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Opened 6 years ago
Closed 6 years ago
#2990 closed defect (fixed)
isolde.openmm.openmm_interface: 'coords' is None
| Reported by: | Owned by: | Tristan Croll | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Third Party | Version: | 0.91 |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description (last modified by )
The following bug report has been submitted: Platform: Darwin-19.3.0-x86_64-i386-64bit ChimeraX Version: 0.91 (2019-12-23) Description (Describe the actions that caused this problem to occur here) Log: Startup Messages --- warning | 'clip' is a prefix of an existing command 'clipper' UCSF ChimeraX version: 0.91 (2019-12-23) © 2016-2019 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > isolde tutorial > toolshed show ISOLDE > set selectionWidth 4 Done loading forcefield > isolde demo cryo_em_intro modelOnly true startIsolde false 6out.pdb title: Asymmetric focused reconstruction of human norovirus gi.1 norwalk strain VLP asymmetric unit In T=3 symmetry [more info...] Chain information for 6out.pdb #1 --- Chain | Description A B C | capsid protein VP1 Loaded cryo-EM demo: PDB ID 6out, EMDB ID 20205 > open 20205 fromDatabase emdb Summary of feedback from opening 20205 fetched from emdb --- note | Fetching compressed map 20205 from ftp://ftp.ebi.ac.uk/pub/databases/emdb/structures/EMD-20205/map/emd_20205.map.gz Opened emd_20205.map, grid size 98,112,104, pixel 1.07,1.07,1.07, shown at level 0.287, step 1, values float32 > clipper associate #2 toModel #1 6out.pdb title: Asymmetric focused reconstruction of human norovirus gi.1 norwalk strain VLP asymmetric unit In T=3 symmetry [more info...] Chain information for 6out.pdb --- Chain | Description 1.1/A 1.1/B 1.1/C | capsid protein VP1 > isolde start > set selectionWidth 4 Done loading forcefield QWidget::repaint: Recursive repaint detected > set bgColor white > clipper spotlight radius 13.00 > clipper spotlight radius 14.00 > clipper spotlight radius 15.00 > clipper spotlight radius 16.00 > clipper spotlight radius 17.00 > clipper spotlight radius 16.00 > clipper spotlight radius 15.00 > clipper spotlight radius 14.00 > clipper spotlight radius 13.00 > clipper spotlight radius 12.00 > clipper spotlight radius 11.00 > clipper spotlight radius 10.00 > clipper spotlight radius 9.00 > clipper spotlight radius 8.00 > clipper spotlight radius 9.00 > clipper spotlight radius 10.00 > clipper spotlight radius 11.00 > set bgColor white > addh Summary of feedback from adding hydrogens to 6out.pdb #1.1 --- notes | Termini for 6out.pdb (#1.1) chain A determined from SEQRES records Termini for 6out.pdb (#1.1) chain B determined from SEQRES records Termini for 6out.pdb (#1.1) chain C determined from SEQRES records Chain-initial residues that are actual N termini: /B THR 9 Chain-initial residues that are not actual N termini: /A ASP 29, /C ASP 29 Chain-final residues that are actual C termini: /A SER 520 Chain-final residues that are not actual C termini: /B ALA 519, /C ALA 519 Missing OXT added to C-terminal residue /A SER 520 1438 hydrogen bonds Adding 'H' to /A ASP 29 Adding 'H' to /C ASP 29 /B ALA 519 is not terminus, removing H atom from 'C' /C ALA 519 is not terminus, removing H atom from 'C' 11439 hydrogens added > hide HC Unknown command: isolde restain ligands #1 Unknown command: isolde restain ligands #1 > isolde restrain ligands #1 > select #1 22945 atoms, 23062 bonds, 14 models selected > transparency 50 > transparency 0 No rotamer preview selected! Ignoring command. No rotamer preview selected! Ignoring command. No rotamer preview selected! Ignoring command. No rotamer preview selected! Ignoring command. No rotamer preview selected! Ignoring command. > select clear > select clear > cview /B:375 > cview /A:375 > cview /C:375 > cview /B:383 > clipper spotlight > cview /B:383 > volume gaussian #1 bfactor 50 > clipper associate #2 toModel #1 > volume #1.2.1.1 level 1.6 > volume #1.2.1.1 style surface > volume #1.2.1.1 level 0.1698 > volume #1.2.1.1 style image > volume #1.2.1.1 maximumIntensityProjection true > volume #1.2.1.1 style surface > transparency 50 > volume #1.2.1.1 change image level -0.01372,0 level 0.2156,0.8 level > 0.4259,1 > volume #1.2.1.1 level 0.1757 > transparency 0 > transparency 50 > volume #1.2.1.2 level 0.1032 > select clear > cview /A:383 > cview /C:383 > cview /B:383 > clipper spotlight > cview /B:383 > clipper spotlight > cview /A:383 > select clear > volume #1.2.1.2 level 0.08822 > volume #1.2.1.2 level 0.07667 > select #1 22945 atoms, 23062 bonds, 22 models selected > isolde demo cryo_em_intro modelOnly true startIsolde false 6out.pdb title: Asymmetric focused reconstruction of human norovirus gi.1 norwalk strain VLP asymmetric unit In T=3 symmetry [more info...] Chain information for 6out.pdb #2 --- Chain | Description A B C | capsid protein VP1 Loaded cryo-EM demo: PDB ID 6out, EMDB ID 20205 > select #1 22945 atoms, 23062 bonds, 22 models selected > select #1 22945 atoms, 23062 bonds, 22 models selected > select #1 22945 atoms, 23062 bonds, 22 models selected > close #1 6out.pdb title: Asymmetric focused reconstruction of human norovirus gi.1 norwalk strain VLP asymmetric unit In T=3 symmetry [more info...] Chain information for 6out.pdb --- Chain | Description 1.1/A 1.1/B 1.1/C | capsid protein VP1 > isolde demo cryo_em_intro modelOnly true startIsolde false 6out.pdb title: Asymmetric focused reconstruction of human norovirus gi.1 norwalk strain VLP asymmetric unit In T=3 symmetry [more info...] Chain information for 6out.pdb #2 --- Chain | Description A B C | capsid protein VP1 Loaded cryo-EM demo: PDB ID 6out, EMDB ID 20205 > close #1 6out.pdb title: Asymmetric focused reconstruction of human norovirus gi.1 norwalk strain VLP asymmetric unit In T=3 symmetry [more info...] Chain information for 6out.pdb --- Chain | Description 1.1/A 1.1/B 1.1/C | capsid protein VP1 > close #1 > isolde demo cryo_em_intro modelOnly true startIsolde false 6out.pdb title: Asymmetric focused reconstruction of human norovirus gi.1 norwalk strain VLP asymmetric unit In T=3 symmetry [more info...] Chain information for 6out.pdb #1 --- Chain | Description A B C | capsid protein VP1 6out.pdb title: Asymmetric focused reconstruction of human norovirus gi.1 norwalk strain VLP asymmetric unit In T=3 symmetry [more info...] Chain information for 6out.pdb --- Chain | Description 1.1/A 1.1/B 1.1/C | capsid protein VP1 Loaded cryo-EM demo: PDB ID 6out, EMDB ID 20205 > close #1 > open 20205 fromDatabase emdb Opened emd_20205.map, grid size 98,112,104, pixel 1.07,1.07,1.07, shown at level 0.287, step 1, values float32 > save /Users/km503/Documents/ISOLDE-tut/tut-6out.mrc models #1 > close #1 > open "/Users/km503/Documents/VRC40/higher resolution/VRC40-trimer- > rsr40_real_space_refined-coot-0.pdb" Summary of feedback from opening /Users/km503/Documents/VRC40/higher resolution/VRC40-trimer-rsr40_real_space_refined-coot-0.pdb --- warnings | Start residue of secondary structure not found: HELIX 16 16 PHE H 29 ASP H 31 5 3 Start residue of secondary structure not found: HELIX 17 17 HIS H 62 PHE H 64 5 3 Start residue of secondary structure not found: HELIX 18 18 SER H 93 ASP H 95 5 3 Start residue of secondary structure not found: HELIX 19 19 ASN H 170 GLY H 172 5 3 Start residue of secondary structure not found: HELIX 20 20 SER H 201 SER H 203 5 3 43 messages similar to the above omitted End residue of secondary structure not found: HELIX 67 67 SER K 80 ASP K 82 5 3 Start