Opened 3 years ago

Closed 3 years ago

#7810 closed defect (nonchimerax)

UNK residues that should not be UNK

Reported by: Elaine Meng Owned by: pett
Priority: normal Milestone:
Component: Structure Editing Version:
Keywords: Cc:
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        macOS-12.6-arm64-arm-64bit
ChimeraX Version: 1.5.dev202210150056 (2022-10-15 00:56:37 UTC)
Description
tried to use dockprep with defaults on 3j5q

Have not investigated carefully but I think it has a bunch of truncated side chains and maybe some are incorrectly named ALA

Log:
> open /Users/meng/Desktop/startup.cxc

> alias reset view orient; view initial

> alias start tool show $1

> alias whereprefs info path user unversioned config

> alias captut open help:user/tutorials/binding-sites.html#cap-example

> alias previewts toolshed url https://cxtoolshed-
> preview.rbvi.ucsf.edu;toolshed reload available

> alias normalts toolshed url https://cxtoolshed.rbvi.ucsf.edu;toolshed reload
> available

> alias btut open
> https://www.cgl.ucsf.edu/home/meng/chimerax/vdocs/user/tutorials/binding-
> sites.html

> alias stut open https://www.rbvi.ucsf.edu/chimerax/data/conservation-
> coloring/conservation-coloring.html

> alias ltut open https://www.rbvi.ucsf.edu/chimerax/data/loop-modeling/loop-
> modeling.html; ui dockable false "Help Viewer"

executed startup.cxc  
UCSF ChimeraX version: 1.5.dev202210150056 (2022-10-15)  
© 2016-2022 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open molepore-3j5q.json

Opened 1 Mole channels in PDB 3j5q  

> open 3j5q

Summary of feedback from opening 3j5q fetched from pdb  
---  
warnings | Atom SG is not in the residue template for UNK /A:2  
Atom HA2 is not in the residue template for UNK /A:7  
Atom HA2 is not in the residue template for UNK /A:8  
Atom SG is not in the residue template for UNK /A:9  
Atom SG is not in the residue template for UNK /A:15  
Atom SG is not in the residue template for UNK /A:16  
Atom HA2 is not in the residue template for UNK /A:20  
Atom SG is not in the residue template for UNK /A:21  
Atom SG is not in the residue template for UNK /A:28  
Atom HB3 is not in the residue template for UNK /A:29  
Atom SG is not in the residue template for UNK /C:2  
Atom HA2 is not in the residue template for UNK /C:7  
Atom HA2 is not in the residue template for UNK /C:8  
Atom SG is not in the residue template for UNK /C:9  
Atom SG is not in the residue template for UNK /C:15  
Atom SG is not in the residue template for UNK /C:16  
Atom HA2 is not in the residue template for UNK /C:20  
Atom SG is not in the residue template for UNK /C:21  
Atom SG is not in the residue template for UNK /C:28  
Atom HB3 is not in the residue template for UNK /C:29  
Atom SG is not in the residue template for UNK /F:2  
Atom HA2 is not in the residue template for UNK /F:7  
Too many hydrogens missing from residue template(s) to warn about  
Atom SG is not in the residue template for UNK /F:9  
Atom SG is not in the residue template for UNK /F:15  
Atom SG is not in the residue template for UNK /F:16  
Atom SG is not in the residue template for UNK /F:21  
Atom SG is not in the residue template for UNK /F:28  
6 messages similar to the above omitted  
note | Fetching compressed mmCIF 3j5q from
http://files.rcsb.org/download/3j5q.cif  
  
3j5q title:  
Structure of TRPV1 ion channel in complex with DkTx and RTX determined by
single particle electron cryo-microscopy [more info...]  
  
Chain information for 3j5q #2  
---  
Chain | Description | UniProt  
A C F H | Double-knot toxin |  
B D E G | Transient receptor potential cation channel subfamily V member 1 |
TRPV1_RAT  
  

> ribbon

> hide #2

> view

> surface #1.1

> style #1 stick

Changed 906 atom styles  

> mlp protein surfaces #1.1

Map values for surface "Path 1_A SES surface": minimum -18.41, mean -1.174,
maximum 20.09  

> coulombic protein surfaces #1.1

Using Amber 20 recommended default charges and atom types for standard
residues  
Nonstandard name for heavy atom copy of 3j5q #/F UNK 15 SG  

