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Opened 2 years ago
Closed 2 years ago
#10168 closed defect (fixed)
Error when no output models from Modeller
| Reported by: | Owned by: | Eric Pettersen | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Structure Prediction | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-14.1.1-arm64-arm-64bit
ChimeraX Version: 1.7rc202311150127 (2023-11-15 01:27:09 UTC)
Description
(Describe the actions that caused this problem to occur here)
Log:
UCSF ChimeraX version: 1.7rc202311150127 (2023-11-15)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open /Users/guzelminibaeva/PycharmProjects/docking-
> files/CDK6/6OQO/A/6oqo_protein.pdb
Chain information for 6oqo_protein.pdb #1
---
Chain | Description
A | No description available
> ui tool show "Show Sequence Viewer"
> sequence chain /A
Alignment identifier is 1/A
> close session
> open /Users/guzelminibaeva/PycharmProjects/docking-
> files/CDK7/8P4Z/A/8p4z_start.pdb
8p4z_start.pdb title:
Crystal structure of the human CDK7 kinase domain In complex with LDC4297
[more info...]
Chain information for 8p4z_start.pdb #1
---
Chain | Description | UniProt
A B | cyclin-dependent kinase 7 | CDK7_HUMAN 10-311
Non-standard residues in 8p4z_start.pdb #1
---
1PE — pentaethylene glycol (PEG400)
GOL — glycerol (glycerin; propane-1,2,3-triol)
PGE — triethylene glycol
WZ8 —
2-[(3R)-piperidin-3-yl]oxy-8-propan-2-yl-N-[(2-pyrazol-1-ylphenyl)methyl]pyrazolo[1,5-A][1,3,5]triazin-4-amine
> select /A
2234 atoms, 2282 bonds, 3 pseudobonds, 280 residues, 2 models selected
> select ~sel & ##selected
2324 atoms, 2350 bonds, 3 pseudobonds, 309 residues, 2 models selected
> delete atoms (#!1 & sel)
> delete bonds (#!1 & sel)
> ui tool show "Show Sequence Viewer"
> sequence chain /A
Alignment identifier is 1/A
> ui tool show "Model Loops"
> modeller refine 1/A:1:internal-missing numModels 5 fast false
> adjacentFlexible 1 protocol standard
Webservices job id: UR8FIBW3AM3VQ5H3
Modeller job (ID UR8FIBW3AM3VQ5H3) finished
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 8p4z_start.pdb, chain A (#1) with chain_A, chain A (#), sequence
alignment score = 1515.7
RMSD between 272 pruned atom pairs is 0.045 angstroms; (across all 272 pairs:
0.045)
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 8p4z_start.pdb, chain A (#1) with chain_A, chain A (#), sequence
alignment score = 1515.1
RMSD between 272 pruned atom pairs is 0.120 angstroms; (across all 272 pairs:
0.120)
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 8p4z_start.pdb, chain A (#1) with chain_A, chain A (#), sequence
alignment score = 1515.1
RMSD between 272 pruned atom pairs is 0.082 angstroms; (across all 272 pairs:
0.082)
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 8p4z_start.pdb, chain A (#1) with chain_A, chain A (#), sequence
alignment score = 1509.7
RMSD between 272 pruned atom pairs is 0.164 angstroms; (across all 272 pairs:
0.164)
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 8p4z_start.pdb, chain A (#1) with chain_A, chain A (#), sequence
alignment score = 1515.7
RMSD between 272 pruned atom pairs is 0.119 angstroms; (across all 272 pairs:
0.119)
Associated chain_A chain A to chain A with 0 mismatches
[Repeated 4 time(s)] Chain information for chain_A
---
Chain | Description
2.1/A 2.2/A 2.3/A 2.4/A 2.5/A | No description available
> hide #2.2 models
> hide #2.3 models
> hide #2.5 models
> hide #2.4 models
> show #2.2 models
> hide #2.1 models
> show #2.3 models
> hide #2.2 models
> show #2.4 models
> hide #2.3 models
> show #2.5 models
> hide #2.4 models
> show #2.2 models
> hide #2.5 models
> ui tool show "Dock Prep"
Starting dock prep
Deleting solvent
Deleting non-current alt locs
Summary of feedback from adding hydrogens to chain_A #2.2
---
notes | No usable SEQRES records for chain_A (#2.2) chain A; guessing termini
instead
Chain-initial residues that are actual N termini: chain_A #2.2/A ARG 11
Chain-initial residues that are not actual N termini:
Chain-final residues that are actual C termini: chain_A #2.2/A PRO 310
Chain-final residues that are not actual C termini:
244 hydrogen bonds
2475 hydrogens added
Dock prep finished
> select protein
16562 atoms, 16913 bonds, 3 pseudobonds, 1772 residues, 7 models selected
> save /Users/guzelminibaeva/PycharmProjects/docking-
> files/CDK7/8P4Z/A/8p4z_protein.pdb models #2.2 selectedOnly true
> select ligand
383 atoms, 389 bonds, 24 residues, 6 models selected
> select ::name="GOL"
88 atoms, 76 bonds, 12 residues, 6 models selected
> delete atoms (#2.2#!1 & sel)
> delete bonds (#2.2#!1 & sel)
> select ::name="HOH"
20 atoms, 20 residues, 5 models selected
> delete atoms (#!1 & sel)
> delete bonds (#!1 & sel)
> select ::name="PGE"
74 atoms, 68 bonds, 6 residues, 6 models selected
> select ligand
343 atoms, 353 bonds, 20 residues, 6 models selected
> select ::name="PGE"
74 atoms, 68 bonds, 6 residues, 6 models selected
> delete atoms (#2.2#!1 & sel)
> delete bonds (#2.2#!1 & sel)
> select ::name="WZ8"
221 atoms, 245 bonds, 6 residues, 6 models selected
> select ligand
309 atoms, 321 bonds, 18 residues, 6 models selected
> save /Users/guzelminibaeva/PycharmProjects/docking-
> files/CDK7/8P4Z/A/8p4z_ligand.pdb models #2.2 selectedOnly true
> close session
> open /Users/guzelminibaeva/PycharmProjects/docking-
> files/CDK16/5G6V/A/5g6v_start.pdb
5g6v_start.pdb title:
Crystal structure of the PCTAIRE1 kinase In complex with inhibitor [more
info...]
Chain information for 5g6v_start.pdb #1
---
Chain | Description | UniProt
A B | cyclin-dependent kinase 16 | CDK16_HUMAN 163-478
Non-standard residues in 5g6v_start.pdb #1
---
919 — 4-[4-({[3-tert-
butyl-1-(quinolin-6-yl)-1H-pyrazol-5-yl]carbamoyl}amino)-3-fluorophenoxy]-N-methylpyridine-2-carboxamide
(DCC-2036)
EDO — 1,2-ethanediol (ethylene glycol)
> select /A
2576 atoms, 2507 bonds, 1 pseudobond, 433 residues, 2 models selected
> delete atoms (#!1 & sel)
> delete bonds (#!1 & sel)
> close session
> open /Users/guzelminibaeva/PycharmProjects/docking-
> files/CDK16/5G6V/A/5g6v_start.pdb
5g6v_start.pdb title:
Crystal structure of the PCTAIRE1 kinase In complex with inhibitor [more
info...]
Chain information for 5g6v_start.pdb #1
---
Chain | Description | UniProt
A B | cyclin-dependent kinase 16 | CDK16_HUMAN 163-478
Non-standard residues in 5g6v_start.pdb #1
---
919 — 4-[4-({[3-tert-
butyl-1-(quinolin-6-yl)-1H-pyrazol-5-yl]carbamoyl}amino)-3-fluorophenoxy]-N-methylpyridine-2-carboxamide
(DCC-2036)
EDO — 1,2-ethanediol (ethylene glycol)
> select /A
2576 atoms, 2507 bonds, 1 pseudobond, 433 residues, 2 models selected
> select ~sel & ##selected
2596 atoms, 2510 bonds, 1 pseudobond, 445 residues, 2 models selected
> delete atoms (#!1 & sel)
> delete bonds (#!1 & sel)
> ui tool show "Show Sequence Viewer"
> sequence chain /A
Alignment identifier is 1/A
> ui tool show "Model Loops"
> modeller refine 1/A:1:internal-missing numModels 5 fast false
> adjacentFlexible 1 protocol standard
Webservices job id: FXB9600QUZRDNJM8
Modeller job (ID FXB9600QUZRDNJM8) finished
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 5g6v_start.pdb, chain A (#1) with chain_A, chain A (#), sequence
alignment score = 1612.7
RMSD between 308 pruned atom pairs is 0.016 angstroms; (across all 308 pairs:
0.016)
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 5g6v_start.pdb, chain A (#1) with chain_A, chain A (#), sequence
alignment score = 1612.7
RMSD between 308 pruned atom pairs is 0.028 angstroms; (across all 308 pairs:
0.028)
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 5g6v_start.pdb, chain A (#1) with chain_A, chain A (#), sequence
alignment score = 1612.7
RMSD between 308 pruned atom pairs is 0.010 angstroms; (across all 308 pairs:
0.010)
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 5g6v_start.pdb, chain A (#1) with chain_A, chain A (#), sequence
alignment score = 1612.7
RMSD between 308 pruned atom pairs is 0.010 angstroms; (across all 308 pairs:
0.010)
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 5g6v_start.pdb, chain A (#1) with chain_A, chain A (#), sequence
alignment score = 1612.7
RMSD between 308 pruned atom pairs is 0.083 angstroms; (across all 308 pairs:
0.083)
Associated chain_A chain A to chain A with 0 mismatches
[Repeated 4 time(s)] Chain information for chain_A
---
Chain | Description
2.1/A 2.2/A 2.3/A 2.4/A 2.5/A | No description available
> hide #2.2 models
> show #2.2 models
> hide #2.3 models
> hide #2.4 models
> hide #2.5 models
> hide #2.1 models
> hide #2.2 models
> show #2.1 models
> ui tool show "Dock Prep"
Starting dock prep
Deleting solvent
Deleting non-current alt locs
Summary of feedback from adding hydrogens to chain_A #2.1
---
notes | No usable SEQRES records for chain_A (#2.1) chain A; guessing termini
instead
Chain-initial residues that are actual N termini: chain_A #2.1/A MET 162
Chain-initial residues that are not actual N termini:
Chain-final residues that are actual C termini: chain_A #2.1/A ALA 474
Chain-final residues that are not actual C termini:
285 hydrogen bonds
2598 hydrogens added
Dock prep finished
> select protein
17628 atoms, 17954 bonds, 1 pseudobond, 1873 residues, 7 models selected
> save /Users/guzelminibaeva/PycharmProjects/docking-
> files/CDK16/5G6V/A/5g6v_protein.pdb models #2.1 selectedOnly true
> select ligand
334 atoms, 346 bonds, 18 residues, 6 models selected
> select ::name="919"
274 atoms, 298 bonds, 6 residues, 6 models selected
> select ::name="EDO"
60 atoms, 48 bonds, 12 residues, 6 models selected
> delete atoms (#2.1#!1 & sel)
> delete bonds (#2.1#!1 & sel)
> select ::name="HOH"
610 atoms, 610 residues, 5 models selected
> delete atoms (#!1 & sel)
> delete bonds (#!1 & sel)
> select ligand
306 atoms, 322 bonds, 14 residues, 6 models selected
> save /Users/guzelminibaeva/PycharmProjects/docking-
> files/CDK16/5G6V/A/5g6v_ligand.pdb selectedOnly true
> close session
> open /Users/guzelminibaeva/PycharmProjects/docking-
> files/MAPK13/5EKO/5eko_start.pdb
5eko_start.pdb title:
Crystal structure of MAPK13 complex with inhibitor [more info...]