residue of secondary structure not found: HELIX 68 68 ASP K 122 LEU K 125 1 4 Start residue of secondary structure not found: HELIX 69 69 LYS K 183 LYS K 188 1 6 Start residue of secondary structure not found: SHEET 1 K 4 GLN H 3 GLN H 6 0 Start residue of secondary structure not found: SHEET 2 K 4 VAL H 18 SER H 25 -1 N SER H 25 O GLN H 3 Start residue of secondary structure not found: SHEET 3 K 4 LEU H 81 LEU H 88 -1 N LEU H 88 O VAL H 18 2 messages similar to the above omitted End residue of secondary structure not found: SHEET 2 L 6 SER H 121 VAL H 125 1 N ILE H 124 O GLN H 10 Start residue of secondary structure not found: SHEET 3 L 6 ALA H 97 ARG H 103 -1 N TYR H 99 O SER H 121 Start residue of secondary structure not found: SHEET 4 L 6 LEU H 33 LEU H 39 -1 N LEU H 39 O ILE H 98 Start residue of secondary structure not found: SHEET 5 L 6 LEU H 45 ASN H 52 -1 N ILE H 51 O ILE H 34 Start residue of secondary structure not found: SHEET 6 L 6 MET H 58 LEU H 60 -1 N TYR H 59 O ARG H 50 Start residue of secondary structure not found: SHEET 1 M 4 SER H 135 LEU H 139 0 6 messages similar to the above omitted End residue of secondary structure not found: SHEET 1 T 2 TRP C 36 TYR C 41 0 Start residue of secondary structure not found: SHEET 2 T 2 LEU C 494 THR C 499 -1 N THR C 499 O TRP C 36 Start residue of secondary structure not found: SHEET 1 U 2 CYS C 55 SER C 57 0 Start residue of secondary structure not found: SHEET 2 U 2 ILE C 216 TYR C 218 -1 N HIS C 217 O ALA C 56 Start residue of secondary structure not found: SHEET 1 V 4 GLU C 84 HIS C 86 0 Start residue of secondary structure not found: SHEET 2 V 4 VAL C 243 VAL C 246 -1 N THR C 245 O ILE C 85 52 messages similar to the above omitted End residue of secondary structure not found: SHEET 1 AM 2 TRP G 36 TYR G 41 0 Start residue of secondary structure not found: SHEET 2 AM 2 LEU G 494 THR G 499 -1 N THR G 499 O TRP G 36 Start residue of secondary structure not found: SHEET 1 AN 2 CYS G 55 SER G 57 0 Start residue of secondary structure not found: SHEET 2 AN 2 ILE G 216 TYR G 218 -1 N HIS G 217 O ALA G 56 Start residue of secondary structure not found: SHEET 1 AO 4 GLU G 84 HIS G 86 0 Start residue of secondary structure not found: SHEET 2 AO 4 VAL G 243 VAL G 246 -1 N THR G 245 O ILE G 85 41 messages similar to the above omitted End residue of secondary structure not found: SHEET 2 BB 2 ARG K 103 MET K 106 1 N ARG K 103 O LEU K 11 Start residue of secondary structure not found: SHEET 1 BC 3 LEU K 85 GLN K 90 0 Start residue of secondary structure not found: SHEET 2 BC 3 ILE K 33 LEU K 38 -1 N LEU K 38 O LEU K 85 Start residue of secondary structure not found: SHEET 3 BC 3 ARG K 45 VAL K 48 -1 N VAL K 48 O TRP K 35 Start residue of secondary structure not found: SHEET 1 BD 4 SER K 114 PHE K 118 0 Start residue of secondary structure not found: SHEET 2 BD 4 THR K 129 ASN K 137 -1 N ASN K 137 O SER K 114 5 messages similar to the above omitted Cannot find LINK/SSBOND residue CYS (22 ) Cannot find LINK/SSBOND residue CYS (155 ) Cannot find LINK/SSBOND residue CYS (120 ) Cannot find LINK/SSBOND residue CYS (127 ) Cannot find LINK/SSBOND residue CYS (132 ) 27 messages similar to the above omitted Chain information for VRC40-trimer-rsr40_real_space_refined-coot-0.pdb #1 --- Chain | Description A E I | No description available B F J | No description available C G K | No description available D H L | No description available The following atoms were found to have physically impossible anisotropic B-factor (ANISOU) entries. These have been removed in favour of their isotropic B-factors. C1: N C1: CA C1: C C1: O C1: CB C1: CG C1: CD C1: OE1 [lots of this removed] L212: N L212: CA L212: C L212: O L213: N L213: CA L213: C L213: O L213: CB L213: CG L213: CD L213: OE1 L213: OE2 L214: N L214: CA L214: C L214: O L214: CB L214: SG Chain information for VRC40-trimer-rsr40_real_space_refined-coot-0.pdb --- Chain | Description 1.1/A 1.1/E 1.1/I | No description available 1.1/B 1.1/F 1.1/J | No description available 1.1/C 1.1/G 1.1/K | No description available 1.1/D 1.1/H 1.1/L | No description available > close #1 > open "/Users/km503/Documents/VRC40/higher resolution/VRC40-trimer- > rsr40_real_space_refined-coot-0.pdb" Summary of feedback from opening /Users/km503/Documents/VRC40/higher resolution/VRC40-trimer-rsr40_real_space_refined-coot-0.pdb --- warnings | Start residue of secondary structure not found: HELIX 16 16 PHE H 29 ASP H 31 5 3 Start residue of secondary structure not found: HELIX 17 17 HIS H 62 PHE H 64 5 3 Start residue of secondary structure not found: HELIX 18 18 SER H 93 ASP H 95 5 3 Start residue of secondary structure not found: HELIX 19 19 ASN H 170 GLY H 172 5 3 Start residue of secondary structure not found: HELIX 20 20 SER H 201 SER H 203 5 3 43 messages similar to the above omitted End residue of secondary structure not found: HELIX 67 67 SER K 80 ASP K 82 5 3 Start residue of secondary structure not found: HELIX 68 68 ASP K 122 LEU K 125 1 4 Start residue of secondary structure not found: HELIX 69 69 LYS K 183 LYS K 188 1 6 Start residue of secondary structure not found: SHEET 1 K 4 GLN H 3 GLN H 6 0 Start residue of secondary structure not found: SHEET 2 K 4 VAL H 18 SER H 25 -1 N SER H 25 O GLN H 3 Start residue of secondary structure not found: SHEET 3 K 4 LEU H 81 LEU H 88 -1 N LEU H 88 O VAL H 18 2 messages similar to the above omitted End residue of secondary structure not found: SHEET 2 L 6 SER H 121 VAL H 125 1 N ILE H 124 O GLN H 10 Start residue of secondary structure not found: SHEET 3 L 6 ALA H 97 ARG H 103 -1 N TYR H 99 O SER H 121 Start residue of secondary structure not found: SHEET 4 L 6 LEU H 33 LEU H 39 -1 N LEU H 39 O ILE H 98 Start residue of secondary structure not found: SHEET 5 L 6 LEU H 45 ASN H 52 -1 N ILE H 51 O ILE H 34 Start residue of secondary structure not found: SHEET 6 L 6 MET H 58 LEU H 60 -1 N TYR H 59 O ARG H 50 Start residue of secondary structure not found: SHEET 1 M 4 SER H 135 LEU H 139 0 6 messages similar to the above omitted End residue of secondary structure not found: SHEET 1 T 2 TRP C 36 TYR C 41 0 Start residue of secondary structure not found: SHEET 2 T 2 LEU C 494 THR C 499 -1 N THR C 499 O TRP C 36 Start residue of secondary structure not found: SHEET 1 U 2 CYS C 55 SER C 57 0 Start residue of secondary structure not found: SHEET 2 U 2 ILE C 216 TYR C 218 -1 N HIS C 217 O ALA C 56 Start residue of secondary structure not found: SHEET 1 V 4 GLU C 84 HIS C 86 0 Start residue of secondary structure not found: SHEET 2 V 4 VAL C 243 VAL C 246 -1 N THR C 245 O ILE C 85 52 messages similar to the above omitted End residue of secondary structure not found: SHEET 1 AM 2 TRP G 36 TYR G 41 0 Start residue of secondary structure not found: SHEET 2 AM 2 LEU G 494 THR G 499 -1 N THR G 499 O TRP G 36 Start residue of secondary structure not found: SHEET 1 AN 2 CYS G 55 SER G 57 0 Start residue of secondary structure not found: SHEET 2 AN 2 ILE G 216 TYR G 218 -1 N HIS G 217 O ALA G 56 Start residue of secondary structure not found: SHEET 1 AO 4 GLU G 84 HIS G 86 0 Start residue of secondary structure not found: SHEET 2 AO 4 VAL G 243 VAL G 246 -1 N THR G 245 O ILE G 85 41 messages similar to the above omitted End residue of secondary structure not found: SHEET 2 BB 2 ARG K 103 MET K 106 1 N ARG K 103 O LEU K 11 Start residue of secondary structure not found: SHEET 1 BC 3 LEU K 85 GLN K 90 0 Start residue of secondary structure not found: SHEET 2 BC 3 ILE K 33 LEU K 38 -1 N LEU K 38 O LEU K 85 