> dockprep #2

Deleting solvent  
Deleting non-metal-complex ions  
Deleting non-current alt locs  
Filling out missing side chains  
3j5q #2/D ARG 355: phi -81.4, psi 71.2 trans  
3j5q #2/D GLU 356: phi -64.3, psi 140.2 trans  
3j5q #2/D ILE 357: phi -123.7, psi 134.8 trans  
3j5q #2/D GLU 361: phi 79.5, psi 4.8 trans  
3j5q #2/D ARG 363: phi -61.5, psi -39.8 trans  
3j5q #2/D LEU 365: phi -69.4, psi -42.3 trans  
3j5q #2/D LYS 368: phi -115.7, psi 131.6 trans  
3j5q #2/D THR 370: phi -120.9, psi 130.6 trans  
3j5q #2/D GLU 371: phi -151.3, psi 69.7 trans  
3j5q #2/D TYR 374: phi -112.6, psi 152.3 trans  
3j5q #2/D VAL 377: phi -127.9, psi 161.0 trans  
3j5q #2/D HIS 378: phi -152.2, psi 155.1 trans  
3j5q #2/D SER 380: phi -123.2, psi 137.9 trans  
3j5q #2/D ILE 387: phi -62.7, psi -39.8 trans  
3j5q #2/D ASP 388: phi -62.8, psi -39.0 trans  
3j5q #2/D THR 389: phi -59.9, psi 131.1 trans  
3j5q #2/D GLU 391: phi -59.7, psi -41.1 trans  
3j5q #2/D LYS 392: phi -73.6, psi 158.4 trans  
3j5q #2/D SER 394: phi 81.5, psi 169.6 trans  
3j5q #2/D VAL 395: phi -66.7, psi -46.0 trans  
3j5q #2/D LEU 396: phi -65.4, psi -44.0 trans  
3j5q #2/D GLU 397: phi -63.7, psi -43.6 trans  
3j5q #2/D VAL 398: phi -63.3, psi -42.3 trans  
3j5q #2/D GLU 405: phi -67.1, psi -41.0 trans  
3j5q #2/D THR 406: phi 87.8, psi -5.6 trans  
3j5q #2/D ARG 409: phi -40.7, psi -43.2 trans  
3j5q #2/D HIS 410: phi -64.9, psi -41.7 trans  
3j5q #2/D ASP 411: phi -70.6, psi -41.1 trans  
3j5q #2/D MET 412: phi -62.9, psi -38.9 trans  
3j5q #2/D VAL 415: phi -141.5, psi 171.5 trans  
3j5q #2/D GLU 416: phi -67.0, psi -40.8 cis  
3j5q #2/D LEU 418: phi -60.9, psi -48.2 trans  
3j5q #2/D ASN 419: phi -68.5, psi -46.2 trans  
3j5q #2/D ARG 420: phi -65.3, psi -44.5 trans  
3j5q #2/D LEU 422: phi -62.9, psi -42.5 trans  
3j5q #2/D ASP 424: phi -65.0, psi -41.4 trans  
3j5q #2/D ASP 427: phi -60.9, psi -42.7 trans  
3j5q #2/D ARG 428: phi -64.3, psi -45.5 trans  
3j5q #2/D LYS 431: phi -57.0, psi -41.2 trans  
3j5q #2/D ARG 432: phi -63.5, psi -41.6 trans  
3j5q #2/D LEU 443: phi -63.8, psi -37.9 trans  
3j5q #2/D THR 449: phi -67.6, psi -40.6 trans  
3j5q #2/D VAL 457: phi -63.0, psi -40.4 trans  
3j5q #2/D GLU 458: phi 57.6, psi -133.8 trans  
3j5q #2/D LEU 460: phi -125.0, psi 125.2 trans  
3j5q #2/D PRO 461: phi 54.8, psi -131.4 trans  
3j5q #2/D PRO 462: phi -72.5, psi 157.5 trans  
3j5q #2/D TYR 463: phi -71.5, psi 143.0 cis  
3j5q #2/D LYS 464: phi -120.7, psi 127.6 trans  
3j5q #2/D LYS 466: phi 56.3, psi 38.6 trans  
3j5q #2/D THR 468: phi 83.6, psi 178.6 trans  
3j5q #2/D VAL 469: phi -63.7, psi -42.0 trans  
3j5q #2/D ASP 471: phi -86.9, psi -7.8 trans  
3j5q #2/D THR 476: phi -62.6, psi -43.1 trans  
3j5q #2/D GLU 478: phi -63.2, psi -44.4 trans  
3j5q #2/D ILE 479: phi -64.6, psi -42.0 trans  
3j5q #2/D LEU 480: phi -63.5, psi -42.6 trans  
3j5q #2/D SER 481: phi -63.9, psi -43.9 trans  
3j5q #2/D SER 483: phi -62.6, psi -39.5 trans  
3j5q #2/D VAL 486: phi -62.5, psi -37.5 trans  
3j5q #2/D PHE 489: phi -67.4, psi -44.3 trans  
3j5q #2/D ARG 491: phi -66.9, psi -40.7 trans  
3j5q #2/D ILE 493: phi -61.9, psi -39.8 trans  
3j5q #2/D GLN 494: phi -62.3, psi -40.2 trans  
3j5q #2/D LEU 497: phi -69.4, psi -44.7 trans  
3j5q #2/D ARG 500: phi -62.9, psi -40.3 trans  
3j5q #2/D PRO 501: phi -63.7, psi 139.5 trans  
3j5q #2/D ASP 509: phi -107.6, psi 131.2 trans  
3j5q #2/D LEU 524: phi -62.5, psi -40.1 trans  
3j5q #2/D VAL 527: phi -64.8, psi -42.7 trans  
3j5q #2/D VAL 528: phi -62.5, psi -40.6 trans  
3j5q #2/D LEU 529: phi -63.2, psi -40.3 trans  
3j5q #2/D GLN 533: phi 82.4, psi 8.1 trans  
3j5q #2/D LYS 535: phi -61.0, psi -34.4 trans  
3j5q #2/D GLU 536: phi -61.9, psi -19.4 trans  
3j5q #2/D SER 540: phi -63.4, psi -41.3 trans  
3j5q #2/D MET 541: phi -63.5, psi -39.6 trans  
3j5q #2/D ASN 551: phi -62.7, psi -36.0 trans  
3j5q #2/D THR 556: phi -62.0, psi -21.3 trans  
3j5q #2/D GLN 561: phi -64.6, psi -57.6 trans  
3j5q #2/D ASP 601: phi 53.6, psi -137.0 trans  
3j5q #2/D LYS 656: phi -62.1, psi -41.7 trans  
3j5q #2/D LYS 698: phi -62.6, psi -45.7 trans  
3j5q #2/D GLN 700: phi -57.1, psi -42.6 trans  
3j5q #2/D ILE 703: phi -63.0, psi -41.7 trans  
3j5q #2/D THR 704: phi -62.5, psi -43.3 trans  
3j5q #2/D LEU 706: phi -64.0, psi -43.8 trans  
3j5q #2/D ASP 707: phi -63.7, psi -43.4 trans  
3j5q #2/D THR 708: phi -63.1, psi -41.7 trans  
3j5q #2/D GLU 709: phi -62.6, psi -42.5 trans  
3j5q #2/D PHE 712: phi -80.5, psi 15.4 trans  
3j5q #2/D LYS 714: phi 51.8, psi 40.5 trans  
3j5q #2/D CYS 715: phi -69.9, psi 163.2 trans  
3j5q #2/D MET 716: phi -57.0, psi 133.2 trans  
3j5q #2/D ARG 717: phi -160.3, psi 169.6 trans  
3j5q #2/D LYS 718: phi -57.6, psi 132.9 trans  
3j5q #2/B ARG 355: phi -81.3, psi 71.2 trans  
3j5q #2/B GLU 356: phi -64.3, psi 140.2 trans  
3j5q #2/B ILE 357: phi -123.7, psi 134.7 trans  
3j5q #2/B GLU 361: phi 79.5, psi 4.8 trans  
3j5q #2/B ARG 363: phi -61.5, psi -39.8 trans  
3j5q #2/B LEU 365: phi -69.3, psi -42.4 trans  
3j5q #2/B LYS 368: phi -115.6, psi 131.6 trans  
3j5q #2/B THR 370: phi -120.9, psi 130.6 trans  
3j5q #2/B GLU 371: phi -151.2, psi 69.6 trans  
3j5q #2/B TYR 374: phi -112.5, psi 152.3 trans  
3j5q #2/B VAL 377: phi -127.8, psi 161.0 trans  
3j5q #2/B HIS 378: phi -152.2, psi 155.1 trans  
3j5q #2/B SER 380: phi -123.1, psi 137.9 trans  
3j5q #2/B ILE 387: phi -62.6, psi -39.8 trans  
3j5q #2/B ASP 388: phi -62.8, psi -39.0 trans  
3j5q #2/B THR 389: phi -59.9, psi 131.1 trans  
3j5q #2/B GLU 391: phi -59.8, psi -41.1 trans  
3j5q #2/B LYS 392: phi -73.5, psi 158.3 trans  
3j5q #2/B SER 394: phi 81.5, psi 169.5 trans  
3j5q #2/B VAL 395: phi -66.7, psi -46.0 trans  
3j5q #2/B LEU 396: phi -65.4, psi -44.0 trans  
3j5q #2/B GLU 397: phi -63.7, psi -43.6 trans  
3j5q #2/B VAL 398: phi -63.3, psi -42.3 trans  
3j5q #2/B GLU 405: phi -67.1, psi -40.9 trans  
3j5q #2/B THR 406: phi 87.8, psi -5.6 trans  
3j5q #2/B ARG 409: phi -40.7, psi -43.2 trans  
3j5q #2/B HIS 410: phi -64.9, psi -41.7 trans  
3j5q #2/B ASP 411: phi -70.6, psi -41.1 trans  
3j5q #2/B MET 412: phi -62.8, psi -39.0 trans  
3j5q #2/B VAL 415: phi -141.5, psi 171.5 trans  
3j5q #2/B GLU 416: phi -67.0, psi -40.8 cis  
3j5q #2/B LEU 418: phi -60.9, psi -48.2 trans  
3j5q #2/B ASN 419: phi -68.5, psi -46.2 trans  
3j5q #2/B ARG 420: phi -65.2, psi -44.6 trans  
3j5q #2/B LEU 422: phi -62.9, psi -42.5 trans  
3j5q #2/B ASP 424: phi -64.9, psi -41.5 trans  
3j5q #2/B ASP 427: phi -60.9, psi -42.8 trans  
3j5q #2/B ARG 428: phi -64.3, psi -45.5 trans  
3j5q #2/B LYS 431: phi -56.9, psi -41.3 trans  
3j5q #2/B ARG 432: phi -63.5, psi -41.6 trans  
3j5q #2/B LEU 443: phi -63.8, psi -37.8 trans  
3j5q #2/B THR 449: phi -67.6, psi -40.6 trans  
3j5q #2/B VAL 457: phi -63.0, psi -40.3 trans  
3j5q #2/B GLU 458: phi 57.6, psi -133.8 trans  
3j5q #2/B LEU 460: phi -124.9, psi 125.3 trans  
3j5q #2/B PRO 461: phi 54.8, psi -131.3 trans  
3j5q #2/B PRO 462: phi -72.5, psi 157.5 trans  
3j5q #2/B TYR 463: phi -71.5, psi 143.0 cis  
3j5q #2/B LYS 464: phi -120.7, psi 127.5 trans  
3j5q #2/B LYS 466: phi 56.3, psi 38.6 trans  
3j5q #2/B THR 468: phi 83.6, psi 178.6 trans  
3j5q #2/B VAL 469: phi -63.7, psi -42.1 trans  
3j5q #2/B ASP 471: phi -86.9, psi -7.8 trans  
3j5q #2/B THR 476: phi -62.6, psi -43.2 trans  
3j5q #2/B GLU 478: phi -63.3, psi -44.4 trans  
3j5q #2/B ILE 479: phi -64.6, psi -42.0 trans  
3j5q #2/B LEU 480: phi -63.5, psi -42.6 trans  
3j5q #2/B SER 481: phi -64.0, psi -43.9 trans  
3j5q #2/B SER 483: phi -62.4, psi -39.6 trans  
3j5q #2/B VAL 486: phi -62.6, psi -37.4 trans  
3j5q #2/B PHE 489: phi -67.3, psi -44.3 trans  
3j5q #2/B ARG 491: phi -66.9, psi -40.7 trans  
3j5q #2/B ILE 493: phi -61.9, psi -39.8 trans  
3j5q #2/B GLN 494: phi -62.3, psi -40.3 trans  
3j5q #2/B LEU 497: phi -69.4, psi -44.7 trans  
3j5q #2/B ARG 500: phi -63.0, psi -40.2 trans  
3j5q #2/B PRO 501: phi -63.8, psi 139.4 trans  
3j5q #2/B ASP 509: phi -107.5, psi 131.2 trans  
3j5q #2/B LEU 524: phi -62.5, psi -40.1 trans  
3j5q #2/B VAL 527: phi -64.8, psi -42.7 trans  
3j5q #2/B VAL 528: phi -62.5, psi -40.7 trans  
3j5q #2/B LEU 529: phi -63.3, psi -40.2 trans  
3j5q #2/B GLN 533: phi 82.5, psi 8.1 trans  
3j5q #2/B LYS 535: phi -61.1, psi -34.3 trans  
3j5q #2/B GLU 536: phi -62.0, psi -19.4 trans  
3j5q #2/B SER 540: phi -63.4, psi -41.3 trans  
3j5q #2/B MET 541: phi -63.5, psi -39.6 trans  
3j5q #2/B ASN 551: phi -62.8, psi -36.0 trans  
3j5q #2/B THR 556: phi -62.0, psi -21.3 trans  
3j5q #2/B GLN 561: phi -64.6, psi -57.6 trans  
3j5q #2/B ASP 601: phi 53.6, psi -136.9 trans  
3j5q #2/B LYS 656: phi -62.1, psi -41.7 trans  
3j5q #2/B LYS 698: phi -62.7, psi -45.7 trans  
3j5q #2/B GLN 700: phi -57.1, psi -42.6 trans  
3j5q #2/B ILE 703: phi -63.0, psi -41.7 trans  
3j5q #2/B THR 704: phi -62.5, psi -43.2 trans  
3j5q #2/B LEU 706: phi -64.0, psi -43.8 trans  
3j5q #2/B ASP 707: phi -63.7, psi -43.4 trans  
3j5q #2/B THR 708: phi -63.2, psi -41.7 trans  
3j5q #2/B GLU 709: phi -62.6, psi -42.5 trans  
3j5q #2/B PHE 712: phi -80.6, psi 15.5 trans  
3j5q #2/B LYS 714: phi 51.8, psi 40.5 trans  
3j5q #2/B CYS 715: phi -69.8, psi 163.3 trans  
3j5q #2/B MET 716: phi -57.0, psi 133.2 trans  
3j5q #2/B ARG 717: phi -160.3, psi 169.6 trans  
