to form bonds with according to residue template for
C /2:909
Atom OP2 has no neighbors to form bonds with according to residue template for
U /2:910
Atom N3 has no neighbors to form bonds with according to residue template for
A /2:939
Atom O3' has no neighbors to form bonds with according to residue template for
G /2:1108
Atom O2' has no neighbors to form bonds with according to residue template for
C /2:1133
Atom O2 has no neighbors to form bonds with according to residue template for
C /2:1133
Atom C8 has no neighbors to form bonds with according to residue template for
G /2:1140
Atom OP1 has no neighbors to form bonds with according to residue template for
A /2:1141
Atom OP2 has no neighbors to form bonds with according to residue template for
A /2:1141
Atom OP2 has no neighbors to form bonds with according to residue template for
C /2:1176
Atom C5' has no neighbors to form bonds with according to residue template for
A /2:1188
Atom O3' has no neighbors to form bonds with according to residue template for
C /2:1454
Atom O2' has no neighbors to form bonds with according to residue template for
C /2:1454
Atom OP2 has no neighbors to form bonds with according to residue template for
G /2:1456
Atom OP2 has no neighbors to form bonds with according to residue template for
C /2:1463
Atom N4 has no neighbors to form bonds with according to residue template for
C /2:1463
Atom O3' has no neighbors to form bonds with according to residue template for
C /2:1617
Atom O2' has no neighbors to form bonds with according to residue template for
C /2:1617
Atom O3' has no neighbors to form bonds with according to residue template for
U /2:1619
Atom OP1 has no neighbors to form bonds with according to residue template for
C /2:1632
Atom O5' has no neighbors to form bonds with according to residue template for
A /2:1744
Atom O4' has no neighbors to form bonds with according to residue template for
U /2:1793
Atom N has no neighbors to form bonds with according to residue template for
ARG /B:8
Atom O has no neighbors to form bonds with according to residue template for
ARG /B:8
Atom CG1 has no neighbors to form bonds with according to residue template for
VAL /F:222
Atom O has no neighbors to form bonds with according to residue template for
ARG /O:90
Atom NH1 has no neighbors to form bonds with according to residue template for
ARG /O:103
Atom NH2 has no neighbors to form bonds with according to residue template for
ARG /O:103
Atom N has no neighbors to form bonds with according to residue template for
THR /S:140
Atom CG2 has no neighbors to form bonds with according to residue template for
THR /S:140
Atom O has no neighbors to form bonds with according to residue template for
CYS /X:71
Atom N has no neighbors to form bonds with according to residue template for
VAL /X:120
Atom CG2 has no neighbors to form bonds with according to residue template for
VAL /X:120
Atom O has no neighbors to form bonds with according to residue template for
ASN /a:8
Atom N has no neighbors to form bonds with according to residue template for
VAL /a:18
Atom O has no neighbors to form bonds with according to residue template for
VAL /a:18
Atom CG1 has no neighbors to form bonds with according to residue template for
VAL /a:21
Atom O has no neighbors to form bonds with according to residue template for
LEU /a:71
Atom CD1 has no neighbors to form bonds with according to residue template for
LEU /a:71
Atom N has no neighbors to form bonds with according to residue template for
ILE /a:83
Atom N has no neighbors to form bonds with according to residue template for
ARG /h:21
Atom NH1 has no neighbors to form bonds with according to residue template for
ARG /h:21
Atom CG has no neighbors to form bonds with according to residue template for
ARG /i:24
Atom O has no neighbors to form bonds with according to residue template for
GLU /i:34
Atom N has no neighbors to form bonds with according to residue template for
ASP /i:53
Atom C has no neighbors to form bonds with according to residue template for
ASP /i:53
Atom N has no neighbors to form bonds with according to residue template for
ASP /i:83
Atom C has no neighbors to form bonds with according to residue template for
ASP /i:83
Atom N has no neighbors to form bonds with according to residue template for
ARG /i:101
Atom CD1 has no neighbors to form bonds with according to residue template for
LEU /i:109
Atom CD2 has no neighbors to form bonds with according to residue template for
LEU /i:109
Atom CG2 has no neighbors to form bonds with according to residue template for
ILE /j:19
Atom CD1 has no neighbors to form bonds with according to residue template for
ILE /j:19
Atom CG2 has no neighbors to form bonds with according to residue template for
ILE /j:46
Atom OE1 has no neighbors to form bonds with according to residue template for
GLN /j:60
Atom N has no neighbors to form bonds with according to residue template for
ARG /j:75
Atom N has no neighbors to form bonds with according to residue template for
GLY /k:277
Atom O has no neighbors to form bonds with according to residue template for
GLY /k:277
Atom O has no neighbors to form bonds with according to residue template for
ILE /k:291
Atom O has no neighbors to form bonds with according to residue template for
ASN /k:295
Atom N has no neighbors to form bonds with according to residue template for
LYS /k:300
Atom N has no neighbors to form bonds with according to residue template for
ILE /k:495
Atom CD1 has no neighbors to form bonds with according to residue template for
TYR /p:248
Atom OG has no neighbors to form bonds with according to residue template for
SER /p:275
Atom CD2 has no neighbors to form bonds with according to residue template for
LEU /p:284
Atom CD1 has no neighbors to form bonds with according to residue template for
TRP /p:336
Atom N has no neighbors to form bonds with according to residue template for
ASP /p:360
Atom O has no neighbors to form bonds with according to residue template for
ASP /p:360
Atom N has no neighbors to form bonds with according to residue template for
ALA /p:370
Atom O has no neighbors to form bonds with according to residue template for
ALA /p:370
Atom N has no neighbors to form bonds with according to residue template for
VAL /q:112
Chain information for 0057_6gsm_m.cif #1
---
Chain | Description
1 | Met-tRNAi
2 | 18S ribosomal RNA
3 | mRNA (5'-R(P*AP*AP*U)-3')
B | 40S ribosomal protein S1
F | KLLA0D10659p
O | 40S ribosomal protein S14
P | KLLA0F07843p
Q | 40S ribosomal protein S16
S | KLLA0B01562p
X | KLLA0B11231p
a | 40S ribosomal protein S26
c | 40S ribosomal protein S28
e | 40S ribosomal protein S30
h | 60S ribosomal protein L41-A
i | Eukaryotic translation initiation factor 1A
j | Eukaryotic translation initiation factor 2 subunit alpha
k | Eukaryotic translation initiation factor 2 subunit gamma
l | Eukaryotic translation initiation factor 2 subunit beta
m | Eukaryotic translation initiation factor eIF-1
o | Eukaryotic translation initiation factor 3 subunit A,Eukaryotic
translation initiation factor 3 subunit A,eIF3a
p | Eukaryotic translation initiation factor 3 subunit B
q | Eukaryotic translation initiation factor 3 subunit C
> open /scratch/cs-
> bioinfo/tngu/6k_data/Box_Chains_new/0057_6gsm/0057_6gsm_m.mrc
Opened 0057_6gsm_m.mrc as #2, grid size 104,72,72, pixel 1, shown at level
0.134, step 1, values float32
> fitmap #1 inMap #2
Fit molecule 0057_6gsm_m.cif (#1) to map 0057_6gsm_m.mrc (#2) using 12721
atoms
average map value = 0.0659, steps = 112
shifted from previous position = 0.523
rotated from previous position = 0.124 degrees
atoms outside contour = 12229, contour level = 0.13429
Position of 0057_6gsm_m.cif (#1) relative to 0057_6gsm_m.mrc (#2) coordinates:
Matrix rotation and translation
0.99999779 0.00130994 0.00164375 -1.03339978
-0.00130910 0.99999901 -0.00050917 0.23869542
-0.00164441 0.00050701 0.99999852 0.15046608
Axis 0.23496469 0.76030197 -0.60558444
Axis point 34.81184266 0.00000000 606.93991431
Rotation angle (degrees) 0.12389672
Shift along axis -0.15245178
> save /scratch/cs-
> bioinfo/tngu/6k_data/Box_Chains_new/0057_6gsm/0057_6gsm_m_fitted.cif #1
> close #1
> close #2
> open /scratch/cs-
> bioinfo/tngu/6k_data/Box_Chains_new/0057_6gsm/0057_6gsm_T.cif
Summary of feedback from opening /scratch/cs-
bioinfo/tngu/6k_data/Box_Chains_new/0057_6gsm/0057_6gsm_T.cif
---
warnings | Invalid residue range for struct_conf "HELX1": invalid chain "C",
near line 44599
Invalid residue range for struct_conf "HELX2": invalid chain "C", near line
44600
Invalid residue range for struct_conf "HELX3": invalid chain "C", near line
44601
Invalid residue range for struct_conf "HELX4": invalid chain "C", near line
44602
Invalid residue range for struct_conf "HELX5": invalid chain "C", near line
44603
174 messages similar to the above omitted
Invalid sheet range for struct_sheet_range "? 1": invalid chain "C", near line
44852
Invalid sheet range for struct_sheet_range "? 2": invalid chain "C", near line
44853
Invalid sheet range for struct_sheet_range "? 3": invalid chain "C", near line
44854
Invalid sheet range for struct_sheet_range "? 4": invalid chain "C", near line
44855
Invalid sheet range for struct_sheet_range "? 5": invalid chain "C", near line
44856
183 messages similar to the above omitted
Atom O4' has no neighbors to form bonds with according to residue template for
G /1:43
Atom O3' has no neighbors to form bonds with according to residue template for
C /2:1158
Atom O2' has no neighbors to form bonds with according to residue template for
C /2:1158
Atom OP2 has no neighbors to form bonds with according to residue template for
A /2:1159
Atom O6 has no neighbors to form bonds with according to residue template for
G /2:1197
Atom OP1 has no neighbors to form bonds with according to residue template for
U /2:1448
Atom O2 has no neighbors to form bonds with according to residue template for
C /2:1617
Atom N3 has no neighbors to form bonds with according to residue template for
C /2:1617
Atom CG1 has no neighbors to form bonds with according to residue template for
VAL /D:41
Atom CG2 has no neighbors to form bonds with according to residue template for
VAL /D:41
Atom CD1 has no neighbors to form bonds with according to residue template for
ILE /F:42
Atom CG2 has no neighbors to form bonds with according to residue template for
ILE /F:64
Atom C has no neighbors to form bonds with according to residue template for
VAL /F:134
Atom CB has no neighbors to form bonds with according to residue template for
ALA /F:138
Atom O has no neighbors to form bonds with according to residue template for
SER /F:142
Atom N has no neighbors to form bonds with according to residue template for
ARG /F:159
Atom CG1 has no neighbors to form bonds with according to residue template for
VAL /F:222
Atom CG2 has no neighbors to form bonds with according to residue template for
VAL /F:222
Atom C has no neighbors to form bonds with according to residue template for
ASN /K:28
Atom CB has no neighbors to form bonds with according to residue template for
ASN /K:28
Atom OE1 has no neighbors to form bonds with according to residue template for
GLU /P:23
Atom OE2 has no neighbors to form bonds with according to residue template for
GLU /P:23
Atom O has no neighbors to form bonds with according to residue template for
GLY /P:48
Atom O has no neighbors to form bonds with according to residue template for
ILE /P:85
Atom O has no neighbors to form bonds with according to residue template for
VAL /P:94
Atom CG2 has no neighbors to form bonds with according to residue template for
VAL /P:94
Atom N has no neighbors to form bonds with according to residue template for
ARG /P:127
Atom O has no neighbors to form bonds with according to residue template for
ARG /P:127
Atom N has no neighbors to form bonds with according to residue template for
TRP /S:129
Atom C has no neighbors to form bonds with according to residue template for
TRP /S:129
Atom CB has no neighbors to form bonds with according to residue template for
TRP /S:129
Atom CD1 has no neighbors to form bonds with according to residue template for
TRP /S:129
Atom N has no neighbors to form bonds with according to residue template for
GLU /U:46
Atom CD1 has no neighbors to form bonds with according to residue template for
ILE /U:99
Atom CG2 has no neighbors to form bonds with according to residue template for
VAL /c:25
Atom C has no neighbors to form bonds with according to residue template for
LYS /c:45
Atom O has no neighbors to form bonds with according to residue template for
TYR /d:8
Atom OH has no neighbors to form bonds with according to residue template for
TYR /d:8
Atom O has no neighbors to form bonds with according to residue template for
ILE /d:38
Atom CG1 has no neighbors to form bonds with according to residue template for
VAL /g:35
Atom N has no neighbors to form bonds with according to residue template for
VAL /g:72
Atom CD2 has no neighbors to form bonds with according to residue template for
LEU /g:112
Atom N has no neighbors to form bonds with according to residue template for
ALA /g:249
Atom CB has no neighbors to form bonds with according to residue template for
ALA /g:249
Atom N has no neighbors to form bonds with according to residue template for
ARG /j:54
Atom NZ has no neighbors to form bonds with according to residue template for
LYS /j:87
Chain information for 0057_6gsm_T.cif #1
---
Chain | Description
1 | Met-tRNAi
2 | 18S ribosomal RNA
D | KLLA0D08305p
F | KLLA0D10659p
K | KLLA0B08173p
P | KLLA0F07843p
Q | 40S ribosomal protein S16
R | KLLA0B01474p
S | KLLA0B01562p
T | KLLA0A07194p
U | KLLA0F25542p
Z | KLLA0B06182p
c | 40S ribosomal protein S28
d | 40S ribosomal protein S29
g | KLLA0E12277p
j | Eukaryotic translation initiation factor 2 subunit alpha
> open /scratch/cs-
> bioinfo/tngu/6k_data/Box_Chains_new/0057_6gsm/0057_6gsm_T.mrc
Opened 0057_6gsm_T.mrc as #2, grid size 88,88,80, pixel 1, shown at level
0.133, step 1, values float32
> fitmap #1 inMap #2
Fit molecule 0057_6gsm_T.cif (#1) to map 0057_6gsm_T.mrc (#2) using 13497
atoms
average map value = 0.07745, steps = 60
shifted from previous position = 0.338
rotated from previous position = 0.083 degrees
atoms outside contour = 12958, contour level = 0.13258
Position of 0057_6gsm_T.cif (#1) relative to 0057_6gsm_T.mrc (#2) coordinates:
Matrix rotation and translation
0.99999979 -0.00028336 0.00058636 -0.30702594
0.00028412 0.99999912 -0.00129319 0.23254354
-0.00058599 0.00129335 0.99999899 -0.30519742
Axis 0.89315267 0.40482004 0.19595673
Axis point -0.00000000 199.82647397 254.78106719
Rotation angle (degrees) 0.08296346
Shift along axis -0.23988825
> save /scratch/cs-
> bioinfo/tngu/6k_data/Box_Chains_new/0057_6gsm/0057_6gsm_T_fitted.cif #1
> close #1
> close #2
> open /scratch/cs-
> bioinfo/tngu/6k_data/Box_Chains_new/0057_6gsm/0057_6gsm_Y.cif
Summary of feedback from opening /scratch/cs-
bioinfo/tngu/6k_data/Box_Chains_new/0057_6gsm/0057_6gsm_Y.cif
---
warnings | Invalid residue range for struct_conf "HELX1": invalid chain "C",
near line 43436
Invalid residue range for struct_conf "HELX2": invalid chain "C", near line
43437
Invalid residue range for struct_conf "HELX3": invalid chain "C", near line
43438
Invalid residue range for struct_conf "HELX4": invalid chain "C", near line
43439
Invalid residue range for struct_conf "HELX5": invalid chain "C", near line
43440
161 messages similar to the above omitted
Invalid sheet range for struct_sheet_range "? 1": invalid chain "C", near line
43689
Invalid sheet range for struct_sheet_range "? 2": invalid chain "C", near line
43690
Invalid sheet range for struct_sheet_range "? 3": invalid chain "C", near line
43691
Invalid sheet range for struct_sheet_range "? 4": invalid chain "C", near line
43692
Invalid sheet range for struct_sheet_range "? 5": invalid chain "C", near line
43693
187 messages similar to the above omitted
Atom N2 has no neighbors to form bonds with according to residue template for
G /2:23
Atom C8 has no neighbors to form bonds with according to residue template for
A /2:28
Atom O4 has no neighbors to form bonds with according to residue template for
U /2:29
Atom O3' has no neighbors to form bonds with according to residue template for
U /2:77
Atom O2' has no neighbors to form bonds with according to residue template for
U /2:173
Atom OP2 has no neighbors to form bonds with according to residue template for
U /2:271
Atom N7 has no neighbors to form bonds with according to residue template for
G /2:290
Atom O6 has no neighbors to form bonds with according to residue template for
G /2:290
Atom C4' has no neighbors to form bonds with according to residue template for
C /2:297
Atom O2' has no neighbors to form bonds with according to residue template for
C /2:297
Atom O3' has no neighbors to form bonds with according to residue template for
A /2:359
Atom OP2 has no neighbors to form bonds with according to residue template for
G /2:389
Atom N4 has no neighbors to form bonds with according to residue template for
C /2:392
Atom N3 has no neighbors to form bonds with according to residue template for
G /2:395
Atom OP1 has no neighbors to form bonds with according to residue template for
A /2:396
Atom O2' has no neighbors to form bonds with according to residue template for
A /2:398
Atom O3' has no neighbors to form bonds with according to residue template for
G /2:508
Atom OP1 has no neighbors to form bonds with according to residue template for
C /2:542
Atom C5' has no neighbors to form bonds with according to residue template for
U /2:592
Atom N6 has no neighbors to form bonds with according to residue template for
A /2:593
Atom O2' has no neighbors to form bonds with according to residue template for
U /2:1659
Atom N4 has no neighbors to form bonds with according to residue template for
C /2:1684
Atom C8 has no neighbors to form bonds with according to residue template for
G /2:1711
Atom N3 has no neighbors to form bonds with according to residue template for
A /2:1720
Atom N has no neighbors to form bonds with according to residue template for
GLN /C:155
Atom O has no neighbors to form bonds with according to residue template for
GLN /C:155
Atom CB has no neighbors to form bonds with according to residue template for
PRO /C:178
Atom O has no neighbors to form bonds with according to residue template for
ALA /E:2
Atom CB has no neighbors to form bonds with according to residue template for
ALA /E:2
Atom N has no neighbors to form bonds with according to residue template for
TYR /E:121
Atom O has no neighbors to form bonds with according to residue template for
TYR /E:121
Atom N has no neighbors to form bonds with according to residue template for
PHE /G:145
Atom CG1 has no neighbors to form bonds with according to residue template for
VAL /G:153
Atom CG2 has no neighbors to form bonds with according to residue template for
VAL /G:153
Atom NH1 has no neighbors to form bonds with according to residue template for
ARG /G:159
Atom O has no neighbors to form bonds with according to residue template for
GLU /J:183
Atom O has no neighbors to form bonds with according to residue template for
ARG /p:663
Atom N has no neighbors to form bonds with according to residue template for
ALA /p:692
Atom CB has no neighbors to form bonds with according to residue template for
ALA /p:692
Chain information for 0057_6gsm_Y.cif #1
---
Chain | Description
2 | 18S ribosomal RNA
C | KLLA0F09812p
E | 40S ribosomal protein S4
G | 40S ribosomal protein S6
J | KLLA0E23673p
Y | 40S ribosomal protein S24
o | Eukaryotic translation initiation factor 3 subunit A,Eukaryotic
translation initiation factor 3 subunit A,eIF3a
p | Eukaryotic translation initiation factor 3 subunit B
> open /scratch/cs-
> bioinfo/tngu/6k_data/Box_Chains_new/0057_6gsm/0057_6gsm_Y.mrc
Opened 0057_6gsm_Y.mrc as #2, grid size 128,80,72, pixel 1, shown at level
0.142, step 1, values float32
> fitmap #1 inMap #2
Fit molecule 0057_6gsm_Y.cif (#1) to map 0057_6gsm_Y.mrc (#2) using 12319
atoms
average map value = 0.08353, steps = 48
shifted from previous position = 0.466
rotated from previous position = 0.137 degrees
atoms outside contour = 11679, contour level = 0.14216
Position of 0057_6gsm_Y.cif (#1) relative to 0057_6gsm_Y.mrc (#2) coordinates:
Matrix rotation and translation
0.99999809 -0.00071326 -0.00182141 0.23329565
0.00071574 0.99999882 0.00136215 -0.76507248
0.00182043 -0.00136345 0.99999741 0.02693523
Axis -0.57164385 -0.76380649 0.29970477
Axis point 61.17022831 0.00000000 272.10136371
Rotation angle (degrees) 0.13659378
Shift along axis 0.45907793
> save /scratch/cs-
> bioinfo/tngu/6k_data/Box_Chains_new/0057_6gsm/0057_6gsm_Y_fitted.cif #1
> close #1
> close #2
> open /scratch/cs-
> bioinfo/tngu/6k_data/Box_Chains_new/0057_6gsm/0057_6gsm_F.cif
Summary of feedback from opening /scratch/cs-
bioinfo/tngu/6k_data/Box_Chains_new/0057_6gsm/0057_6gsm_F.cif
---
warnings | Invalid residue range for struct_conf "HELX27": invalid chain "H",
near line 47739
Invalid residue range for struct_conf "HELX28": invalid chain "H", near line
47740
Invalid residue range for struct_conf "HELX29": invalid chain "H", near line
47741
Invalid residue range for struct_conf "HELX30": invalid chain "H", near line
47742
Invalid residue range for struct_conf "HELX31": invalid chain "H", near line
47743
112 messages similar to the above omitted
Invalid sheet range for struct_sheet_range "? 32": invalid chain "H", near
line 47997
Invalid sheet range for struct_sheet_range "? 33": invalid chain "H", near
line 47998
Invalid sheet range for struct_sheet_range "? 34": invalid chain "H", near
line 47999
Invalid sheet range for struct_sheet_range "? 35": invalid chain "H", near
line 48000
Invalid sheet range for struct_sheet_range "? 36": invalid chain "H", near
line 48001
139 messages similar to the above omitted
Atom OP1 has no neighbors to form bonds with according to residue template for
G /1:22
Atom OP2 has no neighbors to form bonds with according to residue template for
G /1:22
Atom C5' has no neighbors to form bonds with according to residue template for
G /1:22
Atom O3' has no neighbors to form bonds with according to residue template for
G /1:22
Atom O3' has no neighbors to form bonds with according to residue template for
C /1:23
Atom O3' has no neighbors to form bonds with according to residue template for
G /1:24
Atom O4 has no neighbors to form bonds with according to residue template for
U /1:45
Atom C5 has no neighbors to form bonds with according to residue template for
U /1:45
Atom C8 has no neighbors to form bonds with according to residue template for
A /2:899
Atom O2' has no neighbors to form bonds with according to residue template for
A /2:987
Atom N3 has no neighbors to form bonds with according to residue template for
A /2:987
Atom O2 has no neighbors to form bonds with according to residue template for
C /2:999
Atom OP1 has no neighbors to form bonds with according to residue template for
G /2:1145
Atom O2' has no neighbors to form bonds with according to residue template for
G /2:1145
Atom OP2 has no neighbors to form bonds with according to residue template for
C /2:1273
Atom OP2 has no neighbors to form bonds with according to residue template for
C /2:1278
Atom OP2 has no neighbors to form bonds with according to residue template for
A /2:1347
Atom O4' has no neighbors to form bonds with according to residue template for
C /2:1354
Atom OP2 has no neighbors to form bonds with according to residue template for
U /2:1355
Atom C2' has no neighbors to form bonds with according to residue template for