Chain information for 5eko_start.pdb #1
---
Chain | Description | UniProt
A | mitogen-activated protein kinase 13 | MK13_HUMAN 1-352
Non-standard residues in 5eko_start.pdb #1
---
N17 — 3-(4-methyl-1H-imidazol-1-yl)-N-[4-(pyridin-4-yloxy)phenyl]benzamide
> select /A
3013 atoms, 2870 bonds, 1 pseudobond, 555 residues, 2 models selected
> select clear
> ui tool show "Show Sequence Viewer"
> sequence chain /A
Alignment identifier is 1/A
> ui tool show "Model Loops"
> modeller refine 1/A:1:internal-missing numModels 5 fast false
> adjacentFlexible 1 protocol standard
Webservices job id: Z6Y5VTRZL56KJ0IT
Modeller job (ID Z6Y5VTRZL56KJ0IT) finished
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 5eko_start.pdb, chain A (#1) with chain_A, chain A (#), sequence
alignment score = 1799
RMSD between 340 pruned atom pairs is 0.030 angstroms; (across all 341 pairs:
0.117)
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 5eko_start.pdb, chain A (#1) with chain_A, chain A (#), sequence
alignment score = 1799
RMSD between 340 pruned atom pairs is 0.018 angstroms; (across all 341 pairs:
0.116)
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 5eko_start.pdb, chain A (#1) with chain_A, chain A (#), sequence
alignment score = 1799
RMSD between 341 pruned atom pairs is 0.098 angstroms; (across all 341 pairs:
0.098)
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 5eko_start.pdb, chain A (#1) with chain_A, chain A (#), sequence
alignment score = 1799
RMSD between 340 pruned atom pairs is 0.037 angstroms; (across all 341 pairs:
0.120)
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 5eko_start.pdb, chain A (#1) with chain_A, chain A (#), sequence
alignment score = 1799
RMSD between 341 pruned atom pairs is 0.099 angstroms; (across all 341 pairs:
0.099)
Associated chain_A chain A to chain A with 0 mismatches
[Repeated 4 time(s)] Chain information for chain_A
---
Chain | Description
2.1/A 2.2/A 2.3/A 2.4/A 2.5/A | No description available
> hide #2.2 models
> hide #2.3 models
> hide #2.4 models
> show #2.4 models
> hide #2.4 models
> hide #2.5 models
> show #2.2 models
> hide #2.2 models
> ui tool show "Dock Prep"
Starting dock prep
Deleting solvent
Deleting non-current alt locs
Summary of feedback from adding hydrogens to chain_A #2.1
---
notes | No usable SEQRES records for chain_A (#2.1) chain A; guessing termini
instead
Chain-initial residues that are actual N termini: chain_A #2.1/A SER 2
Chain-initial residues that are not actual N termini:
Chain-final residues that are actual C termini: chain_A #2.1/A PRO 351
Chain-final residues that are not actual C termini:
303 hydrogen bonds
2860 hydrogens added
Dock prep finished
> select protein
19819 atoms, 20231 bonds, 1 pseudobond, 2091 residues, 7 models selected
> save /Users/guzelminibaeva/PycharmProjects/docking-
> files/MAPK13/5EKO/5eko_protein.pdb models #2.1 selectedOnly true
> select ::name="HOH"
1065 atoms, 1065 residues, 5 models selected
> delete atoms (#!1 & sel)
> delete bonds (#!1 & sel)
> select ligand
186 atoms, 204 bonds, 6 residues, 6 models selected
> save /Users/guzelminibaeva/PycharmProjects/docking-
> files/MAPK13/5EKO/5eko_ligand.pdb selectedOnly true
> close session
> open /Users/guzelminibaeva/PycharmProjects/docking-
> files/ERK5/5BYZ/A/5byz_start.pdb
5byz_start.pdb title:
ERK5 In complex with small molecule [more info...]
Chain information for 5byz_start.pdb #1
---
Chain | Description | UniProt
A | mitogen-activated protein kinase 7 | MK07_HUMAN 48-395
Non-standard residues in 5byz_start.pdb #1
---
4WE —
4-({5-fluoro-4-[2-methyl-1-(propan-2-yl)-1H-imidazol-5-yl]pyrimidin-2-yl}amino)-N-[2-(piperidin-1-yl)ethyl]benzamide
GOL — glycerol (glycerin; propane-1,2,3-triol)
> select /A
3210 atoms, 2940 bonds, 691 residues, 1 model selected
> select clear
> ui tool show "Show Sequence Viewer"
> sequence chain /A
Alignment identifier is 1/A
> ui tool show "Model Loops"
> modeller refine 1/A:1:internal-missing numModels 5 fast false
> adjacentFlexible 1 protocol standard
Webservices job id: 3PM1UTKJWLVK1NFV
Modeller job (ID 3PM1UTKJWLVK1NFV) finished
Modeller error output
Traceback (most recent call last):
File "ModellerModelling.py", line 93, in <module>
a.make()
File "/usr/lib64/python3.8/site-packages/modeller/automodel/loopmodel.py",
line 42, in make
AutoModel.make(self, exit_stage)
File "/usr/lib64/python3.8/site-packages/modeller/automodel/automodel.py",
line 151, in make
atmsel = self._check_select_atoms()
File "/usr/lib64/python3.8/site-packages/modeller/automodel/automodel.py",
line 701, in _check_select_atoms
raise ModellerError("no atoms selected for optimization")
_modeller.ModellerError: no atoms selected for optimization
Modeller run output
MODELLER 10.4, 2022/10/28, r12463
PROTEIN STRUCTURE MODELLING BY SATISFACTION OF SPATIAL RESTRAINTS
Copyright(c) 1989-2022 Andrej Sali
All Rights Reserved
Written by A. Sali
with help from
B. Webb, M.S. Madhusudhan, M-Y. Shen, G.Q. Dong,
M.A. Marti-Renom, N. Eswar, F. Alber, M. Topf, B. Oliva,
A. Fiser, R. Sanchez, B. Yerkovich, A. Badretdinov,
F. Melo, J.P. Overington, E. Feyfant
University of California, San Francisco, USA
Rockefeller University, New York, USA
Harvard University, Cambridge, USA
Imperial Cancer Research Fund, London, UK
Birkbeck College, University of London, London, UK
Kind, OS, HostName, Kernel, Processor: 4, Linux wilkins.cgl.ucsf.edu
4.18.0-477.21.1.el8_8.x86_64 x86_64
Date and time of compilation : 2022/10/28 21:02:55
MODELLER executable type : x86_64-intel8
Job starting time (YY/MM/DD HH:MM:SS): 2023/11/16 08:03:34
environ____W> The class 'environ' is deprecated; use 'Environ' instead
openf___224_> Open $(LIB)/restyp.lib
openf___224_> Open ${MODINSTALL10v4}/modlib/resgrp.lib
rdresgr_266_> Number of residue groups: 2
openf___224_> Open ${MODINSTALL10v4}/modlib/sstruc.lib
Dynamically allocated memory at amaxlibraries [B,KiB,MiB]: 191566 187.076
0.183
Dynamically allocated memory at amaxlibraries [B,KiB,MiB]: 192094 187.592
0.183
openf___224_> Open ${MODINSTALL10v4}/modlib/resdih.lib
Dynamically allocated memory at amaxlibraries [B,KiB,MiB]: 240694 235.053
0.230
rdrdih__263_> Number of dihedral angle types : 9
Maximal number of dihedral angle optima: 3
Dihedral angle names : Alph Phi Psi Omeg chi1 chi2 chi3 chi4 chi5
openf___224_> Open ${MODINSTALL10v4}/modlib/radii.lib
Dynamically allocated memory at amaxlibraries [B,KiB,MiB]: 253994 248.041
0.242
openf___224_> Open ${MODINSTALL10v4}/modlib/af_mnchdef.lib
rdwilmo_274_> Mainchain residue conformation classes: APBLE
openf___224_> Open ${MODINSTALL10v4}/modlib/mnch.lib
rdclass_257_> Number of classes: 5
openf___224_> Open ${MODINSTALL10v4}/modlib/mnch1.lib
openf___224_> Open ${MODINSTALL10v4}/modlib/mnch2.lib
openf___224_> Open ${MODINSTALL10v4}/modlib/mnch3.lib
openf___224_> Open ${MODINSTALL10v4}/modlib/xs4.mat
rdrrwgh_268_> Number of residue types: 21
loopmodel__W> The class 'loopmodel' is deprecated; use 'LoopModel' instead
openf___224_> Open alignment.ali
Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 282617 275.993
0.270
Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 297709 290.731
0.284
Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 313109 305.771
0.299
Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 343909 335.849
0.328
Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 405509 396.005
0.387
Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 528709 516.317
0.504
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 531469 519.013 0.507
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 534229 521.708 0.509
read_al_374_> Non-standard residue type,position,sequence: . 349 1
read_al_374_> Non-standard residue type,position,sequence: . 350 1
read_al_374_> Non-standard residue type,position,sequence: . 351 1
read_al_374_> Non-standard residue type,position,sequence: . 352 1
read_al_374_> Non-standard residue type,position,sequence: . 353 1
read_al_374_> Non-standard residue type,position,sequence: . 354 1
read_al_374_> Non-standard residue type,position,sequence: . 355 1
read_al_374_> Non-standard residue type,position,sequence: w 356 1
read_al_374_> Non-standard residue type,position,sequence: w 357 1
read_al_374_> Non-standard residue type,position,sequence: w 358 1
read_al_374_> Non-standard residue type,position,sequence: w 359 1
read_al_374_> Non-standard residue type,position,sequence: w 360 1
read_al_374_> Non-standard residue type,position,sequence: w 361 1
read_al_374_> Non-standard residue type,position,sequence: w 362 1
read_al_374_> Non-standard residue type,position,sequence: w 363 1
read_al_374_> Non-standard residue type,position,sequence: w 364 1
read_al_374_> Non-standard residue type,position,sequence: w 365 1
read_al_374_> Non-standard residue type,position,sequence: w 366 1
read_al_374_> Non-standard residue type,position,sequence: w 367 1
read_al_374_> Non-standard residue type,position,sequence: w 368 1
read_al_374_> Non-standard residue type,position,sequence: w 369 1
read_al_374_> Non-standard residue type,position,sequence: w 370 1
read_al_374_> Non-standard residue type,position,sequence: w 371 1
read_al_374_> Non-standard residue type,position,sequence: w 372 1
read_al_374_> Non-standard residue type,position,sequence: w 373 1
read_al_374_> Non-standard residue type,position,sequence: w 374 1
read_al_374_> Non-standard residue type,position,sequence: w 375 1
read_al_374_> Non-standard residue type,position,sequence: w 376 1
read_al_374_> Non-standard residue type,position,sequence: w 377 1
read_al_374_> Non-standard residue type,position,sequence: w 378 1
read_al_374_> Non-standard residue type,position,sequence: w 379 1
read_al_374_> Non-standard residue type,position,sequence: w 380 1
read_al_374_> Non-standard residue type,position,sequence: w 381 1
read_al_374_> Non-standard residue type,position,sequence: w 382 1
read_al_374_> Non-standard residue type,position,sequence: w 383 1
read_al_374_> Non-standard residue type,position,sequence: w 384 1
read_al_374_> Non-standard residue type,position,sequence: w 385 1
read_al_374_> Non-standard residue type,position,sequence: w 386 1
read_al_374_> Non-standard residue type,position,sequence: w 387 1
read_al_374_> Non-standard residue type,position,sequence: w 388 1
read_al_374_> Non-standard residue type,position,sequence: w 389 1
read_al_374_> Non-standard residue type,position,sequence: w 390 1
read_al_374_> Non-standard residue type,position,sequence: w 391 1
read_al_374_> Non-standard residue type,position,sequence: w 392 1
read_al_374_> Non-standard residue type,position,sequence: w 393 1
read_al_374_> Non-standard residue type,position,sequence: w 394 1
read_al_374_> Non-standard residue type,position,sequence: w 395 1