3j5q #2/B LYS 718: phi -57.6, psi 132.9 trans  
3j5q #2/E ARG 355: phi -81.3, psi 71.2 trans  
3j5q #2/E GLU 356: phi -64.3, psi 140.1 trans  
3j5q #2/E ILE 357: phi -123.7, psi 134.7 trans  
3j5q #2/E GLU 361: phi 79.5, psi 4.8 trans  
3j5q #2/E ARG 363: phi -61.5, psi -39.8 trans  
3j5q #2/E LEU 365: phi -69.4, psi -42.3 trans  
3j5q #2/E LYS 368: phi -115.7, psi 131.6 trans  
3j5q #2/E THR 370: phi -120.9, psi 130.6 trans  
3j5q #2/E GLU 371: phi -151.3, psi 69.7 trans  
3j5q #2/E TYR 374: phi -112.5, psi 152.3 trans  
3j5q #2/E VAL 377: phi -127.9, psi 160.9 trans  
3j5q #2/E HIS 378: phi -152.1, psi 155.1 trans  
3j5q #2/E SER 380: phi -123.2, psi 137.9 trans  
3j5q #2/E ILE 387: phi -62.6, psi -39.8 trans  
3j5q #2/E ASP 388: phi -62.8, psi -38.9 trans  
3j5q #2/E THR 389: phi -59.9, psi 131.1 trans  
3j5q #2/E GLU 391: phi -59.7, psi -41.1 trans  
3j5q #2/E LYS 392: phi -73.6, psi 158.3 trans  
3j5q #2/E SER 394: phi 81.4, psi 169.5 trans  
3j5q #2/E VAL 395: phi -66.7, psi -46.0 trans  
3j5q #2/E LEU 396: phi -65.4, psi -44.1 trans  
3j5q #2/E GLU 397: phi -63.7, psi -43.6 trans  
3j5q #2/E VAL 398: phi -63.3, psi -42.3 trans  
3j5q #2/E GLU 405: phi -67.1, psi -40.9 trans  
3j5q #2/E THR 406: phi 87.8, psi -5.6 trans  
3j5q #2/E ARG 409: phi -40.7, psi -43.3 trans  
3j5q #2/E HIS 410: phi -64.9, psi -41.7 trans  
3j5q #2/E ASP 411: phi -70.6, psi -41.1 trans  
3j5q #2/E MET 412: phi -62.9, psi -39.0 trans  
3j5q #2/E VAL 415: phi -141.4, psi 171.6 trans  
3j5q #2/E GLU 416: phi -67.0, psi -40.8 cis  
3j5q #2/E LEU 418: phi -60.9, psi -48.2 trans  
3j5q #2/E ASN 419: phi -68.4, psi -46.3 trans  
3j5q #2/E ARG 420: phi -65.2, psi -44.6 trans  
3j5q #2/E LEU 422: phi -62.9, psi -42.5 trans  
3j5q #2/E ASP 424: phi -65.1, psi -41.4 trans  
3j5q #2/E ASP 427: phi -60.9, psi -42.8 trans  
3j5q #2/E ARG 428: phi -64.3, psi -45.6 trans  
3j5q #2/E LYS 431: phi -56.9, psi -41.3 trans  
3j5q #2/E ARG 432: phi -63.5, psi -41.6 trans  
3j5q #2/E LEU 443: phi -63.7, psi -37.9 trans  
3j5q #2/E THR 449: phi -67.5, psi -40.7 trans  
3j5q #2/E VAL 457: phi -63.0, psi -40.4 trans  
3j5q #2/E GLU 458: phi 57.6, psi -133.8 trans  
3j5q #2/E LEU 460: phi -125.0, psi 125.2 trans  
3j5q #2/E PRO 461: phi 54.8, psi -131.4 trans  
3j5q #2/E PRO 462: phi -72.5, psi 157.5 trans  
3j5q #2/E TYR 463: phi -71.5, psi 143.0 cis  
3j5q #2/E LYS 464: phi -120.7, psi 127.5 trans  
3j5q #2/E LYS 466: phi 56.3, psi 38.6 trans  
3j5q #2/E THR 468: phi 83.6, psi 178.6 trans  
3j5q #2/E VAL 469: phi -63.7, psi -42.0 trans  
3j5q #2/E ASP 471: phi -86.9, psi -7.8 trans  
3j5q #2/E THR 476: phi -62.5, psi -43.2 trans  
3j5q #2/E GLU 478: phi -63.3, psi -44.4 trans  
3j5q #2/E ILE 479: phi -64.5, psi -42.0 trans  
3j5q #2/E LEU 480: phi -63.5, psi -42.6 trans  
3j5q #2/E SER 481: phi -63.9, psi -43.9 trans  
3j5q #2/E SER 483: phi -62.5, psi -39.5 trans  
3j5q #2/E VAL 486: phi -62.5, psi -37.5 trans  
3j5q #2/E PHE 489: phi -67.4, psi -44.2 trans  
3j5q #2/E ARG 491: phi -66.8, psi -40.8 trans  
3j5q #2/E ILE 493: phi -61.9, psi -39.8 trans  
3j5q #2/E GLN 494: phi -62.2, psi -40.3 trans  
3j5q #2/E LEU 497: phi -69.4, psi -44.7 trans  
3j5q #2/E ARG 500: phi -63.0, psi -40.3 trans  
3j5q #2/E PRO 501: phi -63.7, psi 139.4 trans  
3j5q #2/E ASP 509: phi -107.6, psi 131.2 trans  
3j5q #2/E LEU 524: phi -62.5, psi -40.1 trans  
3j5q #2/E VAL 527: phi -64.8, psi -42.6 trans  
3j5q #2/E VAL 528: phi -62.5, psi -40.6 trans  
3j5q #2/E LEU 529: phi -63.3, psi -40.3 trans  
3j5q #2/E GLN 533: phi 82.4, psi 8.1 trans  
3j5q #2/E LYS 535: phi -61.2, psi -34.4 trans  
3j5q #2/E GLU 536: phi -61.9, psi -19.4 trans  
3j5q #2/E SER 540: phi -63.4, psi -41.3 trans  
3j5q #2/E MET 541: phi -63.5, psi -39.6 trans  
3j5q #2/E ASN 551: phi -62.7, psi -36.0 trans  
3j5q #2/E THR 556: phi -61.9, psi -21.4 trans  
3j5q #2/E GLN 561: phi -64.6, psi -57.6 trans  
3j5q #2/E ASP 601: phi 53.6, psi -137.0 trans  
3j5q #2/E LYS 656: phi -62.1, psi -41.7 trans  
3j5q #2/E LYS 698: phi -62.6, psi -45.7 trans  
3j5q #2/E GLN 700: phi -57.1, psi -42.6 trans  
3j5q #2/E ILE 703: phi -63.0, psi -41.7 trans  
3j5q #2/E THR 704: phi -62.5, psi -43.3 trans  
3j5q #2/E LEU 706: phi -64.1, psi -43.7 trans  
3j5q #2/E ASP 707: phi -63.7, psi -43.4 trans  
3j5q #2/E THR 708: phi -63.1, psi -41.7 trans  
3j5q #2/E GLU 709: phi -62.6, psi -42.5 trans  
3j5q #2/E PHE 712: phi -80.5, psi 15.5 trans  
3j5q #2/E LYS 714: phi 51.7, psi 40.6 trans  
3j5q #2/E CYS 715: phi -69.9, psi 163.3 trans  
3j5q #2/E MET 716: phi -57.1, psi 133.1 trans  
3j5q #2/E ARG 717: phi -160.3, psi 169.6 trans  
3j5q #2/E LYS 718: phi -57.6, psi 132.9 trans  
3j5q #2/G ARG 355: phi -81.3, psi 71.2 trans  
3j5q #2/G GLU 356: phi -64.3, psi 140.2 trans  
3j5q #2/G ILE 357: phi -123.7, psi 134.8 trans  
3j5q #2/G GLU 361: phi 79.5, psi 4.8 trans  
3j5q #2/G ARG 363: phi -61.5, psi -39.7 trans  
3j5q #2/G LEU 365: phi -69.4, psi -42.3 trans  
3j5q #2/G LYS 368: phi -115.7, psi 131.6 trans  
3j5q #2/G THR 370: phi -120.9, psi 130.6 trans  
3j5q #2/G GLU 371: phi -151.2, psi 69.7 trans  
3j5q #2/G TYR 374: phi -112.6, psi 152.3 trans  
3j5q #2/G VAL 377: phi -127.9, psi 160.9 trans  
3j5q #2/G HIS 378: phi -152.1, psi 155.1 trans  
3j5q #2/G SER 380: phi -123.2, psi 137.8 trans  
3j5q #2/G ILE 387: phi -62.6, psi -39.8 trans  
3j5q #2/G ASP 388: phi -62.8, psi -39.0 trans  
3j5q #2/G THR 389: phi -59.9, psi 131.1 trans  
3j5q #2/G GLU 391: phi -59.7, psi -41.1 trans  
3j5q #2/G LYS 392: phi -73.6, psi 158.3 trans  
3j5q #2/G SER 394: phi 81.5, psi 169.5 trans  
3j5q #2/G VAL 395: phi -66.6, psi -46.0 trans  
3j5q #2/G LEU 396: phi -65.4, psi -44.0 trans  
3j5q #2/G GLU 397: phi -63.8, psi -43.6 trans  
3j5q #2/G VAL 398: phi -63.3, psi -42.3 trans  
3j5q #2/G GLU 405: phi -67.1, psi -40.9 trans  
3j5q #2/G THR 406: phi 87.8, psi -5.6 trans  
3j5q #2/G ARG 409: phi -40.7, psi -43.2 trans  
3j5q #2/G HIS 410: phi -64.9, psi -41.6 trans  
3j5q #2/G ASP 411: phi -70.6, psi -41.1 trans  
3j5q #2/G MET 412: phi -62.9, psi -39.0 trans  
3j5q #2/G VAL 415: phi -141.5, psi 171.5 trans  
3j5q #2/G GLU 416: phi -67.1, psi -40.8 cis  
3j5q #2/G LEU 418: phi -60.9, psi -48.2 trans  
3j5q #2/G ASN 419: phi -68.5, psi -46.2 trans  
3j5q #2/G ARG 420: phi -65.2, psi -44.6 trans  
3j5q #2/G LEU 422: phi -62.9, psi -42.5 trans  
3j5q #2/G ASP 424: phi -65.0, psi -41.4 trans  
3j5q #2/G ASP 427: phi -60.9, psi -42.8 trans  
3j5q #2/G ARG 428: phi -64.3, psi -45.5 trans  
3j5q #2/G LYS 431: phi -56.9, psi -41.3 trans  
3j5q #2/G ARG 432: phi -63.5, psi -41.6 trans  
3j5q #2/G LEU 443: phi -63.7, psi -37.9 trans  
3j5q #2/G THR 449: phi -67.5, psi -40.6 trans  
3j5q #2/G VAL 457: phi -63.0, psi -40.4 trans  
3j5q #2/G GLU 458: phi 57.6, psi -133.9 trans  
3j5q #2/G LEU 460: phi -125.0, psi 125.2 trans  
3j5q #2/G PRO 461: phi 54.8, psi -131.4 trans  
3j5q #2/G PRO 462: phi -72.5, psi 157.5 trans  
3j5q #2/G TYR 463: phi -71.5, psi 143.0 cis  
3j5q #2/G LYS 464: phi -120.7, psi 127.5 trans  
3j5q #2/G LYS 466: phi 56.3, psi 38.6 trans  
3j5q #2/G THR 468: phi 83.6, psi 178.6 trans  
3j5q #2/G VAL 469: phi -63.6, psi -42.1 trans  
3j5q #2/G ASP 471: phi -86.9, psi -7.8 trans  
3j5q #2/G THR 476: phi -62.5, psi -43.1 trans  
3j5q #2/G GLU 478: phi -63.2, psi -44.4 trans  
3j5q #2/G ILE 479: phi -64.6, psi -42.0 trans  
3j5q #2/G LEU 480: phi -63.5, psi -42.6 trans  
3j5q #2/G SER 481: phi -64.0, psi -43.8 trans  
3j5q #2/G SER 483: phi -62.5, psi -39.6 trans  
3j5q #2/G VAL 486: phi -62.5, psi -37.4 trans  
3j5q #2/G PHE 489: phi -67.4, psi -44.3 trans  
3j5q #2/G ARG 491: phi -66.8, psi -40.7 trans  
3j5q #2/G ILE 493: phi -61.9, psi -39.8 trans  
3j5q #2/G GLN 494: phi -62.3, psi -40.2 trans  
3j5q #2/G LEU 497: phi -69.4, psi -44.7 trans  
3j5q #2/G ARG 500: phi -63.0, psi -40.3 trans  
3j5q #2/G PRO 501: phi -63.7, psi 139.5 trans  
3j5q #2/G ASP 509: phi -107.6, psi 131.1 trans  
3j5q #2/G LEU 524: phi -62.5, psi -40.0 trans  
3j5q #2/G VAL 527: phi -64.8, psi -42.7 trans  
3j5q #2/G VAL 528: phi -62.5, psi -40.6 trans  
3j5q #2/G LEU 529: phi -63.3, psi -40.2 trans  
3j5q #2/G GLN 533: phi 82.4, psi 8.1 trans  
3j5q #2/G LYS 535: phi -61.1, psi -34.4 trans  
3j5q #2/G GLU 536: phi -61.9, psi -19.4 trans  
3j5q #2/G SER 540: phi -63.4, psi -41.3 trans  
3j5q #2/G MET 541: phi -63.5, psi -39.6 trans  
3j5q #2/G ASN 551: phi -62.7, psi -36.0 trans  
3j5q #2/G THR 556: phi -62.0, psi -21.4 trans  
3j5q #2/G GLN 561: phi -64.6, psi -57.6 trans  
3j5q #2/G ASP 601: phi 53.6, psi -137.0 trans  
3j5q #2/G LYS 656: phi -62.0, psi -41.7 trans  
3j5q #2/G LYS 698: phi -62.7, psi -45.7 trans  
3j5q #2/G GLN 700: phi -57.1, psi -42.6 trans  
3j5q #2/G ILE 703: phi -63.0, psi -41.7 trans  
3j5q #2/G THR 704: phi -62.5, psi -43.3 trans  
3j5q #2/G LEU 706: phi -64.0, psi -43.8 trans  
3j5q #2/G ASP 707: phi -63.6, psi -43.4 trans  
3j5q #2/G THR 708: phi -63.1, psi -41.7 trans  
3j5q #2/G GLU 709: phi -62.6, psi -42.5 trans  
3j5q #2/G PHE 712: phi -80.6, psi 15.5 trans  
3j5q #2/G LYS 714: phi 51.7, psi 40.6 trans  
3j5q #2/G CYS 715: phi -69.8, psi 163.3 trans  
3j5q #2/G MET 716: phi -57.0, psi 133.2 trans  
3j5q #2/G ARG 717: phi -160.3, psi 169.6 trans  
3j5q #2/G LYS 718: phi -57.7, psi 132.9 trans  