Start residue of secondary structure not found: SHEET 3 BC 3 ARG K 45 VAL K 48 -1 N VAL K 48 O TRP K 35 Start residue of secondary structure not found: SHEET 1 BD 4 SER K 114 PHE K 118 0 Start residue of secondary structure not found: SHEET 2 BD 4 THR K 129 ASN K 137 -1 N ASN K 137 O SER K 114 5 messages similar to the above omitted Cannot find LINK/SSBOND residue CYS (22 ) Cannot find LINK/SSBOND residue CYS (155 ) Cannot find LINK/SSBOND residue CYS (120 ) Cannot find LINK/SSBOND residue CYS (127 ) Cannot find LINK/SSBOND residue CYS (132 ) 27 messages similar to the above omitted Chain information for VRC40-trimer-rsr40_real_space_refined-coot-0.pdb #1 --- Chain | Description A E I | No description available B F J | No description available C G K | No description available D H L | No description available > open "/Users/km503/Documents/VRC40/higher > resolution/cryosparc_P4_J12_008_volume_map_sharp_local-zflip.mrc" Opened cryosparc_P4_J12_008_volume_map_sharp_local-zflip.mrc, grid size 320,320,320, pixel 1.08, shown at level 0.667, step 2, values float32 > clipper associate #2 toModel #1 The following atoms were found to have physically impossible anisotropic B-factor (ANISOU) entries. These have been removed in favour of their isotropic B-factors. C1: N C1: CA C1: C C1: O C1: CB C1: CG C1: CD C1: OE1 C1: NE2 C2: N C2: CA C2: C C2: O C2: CB C2: CG1 C2: CG2 C3: N C3: CA C3: C C3: O C3: CB C3: CG C3: CD C3: OE1 C3: NE2 C4: N C4: CA C4: C C4: O C4: CB C4: CG C4: CD1 C4: CD2 C5: N C5: CA C5: C [lots of this removed] L206: C L206: O L206: CB L206: OG1 L206: CG2 L207: N L207: CA L207: C L207: O L207: CB L207: CG L207: CD L207: CE L207: NZ L208: N L208: CA L208: C L208: O L208: CB L208: OG L209: N L209: CA L209: C L209: O L209: CB L209: CG L209: CD1 L209: CD2 L209: CE1 L209: CE2 L209: CZ L210: N L210: CA L210: C L210: O L210: CB L210: CG L210: OD1 L210: ND2 L211: N L211: CA L211: C L211: O L211: CB L211: CG L211: CD L211: NE L211: CZ L211: NH1 L211: NH2 L212: N L212: CA L212: C L212: O L213: N L213: CA L213: C L213: O L213: CB L213: CG L213: CD L213: OE1 L213: OE2 L214: N L214: CA L214: C L214: O L214: CB L214: SG Chain information for VRC40-trimer-rsr40_real_space_refined-coot-0.pdb --- Chain | Description 1.1/A 1.1/E 1.1/I | No description available 1.1/B 1.1/F 1.1/J | No description available 1.1/C 1.1/G 1.1/K | No description available 1.1/D 1.1/H 1.1/L | No description available > isolde start > set selectionWidth 4 Done loading forcefield > set bgColor white > addh Summary of feedback from adding hydrogens to VRC40-trimer- rsr40_real_space_refined-coot-0.pdb #1.1 --- warning | Skipped 15 atom(s) with bad connectivities; see log for details notes | No usable SEQRES records for VRC40-trimer-rsr40_real_space_refined- coot-0.pdb (#1.1) chain A; guessing termini instead No usable SEQRES records for VRC40-trimer-rsr40_real_space_refined-coot-0.pdb (#1.1) chain B; guessing termini instead No usable SEQRES records for VRC40-trimer-rsr40_real_space_refined-coot-0.pdb (#1.1) chain C; guessing termini instead No usable SEQRES records for VRC40-trimer-rsr40_real_space_refined-coot-0.pdb (#1.1) chain D; guessing termini instead No usable SEQRES records for VRC40-trimer-rsr40_real_space_refined-coot-0.pdb (#1.1) chain E; guessing termini instead 7 messages similar to the above omitted Chain-initial residues that are actual N termini: /C GLN 1, /D GLN 1, /G GLN 1, /H GLN 1, /K GLN 1, /L GLN 1 Chain-initial residues that are not actual N termini: /A ALA 32, /B ALA 512, /E ALA 32, /F ALA 512, /I ALA 32, /J ALA 512 Chain-final residues that are actual C termini: Chain-final residues that are not actual C termini: /A VAL 505, /B ASP 664, /C SER 230, /D CYS 214, /E VAL 505, /F ASP 664, /G SER 230, /H CYS 214, /I VAL 505, /J ASP 664, /K SER 230, /L CYS 214 Skipping possible acceptor with bad geometry: /A NAG 3932 O7 Wrong number of grandchild atoms for phi/psi acceptor /A NAG 3932 O7 Skipping possible acceptor with bad geometry: /E NAG 3932 O7 Wrong number of grandchild atoms for phi/psi acceptor /E NAG 3932 O7 Skipping possible acceptor with bad geometry: /I NAG 3932 O7 Wrong number of grandchild atoms for phi/psi acceptor /I NAG 3932 O7 Skipping possible acceptor with bad geometry: /A NAG 3932 O7 Wrong number of grandchild atoms for phi/psi acceptor /A NAG 3932 O7 Skipping possible acceptor with bad geometry: /E NAG 3932 O7 Wrong number of grandchild atoms for phi/psi acceptor /E NAG 3932 O7 10 messages similar to the above omitted 2010 hydrogen bonds /A VAL 505 is not terminus, removing H atom from 'C' /B ASP 664 is not terminus, removing H atom from 'C' /C SER 230 is not terminus, removing H atom from 'C' /D CYS 214 is not terminus, removing H atom from 'C' /E VAL 505 is not terminus, removing H atom from 'C' 7 messages similar to the above omitted 5956 hydrogens added > hide HC > show HC > hide HC > isolde restrain ligands #1 > hide #1.1.5 models > show #1.1.5 models > addh hbond true Summary of feedback from adding hydrogens to VRC40-trimer- rsr40_real_space_refined-coot-0.pdb #1.1 --- warning | Skipped 15 atom(s) with bad connectivities; see log for details notes | No usable SEQRES records for VRC40-trimer-rsr40_real_space_refined- coot-0.pdb (#1.1) chain A; guessing termini instead No usable SEQRES records for VRC40-trimer-rsr40_real_space_refined-coot-0.pdb (#1.1) chain B; guessing termini instead No usable SEQRES records for VRC40-trimer-rsr40_real_space_refined-coot-0.pdb (#1.1) chain C; guessing termini instead No usable SEQRES records for VRC40-trimer-rsr40_real_space_refined-coot-0.pdb (#1.1) chain D; guessing termini instead No usable SEQRES records for VRC40-trimer-rsr40_real_space_refined-coot-0.pdb (#1.1) chain E; guessing termini instead 7 messages similar to the above omitted Chain-initial residues that are actual N termini: /C GLN 1, /D GLN 1, /G GLN 1, /H GLN 1, /K GLN 1, /L GLN 1 Chain-initial residues that are not actual N termini: /A ALA 32, /B ALA 512, /E ALA 32, /F ALA 512, /I ALA 32, /J ALA 512 Chain-final residues that are actual C termini: Chain-final residues that are not actual C termini: /A VAL 505, /B ASP 664, /C SER 230, /D CYS 214, /E VAL 505, /F ASP 664, /G SER 230, /H CYS 214, /I VAL 505, /J ASP 664, /K SER 230, /L CYS 214 Skipping possible acceptor with bad geometry: /A NAG 3932 O7 Wrong number of grandchild atoms for phi/psi acceptor /A NAG 3932 O7 Skipping possible acceptor with bad geometry: /E NAG 3932 O7 Wrong number of grandchild atoms for phi/psi acceptor /E NAG 3932 O7 Skipping possible acceptor with bad geometry: /E NAG 3932 O7 Wrong number of grandchild atoms for phi/psi acceptor /E NAG 3932 O7 Skipping possible acceptor with bad geometry: /I NAG 3932 O7 Wrong number of grandchild atoms for phi/psi acceptor /I NAG 3932 O7 Skipping possible acceptor with bad geometry: /A NAG 3932 O7 Wrong number of grandchild atoms for phi/psi acceptor /A NAG 3932 O7 10 messages similar to the above omitted 1974 hydrogen bonds /A VAL 505 is not terminus, removing H atom from 'C' /B ASP 664 is not terminus, removing H atom from 'C' /C SER 230 is not terminus, removing H atom from 'C' /D CYS 214 is not terminus, removing H atom from 'C' /E VAL 505 is not terminus, removing H atom from 'C' 7 messages similar to the above omitted 0 hydrogens added > show HC > hide HC > volume #1.2.1.1 level 1.102 QWidget::repaint: Recursive repaint detected > select #1 51607 atoms, 52256 bonds, 14 models selected > isolde sim start sel No template found for residue A3932 (NAG) Adding hydrogens