A /2:1371
Atom C6 has no neighbors to form bonds with according to residue template for
U /2:1520
Atom O3' has no neighbors to form bonds with according to residue template for
A /2:1598
Atom O2' has no neighbors to form bonds with according to residue template for
A /2:1598
Atom OP1 has no neighbors to form bonds with according to residue template for
U /2:1783
Atom C5' has no neighbors to form bonds with according to residue template for
U /2:1783
Atom OP2 has no neighbors to form bonds with according to residue template for
U /2:1796
Atom N has no neighbors to form bonds with according to residue template for
TYR /A:81
Atom CB has no neighbors to form bonds with according to residue template for
GLN /A:83
Atom N has no neighbors to form bonds with according to residue template for
VAL /B:3
Atom OG1 has no neighbors to form bonds with according to residue template for
THR /B:107
Atom NZ has no neighbors to form bonds with according to residue template for
LYS /B:116
Atom CG1 has no neighbors to form bonds with according to residue template for
VAL /D:126
Atom CG2 has no neighbors to form bonds with according to residue template for
VAL /D:126
Atom N has no neighbors to form bonds with according to residue template for
ILE /D:138
Atom N has no neighbors to form bonds with according to residue template for
MET /D:150
Atom N has no neighbors to form bonds with according to residue template for
ASP /D:154
Atom CG1 has no neighbors to form bonds with according to residue template for
VAL /D:186
Atom N has no neighbors to form bonds with according to residue template for
GLU /D:214
Atom N has no neighbors to form bonds with according to residue template for
LYS /O:72
Atom OD1 has no neighbors to form bonds with according to residue template for
ASP /O:124
Atom N has no neighbors to form bonds with according to residue template for
LEU /S:18
Atom O has no neighbors to form bonds with according to residue template for
LEU /S:18
Atom O has no neighbors to form bonds with according to residue template for
LYS /T:38
Atom CG has no neighbors to form bonds with according to residue template for
LYS /T:38
Atom N has no neighbors to form bonds with according to residue template for
ASN /U:36
Atom OD1 has no neighbors to form bonds with according to residue template for
ASN /U:36
Atom ND2 has no neighbors to form bonds with according to residue template for
ASN /U:36
Atom N has no neighbors to form bonds with according to residue template for
LYS /U:61
Atom OG1 has no neighbors to form bonds with according to residue template for
THR /U:67
Atom N has no neighbors to form bonds with according to residue template for
SER /a:57
Atom OG has no neighbors to form bonds with according to residue template for
SER /a:57
Atom N has no neighbors to form bonds with according to residue template for
SER /a:88
Atom CB has no neighbors to form bonds with according to residue template for
SER /a:88
Atom OD1 has no neighbors to form bonds with according to residue template for
ASN /d:48
Atom ND2 has no neighbors to form bonds with according to residue template for
ASN /d:48
Atom CG1 has no neighbors to form bonds with according to residue template for
VAL /g:35
Atom CD2 has no neighbors to form bonds with according to residue template for
LEU /g:48
Atom N has no neighbors to form bonds with according to residue template for
VAL /g:72
Atom N has no neighbors to form bonds with according to residue template for
ALA /g:249
Atom CB has no neighbors to form bonds with according to residue template for
ALA /g:249
Atom N has no neighbors to form bonds with according to residue template for
LYS /g:268
Atom N has no neighbors to form bonds with according to residue template for
LEU /g:299
Atom CD2 has no neighbors to form bonds with according to residue template for
LEU /g:299
Atom CB has no neighbors to form bonds with according to residue template for
TYR /j:9
Atom OG has no neighbors to form bonds with according to residue template for
SER /j:91
Atom N has no neighbors to form bonds with according to residue template for
LEU /j:123
Atom C has no neighbors to form bonds with according to residue template for
LEU /j:123
Atom NE1 has no neighbors to form bonds with according to residue template for
TRP /j:132
Atom O has no neighbors to form bonds with according to residue template for
ILE /l:173
Atom NH1 has no neighbors to form bonds with according to residue template for
ARG /m:36
Chain information for 0057_6gsm_F.cif #1
---
Chain | Description
1 | Met-tRNAi
2 | 18S ribosomal RNA
3 | mRNA (5'-R(P*AP*AP*U)-3')
A | 40S ribosomal protein S0
B | 40S ribosomal protein S1
C | KLLA0F09812p
D | KLLA0D08305p
F | KLLA0D10659p
O | 40S ribosomal protein S14
Q | 40S ribosomal protein S16
R | KLLA0B01474p
S | KLLA0B01562p
T | KLLA0A07194p
U | KLLA0F25542p
Z | KLLA0B06182p
a | 40S ribosomal protein S26
c | 40S ribosomal protein S28
d | 40S ribosomal protein S29
g | KLLA0E12277p
i | Eukaryotic translation initiation factor 1A
j | Eukaryotic translation initiation factor 2 subunit alpha
l | Eukaryotic translation initiation factor 2 subunit beta
m | Eukaryotic translation initiation factor eIF-1
> open /scratch/cs-
> bioinfo/tngu/6k_data/Box_Chains_new/0057_6gsm/0057_6gsm_F.mrc
Opened 0057_6gsm_F.mrc as #2, grid size 96,104,80, pixel 1, shown at level
0.132, step 1, values float32
> fitmap #1 inMap #2
Fit molecule 0057_6gsm_F.cif (#1) to map 0057_6gsm_F.mrc (#2) using 16573
atoms
average map value = 0.07465, steps = 48
shifted from previous position = 0.482
rotated from previous position = 0.311 degrees
atoms outside contour = 15915, contour level = 0.13241
Position of 0057_6gsm_F.cif (#1) relative to 0057_6gsm_F.mrc (#2) coordinates:
Matrix rotation and translation
0.99999869 -0.00155151 -0.00047107 0.19682187
0.00154904 0.99998536 -0.00518424 0.71416720
0.00047911 0.00518351 0.99998645 -1.35461568
Axis 0.95440247 -0.08746900 0.28542090
Axis point -0.00000000 247.29302550 132.65108473
Rotation angle (degrees) 0.31120585
Shift along axis -0.26125584
> save /scratch/cs-
> bioinfo/tngu/6k_data/Box_Chains_new/0057_6gsm/0057_6gsm_F_fitted.cif #1
> close #1
> close #2
> open /scratch/cs-
> bioinfo/tngu/6k_data/Box_Chains_new/0057_6gsm/0057_6gsm_L.cif
Summary of feedback from opening /scratch/cs-
bioinfo/tngu/6k_data/Box_Chains_new/0057_6gsm/0057_6gsm_L.cif
---
warnings | Invalid residue range for struct_conf "HELX1": invalid chain "C",
near line 51957
Invalid residue range for struct_conf "HELX2": invalid chain "C", near line
51958
Invalid residue range for struct_conf "HELX3": invalid chain "C", near line
51959
Invalid residue range for struct_conf "HELX4": invalid chain "C", near line
51960
Invalid residue range for struct_conf "HELX5": invalid chain "C", near line
51961
107 messages similar to the above omitted
Invalid sheet range for struct_sheet_range "? 1": invalid chain "C", near line
52210
Invalid sheet range for struct_sheet_range "? 2": invalid chain "C", near line
52211
Invalid sheet range for struct_sheet_range "? 3": invalid chain "C", near line
52212
Invalid sheet range for struct_sheet_range "? 4": invalid chain "C", near line
52213
Invalid sheet range for struct_sheet_range "? 5": invalid chain "C", near line
52214
152 messages similar to the above omitted
Atom OP2 has no neighbors to form bonds with according to residue template for
G /2:20
Atom O2' has no neighbors to form bonds with according to residue template for
U /2:24
Atom O2 has no neighbors to form bonds with according to residue template for
U /2:24
Atom OP1 has no neighbors to form bonds with according to residue template for
A /2:26
Atom O2' has no neighbors to form bonds with according to residue template for
A /2:43
Atom OP1 has no neighbors to form bonds with according to residue template for
A /2:47
Atom C6 has no neighbors to form bonds with according to residue template for
C /2:90
Atom OP1 has no neighbors to form bonds with according to residue template for
A /2:135
Atom O3' has no neighbors to form bonds with according to residue template for
A /2:135
Atom OP2 has no neighbors to form bonds with according to residue template for
A /2:196
Atom N7 has no neighbors to form bonds with according to residue template for
A /2:196
Atom N6 has no neighbors to form bonds with according to residue template for
A /2:196
Atom O4' has no neighbors to form bonds with according to residue template for
C /2:229
Atom O2 has no neighbors to form bonds with according to residue template for
C /2:229
Atom O2' has no neighbors to form bonds with according to residue template for
G /2:273
Atom N2 has no neighbors to form bonds with according to residue template for
G /2:273
Atom OP1 has no neighbors to form bonds with according to residue template for
C /2:281
Atom OP2 has no neighbors to form bonds with according to residue template for
G /2:286
Atom C5' has no neighbors to form bonds with according to residue template for
G /2:286
Atom N7 has no neighbors to form bonds with according to residue template for
G /2:286
Atom O6 has no neighbors to form bonds with according to residue template for
G /2:286
Atom OP1 has no neighbors to form bonds with according to residue template for
A /2:287
Atom OP2 has no neighbors to form bonds with according to residue template for
A /2:287
Atom OP2 has no neighbors to form bonds with according to residue template for
U /2:288
Atom OP1 has no neighbors to form bonds with according to residue template for
G /2:387
Atom C5' has no neighbors to form bonds with according to residue template for
C /2:571
Atom O4' has no neighbors to form bonds with according to residue template for
C /2:571
Atom O2' has no neighbors to form bonds with according to residue template for
A /2:619
Atom OP1 has no neighbors to form bonds with according to residue template for
U /2:695
Atom OP2 has no neighbors to form bonds with according to residue template for
U /2:695
Atom O3' has no neighbors to form bonds with according to residue template for
U /2:695
Atom OP1 has no neighbors to form bonds with according to residue template for
G /2:729
Atom O3' has no neighbors to form bonds with according to residue template for
G /2:729
Atom O3' has no neighbors to form bonds with according to residue template for
C /2:731
Atom O3' has no neighbors to form bonds with according to residue template for
G /2:786
Atom O2' has no neighbors to form bonds with according to residue template for
C /2:949
Atom OP1 has no neighbors to form bonds with according to residue template for
A /2:1019
Atom O3' has no neighbors to form bonds with according to residue template for
A /2:1019
Atom O3' has no neighbors to form bonds with according to residue template for
U /2:1048
Atom O2' has no neighbors to form bonds with according to residue template for
U /2:1048
Atom OP2 has no neighbors to form bonds with according to residue template for
G /2:1109
Atom O6 has no neighbors to form bonds with according to residue template for
G /2:1109
Atom N2 has no neighbors to form bonds with according to residue template for
G /2:1125
Atom O2' has no neighbors to form bonds with according to residue template for
G /2:1647
Atom O2' has no neighbors to form bonds with according to residue template for
G /2:1678
Atom OP2 has no neighbors to form bonds with according to residue template for
U /2:1706
Atom C5' has no neighbors to form bonds with according to residue template for
U /2:1706
Atom N6 has no neighbors to form bonds with according to residue template for
A /2:1720
Atom C5' has no neighbors to form bonds with according to residue template for
A /2:1744
Atom O4' has no neighbors to form bonds with according to residue template for
A /2:1744
Atom OG1 has no neighbors to form bonds with according to residue template for
THR /C:163
Atom O has no neighbors to form bonds with according to residue template for
PRO /C:178
Atom N has no neighbors to form bonds with according to residue template for
LEU /C:192
Atom CB has no neighbors to form bonds with according to residue template for
LEU /C:192
Atom N has no neighbors to form bonds with according to residue template for
ARG /C:210
Atom CG has no neighbors to form bonds with according to residue template for
ARG /C:210
Atom OG1 has no neighbors to form bonds with according to residue template for
THR /E:81
Atom N has no neighbors to form bonds with according to residue template for
GLU /E:250
Atom C has no neighbors to form bonds with according to residue template for
GLU /E:250
Atom CB has no neighbors to form bonds with according to residue template for
GLU /E:250
Atom O has no neighbors to form bonds with according to residue template for
ARG /G:88
Atom O has no neighbors to form bonds with according to residue template for
ARG /G:183
Atom NH2 has no neighbors to form bonds with according to residue template for
ARG /G:183
Atom CD2 has no neighbors to form bonds with according to residue template for
LEU /G:184
Atom C has no neighbors to form bonds with according to residue template for
ARG /H:96
Atom CB has no neighbors to form bonds with according to residue template for
ARG /H:96
Atom NH2 has no neighbors to form bonds with according to residue template for
ARG /H:96
Atom N has no neighbors to form bonds with according to residue template for
VAL /H:121
Atom CG2 has no neighbors to form bonds with according to residue template for
VAL /H:121
Atom CG has no neighbors to form bonds with according to residue template for
LYS /I:138
Atom O has no neighbors to form bonds with according to residue template for
LYS /J:16
Atom NH1 has no neighbors to form bonds with according to residue template for
ARG /N:104
Atom N has no neighbors to form bonds with according to residue template for
ASN /N:105
Atom O has no neighbors to form bonds with according to residue template for
ASN /N:105
Atom CD1 has no neighbors to form bonds with according to residue template for
ILE /W:14
Atom CD1 has no neighbors to form bonds with according to residue template for
LEU /W:26
Atom C has no neighbors to form bonds with according to residue template for
LYS /W:71
Atom O has no neighbors to form bonds with according to residue template for
ASN /X:79
Atom O has no neighbors to form bonds with according to residue template for
ALA /X:113
Atom N has no neighbors to form bonds with according to residue template for
LYS /b:72
Atom O has no neighbors to form bonds with according to residue template for
LYS /b:72
Atom N has no neighbors to form bonds with according to residue template for
ARG /h:23
Atom O has no neighbors to form bonds with according to residue template for
UNK /o:734
Atom C has no neighbors to form bonds with according to residue template for
ASP /p:360
Atom CA has no neighbors to form bonds with according to residue template for
ASP /p:397
Atom N has no neighbors to form bonds with according to residue template for
ARG /p:677
Atom CB has no neighbors to form bonds with according to residue template for
ARG /p:677
Atom N has no neighbors to form bonds with according to residue template for
LYS /q:113
Chain information for 0057_6gsm_L.cif #1
---
Chain | Description
2 | 18S ribosomal RNA
C | KLLA0F09812p
E | 40S ribosomal protein S4
G | 40S ribosomal protein S6
H | 40S ribosomal protein S7
I | 40S ribosomal protein S8
J | KLLA0E23673p
L | KLLA0A10483p
N | KLLA0F18040p
W | 40S ribosomal protein S22
X | KLLA0B11231p
b | 40S ribosomal protein S27
h | 60S ribosomal protein L41-A
o | Eukaryotic translation initiation factor 3 subunit A,Eukaryotic
translation initiation factor 3 subunit A,eIF3a
p | Eukaryotic translation initiation factor 3 subunit B
q | Eukaryotic translation initiation factor 3 subunit C
> open /scratch/cs-
> bioinfo/tngu/6k_data/Box_Chains_new/0057_6gsm/0057_6gsm_L.mrc
Opened 0057_6gsm_L.mrc as #2, grid size 88,112,104, pixel 1, shown at level
0.147, step 1, values float32
> fitmap #1 inMap #2
Fit molecule 0057_6gsm_L.cif (#1) to map 0057_6gsm_L.mrc (#2) using 20625
atoms
average map value = 0.0855, steps = 64
shifted from previous position = 0.562
rotated from previous position = 0.106 degrees
atoms outside contour = 19726, contour level = 0.14692
Position of 0057_6gsm_L.cif (#1) relative to 0057_6gsm_L.mrc (#2) coordinates:
Matrix rotation and translation
0.99999903 0.00135370 -0.00033389 -0.56069105
-0.00135329 0.99999833 0.00122632 -0.32874382
0.00033555 -0.00122587 0.99999919 -0.08200758
Axis -0.66036488 -0.18027934 -0.72898394
Axis point -177.95394095 175.36755179 0.00000000
Rotation angle (degrees) 0.10638074
Shift along axis 0.48930860
> save /scratch/cs-
> bioinfo/tngu/6k_data/Box_Chains_new/0057_6gsm/0057_6gsm_L_fitted.cif #1
> close #1
> close #2
> open /scratch/cs-
> bioinfo/tngu/6k_data/Box_Chains_new/0057_6gsm/0057_6gsm_3.cif
Summary of feedback from opening /scratch/cs-
bioinfo/tngu/6k_data/Box_Chains_new/0057_6gsm/0057_6gsm_3.cif
---
warnings | Invalid residue range for struct_conf "HELX1": invalid chain "C",
near line 35563
Invalid residue range for struct_conf "HELX2": invalid chain "C", near line
35564
Invalid residue range for struct_conf "HELX3": invalid chain "C", near line
35565
Invalid residue range for struct_conf "HELX4": invalid chain "C", near line
35566
Invalid residue range for struct_conf "HELX5": invalid chain "C", near line
35567
172 messages similar to the above omitted
Invalid sheet range for struct_sheet_range "? 1": invalid chain "C", near line
35816
Invalid sheet range for struct_sheet_range "? 2": invalid chain "C", near line
35817
Invalid sheet range for struct_sheet_range "? 3": invalid chain "C", near line
35818
Invalid sheet range for struct_sheet_range "? 4": invalid chain "C", near line
35819
Invalid sheet range for struct_sheet_range "? 5": invalid chain "C", near line
35820
187 messages similar to the above omitted
Atom O5' has no neighbors to form bonds with according to residue template for
C /1:11
Atom N6 has no neighbors to form bonds with according to residue template for
A /1:28
Atom O4' has no neighbors to form bonds with according to residue template for
A /2:11
Atom OP2 has no neighbors to form bonds with according to residue template for
U /2:12
Atom O3' has no neighbors to form bonds with according to residue template for
A /2:579
Atom C2' has no neighbors to form bonds with according to residue template for
U /2:580
Atom O3' has no neighbors to form bonds with according to residue template for
A /2:906
Atom O3' has no neighbors to form bonds with according to residue template for
A /2:991
Atom C8 has no neighbors to form bonds with according to residue template for
G /2:993
Atom OP1 has no neighbors to form bonds with according to residue template for
A /2:1029
Atom O2' has no neighbors to form bonds with according to residue template for
A /2:1087
Atom OP1 has no neighbors to form bonds with according to residue template for
A /2:1137
Atom O5' has no neighbors to form bonds with according to residue template for
A /2:1137
Atom O3' has no neighbors to form bonds with according to residue template for
A /2:1137
Atom O6 has no neighbors to form bonds with according to residue template for
G /2:1152
Atom N6 has no neighbors to form bonds with according to residue template for
A /2:1156
Atom N1 has no neighbors to form bonds with according to residue template for
A /2:1156
Atom N3 has no neighbors to form bonds with according to residue template for
A /2:1159
Atom C2' has no neighbors to form bonds with according to residue template for
G /2:1187
Atom C5' has no neighbors to form bonds with according to residue template for
C /2:1196
Atom OP1 has no neighbors to form bonds with according to residue template for
G /2:1272
Atom O3' has no neighbors to form bonds with according to residue template for
A /2:1274
Atom OP1 has no neighbors to form bonds with according to residue template for
C /2:1424
Atom OP1 has no neighbors to form bonds with according to residue template for
G /2:1462
Atom C6 has no neighbors to form bonds with according to residue template for
U /2:1577
Atom O4' has no neighbors to form bonds with according to residue template for
C /2:1578
Atom OP1 has no neighbors to form bonds with according to residue template for
C /2:1749
Atom OP2 has no neighbors to form bonds with according to residue template for
C /2:1749
Atom OP2 has no neighbors to form bonds with according to residue template for
A /2:1751
Atom O3' has no neighbors to form bonds with according to residue template for
A /2:1751
Atom OP2 has no neighbors to form bonds with according to residue template for
U /2:1773
Atom OP2 has no neighbors to form bonds with according to residue template for
G /2:1784
Atom O6 has no neighbors to form bonds with according to residue template for
G /2:1784
Atom O2' has no neighbors to form bonds with according to residue template for
A /2:1788
Atom OP1 has no neighbors to form bonds with according to residue template for
C /2:1794
Atom OP2 has no neighbors to form bonds with according to residue template for
C /2:1794
Atom N has no neighbors to form bonds with according to residue template for
ILE /X:68
Atom C has no neighbors to form bonds with according to residue template for
THR /c:19
Atom CG2 has no neighbors to form bonds with according to residue template for
THR /c:19
Atom N has no neighbors to form bonds with according to residue template for
GLY /c:23
Atom O has no neighbors to form bonds with according to residue template for
GLY /c:23
Atom CG1 has no neighbors to form bonds with according to residue template for
VAL /c:25
Atom CG2 has no neighbors to form bonds with according to residue template for
VAL /c:25
Atom N has no neighbors to form bonds with according to residue template for
LEU /h:13
Atom O has no neighbors to form bonds with according to residue template for
ASN /i:55
Atom N has no neighbors to form bonds with according to residue template for
LEU /i:78
Atom N has no neighbors to form bonds with according to residue template for
VAL /j:90
Atom N has no neighbors to form bonds with according to residue template for
ILE /l:180
Atom N has no neighbors to form bonds with according to residue template for
THR /m:41
Atom OG1 has no neighbors to form bonds with according to residue template for
THR /m:41
Atom CG2 has no neighbors to form bonds with according to residue template for
THR /m:41
Atom N has no neighbors to form bonds with according to residue template for
ASP /m:61
Atom C has no neighbors to form bonds with according to residue template for
ASP /m:61
Chain information for 0057_6gsm_3.cif #1
---
Chain | Description
1 | Met-tRNAi
2 | 18S ribosomal RNA
3 | mRNA (5'-R(P*AP*AP*U)-3')
C | KLLA0F09812p
D | KLLA0D08305p
F | KLLA0D10659p
O | 40S ribosomal protein S14
Q | 40S ribosomal protein S16
U | KLLA0F25542p
X | KLLA0B11231p
a | 40S ribosomal protein S26
c | 40S ribosomal protein S28
h | 60S ribosomal protein L41-A
i | Eukaryotic translation initiation factor 1A
j | Eukaryotic translation initiation factor 2 subunit alpha
l | Eukaryotic translation initiation factor 2 subunit beta
m | Eukaryotic translation initiation factor eIF-1
> open /scratch/cs-
> bioinfo/tngu/6k_data/Box_Chains_new/0057_6gsm/0057_6gsm_3.mrc
Opened 0057_6gsm_3.mrc as #2, grid size 48,56,56, pixel 1, shown at level
0.147, step 1, values float32
> fitmap #1 inMap #2
Fit molecule 0057_6gsm_3.cif (#1) to map 0057_6gsm_3.mrc (#2) using 4594 atoms
average map value = 0.0782, steps = 56
shifted from previous position = 0.482
rotated from previous position = 0.264 degrees
atoms outside contour = 4481, contour level = 0.14686
Position of 0057_6gsm_3.cif (#1) relative to 0057_6gsm_3.mrc (#2) coordinates:
Matrix rotation and translation
0.99999048 0.00086917 -0.00427518 0.27803584
-0.00087555 0.99999851 -0.00149093 0.24639436
0.00427388 0.00149466 0.99998975 -1.25590328
Axis 0.32374789 -0.92703488 -0.18919205
Axis point 289.60036558 0.00000000 56.87772451
Rotation angle (degrees) 0.26419021
Shift along axis 0.09920427
> save /scratch/cs-
> bioinfo/tngu/6k_data/Box_Chains_new/0057_6gsm/0057_6gsm_3_fitted.cif #1
> close #1
> close #2
> open /scratch/cs-
> bioinfo/tngu/6k_data/Box_Chains_new/0057_6gsm/0057_6gsm_J.cif
Summary of feedback from opening /scratch/cs-
bioinfo/tngu/6k_data/Box_Chains_new/0057_6gsm/0057_6gsm_J.cif
---
warnings | Invalid residue range for struct_conf "HELX7": invalid chain "E",
near line 51987
Invalid residue range for struct_conf "HELX8": invalid chain "E", near line
51988
Invalid residue range for struct_conf "HELX9": invalid chain "E", near line
51989
Invalid residue range for struct_conf "HELX10": invalid chain "E", near line
51990
Invalid residue range for struct_conf "HELX11": invalid chain "E", near line
51991
147 messages similar to the above omitted
Invalid sheet range for struct_sheet_range "? 8": invalid chain "E", near line
52241
Invalid sheet range for struct_sheet_range "? 9": invalid chain "E", near line
52242
Invalid sheet range for struct_sheet_range "? 10": invalid chain "E", near
line 52243
Invalid sheet range for struct_sheet_range "? 11": invalid chain "E", near
line 52244
Invalid sheet range for struct_sheet_range "? 12": invalid chain "E", near
line 52245
130 messages similar to the above omitted
Atom OP1 has no neighbors to form bonds with according to residue template for
A /2:11
Atom OP2 has no neighbors to form bonds with according to residue template for
C /2:49
Atom OP2 has no neighbors to form bonds with according to residue template for
U /2:295
Atom O5' has no neighbors to form bonds with according to residue template for
U /2:295
Atom OP2 has no neighbors to form bonds with according to residue template for
A /2:322
Atom N7 has no neighbors to form bonds with according to residue template for
G /2:325
Atom C4' has no neighbors to form bonds with according to residue template for
A /2:327
Atom OP1 has no neighbors to form bonds with according to residue template for
G /2:328
Atom OP2 has no neighbors to form bonds with according to residue template for
G /2:328
Atom O4' has no neighbors to form bonds with according to residue template for
C /2:430
Atom OP2 has no neighbors to form bonds with according to residue template for
G /2:431
Atom OP2 has no neighbors to form bonds with according to residue template for
C /2:432
Atom OP2 has no neighbors to form bonds with according to residue template for
C /2:565
Atom O2' has no neighbors to form bonds with according to residue template for
A /2:629
Atom O4 has no neighbors to form bonds with according to residue template for
U /2:666
Atom OP1 has no neighbors to form bonds with according to residue template for
A /2:707
Atom O3' has no neighbors to form bonds with according to residue template for
G /2:722
Atom O2' has no neighbors to form bonds with according to residue template for
G /2:722
Atom OP1 has no neighbors to form bonds with according to residue template for
U /2:745
Atom O4' has no neighbors to form bonds with according to residue template for
A /2:805
Atom O2' has no neighbors to form bonds with according to residue template for
A /2:978
Atom N3 has no neighbors to form bonds with according to residue template for
A /2:978
Atom C4' has no neighbors to form bonds with according to residue template for
G /2:979
Atom O3' has no neighbors to form bonds with according to residue template for
G /2:979
Atom O2' has no neighbors to form bonds with according to residue template for
G /2:979
Atom O3' has no neighbors to form bonds with according to residue template for
C /2:1021
Atom O2' has no neighbors to form bonds with according to residue template for
C /2:1021
Atom OP2 has no neighbors to form bonds with according to residue template for
C /2:1032
Atom C5' has no neighbors to form bonds with according to residue template for
A /2:1038
Atom O4' has no neighbors to form bonds with according to residue template for
A /2:1038
Atom OP2 has no neighbors to form bonds with according to residue template for
U /2:1088
Atom O2' has no neighbors to form bonds with according to residue template for
A /2:1142
Atom C5' has no neighbors to form bonds with according to residue template for
G /2:1294
Atom O3' has no neighbors to form bonds with according to residue template for
G /2:1294
Atom O4' has no neighbors to form bonds with according to residue template for
A /2:1299
Atom OP1 has no neighbors to form bonds with according to residue template for
A /2:1738
Atom O3' has no neighbors to form bonds with according to residue template for
A /2:1747
Atom O2' has no neighbors to form bonds with according to residue template for
A /2:1747
Atom C2 has no neighbors to form bonds with according to residue template for
A /2:1747
Atom OP1 has no neighbors to form bonds with according to residue template for
A /2:1753
Atom N6 has no neighbors to form bonds with according to residue template for
A /2:1753
Atom O3' has no neighbors to form bonds with according to residue template for
C /2:1770
Atom O2' has no neighbors to form bonds with according to residue template for
C /2:1770
Atom O3' has no neighbors to form bonds with according to residue template for
A /2:1788
Atom O2' has no neighbors to form bonds with according to residue template for
A /2:1788
Atom O4' has no neighbors to form bonds with according to residue template for
G /2:1790
Atom CD1 has no neighbors to form bonds with according to residue template for
LEU /A:59
Atom OG1 has no neighbors to form bonds with according to residue template for
THR /A:108
Atom CG2 has no neighbors to form bonds with according to residue template for
THR /A:108
Atom O has no neighbors to form bonds with according to residue template for
LEU /A:177
Atom NH1 has no neighbors to form bonds with according to residue template for
ARG /C:48
Atom N has no neighbors to form bonds with according to residue template for
VAL /C:91
Atom CD1 has no neighbors to form bonds with according to residue template for
PHE /C:103
Atom OG1 has no neighbors to form bonds with according to residue template for
THR /C:122
Atom N has no neighbors to form bonds with according to residue template for
GLY /C:128
Atom OD1 has no neighbors to form bonds with according to residue template for
ASP /C:250
Atom N has no neighbors to form bonds with according to residue template for
PRO /E:35
Atom C has no neighbors to form bonds with according to residue template for
ASP /E:79
Atom O has no neighbors to form bonds with according to residue template for
HIS /E:142
Atom C has no neighbors to form bonds with according to residue template for
LEU /E:238
Atom CA has no neighbors to form bonds with according to residue template for
GLY /H:145
Atom O has no neighbors to form bonds with according to residue template for
GLY /H:145
Atom N has no neighbors to form bonds with according to residue template for
THR /L:72
Atom O has no neighbors to form bonds with according to residue template for
THR /L:72
Atom C has no neighbors to form bonds with according to residue template for
ARG /L:87
Atom OE2 has no neighbors to form bonds with according to residue template for
GLU /V:64
Atom O has no neighbors to form bonds with according to residue template for
LEU /V:69
Atom O has no neighbors to form bonds with according to residue template for
LYS /Y:52
Atom N has no neighbors to form bonds with according to residue template for
VAL /Y:75
Atom CG2 has no neighbors to form bonds with according to residue template for
VAL /Y:75
Atom CE2 has no neighbors to form bonds with according to residue template for
TYR /Y:76
Atom OH has no neighbors to form bonds with according to residue template for
TYR /Y:76
Atom CD1 has no neighbors to form bonds with according to residue template for
LEU /Y:96
Atom N has no neighbors to form bonds with according to residue template for
TRP /h:5
Atom CD has no neighbors to form bonds with according to residue template for
ARG /i:57
Atom NH1 has no neighbors to form bonds with according to residue template for
ARG /i:57
Chain information for 0057_6gsm_J.cif #1
---
Chain | Description
2 | 18S ribosomal RNA
A | 40S ribosomal protein S0
C | KLLA0F09812p
E | 40S ribosomal protein S4
H | 40S ribosomal protein S7
I | 40S ribosomal protein S8
J | KLLA0E23673p
L | KLLA0A10483p
V | 40S ribosomal protein S21
W | 40S ribosomal protein S22
X | KLLA0B11231p
Y | 40S ribosomal protein S24
a | 40S ribosomal protein S26
e | 40S ribosomal protein S30
h | 60S ribosomal protein L41-A
i | Eukaryotic translation initiation factor 1A
> open /scratch/cs-
> bioinfo/tngu/6k_data/Box_Chains_new/0057_6gsm/0057_6gsm_J.mrc
Opened 0057_6gsm_J.mrc as #2, grid size 96,88,128, pixel 1, shown at level
0.146, step 1, values float32
> fitmap #1 inMap #2
Fit molecule 0057_6gsm_J.cif (#1) to map 0057_6gsm_J.mrc (#2) using 20634
atoms
average map value = 0.08539, steps = 48
shifted from previous position = 0.283
rotated from previous position = 0.0807 degrees
atoms outside contour = 19712, contour level = 0.14584
Position of 0057_6gsm_J.cif (#1) relative to 0057_6gsm_J.mrc (#2) coordinates:
Matrix rotation and translation
0.99999926 0.00084597 0.00087723 -0.52834288
-0.00084659 0.99999939 0.00070453 -0.19287997
-0.00087663 -0.00070527 0.99999937 0.28359637
Axis -0.50068506 0.62287955 -0.60111192
Axis point 305.17755694 0.00000000 617.43129214
Rotation angle (degrees) 0.08066466
Shift along axis -0.02608076
> save /scratch/cs-
> bioinfo/tngu/6k_data/Box_Chains_new/0057_6gsm/0057_6gsm_J_fitted.cif #1
> close #1
> close #2
> open /scratch/cs-
> bioinfo/tngu/6k_data/Box_Chains_new/0057_6gsm/0057_6gsm_b.cif
Summary of feedback from opening /scratch/cs-
bioinfo/tngu/6k_data/Box_Chains_new/0057_6gsm/0057_6gsm_b.cif
---
warnings | Invalid residue range for struct_conf "HELX21": invalid chain "G",
near line 44712
Invalid residue range for struct_conf "HELX22": invalid chain "G", near line
44713
Invalid residue range for struct_conf "HELX23": invalid chain "G", near line
44714
Invalid residue range for struct_conf "HELX24": invalid chain "G", near line
44715
Invalid residue range for struct_conf "HELX25": invalid chain "G", near line
44716
111 messages similar to the above omitted
Invalid sheet range for struct_sheet_range "? 25": invalid chain "G", near
line 44969
Invalid sheet range for struct_sheet_range "? 26": invalid chain "G", near
line 44970
Invalid sheet range for struct_sheet_range "? 27": invalid chain "G", near
line 44971
Invalid sheet range for struct_sheet_range "? 28": invalid chain "G", near
line 44972
Invalid sheet range for struct_sheet_range "? 29": invalid chain "G", near
line 44973
189 messages similar to the above omitted
Atom OP1 has no neighbors to form bonds with according to residue template for
G /2:306
Atom O2' has no neighbors to form bonds with according to residue template for
G /2:306
Atom OP1 has no neighbors to form bonds with according to residue template for
C /2:308
Atom OP2 has no neighbors to form bonds with according to residue template for
C /2:308
Atom OP1 has no neighbors to form bonds with according to residue template for
U /2:348
Atom O3' has no neighbors to form bonds with according to residue template for
U /2:348
Atom O2 has no neighbors to form bonds with according to residue template for
U /2:349
Atom O4 has no neighbors to form bonds with according to residue template for
U /2:637
Atom O2' has no neighbors to form bonds with according to residue template for
U /2:639
Atom O2' has no neighbors to form bonds with according to residue template for
U /2:794
Atom O2 has no neighbors to form bonds with according to residue template for
U /2:794
Atom OP2 has no neighbors to form bonds with according to residue template for
U /2:1023
Atom C5 has no neighbors to form bonds with according to residue template for
U /2:1023
Atom OP2 has no neighbors to form bonds with according to residue template for
G /2:1113
Atom O3' has no neighbors to form bonds with according to residue template for
U /2:1302
Atom O2' has no neighbors to form bonds with according to residue template for
U /2:1302
Atom OP1 has no neighbors to form bonds with according to residue template for
U /2:1626
Atom C5' has no neighbors to form bonds with according to residue template for
U /2:1626
Atom O3' has no neighbors to form bonds with according to residue template for
U /2:1626
Atom O4' has no neighbors to form bonds with according to residue template for
G /2:1772
Atom OP2 has no neighbors to form bonds with according to residue template for
G /2:1786
Atom N has no neighbors to form bonds with according to residue template for
THR /A:10
Atom NZ has no neighbors to form bonds with according to residue template for
LYS /A:88
Atom ND1 has no neighbors to form bonds with according to residue template for
HIS /A:92
Atom N has no neighbors to form bonds with according to residue template for
GLY /A:100
Atom NH2 has no neighbors to form bonds with according to residue template for
ARG /A:179
Atom OE1 has no neighbors to form bonds with according to residue template for
GLU /B:122
Atom CE has no neighbors to form bonds with according to residue template for
LYS /B:145
Atom N has no neighbors to form bonds with according to residue template for
LEU /B:172
Atom C has no neighbors to form bonds with according to residue template for
LEU /B:172
Atom CB has no neighbors to form bonds with according to residue template for
LEU /B:172
Atom CD1 has no neighbors to form bonds with according to residue template for
LEU /B:172
Atom CE has no neighbors to form bonds with according to residue template for
MET /C:245
Atom OD1 has no neighbors to form bonds with according to residue template for
ASP /H:87
Atom OD2 has no neighbors to form bonds with according to residue template for
ASP /H:87
Atom O has no neighbors to form bonds with according to residue template for
ARG /H:114
Atom O has no neighbors to form bonds with according to residue template for
HIS /L:104
Atom NH1 has no neighbors to form bonds with according to residue template for
ARG /N:99
Atom NH2 has no neighbors to form bonds with according to residue template for
ARG /N:99
Atom CB has no neighbors to form bonds with according to residue template for
LYS /N:100
Atom CE has no neighbors to form bonds with according to residue template for
LYS /N:100
Atom CG has no neighbors to form bonds with according to residue template for
LYS /N:140
Atom N has no neighbors to form bonds with according to residue template for
ARG /O:133
Atom N has no neighbors to form bonds with according to residue template for
SER /R:96
Atom OG has no neighbors to form bonds with according to residue template for
SER /R:96
Atom C has no neighbors to form bonds with according to residue template for
VAL /V:13
Atom N has no neighbors to form bonds with according to residue template for
VAL /V:39
Atom OD1 has no neighbors to form bonds with according to residue template for
ASP /q:393
Atom CG2 has no neighbors to form bonds with according to residue template for
ILE /q:448
Atom NE1 has no neighbors to form bonds with according to residue template for
TRP /q:456
Atom CZ2 has no neighbors to form bonds with according to residue template for
TRP /q:456
Atom OD1 has no neighbors to form bonds with according to residue template for
ASP /q:484
Atom CA has no neighbors to form bonds with according to residue template for
GLN /q:517
Atom CB has no neighbors to form bonds with according to residue template for
ARG /q:654
Chain information for 0057_6gsm_b.cif #1
---
Chain | Description
2 | 18S ribosomal RNA
A | 40S ribosomal protein S0
B | 40S ribosomal protein S1
C | KLLA0F09812p
H | 40S ribosomal protein S7
L | KLLA0A10483p
N | KLLA0F18040p
O | 40S ribosomal protein S14
R | KLLA0B01474p
V | 40S ribosomal protein S21
W | 40S ribosomal protein S22
X | KLLA0B11231p
a | 40S ribosomal protein S26
b | 40S ribosomal protein S27
h | 60S ribosomal protein L41-A
o | Eukaryotic translation initiation factor 3 subunit A,Eukaryotic
translation initiation factor 3 subunit A,eIF3a
q | Eukaryotic translation initiation factor 3 subunit C
> open /scratch/cs-
> bioinfo/tngu/6k_data/Box_Chains_new/0057_6gsm/0057_6gsm_b.mrc
Opened 0057_6gsm_b.mrc as #2, grid size 80,64,104, pixel 1, shown at level
0.145, step 1, values float32
> fitmap #1 inMap #2
Fit molecule 0057_6gsm_b.cif (#1) to map 0057_6gsm_b.mrc (#2) using 13648
atoms
average map value = 0.06975, steps = 120
shifted from previous position = 0.477
rotated from previous position = 0.155 degrees
atoms outside contour = 13183, contour level = 0.1446
Position of 0057_6gsm_b.cif (#1) relative to 0057_6gsm_b.mrc (#2) coordinates:
Matrix rotation and translation
0.99999867 0.00068419 -0.00147724 0.10063725
-0.00068737 0.99999744 -0.00215405 0.39911254
0.00147576 0.00215506 0.99999659 -1.14122012
Axis 0.79784835 -0.54676044 -0.25395084
Axis point 0.00000000 512.00866074 223.23098321
Rotation angle (degrees) 0.15472488
Shift along axis 0.15188813
> save /scratch/cs-
> bioinfo/tngu/6k_data/Box_Chains_new/0057_6gsm/0057_6gsm_b_fitted.cif #1
> close #1
> close #2
> open /scratch/cs-
> bioinfo/tngu/6k_data/Box_Chains_new/0057_6gsm/0057_6gsm_c.cif
Summary of feedback from opening /scratch/cs-
bioinfo/tngu/6k_data/Box_Chains_new/0057_6gsm/0057_6gsm_c.cif
---
warnings | Invalid residue range for struct_conf "HELX27": invalid chain "H",
near line 40502
Invalid residue range for struct_conf "HELX28": invalid chain "H", near line
40503
Invalid residue range for struct_conf "HELX29": invalid chain "H", near line
40504
Invalid residue range for struct_conf "HELX30": invalid chain "H", near line
40505
Invalid residue range for struct_conf "HELX31": invalid chain "H", near line
40506
134 messages similar to the above omitted
Invalid sheet range for struct_sheet_range "? 32": invalid chain "H", near
line 40760
Invalid sheet range for struct_sheet_range "? 33": invalid chain "H", near
line 40761
Invalid sheet range for struct_sheet_range "? 34": invalid chain "H", near
line 40762
Invalid sheet range for struct_sheet_range "? 35": invalid chain "H", near
line 40763
Invalid sheet range for struct_sheet_range "? 36": invalid chain "H", near
line 40764
163 messages similar to the above omitted
Atom N4 has no neighbors to form bonds with according to residue template for
C /1:34
Atom C5 has no neighbors to form bonds with according to residue template for
C /1:34
Atom O2' has no neighbors to form bonds with according to residue template for
C /2:882
Atom C5 has no neighbors to form bonds with according to residue template for
U /2:887
Atom OP1 has no neighbors to form bonds with according to residue template for
G /2:900
Atom OP2 has no neighbors to form bonds with according to residue template for
G /2:900
Atom O4' has no neighbors to form bonds with according to residue template for
A /2:905
Atom O2' has no neighbors to form bonds with according to residue template for
U /2:927
Atom C5' has no neighbors to form bonds with according to residue template for
G /2:1166
Atom O4' has no neighbors to form bonds with according to residue template for
G /2:1166
Atom OP1 has no neighbors to form bonds with according to residue template for
U /2:1284
Atom O3' has no neighbors to form bonds with according to residue template for
A /2:1320
Atom O4' has no neighbors to form bonds with according to residue template for
A /2:1325
Atom C8 has no neighbors to form bonds with according to residue template for
A /2:1330
Atom O4' has no neighbors to form bonds with according to residue template for
C /2:1338
Atom O3' has no neighbors to form bonds with according to residue template for
G /2:1532
Atom O2' has no neighbors to form bonds with according to residue template for
G /2:1532
Atom C1' has no neighbors to form bonds with according to residue template for
G /2:1532
Atom OP2 has no neighbors to form bonds with according to residue template for
C /2:1578
Atom OP1 has no neighbors to form bonds with according to residue template for
U /2:1607
Atom OP2 has no neighbors to form bonds with according to residue template for
U /2:1607
Atom O5' has no neighbors to form bonds with according to residue template for
U /2:1607
Atom C4' has no neighbors to form bonds with according to residue template for
A /2:1631
Atom O4' has no neighbors to form bonds with according to residue template for
U /2:1769
Atom O3' has no neighbors to form bonds with according to residue template for
C /2:1782
Atom O3' has no neighbors to form bonds with according to residue template for
G /2:1791
Atom O2' has no neighbors to form bonds with according to residue template for
G /2:1791
Atom O has no neighbors to form bonds with according to residue template for
ILE /A:111
Atom CG2 has no neighbors to form bonds with according to residue template for
ILE /A:111
Atom CD2 has no neighbors to form bonds with according to residue template for
HIS /A:168
Atom O has no neighbors to form bonds with according to residue template for
TYR /A:204
Atom O4 has no neighbors to form bonds with according to residue template for
U /3:30
Atom OG1 has no neighbors to form bonds with according to residue template for
THR /B:46
Atom N has no neighbors to form bonds with according to residue template for
VAL /B:84
Atom O has no neighbors to form bonds with according to residue template for
VAL /B:84
Atom SD has no neighbors to form bonds with according to residue template for
MET /B:103
Atom OE1 has no neighbors to form bonds with according to residue template for
GLN /B:149
Atom CA has no neighbors to form bonds with according to residue template for
VAL /B:150
Atom O has no neighbors to form bonds with according to residue template for
VAL /B:150
Atom CG1 has no neighbors to form bonds with according to residue template for
VAL /F:25
Atom CG2 has no neighbors to form bonds with according to residue template for
VAL /F:25
Atom O has no neighbors to form bonds with according to residue template for
GLU /F:34
Atom CD has no neighbors to form bonds with according to residue template for
ARG /F:104
Atom NH1 has no neighbors to form bonds with according to residue template for
ARG /F:104
Atom N has no neighbors to form bonds with according to residue template for
ASP /F:128
Atom C has no neighbors to form bonds with according to residue template for
ASP /F:128
Atom N has no neighbors to form bonds with according to residue template for
MET /O:46
Atom N has no neighbors to form bonds with according to residue template for
LYS /Q:14
Atom CG has no neighbors to form bonds with according to residue template for
LYS /Q:14
Atom CE has no neighbors to form bonds with according to residue template for
LYS /Q:14
Atom C has no neighbors to form bonds with according to residue template for
ALA /Q:20
Atom CB has no neighbors to form bonds with according to residue template for
ALA /Q:20
Atom N has no neighbors to form bonds with according to residue template for
GLN /Q:40
Atom N has no neighbors to form bonds with according to residue template for
GLN /Q:77
Atom N has no neighbors to form bonds with according to residue template for
LEU /Q:89
Atom CD1 has no neighbors to form bonds with according to residue template for
LEU /Q:105
Atom OE1 has no neighbors to form bonds with according to residue template for
GLU /R:18
Atom OE2 has no neighbors to form bonds with according to residue template for
GLU /R:18