The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: 3j5q #2/E PRO 461 N; 3j5q #2/D PRO 462 N; 3j5q #2/D PRO 461 N;
3j5q #2/E PRO 462 N; 3j5q #2/E PRO 501 N; 3j5q #2/D PRO 501 N; 3j5q #2/G PRO
461 N; 3j5q #2/G PRO 462 N; 3j5q #2/B PRO 461 N; 3j5q #2/B PRO 462 N; 3j5q
#2/G PRO 501 N; 3j5q #2/B PRO 501 N  

Applying ARG rotamer (chi angles: 66.5 92.9 71.6 -112.0) to 3j5q #2/D ARG 355  
Applying GLU rotamer (chi angles: 60.4 85.9 19.3) to 3j5q #2/D GLU 356  
Applying ILE rotamer (chi angles: -60.7 170.4) to 3j5q #2/D ILE 357  
Applying GLU rotamer (chi angles: -56.4 -66.5 -27.2) to 3j5q #2/D GLU 361  
Applying ARG rotamer (chi angles: -70.7 177.7 -180.0 172.6) to 3j5q #2/D ARG
363  
Applying LEU rotamer (chi angles: -68.3 173.0) to 3j5q #2/D LEU 365  
Applying LYS rotamer (chi angles: 39.0 99.7 98.0 -68.6) to 3j5q #2/D LYS 368  
Applying THR rotamer (chi angles: -179.0) to 3j5q #2/D THR 370  
Applying GLU rotamer (chi angles: -172.7 176.6 -1.7) to 3j5q #2/D GLU 371  
Applying TYR rotamer (chi angles: -66.0 -2.7) to 3j5q #2/D TYR 374  
Applying VAL rotamer (chi angles: 177.9) to 3j5q #2/D VAL 377  
Applying HIS rotamer (chi angles: -62.4 -79.4) to 3j5q #2/D HIS 378  
Applying SER rotamer (chi angles: 61.8) to 3j5q #2/D SER 380  
Applying ILE rotamer (chi angles: -164.1 -80.1) to 3j5q #2/D ILE 387  
Applying ASP rotamer (chi angles: -71.8 -15.3) to 3j5q #2/D ASP 388  
Applying THR rotamer (chi angles: 58.4) to 3j5q #2/D THR 389  
Applying GLU rotamer (chi angles: -67.0 81.2 -0.7) to 3j5q #2/D GLU 391  
Applying LYS rotamer (chi angles: -68.7 179.0 70.3 67.4) to 3j5q #2/D LYS 392  
Applying SER rotamer (chi angles: 66.3) to 3j5q #2/D SER 394  
Applying VAL rotamer (chi angles: 69.3) to 3j5q #2/D VAL 395  
Applying LEU rotamer (chi angles: -177.4 58.8) to 3j5q #2/D LEU 396  
Applying GLU rotamer (chi angles: -178.0 65.6 20.3) to 3j5q #2/D GLU 397  
Applying VAL rotamer (chi angles: 171.5) to 3j5q #2/D VAL 398  
Applying GLU rotamer (chi angles: -68.9 177.5 18.3) to 3j5q #2/D GLU 405  
Applying THR rotamer (chi angles: -60.4) to 3j5q #2/D THR 406  
Applying ARG rotamer (chi angles: -71.4 -178.8 -70.0 169.1) to 3j5q #2/D ARG
409  
Applying HIS rotamer (chi angles: -70.9 -66.4) to 3j5q #2/D HIS 410  
Applying ASP rotamer (chi angles: -172.4 6.0) to 3j5q #2/D ASP 411  
Applying MET rotamer (chi angles: -174.4 63.7 74.6) to 3j5q #2/D MET 412  
Applying VAL rotamer (chi angles: -61.0) to 3j5q #2/D VAL 415  
Applying GLU rotamer (chi angles: -177.3 63.2 19.3) to 3j5q #2/D GLU 416  
Applying LEU rotamer (chi angles: -70.2 171.3) to 3j5q #2/D LEU 418  
Applying ASN rotamer (chi angles: -72.9 -173.8) to 3j5q #2/D ASN 419  
Applying ARG rotamer (chi angles: 179.0 65.5 -178.0 85.8) to 3j5q #2/D ARG 420  
Applying LEU rotamer (chi angles: -69.2 172.7) to 3j5q #2/D LEU 422  
Applying ASP rotamer (chi angles: -71.0 -16.3) to 3j5q #2/D ASP 424  
Applying ASP rotamer (chi angles: -71.8 -15.3) to 3j5q #2/D ASP 427  
Applying ARG rotamer (chi angles: -71.5 -177.7 -70.0 167.4) to 3j5q #2/D ARG
428  
Applying LYS rotamer (chi angles: 39.0 99.7 98.0 -68.6) to 3j5q #2/D LYS 431  
Applying ARG rotamer (chi angles: -71.0 -167.5 -64.0 -87.5) to 3j5q #2/D ARG
432  
Applying LEU rotamer (chi angles: -176.1 153.6) to 3j5q #2/D LEU 443  
Applying THR rotamer (chi angles: -172.0) to 3j5q #2/D THR 449  
Applying VAL rotamer (chi angles: 171.5) to 3j5q #2/D VAL 457  
Applying GLU rotamer (chi angles: -66.2 -66.0 -36.7) to 3j5q #2/D GLU 458  
Applying LEU rotamer (chi angles: -60.7 174.7) to 3j5q #2/D LEU 460  
Applying PRO rotamer (chi angles: -25.1 36.3) to 3j5q #2/D PRO 461  
Applying PRO rotamer (chi angles: 27.0 -34.8) to 3j5q #2/D PRO 462  
Applying TYR rotamer (chi angles: -178.5 76.3) to 3j5q #2/D TYR 463  
Applying LYS rotamer (chi angles: 62.9 85.9 -178.0 62.2) to 3j5q #2/D LYS 464  
Applying LYS rotamer (chi angles: -64.5 -175.5 -71.7 -67.7) to 3j5q #2/D LYS
466  
Applying THR rotamer (chi angles: 63.3) to 3j5q #2/D THR 468  
Applying VAL rotamer (chi angles: 171.5) to 3j5q #2/D VAL 469  
Applying ASP rotamer (chi angles: -66.9 -27.4) to 3j5q #2/D ASP 471  
Applying THR rotamer (chi angles: 58.7) to 3j5q #2/D THR 476  
Applying GLU rotamer (chi angles: -69.9 176.8 -8.7) to 3j5q #2/D GLU 478  
Applying ILE rotamer (chi angles: -68.1 168.5) to 3j5q #2/D ILE 479  
Applying LEU rotamer (chi angles: -69.2 172.7) to 3j5q #2/D LEU 480  
Applying SER rotamer (chi angles: 65.0) to 3j5q #2/D SER 481  
Applying SER rotamer (chi angles: 65.0) to 3j5q #2/D SER 483  
Applying VAL rotamer (chi angles: 171.5) to 3j5q #2/D VAL 486  
Applying PHE rotamer (chi angles: -175.1 75.2) to 3j5q #2/D PHE 489  
Applying ARG rotamer (chi angles: -176.4 175.9 65.4 -163.9) to 3j5q #2/D ARG
491  
Applying ILE rotamer (chi angles: -68.1 168.5) to 3j5q #2/D ILE 493  
Applying GLN rotamer (chi angles: -69.8 176.6 64.1) to 3j5q #2/D GLN 494  
Applying LEU rotamer (chi angles: -177.4 58.8) to 3j5q #2/D LEU 497  
Applying ARG rotamer (chi angles: -178.4 -93.3 177.9 -84.3) to 3j5q #2/D ARG
500  
Applying PRO rotamer (chi angles: -24.5 36.0) to 3j5q #2/D PRO 501  
Applying ASP rotamer (chi angles: -175.8 76.7) to 3j5q #2/D ASP 509  
Applying LEU rotamer (chi angles: -69.2 172.7) to 3j5q #2/D LEU 524  
Applying VAL rotamer (chi angles: 171.5) to 3j5q #2/D VAL 527  
Applying VAL rotamer (chi angles: 171.5) to 3j5q #2/D VAL 528  
Applying LEU rotamer (chi angles: -69.2 172.7) to 3j5q #2/D LEU 529  
Applying GLN rotamer (chi angles: -59.8 -175.6 2.4) to 3j5q #2/D GLN 533  
Applying LYS rotamer (chi angles: -177.5 61.9 67.2 174.7) to 3j5q #2/D LYS 535  
Applying GLU rotamer (chi angles: -64.5 83.4 -60.9) to 3j5q #2/D GLU 536  
Applying SER rotamer (chi angles: -179.9) to 3j5q #2/D SER 540  
Applying MET rotamer (chi angles: -179.6 -178.9 71.4) to 3j5q #2/D MET 541  
Applying ASN rotamer (chi angles: -73.2 3.9) to 3j5q #2/D ASN 551  
Applying THR rotamer (chi angles: 59.5) to 3j5q #2/D THR 556  
Applying GLN rotamer (chi angles: -67.5 83.3 -27.4) to 3j5q #2/D GLN 561  
Applying ASP rotamer (chi angles: -61.8 -32.9) to 3j5q #2/D ASP 601  
Applying LYS rotamer (chi angles: 39.0 99.7 98.0 -68.6) to 3j5q #2/D LYS 656  
Applying LYS rotamer (chi angles: -179.0 178.1 178.3 180.0) to 3j5q #2/D LYS
698  
Applying GLN rotamer (chi angles: -175.4 64.8 78.1) to 3j5q #2/D GLN 700  
Applying ILE rotamer (chi angles: -68.1 168.5) to 3j5q #2/D ILE 703  
Applying THR rotamer (chi angles: 58.7) to 3j5q #2/D THR 704  
Applying LEU rotamer (chi angles: -174.8 -78.8) to 3j5q #2/D LEU 706  
Applying ASP rotamer (chi angles: -71.8 -15.3) to 3j5q #2/D ASP 707  
Applying THR rotamer (chi angles: 58.7) to 3j5q #2/D THR 708  
Applying GLU rotamer (chi angles: -177.3 177.0 -1.2) to 3j5q #2/D GLU 709  
Applying PHE rotamer (chi angles: -178.7 77.3) to 3j5q #2/D PHE 712  
Applying LYS rotamer (chi angles: -61.4 -177.0 175.9 65.8) to 3j5q #2/D LYS
714  
Applying CYS rotamer (chi angles: 70.2) to 3j5q #2/D CYS 715  
Applying MET rotamer (chi angles: -63.3 -62.1 -67.9) to 3j5q #2/D MET 716  
Applying ARG rotamer (chi angles: 85.3 -76.0 87.4 -178.1) to 3j5q #2/D ARG 717  
Applying LYS rotamer (chi angles: -176.5 177.1 179.6 -180.0) to 3j5q #2/D LYS
718  
Applying ARG rotamer (chi angles: -174.1 -89.4 -176.2 -86.8) to 3j5q #2/B ARG
355  
Applying GLU rotamer (chi angles: 60.4 85.9 19.3) to 3j5q #2/B GLU 356  
Applying ILE rotamer (chi angles: -60.7 170.4) to 3j5q #2/B ILE 357  
Applying GLU rotamer (chi angles: -56.4 -66.5 -27.2) to 3j5q #2/B GLU 361  
Applying ARG rotamer (chi angles: -70.7 177.7 -180.0 172.6) to 3j5q #2/B ARG
363  
Applying LEU rotamer (chi angles: -68.3 173.0) to 3j5q #2/B LEU 365  
Applying LYS rotamer (chi angles: 39.0 99.7 98.0 -68.6) to 3j5q #2/B LYS 368  
Applying THR rotamer (chi angles: -179.0) to 3j5q #2/B THR 370  
Applying GLU rotamer (chi angles: -172.7 176.6 -1.7) to 3j5q #2/B GLU 371  
Applying TYR rotamer (chi angles: -66.0 -2.7) to 3j5q #2/B TYR 374  
Applying VAL rotamer (chi angles: 177.9) to 3j5q #2/B VAL 377  
Applying HIS rotamer (chi angles: -62.4 -79.4) to 3j5q #2/B HIS 378  
Applying SER rotamer (chi angles: 61.8) to 3j5q #2/B SER 380  
Applying ILE rotamer (chi angles: -164.1 -80.1) to 3j5q #2/B ILE 387  
Applying ASP rotamer (chi angles: -71.8 -15.3) to 3j5q #2/B ASP 388  
Applying THR rotamer (chi angles: 58.4) to 3j5q #2/B THR 389  
Applying GLU rotamer (chi angles: -67.0 81.2 -0.7) to 3j5q #2/B GLU 391  
Applying LYS rotamer (chi angles: -68.7 179.0 70.3 67.4) to 3j5q #2/B LYS 392  
Applying SER rotamer (chi angles: 66.3) to 3j5q #2/B SER 394  
Applying VAL rotamer (chi angles: 69.3) to 3j5q #2/B VAL 395  
Applying LEU rotamer (chi angles: -177.4 58.8) to 3j5q #2/B LEU 396  
Applying GLU rotamer (chi angles: -178.0 65.6 20.3) to 3j5q #2/B GLU 397  
Applying VAL rotamer (chi angles: 171.5) to 3j5q #2/B VAL 398  
Applying GLU rotamer (chi angles: -68.9 177.5 18.3) to 3j5q #2/B GLU 405  
Applying THR rotamer (chi angles: -60.4) to 3j5q #2/B THR 406  
Applying ARG rotamer (chi angles: -71.4 -178.8 -70.0 169.1) to 3j5q #2/B ARG
409  
Applying HIS rotamer (chi angles: -70.9 -66.4) to 3j5q #2/B HIS 410  
Applying ASP rotamer (chi angles: -172.4 6.0) to 3j5q #2/B ASP 411  
Applying MET rotamer (chi angles: -174.4 63.7 74.6) to 3j5q #2/B MET 412  
Applying VAL rotamer (chi angles: -61.0) to 3j5q #2/B VAL 415  
Applying GLU rotamer (chi angles: -177.3 63.2 19.3) to 3j5q #2/B GLU 416  
Applying LEU rotamer (chi angles: -70.2 171.3) to 3j5q #2/B LEU 418  
Applying ASN rotamer (chi angles: -72.9 -173.8) to 3j5q #2/B ASN 419  
Applying ARG rotamer (chi angles: 179.0 65.5 -178.0 85.8) to 3j5q #2/B ARG 420  
Applying LEU rotamer (chi angles: -89.2 -60.6) to 3j5q #2/B LEU 422  
Applying ASP rotamer (chi angles: -71.8 -15.3) to 3j5q #2/B ASP 424  
Applying ASP rotamer (chi angles: -71.8 -15.3) to 3j5q #2/B ASP 427  
Applying ARG rotamer (chi angles: -71.5 -177.7 -70.0 167.4) to 3j5q #2/B ARG
428  
Applying LYS rotamer (chi angles: 39.0 99.7 98.0 -68.6) to 3j5q #2/B LYS 431  
Applying ARG rotamer (chi angles: -71.0 -167.5 -64.0 -87.5) to 3j5q #2/B ARG