read_al_374_> Non-standard residue type,position,sequence: w 396 1
read_al_374_> Non-standard residue type,position,sequence: w 397 1
read_al_374_> Non-standard residue type,position,sequence: w 398 1
read_al_374_> Non-standard residue type,position,sequence: w 399 1
read_al_374_> Non-standard residue type,position,sequence: w 400 1
read_al_374_> Non-standard residue type,position,sequence: w 401 1
read_al_374_> Non-standard residue type,position,sequence: w 402 1
read_al_374_> Non-standard residue type,position,sequence: w 403 1
read_al_374_> Non-standard residue type,position,sequence: w 404 1
read_al_374_> Non-standard residue type,position,sequence: w 405 1
read_al_374_> Non-standard residue type,position,sequence: w 406 1
read_al_374_> Non-standard residue type,position,sequence: w 407 1
read_al_374_> Non-standard residue type,position,sequence: w 408 1
read_al_374_> Non-standard residue type,position,sequence: w 409 1
read_al_374_> Non-standard residue type,position,sequence: w 410 1
read_al_374_> Non-standard residue type,position,sequence: w 411 1
read_al_374_> Non-standard residue type,position,sequence: w 412 1
read_al_374_> Non-standard residue type,position,sequence: w 413 1
read_al_374_> Non-standard residue type,position,sequence: w 414 1
read_al_374_> Non-standard residue type,position,sequence: w 415 1
read_al_374_> Non-standard residue type,position,sequence: w 416 1
read_al_374_> Non-standard residue type,position,sequence: w 417 1
read_al_374_> Non-standard residue type,position,sequence: w 418 1
read_al_374_> Non-standard residue type,position,sequence: w 419 1
read_al_374_> Non-standard residue type,position,sequence: w 420 1
read_al_374_> Non-standard residue type,position,sequence: w 421 1
read_al_374_> Non-standard residue type,position,sequence: w 422 1
read_al_374_> Non-standard residue type,position,sequence: w 423 1
read_al_374_> Non-standard residue type,position,sequence: w 424 1
read_al_374_> Non-standard residue type,position,sequence: w 425 1
read_al_374_> Non-standard residue type,position,sequence: w 426 1
read_al_374_> Non-standard residue type,position,sequence: w 427 1
read_al_374_> Non-standard residue type,position,sequence: w 428 1
read_al_374_> Non-standard residue type,position,sequence: w 429 1
read_al_374_> Non-standard residue type,position,sequence: w 430 1
read_al_374_> Non-standard residue type,position,sequence: w 431 1
read_al_374_> Non-standard residue type,position,sequence: w 432 1
read_al_374_> Non-standard residue type,position,sequence: w 433 1
read_al_374_> Non-standard residue type,position,sequence: w 434 1
read_al_374_> Non-standard residue type,position,sequence: w 435 1
read_al_374_> Non-standard residue type,position,sequence: w 436 1
read_al_374_> Non-standard residue type,position,sequence: w 437 1
read_al_374_> Non-standard residue type,position,sequence: w 438 1
read_al_374_> Non-standard residue type,position,sequence: w 439 1
read_al_374_> Non-standard residue type,position,sequence: w 440 1
read_al_374_> Non-standard residue type,position,sequence: w 441 1
read_al_374_> Non-standard residue type,position,sequence: w 442 1
read_al_374_> Non-standard residue type,position,sequence: w 443 1
read_al_374_> Non-standard residue type,position,sequence: w 444 1
read_al_374_> Non-standard residue type,position,sequence: w 445 1
read_al_374_> Non-standard residue type,position,sequence: w 446 1
read_al_374_> Non-standard residue type,position,sequence: w 447 1
read_al_374_> Non-standard residue type,position,sequence: w 448 1
read_al_374_> Non-standard residue type,position,sequence: w 449 1
read_al_374_> Non-standard residue type,position,sequence: w 450 1
read_al_374_> Non-standard residue type,position,sequence: w 451 1
read_al_374_> Non-standard residue type,position,sequence: w 452 1
read_al_374_> Non-standard residue type,position,sequence: w 453 1
read_al_374_> Non-standard residue type,position,sequence: w 454 1
read_al_374_> Non-standard residue type,position,sequence: w 455 1
read_al_374_> Non-standard residue type,position,sequence: w 456 1
read_al_374_> Non-standard residue type,position,sequence: w 457 1
read_al_374_> Non-standard residue type,position,sequence: w 458 1
read_al_374_> Non-standard residue type,position,sequence: w 459 1
read_al_374_> Non-standard residue type,position,sequence: w 460 1
read_al_374_> Non-standard residue type,position,sequence: w 461 1
read_al_374_> Non-standard residue type,position,sequence: w 462 1
read_al_374_> Non-standard residue type,position,sequence: w 463 1
read_al_374_> Non-standard residue type,position,sequence: w 464 1
read_al_374_> Non-standard residue type,position,sequence: w 465 1
read_al_374_> Non-standard residue type,position,sequence: w 466 1
read_al_374_> Non-standard residue type,position,sequence: w 467 1
read_al_374_> Non-standard residue type,position,sequence: w 468 1
read_al_374_> Non-standard residue type,position,sequence: w 469 1
read_al_374_> Non-standard residue type,position,sequence: w 470 1
read_al_374_> Non-standard residue type,position,sequence: w 471 1
read_al_374_> Non-standard residue type,position,sequence: w 472 1
read_al_374_> Non-standard residue type,position,sequence: w 473 1
read_al_374_> Non-standard residue type,position,sequence: w 474 1
read_al_374_> Non-standard residue type,position,sequence: w 475 1
read_al_374_> Non-standard residue type,position,sequence: w 476 1
read_al_374_> Non-standard residue type,position,sequence: w 477 1
read_al_374_> Non-standard residue type,position,sequence: w 478 1
read_al_374_> Non-standard residue type,position,sequence: w 479 1
read_al_374_> Non-standard residue type,position,sequence: w 480 1
read_al_374_> Non-standard residue type,position,sequence: w 481 1
read_al_374_> Non-standard residue type,position,sequence: w 482 1
read_al_374_> Non-standard residue type,position,sequence: w 483 1
read_al_374_> Non-standard residue type,position,sequence: w 484 1
read_al_374_> Non-standard residue type,position,sequence: w 485 1
read_al_374_> Non-standard residue type,position,sequence: w 486 1
read_al_374_> Non-standard residue type,position,sequence: w 487 1
read_al_374_> Non-standard residue type,position,sequence: w 488 1
read_al_374_> Non-standard residue type,position,sequence: w 489 1
read_al_374_> Non-standard residue type,position,sequence: w 490 1
read_al_374_> Non-standard residue type,position,sequence: w 491 1
read_al_374_> Non-standard residue type,position,sequence: w 492 1
read_al_374_> Non-standard residue type,position,sequence: w 493 1
read_al_374_> Non-standard residue type,position,sequence: w 494 1
read_al_374_> Non-standard residue type,position,sequence: w 495 1
read_al_374_> Non-standard residue type,position,sequence: w 496 1
read_al_374_> Non-standard residue type,position,sequence: w 497 1
read_al_374_> Non-standard residue type,position,sequence: w 498 1
read_al_374_> Non-standard residue type,position,sequence: w 499 1
read_al_374_> Non-standard residue type,position,sequence: w 500 1
read_al_374_> Non-standard residue type,position,sequence: w 501 1
read_al_374_> Non-standard residue type,position,sequence: w 502 1
read_al_374_> Non-standard residue type,position,sequence: w 503 1
read_al_374_> Non-standard residue type,position,sequence: w 504 1
read_al_374_> Non-standard residue type,position,sequence: w 505 1
read_al_374_> Non-standard residue type,position,sequence: w 506 1
read_al_374_> Non-standard residue type,position,sequence: w 507 1
read_al_374_> Non-standard residue type,position,sequence: w 508 1
read_al_374_> Non-standard residue type,position,sequence: w 509 1
read_al_374_> Non-standard residue type,position,sequence: w 510 1
read_al_374_> Non-standard residue type,position,sequence: w 511 1
read_al_374_> Non-standard residue type,position,sequence: w 512 1
read_al_374_> Non-standard residue type,position,sequence: w 513 1
read_al_374_> Non-standard residue type,position,sequence: w 514 1
read_al_374_> Non-standard residue type,position,sequence: w 515 1
read_al_374_> Non-standard residue type,position,sequence: w 516 1
read_al_374_> Non-standard residue type,position,sequence: w 517 1
read_al_374_> Non-standard residue type,position,sequence: w 518 1
read_al_374_> Non-standard residue type,position,sequence: w 519 1
read_al_374_> Non-standard residue type,position,sequence: w 520 1
read_al_374_> Non-standard residue type,position,sequence: w 521 1
read_al_374_> Non-standard residue type,position,sequence: w 522 1
read_al_374_> Non-standard residue type,position,sequence: w 523 1
read_al_374_> Non-standard residue type,position,sequence: w 524 1
read_al_374_> Non-standard residue type,position,sequence: w 525 1
read_al_374_> Non-standard residue type,position,sequence: w 526 1
read_al_374_> Non-standard residue type,position,sequence: w 527 1
read_al_374_> Non-standard residue type,position,sequence: w 528 1
read_al_374_> Non-standard residue type,position,sequence: w 529 1
read_al_374_> Non-standard residue type,position,sequence: w 530 1
read_al_374_> Non-standard residue type,position,sequence: w 531 1
read_al_374_> Non-standard residue type,position,sequence: w 532 1
read_al_374_> Non-standard residue type,position,sequence: w 533 1
read_al_374_> Non-standard residue type,position,sequence: w 534 1
read_al_374_> Non-standard residue type,position,sequence: w 535 1
read_al_374_> Non-standard residue type,position,sequence: w 536 1
read_al_374_> Non-standard residue type,position,sequence: w 537 1
read_al_374_> Non-standard residue type,position,sequence: w 538 1
read_al_374_> Non-standard residue type,position,sequence: w 539 1
read_al_374_> Non-standard residue type,position,sequence: w 540 1
read_al_374_> Non-standard residue type,position,sequence: w 541 1
read_al_374_> Non-standard residue type,position,sequence: w 542 1
read_al_374_> Non-standard residue type,position,sequence: w 543 1
read_al_374_> Non-standard residue type,position,sequence: w 544 1
read_al_374_> Non-standard residue type,position,sequence: w 545 1
read_al_374_> Non-standard residue type,position,sequence: w 546 1
read_al_374_> Non-standard residue type,position,sequence: w 547 1
read_al_374_> Non-standard residue type,position,sequence: w 548 1
read_al_374_> Non-standard residue type,position,sequence: w 549 1
read_al_374_> Non-standard residue type,position,sequence: w 550 1
read_al_374_> Non-standard residue type,position,sequence: w 551 1
read_al_374_> Non-standard residue type,position,sequence: w 552 1
read_al_374_> Non-standard residue type,position,sequence: w 553 1
read_al_374_> Non-standard residue type,position,sequence: w 554 1
read_al_374_> Non-standard residue type,position,sequence: w 555 1
read_al_374_> Non-standard residue type,position,sequence: w 556 1