Atom OG1 has no neighbors to form bonds with according to residue template for
THR /R:54
Atom OG1 has no neighbors to form bonds with according to residue template for
THR /R:55
Atom CG1 has no neighbors to form bonds with according to residue template for
ILE /R:61
Atom O has no neighbors to form bonds with according to residue template for
LYS /a:32
Atom CG has no neighbors to form bonds with according to residue template for
LYS /a:32
Atom CG has no neighbors to form bonds with according to residue template for
LYS /a:34
Atom N has no neighbors to form bonds with according to residue template for
ASP /j:18
Atom O has no neighbors to form bonds with according to residue template for
ASP /j:18
Atom ND2 has no neighbors to form bonds with according to residue template for
ASN /j:23
Atom CD1 has no neighbors to form bonds with according to residue template for
ILE /j:63
Atom NH1 has no neighbors to form bonds with according to residue template for
ARG /j:64
Atom N has no neighbors to form bonds with according to residue template for
VAL /o:48
Atom NZ has no neighbors to form bonds with according to residue template for
LYS /o:76
Chain information for 0057_6gsm_c.cif #1
---
Chain | Description
1 | Met-tRNAi
2 | 18S ribosomal RNA
3 | mRNA (5'-R(P*AP*AP*U)-3')
A | 40S ribosomal protein S0
B | 40S ribosomal protein S1
C | KLLA0F09812p
D | KLLA0D08305p
F | KLLA0D10659p
O | 40S ribosomal protein S14
Q | 40S ribosomal protein S16
R | KLLA0B01474p
Z | KLLA0B06182p
a | 40S ribosomal protein S26
c | 40S ribosomal protein S28
g | KLLA0E12277p
j | Eukaryotic translation initiation factor 2 subunit alpha
o | Eukaryotic translation initiation factor 3 subunit A,Eukaryotic
translation initiation factor 3 subunit A,eIF3a
> open /scratch/cs-
> bioinfo/tngu/6k_data/Box_Chains_new/0057_6gsm/0057_6gsm_c.mrc
Opened 0057_6gsm_c.mrc as #2, grid size 72,80,72, pixel 1, shown at level
0.137, step 1, values float32
> fitmap #1 inMap #2
Fit molecule 0057_6gsm_c.cif (#1) to map 0057_6gsm_c.mrc (#2) using 9480 atoms
average map value = 0.07507, steps = 48
shifted from previous position = 0.58
rotated from previous position = 0.323 degrees
atoms outside contour = 9159, contour level = 0.13696
Position of 0057_6gsm_c.cif (#1) relative to 0057_6gsm_c.mrc (#2) coordinates:
Matrix rotation and translation
0.99999841 -0.00143913 0.00105503 -0.05309246
0.00144474 0.99998470 -0.00534025 0.88891144
-0.00104733 0.00534177 0.99998518 -1.26219123
Axis 0.94846552 0.18667082 0.25606087
Axis point 0.00000000 226.81472737 173.06242894
Rotation angle (degrees) 0.32264642
Shift along axis -0.20762033
> save /scratch/cs-
> bioinfo/tngu/6k_data/Box_Chains_new/0057_6gsm/0057_6gsm_c_fitted.cif #1
> close #1
> close #2
> open /scratch/cs-
> bioinfo/tngu/6k_data/Box_Chains_new/0057_6gsm/0057_6gsm_i.cif
Summary of feedback from opening /scratch/cs-
bioinfo/tngu/6k_data/Box_Chains_new/0057_6gsm/0057_6gsm_i.cif
---
warnings | Invalid residue range for struct_conf "HELX1": invalid chain "C",
near line 41478
Invalid residue range for struct_conf "HELX2": invalid chain "C", near line
41479
Invalid residue range for struct_conf "HELX3": invalid chain "C", near line
41480
Invalid residue range for struct_conf "HELX4": invalid chain "C", near line
41481
Invalid residue range for struct_conf "HELX5": invalid chain "C", near line
41482
130 messages similar to the above omitted
Invalid sheet range for struct_sheet_range "? 1": invalid chain "C", near line
41731
Invalid sheet range for struct_sheet_range "? 2": invalid chain "C", near line
41732
Invalid sheet range for struct_sheet_range "? 3": invalid chain "C", near line
41733
Invalid sheet range for struct_sheet_range "? 4": invalid chain "C", near line
41734
Invalid sheet range for struct_sheet_range "? 5": invalid chain "C", near line
41735
155 messages similar to the above omitted
Atom O2 has no neighbors to form bonds with according to residue template for
C /1:11
Atom OP1 has no neighbors to form bonds with according to residue template for
G /1:12
Atom O3' has no neighbors to form bonds with according to residue template for
G /1:12
Atom N2 has no neighbors to form bonds with according to residue template for
G /1:24
Atom N3 has no neighbors to form bonds with according to residue template for
G /1:24
Atom OP2 has no neighbors to form bonds with according to residue template for
G /1:29
Atom O2 has no neighbors to form bonds with according to residue template for
C /1:69
Atom O4' has no neighbors to form bonds with according to residue template for
U /1:72
Atom OP2 has no neighbors to form bonds with according to residue template for
C /2:4
Atom OP2 has no neighbors to form bonds with according to residue template for
C /2:13
Atom N6 has no neighbors to form bonds with according to residue template for
A /2:540
Atom O3' has no neighbors to form bonds with according to residue template for
A /2:544
Atom O2' has no neighbors to form bonds with according to residue template for
A /2:544
Atom OP2 has no neighbors to form bonds with according to residue template for
A /2:555
Atom OP2 has no neighbors to form bonds with according to residue template for
G /2:556
Atom OP2 has no neighbors to form bonds with according to residue template for
U /2:557
Atom OP2 has no neighbors to form bonds with according to residue template for
C /2:588
Atom O5' has no neighbors to form bonds with according to residue template for
C /2:588
Atom OP2 has no neighbors to form bonds with according to residue template for
U /2:601
Atom N7 has no neighbors to form bonds with according to residue template for
G /2:609
Atom O6 has no neighbors to form bonds with according to residue template for
G /2:609
Atom C8 has no neighbors to form bonds with according to residue template for
G /2:612
Atom O4' has no neighbors to form bonds with according to residue template for
A /2:1085
Atom O2' has no neighbors to form bonds with according to residue template for
A /2:1085
Atom O2' has no neighbors to form bonds with according to residue template for
U /2:1114
Atom O2' has no neighbors to form bonds with according to residue template for
A /2:1142
Atom OP1 has no neighbors to form bonds with according to residue template for
G /2:1149
Atom OP2 has no neighbors to form bonds with according to residue template for
G /2:1149
Atom OP2 has no neighbors to form bonds with according to residue template for
C /2:1158
Atom O3' has no neighbors to form bonds with according to residue template for
G /2:1175
Atom O2' has no neighbors to form bonds with according to residue template for
G /2:1175
Atom O2 has no neighbors to form bonds with according to residue template for
C /2:1176
Atom O2 has no neighbors to form bonds with according to residue template for
U /2:1184
Atom C5' has no neighbors to form bonds with according to residue template for
G /2:1199
Atom OP2 has no neighbors to form bonds with according to residue template for
U /2:1213
Atom O2' has no neighbors to form bonds with according to residue template for
C /2:1214
Atom O3' has no neighbors to form bonds with according to residue template for
C /2:1215
Atom N3 has no neighbors to form bonds with according to residue template for
A /2:1216
Atom O4' has no neighbors to form bonds with according to residue template for
G /2:1264
Atom O3' has no neighbors to form bonds with according to residue template for
G /2:1280
Atom O5' has no neighbors to form bonds with according to residue template for
U /2:1281
Atom O2 has no neighbors to form bonds with according to residue template for
U /2:1281
Atom O2 has no neighbors to form bonds with according to residue template for
U /2:1282
Atom N3 has no neighbors to form bonds with according to residue template for
A /2:1423
Atom O4 has no neighbors to form bonds with according to residue template for
U /2:1435
Atom OP2 has no neighbors to form bonds with according to residue template for
G /2:1436
Atom O2' has no neighbors to form bonds with according to residue template for
G /2:1462
Atom OP1 has no neighbors to form bonds with according to residue template for
A /2:1575
Atom O5' has no neighbors to form bonds with according to residue template for
A /2:1575
Atom O2' has no neighbors to form bonds with according to residue template for
A /2:1575
Atom O4' has no neighbors to form bonds with according to residue template for
C /2:1622
Atom OP2 has no neighbors to form bonds with according to residue template for
C /2:1623
Atom O6 has no neighbors to form bonds with according to residue template for
G /2:1627
Atom N1 has no neighbors to form bonds with according to residue template for
G /2:1627
Atom N2 has no neighbors to form bonds with according to residue template for
G /2:1627
Atom OP1 has no neighbors to form bonds with according to residue template for
U /2:1740
Atom OP2 has no neighbors to form bonds with according to residue template for
U /2:1740
Atom C5' has no neighbors to form bonds with according to residue template for
U /2:1740
Atom N3 has no neighbors to form bonds with according to residue template for
A /2:1780
Atom N has no neighbors to form bonds with according to residue template for
ALA /C:97
Atom NH1 has no neighbors to form bonds with according to residue template for
ARG /J:23
Atom NH2 has no neighbors to form bonds with according to residue template for
ARG /J:23
Atom N has no neighbors to form bonds with according to residue template for
LYS /U:77
Atom CD has no neighbors to form bonds with according to residue template for
LYS /X:39
Atom N has no neighbors to form bonds with according to residue template for
LYS /X:78
Atom C has no neighbors to form bonds with according to residue template for
LYS /X:78
Atom N has no neighbors to form bonds with according to residue template for
LYS /f:90
Atom O has no neighbors to form bonds with according to residue template for
LYS /f:90
Atom O has no neighbors to form bonds with according to residue template for
ILE /l:141
Atom CG2 has no neighbors to form bonds with according to residue template for
ILE /l:141
Atom CD has no neighbors to form bonds with according to residue template for
ARG /l:253
Atom CD1 has no neighbors to form bonds with according to residue template for
ILE /m:54
Atom CA has no neighbors to form bonds with according to residue template for
LEU /m:55
Atom O has no neighbors to form bonds with according to residue template for
LEU /m:55
Atom N has no neighbors to form bonds with according to residue template for
ASN /m:67
Atom O has no neighbors to form bonds with according to residue template for
ASN /m:67
Atom N has no neighbors to form bonds with according to residue template for
TRP /p:315
Atom N has no neighbors to form bonds with according to residue template for
GLY /p:320
Atom CG1 has no neighbors to form bonds with according to residue template for
VAL /p:480
Atom CG2 has no neighbors to form bonds with according to residue template for
VAL /p:480
Chain information for 0057_6gsm_i.cif #1
---
Chain | Description
1 | Met-tRNAi
2 | 18S ribosomal RNA
3 | mRNA (5'-R(P*AP*AP*U)-3')
C | KLLA0F09812p
D | KLLA0D08305p
J | KLLA0E23673p
Q | 40S ribosomal protein S16
U | KLLA0F25542p
X | KLLA0B11231p
d | 40S ribosomal protein S29
e | 40S ribosomal protein S30
f | Ubiquitin-40S ribosomal protein S27a
h | 60S ribosomal protein L41-A
i | Eukaryotic translation initiation factor 1A
j | Eukaryotic translation initiation factor 2 subunit alpha
k | Eukaryotic translation initiation factor 2 subunit gamma
l | Eukaryotic translation initiation factor 2 subunit beta
m | Eukaryotic translation initiation factor eIF-1
o | Eukaryotic translation initiation factor 3 subunit A,Eukaryotic
translation initiation factor 3 subunit A,eIF3a
p | Eukaryotic translation initiation factor 3 subunit B
> open /scratch/cs-
> bioinfo/tngu/6k_data/Box_Chains_new/0057_6gsm/0057_6gsm_i.mrc
Opened 0057_6gsm_i.mrc as #2, grid size 80,80,72, pixel 1, shown at level
0.139, step 1, values float32
> fitmap #1 inMap #2
Fit molecule 0057_6gsm_i.cif (#1) to map 0057_6gsm_i.mrc (#2) using 10393
atoms
average map value = 0.07196, steps = 56
shifted from previous position = 0.474
rotated from previous position = 0.143 degrees
atoms outside contour = 9995, contour level = 0.13898
Position of 0057_6gsm_i.cif (#1) relative to 0057_6gsm_i.mrc (#2) coordinates:
Matrix rotation and translation
0.99999692 0.00018283 0.00247368 -0.90601607
-0.00018207 0.99999994 -0.00030762 -0.12008924
-0.00247373 0.00030717 0.99999689 0.50653629
Axis 0.12298613 0.98972007 -0.07299718
Axis point 196.43577144 0.00000000 353.21954976
Rotation angle (degrees) 0.14320519
Shift along axis -0.26725786
> save /scratch/cs-
> bioinfo/tngu/6k_data/Box_Chains_new/0057_6gsm/0057_6gsm_i_fitted.cif #1
> close #1
> close #2
> open /scratch/cs-
> bioinfo/tngu/6k_data/Box_Chains_new/0057_6gsm/0057_6gsm_X.cif
Summary of feedback from opening /scratch/cs-
bioinfo/tngu/6k_data/Box_Chains_new/0057_6gsm/0057_6gsm_X.cif
---
warnings | Invalid residue range for struct_conf "HELX32": invalid chain "I",
near line 55763
Invalid residue range for struct_conf "HELX33": invalid chain "I", near line
55764
Invalid residue range for struct_conf "HELX34": invalid chain "I", near line
55765
Invalid residue range for struct_conf "HELX35": invalid chain "I", near line
55766
Invalid residue range for struct_conf "HELX36": invalid chain "I", near line
55767
58 messages similar to the above omitted
Invalid sheet range for struct_sheet_range "? 47": invalid chain "I", near
line 56031
Invalid sheet range for struct_sheet_range "? 48": invalid chain "I", near
line 56032
Invalid sheet range for struct_sheet_range "? 79": invalid chain "P", near
line 56063
Invalid sheet range for struct_sheet_range "? 80": invalid chain "P", near
line 56064
Invalid sheet range for struct_sheet_range "? 86": invalid chain "S", near
line 56070
104 messages similar to the above omitted
Atom N7 has no neighbors to form bonds with according to residue template for
G /2:325
Atom O6 has no neighbors to form bonds with according to residue template for
G /2:325
Atom O3' has no neighbors to form bonds with according to residue template for
C /2:338
Atom N4 has no neighbors to form bonds with according to residue template for
C /2:341
Atom C5 has no neighbors to form bonds with according to residue template for
C /2:341
Atom O4' has no neighbors to form bonds with according to residue template for
G /2:391
Atom OP1 has no neighbors to form bonds with according to residue template for
A /2:415
Atom O3' has no neighbors to form bonds with according to residue template for
A /2:459
Atom OP2 has no neighbors to form bonds with according to residue template for
G /2:479
Atom O2' has no neighbors to form bonds with according to residue template for
U /2:481
Atom N6 has no neighbors to form bonds with according to residue template for
A /2:525
Atom O2' has no neighbors to form bonds with according to residue template for
G /2:809
Atom O2' has no neighbors to form bonds with according to residue template for
U /2:888
Atom O3' has no neighbors to form bonds with according to residue template for
A /2:925
Atom O2' has no neighbors to form bonds with according to residue template for
C /2:926
Atom O2' has no neighbors to form bonds with according to residue template for
A /2:928
Atom OP1 has no neighbors to form bonds with according to residue template for
C /2:930
Atom OP2 has no neighbors to form bonds with according to residue template for
C /2:930
Atom OP2 has no neighbors to form bonds with according to residue template for
C /2:936
Atom OP2 has no neighbors to form bonds with according to residue template for
G /2:937
Atom OP2 has no neighbors to form bonds with according to residue template for
A /2:943
Atom N7 has no neighbors to form bonds with according to residue template for
A /2:943
Atom C6 has no neighbors to form bonds with according to residue template for
U /2:964
Atom O3' has no neighbors to form bonds with according to residue template for
G /2:1001
Atom O2' has no neighbors to form bonds with according to residue template for
G /2:1001
Atom OP1 has no neighbors to form bonds with according to residue template for
A /2:1002
Atom O2' has no neighbors to form bonds with according to residue template for
A /2:1002
Atom OP2 has no neighbors to form bonds with according to residue template for
U /2:1016
Atom O2' has no neighbors to form bonds with according to residue template for
U /2:1043
Atom O3' has no neighbors to form bonds with according to residue template for
C /2:1071
Atom OP1 has no neighbors to form bonds with according to residue template for
A /2:1150
Atom O6 has no neighbors to form bonds with according to residue template for
G /2:1290
Atom O2' has no neighbors to form bonds with according to residue template for
A /2:1318
Atom OP1 has no neighbors to form bonds with according to residue template for
U /2:1421
Atom O3' has no neighbors to form bonds with according to residue template for
U /2:1435
Atom O2' has no neighbors to form bonds with according to residue template for
U /2:1435
Atom OP1 has no neighbors to form bonds with according to residue template for
C /2:1623
Atom C5' has no neighbors to form bonds with according to residue template for
C /2:1623
Atom O3' has no neighbors to form bonds with according to residue template for
C /2:1623
Atom O2 has no neighbors to form bonds with according to residue template for
C /2:1635
Atom OP2 has no neighbors to form bonds with according to residue template for
U /2:1667
Atom OP1 has no neighbors to form bonds with according to residue template for
A /3:29
Atom O has no neighbors to form bonds with according to residue template for
LEU /C:159
Atom N has no neighbors to form bonds with according to residue template for
LEU /C:195
Atom O has no neighbors to form bonds with according to residue template for
VAL /C:198
Atom CG1 has no neighbors to form bonds with according to residue template for
VAL /C:198
Atom CG2 has no neighbors to form bonds with according to residue template for
VAL /C:198
Atom CE has no neighbors to form bonds with according to residue template for
MET /D:105
Atom N has no neighbors to form bonds with according to residue template for
TYR /D:120
Atom N has no neighbors to form bonds with according to residue template for
ALA /D:153
Atom CB has no neighbors to form bonds with according to residue template for
ALA /D:153
Atom NH1 has no neighbors to form bonds with according to residue template for
ARG /D:173
Atom N has no neighbors to form bonds with according to residue template for
SER /H:106
Atom N has no neighbors to form bonds with according to residue template for
GLN /H:110
Atom O has no neighbors to form bonds with according to residue template for
GLN /H:110
Atom N has no neighbors to form bonds with according to residue template for
LYS /J:65
Atom O has no neighbors to form bonds with according to residue template for
LEU /J:93
Atom N has no neighbors to form bonds with according to residue template for
ALA /J:177
Atom CB has no neighbors to form bonds with according to residue template for
ALA /J:177
Atom N has no neighbors to form bonds with according to residue template for
PHE /K:54
Atom CE1 has no neighbors to form bonds with according to residue template for
PHE /K:54
Atom NE has no neighbors to form bonds with according to residue template for
ARG /L:116
Atom NH2 has no neighbors to form bonds with according to residue template for
ARG /L:116
Atom O has no neighbors to form bonds with according to residue template for
VAL /L:125
Atom C has no neighbors to form bonds with according to residue template for
SER /L:132
Atom N has no neighbors to form bonds with according to residue template for
ARG /L:136
Atom CA has no neighbors to form bonds with according to residue template for
GLY /L:147
Atom O has no neighbors to form bonds with according to residue template for
GLY /L:147
Atom O has no neighbors to form bonds with according to residue template for
ILE /N:116
Atom O has no neighbors to form bonds with according to residue template for
THR /O:89
Atom N has no neighbors to form bonds with according to residue template for
SER /O:125
Atom OG has no neighbors to form bonds with according to residue template for
SER /O:125
Atom N has no neighbors to form bonds with according to residue template for
GLN /W:39
Atom N has no neighbors to form bonds with according to residue template for
MET /W:41
Atom CD1 has no neighbors to form bonds with according to residue template for
LEU /W:69
Atom CD2 has no neighbors to form bonds with according to residue template for
LEU /W:69
Atom O has no neighbors to form bonds with according to residue template for
ASN /Y:31
Atom N has no neighbors to form bonds with according to residue template for
ASN /a:25
Atom C has no neighbors to form bonds with according to residue template for
ASN /a:25
Atom CB has no neighbors to form bonds with according to residue template for
ASN /a:25
Atom ND2 has no neighbors to form bonds with according to residue template for
ASN /a:25
Atom N has no neighbors to form bonds with according to residue template for
MET /a:39
Atom N has no neighbors to form bonds with according to residue template for
GLN /a:99
Atom N has no neighbors to form bonds with according to residue template for
VAL /e:47
Atom CG1 has no neighbors to form bonds with according to residue template for
VAL /e:47
Atom O has no neighbors to form bonds with according to residue template for
ARG /m:36
Atom O has no neighbors to form bonds with according to residue template for
THR /m:38
Atom OG1 has no neighbors to form bonds with according to residue template for
THR /m:38
Atom OE2 has no neighbors to form bonds with according to residue template for
GLU /m:47
Atom OD1 has no neighbors to form bonds with according to residue template for
ASN /m:67
Atom O has no neighbors to form bonds with according to residue template for
ILE /m:103
Atom O has no neighbors to form bonds with according to residue template for
PRO /p:88
Atom N has no neighbors to form bonds with according to residue template for
ILE /p:116
Atom CD1 has no neighbors to form bonds with according to residue template for
ILE /p:116
Atom N has no neighbors to form bonds with according to residue template for
ASP /p:380
Atom N has no neighbors to form bonds with according to residue template for
GLN /p:444
Atom O has no neighbors to form bonds with according to residue template for
GLN /p:444
Atom N has no neighbors to form bonds with according to residue template for
GLU /p:455
Atom CD2 has no neighbors to form bonds with according to residue template for
LEU /p:468
Atom OD1 has no neighbors to form bonds with according to residue template for
ASN /p:592
Atom ND2 has no neighbors to form bonds with according to residue template for
ASN /p:592
Atom N has no neighbors to form bonds with according to residue template for
VAL /p:595
Atom CG1 has no neighbors to form bonds with according to residue template for
VAL /p:595
Chain information for 0057_6gsm_X.cif #1
---
Chain | Description
2 | 18S ribosomal RNA
3 | mRNA (5'-R(P*AP*AP*U)-3')
B | 40S ribosomal protein S1
C | KLLA0F09812p
D | KLLA0D08305p
E | 40S ribosomal protein S4
H | 40S ribosomal protein S7
I | 40S ribosomal protein S8
J | KLLA0E23673p
K | KLLA0B08173p
L | KLLA0A10483p
N | KLLA0F18040p
O | 40S ribosomal protein S14
V | 40S ribosomal protein S21
W | 40S ribosomal protein S22
X | KLLA0B11231p
Y | 40S ribosomal protein S24
a | 40S ribosomal protein S26
b | 40S ribosomal protein S27
e | 40S ribosomal protein S30
h | 60S ribosomal protein L41-A