432  
Applying LEU rotamer (chi angles: -176.1 153.6) to 3j5q #2/B LEU 443  
Applying THR rotamer (chi angles: -172.0) to 3j5q #2/B THR 449  
Applying VAL rotamer (chi angles: 171.5) to 3j5q #2/B VAL 457  
Applying GLU rotamer (chi angles: -66.2 -66.0 -36.7) to 3j5q #2/B GLU 458  
Applying LEU rotamer (chi angles: -60.7 174.7) to 3j5q #2/B LEU 460  
Applying PRO rotamer (chi angles: -25.1 36.3) to 3j5q #2/B PRO 461  
Applying PRO rotamer (chi angles: 27.0 -34.8) to 3j5q #2/B PRO 462  
Applying TYR rotamer (chi angles: -178.5 76.3) to 3j5q #2/B TYR 463  
Applying LYS rotamer (chi angles: 62.9 85.9 -178.0 62.2) to 3j5q #2/B LYS 464  
Applying LYS rotamer (chi angles: -64.5 -175.5 -71.7 -67.7) to 3j5q #2/B LYS
466  
Applying THR rotamer (chi angles: 63.3) to 3j5q #2/B THR 468  
Applying VAL rotamer (chi angles: 171.5) to 3j5q #2/B VAL 469  
Applying ASP rotamer (chi angles: -66.9 -27.4) to 3j5q #2/B ASP 471  
Applying THR rotamer (chi angles: 58.7) to 3j5q #2/B THR 476  
Applying GLU rotamer (chi angles: -69.9 176.8 -8.7) to 3j5q #2/B GLU 478  
Applying ILE rotamer (chi angles: -68.1 168.5) to 3j5q #2/B ILE 479  
Applying LEU rotamer (chi angles: -69.2 172.7) to 3j5q #2/B LEU 480  
Applying SER rotamer (chi angles: 65.0) to 3j5q #2/B SER 481  
Applying SER rotamer (chi angles: 65.0) to 3j5q #2/B SER 483  
Applying VAL rotamer (chi angles: 171.5) to 3j5q #2/B VAL 486  
Applying PHE rotamer (chi angles: -175.1 75.2) to 3j5q #2/B PHE 489  
Applying ARG rotamer (chi angles: -176.4 175.9 65.4 -163.9) to 3j5q #2/B ARG
491  
Applying ILE rotamer (chi angles: -68.1 168.5) to 3j5q #2/B ILE 493  
Applying GLN rotamer (chi angles: -69.8 176.6 64.1) to 3j5q #2/B GLN 494  
Applying LEU rotamer (chi angles: -177.4 58.8) to 3j5q #2/B LEU 497  
Applying ARG rotamer (chi angles: -178.4 -93.3 177.9 -84.3) to 3j5q #2/B ARG
500  
Applying PRO rotamer (chi angles: -24.5 36.0) to 3j5q #2/B PRO 501  
Applying ASP rotamer (chi angles: -175.8 76.7) to 3j5q #2/B ASP 509  
Applying LEU rotamer (chi angles: -69.2 172.7) to 3j5q #2/B LEU 524  
Applying VAL rotamer (chi angles: 171.5) to 3j5q #2/B VAL 527  
Applying VAL rotamer (chi angles: 171.5) to 3j5q #2/B VAL 528  
Applying LEU rotamer (chi angles: -69.2 172.7) to 3j5q #2/B LEU 529  
Applying GLN rotamer (chi angles: -59.8 -175.6 2.4) to 3j5q #2/B GLN 533  
Applying LYS rotamer (chi angles: -177.5 61.9 67.2 174.7) to 3j5q #2/B LYS 535  
Applying GLU rotamer (chi angles: -64.5 83.4 -60.9) to 3j5q #2/B GLU 536  
Applying SER rotamer (chi angles: -179.9) to 3j5q #2/B SER 540  
Applying MET rotamer (chi angles: -179.6 -178.9 71.4) to 3j5q #2/B MET 541  
Applying ASN rotamer (chi angles: -73.2 3.9) to 3j5q #2/B ASN 551  
Applying THR rotamer (chi angles: 59.5) to 3j5q #2/B THR 556  
Applying GLN rotamer (chi angles: -67.5 83.3 -27.4) to 3j5q #2/B GLN 561  
Applying ASP rotamer (chi angles: -61.8 -32.9) to 3j5q #2/B ASP 601  
Applying LYS rotamer (chi angles: 39.0 99.7 98.0 -68.6) to 3j5q #2/B LYS 656  
Applying LYS rotamer (chi angles: -179.0 178.1 178.3 180.0) to 3j5q #2/B LYS
698  
Applying GLN rotamer (chi angles: -175.4 64.8 78.1) to 3j5q #2/B GLN 700  
Applying ILE rotamer (chi angles: -68.1 168.5) to 3j5q #2/B ILE 703  
Applying THR rotamer (chi angles: 58.7) to 3j5q #2/B THR 704  
Applying LEU rotamer (chi angles: -174.8 -78.8) to 3j5q #2/B LEU 706  
Applying ASP rotamer (chi angles: -71.8 -15.3) to 3j5q #2/B ASP 707  
Applying THR rotamer (chi angles: 58.7) to 3j5q #2/B THR 708  
Applying GLU rotamer (chi angles: -177.3 177.0 -1.2) to 3j5q #2/B GLU 709  
Applying PHE rotamer (chi angles: -178.7 77.3) to 3j5q #2/B PHE 712  
Applying LYS rotamer (chi angles: -61.4 -177.0 175.9 65.8) to 3j5q #2/B LYS
714  
Applying CYS rotamer (chi angles: 70.2) to 3j5q #2/B CYS 715  
Applying MET rotamer (chi angles: -63.3 -62.1 -67.9) to 3j5q #2/B MET 716  
Applying ARG rotamer (chi angles: 85.3 -76.0 87.4 -178.1) to 3j5q #2/B ARG 717  
Applying LYS rotamer (chi angles: -176.5 177.1 179.6 -180.0) to 3j5q #2/B LYS
718  
Applying ARG rotamer (chi angles: 66.5 92.9 71.6 -112.0) to 3j5q #2/E ARG 355  
Applying GLU rotamer (chi angles: 60.4 85.9 19.3) to 3j5q #2/E GLU 356  
Applying ILE rotamer (chi angles: -60.7 170.4) to 3j5q #2/E ILE 357  
Applying GLU rotamer (chi angles: -56.4 -66.5 -27.2) to 3j5q #2/E GLU 361  
Applying ARG rotamer (chi angles: -70.7 177.7 -180.0 172.6) to 3j5q #2/E ARG
363  
Applying LEU rotamer (chi angles: -68.3 173.0) to 3j5q #2/E LEU 365  
Applying LYS rotamer (chi angles: 39.0 99.7 98.0 -68.6) to 3j5q #2/E LYS 368  
Applying THR rotamer (chi angles: -179.0) to 3j5q #2/E THR 370  
Applying GLU rotamer (chi angles: -172.7 176.6 -1.7) to 3j5q #2/E GLU 371  
Applying TYR rotamer (chi angles: -66.0 -2.7) to 3j5q #2/E TYR 374  
Applying VAL rotamer (chi angles: 177.9) to 3j5q #2/E VAL 377  
Applying HIS rotamer (chi angles: -62.4 -79.4) to 3j5q #2/E HIS 378  
Applying SER rotamer (chi angles: 61.8) to 3j5q #2/E SER 380  
Applying ILE rotamer (chi angles: -164.1 -80.1) to 3j5q #2/E ILE 387  
Applying ASP rotamer (chi angles: -71.8 -15.3) to 3j5q #2/E ASP 388  
Applying THR rotamer (chi angles: 58.4) to 3j5q #2/E THR 389  
Applying GLU rotamer (chi angles: -67.0 81.2 -0.7) to 3j5q #2/E GLU 391  
Applying LYS rotamer (chi angles: -68.7 179.0 70.3 67.4) to 3j5q #2/E LYS 392  
Applying SER rotamer (chi angles: 66.3) to 3j5q #2/E SER 394  
Applying VAL rotamer (chi angles: 69.3) to 3j5q #2/E VAL 395  
Applying LEU rotamer (chi angles: -177.4 58.8) to 3j5q #2/E LEU 396  
Applying GLU rotamer (chi angles: -178.0 65.6 20.3) to 3j5q #2/E GLU 397  
Applying VAL rotamer (chi angles: 171.5) to 3j5q #2/E VAL 398  
Applying GLU rotamer (chi angles: -68.9 177.5 18.3) to 3j5q #2/E GLU 405  
Applying THR rotamer (chi angles: -60.4) to 3j5q #2/E THR 406  
Applying ARG rotamer (chi angles: -71.4 -178.8 -70.0 169.1) to 3j5q #2/E ARG
409  
Applying HIS rotamer (chi angles: -70.9 -66.4) to 3j5q #2/E HIS 410  
Applying ASP rotamer (chi angles: -172.4 6.0) to 3j5q #2/E ASP 411  
Applying MET rotamer (chi angles: -174.4 63.7 74.6) to 3j5q #2/E MET 412  
Applying VAL rotamer (chi angles: -61.0) to 3j5q #2/E VAL 415  
Applying GLU rotamer (chi angles: -177.3 63.2 19.3) to 3j5q #2/E GLU 416  
Applying LEU rotamer (chi angles: -70.2 171.3) to 3j5q #2/E LEU 418  
Applying ASN rotamer (chi angles: -72.9 -173.8) to 3j5q #2/E ASN 419  
Applying ARG rotamer (chi angles: 179.0 65.5 -178.0 85.8) to 3j5q #2/E ARG 420  
Applying LEU rotamer (chi angles: -69.2 172.7) to 3j5q #2/E LEU 422  
Applying ASP rotamer (chi angles: -71.0 -16.3) to 3j5q #2/E ASP 424  
Applying ASP rotamer (chi angles: -71.8 -15.3) to 3j5q #2/E ASP 427  
Applying ARG rotamer (chi angles: -71.5 -177.7 -70.0 167.4) to 3j5q #2/E ARG
428  
Applying LYS rotamer (chi angles: 39.0 99.7 98.0 -68.6) to 3j5q #2/E LYS 431  
Applying ARG rotamer (chi angles: -71.0 -167.5 -64.0 -87.5) to 3j5q #2/E ARG
432  
Applying LEU rotamer (chi angles: -176.1 153.6) to 3j5q #2/E LEU 443  
Applying THR rotamer (chi angles: -172.0) to 3j5q #2/E THR 449  
Applying VAL rotamer (chi angles: 171.5) to 3j5q #2/E VAL 457  
Applying GLU rotamer (chi angles: -66.2 -66.0 -36.7) to 3j5q #2/E GLU 458  
Applying LEU rotamer (chi angles: -60.7 174.7) to 3j5q #2/E LEU 460  
Applying PRO rotamer (chi angles: -25.1 36.3) to 3j5q #2/E PRO 461  
Applying PRO rotamer (chi angles: 27.0 -34.8) to 3j5q #2/E PRO 462  
Applying TYR rotamer (chi angles: -178.5 76.3) to 3j5q #2/E TYR 463  
Applying LYS rotamer (chi angles: 62.9 85.9 -178.0 62.2) to 3j5q #2/E LYS 464  
Applying LYS rotamer (chi angles: -64.5 -175.5 -71.7 -67.7) to 3j5q #2/E LYS
466  
Applying THR rotamer (chi angles: 63.3) to 3j5q #2/E THR 468  
Applying VAL rotamer (chi angles: 171.5) to 3j5q #2/E VAL 469  
Applying ASP rotamer (chi angles: -66.9 -27.4) to 3j5q #2/E ASP 471  
Applying THR rotamer (chi angles: 58.7) to 3j5q #2/E THR 476  
Applying GLU rotamer (chi angles: -69.9 176.8 -8.7) to 3j5q #2/E GLU 478  
Applying ILE rotamer (chi angles: -68.1 168.5) to 3j5q #2/E ILE 479  
Applying LEU rotamer (chi angles: -69.2 172.7) to 3j5q #2/E LEU 480  
Applying SER rotamer (chi angles: 65.0) to 3j5q #2/E SER 481  
Applying SER rotamer (chi angles: 65.0) to 3j5q #2/E SER 483  
Applying VAL rotamer (chi angles: 171.5) to 3j5q #2/E VAL 486  
Applying PHE rotamer (chi angles: -175.1 75.2) to 3j5q #2/E PHE 489  
Applying ARG rotamer (chi angles: -176.4 175.9 65.4 -163.9) to 3j5q #2/E ARG
491  
Applying ILE rotamer (chi angles: -68.1 168.5) to 3j5q #2/E ILE 493  
Applying GLN rotamer (chi angles: -69.8 176.6 64.1) to 3j5q #2/E GLN 494  
Applying LEU rotamer (chi angles: -177.4 58.8) to 3j5q #2/E LEU 497  
Applying ARG rotamer (chi angles: -178.4 -93.3 177.9 -84.3) to 3j5q #2/E ARG
500  
Applying PRO rotamer (chi angles: -24.5 36.0) to 3j5q #2/E PRO 501  
Applying ASP rotamer (chi angles: -175.8 76.7) to 3j5q #2/E ASP 509  
Applying LEU rotamer (chi angles: -69.2 172.7) to 3j5q #2/E LEU 524  
Applying VAL rotamer (chi angles: 171.5) to 3j5q #2/E VAL 527  
Applying VAL rotamer (chi angles: 171.5) to 3j5q #2/E VAL 528  
Applying LEU rotamer (chi angles: -69.2 172.7) to 3j5q #2/E LEU 529  
Applying GLN rotamer (chi angles: -59.8 -175.6 2.4) to 3j5q #2/E GLN 533  
Applying LYS rotamer (chi angles: -177.5 61.9 67.2 174.7) to 3j5q #2/E LYS 535  
Applying GLU rotamer (chi angles: -64.5 83.4 -60.9) to 3j5q #2/E GLU 536  
Applying SER rotamer (chi angles: -179.9) to 3j5q #2/E SER 540  
Applying MET rotamer (chi angles: -179.6 -178.9 71.4) to 3j5q #2/E MET 541  
Applying ASN rotamer (chi angles: -73.2 3.9) to 3j5q #2/E ASN 551  
Applying THR rotamer (chi angles: 59.5) to 3j5q #2/E THR 556  
Applying GLN rotamer (chi angles: -67.5 83.3 -27.4) to 3j5q #2/E GLN 561  
Applying ASP rotamer (chi angles: -61.8 -32.9) to 3j5q #2/E ASP 601  
Applying LYS rotamer (chi angles: 39.0 99.7 98.0 -68.6) to 3j5q #2/E LYS 656  
Applying LYS rotamer (chi angles: -179.0 178.1 178.3 180.0) to 3j5q #2/E LYS
698  
Applying GLN rotamer (chi angles: -175.4 64.8 78.1) to 3j5q #2/E GLN 700  
Applying ILE rotamer (chi angles: -68.1 168.5) to 3j5q #2/E ILE 703  