Summary of feedback from adding hydrogens to VRC40-trimer- rsr40_real_space_refined-coot-0.pdb #1.1 --- warning | Skipped 15 atom(s) with bad connectivities; see log for details notes | No usable SEQRES records for VRC40-trimer-rsr40_real_space_refined- coot-0.pdb (#1.1) chain A; guessing termini instead No usable SEQRES records for VRC40-trimer-rsr40_real_space_refined-coot-0.pdb (#1.1) chain B; guessing termini instead No usable SEQRES records for VRC40-trimer-rsr40_real_space_refined-coot-0.pdb (#1.1) chain C; guessing termini instead No usable SEQRES records for VRC40-trimer-rsr40_real_space_refined-coot-0.pdb (#1.1) chain D; guessing termini instead No usable SEQRES records for VRC40-trimer-rsr40_real_space_refined-coot-0.pdb (#1.1) chain E; guessing termini instead 7 messages similar to the above omitted Chain-initial residues that are actual N termini: /C GLN 1, /D GLN 1, /G GLN 1, /H GLN 1, /K GLN 1, /L GLN 1 Chain-initial residues that are not actual N termini: /A ALA 32, /B ALA 512, /E ALA 32, /F ALA 512, /I ALA 32, /J ALA 512 Chain-final residues that are actual C termini: Chain-final residues that are not actual C termini: /A VAL 505, /B ASP 664, /C SER 230, /D CYS 214, /E VAL 505, /F ASP 664, /G SER 230, /H CYS 214, /I VAL 505, /J ASP 664, /K SER 230, /L CYS 214 Skipping possible acceptor with bad geometry: /A NAG 3932 O7 Wrong number of grandchild atoms for phi/psi acceptor /A NAG 3932 O7 Skipping possible acceptor with bad geometry: /E NAG 3932 O7 Wrong number of grandchild atoms for phi/psi acceptor /E NAG 3932 O7 Skipping possible acceptor with bad geometry: /E NAG 3932 O7 Wrong number of grandchild atoms for phi/psi acceptor /E NAG 3932 O7 Skipping possible acceptor with bad geometry: /A NAG 3932 O7 Wrong number of grandchild atoms for phi/psi acceptor /A NAG 3932 O7 Skipping possible acceptor with bad geometry: /I NAG 3932 O7 Wrong number of grandchild atoms for phi/psi acceptor /I NAG 3932 O7 10 messages similar to the above omitted 1974 hydrogen bonds /A VAL 505 is not terminus, removing H atom from 'C' /B ASP 664 is not terminus, removing H atom from 'C' /C SER 230 is not terminus, removing H atom from 'C' /D CYS 214 is not terminus, removing H atom from 'C' /E VAL 505 is not terminus, removing H atom from 'C' 7 messages similar to the above omitted 0 hydrogens added No template found for residue A3932 (NAG) Adding hydrogens Summary of feedback from adding hydrogens to VRC40-trimer- rsr40_real_space_refined-coot-0.pdb #1.1 --- warning | Skipped 15 atom(s) with bad connectivities; see log for details notes | No usable SEQRES records for VRC40-trimer-rsr40_real_space_refined- coot-0.pdb (#1.1) chain A; guessing termini instead No usable SEQRES records for VRC40-trimer-rsr40_real_space_refined-coot-0.pdb (#1.1) chain B; guessing termini instead No usable SEQRES records for VRC40-trimer-rsr40_real_space_refined-coot-0.pdb (#1.1) chain C; guessing termini instead No usable SEQRES records for VRC40-trimer-rsr40_real_space_refined-coot-0.pdb (#1.1) chain D; guessing termini instead No usable SEQRES records for VRC40-trimer-rsr40_real_space_refined-coot-0.pdb (#1.1) chain E; guessing termini instead 7 messages similar to the above omitted Chain-initial residues that are actual N termini: /C GLN 1, /D GLN 1, /G GLN 1, /H GLN 1, /K GLN 1, /L GLN 1 Chain-initial residues that are not actual N termini: /A ALA 32, /B ALA 512, /E ALA 32, /F ALA 512, /I ALA 32, /J ALA 512 Chain-final residues that are actual C termini: Chain-final residues that are not actual C termini: /A VAL 505, /B ASP 664, /C SER 230, /D CYS 214, /E VAL 505, /F ASP 664, /G SER 230, /H CYS 214, /I VAL 505, /J ASP 664, /K SER 230, /L CYS 214 Skipping possible acceptor with bad geometry: /A NAG 3932 O7 Wrong number of grandchild atoms for phi/psi acceptor /A NAG 3932 O7 Skipping possible acceptor with bad geometry: /E NAG 3932 O7 Wrong number of grandchild atoms for phi/psi acceptor /E NAG 3932 O7 Skipping possible acceptor with bad geometry: /E NAG 3932 O7 Wrong number of grandchild atoms for phi/psi acceptor /E NAG 3932 O7 Skipping possible acceptor with bad geometry: /I NAG 3932 O7 Wrong number of grandchild atoms for phi/psi acceptor /I NAG 3932 O7 Skipping possible acceptor with bad geometry: /A NAG 3932 O7 Wrong number of grandchild atoms for phi/psi acceptor /A NAG 3932 O7 10 messages similar to the above omitted 1974 hydrogen bonds /A VAL 505 is not terminus, removing H atom from 'C' /B ASP 664 is not terminus, removing H atom from 'C' /C SER 230 is not terminus, removing H atom from 'C' /D CYS 214 is not terminus, removing H atom from 'C' /E VAL 505 is not terminus, removing H atom from 'C' 7 messages similar to the above omitted 0 hydrogens added No template found for residue A3932 (NAG) Doing nothing No template found for residue A3932 (NAG) Adding hydrogens Summary of feedback from adding hydrogens to VRC40-trimer- rsr40_real_space_refined-coot-0.pdb #1.1 --- warning | Skipped 15 atom(s) with bad connectivities; see log for details notes | No usable SEQRES records for VRC40-trimer-rsr40_real_space_refined- coot-0.pdb (#1.1) chain A; guessing termini instead No usable SEQRES records for VRC40-trimer-rsr40_real_space_refined-coot-0.pdb (#1.1) chain B; guessing termini instead No usable SEQRES records for VRC40-trimer-rsr40_real_space_refined-coot-0.pdb (#1.1) chain C; guessing termini instead No usable SEQRES records for VRC40-trimer-rsr40_real_space_refined-coot-0.pdb (#1.1) chain D; guessing termini instead No usable SEQRES records for VRC40-trimer-rsr40_real_space_refined-coot-0.pdb (#1.1) chain E; guessing termini instead 7 messages similar to the above omitted Chain-initial residues that are actual N termini: /C GLN 1, /D GLN 1, /G GLN 1, /H GLN 1, /K GLN 1, /L GLN 1 Chain-initial residues that are not actual N termini: /A ALA 32, /B ALA 512, /E ALA 32, /F ALA 512, /I ALA 32, /J ALA 512 Chain-final residues that are actual C termini: Chain-final residues that are not actual C termini: /A VAL 505, /B ASP 664, /C SER 230, /D CYS 214, /E VAL 505, /F ASP 664, /G SER 230, /H CYS 214, /I VAL 505, /J ASP 664, /K SER 230, /L CYS 214 Skipping possible acceptor with bad geometry: /A NAG 3932 O7 Wrong number of grandchild atoms for phi/psi acceptor /A NAG 3932 O7 Skipping possible acceptor with bad geometry: /E NAG 3932 O7 Wrong number of grandchild atoms for phi/psi acceptor /E NAG 3932 O7 Skipping possible acceptor with bad geometry: /E NAG 3932 O7 Wrong number of grandchild atoms for phi/psi acceptor /E NAG 3932 O7 Skipping possible acceptor with bad geometry: /A NAG 3932 O7 Wrong number of grandchild atoms for phi/psi acceptor /A NAG 3932 O7 Skipping possible acceptor with bad geometry: /I NAG 3932 O7 Wrong number of grandchild atoms for phi/psi acceptor /I NAG 3932 O7 10 messages similar to the above omitted 1974 hydrogen bonds /A VAL 505 is not terminus, removing H atom from 'C' /B ASP 664 is not terminus, removing H atom from 'C' /C SER 230 is not terminus, removing H atom from 'C' /D CYS 214 is not terminus, removing H atom from 'C' /E VAL 505 is not terminus, removing H atom from 'C' 7 messages similar to the above omitted 0 hydrogens added No template found for residue A3932 (NAG) Adding hydrogens Summary of feedback from adding hydrogens to VRC40-trimer- rsr40_real_space_refined-coot-0.pdb #1.1 --- warning | Skipped 15 atom(s) with bad connectivities; see log for details notes | No usable SEQRES records for VRC40-trimer-rsr40_real_space_refined- coot-0.pdb (#1.1) chain A; guessing termini instead