i | Eukaryotic translation initiation factor 1A
l | Eukaryotic translation initiation factor 2 subunit beta
m | Eukaryotic translation initiation factor eIF-1
o | Eukaryotic translation initiation factor 3 subunit A,Eukaryotic
translation initiation factor 3 subunit A,eIF3a
p | Eukaryotic translation initiation factor 3 subunit B
q | Eukaryotic translation initiation factor 3 subunit C
> open /scratch/cs-
> bioinfo/tngu/6k_data/Box_Chains_new/0057_6gsm/0057_6gsm_X.mrc
Opened 0057_6gsm_X.mrc as #2, grid size 88,88,112, pixel 1, shown at level
0.153, step 1, values float32
> fitmap #1 inMap #2
Fit molecule 0057_6gsm_X.cif (#1) to map 0057_6gsm_X.mrc (#2) using 24244
atoms
average map value = 0.08409, steps = 40
shifted from previous position = 0.373
rotated from previous position = 0.099 degrees
atoms outside contour = 23533, contour level = 0.15287
Position of 0057_6gsm_X.cif (#1) relative to 0057_6gsm_X.mrc (#2) coordinates:
Matrix rotation and translation
0.99999908 0.00000025 0.00135501 -0.57857011
-0.00000170 0.99999943 0.00107085 -0.40116203
-0.00135501 -0.00107086 0.99999851 0.45634782
Axis -0.62003964 0.78457028 -0.00056271
Axis point 336.35507218 0.00000000 407.19792982
Rotation angle (degrees) 0.09895421
Shift along axis 0.04373981
> save /scratch/cs-
> bioinfo/tngu/6k_data/Box_Chains_new/0057_6gsm/0057_6gsm_X_fitted.cif #1
> close #1
> close #2
> open /scratch/cs-
> bioinfo/tngu/6k_data/Box_Chains_new/0057_6gsm/0057_6gsm_1.cif
Summary of feedback from opening /scratch/cs-
bioinfo/tngu/6k_data/Box_Chains_new/0057_6gsm/0057_6gsm_1.cif
---
warnings | Invalid residue range for struct_conf "HELX1": invalid chain "C",
near line 49791
Invalid residue range for struct_conf "HELX2": invalid chain "C", near line
49792
Invalid residue range for struct_conf "HELX3": invalid chain "C", near line
49793
Invalid residue range for struct_conf "HELX4": invalid chain "C", near line
49794
Invalid residue range for struct_conf "HELX5": invalid chain "C", near line
49795
111 messages similar to the above omitted
Invalid sheet range for struct_sheet_range "? 1": invalid chain "C", near line
50044
Invalid sheet range for struct_sheet_range "? 2": invalid chain "C", near line
50045
Invalid sheet range for struct_sheet_range "? 3": invalid chain "C", near line
50046
Invalid sheet range for struct_sheet_range "? 4": invalid chain "C", near line
50047
Invalid sheet range for struct_sheet_range "? 5": invalid chain "C", near line
50048
131 messages similar to the above omitted
Atom OP1 has no neighbors to form bonds with according to residue template for
U /2:577
Atom OP2 has no neighbors to form bonds with according to residue template for
U /2:577
Atom O2' has no neighbors to form bonds with according to residue template for
U /2:577
Atom C5' has no neighbors to form bonds with according to residue template for
U /2:910
Atom OP2 has no neighbors to form bonds with according to residue template for
A /2:1012
Atom O4' has no neighbors to form bonds with according to residue template for
U /2:1181
Atom OP1 has no neighbors to form bonds with according to residue template for
G /2:1270
Atom C5' has no neighbors to form bonds with according to residue template for
G /2:1270
Atom O3' has no neighbors to form bonds with according to residue template for
A /2:1286
Atom O2' has no neighbors to form bonds with according to residue template for
A /2:1286
Atom OP1 has no neighbors to form bonds with according to residue template for
G /2:1287
Atom O2' has no neighbors to form bonds with according to residue template for
G /2:1287
Atom O2' has no neighbors to form bonds with according to residue template for
U /2:1306
Atom OP1 has no neighbors to form bonds with according to residue template for
C /2:1308
Atom OP2 has no neighbors to form bonds with according to residue template for
C /2:1308
Atom O2' has no neighbors to form bonds with according to residue template for
U /2:1435
Atom O2' has no neighbors to form bonds with according to residue template for
G /2:1436
Atom OP2 has no neighbors to form bonds with according to residue template for
U /2:1526
Atom C4' has no neighbors to form bonds with according to residue template for
U /2:1556
Atom O3' has no neighbors to form bonds with according to residue template for
U /2:1556
Atom N4 has no neighbors to form bonds with according to residue template for
C /2:1589
Atom O2' has no neighbors to form bonds with according to residue template for
G /2:1592
Atom OP2 has no neighbors to form bonds with according to residue template for
U /2:1596
Atom O5' has no neighbors to form bonds with according to residue template for
U /2:1596
Atom O4' has no neighbors to form bonds with according to residue template for
U /2:1602
Atom C8 has no neighbors to form bonds with according to residue template for
G /2:1784
Atom CD has no neighbors to form bonds with according to residue template for
LYS /C:93
Atom NZ has no neighbors to form bonds with according to residue template for
LYS /C:93
Atom N has no neighbors to form bonds with according to residue template for
ARG /D:143
Atom C has no neighbors to form bonds with according to residue template for
ARG /D:143
Atom CG1 has no neighbors to form bonds with according to residue template for
VAL /F:55
Atom CB has no neighbors to form bonds with according to residue template for
ARG /F:94
Atom N has no neighbors to form bonds with according to residue template for
ASN /F:130
Atom N has no neighbors to form bonds with according to residue template for
LEU /F:132
Atom NE2 has no neighbors to form bonds with according to residue template for
GLN /F:133
Atom N has no neighbors to form bonds with according to residue template for
LYS /O:92
Atom O has no neighbors to form bonds with according to residue template for
THR /O:93
Atom CB has no neighbors to form bonds with according to residue template for
VAL /S:52
Atom O has no neighbors to form bonds with according to residue template for
LEU /S:66
Atom N has no neighbors to form bonds with according to residue template for
ALA /S:83
Atom CE3 has no neighbors to form bonds with according to residue template for
TRP /S:84
Atom CD1 has no neighbors to form bonds with according to residue template for
PHE /S:128
Atom CB has no neighbors to form bonds with according to residue template for
PRO /T:31
Atom N has no neighbors to form bonds with according to residue template for
PHE /T:54
Atom CB has no neighbors to form bonds with according to residue template for
ARG /Z:49
Atom CD has no neighbors to form bonds with according to residue template for
ARG /Z:49
Atom O has no neighbors to form bonds with according to residue template for
GLU /Z:84
Atom N has no neighbors to form bonds with according to residue template for
VAL /Z:92
Atom CG2 has no neighbors to form bonds with according to residue template for
VAL /Z:92
Atom NH1 has no neighbors to form bonds with according to residue template for
ARG /a:89
Atom OE2 has no neighbors to form bonds with according to residue template for
GLU /c:31
Atom OE1 has no neighbors to form bonds with according to residue template for
GLU /c:34
Atom OE2 has no neighbors to form bonds with according to residue template for
GLU /c:34
Atom N has no neighbors to form bonds with according to residue template for
TYR /i:28
Atom N has no neighbors to form bonds with according to residue template for
GLU /i:30
Atom OE1 has no neighbors to form bonds with according to residue template for
GLU /i:30
Atom O has no neighbors to form bonds with according to residue template for
SER /i:50
Atom N has no neighbors to form bonds with according to residue template for
GLN /k:175
Atom N has no neighbors to form bonds with according to residue template for
LEU /k:260
Atom N has no neighbors to form bonds with according to residue template for
MET /k:310
Atom N has no neighbors to form bonds with according to residue template for
GLU /k:457
Atom N has no neighbors to form bonds with according to residue template for
ALA /k:477
Atom OH has no neighbors to form bonds with according to residue template for
TYR /l:131
Atom ND1 has no neighbors to form bonds with according to residue template for
HIS /p:145
Atom O has no neighbors to form bonds with according to residue template for
LEU /p:149
Atom O has no neighbors to form bonds with according to residue template for
ASP /q:97
Chain information for 0057_6gsm_1.cif #1
---
Chain | Description
1 | Met-tRNAi
2 | 18S ribosomal RNA
3 | mRNA (5'-R(P*AP*AP*U)-3')
B | 40S ribosomal protein S1
C | KLLA0F09812p
D | KLLA0D08305p
F | KLLA0D10659p
O | 40S ribosomal protein S14
P | KLLA0F07843p
Q | 40S ribosomal protein S16
S | KLLA0B01562p
T | KLLA0A07194p
U | KLLA0F25542p
Z | KLLA0B06182p
a | 40S ribosomal protein S26
c | 40S ribosomal protein S28
d | 40S ribosomal protein S29
i | Eukaryotic translation initiation factor 1A
j | Eukaryotic translation initiation factor 2 subunit alpha
k | Eukaryotic translation initiation factor 2 subunit gamma
l | Eukaryotic translation initiation factor 2 subunit beta
m | Eukaryotic translation initiation factor eIF-1
p | Eukaryotic translation initiation factor 3 subunit B
q | Eukaryotic translation initiation factor 3 subunit C
> open /scratch/cs-
> bioinfo/tngu/6k_data/Box_Chains_new/0057_6gsm/0057_6gsm_1.mrc
Opened 0057_6gsm_1.mrc as #2, grid size 128,96,80, pixel 1, shown at level
0.126, step 1, values float32
> fitmap #1 inMap #2
Fit molecule 0057_6gsm_1.cif (#1) to map 0057_6gsm_1.mrc (#2) using 18608
atoms
average map value = 0.0684, steps = 64
shifted from previous position = 0.53
rotated from previous position = 0.158 degrees
atoms outside contour = 17745, contour level = 0.126
Position of 0057_6gsm_1.cif (#1) relative to 0057_6gsm_1.mrc (#2) coordinates:
Matrix rotation and translation
0.99999827 0.00173579 0.00066214 -0.84382811
-0.00173443 0.99999640 -0.00204519 0.72064419
-0.00066568 0.00204403 0.99999769 -0.47427235
Axis 0.74010988 0.24032262 -0.62807835
Axis point 0.00000000 279.59960222 369.90215785
Rotation angle (degrees) 0.15828409
Shift along axis -0.15345823
> save /scratch/cs-
> bioinfo/tngu/6k_data/Box_Chains_new/0057_6gsm/0057_6gsm_1_fitted.cif #1
> close #1
> close #2
> open /scratch/cs-
> bioinfo/tngu/6k_data/Box_Chains_new/0057_6gsm/0057_6gsm_Z.cif
Summary of feedback from opening /scratch/cs-
bioinfo/tngu/6k_data/Box_Chains_new/0057_6gsm/0057_6gsm_Z.cif
---
warnings | Invalid residue range for struct_conf "HELX1": invalid chain "C",
near line 37310
Invalid residue range for struct_conf "HELX2": invalid chain "C", near line
37311
Invalid residue range for struct_conf "HELX3": invalid chain "C", near line
37312
Invalid residue range for struct_conf "HELX4": invalid chain "C", near line
37313
Invalid residue range for struct_conf "HELX5": invalid chain "C", near line
37314
197 messages similar to the above omitted
Invalid sheet range for struct_sheet_range "? 1": invalid chain "C", near line
37563
Invalid sheet range for struct_sheet_range "? 2": invalid chain "C", near line
37564
Invalid sheet range for struct_sheet_range "? 3": invalid chain "C", near line
37565
Invalid sheet range for struct_sheet_range "? 4": invalid chain "C", near line
37566
Invalid sheet range for struct_sheet_range "? 5": invalid chain "C", near line
37567
227 messages similar to the above omitted
Atom O3' has no neighbors to form bonds with according to residue template for
G /1:43
Atom O3' has no neighbors to form bonds with according to residue template for
A /1:44
Atom O3' has no neighbors to form bonds with according to residue template for
H2U /1:47
Atom O3' has no neighbors to form bonds with according to residue template for
G /2:1166
Atom O3' has no neighbors to form bonds with according to residue template for
G /2:1169
Atom O2' has no neighbors to form bonds with according to residue template for
G /2:1348
Atom N2 has no neighbors to form bonds with according to residue template for
G /2:1357
Atom N3 has no neighbors to form bonds with according to residue template for
G /2:1357
Atom O2 has no neighbors to form bonds with according to residue template for
C /2:1358
Atom O3' has no neighbors to form bonds with according to residue template for
C /2:1364
Atom O2 has no neighbors to form bonds with according to residue template for
C /2:1365
Atom O2' has no neighbors to form bonds with according to residue template for
G /2:1367
Atom O2 has no neighbors to form bonds with according to residue template for
C /2:1377
Atom OP1 has no neighbors to form bonds with according to residue template for
C /2:1465
Atom OP2 has no neighbors to form bonds with according to residue template for
C /2:1483
Atom O4' has no neighbors to form bonds with according to residue template for
U /2:1542
Atom O3' has no neighbors to form bonds with according to residue template for
U /2:1564
Atom OD1 has no neighbors to form bonds with according to residue template for
ASP /F:62
Atom N has no neighbors to form bonds with according to residue template for
ARG /F:145
Atom CD2 has no neighbors to form bonds with according to residue template for
LEU /Q:28
Atom O has no neighbors to form bonds with according to residue template for
ASP /Q:120
Atom NH1 has no neighbors to form bonds with according to residue template for
ARG /S:41
Atom N has no neighbors to form bonds with according to residue template for
ARG /S:68
Atom N has no neighbors to form bonds with according to residue template for
VAL /S:70
Atom N has no neighbors to form bonds with according to residue template for
ARG /S:143
Atom CG1 has no neighbors to form bonds with according to residue template for
VAL /T:34
Atom N has no neighbors to form bonds with according to residue template for
THR /T:39
Atom N has no neighbors to form bonds with according to residue template for
GLN /T:70
Atom O has no neighbors to form bonds with according to residue template for
GLN /T:70
Atom CD2 has no neighbors to form bonds with according to residue template for
LEU /T:76
Atom OD1 has no neighbors to form bonds with according to residue template for
ASP /T:95
Atom N has no neighbors to form bonds with according to residue template for
VAL /T:114
Atom OG has no neighbors to form bonds with according to residue template for
SER /T:125
Atom CG2 has no neighbors to form bonds with according to residue template for
ILE /c:53
Atom CD1 has no neighbors to form bonds with according to residue template for
ILE /c:53
Atom N has no neighbors to form bonds with according to residue template for
ILE /j:27
Atom O has no neighbors to form bonds with according to residue template for
ILE /j:27
Atom CG has no neighbors to form bonds with according to residue template for
LYS /j:67
Atom CG1 has no neighbors to form bonds with according to residue template for
VAL /j:73
Atom CG2 has no neighbors to form bonds with according to residue template for
VAL /j:73
Atom O has no neighbors to form bonds with according to residue template for
ASP /j:84
Chain information for 0057_6gsm_Z.cif #1
---
Chain | Description
1 | Met-tRNAi
2 | 18S ribosomal RNA
F | KLLA0D10659p
Q | 40S ribosomal protein S16
S | KLLA0B01562p
T | KLLA0A07194p
Z | KLLA0B06182p
c | 40S ribosomal protein S28
j | Eukaryotic translation initiation factor 2 subunit alpha
> open /scratch/cs-
> bioinfo/tngu/6k_data/Box_Chains_new/0057_6gsm/0057_6gsm_Z.mrc
Opened 0057_6gsm_Z.mrc as #2, grid size 88,72,72, pixel 1, shown at level
0.12, step 1, values float32
> fitmap #1 inMap #2
Fit molecule 0057_6gsm_Z.cif (#1) to map 0057_6gsm_Z.mrc (#2) using 6379 atoms
average map value = 0.07059, steps = 52
shifted from previous position = 0.758
rotated from previous position = 0.382 degrees
atoms outside contour = 6034, contour level = 0.1198
Position of 0057_6gsm_Z.cif (#1) relative to 0057_6gsm_Z.mrc (#2) coordinates:
Matrix rotation and translation
0.99999732 -0.00041871 0.00227831 -0.60321734
0.00043294 0.99998038 -0.00624984 1.37470602
-0.00227564 0.00625081 0.99997787 -1.05746611
Axis 0.93767464 0.34159226 0.06388265
Axis point 0.00000000 168.30919662 228.37113330
Rotation angle (degrees) 0.38192337
Shift along axis -0.16358642
> save /scratch/cs-
> bioinfo/tngu/6k_data/Box_Chains_new/0057_6gsm/0057_6gsm_Z_fitted.cif #1
> close #1
> close #2
> open /scratch/cs-
> bioinfo/tngu/6k_data/Box_Chains_new/0057_6gsm/0057_6gsm_H.cif
Summary of feedback from opening /scratch/cs-
bioinfo/tngu/6k_data/Box_Chains_new/0057_6gsm/0057_6gsm_H.cif
---
warnings | Invalid residue range for struct_conf "HELX21": invalid chain "G",
near line 46024
Invalid residue range for struct_conf "HELX22": invalid chain "G", near line
46025
Invalid residue range for struct_conf "HELX23": invalid chain "G", near line
46026
Invalid residue range for struct_conf "HELX24": invalid chain "G", near line
46027
Invalid residue range for struct_conf "HELX25": invalid chain "G", near line
46028
132 messages similar to the above omitted
Invalid sheet range for struct_sheet_range "? 25": invalid chain "G", near
line 46281
Invalid sheet range for struct_sheet_range "? 26": invalid chain "G", near
line 46282
Invalid sheet range for struct_sheet_range "? 27": invalid chain "G", near
line 46283
Invalid sheet range for struct_sheet_range "? 28": invalid chain "G", near
line 46284
Invalid sheet range for struct_sheet_range "? 29": invalid chain "G", near
line 46285
179 messages similar to the above omitted
Atom O3' has no neighbors to form bonds with according to residue template for
C /2:14
Atom O2 has no neighbors to form bonds with according to residue template for
C /2:14
Atom OP1 has no neighbors to form bonds with according to residue template for
U /2:15
Atom O2' has no neighbors to form bonds with according to residue template for
G /2:213
Atom O3' has no neighbors to form bonds with according to residue template for
C /2:307
Atom O2' has no neighbors to form bonds with according to residue template for
G /2:370
Atom N2 has no neighbors to form bonds with according to residue template for
G /2:370
Atom OP1 has no neighbors to form bonds with according to residue template for
G /2:371
Atom O3' has no neighbors to form bonds with according to residue template for
G /2:372
Atom O3' has no neighbors to form bonds with according to residue template for
U /2:628
Atom OP1 has no neighbors to form bonds with according to residue template for
U /2:718
Atom N6 has no neighbors to form bonds with according to residue template for
A /2:728
Atom OP1 has no neighbors to form bonds with according to residue template for
U /2:793
Atom C6 has no neighbors to form bonds with according to residue template for
U /2:840
Atom N4 has no neighbors to form bonds with according to residue template for
C /2:841
Atom N7 has no neighbors to form bonds with according to residue template for
G /2:877
Atom O6 has no neighbors to form bonds with according to residue template for
G /2:877
Atom N2 has no neighbors to form bonds with according to residue template for
G /2:935
Atom OP2 has no neighbors to form bonds with according to residue template for
G /2:941
Atom C1' has no neighbors to form bonds with according to residue template for
C /2:942
Atom OP2 has no neighbors to form bonds with according to residue template for
G /2:947
Atom O5' has no neighbors to form bonds with according to residue template for
G /2:947
Atom O3' has no neighbors to form bonds with according to residue template for
U /2:1060
Atom C8 has no neighbors to form bonds with according to residue template for
G /2:1296
Atom O has no neighbors to form bonds with according to residue template for
ILE /A:133
Atom CG2 has no neighbors to form bonds with according to residue template for
ILE /A:133
Atom N has no neighbors to form bonds with according to residue template for
ALA /A:145
Atom O has no neighbors to form bonds with according to residue template for
ALA /A:145
Atom CA has no neighbors to form bonds with according to residue template for
VAL /A:181
Atom O has no neighbors to form bonds with according to residue template for
VAL /A:181
Atom NE has no neighbors to form bonds with according to residue template for
ARG /A:185
Atom CB has no neighbors to form bonds with according to residue template for
ARG /C:173
Atom O has no neighbors to form bonds with according to residue template for
VAL /C:221
Atom N has no neighbors to form bonds with according to residue template for
TYR /C:251
Atom C has no neighbors to form bonds with according to residue template for
TYR /C:251
Atom N has no neighbors to form bonds with according to residue template for
ARG /E:233
Atom CB has no neighbors to form bonds with according to residue template for
ARG /E:233
Atom N has no neighbors to form bonds with according to residue template for
LYS /L:46
Atom CG1 has no neighbors to form bonds with according to residue template for
VAL /L:125
Atom CG has no neighbors to form bonds with according to residue template for
GLU /V:2
Atom OE1 has no neighbors to form bonds with according to residue template for
GLU /V:2
Atom C has no neighbors to form bonds with according to residue template for
ALA /X:25
Atom CB has no neighbors to form bonds with according to residue template for
ALA /X:25
Atom NH1 has no neighbors to form bonds with according to residue template for
ARG /a:15
Atom O has no neighbors to form bonds with according to residue template for
PHE /q:254
Atom O has no neighbors to form bonds with according to residue template for
PHE /q:255
Atom O has no neighbors to form bonds with according to residue template for
VAL /q:270
Atom OE2 has no neighbors to form bonds with according to residue template for
GLU /q:281
Atom OE2 has no neighbors to form bonds with according to residue template for
GLU /q:287
Atom NH1 has no neighbors to form bonds with according to residue template for
ARG /q:303
Atom N has no neighbors to form bonds with according to residue template for
GLN /q:334
Atom CB has no neighbors to form bonds with according to residue template for
GLN /q:334
Atom NE2 has no neighbors to form bonds with according to residue template for
GLN /q:334
Atom N has no neighbors to form bonds with according to residue template for
THR /q:335
Atom N has no neighbors to form bonds with according to residue template for
LYS /q:443
Atom CG has no neighbors to form bonds with according to residue template for
LYS /q:443
Atom CE has no neighbors to form bonds with according to residue template for
LYS /q:443
Atom CD2 has no neighbors to form bonds with according to residue template for
LEU /q:486
Atom CG2 has no neighbors to form bonds with according to residue template for
THR /q:488
Atom CG2 has no neighbors to form bonds with according to residue template for
ILE /q:560
Atom CD1 has no neighbors to form bonds with according to residue template for
LEU /q:576
Atom N has no neighbors to form bonds with according to residue template for
GLN /q:583
Atom O has no neighbors to form bonds with according to residue template for
SER /q:592
Atom OG has no neighbors to form bonds with according to residue template for
SER /q:592
Atom CA has no neighbors to form bonds with according to residue template for
SER /q:593
Atom OG has no neighbors to form bonds with according to residue template for
SER /q:593
Atom N has no neighbors to form bonds with according to residue template for
THR /q:634
Atom C has no neighbors to form bonds with according to residue template for
THR /q:634
Atom N has no neighbors to form bonds with according to residue template for
ARG /q:654
Chain information for 0057_6gsm_H.cif #1
---
Chain | Description
2 | 18S ribosomal RNA
A | 40S ribosomal protein S0
B | 40S ribosomal protein S1