Applying THR rotamer (chi angles: 58.7) to 3j5q #2/E THR 704  
Applying LEU rotamer (chi angles: -174.8 -78.8) to 3j5q #2/E LEU 706  
Applying ASP rotamer (chi angles: -71.8 -15.3) to 3j5q #2/E ASP 707  
Applying THR rotamer (chi angles: 58.7) to 3j5q #2/E THR 708  
Applying GLU rotamer (chi angles: -177.3 177.0 -1.2) to 3j5q #2/E GLU 709  
Applying PHE rotamer (chi angles: -178.7 77.3) to 3j5q #2/E PHE 712  
Applying LYS rotamer (chi angles: -61.4 -177.0 175.9 65.8) to 3j5q #2/E LYS
714  
Applying CYS rotamer (chi angles: 70.2) to 3j5q #2/E CYS 715  
Applying MET rotamer (chi angles: -63.3 -62.1 -67.9) to 3j5q #2/E MET 716  
Applying ARG rotamer (chi angles: 85.3 -76.0 87.4 -178.1) to 3j5q #2/E ARG 717  
Applying LYS rotamer (chi angles: -176.5 177.1 179.6 -180.0) to 3j5q #2/E LYS
718  
Applying ARG rotamer (chi angles: 66.5 92.9 71.6 -112.0) to 3j5q #2/G ARG 355  
Applying GLU rotamer (chi angles: 60.4 85.9 19.3) to 3j5q #2/G GLU 356  
Applying ILE rotamer (chi angles: -60.7 170.4) to 3j5q #2/G ILE 357  
Applying GLU rotamer (chi angles: -56.4 -66.5 -27.2) to 3j5q #2/G GLU 361  
Applying ARG rotamer (chi angles: -70.7 177.7 -180.0 172.6) to 3j5q #2/G ARG
363  
Applying LEU rotamer (chi angles: -68.3 173.0) to 3j5q #2/G LEU 365  
Applying LYS rotamer (chi angles: 39.0 99.7 98.0 -68.6) to 3j5q #2/G LYS 368  
Applying THR rotamer (chi angles: -179.0) to 3j5q #2/G THR 370  
Applying GLU rotamer (chi angles: -172.7 176.6 -1.7) to 3j5q #2/G GLU 371  
Applying TYR rotamer (chi angles: -66.0 -2.7) to 3j5q #2/G TYR 374  
Applying VAL rotamer (chi angles: 177.9) to 3j5q #2/G VAL 377  
Applying HIS rotamer (chi angles: -62.4 -79.4) to 3j5q #2/G HIS 378  
Applying SER rotamer (chi angles: 61.8) to 3j5q #2/G SER 380  
Applying ILE rotamer (chi angles: -164.1 -80.1) to 3j5q #2/G ILE 387  
Applying ASP rotamer (chi angles: -71.8 -15.3) to 3j5q #2/G ASP 388  
Applying THR rotamer (chi angles: 58.4) to 3j5q #2/G THR 389  
Applying GLU rotamer (chi angles: -67.0 81.2 -0.7) to 3j5q #2/G GLU 391  
Applying LYS rotamer (chi angles: -68.7 179.0 70.3 67.4) to 3j5q #2/G LYS 392  
Applying SER rotamer (chi angles: 66.3) to 3j5q #2/G SER 394  
Applying VAL rotamer (chi angles: 69.3) to 3j5q #2/G VAL 395  
Applying LEU rotamer (chi angles: -177.4 58.8) to 3j5q #2/G LEU 396  
Applying GLU rotamer (chi angles: -178.0 65.6 20.3) to 3j5q #2/G GLU 397  
Applying VAL rotamer (chi angles: 171.5) to 3j5q #2/G VAL 398  
Applying GLU rotamer (chi angles: -68.9 177.5 18.3) to 3j5q #2/G GLU 405  
Applying THR rotamer (chi angles: -60.4) to 3j5q #2/G THR 406  
Applying ARG rotamer (chi angles: -71.4 -178.8 -70.0 169.1) to 3j5q #2/G ARG
409  
Applying HIS rotamer (chi angles: -70.9 -66.4) to 3j5q #2/G HIS 410  
Applying ASP rotamer (chi angles: -172.4 6.0) to 3j5q #2/G ASP 411  
Applying MET rotamer (chi angles: -174.4 63.7 74.6) to 3j5q #2/G MET 412  
Applying VAL rotamer (chi angles: -61.0) to 3j5q #2/G VAL 415  
Applying GLU rotamer (chi angles: -177.3 63.2 19.3) to 3j5q #2/G GLU 416  
Applying LEU rotamer (chi angles: -70.2 171.3) to 3j5q #2/G LEU 418  
Applying ASN rotamer (chi angles: -72.9 -173.8) to 3j5q #2/G ASN 419  
Applying ARG rotamer (chi angles: 179.0 65.5 -178.0 85.8) to 3j5q #2/G ARG 420  
Applying LEU rotamer (chi angles: -69.2 172.7) to 3j5q #2/G LEU 422  
Applying ASP rotamer (chi angles: -71.0 -16.3) to 3j5q #2/G ASP 424  
Applying ASP rotamer (chi angles: -71.8 -15.3) to 3j5q #2/G ASP 427  
Applying ARG rotamer (chi angles: -71.5 -177.7 -70.0 167.4) to 3j5q #2/G ARG
428  
Applying LYS rotamer (chi angles: 39.0 99.7 98.0 -68.6) to 3j5q #2/G LYS 431  
Applying ARG rotamer (chi angles: -71.0 -167.5 -64.0 -87.5) to 3j5q #2/G ARG
432  
Applying LEU rotamer (chi angles: -176.1 153.6) to 3j5q #2/G LEU 443  
Applying THR rotamer (chi angles: -172.0) to 3j5q #2/G THR 449  
Applying VAL rotamer (chi angles: 171.5) to 3j5q #2/G VAL 457  
Applying GLU rotamer (chi angles: -66.2 -66.0 -36.7) to 3j5q #2/G GLU 458  
Applying LEU rotamer (chi angles: -60.7 174.7) to 3j5q #2/G LEU 460  
Applying PRO rotamer (chi angles: -25.1 36.3) to 3j5q #2/G PRO 461  
Applying PRO rotamer (chi angles: 27.0 -34.8) to 3j5q #2/G PRO 462  
Applying TYR rotamer (chi angles: -178.5 76.3) to 3j5q #2/G TYR 463  
Applying LYS rotamer (chi angles: 62.9 85.9 -178.0 62.2) to 3j5q #2/G LYS 464  
Applying LYS rotamer (chi angles: -64.5 -175.5 -71.7 -67.7) to 3j5q #2/G LYS
466  
Applying THR rotamer (chi angles: 63.3) to 3j5q #2/G THR 468  
Applying VAL rotamer (chi angles: 171.5) to 3j5q #2/G VAL 469  
Applying ASP rotamer (chi angles: -66.9 -27.4) to 3j5q #2/G ASP 471  
Applying THR rotamer (chi angles: 58.7) to 3j5q #2/G THR 476  
Applying GLU rotamer (chi angles: -69.9 176.8 -8.7) to 3j5q #2/G GLU 478  
Applying ILE rotamer (chi angles: -68.1 168.5) to 3j5q #2/G ILE 479  
Applying LEU rotamer (chi angles: -69.2 172.7) to 3j5q #2/G LEU 480  
Applying SER rotamer (chi angles: 65.0) to 3j5q #2/G SER 481  
Applying SER rotamer (chi angles: 65.0) to 3j5q #2/G SER 483  
Applying VAL rotamer (chi angles: 171.5) to 3j5q #2/G VAL 486  
Applying PHE rotamer (chi angles: -175.1 75.2) to 3j5q #2/G PHE 489  
Applying ARG rotamer (chi angles: -176.4 175.9 65.4 -163.9) to 3j5q #2/G ARG
491  
Applying ILE rotamer (chi angles: -68.1 168.5) to 3j5q #2/G ILE 493  
Applying GLN rotamer (chi angles: -69.8 176.6 64.1) to 3j5q #2/G GLN 494  
Applying LEU rotamer (chi angles: -177.4 58.8) to 3j5q #2/G LEU 497  
Applying ARG rotamer (chi angles: -178.4 -93.3 177.9 -84.3) to 3j5q #2/G ARG
500  
Applying PRO rotamer (chi angles: -24.5 36.0) to 3j5q #2/G PRO 501  
Applying ASP rotamer (chi angles: -175.8 76.7) to 3j5q #2/G ASP 509  
Applying LEU rotamer (chi angles: -69.2 172.7) to 3j5q #2/G LEU 524  
Applying VAL rotamer (chi angles: 171.5) to 3j5q #2/G VAL 527  
Applying VAL rotamer (chi angles: 171.5) to 3j5q #2/G VAL 528  
Applying LEU rotamer (chi angles: -69.2 172.7) to 3j5q #2/G LEU 529  
Applying GLN rotamer (chi angles: -59.8 -175.6 2.4) to 3j5q #2/G GLN 533  
Applying LYS rotamer (chi angles: -177.5 61.9 67.2 174.7) to 3j5q #2/G LYS 535  
Applying GLU rotamer (chi angles: -64.5 83.4 -60.9) to 3j5q #2/G GLU 536  
Applying SER rotamer (chi angles: -179.9) to 3j5q #2/G SER 540  
Applying MET rotamer (chi angles: -179.6 -178.9 71.4) to 3j5q #2/G MET 541  
Applying ASN rotamer (chi angles: -73.2 3.9) to 3j5q #2/G ASN 551  
Applying THR rotamer (chi angles: 59.5) to 3j5q #2/G THR 556  
Applying GLN rotamer (chi angles: -67.5 83.3 -27.4) to 3j5q #2/G GLN 561  
Applying ASP rotamer (chi angles: -61.8 -32.9) to 3j5q #2/G ASP 601  
Applying LYS rotamer (chi angles: 39.0 99.7 98.0 -68.6) to 3j5q #2/G LYS 656  
Applying LYS rotamer (chi angles: -179.0 178.1 178.3 180.0) to 3j5q #2/G LYS
698  
Applying GLN rotamer (chi angles: -175.4 64.8 78.1) to 3j5q #2/G GLN 700  
Applying ILE rotamer (chi angles: -68.1 168.5) to 3j5q #2/G ILE 703  
Applying THR rotamer (chi angles: 58.7) to 3j5q #2/G THR 704  
Applying LEU rotamer (chi angles: -174.8 -78.8) to 3j5q #2/G LEU 706  
Applying ASP rotamer (chi angles: -71.8 -15.3) to 3j5q #2/G ASP 707  
Applying THR rotamer (chi angles: 58.7) to 3j5q #2/G THR 708  
Applying GLU rotamer (chi angles: -177.3 177.0 -1.2) to 3j5q #2/G GLU 709  
Applying PHE rotamer (chi angles: -178.7 77.3) to 3j5q #2/G PHE 712  
Applying LYS rotamer (chi angles: -61.4 -177.0 175.9 65.8) to 3j5q #2/G LYS
714  
Applying CYS rotamer (chi angles: 70.2) to 3j5q #2/G CYS 715  
Applying MET rotamer (chi angles: -63.3 -62.1 -67.9) to 3j5q #2/G MET 716  
Applying ARG rotamer (chi angles: 85.3 -76.0 87.4 -178.1) to 3j5q #2/G ARG 717  
Applying LYS rotamer (chi angles: -176.5 177.1 179.6 -180.0) to 3j5q #2/G LYS
718  
Summary of feedback from adding hydrogens to 3j5q #2  
---  
warnings | Not adding hydrogens to 3j5q #2/D UNK 752 CB because it is missing
heavy-atom bond partners  
Not adding hydrogens to 3j5q #2/D UNK 753 CB because it is missing heavy-atom
bond partners  
Not adding hydrogens to 3j5q #2/D UNK 754 CA because it is missing heavy-atom
bond partners  
Not adding hydrogens to 3j5q #2/D UNK 755 CB because it is missing heavy-atom
bond partners  
Not adding hydrogens to 3j5q #2/D UNK 756 CB because it is missing heavy-atom
bond partners  
347 messages similar to the above omitted  
notes | Termini for 3j5q (#2) chain D determined from SEQRES records  
Termini for 3j5q (#2) chain B determined from SEQRES records  
Termini for 3j5q (#2) chain E determined from SEQRES records  
Termini for 3j5q (#2) chain G determined from SEQRES records  
Termini for 3j5q (#2) chain A determined from SEQRES records  
3 messages similar to the above omitted  
Chain-initial residues that are actual N termini: 3j5q #2/D LEU 111, 3j5q #2/B
LEU 111, 3j5q #2/E LEU 111, 3j5q #2/G LEU 111, 3j5q #2/A UNK 1, 3j5q #2/C UNK
1, 3j5q #2/F UNK 1, 3j5q #2/H UNK 1  
Chain-initial residues that are not actual N termini: 3j5q #2/D VAL 508, 3j5q
#2/D UNK 752, 3j5q #2/B VAL 508, 3j5q #2/B UNK 752, 3j5q #2/E VAL 508, 3j5q
#2/E UNK 752, 3j5q #2/G VAL 508, 3j5q #2/G UNK 752  
Chain-final residues that are actual C termini: 3j5q #2/D UNK 762, 3j5q #2/B
UNK 762, 3j5q #2/E UNK 762, 3j5q #2/G UNK 762, 3j5q #2/A UNK 31, 3j5q #2/C UNK
31, 3j5q #2/F UNK 31, 3j5q #2/H UNK 31  
Chain-final residues that are not actual C termini: 3j5q #2/D SER 502, 3j5q
#2/D ALA 719, 3j5q #2/B SER 502, 3j5q #2/B ALA 719, 3j5q #2/E SER 502, 3j5q
#2/E ALA 719, 3j5q #2/G SER 502, 3j5q #2/G ALA 719  
Missing OXT added to C-terminal residue 3j5q #2/D UNK 762  
Missing OXT added to C-terminal residue 3j5q #2/B UNK 762  
Missing OXT added to C-terminal residue 3j5q #2/E UNK 762  
Missing OXT added to C-terminal residue 3j5q #2/G UNK 762  
Missing OXT added to C-terminal residue 3j5q #2/A UNK 31  
3 messages similar to the above omitted  
2086 hydrogen bonds  
Adding 'H' to 3j5q #2/D VAL 508  
Adding 'H' to 3j5q #2/D UNK 752  
Adding 'H' to 3j5q #2/B VAL 508  
Adding 'H' to 3j5q #2/B UNK 752  
Adding 'H' to 3j5q #2/E VAL 508  
3 messages similar to the above omitted  
19124 hydrogens added  
  