No usable SEQRES records for VRC40-trimer-rsr40_real_space_refined-coot-0.pdb (#1.1) chain B; guessing termini instead No usable SEQRES records for VRC40-trimer-rsr40_real_space_refined-coot-0.pdb (#1.1) chain C; guessing termini instead No usable SEQRES records for VRC40-trimer-rsr40_real_space_refined-coot-0.pdb (#1.1) chain D; guessing termini instead No usable SEQRES records for VRC40-trimer-rsr40_real_space_refined-coot-0.pdb (#1.1) chain E; guessing termini instead 7 messages similar to the above omitted Chain-initial residues that are actual N termini: /C GLN 1, /D GLN 1, /G GLN 1, /H GLN 1, /K GLN 1, /L GLN 1 Chain-initial residues that are not actual N termini: /A ALA 32, /B ALA 512, /E ALA 32, /F ALA 512, /I ALA 32, /J ALA 512 Chain-final residues that are actual C termini: Chain-final residues that are not actual C termini: /A VAL 505, /B ASP 664, /C SER 230, /D CYS 214, /E VAL 505, /F ASP 664, /G SER 230, /H CYS 214, /I VAL 505, /J ASP 664, /K SER 230, /L CYS 214 Skipping possible acceptor with bad geometry: /A NAG 3932 O7 Wrong number of grandchild atoms for phi/psi acceptor /A NAG 3932 O7 Skipping possible acceptor with bad geometry: /E NAG 3932 O7 Wrong number of grandchild atoms for phi/psi acceptor /E NAG 3932 O7 Skipping possible acceptor with bad geometry: /A NAG 3932 O7 Wrong number of grandchild atoms for phi/psi acceptor /A NAG 3932 O7 Skipping possible acceptor with bad geometry: /E NAG 3932 O7 Wrong number of grandchild atoms for phi/psi acceptor /E NAG 3932 O7 Skipping possible acceptor with bad geometry: /I NAG 3932 O7 Wrong number of grandchild atoms for phi/psi acceptor /I NAG 3932 O7 10 messages similar to the above omitted 1974 hydrogen bonds /A VAL 505 is not terminus, removing H atom from 'C' /B ASP 664 is not terminus, removing H atom from 'C' /C SER 230 is not terminus, removing H atom from 'C' /D CYS 214 is not terminus, removing H atom from 'C' /E VAL 505 is not terminus, removing H atom from 'C' 7 messages similar to the above omitted 0 hydrogens added No template found for residue A3932 (NAG) Adding hydrogens Summary of feedback from adding hydrogens to VRC40-trimer- rsr40_real_space_refined-coot-0.pdb #1.1 --- warning | Skipped 15 atom(s) with bad connectivities; see log for details notes | No usable SEQRES records for VRC40-trimer-rsr40_real_space_refined- coot-0.pdb (#1.1) chain A; guessing termini instead No usable SEQRES records for VRC40-trimer-rsr40_real_space_refined-coot-0.pdb (#1.1) chain B; guessing termini instead No usable SEQRES records for VRC40-trimer-rsr40_real_space_refined-coot-0.pdb (#1.1) chain C; guessing termini instead No usable SEQRES records for VRC40-trimer-rsr40_real_space_refined-coot-0.pdb (#1.1) chain D; guessing termini instead No usable SEQRES records for VRC40-trimer-rsr40_real_space_refined-coot-0.pdb (#1.1) chain E; guessing termini instead 7 messages similar to the above omitted Chain-initial residues that are actual N termini: /C GLN 1, /D GLN 1, /G GLN 1, /H GLN 1, /K GLN 1, /L GLN 1 Chain-initial residues that are not actual N termini: /A ALA 32, /B ALA 512, /E ALA 32, /F ALA 512, /I ALA 32, /J ALA 512 Chain-final residues that are actual C termini: Chain-final residues that are not actual C termini: /A VAL 505, /B ASP 664, /C SER 230, /D CYS 214, /E VAL 505, /F ASP 664, /G SER 230, /H CYS 214, /I VAL 505, /J ASP 664, /K SER 230, /L CYS 214 Skipping possible acceptor with bad geometry: /A NAG 3932 O7 Wrong number of grandchild atoms for phi/psi acceptor /A NAG 3932 O7 Skipping possible acceptor with bad geometry: /E NAG 3932 O7 Wrong number of grandchild atoms for phi/psi acceptor /E NAG 3932 O7 Skipping possible acceptor with bad geometry: /E NAG 3932 O7 Wrong number of grandchild atoms for phi/psi acceptor /E NAG 3932 O7 Skipping possible acceptor with bad geometry: /A NAG 3932 O7 Wrong number of grandchild atoms for phi/psi acceptor /A NAG 3932 O7 Skipping possible acceptor with bad geometry: /I NAG 3932 O7 Wrong number of grandchild atoms for phi/psi acceptor /I NAG 3932 O7 10 messages similar to the above omitted 1974 hydrogen bonds /A VAL 505 is not terminus, removing H atom from 'C' /B ASP 664 is not terminus, removing H atom from 'C' /C SER 230 is not terminus, removing H atom from 'C' /D CYS 214 is not terminus, removing H atom from 'C' /E VAL 505 is not terminus, removing H atom from 'C' 7 messages similar to the above omitted 0 hydrogens added No template found for residue A3932 (NAG) Adding hydrogens Summary of feedback from adding hydrogens to VRC40-trimer- rsr40_real_space_refined-coot-0.pdb #1.1 --- warning | Skipped 15 atom(s) with bad connectivities; see log for details notes | No usable SEQRES records for VRC40-trimer-rsr40_real_space_refined- coot-0.pdb (#1.1) chain A; guessing termini instead No usable SEQRES records for VRC40-trimer-rsr40_real_space_refined-coot-0.pdb (#1.1) chain B; guessing termini instead No usable SEQRES records for VRC40-trimer-rsr40_real_space_refined-coot-0.pdb (#1.1) chain C; guessing termini instead No usable SEQRES records for VRC40-trimer-rsr40_real_space_refined-coot-0.pdb (#1.1) chain D; guessing termini instead No usable SEQRES records for VRC40-trimer-rsr40_real_space_refined-coot-0.pdb (#1.1) chain E; guessing termini instead 7 messages similar to the above omitted Chain-initial residues that are actual N termini: /C GLN 1, /D GLN 1, /G GLN 1, /H GLN 1, /K GLN 1, /L GLN 1 Chain-initial residues that are not actual N termini: /A ALA 32, /B ALA 512, /E ALA 32, /F ALA 512, /I ALA 32, /J ALA 512 Chain-final residues that are actual C termini: Chain-final residues that are not actual C termini: /A VAL 505, /B ASP 664, /C SER 230, /D CYS 214, /E VAL 505, /F ASP 664, /G SER 230, /H CYS 214, /I VAL 505, /J ASP 664, /K SER 230, /L CYS 214 Skipping possible acceptor with bad geometry: /A NAG 3932 O7 Wrong number of grandchild atoms for phi/psi acceptor /A NAG 3932 O7 Skipping possible acceptor with bad geometry: /E NAG 3932 O7 Wrong number of grandchild atoms for phi/psi acceptor /E NAG 3932 O7 Skipping possible acceptor with bad geometry: /I NAG 3932 O7 Wrong number of grandchild atoms for phi/psi acceptor /I NAG 3932 O7 Skipping possible acceptor with bad geometry: /A NAG 3932 O7 Wrong number of grandchild atoms for phi/psi acceptor /A NAG 3932 O7 Skipping possible acceptor with bad geometry: /E NAG 3932 O7 Wrong number of grandchild atoms for phi/psi acceptor /E NAG 3932 O7 10 messages similar to the above omitted 1974 hydrogen bonds /A VAL 505 is not terminus, removing H atom from 'C' /B ASP 664 is not terminus, removing H atom from 'C' /C SER 230 is not terminus, removing H atom from 'C' /D CYS 214 is not terminus, removing H atom from 'C' /E VAL 505 is not terminus, removing H atom from 'C' 7 messages similar to the above omitted 0 hydrogens added No template found for residue A3932 (NAG) Adding hydrogens Summary of feedback from adding hydrogens to VRC40-trimer- rsr40_real_space_refined-coot-0.pdb #1.1 --- warning | Skipped 15 atom(s) with bad connectivities; see log for details notes | No usable SEQRES records for VRC40-trimer-rsr40_real_space_refined- coot-0.pdb (#1.1) chain A; guessing termini instead No usable SEQRES records for VRC40-trimer-rsr40_real_space_refined-coot-0.pdb (#1.1) chain B; guessing termini instead No usable SEQRES records for VRC40-trimer-rsr40_real_space_refined-coot-0.pdb (#1.1) chain C; guessing termini instead No usable SEQRES records for VRC40-trimer-rsr40_real_space_refined-coot-0.pdb (#1.1) chain D; guessing termini instead