C | KLLA0F09812p
E | 40S ribosomal protein S4
H | 40S ribosomal protein S7
L | KLLA0A10483p
N | KLLA0F18040p
R | KLLA0B01474p
V | 40S ribosomal protein S21
W | 40S ribosomal protein S22
X | KLLA0B11231p
a | 40S ribosomal protein S26
b | 40S ribosomal protein S27
q | Eukaryotic translation initiation factor 3 subunit C
> open /scratch/cs-
> bioinfo/tngu/6k_data/Box_Chains_new/0057_6gsm/0057_6gsm_H.mrc
Opened 0057_6gsm_H.mrc as #2, grid size 88,96,104, pixel 1, shown at level
0.137, step 1, values float32
> fitmap #1 inMap #2
Fit molecule 0057_6gsm_H.cif (#1) to map 0057_6gsm_H.mrc (#2) using 14921
atoms
average map value = 0.07261, steps = 80
shifted from previous position = 0.499
rotated from previous position = 0.179 degrees
atoms outside contour = 14137, contour level = 0.1369
Position of 0057_6gsm_H.cif (#1) relative to 0057_6gsm_H.mrc (#2) coordinates:
Matrix rotation and translation
0.99999531 -0.00126111 -0.00279203 0.90794240
0.00125934 0.99999900 -0.00063652 -0.43925796
0.00279283 0.00063300 0.99999590 -1.02865610
Axis 0.20288211 -0.89252153 0.40279544
Axis point 392.13097233 0.00000000 312.76567637
Rotation angle (degrees) 0.17926176
Shift along axis 0.16191447
> save /scratch/cs-
> bioinfo/tngu/6k_data/Box_Chains_new/0057_6gsm/0057_6gsm_H_fitted.cif #1
> close #1
> close #2
> open /scratch/cs-
> bioinfo/tngu/6k_data/Box_Chains_new/0057_6gsm/0057_6gsm_l.cif
Summary of feedback from opening /scratch/cs-
bioinfo/tngu/6k_data/Box_Chains_new/0057_6gsm/0057_6gsm_l.cif
---
warnings | Invalid residue range for struct_conf "HELX1": invalid chain "C",
near line 42944
Invalid residue range for struct_conf "HELX2": invalid chain "C", near line
42945
Invalid residue range for struct_conf "HELX3": invalid chain "C", near line
42946
Invalid residue range for struct_conf "HELX4": invalid chain "C", near line
42947
Invalid residue range for struct_conf "HELX5": invalid chain "C", near line
42948
140 messages similar to the above omitted
Invalid sheet range for struct_sheet_range "? 1": invalid chain "C", near line
43197
Invalid sheet range for struct_sheet_range "? 2": invalid chain "C", near line
43198
Invalid sheet range for struct_sheet_range "? 3": invalid chain "C", near line
43199
Invalid sheet range for struct_sheet_range "? 4": invalid chain "C", near line
43200
Invalid sheet range for struct_sheet_range "? 5": invalid chain "C", near line
43201
168 messages similar to the above omitted
Atom O3' has no neighbors to form bonds with according to residue template for
G /1:19
Atom OP1 has no neighbors to form bonds with according to residue template for
U /2:562
Atom OP2 has no neighbors to form bonds with according to residue template for
U /2:562
Atom C5' has no neighbors to form bonds with according to residue template for
U /2:1003
Atom C8 has no neighbors to form bonds with according to residue template for
A /2:1151
Atom O4' has no neighbors to form bonds with according to residue template for
C /2:1191
Atom OP1 has no neighbors to form bonds with according to residue template for
A /2:1193
Atom OP2 has no neighbors to form bonds with according to residue template for
A /2:1193
Atom OP2 has no neighbors to form bonds with according to residue template for
A /2:1207
Atom O6 has no neighbors to form bonds with according to residue template for
G /2:1217
Atom N1 has no neighbors to form bonds with according to residue template for
G /2:1217
Atom N2 has no neighbors to form bonds with according to residue template for
G /2:1217
Atom OP1 has no neighbors to form bonds with according to residue template for
A /2:1243
Atom OP2 has no neighbors to form bonds with according to residue template for
G /2:1269
Atom OP1 has no neighbors to form bonds with according to residue template for
C /2:1273
Atom O5' has no neighbors to form bonds with according to residue template for
C /2:1273
Atom OP1 has no neighbors to form bonds with according to residue template for
A /2:1425
Atom N7 has no neighbors to form bonds with according to residue template for
G /2:1446
Atom O2' has no neighbors to form bonds with according to residue template for
G /2:1540
Atom C6 has no neighbors to form bonds with according to residue template for
U /2:1542
Atom O3' has no neighbors to form bonds with according to residue template for
A /2:1553
Atom O2' has no neighbors to form bonds with according to residue template for
A /2:1553
Atom OP1 has no neighbors to form bonds with according to residue template for
A /2:1554
Atom O2' has no neighbors to form bonds with according to residue template for
A /2:1554
Atom O2' has no neighbors to form bonds with according to residue template for
A /2:1567
Atom O4' has no neighbors to form bonds with according to residue template for
U /2:1577
Atom O2 has no neighbors to form bonds with according to residue template for
C /2:1617
Atom O2' has no neighbors to form bonds with according to residue template for
U /2:1626
Atom O2 has no neighbors to form bonds with according to residue template for
U /2:1626
Atom O3' has no neighbors to form bonds with according to residue template for
U /2:1768
Atom O3' has no neighbors to form bonds with according to residue template for
G /2:1776
Atom O3' has no neighbors to form bonds with according to residue template for
G /2:1790
Atom O2' has no neighbors to form bonds with according to residue template for
G /2:1790
Atom C1' has no neighbors to form bonds with according to residue template for
G /2:1790
Atom N has no neighbors to form bonds with according to residue template for
GLU /F:183
Atom OE1 has no neighbors to form bonds with according to residue template for
GLU /F:218
Atom OE2 has no neighbors to form bonds with according to residue template for
GLU /F:218
Atom C has no neighbors to form bonds with according to residue template for
LYS /P:59
Atom CG has no neighbors to form bonds with according to residue template for
LYS /P:64
Atom CE has no neighbors to form bonds with according to residue template for
LYS /P:64
Atom N has no neighbors to form bonds with according to residue template for
VAL /P:86
Atom CG2 has no neighbors to form bonds with according to residue template for
VAL /P:86
Atom O has no neighbors to form bonds with according to residue template for
PRO /a:2
Atom OD1 has no neighbors to form bonds with according to residue template for
ASP /i:90
Atom O has no neighbors to form bonds with according to residue template for
LYS /j:35
Atom O has no neighbors to form bonds with according to residue template for
ILE /j:46
Atom CD1 has no neighbors to form bonds with according to residue template for
ILE /j:46
Atom O has no neighbors to form bonds with according to residue template for
ILE /j:95
Atom CG2 has no neighbors to form bonds with according to residue template for
ILE /j:96
Atom O has no neighbors to form bonds with according to residue template for
LYS /j:106
Atom SG has no neighbors to form bonds with according to residue template for
CYS /j:262
Atom N has no neighbors to form bonds with according to residue template for
ASN /j:263
Atom O has no neighbors to form bonds with according to residue template for
LYS /p:142
Atom CG has no neighbors to form bonds with according to residue template for
GLU /p:290
Atom OE1 has no neighbors to form bonds with according to residue template for
GLU /p:290
Atom N has no neighbors to form bonds with according to residue template for
ILE /p:292
Atom N has no neighbors to form bonds with according to residue template for
HIS /p:310
Atom CE1 has no neighbors to form bonds with according to residue template for
HIS /p:310
Chain information for 0057_6gsm_l.cif #1
---
Chain | Description
1 | Met-tRNAi
2 | 18S ribosomal RNA
3 | mRNA (5'-R(P*AP*AP*U)-3')
F | KLLA0D10659p
P | KLLA0F07843p
Q | 40S ribosomal protein S16
S | KLLA0B01562p
c | 40S ribosomal protein S28
e | 40S ribosomal protein S30
f | Ubiquitin-40S ribosomal protein S27a
h | 60S ribosomal protein L41-A
i | Eukaryotic translation initiation factor 1A
j | Eukaryotic translation initiation factor 2 subunit alpha
k | Eukaryotic translation initiation factor 2 subunit gamma
l | Eukaryotic translation initiation factor 2 subunit beta
m | Eukaryotic translation initiation factor eIF-1
p | Eukaryotic translation initiation factor 3 subunit B
q | Eukaryotic translation initiation factor 3 subunit C
> open /scratch/cs-
> bioinfo/tngu/6k_data/Box_Chains_new/0057_6gsm/0057_6gsm_l.mrc
Opened 0057_6gsm_l.mrc as #2, grid size 120,72,88, pixel 1, shown at level
0.117, step 1, values float32
> fitmap #1 inMap #2
Fit molecule 0057_6gsm_l.cif (#1) to map 0057_6gsm_l.mrc (#2) using 11892
atoms
average map value = 0.06384, steps = 72
shifted from previous position = 0.608
rotated from previous position = 0.153 degrees
atoms outside contour = 11222, contour level = 0.11707
Position of 0057_6gsm_l.cif (#1) relative to 0057_6gsm_l.mrc (#2) coordinates:
Matrix rotation and translation
0.99999771 0.00015409 0.00213271 -0.96507720
-0.00015068 0.99999871 -0.00159690 0.08959189
-0.00213295 0.00159657 0.99999645 0.13446134
Axis 0.59832829 0.79921371 -0.05710259
Axis point 48.77929787 0.00000000 308.50125021
Rotation angle (degrees) 0.15290296
Shift along axis -0.51350801
> save /scratch/cs-
> bioinfo/tngu/6k_data/Box_Chains_new/0057_6gsm/0057_6gsm_l_fitted.cif #1
> close #1
> close #2
> open /scratch/cs-
> bioinfo/tngu/6k_data/Box_Chains_new/0057_6gsm/0057_6gsm_f.cif
Summary of feedback from opening /scratch/cs-
bioinfo/tngu/6k_data/Box_Chains_new/0057_6gsm/0057_6gsm_f.cif
---
warnings | Invalid residue range for struct_conf "HELX1": invalid chain "C",
near line 41078
Invalid residue range for struct_conf "HELX2": invalid chain "C", near line
41079
Invalid residue range for struct_conf "HELX3": invalid chain "C", near line
41080
Invalid residue range for struct_conf "HELX4": invalid chain "C", near line
41081
Invalid residue range for struct_conf "HELX5": invalid chain "C", near line
41082
193 messages similar to the above omitted
Invalid sheet range for struct_sheet_range "? 1": invalid chain "C", near line
41331
Invalid sheet range for struct_sheet_range "? 2": invalid chain "C", near line
41332
Invalid sheet range for struct_sheet_range "? 3": invalid chain "C", near line
41333
Invalid sheet range for struct_sheet_range "? 4": invalid chain "C", near line
41334
Invalid sheet range for struct_sheet_range "? 5": invalid chain "C", near line
41335
220 messages similar to the above omitted
Atom OP2 has no neighbors to form bonds with according to residue template for
A /2:1193
Atom O2' has no neighbors to form bonds with according to residue template for
G /2:1280
Atom OP2 has no neighbors to form bonds with according to residue template for
C /2:1424
Atom O2' has no neighbors to form bonds with according to residue template for
G /2:1464
Atom O2 has no neighbors to form bonds with according to residue template for
C /2:1465
Atom OP2 has no neighbors to form bonds with according to residue template for
C /2:1483
Atom O4' has no neighbors to form bonds with according to residue template for
G /2:1496
Atom O3' has no neighbors to form bonds with according to residue template for
G /2:1502
Atom OP1 has no neighbors to form bonds with according to residue template for
G /2:1588
Atom O5' has no neighbors to form bonds with according to residue template for
G /2:1603
Atom O has no neighbors to form bonds with according to residue template for
VAL /D:37
Atom O has no neighbors to form bonds with according to residue template for
ASP /D:57
Atom O has no neighbors to form bonds with according to residue template for
ARG /D:64
Atom N has no neighbors to form bonds with according to residue template for
SER /D:129
Atom CB has no neighbors to form bonds with according to residue template for
SER /D:129
Atom O has no neighbors to form bonds with according to residue template for
LYS /D:190
Atom CG has no neighbors to form bonds with according to residue template for
LYS /D:190
Atom N has no neighbors to form bonds with according to residue template for
GLN /M:122
Atom C has no neighbors to form bonds with according to residue template for
GLN /M:122
Atom CB has no neighbors to form bonds with according to residue template for
GLN /M:122
Atom N has no neighbors to form bonds with according to residue template for
MET /P:28
Atom NH2 has no neighbors to form bonds with according to residue template for
ARG /S:110
Atom CB has no neighbors to form bonds with according to residue template for
ALA /T:41
Atom N has no neighbors to form bonds with according to residue template for
TYR /T:80
Atom N has no neighbors to form bonds with according to residue template for
ALA /T:96
Atom O has no neighbors to form bonds with according to residue template for
ALA /T:96
Atom O has no neighbors to form bonds with according to residue template for
THR /U:29
Atom N has no neighbors to form bonds with according to residue template for
ARG /d:56
Atom CD2 has no neighbors to form bonds with according to residue template for
LEU /i:65
Atom N has no neighbors to form bonds with according to residue template for
LEU /i:78
Atom CB has no neighbors to form bonds with according to residue template for
LEU /i:78
Atom N has no neighbors to form bonds with according to residue template for
LEU /i:109
Atom O has no neighbors to form bonds with according to residue template for
ARG /l:167
Atom N has no neighbors to form bonds with according to residue template for
GLN /l:178
Atom CB has no neighbors to form bonds with according to residue template for
GLN /l:178
Atom N has no neighbors to form bonds with according to residue template for
ASP /l:179
Chain information for 0057_6gsm_f.cif #1
---
Chain | Description
1 | Met-tRNAi
2 | 18S ribosomal RNA
D | KLLA0D08305p
K | KLLA0B08173p
M | 40S ribosomal protein S12
P | KLLA0F07843p
S | KLLA0B01562p
T | KLLA0A07194p
U | KLLA0F25542p
d | 40S ribosomal protein S29
f | Ubiquitin-40S ribosomal protein S27a
i | Eukaryotic translation initiation factor 1A
l | Eukaryotic translation initiation factor 2 subunit beta
> open /scratch/cs-
> bioinfo/tngu/6k_data/Box_Chains_new/0057_6gsm/0057_6gsm_f.mrc
Opened 0057_6gsm_f.mrc as #2, grid size 80,72,120, pixel 1, shown at level
0.121, step 1, values float32
> fitmap #1 inMap #2
Fit molecule 0057_6gsm_f.cif (#1) to map 0057_6gsm_f.mrc (#2) using 10038
atoms
average map value = 0.07064, steps = 48
shifted from previous position = 0.453
rotated from previous position = 0.191 degrees
atoms outside contour = 9477, contour level = 0.12053
Position of 0057_6gsm_f.cif (#1) relative to 0057_6gsm_f.mrc (#2) coordinates:
Matrix rotation and translation
0.99999742 0.00017353 -0.00226392 0.00548192
-0.00016801 0.99999701 0.00243768 -0.65676907
0.00226434 -0.00243729 0.99999447 0.03413541
Axis -0.73171784 -0.67967718 -0.05126334
Axis point 0.00000000 22.94036133 146.59506449
Rotation angle (degrees) 0.19086294
Shift along axis 0.44062983
> save /scratch/cs-
> bioinfo/tngu/6k_data/Box_Chains_new/0057_6gsm/0057_6gsm_f_fitted.cif #1
> close #1
> close #2
> open /scratch/cs-
> bioinfo/tngu/6k_data/Box_Chains_new/0057_6gsm/0057_6gsm_R.cif
Summary of feedback from opening /scratch/cs-
bioinfo/tngu/6k_data/Box_Chains_new/0057_6gsm/0057_6gsm_R.cif
---
warnings | Invalid residue range for struct_conf "HELX27": invalid chain "H",
near line 47208
Invalid residue range for struct_conf "HELX28": invalid chain "H", near line
47209
Invalid residue range for struct_conf "HELX29": invalid chain "H", near line
47210
Invalid residue range for struct_conf "HELX30": invalid chain "H", near line
47211
Invalid residue range for struct_conf "HELX31": invalid chain "H", near line
47212
88 messages similar to the above omitted
Invalid sheet range for struct_sheet_range "? 32": invalid chain "H", near
line 47466
Invalid sheet range for struct_sheet_range "? 33": invalid chain "H", near
line 47467
Invalid sheet range for struct_sheet_range "? 34": invalid chain "H", near
line 47468
Invalid sheet range for struct_sheet_range "? 35": invalid chain "H", near
line 47469
Invalid sheet range for struct_sheet_range "? 36": invalid chain "H", near
line 47470
155 messages similar to the above omitted
Atom O3' has no neighbors to form bonds with according to residue template for
A /2:2
Atom O2' has no neighbors to form bonds with according to residue template for
A /2:2
Atom O3' has no neighbors to form bonds with according to residue template for
C /2:4
Atom OP1 has no neighbors to form bonds with according to residue template for
U /2:12
Atom O2' has no neighbors to form bonds with according to residue template for
C /2:13
Atom OP1 has no neighbors to form bonds with according to residue template for
G /2:591
Atom OP2 has no neighbors to form bonds with according to residue template for
G /2:591
Atom O2' has no neighbors to form bonds with according to residue template for
C /2:955
Atom O3' has no neighbors to form bonds with according to residue template for
G /2:1034
Atom O2' has no neighbors to form bonds with according to residue template for
G /2:1034
Atom OP2 has no neighbors to form bonds with according to residue template for
C /2:1044
Atom OP2 has no neighbors to form bonds with according to residue template for
G /2:1047
Atom OP2 has no neighbors to form bonds with according to residue template for
G /2:1063
Atom OP2 has no neighbors to form bonds with according to residue template for
A /2:1064
Atom OP2 has no neighbors to form bonds with according to residue template for
A /2:1085
Atom O3' has no neighbors to form bonds with according to residue template for
A /2:1087
Atom O3' has no neighbors to form bonds with according to residue template for
G /2:1099
Atom O3' has no neighbors to form bonds with according to residue template for
A /2:1142
Atom O2' has no neighbors to form bonds with according to residue template for
A /2:1142
Atom O2' has no neighbors to form bonds with according to residue template for
U /2:1143
Atom O3' has no neighbors to form bonds with according to residue template for
G /2:1152
Atom N7 has no neighbors to form bonds with according to residue template for
A /2:1159
Atom O2' has no neighbors to form bonds with according to residue template for
A /2:1162
Atom O2' has no neighbors to form bonds with according to residue template for
G /2:1163
Atom N2 has no neighbors to form bonds with according to residue template for
G /2:1163
Atom O5' has no neighbors to form bonds with according to residue template for
G /2:1198
Atom OP1 has no neighbors to form bonds with according to residue template for
G /2:1200
Atom C4 has no neighbors to form bonds with according to residue template for
G /2:1200
Atom N1 has no neighbors to form bonds with according to residue template for
G /2:1272
Atom N2 has no neighbors to form bonds with according to residue template for
G /2:1272
Atom O6 has no neighbors to form bonds with according to residue template for
G /2:1276
Atom C6 has no neighbors to form bonds with according to residue template for
U /2:1375
Atom O3' has no neighbors to form bonds with according to residue template for
C /2:1377
Atom OP2 has no neighbors to form bonds with according to residue template for
C /2:1424
Atom O3' has no neighbors to form bonds with according to residue template for
A /2:1513
Atom O2' has no neighbors to form bonds with according to residue template for
A /2:1513
Atom OP2 has no neighbors to form bonds with according to residue template for
C /2:1600
Atom N4 has no neighbors to form bonds with according to residue template for
C /2:1616
Atom C5 has no neighbors to form bonds with according to residue template for
C /2:1616
Atom O2' has no neighbors to form bonds with according to residue template for
C /2:1621
Atom O2 has no neighbors to form bonds with according to residue template for
C /2:1621
Atom O2 has no neighbors to form bonds with according to residue template for
U /2:1797
Atom CB has no neighbors to form bonds with according to residue template for
LYS /B:202
Atom C has no neighbors to form bonds with according to residue template for
ARG /C:96
Atom N has no neighbors to form bonds with according to residue template for
THR /C:231
Atom OG1 has no neighbors to form bonds with according to residue template for
THR /C:231
Atom CG2 has no neighbors to form bonds with according to residue template for
THR /C:231
Atom N has no neighbors to form bonds with according to residue template for
ARG /D:94
Atom C has no neighbors to form bonds with according to residue template for
ARG /D:94
Atom NE has no neighbors to form bonds with according to residue template for
ARG /D:94
Atom CB has no neighbors to form bonds with according to residue template for
ALA /D:114
Atom N has no neighbors to form bonds with according to residue template for
SER /D:221
Atom CD1 has no neighbors to form bonds with according to residue template for
LEU /F:60
Atom N has no neighbors to form bonds with according to residue template for
CYS /F:89
Atom SG has no neighbors to form bonds with according to residue template for
CYS /F:89
Atom OE1 has no neighbors to form bonds with according to residue template for
GLU /J:33
Atom OE2 has no neighbors to form bonds with according to residue template for
GLU /J:33
Atom N has no neighbors to form bonds with according to residue template for
HIS /N:58
Atom CG has no neighbors to form bonds with according to residue template for
LYS /Q:14
Atom CE has no neighbors to form bonds with according to residue template for
LYS /Q:14
Atom N has no neighbors to form bonds with according to residue template for
PHE /Q:138
Atom O has no neighbors to form bonds with according to residue template for
LEU /U:26
Atom N has no neighbors to form bonds with according to residue template for
PHE /U:48
Atom C has no neighbors to form bonds with according to residue template for
PHE /U:48
Atom OD1 has no neighbors to form bonds with according to residue template for
ASN /W:66
Atom CD1 has no neighbors to form bonds with according to residue template for
LEU /W:69
Atom N has no neighbors to form bonds with according to residue template for
CYS /W:72
Atom O has no neighbors to form bonds with according to residue template for
CYS /W:72
Atom O has no neighbors to form bonds with according to residue template for
CYS /b:40
Atom SG has no neighbors to form bonds with according to residue template for
CYS /b:40
Atom O has no neighbors to form bonds with according to residue template for
VAL /b:54
Atom CG1 has no neighbors to form bonds with according to residue template for
VAL /b:62
Atom N has no neighbors to form bonds with according to residue template for
THR /b:65
Atom O has no neighbors to form bonds with according to residue template for
THR /b:65
Atom OG1 has no neighbors to form bonds with according to residue template for
THR /b:65
Atom CG1 has no neighbors to form bonds with according to residue template for
ILE /c:40
Atom O has no neighbors to form bonds with according to residue template for
VAL /c:44
Atom OD2 has no neighbors to form bonds with according to residue template for
ASP /d:49
Atom CE has no neighbors to form bonds with according to residue template for
MET /e:56
Atom N has no neighbors to form bonds with according to residue template for
ASN /g:79
Atom C has no neighbors to form bonds with according to residue template for
ASN /g:79
Atom OE1 has no neighbors to form bonds with according to residue template for
GLU /g:101
Atom OD1 has no neighbors to form bonds with according to residue template for
ASP /g:117
Atom N has no neighbors to form bonds with according to residue template for
TRP /g:186