Using Amber 20 recommended default charges and atom types for standard
residues  
Traceback (most recent call last):  
File
"/Users/meng/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/add_charge/charge.py", line 117, in add_standard_charges  
a.charge, a.gaff_type = heavy_charge_type_data[(a.residue.amber_name,
a.name.lower())]  
KeyError: ('ALA', 'sg')  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File
"/Users/meng/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/cmd_line/tool.py", line 319, in execute  
cmd.run(cmd_text)  
File
"/Users/meng/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File
"/Users/meng/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/dock_prep/cmd.py", line 133, in dock_prep_cmd  
dock_prep_caller(session, structures, memorization=memorize, nogui=True, **kw)  
File
"/Users/meng/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/dock_prep/cmd.py", line 112, in dock_prep_caller  
run_steps(session, state)  
File
"/Users/meng/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/dock_prep/cmd.py", line 124, in run_steps  
step_mod.run_for_dock_prep(session, state, run_steps, state['memorization'],
state['memorize_name'],  
File
"/Users/meng/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/dock_prep/prep.py", line 85, in prep  
callback(session, state)  
File
"/Users/meng/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/dock_prep/cmd.py", line 124, in run_steps  
step_mod.run_for_dock_prep(session, state, run_steps, state['memorization'],
state['memorize_name'],  
File
"/Users/meng/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/addh/dock_prep.py", line 36, in run_for_dock_prep  
callback(session, state)  
File
"/Users/meng/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/dock_prep/cmd.py", line 124, in run_steps  
step_mod.run_for_dock_prep(session, state, run_steps, state['memorization'],
state['memorize_name'],  
File
"/Users/meng/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/add_charge/dock_prep.py", line 37, in run_for_dock_prep  
cmd_addcharge(session, structures.residues, **active_settings)  
File
"/Users/meng/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/add_charge/cmd.py", line 31, in cmd_addcharge  
add_charges(session, residues, method=method, status=session.logger.status,  
File
"/Users/meng/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/add_charge/charge.py", line 23, in add_charges  
uncharged_res_types = add_standard_charges(session, residues, status=status,  
File
"/Users/meng/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/add_charge/charge.py", line 119, in add_standard_charges  
raise ChargeError("Nonstandard name for heavy atom %s" % a)  
chimerax.add_charge.charge.ChargeError: Nonstandard name for heavy atom 3j5q
#2/A UNK 2 SG  
  