No usable SEQRES records for VRC40-trimer-rsr40_real_space_refined-coot-0.pdb (#1.1) chain E; guessing termini instead 7 messages similar to the above omitted Chain-initial residues that are actual N termini: /C GLN 1, /D GLN 1, /G GLN 1, /H GLN 1, /K GLN 1, /L GLN 1 Chain-initial residues that are not actual N termini: /A ALA 32, /B ALA 512, /E ALA 32, /F ALA 512, /I ALA 32, /J ALA 512 Chain-final residues that are actual C termini: Chain-final residues that are not actual C termini: /A VAL 505, /B ASP 664, /C SER 230, /D CYS 214, /E VAL 505, /F ASP 664, /G SER 230, /H CYS 214, /I VAL 505, /J ASP 664, /K SER 230, /L CYS 214 Skipping possible acceptor with bad geometry: /A NAG 3932 O7 Wrong number of grandchild atoms for phi/psi acceptor /A NAG 3932 O7 Skipping possible acceptor with bad geometry: /E NAG 3932 O7 Wrong number of grandchild atoms for phi/psi acceptor /E NAG 3932 O7 Skipping possible acceptor with bad geometry: /I NAG 3932 O7 Wrong number of grandchild atoms for phi/psi acceptor /I NAG 3932 O7 Skipping possible acceptor with bad geometry: /E NAG 3932 O7 Wrong number of grandchild atoms for phi/psi acceptor /E NAG 3932 O7 Skipping possible acceptor with bad geometry: /A NAG 3932 O7 Wrong number of grandchild atoms for phi/psi acceptor /A NAG 3932 O7 10 messages similar to the above omitted 1974 hydrogen bonds /A VAL 505 is not terminus, removing H atom from 'C' /B ASP 664 is not terminus, removing H atom from 'C' /C SER 230 is not terminus, removing H atom from 'C' /D CYS 214 is not terminus, removing H atom from 'C' /E VAL 505 is not terminus, removing H atom from 'C' 7 messages similar to the above omitted 0 hydrogens added No template found for residue A3932 (NAG) Adding hydrogens Summary of feedback from adding hydrogens to VRC40-trimer- rsr40_real_space_refined-coot-0.pdb #1.1 --- warning | Skipped 15 atom(s) with bad connectivities; see log for details notes | No usable SEQRES records for VRC40-trimer-rsr40_real_space_refined- coot-0.pdb (#1.1) chain A; guessing termini instead No usable SEQRES records for VRC40-trimer-rsr40_real_space_refined-coot-0.pdb (#1.1) chain B; guessing termini instead No usable SEQRES records for VRC40-trimer-rsr40_real_space_refined-coot-0.pdb (#1.1) chain C; guessing termini instead No usable SEQRES records for VRC40-trimer-rsr40_real_space_refined-coot-0.pdb (#1.1) chain D; guessing termini instead No usable SEQRES records for VRC40-trimer-rsr40_real_space_refined-coot-0.pdb (#1.1) chain E; guessing termini instead 7 messages similar to the above omitted Chain-initial residues that are actual N termini: /C GLN 1, /D GLN 1, /G GLN 1, /H GLN 1, /K GLN 1, /L GLN 1 Chain-initial residues that are not actual N termini: /A ALA 32, /B ALA 512, /E ALA 32, /F ALA 512, /I ALA 32, /J ALA 512 Chain-final residues that are actual C termini: Chain-final residues that are not actual C termini: /A VAL 505, /B ASP 664, /C SER 230, /D CYS 214, /E VAL 505, /F ASP 664, /G SER 230, /H CYS 214, /I VAL 505, /J ASP 664, /K SER 230, /L CYS 214 Skipping possible acceptor with bad geometry: /A NAG 3932 O7 Wrong number of grandchild atoms for phi/psi acceptor /A NAG 3932 O7 Skipping possible acceptor with bad geometry: /E NAG 3932 O7 Wrong number of grandchild atoms for phi/psi acceptor /E NAG 3932 O7 Skipping possible acceptor with bad geometry: /I NAG 3932 O7 Wrong number of grandchild atoms for phi/psi acceptor /I NAG 3932 O7 Skipping possible acceptor with bad geometry: /E NAG 3932 O7 Wrong number of grandchild atoms for phi/psi acceptor /E NAG 3932 O7 Skipping possible acceptor with bad geometry: /A NAG 3932 O7 Wrong number of grandchild atoms for phi/psi acceptor /A NAG 3932 O7 10 messages similar to the above omitted 1974 hydrogen bonds /A VAL 505 is not terminus, removing H atom from 'C' /B ASP 664 is not terminus, removing H atom from 'C' /C SER 230 is not terminus, removing H atom from 'C' /D CYS 214 is not terminus, removing H atom from 'C' /E VAL 505 is not terminus, removing H atom from 'C' 7 messages similar to the above omitted 0 hydrogens added No template found for residue A3932 (NAG) Adding hydrogens Summary of feedback from adding hydrogens to VRC40-trimer- rsr40_real_space_refined-coot-0.pdb #1.1 --- warning | Skipped 15 atom(s) with bad connectivities; see log for details notes | No usable SEQRES records for VRC40-trimer-rsr40_real_space_refined- coot-0.pdb (#1.1) chain A; guessing termini instead No usable SEQRES records for VRC40-trimer-rsr40_real_space_refined-coot-0.pdb (#1.1) chain B; guessing termini instead No usable SEQRES records for VRC40-trimer-rsr40_real_space_refined-coot-0.pdb (#1.1) chain C; guessing termini instead No usable SEQRES records for VRC40-trimer-rsr40_real_space_refined-coot-0.pdb (#1.1) chain D; guessing termini instead No usable SEQRES records for VRC40-trimer-rsr40_real_space_refined-coot-0.pdb (#1.1) chain E; guessing termini instead 7 messages similar to the above omitted Chain-initial residues that are actual N termini: /C GLN 1, /D GLN 1, /G GLN 1, /H GLN 1, /K GLN 1, /L GLN 1 Chain-initial residues that are not actual N termini: /A ALA 32, /B ALA 512, /E ALA 32, /F ALA 512, /I ALA 32, /J ALA 512 Chain-final residues that are actual C termini: Chain-final residues that are not actual C termini: /A VAL 505, /B ASP 664, /C SER 230, /D CYS 214, /E VAL 505, /F ASP 664, /G SER 230, /H CYS 214, /I VAL 505, /J ASP 664, /K SER 230, /L CYS 214 Skipping possible acceptor with bad geometry: /A NAG 3932 O7 Wrong number of grandchild atoms for phi/psi acceptor /A NAG 3932 O7 Skipping possible acceptor with bad geometry: /E NAG 3932 O7 Wrong number of grandchild atoms for phi/psi acceptor /E NAG 3932 O7 Skipping possible acceptor with bad geometry: /E NAG 3932 O7 Wrong number of grandchild atoms for phi/psi acceptor /E NAG 3932 O7 Skipping possible acceptor with bad geometry: /A NAG 3932 O7 Wrong number of grandchild atoms for phi/psi acceptor /A NAG 3932 O7 Skipping possible acceptor with bad geometry: /I NAG 3932 O7 Wrong number of grandchild atoms for phi/psi acceptor /I NAG 3932 O7 10 messages similar to the above omitted 1974 hydrogen bonds /A VAL 505 is not terminus, removing H atom from 'C' /B ASP 664 is not terminus, removing H atom from 'C' /C SER 230 is not terminus, removing H atom from 'C' /D CYS 214 is not terminus, removing H atom from 'C' /E VAL 505 is not terminus, removing H atom from 'C' 7 messages similar to the above omitted 0 hydrogens added No template found for residue A3932 (NAG) Adding hydrogens Summary of feedback from adding hydrogens to VRC40-trimer- rsr40_real_space_refined-coot-0.pdb #1.1 --- warning | Skipped 15 atom(s) with bad connectivities; see log for details notes | No usable SEQRES records for VRC40-trimer-rsr40_real_space_refined- coot-0.pdb (#1.1) chain A; guessing termini instead No usable SEQRES records for VRC40-trimer-rsr40_real_space_refined-coot-0.pdb (#1.1) chain B; guessing termini instead No usable SEQRES records for VRC40-trimer-rsr40_real_space_refined-coot-0.pdb (#1.1) chain C; guessing termini instead No usable SEQRES records for VRC40-trimer-rsr40_real_space_refined-coot-0.pdb (#1.1) chain D; guessing termini instead No usable SEQRES records for VRC40-trimer-rsr40_real_space_refined-coot-0.pdb (#1.1) chain E; guessing termini instead 7 messages similar to the above omitted Chain-initial residues that are actual N termini: /C GLN 1, /D GLN 1, /G GLN 1, /H GLN 1, /K GLN 1, /L GLN 1 Chain-initial residues that are not actual N termini: /A ALA 32, /B ALA 512, /E ALA 32, /F