read_al_374_> Non-standard residue type,position,sequence: w 557 1
read_al_374_> Non-standard residue type,position,sequence: w 558 1
read_al_374_> Non-standard residue type,position,sequence: w 559 1
read_al_374_> Non-standard residue type,position,sequence: w 560 1
read_al_374_> Non-standard residue type,position,sequence: w 561 1
read_al_374_> Non-standard residue type,position,sequence: w 562 1
read_al_374_> Non-standard residue type,position,sequence: w 563 1
read_al_374_> Non-standard residue type,position,sequence: w 564 1
read_al_374_> Non-standard residue type,position,sequence: w 565 1
read_al_374_> Non-standard residue type,position,sequence: w 566 1
read_al_374_> Non-standard residue type,position,sequence: w 567 1
read_al_374_> Non-standard residue type,position,sequence: w 568 1
read_al_374_> Non-standard residue type,position,sequence: w 569 1
read_al_374_> Non-standard residue type,position,sequence: w 570 1
read_al_374_> Non-standard residue type,position,sequence: w 571 1
read_al_374_> Non-standard residue type,position,sequence: w 572 1
read_al_374_> Non-standard residue type,position,sequence: w 573 1
read_al_374_> Non-standard residue type,position,sequence: w 574 1
read_al_374_> Non-standard residue type,position,sequence: w 575 1
read_al_374_> Non-standard residue type,position,sequence: w 576 1
read_al_374_> Non-standard residue type,position,sequence: w 577 1
read_al_374_> Non-standard residue type,position,sequence: w 578 1
read_al_374_> Non-standard residue type,position,sequence: w 579 1
read_al_374_> Non-standard residue type,position,sequence: w 580 1
read_al_374_> Non-standard residue type,position,sequence: w 581 1
read_al_374_> Non-standard residue type,position,sequence: w 582 1
read_al_374_> Non-standard residue type,position,sequence: w 583 1
read_al_374_> Non-standard residue type,position,sequence: w 584 1
read_al_374_> Non-standard residue type,position,sequence: w 585 1
read_al_374_> Non-standard residue type,position,sequence: w 586 1
read_al_374_> Non-standard residue type,position,sequence: w 587 1
read_al_374_> Non-standard residue type,position,sequence: w 588 1
read_al_374_> Non-standard residue type,position,sequence: w 589 1
read_al_374_> Non-standard residue type,position,sequence: w 590 1
read_al_374_> Non-standard residue type,position,sequence: w 591 1
read_al_374_> Non-standard residue type,position,sequence: w 592 1
read_al_374_> Non-standard residue type,position,sequence: w 593 1
read_al_374_> Non-standard residue type,position,sequence: w 594 1
read_al_374_> Non-standard residue type,position,sequence: w 595 1
read_al_374_> Non-standard residue type,position,sequence: w 596 1
read_al_374_> Non-standard residue type,position,sequence: w 597 1
read_al_374_> Non-standard residue type,position,sequence: w 598 1
read_al_374_> Non-standard residue type,position,sequence: w 599 1
read_al_374_> Non-standard residue type,position,sequence: w 600 1
read_al_374_> Non-standard residue type,position,sequence: w 601 1
read_al_374_> Non-standard residue type,position,sequence: w 602 1
read_al_374_> Non-standard residue type,position,sequence: w 603 1
read_al_374_> Non-standard residue type,position,sequence: w 604 1
read_al_374_> Non-standard residue type,position,sequence: w 605 1
read_al_374_> Non-standard residue type,position,sequence: w 606 1
read_al_374_> Non-standard residue type,position,sequence: w 607 1
read_al_374_> Non-standard residue type,position,sequence: w 608 1
read_al_374_> Non-standard residue type,position,sequence: w 609 1
read_al_374_> Non-standard residue type,position,sequence: w 610 1
read_al_374_> Non-standard residue type,position,sequence: w 611 1
read_al_374_> Non-standard residue type,position,sequence: w 612 1
read_al_374_> Non-standard residue type,position,sequence: w 613 1
read_al_374_> Non-standard residue type,position,sequence: w 614 1
read_al_374_> Non-standard residue type,position,sequence: w 615 1
read_al_374_> Non-standard residue type,position,sequence: w 616 1
read_al_374_> Non-standard residue type,position,sequence: w 617 1
read_al_374_> Non-standard residue type,position,sequence: w 618 1
read_al_374_> Non-standard residue type,position,sequence: w 619 1
read_al_374_> Non-standard residue type,position,sequence: w 620 1
read_al_374_> Non-standard residue type,position,sequence: w 621 1
read_al_374_> Non-standard residue type,position,sequence: w 622 1
read_al_374_> Non-standard residue type,position,sequence: w 623 1
read_al_374_> Non-standard residue type,position,sequence: w 624 1
read_al_374_> Non-standard residue type,position,sequence: w 625 1
read_al_374_> Non-standard residue type,position,sequence: w 626 1
read_al_374_> Non-standard residue type,position,sequence: w 627 1
read_al_374_> Non-standard residue type,position,sequence: w 628 1
read_al_374_> Non-standard residue type,position,sequence: w 629 1
read_al_374_> Non-standard residue type,position,sequence: w 630 1
read_al_374_> Non-standard residue type,position,sequence: w 631 1
read_al_374_> Non-standard residue type,position,sequence: w 632 1
read_al_374_> Non-standard residue type,position,sequence: w 633 1
read_al_374_> Non-standard residue type,position,sequence: w 634 1
read_al_374_> Non-standard residue type,position,sequence: w 635 1
read_al_374_> Non-standard residue type,position,sequence: w 636 1
read_al_374_> Non-standard residue type,position,sequence: w 637 1
read_al_374_> Non-standard residue type,position,sequence: w 638 1
read_al_374_> Non-standard residue type,position,sequence: w 639 1
read_al_374_> Non-standard residue type,position,sequence: w 640 1
read_al_374_> Non-standard residue type,position,sequence: w 641 1
read_al_374_> Non-standard residue type,position,sequence: w 642 1
read_al_374_> Non-standard residue type,position,sequence: w 643 1
read_al_374_> Non-standard residue type,position,sequence: w 644 1
read_al_374_> Non-standard residue type,position,sequence: w 645 1
read_al_374_> Non-standard residue type,position,sequence: w 646 1
read_al_374_> Non-standard residue type,position,sequence: w 647 1
read_al_374_> Non-standard residue type,position,sequence: w 648 1
read_al_374_> Non-standard residue type,position,sequence: w 649 1
read_al_374_> Non-standard residue type,position,sequence: w 650 1
read_al_374_> Non-standard residue type,position,sequence: w 651 1
read_al_374_> Non-standard residue type,position,sequence: w 652 1
read_al_374_> Non-standard residue type,position,sequence: w 653 1
read_al_374_> Non-standard residue type,position,sequence: w 654 1
read_al_374_> Non-standard residue type,position,sequence: w 655 1
read_al_374_> Non-standard residue type,position,sequence: w 656 1
read_al_374_> Non-standard residue type,position,sequence: w 657 1
read_al_374_> Non-standard residue type,position,sequence: w 658 1
read_al_374_> Non-standard residue type,position,sequence: w 659 1
read_al_374_> Non-standard residue type,position,sequence: w 660 1
read_al_374_> Non-standard residue type,position,sequence: w 661 1
read_al_374_> Non-standard residue type,position,sequence: w 662 1
read_al_374_> Non-standard residue type,position,sequence: w 663 1
read_al_374_> Non-standard residue type,position,sequence: w 664 1
read_al_374_> Non-standard residue type,position,sequence: w 665 1
read_al_374_> Non-standard residue type,position,sequence: w 666 1
read_al_374_> Non-standard residue type,position,sequence: w 667 1
read_al_374_> Non-standard residue type,position,sequence: w 668 1
read_al_374_> Non-standard residue type,position,sequence: w 669 1
read_al_374_> Non-standard residue type,position,sequence: w 670 1
read_al_374_> Non-standard residue type,position,sequence: w 671 1
read_al_374_> Non-standard residue type,position,sequence: w 672 1
read_al_374_> Non-standard residue type,position,sequence: w 673 1
read_al_374_> Non-standard residue type,position,sequence: w 674 1
read_al_374_> Non-standard residue type,position,sequence: w 675 1
read_al_374_> Non-standard residue type,position,sequence: w 676 1
read_al_374_> Non-standard residue type,position,sequence: w 677 1
read_al_374_> Non-standard residue type,position,sequence: w 678 1
read_al_374_> Non-standard residue type,position,sequence: w 679 1
read_al_374_> Non-standard residue type,position,sequence: w 680 1
read_al_374_> Non-standard residue type,position,sequence: w 681 1
read_al_374_> Non-standard residue type,position,sequence: w 682 1
read_al_374_> Non-standard residue type,position,sequence: w 683 1
read_al_374_> Non-standard residue type,position,sequence: w 684 1
read_al_374_> Non-standard residue type,position,sequence: w 685 1
read_al_374_> Non-standard residue type,position,sequence: w 686 1
read_al_374_> Non-standard residue type,position,sequence: w 687 1
read_al_374_> Non-standard residue type,position,sequence: w 688 1
read_al_374_> Non-standard residue type,position,sequence: w 689 1
read_al_374_> Non-standard residue type,position,sequence: w 690 1
read_al_374_> Non-standard residue type,position,sequence: w 691 1
read_al_374_> Non-standard residue type,position,sequence: . 349 2
read_al_374_> Non-standard residue type,position,sequence: . 350 2
read_al_374_> Non-standard residue type,position,sequence: . 351 2
read_al_374_> Non-standard residue type,position,sequence: . 352 2
read_al_374_> Non-standard residue type,position,sequence: . 353 2
read_al_374_> Non-standard residue type,position,sequence: . 354 2
read_al_374_> Non-standard residue type,position,sequence: . 355 2
read_al_374_> Non-standard residue type,position,sequence: w 356 2
read_al_374_> Non-standard residue type,position,sequence: w 357 2
read_al_374_> Non-standard residue type,position,sequence: w 358 2
read_al_374_> Non-standard residue type,position,sequence: w 359 2
read_al_374_> Non-standard residue type,position,sequence: w 360 2
read_al_374_> Non-standard residue type,position,sequence: w 361 2
read_al_374_> Non-standard residue type,position,sequence: w 362 2
read_al_374_> Non-standard residue type,position,sequence: w 363 2
read_al_374_> Non-standard residue type,position,sequence: w 364 2
read_al_374_> Non-standard residue type,position,sequence: w 365 2
read_al_374_> Non-standard residue type,position,sequence: w 366 2
read_al_374_> Non-standard residue type,position,sequence: w 367 2
read_al_374_> Non-standard residue type,position,sequence: w 368 2
read_al_374_> Non-standard residue type,position,sequence: w 369 2
read_al_374_> Non-standard residue type,position,sequence: w 370 2
read_al_374_> Non-standard residue type,position,sequence: w 371 2
read_al_374_> Non-standard residue type,position,sequence: w 372 2
read_al_374_> Non-standard residue type,position,sequence: w 373 2