Atom CD1 has no neighbors to form bonds with according to residue template for
LEU /g:188
Atom CD2 has no neighbors to form bonds with according to residue template for
LEU /g:188
Atom O has no neighbors to form bonds with according to residue template for
TYR /g:193
Atom N has no neighbors to form bonds with according to residue template for
PHE /g:238
Atom N has no neighbors to form bonds with according to residue template for
GLU /o:9
Atom OE2 has no neighbors to form bonds with according to residue template for
GLU /o:9
Atom O has no neighbors to form bonds with according to residue template for
ALA /o:15
Atom N has no neighbors to form bonds with according to residue template for
GLU /o:61
Atom C has no neighbors to form bonds with according to residue template for
GLU /o:61
Atom O has no neighbors to form bonds with according to residue template for
ARG /o:156
Atom NH1 has no neighbors to form bonds with according to residue template for
ARG /o:201
Atom OH has no neighbors to form bonds with according to residue template for
TYR /o:257
Atom ND2 has no neighbors to form bonds with according to residue template for
ASN /q:309
Atom N has no neighbors to form bonds with according to residue template for
GLN /q:604
Chain information for 0057_6gsm_R.cif #1
---
Chain | Description
2 | 18S ribosomal RNA
A | 40S ribosomal protein S0
B | 40S ribosomal protein S1
C | KLLA0F09812p
D | KLLA0D08305p
F | KLLA0D10659p
H | 40S ribosomal protein S7
J | KLLA0E23673p
N | KLLA0F18040p
Q | 40S ribosomal protein S16
R | KLLA0B01474p
U | KLLA0F25542p
V | 40S ribosomal protein S21
W | 40S ribosomal protein S22
a | 40S ribosomal protein S26
b | 40S ribosomal protein S27
c | 40S ribosomal protein S28
d | 40S ribosomal protein S29
e | 40S ribosomal protein S30
g | KLLA0E12277p
o | Eukaryotic translation initiation factor 3 subunit A,Eukaryotic
translation initiation factor 3 subunit A,eIF3a
q | Eukaryotic translation initiation factor 3 subunit C
> open /scratch/cs-
> bioinfo/tngu/6k_data/Box_Chains_new/0057_6gsm/0057_6gsm_R.mrc
Opened 0057_6gsm_R.mrc as #2, grid size 72,96,120, pixel 1, shown at level
0.129, step 1, values float32
> fitmap #1 inMap #2
Fit molecule 0057_6gsm_R.cif (#1) to map 0057_6gsm_R.mrc (#2) using 16133
atoms
average map value = 0.06832, steps = 40
shifted from previous position = 0.394
rotated from previous position = 0.046 degrees
atoms outside contour = 15398, contour level = 0.12946
Position of 0057_6gsm_R.cif (#1) relative to 0057_6gsm_R.mrc (#2) coordinates:
Matrix rotation and translation
0.99999986 0.00050653 0.00015865 -0.10325212
-0.00050643 0.99999969 -0.00060125 -0.02149171
-0.00015896 0.00060117 0.99999981 -0.39826988
Axis 0.74964305 0.19801208 -0.63152713
Axis point 0.00000000 484.02758995 -91.93522150
Rotation angle (degrees) 0.04595060
Shift along axis 0.16986038
> save /scratch/cs-
> bioinfo/tngu/6k_data/Box_Chains_new/0057_6gsm/0057_6gsm_R_fitted.cif #1
> close #1
> close #2
> open /scratch/cs-
> bioinfo/tngu/6k_data/Box_Chains_new/0057_6gsm/0057_6gsm_V.cif
Summary of feedback from opening /scratch/cs-
bioinfo/tngu/6k_data/Box_Chains_new/0057_6gsm/0057_6gsm_V.cif
---
warnings | Invalid residue range for struct_conf "HELX32": invalid chain "I",
near line 42239
Invalid residue range for struct_conf "HELX33": invalid chain "I", near line
42240
Invalid residue range for struct_conf "HELX34": invalid chain "I", near line
42241
Invalid residue range for struct_conf "HELX35": invalid chain "I", near line
42242
Invalid residue range for struct_conf "HELX36": invalid chain "I", near line
42243
155 messages similar to the above omitted
Invalid sheet range for struct_sheet_range "? 47": invalid chain "I", near
line 42507
Invalid sheet range for struct_sheet_range "? 48": invalid chain "I", near
line 42508
Invalid sheet range for struct_sheet_range "? 49": invalid chain "J", near
line 42509
Invalid sheet range for struct_sheet_range "? 50": invalid chain "J", near
line 42510
Invalid sheet range for struct_sheet_range "? 51": invalid chain "J", near
line 42511
179 messages similar to the above omitted
Atom OP1 has no neighbors to form bonds with according to residue template for
A /2:11
Atom OP1 has no neighbors to form bonds with according to residue template for
A /2:604
Atom O3' has no neighbors to form bonds with according to residue template for
A /2:604
Atom O2' has no neighbors to form bonds with according to residue template for
A /2:604
Atom OP1 has no neighbors to form bonds with according to residue template for
G /2:606
Atom O6 has no neighbors to form bonds with according to residue template for
G /2:612
Atom C5' has no neighbors to form bonds with according to residue template for
C /2:613
Atom O3' has no neighbors to form bonds with according to residue template for
C /2:613
Atom OP1 has no neighbors to form bonds with according to residue template for
G /2:633
Atom O2' has no neighbors to form bonds with according to residue template for
G /2:633
Atom O2' has no neighbors to form bonds with according to residue template for
C /2:657
Atom O2' has no neighbors to form bonds with according to residue template for
U /2:679
Atom O3' has no neighbors to form bonds with according to residue template for
U /2:680
Atom C5' has no neighbors to form bonds with according to residue template for
C /2:696
Atom C3' has no neighbors to form bonds with according to residue template for
C /2:696
Atom O4' has no neighbors to form bonds with according to residue template for
G /2:751
Atom OP2 has no neighbors to form bonds with according to residue template for
A /2:752
Atom O4 has no neighbors to form bonds with according to residue template for
U /2:759
Atom OP2 has no neighbors to form bonds with according to residue template for
A /2:788
Atom OP2 has no neighbors to form bonds with according to residue template for
U /2:789
Atom O4 has no neighbors to form bonds with according to residue template for
U /2:793
Atom C5 has no neighbors to form bonds with according to residue template for
U /2:793
Atom N7 has no neighbors to form bonds with according to residue template for
G /2:865
Atom O6 has no neighbors to form bonds with according to residue template for
G /2:865
Atom N6 has no neighbors to form bonds with according to residue template for
A /2:868
Atom N1 has no neighbors to form bonds with according to residue template for
A /2:868
Atom O3' has no neighbors to form bonds with according to residue template for
A /2:932
Atom O2' has no neighbors to form bonds with according to residue template for
A /2:932
Atom OP2 has no neighbors to form bonds with according to residue template for
C /2:961
Atom N4 has no neighbors to form bonds with according to residue template for
C /2:961
Atom O2' has no neighbors to form bonds with according to residue template for
A /2:962
Atom O5' has no neighbors to form bonds with according to residue template for
G /2:1050
Atom O2' has no neighbors to form bonds with according to residue template for
U /2:1053
Atom O2' has no neighbors to form bonds with according to residue template for
G /2:1063
Atom OP2 has no neighbors to form bonds with according to residue template for
C /2:1074
Atom OP2 has no neighbors to form bonds with according to residue template for
A /2:1075
Atom O3' has no neighbors to form bonds with according to residue template for
A /2:1141
Atom OP2 has no neighbors to form bonds with according to residue template for
G /2:1145
Atom OP1 has no neighbors to form bonds with according to residue template for
U /2:1626
Atom C5' has no neighbors to form bonds with according to residue template for
U /2:1626
Atom C5' has no neighbors to form bonds with according to residue template for
C /2:1794
Atom NZ has no neighbors to form bonds with according to residue template for
LYS /A:88
Atom N has no neighbors to form bonds with according to residue template for
GLY /A:100
Atom CE has no neighbors to form bonds with according to residue template for
LYS /B:145
Atom NE2 has no neighbors to form bonds with according to residue template for
GLN /C:99
Atom OE1 has no neighbors to form bonds with according to residue template for
GLU /D:128
Atom CA has no neighbors to form bonds with according to residue template for
GLU /H:17
Atom CG has no neighbors to form bonds with according to residue template for
GLU /H:17
Atom NE2 has no neighbors to form bonds with according to residue template for
GLN /H:160
Atom N has no neighbors to form bonds with according to residue template for
LEU /J:24
Atom CB has no neighbors to form bonds with according to residue template for
LYS /N:9
Atom N has no neighbors to form bonds with according to residue template for
SER /R:96
Atom OG has no neighbors to form bonds with according to residue template for
SER /R:96
Atom N has no neighbors to form bonds with according to residue template for
LYS /b:70
Atom NZ has no neighbors to form bonds with according to residue template for
LYS /b:70
Chain information for 0057_6gsm_V.cif #1
---
Chain | Description
2 | 18S ribosomal RNA
A | 40S ribosomal protein S0
B | 40S ribosomal protein S1
C | KLLA0F09812p
D | KLLA0D08305p
E | 40S ribosomal protein S4
H | 40S ribosomal protein S7
J | KLLA0E23673p
N | KLLA0F18040p
R | KLLA0B01474p
V | 40S ribosomal protein S21
W | 40S ribosomal protein S22
X | KLLA0B11231p
a | 40S ribosomal protein S26
b | 40S ribosomal protein S27
> open /scratch/cs-
> bioinfo/tngu/6k_data/Box_Chains_new/0057_6gsm/0057_6gsm_V.mrc
Opened 0057_6gsm_V.mrc as #2, grid size 88,80,88, pixel 1, shown at level
0.136, step 1, values float32
> fitmap #1 inMap #2
Fit molecule 0057_6gsm_V.cif (#1) to map 0057_6gsm_V.mrc (#2) using 11207
atoms
average map value = 0.07645, steps = 64
shifted from previous position = 0.297
rotated from previous position = 0.0534 degrees
atoms outside contour = 10696, contour level = 0.13618
Position of 0057_6gsm_V.cif (#1) relative to 0057_6gsm_V.mrc (#2) coordinates:
Matrix rotation and translation
0.99999976 0.00068120 0.00013990 -0.12701812
-0.00068128 0.99999958 0.00061921 -0.23698402
-0.00013948 -0.00061930 0.99999980 -0.01443814
Axis -0.66502858 0.15001438 -0.73159598
Axis point -361.02664137 128.26419762 0.00000000
Rotation angle (degrees) 0.05335215
Shift along axis 0.05948255
> save /scratch/cs-
> bioinfo/tngu/6k_data/Box_Chains_new/0057_6gsm/0057_6gsm_V_fitted.cif #1
> close #1
> close #2
> open /scratch/cs-
> bioinfo/tngu/6k_data/Box_Chains_new/0057_6gsm/0057_6gsm_A.cif
Summary of feedback from opening /scratch/cs-
bioinfo/tngu/6k_data/Box_Chains_new/0057_6gsm/0057_6gsm_A.cif
---
warnings | Invalid residue range for struct_conf "HELX27": invalid chain "H",
near line 45546
Invalid residue range for struct_conf "HELX28": invalid chain "H", near line
45547
Invalid residue range for struct_conf "HELX29": invalid chain "H", near line
45548
Invalid residue range for struct_conf "HELX30": invalid chain "H", near line
45549
Invalid residue range for struct_conf "HELX31": invalid chain "H", near line
45550
84 messages similar to the above omitted
Invalid sheet range for struct_sheet_range "? 32": invalid chain "H", near
line 45804
Invalid sheet range for struct_sheet_range "? 33": invalid chain "H", near
line 45805
Invalid sheet range for struct_sheet_range "? 34": invalid chain "H", near
line 45806
Invalid sheet range for struct_sheet_range "? 35": invalid chain "H", near
line 45807
Invalid sheet range for struct_sheet_range "? 36": invalid chain "H", near
line 45808
149 messages similar to the above omitted
Atom OP1 has no neighbors to form bonds with according to residue template for
A /2:11
Atom O4' has no neighbors to form bonds with according to residue template for
G /2:371
Atom OP1 has no neighbors to form bonds with according to residue template for
A /2:604
Atom O3' has no neighbors to form bonds with according to residue template for
A /2:604
Atom O2' has no neighbors to form bonds with according to residue template for
A /2:604
Atom OP1 has no neighbors to form bonds with according to residue template for
G /2:606
Atom O6 has no neighbors to form bonds with according to residue template for
G /2:612
Atom C5' has no neighbors to form bonds with according to residue template for
C /2:613
Atom O3' has no neighbors to form bonds with according to residue template for
C /2:613
Atom OP1 has no neighbors to form bonds with according to residue template for
G /2:633
Atom O2' has no neighbors to form bonds with according to residue template for
G /2:633
Atom C5' has no neighbors to form bonds with according to residue template for
A /2:635
Atom O4' has no neighbors to form bonds with according to residue template for
A /2:635
Atom N7 has no neighbors to form bonds with according to residue template for
G /2:865
Atom O6 has no neighbors to form bonds with according to residue template for
G /2:865
Atom N6 has no neighbors to form bonds with according to residue template for
A /2:868
Atom N1 has no neighbors to form bonds with according to residue template for
A /2:868
Atom O2' has no neighbors to form bonds with according to residue template for
G /2:870
Atom O3' has no neighbors to form bonds with according to residue template for
A /2:932
Atom O2' has no neighbors to form bonds with according to residue template for
A /2:932
Atom OP2 has no neighbors to form bonds with according to residue template for
C /2:961
Atom N4 has no neighbors to form bonds with according to residue template for
C /2:961
Atom OP2 has no neighbors to form bonds with according to residue template for
C /2:1074
Atom OP2 has no neighbors to form bonds with according to residue template for
A /2:1075
Atom O3' has no neighbors to form bonds with according to residue template for
A /2:1141
Atom O2' has no neighbors to form bonds with according to residue template for
A /2:1151
Atom OP2 has no neighbors to form bonds with according to residue template for
C /2:1160
Atom O3' has no neighbors to form bonds with according to residue template for
C /2:1191
Atom O4' has no neighbors to form bonds with according to residue template for
C /2:1196
Atom O4' has no neighbors to form bonds with according to residue template for
U /2:1334
Atom O2' has no neighbors to form bonds with according to residue template for
G /2:1381
Atom O3' has no neighbors to form bonds with according to residue template for
G /2:1410
Atom O2' has no neighbors to form bonds with according to residue template for
G /2:1410
Atom OP1 has no neighbors to form bonds with according to residue template for
U /2:1411
Atom C3' has no neighbors to form bonds with according to residue template for
G /2:1414
Atom OP2 has no neighbors to form bonds with according to residue template for
G /2:1426
Atom OP1 has no neighbors to form bonds with according to residue template for
C /2:1794
Atom C5' has no neighbors to form bonds with according to residue template for
C /2:1794
Atom CB has no neighbors to form bonds with according to residue template for
ASP /B:78
Atom OD2 has no neighbors to form bonds with according to residue template for
ASP /B:78
Atom O has no neighbors to form bonds with according to residue template for
LYS /B:195
Atom CG1 has no neighbors to form bonds with according to residue template for
VAL /D:126
Atom OE1 has no neighbors to form bonds with according to residue template for
GLU /D:128
Atom N has no neighbors to form bonds with according to residue template for
GLU /D:169
Atom O has no neighbors to form bonds with according to residue template for
GLU /D:169
Atom CB has no neighbors to form bonds with according to residue template for
GLU /H:134
Atom N has no neighbors to form bonds with according to residue template for
GLN /H:160
Atom CG1 has no neighbors to form bonds with according to residue template for
VAL /H:182
Atom CG2 has no neighbors to form bonds with according to residue template for
VAL /H:182
Atom N has no neighbors to form bonds with according to residue template for
LEU /J:24
Atom N has no neighbors to form bonds with according to residue template for
VAL /J:101
Atom CB has no neighbors to form bonds with according to residue template for
LYS /N:9
Atom C has no neighbors to form bonds with according to residue template for
GLN /N:36
Atom CE2 has no neighbors to form bonds with according to residue template for
TYR /N:40
Atom OH has no neighbors to form bonds with according to residue template for
TYR /N:40
Atom N has no neighbors to form bonds with according to residue template for
THR /U:70
Atom N has no neighbors to form bonds with according to residue template for
ASN /V:3
Atom CB has no neighbors to form bonds with according to residue template for
ASN /V:3
Atom N has no neighbors to form bonds with according to residue template for
GLN /W:98
Atom N has no neighbors to form bonds with according to residue template for
TYR /a:62
Atom O has no neighbors to form bonds with according to residue template for
TYR /a:62
Atom OG1 has no neighbors to form bonds with according to residue template for
THR /b:52
Atom O has no neighbors to form bonds with according to residue template for
THR /b:55
Atom C has no neighbors to form bonds with according to residue template for
VAL /b:62
Atom CG2 has no neighbors to form bonds with according to residue template for
ILE /c:13
Atom O has no neighbors to form bonds with according to residue template for
ARG /c:64
Atom O has no neighbors to form bonds with according to residue template for
GLN /g:70
Atom N has no neighbors to form bonds with according to residue template for
ASP /g:87
Atom C has no neighbors to form bonds with according to residue template for
ASP /g:87
Atom NE1 has no neighbors to form bonds with according to residue template for
TRP /g:135
Atom CZ2 has no neighbors to form bonds with according to residue template for
TRP /g:135
Atom O has no neighbors to form bonds with according to residue template for
PRO /g:283
Atom ND2 has no neighbors to form bonds with according to residue template for
ASN /o:10
Atom N has no neighbors to form bonds with according to residue template for
LEU /o:56
Atom N has no neighbors to form bonds with according to residue template for
LYS /o:95
Atom O has no neighbors to form bonds with according to residue template for
GLU /o:204
Atom OE2 has no neighbors to form bonds with according to residue template for
GLU /o:204
Atom O has no neighbors to form bonds with according to residue template for
ASP /o:262
Atom OD1 has no neighbors to form bonds with according to residue template for
ASP /o:262
Atom N has no neighbors to form bonds with according to residue template for
ASP /q:599
Atom OD2 has no neighbors to form bonds with according to residue template for
ASP /q:599
Chain information for 0057_6gsm_A.cif #1
---
Chain | Description
2 | 18S ribosomal RNA
A | 40S ribosomal protein S0
B | 40S ribosomal protein S1
C | KLLA0F09812p
D | KLLA0D08305p
H | 40S ribosomal protein S7
J | KLLA0E23673p
N | KLLA0F18040p
Q | 40S ribosomal protein S16
R | KLLA0B01474p
U | KLLA0F25542p
V | 40S ribosomal protein S21
W | 40S ribosomal protein S22
X | KLLA0B11231p
a | 40S ribosomal protein S26
b | 40S ribosomal protein S27
c | 40S ribosomal protein S28
d | 40S ribosomal protein S29
g | KLLA0E12277p
o | Eukaryotic translation initiation factor 3 subunit A,Eukaryotic
translation initiation factor 3 subunit A,eIF3a
q | Eukaryotic translation initiation factor 3 subunit C
> open /scratch/cs-
> bioinfo/tngu/6k_data/Box_Chains_new/0057_6gsm/0057_6gsm_A.mrc
Opened 0057_6gsm_A.mrc as #2, grid size 88,88,104, pixel 1, shown at level
0.131, step 1, values float32
> fitmap #1 inMap #2
Fit molecule 0057_6gsm_A.cif (#1) to map 0057_6gsm_A.mrc (#2) using 14494
atoms
average map value = 0.07084, steps = 76
shifted from previous position = 0.352
rotated from previous position = 0.118 degrees
atoms outside contour = 13791, contour level = 0.13132
Position of 0057_6gsm_A.cif (#1) relative to 0057_6gsm_A.mrc (#2) coordinates:
Matrix rotation and translation
0.99999821 -0.00143912 0.00122460 0.07260505
0.00143809 0.99999861 0.00083845 -0.68512420
-0.00122581 -0.00083669 0.99999890 0.13899326
Axis -0.40522153 0.59276321 0.69600811
Axis point 336.72037114 -45.36388925 -0.00000000
Rotation angle (degrees) 0.11842687
Shift along axis -0.33879711
> save /scratch/cs-
> bioinfo/tngu/6k_data/Box_Chains_new/0057_6gsm/0057_6gsm_A_fitted.cif #1
> close #1
> close #2
> open /scratch/cs-
> bioinfo/tngu/6k_data/Box_Chains_new/0057_6gsm/0057_6gsm_D.cif
Summary of feedback from opening /scratch/cs-
bioinfo/tngu/6k_data/Box_Chains_new/0057_6gsm/0057_6gsm_D.cif
---
warnings | Invalid residue range for struct_conf "HELX27": invalid chain "H",
near line 58128
Invalid residue range for struct_conf "HELX28": invalid chain "H", near line
58129
Invalid residue range for struct_conf "HELX29": invalid chain "H", near line
58130
Invalid residue range for struct_conf "HELX30": invalid chain "H", near line
58131
Invalid residue range for struct_conf "HELX31": invalid chain "H", near line
58132
113 messages similar to the above omitted
Invalid sheet range for struct_sheet_range "? 32": invalid chain "H", near
line 58386
Invalid sheet range for struct_sheet_range "? 33": invalid chain "H", near
line 58387
Invalid sheet range for struct_sheet_range "? 34": invalid chain "H", near
line 58388
Invalid sheet range for struct_sheet_range "? 35": invalid chain "H", near
line 58389
Invalid sheet range for struct_sheet_range "? 36": invalid chain "H", near
line 58390
127 messages similar to the above omitted
Atom O2' has no neighbors to form bonds with according to residue template for
C /1:39
Atom O2 has no neighbors to form bonds with according to residue template for
C /1:39
Atom O2' has no neighbors to form bonds with according to residue template for
C /1:40
Atom O2 has no neighbors to form bonds with according to residue template for
C /1:40
Atom O2' has no neighbors to form bonds with according to residue template for
C /1:41
Atom OP2 has no neighbors to form bonds with according to residue template for
C /2:488
Atom N7 has no neighbors to form bonds with according to residue template for
A /2:505
Atom OP2 has no neighbors to form bonds with according to residue template for
G /2:935
Atom C2' has no neighbors to form bonds with according to residue template for
G /2:937
Atom OP1 has no neighbors to form bonds with according to residue template for
C /2:1033
Atom OP2 has no neighbors to form bonds with according to residue template for
C /2:1033
Atom O3' has no neighbors to form bonds with according to residue template for
G /2:1072
Atom OP1 has no neighbors to form bonds with according to residue template for
G /2:1107
Atom C5' has no neighbors to form bonds with according to residue template for
G /2:1107
Atom OP2 has no neighbors to form bonds with according to residue template for
C /2:1179
Atom OP1 has no neighbors to form bonds with according to residue template for
A /2:1182
Atom O5' has no neighbors to form bonds with according to residue template for
A /2:1182
Atom O3' has no neighbors to form bonds with according to residue template for
G /2:1228
Atom O2' has no neighbors to form bonds with according to residue template for
G /2:1228
Atom O2' has no neighbors to form bonds with according to residue template for
U /2:1252
Atom O2' has no neighbors to form bonds with according to residue template for
G /2:1350
Atom OP2 has no neighbors to form bonds with according to residue template for
A /2:1371
Atom O3' has no neighbors to form bonds with according to residue template for
A /2:1469
Atom O2' has no neighbors to form bonds with according to residue template for
A /2:1469