ALA 512, /I ALA 32, /J ALA 512 Chain-final residues that are actual C termini: Chain-final residues that are not actual C termini: /A VAL 505, /B ASP 664, /C SER 230, /D CYS 214, /E VAL 505, /F ASP 664, /G SER 230, /H CYS 214, /I VAL 505, /J ASP 664, /K SER 230, /L CYS 214 Skipping possible acceptor with bad geometry: /A NAG 3932 O7 Wrong number of grandchild atoms for phi/psi acceptor /A NAG 3932 O7 Skipping possible acceptor with bad geometry: /E NAG 3932 O7 Wrong number of grandchild atoms for phi/psi acceptor /E NAG 3932 O7 Skipping possible acceptor with bad geometry: /E NAG 3932 O7 Wrong number of grandchild atoms for phi/psi acceptor /E NAG 3932 O7 Skipping possible acceptor with bad geometry: /A NAG 3932 O7 Wrong number of grandchild atoms for phi/psi acceptor /A NAG 3932 O7 Skipping possible acceptor with bad geometry: /I NAG 3932 O7 Wrong number of grandchild atoms for phi/psi acceptor /I NAG 3932 O7 10 messages similar to the above omitted 1974 hydrogen bonds /A VAL 505 is not terminus, removing H atom from 'C' /B ASP 664 is not terminus, removing H atom from 'C' /C SER 230 is not terminus, removing H atom from 'C' /D CYS 214 is not terminus, removing H atom from 'C' /E VAL 505 is not terminus, removing H atom from 'C' 7 messages similar to the above omitted 0 hydrogens added No template found for residue A3932 (NAG) Adding hydrogens Summary of feedback from adding hydrogens to VRC40-trimer- rsr40_real_space_refined-coot-0.pdb #1.1 --- warning | Skipped 15 atom(s) with bad connectivities; see log for details notes | No usable SEQRES records for VRC40-trimer-rsr40_real_space_refined- coot-0.pdb (#1.1) chain A; guessing termini instead No usable SEQRES records for VRC40-trimer-rsr40_real_space_refined-coot-0.pdb (#1.1) chain B; guessing termini instead No usable SEQRES records for VRC40-trimer-rsr40_real_space_refined-coot-0.pdb (#1.1) chain C; guessing termini instead No usable SEQRES records for VRC40-trimer-rsr40_real_space_refined-coot-0.pdb (#1.1) chain D; guessing termini instead No usable SEQRES records for VRC40-trimer-rsr40_real_space_refined-coot-0.pdb (#1.1) chain E; guessing termini instead 7 messages similar to the above omitted Chain-initial residues that are actual N termini: /C GLN 1, /D GLN 1, /G GLN 1, /H GLN 1, /K GLN 1, /L GLN 1 Chain-initial residues that are not actual N termini: /A ALA 32, /B ALA 512, /E ALA 32, /F ALA 512, /I ALA 32, /J ALA 512 Chain-final residues that are actual C termini: Chain-final residues that are not actual C termini: /A VAL 505, /B ASP 664, /C SER 230, /D CYS 214, /E VAL 505, /F ASP 664, /G SER 230, /H CYS 214, /I VAL 505, /J ASP 664, /K SER 230, /L CYS 214 Skipping possible acceptor with bad geometry: /A NAG 3932 O7 Wrong number of grandchild atoms for phi/psi acceptor /A NAG 3932 O7 Skipping possible acceptor with bad geometry: /E NAG 3932 O7 Wrong number of grandchild atoms for phi/psi acceptor /E NAG 3932 O7 Skipping possible acceptor with bad geometry: /A NAG 3932 O7 Wrong number of grandchild atoms for phi/psi acceptor /A NAG 3932 O7 Skipping possible acceptor with bad geometry: /E NAG 3932 O7 Wrong number of grandchild atoms for phi/psi acceptor /E NAG 3932 O7 Skipping possible acceptor with bad geometry: /I NAG 3932 O7 Wrong number of grandchild atoms for phi/psi acceptor /I NAG 3932 O7 10 messages similar to the above omitted 1974 hydrogen bonds /A VAL 505 is not terminus, removing H atom from 'C' /B ASP 664 is not terminus, removing H atom from 'C' /C SER 230 is not terminus, removing H atom from 'C' /D CYS 214 is not terminus, removing H atom from 'C' /E VAL 505 is not terminus, removing H atom from 'C' 7 messages similar to the above omitted 0 hydrogens added No template found for residue A3932 (NAG) Adding hydrogens Summary of feedback from adding hydrogens to VRC40-trimer- rsr40_real_space_refined-coot-0.pdb #1.1 --- warning | Skipped 15 atom(s) with bad connectivities; see log for details notes | No usable SEQRES records for VRC40-trimer-rsr40_real_space_refined- coot-0.pdb (#1.1) chain A; guessing termini instead No usable SEQRES records for VRC40-trimer-rsr40_real_space_refined-coot-0.pdb (#1.1) chain B; guessing termini instead No usable SEQRES records for VRC40-trimer-rsr40_real_space_refined-coot-0.pdb (#1.1) chain C; guessing termini instead No usable SEQRES records for VRC40-trimer-rsr40_real_space_refined-coot-0.pdb (#1.1) chain D; guessing termini instead No usable SEQRES records for VRC40-trimer-rsr40_real_space_refined-coot-0.pdb (#1.1) chain E; guessing termini instead 7 messages similar to the above omitted Chain-initial residues that are actual N termini: /C GLN 1, /D GLN 1, /G GLN 1, /H GLN 1, /K GLN 1, /L GLN 1 Chain-initial residues that are not actual N termini: /A ALA 32, /B ALA 512, /E ALA 32, /F ALA 512, /I ALA 32, /J ALA 512 Chain-final residues that are actual C termini: Chain-final residues that are not actual C termini: /A VAL 505, /B ASP 664, /C SER 230, /D CYS 214, /E VAL 505, /F ASP 664, /G SER 230, /H CYS 214, /I VAL 505, /J ASP 664, /K SER 230, /L CYS 214 Skipping possible acceptor with bad geometry: /A NAG 3932 O7 Wrong number of grandchild atoms for phi/psi acceptor /A NAG 3932 O7 Skipping possible acceptor with bad geometry: /E NAG 3932 O7 Wrong number of grandchild atoms for phi/psi acceptor /E NAG 3932 O7 Skipping possible acceptor with bad geometry: /A NAG 3932 O7 Wrong number of grandchild atoms for phi/psi acceptor /A NAG 3932 O7 Skipping possible acceptor with bad geometry: /I NAG 3932 O7 Wrong number of grandchild atoms for phi/psi acceptor /I NAG 3932 O7 Skipping possible acceptor with bad geometry: /E NAG 3932 O7 Wrong number of grandchild atoms for phi/psi acceptor /E NAG 3932 O7 10 messages similar to the above omitted 1974 hydrogen bonds /A VAL 505 is not terminus, removing H atom from 'C' /B ASP 664 is not terminus, removing H atom from 'C' /C SER 230 is not terminus, removing H atom from 'C' /D CYS 214 is not terminus, removing H atom from 'C' /E VAL 505 is not terminus, removing H atom from 'C' 7 messages similar to the above omitted 0 hydrogens added No template found for residue A3932 (NAG) Adding hydrogens Summary of feedback from adding hydrogens to VRC40-trimer- rsr40_real_space_refined-coot-0.pdb #1.1 --- warning | Skipped 15 atom(s) with bad connectivities; see log for details notes | No usable SEQRES records for VRC40-trimer-rsr40_real_space_refined- coot-0.pdb (#1.1) chain A; guessing termini instead No usable SEQRES records for VRC40-trimer-rsr40_real_space_refined-coot-0.pdb (#1.1) chain B; guessing termini instead No usable SEQRES records for VRC40-trimer-rsr40_real_space_refined-coot-0.pdb (#1.1) chain C; guessing termini instead No usable SEQRES records for VRC40-trimer-rsr40_real_space_refined-coot-0.pdb (#1.1) chain D; guessing termini instead No usable SEQRES records for VRC40-trimer-rsr40_real_space_refined-coot-0.pdb (#1.1) chain E; guessing termini instead 7 messages similar to the above omitted Chain-initial residues that are actual N termini: /C GLN 1, /D GLN 1, /G GLN 1, /H GLN 1, /K GLN 1, /L GLN 1 Chain-initial residues that are not actual N termini: /A ALA 32, /B ALA 512, /E ALA 32, /F ALA 512, /I ALA 32, /J ALA 512 Chain-final residues that are actual C termini: Chain-final residues that are not actual C termini: /A VAL 505, /B ASP 664, /C SER 230, /D CYS 214, /E VAL 505, /F ASP 664, /G SER 230, /H CYS 214, /I VAL 505, /J ASP 664, /K SER 230, /L CYS 214 Skipping possible acceptor with bad geometry: /A NAG 3932 O7 Wrong number of grandchild