chimerax.add_charge.charge.ChargeError: Nonstandard name for heavy atom 3j5q
#2/A UNK 2 SG  
  
File
"/Users/meng/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/add_charge/charge.py", line 119, in add_standard_charges  
raise ChargeError("Nonstandard name for heavy atom %s" % a)  
  
See log for complete Python traceback.  
  

> coulombic protein surfaces #1.1

Using Amber 20 recommended default charges and atom types for standard
residues  
Nonstandard name for heavy atom 3j5q #2/F UNK 15 SG  




OpenGL version: 4.1 Metal - 76.3
OpenGL renderer: Apple M1 Pro
OpenGL vendor: Apple

Python: 3.9.11
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 Pro
      Model Identifier: MacBookPro18,1
      Chip: Apple M1 Pro
      Total Number of Cores: 10 (8 performance and 2 efficiency)
      Memory: 16 GB
      System Firmware Version: 7459.141.1
      OS Loader Version: 7459.141.1

Software:

    System Software Overview:

      System Version: macOS 12.6 (21G115)
      Kernel Version: Darwin 21.6.0
      Time since boot: 5:59

Graphics/Displays:

    Apple M1 Pro:

      Chipset Model: Apple M1 Pro
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 16
      Vendor: Apple (0x106b)
      Metal Family: Supported, Metal GPUFamily Apple 7
      Displays:
        Color LCD:
          Display Type: Built-in Liquid Retina XDR Display
          Resolution: 3456 x 2234 Retina
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: Yes
          Connection Type: Internal


Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    appnope: 0.1.3
    asttokens: 2.0.8
    Babel: 2.10.3
    backcall: 0.2.0
    blockdiag: 3.0.0
    build: 0.8.0
    certifi: 2021.10.8
    cftime: 1.6.2
    charset-normalizer: 2.1.1
    ChimeraX-AddCharge: 1.4
    ChimeraX-AddH: 2.2
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2.2
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.7
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.3
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.43.2
    ChimeraX-AtomicLibrary: 8.0.2
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.3
    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: 2.7.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.2
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.3.1
    ChimeraX-ChangeChains: 1.0.2
    ChimeraX-CheckWaters: 1.3
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.2.4
    ChimeraX-ColorActions: 1.0.3
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.2
    ChimeraX-CommandLine: 1.2.4
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.5.dev202210150056
    ChimeraX-CoreFormats: 1.1
    ChimeraX-coulombic: 1.3.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.2
    ChimeraX-Dicom: 1.1
    ChimeraX-DistMonitor: 1.3
    ChimeraX-DockPrep: 1.0
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ExperimentalCommands: 1.0
    ChimeraX-FileHistory: 1.0.1
    ChimeraX-FunctionKey: 1.0.1
    ChimeraX-Geometry: 1.2
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 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-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.5
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.2
    ChimeraX-Map: 1.1.1
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0.1
    ChimeraX-MapFilter: 2.0
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1.1
    ChimeraX-Markers: 1.0.1
    ChimeraX-Mask: 1.0.1
    ChimeraX-MatchMaker: 2.0.9
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.2
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.8
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.6
    ChimeraX-ModelPanel: 1.3.6
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.1
    ChimeraX-MouseModes: 1.1.1
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.9.1
    ChimeraX-PDB: 2.6.8
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.2
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PhenixUI: 1.0.5
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1
    ChimeraX-PubChem: 2.1
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.0
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 2.0.1
    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
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.7.3
    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
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.1
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.1.3
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.2
    ChimeraX-ToolshedUtils: 1.2.1
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.24.2
    ChimeraX-uniprot: 2.2.1
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.1.3
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.1
    ChimeraX-WebServices: 1.1.0
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.5
    cxservices: 1.2
    cycler: 0.11.0
    Cython: 0.29.32
    debugpy: 1.6.3
    decorator: 5.1.1
    docutils: 0.19
    entrypoints: 0.4
    executing: 1.1.1
    filelock: 3.7.1
    fonttools: 4.37.4
    funcparserlib: 1.0.0
    grako: 3.16.5
    h5py: 3.7.0
    html2text: 2020.1.16
    idna: 3.4
    ihm: 0.33
    imagecodecs: 2022.7.31
    imagesize: 1.4.1
    importlib-metadata: 5.0.0
    ipykernel: 6.15.3
    ipython: 8.4.0
    ipython-genutils: 0.2.0
    jedi: 0.18.1
    Jinja2: 3.1.2
    jupyter-client: 7.3.4
    jupyter-core: 4.11.1
    kiwisolver: 1.4.4
    line-profiler: 3.5.1
    lxml: 4.9.1
    lz4: 4.0.2
    MarkupSafe: 2.1.1
    matplotlib: 3.5.2
    matplotlib-inline: 0.1.6
    msgpack: 1.0.4
    nest-asyncio: 1.5.6
    netCDF4: 1.6.0
    networkx: 2.8.5
    numexpr: 2.8.3
    numpy: 1.23.1
    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: 9.2.0
    pip: 22.2.2
    pkginfo: 1.8.3
    prompt-toolkit: 3.0.31
    psutil: 5.9.1
    ptyprocess: 0.7.0
    pure-eval: 0.2.2
    pycollada: 0.7.2
    pydicom: 2.3.0
    Pygments: 2.12.0
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 3.0.9
    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: 2022.4
    pyzmq: 24.0.1
    qtconsole: 5.3.1
    QtPy: 2.2.1
    RandomWords: 0.4.0
    requests: 2.28.1
    scipy: 1.9.0
    setuptools: 65.1.1
    setuptools-scm: 7.0.5
    sfftk-rw: 0.7.2
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    Sphinx: 5.1.1
    sphinx-autodoc-typehints: 1.19.1
    sphinxcontrib-applehelp: 1.0.2
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 1.0.2
    sphinxcontrib-htmlhelp: 2.0.0
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.5
    stack-data: 0.5.1
    tables: 3.7.0
    tifffile: 2022.7.31
    tinyarray: 1.2.4
    tomli: 2.0.1
    tornado: 6.2
    traitlets: 5.3.0
    typing-extensions: 4.4.0
    urllib3: 1.26.12
    wcwidth: 0.2.5
    webcolors: 1.12
    wheel: 0.37.1
    wheel-filename: 1.4.1
    zipp: 3.9.0

Change History (3)

comment:1 by pett, 3 years ago

Component: Unassigned → Structure Editing
Owner: set to pett
Platform: → all
Project: → ChimeraX
Status: new → accepted
Summary: ChimeraX bug report submission → UNK residues that should not be UNK

comment:2 by pett, 3 years ago

Have sent mail to the RCSB about this entry.

comment:3 by pett, 3 years ago

Resolution: → nonchimerax
Status: accepted → closed

The RCSB will be releasing a corrected version of 3j5q next week..

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