Atom O2' has no neighbors to form bonds with according to residue template for
A /2:1503
Atom OP1 has no neighbors to form bonds with according to residue template for
U /2:1506
Atom OP2 has no neighbors to form bonds with according to residue template for
U /2:1506
Atom OP2 has no neighbors to form bonds with according to residue template for
U /2:1508
Atom O2' has no neighbors to form bonds with according to residue template for
G /2:1538
Atom N3 has no neighbors to form bonds with according to residue template for
G /2:1539
Atom N4 has no neighbors to form bonds with according to residue template for
C /2:1561
Atom C5 has no neighbors to form bonds with according to residue template for
C /2:1561
Atom O2 has no neighbors to form bonds with according to residue template for
C /2:1771
Atom N has no neighbors to form bonds with according to residue template for
SER /A:2
Atom N has no neighbors to form bonds with according to residue template for
THR /A:10
Atom C has no neighbors to form bonds with according to residue template for
GLU /A:12
Atom N has no neighbors to form bonds with according to residue template for
LYS /A:27
Atom CB has no neighbors to form bonds with according to residue template for
LYS /A:27
Atom N has no neighbors to form bonds with according to residue template for
VAL /A:37
Atom CG1 has no neighbors to form bonds with according to residue template for
VAL /A:37
Atom OP2 has no neighbors to form bonds with according to residue template for
U /3:30
Atom O5' has no neighbors to form bonds with according to residue template for
U /3:30
Atom N has no neighbors to form bonds with according to residue template for
LEU /C:63
Atom ND1 has no neighbors to form bonds with according to residue template for
HIS /C:115
Atom N has no neighbors to form bonds with according to residue template for
SER /C:171
Atom OG has no neighbors to form bonds with according to residue template for
SER /C:171
Atom N has no neighbors to form bonds with according to residue template for
LYS /F:111
Atom CB has no neighbors to form bonds with according to residue template for
LYS /F:111
Atom N has no neighbors to form bonds with according to residue template for
THR /F:209
Atom N has no neighbors to form bonds with according to residue template for
ASP /M:32
Atom NH2 has no neighbors to form bonds with according to residue template for
ARG /M:104
Atom CB has no neighbors to form bonds with according to residue template for
LYS /M:105
Atom N has no neighbors to form bonds with according to residue template for
ALA /O:59
Atom C has no neighbors to form bonds with according to residue template for
ALA /O:59
Atom N has no neighbors to form bonds with according to residue template for
ALA /O:64
Atom CB has no neighbors to form bonds with according to residue template for
ALA /O:64
Atom N has no neighbors to form bonds with according to residue template for
GLN /O:65
Atom O has no neighbors to form bonds with according to residue template for
ARG /O:132
Atom NH2 has no neighbors to form bonds with according to residue template for
ARG /O:132
Atom O has no neighbors to form bonds with according to residue template for
ARG /O:135
Atom NH1 has no neighbors to form bonds with according to residue template for
ARG /O:135
Atom N has no neighbors to form bonds with according to residue template for
SER /P:66
Atom O has no neighbors to form bonds with according to residue template for
SER /P:92
Atom O has no neighbors to form bonds with according to residue template for
ASN /P:103
Atom CG1 has no neighbors to form bonds with according to residue template for
VAL /P:112
Atom OG1 has no neighbors to form bonds with according to residue template for
THR /Q:3
Atom CG2 has no neighbors to form bonds with according to residue template for
THR /Q:3
Atom N has no neighbors to form bonds with according to residue template for
HIS /Q:21
Atom O has no neighbors to form bonds with according to residue template for
LYS /Q:47
Atom C has no neighbors to form bonds with according to residue template for
GLU /Q:50
Atom CD2 has no neighbors to form bonds with according to residue template for
LEU /S:131
Atom CD has no neighbors to form bonds with according to residue template for
LYS /T:84
Atom NZ has no neighbors to form bonds with according to residue template for
LYS /T:84
Atom OE2 has no neighbors to form bonds with according to residue template for
GLU /V:49
Atom N has no neighbors to form bonds with according to residue template for
LEU /V:72
Atom C has no neighbors to form bonds with according to residue template for
LEU /V:72
Atom N has no neighbors to form bonds with according to residue template for
GLN /V:74
Atom N has no neighbors to form bonds with according to residue template for
SER /V:84
Atom O has no neighbors to form bonds with according to residue template for
SER /X:66
Atom O has no neighbors to form bonds with according to residue template for
LYS /X:112
Atom O has no neighbors to form bonds with according to residue template for
TRP /X:136
Atom N has no neighbors to form bonds with according to residue template for
ASN /a:43
Atom O has no neighbors to form bonds with according to residue template for
ASN /a:43
Atom CB has no neighbors to form bonds with according to residue template for
ARG /a:51
Atom NH1 has no neighbors to form bonds with according to residue template for
ARG /c:38
Atom O has no neighbors to form bonds with according to residue template for
ASN /e:46
Atom O has no neighbors to form bonds with according to residue template for
LYS /i:64
Atom CE1 has no neighbors to form bonds with according to residue template for
TYR /j:13
Atom OH has no neighbors to form bonds with according to residue template for
TYR /j:13
Atom N has no neighbors to form bonds with according to residue template for
LEU /j:51
Atom CD1 has no neighbors to form bonds with according to residue template for
LEU /j:51
Atom N has no neighbors to form bonds with according to residue template for
LEU /j:85
Atom O has no neighbors to form bonds with according to residue template for
LEU /j:85
Chain information for 0057_6gsm_D.cif #1
---
Chain | Description
1 | Met-tRNAi
2 | 18S ribosomal RNA
3 | mRNA (5'-R(P*AP*AP*U)-3')
A | 40S ribosomal protein S0
B | 40S ribosomal protein S1
C | KLLA0F09812p
D | KLLA0D08305p
F | KLLA0D10659p
K | KLLA0B08173p
M | 40S ribosomal protein S12
N | KLLA0F18040p
O | 40S ribosomal protein S14
P | KLLA0F07843p
Q | 40S ribosomal protein S16
R | KLLA0B01474p
S | KLLA0B01562p
T | KLLA0A07194p
U | KLLA0F25542p
V | 40S ribosomal protein S21
W | 40S ribosomal protein S22
X | KLLA0B11231p
a | 40S ribosomal protein S26
b | 40S ribosomal protein S27
c | 40S ribosomal protein S28
d | 40S ribosomal protein S29
e | 40S ribosomal protein S30
f | Ubiquitin-40S ribosomal protein S27a
g | KLLA0E12277p
i | Eukaryotic translation initiation factor 1A
j | Eukaryotic translation initiation factor 2 subunit alpha
> open /scratch/cs-
> bioinfo/tngu/6k_data/Box_Chains_new/0057_6gsm/0057_6gsm_D.mrc
Opened 0057_6gsm_D.mrc as #2, grid size 128,96,128, pixel 1, shown at level
0.13, step 1, values float32
> fitmap #1 inMap #2
Fit molecule 0057_6gsm_D.cif (#1) to map 0057_6gsm_D.mrc (#2) using 26755
atoms
average map value = 0.07567, steps = 60
shifted from previous position = 0.287
rotated from previous position = 0.0358 degrees
atoms outside contour = 25381, contour level = 0.13032
Position of 0057_6gsm_D.cif (#1) relative to 0057_6gsm_D.mrc (#2) coordinates:
Matrix rotation and translation
0.99999997 0.00024737 -0.00006156 -0.14997849
-0.00024741 0.99999981 -0.00057026 -0.03289269
0.00006142 0.00057028 0.99999984 -0.29491317
Axis 0.91294090 -0.09843458 -0.39604236
Axis point 0.00000000 528.85055684 -60.77398035
Rotation angle (degrees) 0.03578978
Shift along axis -0.01688561
> save /scratch/cs-
> bioinfo/tngu/6k_data/Box_Chains_new/0057_6gsm/0057_6gsm_D_fitted.cif #1
> close #1
> close #2
> open /scratch/cs-
> bioinfo/tngu/6k_data/Box_Chains_new/0057_6gsm/0057_6gsm_N.cif
Summary of feedback from opening /scratch/cs-
bioinfo/tngu/6k_data/Box_Chains_new/0057_6gsm/0057_6gsm_N.cif
---
warnings | Invalid residue range for struct_conf "HELX21": invalid chain "G",
near line 48034
Invalid residue range for struct_conf "HELX22": invalid chain "G", near line
48035
Invalid residue range for struct_conf "HELX23": invalid chain "G", near line
48036
Invalid residue range for struct_conf "HELX24": invalid chain "G", near line
48037
Invalid residue range for struct_conf "HELX25": invalid chain "G", near line
48038
91 messages similar to the above omitted
Invalid sheet range for struct_sheet_range "? 25": invalid chain "G", near
line 48291
Invalid sheet range for struct_sheet_range "? 26": invalid chain "G", near
line 48292
Invalid sheet range for struct_sheet_range "? 27": invalid chain "G", near
line 48293
Invalid sheet range for struct_sheet_range "? 28": invalid chain "G", near
line 48294
Invalid sheet range for struct_sheet_range "? 29": invalid chain "G", near
line 48295
137 messages similar to the above omitted
Atom O3' has no neighbors to form bonds with according to residue template for
U /2:111
Atom OP1 has no neighbors to form bonds with according to residue template for
U /2:302
Atom O2' has no neighbors to form bonds with according to residue template for
U /2:334
Atom O3' has no neighbors to form bonds with according to residue template for
U /2:610
Atom O2' has no neighbors to form bonds with according to residue template for
U /2:610
Atom O2 has no neighbors to form bonds with according to residue template for
U /2:648
Atom OP1 has no neighbors to form bonds with according to residue template for
U /2:682
Atom OP2 has no neighbors to form bonds with according to residue template for
U /2:682
Atom O3' has no neighbors to form bonds with according to residue template for
U /2:682
Atom OP1 has no neighbors to form bonds with according to residue template for
C /2:847
Atom O3' has no neighbors to form bonds with according to residue template for
C /2:847
Atom O4 has no neighbors to form bonds with according to residue template for
U /2:850
Atom C5 has no neighbors to form bonds with according to residue template for
U /2:850
Atom OP2 has no neighbors to form bonds with according to residue template for
C /2:851
Atom O3' has no neighbors to form bonds with according to residue template for
C /2:851
Atom N4 has no neighbors to form bonds with according to residue template for
C /2:851
Atom C5 has no neighbors to form bonds with according to residue template for
C /2:851
Atom N7 has no neighbors to form bonds with according to residue template for
A /2:929
Atom N6 has no neighbors to form bonds with according to residue template for
A /2:929
Atom OP2 has no neighbors to form bonds with according to residue template for
C /2:930
Atom C8 has no neighbors to form bonds with according to residue template for
G /2:993
Atom O2' has no neighbors to form bonds with according to residue template for
G /2:1084
Atom OP2 has no neighbors to form bonds with according to residue template for
A /2:1087
Atom N7 has no neighbors to form bonds with according to residue template for
G /2:1106
Atom O4' has no neighbors to form bonds with according to residue template for
G /2:1129
Atom C5' has no neighbors to form bonds with according to residue template for
G /2:1627
Atom OP1 has no neighbors to form bonds with according to residue template for
A /2:1764
Atom OP2 has no neighbors to form bonds with according to residue template for
A /2:1764
Atom C5' has no neighbors to form bonds with according to residue template for
A /2:1764
Atom O4' has no neighbors to form bonds with according to residue template for
U /2:1777
Atom N3 has no neighbors to form bonds with according to residue template for
C /2:1781
Atom N4 has no neighbors to form bonds with according to residue template for
C /2:1781
Atom N has no neighbors to form bonds with according to residue template for
VAL /A:50
Atom CG1 has no neighbors to form bonds with according to residue template for
VAL /A:50
Atom N has no neighbors to form bonds with according to residue template for
THR /A:80
Atom C has no neighbors to form bonds with according to residue template for
THR /A:80
Atom NH1 has no neighbors to form bonds with according to residue template for
ARG /A:101
Atom CB has no neighbors to form bonds with according to residue template for
PRO /A:118
Atom OE1 has no neighbors to form bonds with according to residue template for
GLU /A:135
Atom CD2 has no neighbors to form bonds with according to residue template for
HIS /A:168
Atom NE1 has no neighbors to form bonds with according to residue template for
TRP /A:174
Atom CZ2 has no neighbors to form bonds with according to residue template for
TRP /A:174
Atom O has no neighbors to form bonds with according to residue template for
PRO /C:232
Atom CD has no neighbors to form bonds with according to residue template for
ARG /H:88
Atom N has no neighbors to form bonds with according to residue template for
THR /L:6
Atom O has no neighbors to form bonds with according to residue template for
LYS /L:57
Atom NH1 has no neighbors to form bonds with according to residue template for
ARG /L:67
Atom N has no neighbors to form bonds with according to residue template for
VAL /L:94
Atom CG2 has no neighbors to form bonds with according to residue template for
VAL /L:94
Atom O has no neighbors to form bonds with according to residue template for
TYR /L:97
Atom CB has no neighbors to form bonds with according to residue template for
TYR /L:97
Atom CG1 has no neighbors to form bonds with according to residue template for
ILE /V:23
Atom N has no neighbors to form bonds with according to residue template for
ILE /V:24
Atom N has no neighbors to form bonds with according to residue template for
GLN /V:74
Atom ND2 has no neighbors to form bonds with according to residue template for
ASN /V:81
Atom N has no neighbors to form bonds with according to residue template for
HIS /W:117
Atom C has no neighbors to form bonds with according to residue template for
HIS /W:117
Atom N has no neighbors to form bonds with according to residue template for
ARG /X:16
Atom CB has no neighbors to form bonds with according to residue template for
ARG /X:16
Atom N has no neighbors to form bonds with according to residue template for
LYS /h:16
Atom CG has no neighbors to form bonds with according to residue template for
LYS /h:16
Atom N has no neighbors to form bonds with according to residue template for
SER /p:89
Atom OG has no neighbors to form bonds with according to residue template for
SER /p:89
Atom N has no neighbors to form bonds with according to residue template for
LEU /q:329
Atom CG2 has no neighbors to form bonds with according to residue template for
ILE /q:408
Atom N has no neighbors to form bonds with according to residue template for
ILE /q:503
Atom CG1 has no neighbors to form bonds with according to residue template for
VAL /q:546
Atom CG2 has no neighbors to form bonds with according to residue template for
VAL /q:546
Atom CG2 has no neighbors to form bonds with according to residue template for
ILE /q:566
Atom O has no neighbors to form bonds with according to residue template for
LEU /q:567
Atom C has no neighbors to form bonds with according to residue template for
THR /q:670
Atom CG2 has no neighbors to form bonds with according to residue template for
THR /q:670
Atom N has no neighbors to form bonds with according to residue template for
ARG /q:672
Atom NH2 has no neighbors to form bonds with according to residue template for
ARG /q:672
Chain information for 0057_6gsm_N.cif #1
---
Chain | Description
2 | 18S ribosomal RNA
A | 40S ribosomal protein S0
B | 40S ribosomal protein S1
C | KLLA0F09812p
E | 40S ribosomal protein S4
H | 40S ribosomal protein S7
I | 40S ribosomal protein S8
L | KLLA0A10483p
N | KLLA0F18040p
O | 40S ribosomal protein S14
R | KLLA0B01474p
V | 40S ribosomal protein S21
W | 40S ribosomal protein S22
X | KLLA0B11231p
a | 40S ribosomal protein S26
b | 40S ribosomal protein S27
h | 60S ribosomal protein L41-A
o | Eukaryotic translation initiation factor 3 subunit A,Eukaryotic
translation initiation factor 3 subunit A,eIF3a
p | Eukaryotic translation initiation factor 3 subunit B
q | Eukaryotic translation initiation factor 3 subunit C
> open /scratch/cs-
> bioinfo/tngu/6k_data/Box_Chains_new/0057_6gsm/0057_6gsm_N.mrc
Opened 0057_6gsm_N.mrc as #2, grid size 96,88,88, pixel 1, shown at level
0.146, step 1, values float32
> fitmap #1 inMap #2
Fit molecule 0057_6gsm_N.cif (#1) to map 0057_6gsm_N.mrc (#2) using 16843
atoms
average map value = 0.07727, steps = 56
shifted from previous position = 0.537
rotated from previous position = 0.0952 degrees
atoms outside contour = 16191, contour level = 0.14631
Position of 0057_6gsm_N.cif (#1) relative to 0057_6gsm_N.mrc (#2) coordinates:
Matrix rotation and translation
0.99999868 0.00059240 -0.00150967 -0.02680054
-0.00059186 0.99999976 0.00036035 -0.23872813
0.00150989 -0.00035945 0.99999880 -0.60628094
Axis -0.21665054 -0.90884921 -0.35644867
Axis point 297.96676729 0.00000000 44.97111143
Rotation angle (degrees) 0.09517979
Shift along axis 0.43888226
> save /scratch/cs-
> bioinfo/tngu/6k_data/Box_Chains_new/0057_6gsm/0057_6gsm_N_fitted.cif #1
> close #1
> close #2
> open /scratch/cs-
> bioinfo/tngu/6k_data/Box_Chains_new/0057_6gsm/0057_6gsm_O.cif
===== Log before crash end =====
Log:
UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
OpenGL version: 4.5 (Core Profile) Mesa 22.3.0
OpenGL renderer: llvmpipe (LLVM 15.0.0, 256 bits)
OpenGL vendor: Mesa/X.org
Python: 3.9.11
Locale: en_US.UTF-8
Qt version: PyQt6 6.4.2, Qt 6.4.2
Qt runtime version: 6.4.3
Qt platform: xcb
XDG_SESSION_TYPE=x11
DESKTOP_SESSION=xfce
XDG_SESSION_DESKTOP=
XDG_CURRENT_DESKTOP=XFCE
DISPLAY=wahab-01:1006.0
Manufacturer: Dell Inc.
Model: PowerEdge C6420
OS: Rocky Linux 8.8 Green Obsidian
Architecture: 64bit
Virtual Machine: none
CPU: 40 Intel(R) Xeon(R) Gold 6148 CPU @ 2.40GHz
Cache Size: 28160 KB
Memory:
MemTotal: 394830924 kB
MemFree: 286321508 kB
MemAvailable: 383571180 kB
Graphics:
unknown
Installed Packages:
alabaster: 0.7.13
appdirs: 1.4.4
asttokens: 2.2.1
Babel: 2.12.1
backcall: 0.2.0
beautifulsoup4: 4.11.2
blockdiag: 3.0.0
build: 0.10.0
certifi: 2023.5.7
cftime: 1.6.2
charset-normalizer: 3.1.0
ChimeraX-AddCharge: 1.5.9.1
ChimeraX-AddH: 2.2.5
ChimeraX-AlignmentAlgorithms: 2.0.1
ChimeraX-AlignmentHdrs: 3.3.1
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.9.3
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.0.3
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.43.10
ChimeraX-AtomicLibrary: 10.0.6
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.3.2
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.1.2
ChimeraX-BondRot: 2.0.1
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.8
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.2.2
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.3.2
ChimeraX-ChangeChains: 1.0.2
ChimeraX-CheckWaters: 1.3.1
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.2.4
ChimeraX-ColorActions: 1.0.3
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.3
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.6.1
ChimeraX-CoreFormats: 1.1
ChimeraX-coulombic: 1.4.2
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2
ChimeraX-DistMonitor: 1.4
ChimeraX-DockPrep: 1.1.1
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ESMFold: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.3
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.1.1
ChimeraX-Hbonds: 2.4
ChimeraX-Help: 1.2.1
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-Label: 1.1.7
ChimeraX-LinuxSupport: 1.0.1
ChimeraX-ListInfo: 1.1.1
ChimeraX-Log: 1.1.5
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.8.2
ChimeraX-Map: 1.1.4
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0.1
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.2
ChimeraX-MatchMaker: 2.0.12
ChimeraX-MDcrds: 2.6
ChimeraX-MedicalToolbar: 1.0.2
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.12
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.9
ChimeraX-ModelPanel: 1.3.7
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.0
ChimeraX-NRRD: 1.0
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.10.1
ChimeraX-PDB: 2.7.2
ChimeraX-PDBBio: 1.0
ChimeraX-PDBLibrary: 1.0.2
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1
ChimeraX-PubChem: 2.1
ChimeraX-QScore: 1.0
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.1
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.1
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 3.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.1
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.8.3
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.1.1
ChimeraX-ShowSequences: 1.0.1
ChimeraX-SideView: 1.0.1
ChimeraX-Smiles: 2.1
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.10.3
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.1.2
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.2.1
ChimeraX-TapeMeasure: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1.2
ChimeraX-ToolshedUtils: 1.2.1
ChimeraX-Topography: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.28.4
ChimeraX-uniprot: 2.2.2
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.2
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.1
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.1.3
contourpy: 1.0.7
cxservices: 1.2.2
cycler: 0.11.0
Cython: 0.29.33
debugpy: 1.6.7
decorator: 5.1.1
distro: 1.7.0
docutils: 0.19
executing: 1.2.0
filelock: 3.9.0
fonttools: 4.39.3
funcparserlib: 1.0.1
grako: 3.16.5
h5py: 3.8.0
html2text: 2020.1.16
idna: 3.4
ihm: 0.35
imagecodecs: 2022.9.26
imagesize: 1.4.1
importlib-metadata: 6.6.0
ipykernel: 6.21.1
ipython: 8.10.0
ipython-genutils: 0.2.0
ipywidgets: 8.0.6
jedi: 0.18.2
Jinja2: 3.1.2
jupyter-client: 8.0.2
jupyter-core: 5.3.0
jupyterlab-widgets: 3.0.7
kiwisolver: 1.4.4
line-profiler: 4.0.2
lxml: 4.9.2
lz4: 4.3.2
MarkupSafe: 2.1.2
matplotlib: 3.6.3
matplotlib-inline: 0.1.6
msgpack: 1.0.4
nest-asyncio: 1.5.6
netCDF4: 1.6.2
networkx: 2.8.8
nibabel: 5.0.1
nptyping: 2.5.0
numexpr: 2.8.4
numpy: 1.23.5
openvr: 1.23.701
packaging: 23.1
ParmEd: 3.4.3
parso: 0.8.3
pep517: 0.13.0
pexpect: 4.8.0
pickleshare: 0.7.5
Pillow: 9.3.0
pip: 23.0
pkginfo: 1.9.6
platformdirs: 3.5.0
prompt-toolkit: 3.0.38
psutil: 5.9.4
ptyprocess: 0.7.0
pure-eval: 0.2.2
pycollada: 0.7.2
pydicom: 2.3.0
Pygments: 2.14.0
pynrrd: 1.0.0
PyOpenGL: 3.1.5
PyOpenGL-accelerate: 3.1.5
pyparsing: 3.0.9
pyproject-hooks: 1.0.0
PyQt6-commercial: 6.4.2
PyQt6-Qt6: 6.4.3
PyQt6-sip: 13.4.1
PyQt6-WebEngine-commercial: 6.4.0
PyQt6-WebEngine-Qt6: 6.4.3
python-dateutil: 2.8.2
pytz: 2023.3
pyzmq: 25.0.2
qtconsole: 5.4.0
QtPy: 2.3.1
RandomWords: 0.4.0
requests: 2.28.2
scipy: 1.9.3
setuptools: 67.4.0
sfftk-rw: 0.7.3
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.4.1
sphinx: 6.1.3
sphinx-autodoc-typehints: 1.22
sphinxcontrib-applehelp: 1.0.4
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.2
sphinxcontrib-htmlhelp: 2.0.1
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.3
sphinxcontrib-serializinghtml: 1.1.5
stack-data: 0.6.2
tables: 3.7.0
tcia-utils: 1.2.0
tifffile: 2022.10.10
tinyarray: 1.2.4
tomli: 2.0.1
torch: 1.13.1+cu117
torchaudio: 0.13.1+cu117
torchvision: 0.14.1+cu117
tornado: 6.3.1
traitlets: 5.9.0
typing-extensions: 4.5.0
tzdata: 2023.3
urllib3: 1.26.15
wcwidth: 0.2.6
webcolors: 1.12
wheel: 0.38.4
wheel-filename: 1.4.1
widgetsnbextension: 4.0.7
zipp: 3.15.0
Note:
See TracTickets
for help on using tickets.