read_al_374_> Non-standard residue type,position,sequence: w 374 2
read_al_374_> Non-standard residue type,position,sequence: w 375 2
read_al_374_> Non-standard residue type,position,sequence: w 376 2
read_al_374_> Non-standard residue type,position,sequence: w 377 2
read_al_374_> Non-standard residue type,position,sequence: w 378 2
read_al_374_> Non-standard residue type,position,sequence: w 379 2
read_al_374_> Non-standard residue type,position,sequence: w 380 2
read_al_374_> Non-standard residue type,position,sequence: w 381 2
read_al_374_> Non-standard residue type,position,sequence: w 382 2
read_al_374_> Non-standard residue type,position,sequence: w 383 2
read_al_374_> Non-standard residue type,position,sequence: w 384 2
read_al_374_> Non-standard residue type,position,sequence: w 385 2
read_al_374_> Non-standard residue type,position,sequence: w 386 2
read_al_374_> Non-standard residue type,position,sequence: w 387 2
read_al_374_> Non-standard residue type,position,sequence: w 388 2
read_al_374_> Non-standard residue type,position,sequence: w 389 2
read_al_374_> Non-standard residue type,position,sequence: w 390 2
read_al_374_> Non-standard residue type,position,sequence: w 391 2
read_al_374_> Non-standard residue type,position,sequence: w 392 2
read_al_374_> Non-standard residue type,position,sequence: w 393 2
read_al_374_> Non-standard residue type,position,sequence: w 394 2
read_al_374_> Non-standard residue type,position,sequence: w 395 2
read_al_374_> Non-standard residue type,position,sequence: w 396 2
read_al_374_> Non-standard residue type,position,sequence: w 397 2
read_al_374_> Non-standard residue type,position,sequence: w 398 2
read_al_374_> Non-standard residue type,position,sequence: w 399 2
read_al_374_> Non-standard residue type,position,sequence: w 400 2
read_al_374_> Non-standard residue type,position,sequence: w 401 2
read_al_374_> Non-standard residue type,position,sequence: w 402 2
read_al_374_> Non-standard residue type,position,sequence: w 403 2
read_al_374_> Non-standard residue type,position,sequence: w 404 2
read_al_374_> Non-standard residue type,position,sequence: w 405 2
read_al_374_> Non-standard residue type,position,sequence: w 406 2
read_al_374_> Non-standard residue type,position,sequence: w 407 2
read_al_374_> Non-standard residue type,position,sequence: w 408 2
read_al_374_> Non-standard residue type,position,sequence: w 409 2
read_al_374_> Non-standard residue type,position,sequence: w 410 2
read_al_374_> Non-standard residue type,position,sequence: w 411 2
read_al_374_> Non-standard residue type,position,sequence: w 412 2
read_al_374_> Non-standard residue type,position,sequence: w 413 2
read_al_374_> Non-standard residue type,position,sequence: w 414 2
read_al_374_> Non-standard residue type,position,sequence: w 415 2
read_al_374_> Non-standard residue type,position,sequence: w 416 2
read_al_374_> Non-standard residue type,position,sequence: w 417 2
read_al_374_> Non-standard residue type,position,sequence: w 418 2
read_al_374_> Non-standard residue type,position,sequence: w 419 2
read_al_374_> Non-standard residue type,position,sequence: w 420 2
read_al_374_> Non-standard residue type,position,sequence: w 421 2
read_al_374_> Non-standard residue type,position,sequence: w 422 2
read_al_374_> Non-standard residue type,position,sequence: w 423 2
read_al_374_> Non-standard residue type,position,sequence: w 424 2
read_al_374_> Non-standard residue type,position,sequence: w 425 2
read_al_374_> Non-standard residue type,position,sequence: w 426 2
read_al_374_> Non-standard residue type,position,sequence: w 427 2
read_al_374_> Non-standard residue type,position,sequence: w 428 2
read_al_374_> Non-standard residue type,position,sequence: w 429 2
read_al_374_> Non-standard residue type,position,sequence: w 430 2
read_al_374_> Non-standard residue type,position,sequence: w 431 2
read_al_374_> Non-standard residue type,position,sequence: w 432 2
read_al_374_> Non-standard residue type,position,sequence: w 433 2
read_al_374_> Non-standard residue type,position,sequence: w 434 2
read_al_374_> Non-standard residue type,position,sequence: w 435 2
read_al_374_> Non-standard residue type,position,sequence: w 436 2
read_al_374_> Non-standard residue type,position,sequence: w 437 2
read_al_374_> Non-standard residue type,position,sequence: w 438 2
read_al_374_> Non-standard residue type,position,sequence: w 439 2
read_al_374_> Non-standard residue type,position,sequence: w 440 2
read_al_374_> Non-standard residue type,position,sequence: w 441 2
read_al_374_> Non-standard residue type,position,sequence: w 442 2
read_al_374_> Non-standard residue type,position,sequence: w 443 2
read_al_374_> Non-standard residue type,position,sequence: w 444 2
read_al_374_> Non-standard residue type,position,sequence: w 445 2
read_al_374_> Non-standard residue type,position,sequence: w 446 2
read_al_374_> Non-standard residue type,position,sequence: w 447 2
read_al_374_> Non-standard residue type,position,sequence: w 448 2
read_al_374_> Non-standard residue type,position,sequence: w 449 2
read_al_374_> Non-standard residue type,position,sequence: w 450 2
read_al_374_> Non-standard residue type,position,sequence: w 451 2
read_al_374_> Non-standard residue type,position,sequence: w 452 2
read_al_374_> Non-standard residue type,position,sequence: w 453 2
read_al_374_> Non-standard residue type,position,sequence: w 454 2
read_al_374_> Non-standard residue type,position,sequence: w 455 2
read_al_374_> Non-standard residue type,position,sequence: w 456 2
read_al_374_> Non-standard residue type,position,sequence: w 457 2
read_al_374_> Non-standard residue type,position,sequence: w 458 2
read_al_374_> Non-standard residue type,position,sequence: w 459 2
read_al_374_> Non-standard residue type,position,sequence: w 460 2
read_al_374_> Non-standard residue type,position,sequence: w 461 2
read_al_374_> Non-standard residue type,position,sequence: w 462 2
read_al_374_> Non-standard residue type,position,sequence: w 463 2
read_al_374_> Non-standard residue type,position,sequence: w 464 2
read_al_374_> Non-standard residue type,position,sequence: w 465 2
read_al_374_> Non-standard residue type,position,sequence: w 466 2
read_al_374_> Non-standard residue type,position,sequence: w 467 2
read_al_374_> Non-standard residue type,position,sequence: w 468 2
read_al_374_> Non-standard residue type,position,sequence: w 469 2
read_al_374_> Non-standard residue type,position,sequence: w 470 2
read_al_374_> Non-standard residue type,position,sequence: w 471 2
read_al_374_> Non-standard residue type,position,sequence: w 472 2
read_al_374_> Non-standard residue type,position,sequence: w 473 2
read_al_374_> Non-standard residue type,position,sequence: w 474 2
read_al_374_> Non-standard residue type,position,sequence: w 475 2
read_al_374_> Non-standard residue type,position,sequence: w 476 2
read_al_374_> Non-standard residue type,position,sequence: w 477 2
read_al_374_> Non-standard residue type,position,sequence: w 478 2
read_al_374_> Non-standard residue type,position,sequence: w 479 2
read_al_374_> Non-standard residue type,position,sequence: w 480 2
read_al_374_> Non-standard residue type,position,sequence: w 481 2
read_al_374_> Non-standard residue type,position,sequence: w 482 2
read_al_374_> Non-standard residue type,position,sequence: w 483 2
read_al_374_> Non-standard residue type,position,sequence: w 484 2
read_al_374_> Non-standard residue type,position,sequence: w 485 2
read_al_374_> Non-standard residue type,position,sequence: w 486 2
read_al_374_> Non-standard residue type,position,sequence: w 487 2
read_al_374_> Non-standard residue type,position,sequence: w 488 2
read_al_374_> Non-standard residue type,position,sequence: w 489 2
read_al_374_> Non-standard residue type,position,sequence: w 490 2
read_al_374_> Non-standard residue type,position,sequence: w 491 2
read_al_374_> Non-standard residue type,position,sequence: w 492 2
read_al_374_> Non-standard residue type,position,sequence: w 493 2
read_al_374_> Non-standard residue type,position,sequence: w 494 2
read_al_374_> Non-standard residue type,position,sequence: w 495 2
read_al_374_> Non-standard residue type,position,sequence: w 496 2
read_al_374_> Non-standard residue type,position,sequence: w 497 2
read_al_374_> Non-standard residue type,position,sequence: w 498 2
read_al_374_> Non-standard residue type,position,sequence: w 499 2
read_al_374_> Non-standard residue type,position,sequence: w 500 2
read_al_374_> Non-standard residue type,position,sequence: w 501 2
read_al_374_> Non-standard residue type,position,sequence: w 502 2
read_al_374_> Non-standard residue type,position,sequence: w 503 2
read_al_374_> Non-standard residue type,position,sequence: w 504 2
read_al_374_> Non-standard residue type,position,sequence: w 505 2
read_al_374_> Non-standard residue type,position,sequence: w 506 2
read_al_374_> Non-standard residue type,position,sequence: w 507 2
read_al_374_> Non-standard residue type,position,sequence: w 508 2
read_al_374_> Non-standard residue type,position,sequence: w 509 2
read_al_374_> Non-standard residue type,position,sequence: w 510 2
read_al_374_> Non-standard residue type,position,sequence: w 511 2
read_al_374_> Non-standard residue type,position,sequence: w 512 2
read_al_374_> Non-standard residue type,position,sequence: w 513 2
read_al_374_> Non-standard residue type,position,sequence: w 514 2
read_al_374_> Non-standard residue type,position,sequence: w 515 2
read_al_374_> Non-standard residue type,position,sequence: w 516 2
read_al_374_> Non-standard residue type,position,sequence: w 517 2
read_al_374_> Non-standard residue type,position,sequence: w 518 2
read_al_374_> Non-standard residue type,position,sequence: w 519 2
read_al_374_> Non-standard residue type,position,sequence: w 520 2
read_al_374_> Non-standard residue type,position,sequence: w 521 2
read_al_374_> Non-standard residue type,position,sequence: w 522 2
read_al_374_> Non-standard residue type,position,sequence: w 523 2
read_al_374_> Non-standard residue type,position,sequence: w 524 2
read_al_374_> Non-standard residue type,position,sequence: w 525 2
read_al_374_> Non-standard residue type,position,sequence: w 526 2
read_al_374_> Non-standard residue type,position,sequence: w 527 2
read_al_374_> Non-standard residue type,position,sequence: w 528 2
read_al_374_> Non-standard residue type,position,sequence: w 529 2
read_al_374_> Non-standard residue type,position,sequence: w 530 2
read_al_374_> Non-standard residue type,position,sequence: w 531 2
read_al_374_> Non-standard residue type,position,sequence: w 532 2
read_al_374_> Non-standard residue type,position,sequence: w 533 2
read_al_374_> Non-standard residue type,position,sequence: w 534 2
read_al_374_> Non-standard residue type,position,sequence: w 535 2
read_al_374_> Non-standard residue type,position,sequence: w 536 2
read_al_374_> Non-standard residue type,position,sequence: w 537 2
read_al_374_> Non-standard residue type,position,sequence: w 538 2
read_al_374_> Non-standard residue type,position,sequence: w 539 2
read_al_374_> Non-standard residue type,position,sequence: w 540 2
read_al_374_> Non-standard residue type,position,sequence: w 541 2
read_al_374_> Non-standard residue type,position,sequence: w 542 2
read_al_374_> Non-standard residue type,position,sequence: w 543 2
read_al_374_> Non-standard residue type,position,sequence: w 544 2
read_al_374_> Non-standard residue type,position,sequence: w 545 2
read_al_374_> Non-standard residue type,position,sequence: w 546 2
read_al_374_> Non-standard residue type,position,sequence: w 547 2
read_al_374_> Non-standard residue type,position,sequence: w 548 2
read_al_374_> Non-standard residue type,position,sequence: w 549 2
read_al_374_> Non-standard residue type,position,sequence: w 550 2
read_al_374_> Non-standard residue type,position,sequence: w 551 2
read_al_374_> Non-standard residue type,position,sequence: w 552 2
read_al_374_> Non-standard residue type,position,sequence: w 553 2
read_al_374_> Non-standard residue type,position,sequence: w 554 2
read_al_374_> Non-standard residue type,position,sequence: w 555 2
read_al_374_> Non-standard residue type,position,sequence: w 556 2
read_al_374_> Non-standard residue type,position,sequence: w 557 2
read_al_374_> Non-standard residue type,position,sequence: w 558 2
read_al_374_> Non-standard residue type,position,sequence: w 559 2
read_al_374_> Non-standard residue type,position,sequence: w 560 2
read_al_374_> Non-standard residue type,position,sequence: w 561 2
read_al_374_> Non-standard residue type,position,sequence: w 562 2
read_al_374_> Non-standard residue type,position,sequence: w 563 2
read_al_374_> Non-standard residue type,position,sequence: w 564 2
read_al_374_> Non-standard residue type,position,sequence: w 565 2
read_al_374_> Non-standard residue type,position,sequence: w 566 2
read_al_374_> Non-standard residue type,position,sequence: w 567 2
read_al_374_> Non-standard residue type,position,sequence: w 568 2
read_al_374_> Non-standard residue type,position,sequence: w 569 2
read_al_374_> Non-standard residue type,position,sequence: w 570 2
read_al_374_> Non-standard residue type,position,sequence: w 571 2
read_al_374_> Non-standard residue type,position,sequence: w 572 2
read_al_374_> Non-standard residue type,position,sequence: w 573 2
read_al_374_> Non-standard residue type,position,sequence: w 574 2
read_al_374_> Non-standard residue type,position,sequence: w 575 2
read_al_374_> Non-standard residue type,position,sequence: w 576 2
read_al_374_> Non-standard residue type,position,sequence: w 577 2
read_al_374_> Non-standard residue type,position,sequence: w 578 2
read_al_374_> Non-standard residue type,position,sequence: w 579 2
read_al_374_> Non-standard residue type,position,sequence: w 580 2
read_al_374_> Non-standard residue type,position,sequence: w 581 2
read_al_374_> Non-standard residue type,position,sequence: w 582 2
read_al_374_> Non-standard residue type,position,sequence: w 583 2
read_al_374_> Non-standard residue type,position,sequence: w 584 2
read_al_374_> Non-standard residue type,position,sequence: w 585 2
read_al_374_> Non-standard residue type,position,sequence: w 586 2
read_al_374_> Non-standard residue type,position,sequence: w 587 2
read_al_374_> Non-standard residue type,position,sequence: w 588 2
read_al_374_> Non-standard residue type,position,sequence: w 589 2
read_al_374_> Non-standard residue type,position,sequence: w 590 2
read_al_374_> Non-standard residue type,position,sequence: w 591 2
read_al_374_> Non-standard residue type,position,sequence: w 592 2
read_al_374_> Non-standard residue type,position,sequence: w 593 2
read_al_374_> Non-standard residue type,position,sequence: w 594 2
read_al_374_> Non-standard residue type,position,sequence: w 595 2
read_al_374_> Non-standard residue type,position,sequence: w 596 2
read_al_374_> Non-standard residue type,position,sequence: w 597 2
read_al_374_> Non-standard residue type,position,sequence: w 598 2
read_al_374_> Non-standard residue type,position,sequence: w 599 2
read_al_374_> Non-standard residue type,position,sequence: w 600 2
read_al_374_> Non-standard residue type,position,sequence: w 601 2
read_al_374_> Non-standard residue type,position,sequence: w 602 2
read_al_374_> Non-standard residue type,position,sequence: w 603 2
read_al_374_> Non-standard residue type,position,sequence: w 604 2
read_al_374_> Non-standard residue type,position,sequence: w 605 2
read_al_374_> Non-standard residue type,position,sequence: w 606 2
read_al_374_> Non-standard residue type,position,sequence: w 607 2
read_al_374_> Non-standard residue type,position,sequence: w 608 2
read_al_374_> Non-standard residue type,position,sequence: w 609 2
read_al_374_> Non-standard residue type,position,sequence: w 610 2
read_al_374_> Non-standard residue type,position,sequence: w 611 2
read_al_374_> Non-standard residue type,position,sequence: w 612 2
read_al_374_> Non-standard residue type,position,sequence: w 613 2
read_al_374_> Non-standard residue type,position,sequence: w 614 2
read_al_374_> Non-standard residue type,position,sequence: w 615 2
read_al_374_> Non-standard residue type,position,sequence: w 616 2
read_al_374_> Non-standard residue type,position,sequence: w 617 2
read_al_374_> Non-standard residue type,position,sequence: w 618 2
read_al_374_> Non-standard residue type,position,sequence: w 619 2
read_al_374_> Non-standard residue type,position,sequence: w 620 2
read_al_374_> Non-standard residue type,position,sequence: w 621 2
read_al_374_> Non-standard residue type,position,sequence: w 622 2
read_al_374_> Non-standard residue type,position,sequence: w 623 2
read_al_374_> Non-standard residue type,position,sequence: w 624 2
read_al_374_> Non-standard residue type,position,sequence: w 625 2
read_al_374_> Non-standard residue type,position,sequence: w 626 2
read_al_374_> Non-standard residue type,position,sequence: w 627 2
read_al_374_> Non-standard residue type,position,sequence: w 628 2
read_al_374_> Non-standard residue type,position,sequence: w 629 2
read_al_374_> Non-standard residue type,position,sequence: w 630 2
read_al_374_> Non-standard residue type,position,sequence: w 631 2
read_al_374_> Non-standard residue type,position,sequence: w 632 2
read_al_374_> Non-standard residue type,position,sequence: w 633 2
read_al_374_> Non-standard residue type,position,sequence: w 634 2
read_al_374_> Non-standard residue type,position,sequence: w 635 2
read_al_374_> Non-standard residue type,position,sequence: w 636 2
read_al_374_> Non-standard residue type,position,sequence: w 637 2
read_al_374_> Non-standard residue type,position,sequence: w 638 2
read_al_374_> Non-standard residue type,position,sequence: w 639 2
read_al_374_> Non-standard residue type,position,sequence: w 640 2
read_al_374_> Non-standard residue type,position,sequence: w 641 2
read_al_374_> Non-standard residue type,position,sequence: w 642 2
read_al_374_> Non-standard residue type,position,sequence: w 643 2
read_al_374_> Non-standard residue type,position,sequence: w 644 2
read_al_374_> Non-standard residue type,position,sequence: w 645 2
read_al_374_> Non-standard residue type,position,sequence: w 646 2
read_al_374_> Non-standard residue type,position,sequence: w 647 2
read_al_374_> Non-standard residue type,position,sequence: w 648 2
read_al_374_> Non-standard residue type,position,sequence: w 649 2
read_al_374_> Non-standard residue type,position,sequence: w 650 2
read_al_374_> Non-standard residue type,position,sequence: w 651 2
read_al_374_> Non-standard residue type,position,sequence: w 652 2
read_al_374_> Non-standard residue type,position,sequence: w 653 2
read_al_374_> Non-standard residue type,position,sequence: w 654 2
read_al_374_> Non-standard residue type,position,sequence: w 655 2
read_al_374_> Non-standard residue type,position,sequence: w 656 2
read_al_374_> Non-standard residue type,position,sequence: w 657 2
read_al_374_> Non-standard residue type,position,sequence: w 658 2
read_al_374_> Non-standard residue type,position,sequence: w 659 2
read_al_374_> Non-standard residue type,position,sequence: w 660 2
read_al_374_> Non-standard residue type,position,sequence: w 661 2
read_al_374_> Non-standard residue type,position,sequence: w 662 2
read_al_374_> Non-standard residue type,position,sequence: w 663 2
read_al_374_> Non-standard residue type,position,sequence: w 664 2
read_al_374_> Non-standard residue type,position,sequence: w 665 2
read_al_374_> Non-standard residue type,position,sequence: w 666 2
read_al_374_> Non-standard residue type,position,sequence: w 667 2
read_al_374_> Non-standard residue type,position,sequence: w 668 2
read_al_374_> Non-standard residue type,position,sequence: w 669 2
read_al_374_> Non-standard residue type,position,sequence: w 670 2
read_al_374_> Non-standard residue type,position,sequence: w 671 2
read_al_374_> Non-standard residue type,position,sequence: w 672 2
read_al_374_> Non-standard residue type,position,sequence: w 673 2
read_al_374_> Non-standard residue type,position,sequence: w 674 2
read_al_374_> Non-standard residue type,position,sequence: w 675 2
read_al_374_> Non-standard residue type,position,sequence: w 676 2
read_al_374_> Non-standard residue type,position,sequence: w 677 2
read_al_374_> Non-standard residue type,position,sequence: w 678 2
read_al_374_> Non-standard residue type,position,sequence: w 679 2
read_al_374_> Non-standard residue type,position,sequence: w 680 2
read_al_374_> Non-standard residue type,position,sequence: w 681 2
read_al_374_> Non-standard residue type,position,sequence: w 682 2
read_al_374_> Non-standard residue type,position,sequence: w 683 2
read_al_374_> Non-standard residue type,position,sequence: w 684 2
read_al_374_> Non-standard residue type,position,sequence: w 685 2
read_al_374_> Non-standard residue type,position,sequence: w 686 2
read_al_374_> Non-standard residue type,position,sequence: w 687 2
read_al_374_> Non-standard residue type,position,sequence: w 688 2
read_al_374_> Non-standard residue type,position,sequence: w 689 2
read_al_374_> Non-standard residue type,position,sequence: w 690 2
read_al_374_> Non-standard residue type,position,sequence: w 691 2
Read the alignment from file : alignment.ali
Total number of alignment positions: 691
# Code #_Res #_Segm PDB_code Name
\-------------------------------------------------------------------------------
1 5byz_star 691 1 5byz_start.
2 chain_A 691 1 chain_A
check_a_343_> >> BEGINNING OF COMMAND
openf___224_> Open ./5byz_start.pdb_1.pdb
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 743254 725.834
0.709
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 743254 725.834 0.709
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 743425 726.001
0.709
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 744275 726.831
0.710
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 745533 728.060
0.711
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 747437 729.919
0.713
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 747437 729.919 0.713
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 747527 730.007
0.713
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 750383 732.796
0.716
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 750383 732.796 0.716
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 750518 732.928
0.716
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 754802 737.111
0.720
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 754802 737.111 0.720
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 755000 737.305
0.720
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 761426 743.580
0.726
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 761426 743.580 0.726
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 761723 743.870
0.726
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 771345 753.267
0.736
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 771345 753.267 0.736
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 771795 753.706
0.736
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 786245 767.817
0.750
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 786245 767.817 0.750
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 786920 768.477
0.750
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 808578 789.627
0.771
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 808578 789.627 0.771
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 809586 790.611
0.772
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 842090 822.354
0.803
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 842090 822.354 0.803
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 843602 823.830
0.805
read_pd_459W> Residue type 4WE not recognized. 'AutoModel' model building
will treat this residue as a rigid body.
To use real parameters, add the residue type to ${LIB}/restyp.lib,
its topology to ${LIB}/top_*.lib, and suitable forcefield
parameters to ${LIB}/par.lib.
read_pd_459W> Residue type GOL not recognized. 'AutoModel' model building
will treat this residue as a rigid body.
To use real parameters, add the residue type to ${LIB}/restyp.lib,
its topology to ${LIB}/top_*.lib, and suitable forcefield
parameters to ${LIB}/par.lib.
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 892358 871.443
0.851
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 892358 871.443 0.851
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 894626 873.658
0.853
Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 894032 873.078
0.853
fndatmi_285W> Only 348 residues out of 691 contain atoms of type CA
(This is usually caused by non-standard residues, such
as ligands, or by PDB files with missing atoms.)
fndatmi_285W> Only 348 residues out of 691 contain atoms of type CA
(This is usually caused by non-standard residues, such
as ligands, or by PDB files with missing atoms.)
check_ali___> Checking the sequence-structure alignment.
Implied intrachain target CA(i)-CA(i+1) distances longer than 8.0 angstroms:
ALN_POS TMPL RID1 RID2 NAM1 NAM2 DIST
\----------------------------------------------
END OF TABLE
check_a_344_> << END OF COMMAND
openf___224_> Open ${LIB}/top_heav.lib
read_to_681_> topology.submodel read from topology file: 3
openf___224_> Open ${LIB}/par.lib
Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 1033284 1009.066
0.985
Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 1034884 1010.629
0.987
Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 1038864 1014.516
0.991
Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 1040864 1016.469
0.993
Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 1043864 1019.398
0.996
Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 1048364 1023.793
1.000
Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 1053936 1029.234
1.005
Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 1056736 1031.969
1.008
Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 1060936 1036.070
1.012
Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 1067236 1042.223
1.018
Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 1070008 1044.930
1.020
Dynamically allocated memory at amaxparameters [B,KiB,MiB]: 1071408 1046.297
1.022
read_pa_232_> parameters BONDS ANGLS DIHEDS IMPROPS MODE
227 561 661 112 0
Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 1179738 1152.088 1.125
Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 1489320 1454.414 1.420
Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 1491378 1456.424 1.422
Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 1493436 1458.434 1.424
Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 1495494 1460.443 1.426
Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 1537982 1501.936 1.467
getf_______W> RTF restraint not found in the atoms list:
residue type, indices: 8 348
atom names : C +N
atom indices : 2803 0
getf_______W> RTF restraint not found in the atoms list:
residue type, indices: 8 348
atom names : C CA +N O
atom indices : 2803 2798 0 2804
mkilst______> segment topology constructed from sequence and RTF:
segments residues atoms bonds angles dihedrals impropers:
1 691 3210 2873 0 0 1219
Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 1658450 1619.580 1.582
patch_______> segment topology patched using RTF: 1 ; THR ; NTER
segments residues atoms bonds angles dihedrals impropers:
1 691 3210 2873 3896 4609 1219
Dynamically allocated memory at amaxmodel [B,KiB,MiB]: 1791026 1749.049 1.708
patch_______> segment topology patched using RTF: 348 ; ILE ; CTER
segments residues atoms bonds angles dihedrals impropers:
1 691 3211 2874 3898 4611 1220
genseg______> segment topology constructed from sequence and RTF:
segments residues atoms bonds angles dihedrals impropers:
1 691 3211 2874 3898 4611 1220
fndatmi_285W> Only 348 residues out of 691 contain atoms of type CA
(This is usually caused by non-standard residues, such
as ligands, or by PDB files with missing atoms.)
transfe_506_> MODEL is an average of all templates.
transfe_511_> Number of templates for coordinate transfer: 1
After transferring coordinates of the equivalent template atoms,
there are defined, undefined atoms in MODEL: 3210 1
openf___224_> Open chain_A.ini
wrpdb___568_> Residues, atoms, selected atoms: 691 3211 3211
make_re_417_> Restraint type to be calculated: stereo
Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 1898475 1853.979
1.811
Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 1906667 1861.979
1.818
Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 1923051 1877.979
1.834
Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 1955819 1909.979
1.865
Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 1988587 1941.979
1.896
Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 2054123 2005.979
1.959
Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 2086891 2037.979
1.990
Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 2119659 2069.979
2.021
Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 2185195 2133.979
2.084
Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 2316267 2261.979
2.209
Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 2381803 2325.979
2.271
Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 2447339 2389.979
2.334
Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 2578411 2517.979
2.459
Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 2840555 2773.979
2.709
Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 2971627 2901.979
2.834
r_stere_606_> Stereochemical restraints were constructed from RTF & PRMF.
Added bond,angle,dihedral,improper restraints : 2874 3898 4424 1199
Total number of restraints before, now : 0 12395
make_re_422_> Number of previous, current restraints : 0 12395
make_re_423_> Number of previous, current selected restraints: 0 12395
make_re_417_> Restraint type to be calculated: phi-psi_binormal
Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 3293355 3216.167
3.141
openf___224_> Open ${MODINSTALL10v4}/modlib/mnch1.bin
openf___224_> Open ${MODINSTALL10v4}/modlib/mnch1.mdt
errdih__638_> Missing atoms in a dihedral, residue index, residue type: 1 347
GLY
errdih__638_> Missing atoms in a dihedral, residue index, residue type: 1 348
ILE
errdih__638_> Missing atoms in a dihedral, residue index, residue type: 3 348
ILE
errdih__638_> Missing atoms in a dihedral, residue index, residue type: 4 348
ILE
getdata_643_> Protein accepted: 5byz_start.pdb_1
getdata_289_> Proteins (all/accepted): 1 1
make_re_422_> Number of previous, current restraints : 12395 12741
make_re_423_> Number of previous, current selected restraints: 12395 12741
make_re_417_> Restraint type to be calculated: omega_dihedral
Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 3293371 3216.183
3.141
openf___224_> Open ${MODINSTALL10v4}/modlib/omega.bin
openf___224_> Open ${MODINSTALL10v4}/modlib/omega.mdt
getdata_643_> Protein accepted: 5byz_start.pdb_1
getdata_289_> Proteins (all/accepted): 1 1
omgdel__425_> Unselected all O C +N +CA dihedrals: 368
(This is to avoid clashes between STEREO
and OMEGA_DIHEDRAL restraints)
make_re_422_> Number of previous, current restraints : 12741 13088
make_re_423_> Number of previous, current selected restraints: 12741 12720
make_re_417_> Restraint type to be calculated: chi1_dihedral
Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 3293371 3216.183
3.141
openf___224_> Open ${MODINSTALL10v4}/modlib/chi1234.bin
openf___224_> Open ${MODINSTALL10v4}/modlib/chi1.mdt
getdata_643_> Protein accepted: 5byz_start.pdb_1
getdata_289_> Proteins (all/accepted): 1 1
Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 3424443 3344.183
3.266
make_re_422_> Number of previous, current restraints : 13088 13387
make_re_423_> Number of previous, current selected restraints: 12720 13019
make_re_417_> Restraint type to be calculated: chi2_dihedral
Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 3424443 3344.183
3.266
openf___224_> Open ${MODINSTALL10v4}/modlib/chi1234.bin
openf___224_> Open ${MODINSTALL10v4}/modlib/chi2.mdt
getdata_643_> Protein accepted: 5byz_start.pdb_1
getdata_289_> Proteins (all/accepted): 1 1
make_re_422_> Number of previous, current restraints : 13387 13629
make_re_423_> Number of previous, current selected restraints: 13019 13261
make_re_417_> Restraint type to be calculated: chi3_dihedral
Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 3424443 3344.183
3.266
openf___224_> Open ${MODINSTALL10v4}/modlib/chi1234.bin
openf___224_> Open ${MODINSTALL10v4}/modlib/chi3.mdt
getdata_643_> Protein accepted: 5byz_start.pdb_1
getdata_289_> Proteins (all/accepted): 1 1
make_re_422_> Number of previous, current restraints : 13629 13739
make_re_423_> Number of previous, current selected restraints: 13261 13371
make_re_417_> Restraint type to be calculated: chi4_dihedral
Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 3424443 3344.183
3.266
openf___224_> Open ${MODINSTALL10v4}/modlib/chi1234.bin
openf___224_> Open ${MODINSTALL10v4}/modlib/chi4.mdt
mdtrsr__446W> A potential that relies on one protein is used, yet you have at
least one known structure available. MDT, not library, potential is used.
getdata_643_> Protein accepted: 5byz_start.pdb_1
getdata_289_> Proteins (all/accepted): 1 1
make_re_422_> Number of previous, current restraints : 13739 13780
make_re_423_> Number of previous, current selected restraints: 13371 13412
make_re_417_> Restraint type to be calculated: DISTANCE
Dynamically allocated memory at amaxhash_contac [B,KiB,MiB]: 4349175 4247.241
4.148
iup2crm_280W> No topology library in memory or assigning a BLK residue.
Default CHARMM atom type assigned: C1 --> CT2
This message is written only for the first such atom.
Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 4611319 4503.241
4.398
Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 4873463 4759.241
4.648
Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 5397751 5271.241
5.148
make_re_422_> Number of previous, current restraints : 13780 20776
make_re_423_> Number of previous, current selected restraints: 13412 20408
make_re_417_> Restraint type to be calculated: DISTANCE
Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 5659895 5527.241
5.398
make_re_422_> Number of previous, current restraints : 20776 27696
make_re_423_> Number of previous, current selected restraints: 20408 27328
make_re_417_> Restraint type to be calculated: DISTANCE
Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 6184183 6039.241
5.898
make_re_422_> Number of previous, current restraints : 27696 33339
make_re_423_> Number of previous, current selected restraints: 27328 32971
make_re_417_> Restraint type to be calculated: DISTANCE
make_re_422_> Number of previous, current restraints : 33339 37114
make_re_423_> Number of previous, current selected restraints: 32971 36746
406 atoms in HETATM/BLK residues constrained
to protein atoms within 2.30 angstroms
and protein CA atoms within 10.00 angstroms
make_re_417_> Restraint type to be calculated: DISTANCE
make_re_422_> Number of previous, current restraints : 37114 37115
make_re_423_> Number of previous, current selected restraints: 36746 36747
make_re_417_> Restraint type to be calculated: DISTANCE
Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 7232759 7063.241
6.898
make_re_422_> Number of previous, current restraints : 37115 43026
make_re_423_> Number of previous, current selected restraints: 36747 42658
make_re_417_> Restraint type to be calculated: DISTANCE
make_re_422_> Number of previous, current restraints : 43026 43026
make_re_423_> Number of previous, current selected restraints: 42658 42658
make_re_417_> Restraint type to be calculated: DISTANCE
make_re_422_> Number of previous, current restraints : 43026 44463
make_re_423_> Number of previous, current selected restraints: 42658 44095
70 atoms in residues without defined topology
constrained to be rigid bodies
make_re_417_> Restraint type to be calculated: DISTANCE
make_re_422_> Number of previous, current restraints : 44463 45553
make_re_423_> Number of previous, current selected restraints: 44095 45185
rmdupl__427_> 2178 redundant cosine dihedral restraints were unselected.
condens_443_> Restraints marked for deletion were removed.
Total number of restraints before, now: 45553 43007
openf___224_> Open chain_A.rsr
openf___224_> Open chain_A.rsr
Dynamically allocated memory at amaxrestraints [B,KiB,MiB]: 7328327 7156.569
6.989
rdcsr2__307_> Number of restraints read : 43007
Number of excluded pairs read: 1
Number of pseudo atoms read : 0
rdcsrs__304_> Restraints in memory, selected restraints: 43007 43007
Explicitly excluded atom pairs in memory : 1
Pseudo atoms in memory : 0
No output models from Modeller; see log for Modeller text output.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.7-rc2023.11.15.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/gui.py", line 717, in customEvent
func(*args, **kw)
File
"/Applications/ChimeraX-1.7-rc2023.11.15.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/modeller/common.py", line 602, in on_finish
self.caller.process_ok_models(model_info, get_pdb_model)
^^^^^^^^^^
UnboundLocalError: cannot access local variable 'model_info' where it is not
associated with a value
UnboundLocalError: cannot access local variable 'model_info' where it is not
associated with a value
File
"/Applications/ChimeraX-1.7-rc2023.11.15.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/modeller/common.py", line 602, in on_finish
self.caller.process_ok_models(model_info, get_pdb_model)
^^^^^^^^^^
See log for complete Python traceback.
OpenGL version: 4.1 Metal - 88
OpenGL renderer: Apple M2
OpenGL vendor: Apple
Python: 3.11.2
Locale: UTF-8
Qt version: PyQt6 6.3.1, Qt 6.3.1
Qt runtime version: 6.3.2
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Air
Model Identifier: Mac14,2
Model Number: Z15W000NACZ/A
Chip: Apple M2
Total Number of Cores: 8 (4 performance and 4 efficiency)
Memory: 16 GB
System Firmware Version: 10151.41.12
OS Loader Version: 10151.41.12
Software:
System Software Overview:
System Version: macOS 14.1.1 (23B81)
Kernel Version: Darwin 23.1.0
Time since boot: 4 days, 10 hours, 10 minutes
Graphics/Displays:
Apple M2:
Chipset Model: Apple M2
Type: GPU
Bus: Built-In
Total Number of Cores: 8
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
Color LCD:
Display Type: Built-in Liquid Retina Display
Resolution: 2560 x 1664 Retina
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
Installed Packages:
alabaster: 0.7.13
appdirs: 1.4.4
appnope: 0.1.3
asttokens: 2.4.1
Babel: 2.13.1
backcall: 0.2.0
beautifulsoup4: 4.11.2
blockdiag: 3.0.0
blosc2: 2.0.0
build: 0.10.0
certifi: 2022.12.7
cftime: 1.6.3
charset-normalizer: 3.3.2
ChimeraX-AddCharge: 1.5.12
ChimeraX-AddH: 2.2.5
ChimeraX-AlignmentAlgorithms: 2.0.1
ChimeraX-AlignmentHdrs: 3.4.1
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.12.1
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.1.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.49.1
ChimeraX-AtomicLibrary: 12.1
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: 2.0.4
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.10.5
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: 1.1
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: 1.5.5
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.7rc202311150127
ChimeraX-CoreFormats: 1.2
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: 1.1.2
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: 1.2.2
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-IUPAC: 1.0
ChimeraX-Label: 1.1.8
ChimeraX-ListInfo: 1.2.1
ChimeraX-Log: 1.1.6
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
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: 2.1.2
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.6
ChimeraX-MedicalToolbar: 1.0.2
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.12.1
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.12
ChimeraX-ModelPanel: 1.4
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0.3
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.1
ChimeraX-NRRD: 1.1
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.13
ChimeraX-PDB: 2.7.2
ChimeraX-PDBBio: 1.0.1
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-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.1
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.2
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 4.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.2
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.11
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.1.1
ChimeraX-ShowSequences: 1.0.2
ChimeraX-SideView: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.12.2
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: 2.2.2
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1.2
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.33.2
ChimeraX-uniprot: 2.3
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.3.2
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-vrml: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.3
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.0
contourpy: 1.2.0
cxservices: 1.2.2
cycler: 0.12.1
Cython: 0.29.33
debugpy: 1.8.0
decorator: 5.1.1
docutils: 0.19
executing: 2.0.1
filelock: 3.9.0
fonttools: 4.44.1
funcparserlib: 1.0.1
glfw: 2.6.2
grako: 3.16.5
h5py: 3.10.0
html2text: 2020.1.16
idna: 3.4
ihm: 0.38
imagecodecs: 2023.9.18
imagesize: 1.4.1
ipykernel: 6.23.2
ipython: 8.14.0
ipython-genutils: 0.2.0
ipywidgets: 8.1.1
jedi: 0.18.2
Jinja2: 3.1.2
jupyter-client: 8.2.0
jupyter-core: 5.5.0
jupyterlab-widgets: 3.0.9
kiwisolver: 1.4.5
line-profiler: 4.0.2
lxml: 4.9.2
lz4: 4.3.2
MarkupSafe: 2.1.3
matplotlib: 3.7.2
matplotlib-inline: 0.1.6
msgpack: 1.0.4
nest-asyncio: 1.5.8
netCDF4: 1.6.2
networkx: 3.1
nibabel: 5.0.1
nptyping: 2.5.0
numexpr: 2.8.7
numpy: 1.25.1
openvr: 1.23.701
packaging: 21.3
ParmEd: 3.4.3
parso: 0.8.3
pep517: 0.13.0
pexpect: 4.8.0
pickleshare: 0.7.5
Pillow: 10.0.1
pip: 23.0
pkginfo: 1.9.6
platformdirs: 4.0.0
prompt-toolkit: 3.0.41
psutil: 5.9.5
ptyprocess: 0.7.0
pure-eval: 0.2.2
py-cpuinfo: 9.0.0
pycollada: 0.7.2
pydicom: 2.3.0
Pygments: 2.16.1
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.2801
pyparsing: 3.0.9
pyproject-hooks: 1.0.0
PyQt6-commercial: 6.3.1
PyQt6-Qt6: 6.3.2
PyQt6-sip: 13.4.0
PyQt6-WebEngine-commercial: 6.3.1
PyQt6-WebEngine-Qt6: 6.3.2
python-dateutil: 2.8.2
pytz: 2023.3.post1
pyzmq: 25.1.1
qtconsole: 5.4.3
QtPy: 2.4.1
RandomWords: 0.4.0
requests: 2.31.0
scipy: 1.11.1
setuptools: 67.4.0
setuptools-scm: 7.0.5
sfftk-rw: 0.7.3
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.5
sphinx: 6.1.3
sphinx-autodoc-typehints: 1.22
sphinxcontrib-applehelp: 1.0.7
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.5
sphinxcontrib-htmlhelp: 2.0.4
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.6
sphinxcontrib-serializinghtml: 1.1.9
stack-data: 0.6.3
superqt: 0.5.0
tables: 3.8.0
tcia-utils: 1.5.1
tifffile: 2023.7.18
tinyarray: 1.2.4
tomli: 2.0.1
tornado: 6.3.3
traitlets: 5.9.0
typing-extensions: 4.8.0
tzdata: 2023.3
urllib3: 2.1.0
wcwidth: 0.2.10
webcolors: 1.12
wheel: 0.38.4
wheel-filename: 1.4.1
widgetsnbextension: 4.0.9
Change History (2)
comment:1 by , 2 years ago
| Component: | Unassigned → Structure Prediction |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → accepted |
| Summary: | ChimeraX bug report submission → Error when no output models from Modeller |
comment:2 by , 2 years ago
| Resolution: | → fixed |
|---|---|
| Status: | accepted → closed |
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Fix: https://github.com/RBVI/ChimeraX/commit/f0937307f0057fe9e0f5f230fb862792517c90fc