atoms for phi/psi acceptor /A NAG 3932 O7 Skipping possible acceptor with bad geometry: /E NAG 3932 O7 Wrong number of grandchild atoms for phi/psi acceptor /E NAG 3932 O7 Skipping possible acceptor with bad geometry: /E NAG 3932 O7 Wrong number of grandchild atoms for phi/psi acceptor /E NAG 3932 O7 Skipping possible acceptor with bad geometry: /A NAG 3932 O7 Wrong number of grandchild atoms for phi/psi acceptor /A NAG 3932 O7 Skipping possible acceptor with bad geometry: /I NAG 3932 O7 Wrong number of grandchild atoms for phi/psi acceptor /I NAG 3932 O7 10 messages similar to the above omitted 1974 hydrogen bonds /A VAL 505 is not terminus, removing H atom from 'C' /B ASP 664 is not terminus, removing H atom from 'C' /C SER 230 is not terminus, removing H atom from 'C' /D CYS 214 is not terminus, removing H atom from 'C' /E VAL 505 is not terminus, removing H atom from 'C' 7 messages similar to the above omitted 0 hydrogens added No template found for residue A3932 (NAG) Adding hydrogens Summary of feedback from adding hydrogens to VRC40-trimer- rsr40_real_space_refined-coot-0.pdb #1.1 --- warning | Skipped 15 atom(s) with bad connectivities; see log for details notes | No usable SEQRES records for VRC40-trimer-rsr40_real_space_refined- coot-0.pdb (#1.1) chain A; guessing termini instead No usable SEQRES records for VRC40-trimer-rsr40_real_space_refined-coot-0.pdb (#1.1) chain B; guessing termini instead No usable SEQRES records for VRC40-trimer-rsr40_real_space_refined-coot-0.pdb (#1.1) chain C; guessing termini instead No usable SEQRES records for VRC40-trimer-rsr40_real_space_refined-coot-0.pdb (#1.1) chain D; guessing termini instead No usable SEQRES records for VRC40-trimer-rsr40_real_space_refined-coot-0.pdb (#1.1) chain E; guessing termini instead 7 messages similar to the above omitted Chain-initial residues that are actual N termini: /C GLN 1, /D GLN 1, /G GLN 1, /H GLN 1, /K GLN 1, /L GLN 1 Chain-initial residues that are not actual N termini: /A ALA 32, /B ALA 512, /E ALA 32, /F ALA 512, /I ALA 32, /J ALA 512 Chain-final residues that are actual C termini: Chain-final residues that are not actual C termini: /A VAL 505, /B ASP 664, /C SER 230, /D CYS 214, /E VAL 505, /F ASP 664, /G SER 230, /H CYS 214, /I VAL 505, /J ASP 664, /K SER 230, /L CYS 214 Skipping possible acceptor with bad geometry: /A NAG 3932 O7 Wrong number of grandchild atoms for phi/psi acceptor /A NAG 3932 O7 Skipping possible acceptor with bad geometry: /E NAG 3932 O7 Wrong number of grandchild atoms for phi/psi acceptor /E NAG 3932 O7 Skipping possible acceptor with bad geometry: /E NAG 3932 O7 Wrong number of grandchild atoms for phi/psi acceptor /E NAG 3932 O7 Skipping possible acceptor with bad geometry: /I NAG 3932 O7 Wrong number of grandchild atoms for phi/psi acceptor /I NAG 3932 O7 Skipping possible acceptor with bad geometry: /A NAG 3932 O7 Wrong number of grandchild atoms for phi/psi acceptor /A NAG 3932 O7 10 messages similar to the above omitted 1974 hydrogen bonds /A VAL 505 is not terminus, removing H atom from 'C' /B ASP 664 is not terminus, removing H atom from 'C' /C SER 230 is not terminus, removing H atom from 'C' /D CYS 214 is not terminus, removing H atom from 'C' /E VAL 505 is not terminus, removing H atom from 'C' 7 messages similar to the above omitted 0 hydrogens added No template found for residue A3932 (NAG) Adding hydrogens Summary of feedback from adding hydrogens to VRC40-trimer- rsr40_real_space_refined-coot-0.pdb #1.1 --- warning | Skipped 15 atom(s) with bad connectivities; see log for details notes | No usable SEQRES records for VRC40-trimer-rsr40_real_space_refined- coot-0.pdb (#1.1) chain A; guessing termini instead No usable SEQRES records for VRC40-trimer-rsr40_real_space_refined-coot-0.pdb (#1.1) chain B; guessing termini instead No usable SEQRES records for VRC40-trimer-rsr40_real_space_refined-coot-0.pdb (#1.1) chain C; guessing termini instead No usable SEQRES records for VRC40-trimer-rsr40_real_space_refined-coot-0.pdb (#1.1) chain D; guessing termini instead No usable SEQRES records for VRC40-trimer-rsr40_real_space_refined-coot-0.pdb (#1.1) chain E; guessing termini instead 7 messages similar to the above omitted Chain-initial residues that are actual N termini: /C GLN 1, /D GLN 1, /G GLN 1, /H GLN 1, /K GLN 1, /L GLN 1 Chain-initial residues that are not actual N termini: /A ALA 32, /B ALA 512, /E ALA 32, /F ALA 512, /I ALA 32, /J ALA 512 Chain-final residues that are actual C termini: Chain-final residues that are not actual C termini: /A VAL 505, /B ASP 664, /C SER 230, /D CYS 214, /E VAL 505, /F ASP 664, /G SER 230, /H CYS 214, /I VAL 505, /J ASP 664, /K SER 230, /L CYS 214 Skipping possible acceptor with bad geometry: /A NAG 3932 O7 Wrong number of grandchild atoms for phi/psi acceptor /A NAG 3932 O7 Skipping possible acceptor with bad geometry: /E NAG 3932 O7 Wrong number of grandchild atoms for phi/psi acceptor /E NAG 3932 O7 Skipping possible acceptor with bad geometry: /E NAG 3932 O7 Wrong number of grandchild atoms for phi/psi acceptor /E NAG 3932 O7 Skipping possible acceptor with bad geometry: /A NAG 3932 O7 Wrong number of grandchild atoms for phi/psi acceptor /A NAG 3932 O7 Skipping possible acceptor with bad geometry: /I NAG 3932 O7 Wrong number of grandchild atoms for phi/psi acceptor /I NAG 3932 O7 10 messages similar to the above omitted 1974 hydrogen bonds /A VAL 505 is not terminus, removing H atom from 'C' /B ASP 664 is not terminus, removing H atom from 'C' /C SER 230 is not terminus, removing H atom from 'C' /D CYS 214 is not terminus, removing H atom from 'C' /E VAL 505 is not terminus, removing H atom from 'C' 7 messages similar to the above omitted 0 hydrogens added No template found for residue A3932 (NAG) Adding hydrogens Summary of feedback from adding hydrogens to VRC40-trimer- rsr40_real_space_refined-coot-0.pdb #1.1 --- warning | Skipped 15 atom(s) with bad connectivities; see log for details notes | No usable SEQRES records for VRC40-trimer-rsr40_real_space_refined- coot-0.pdb (#1.1) chain A; guessing termini instead No usable SEQRES records for VRC40-trimer-rsr40_real_space_refined-coot-0.pdb (#1.1) chain B; guessing termini instead No usable SEQRES records for VRC40-trimer-rsr40_real_space_refined-coot-0.pdb (#1.1) chain C; guessing termini instead No usable SEQRES records for VRC40-trimer-rsr40_real_space_refined-coot-0.pdb (#1.1) chain D; guessing termini instead No usable SEQRES records for VRC40-trimer-rsr40_real_space_refined-coot-0.pdb (#1.1) chain E; guessing termini instead 7 messages similar to the above omitted Chain-initial residues that are actual N termini: /C GLN 1, /D GLN 1, /G GLN 1, /H GLN 1, /K GLN 1, /L GLN 1 Chain-initial residues that are not actual N termini: /A ALA 32, /B ALA 512, /E ALA 32, /F ALA 512, /I ALA 32, /J ALA 512 Chain-final residues that are actual C termini: Chain-final residues that are not actual C termini: /A VAL 505, /B ASP 664, /C SER 230, /D CYS 214, /E VAL 505, /F ASP 664, /G SER 230, /H CYS 214, /I VAL 505, /J ASP 664, /K SER 230, /L CYS 214 Skipping possible acceptor with bad geometry: /A NAG 3932 O7 Wrong number of grandchild atoms for phi/psi acceptor /A NAG 3932 O7 Skipping possible acceptor with bad geometry: /E NAG 3932 O7 Wrong number of grandchild atoms for phi/psi acceptor /E NAG 3932 O7 Skipping possible acceptor with bad geometry: /A NAG 3932 O7 Wrong number of grandchild atoms for phi/psi acceptor /A NAG 3932 O7 Skipping possible acceptor with bad geometry: /E NAG 3932 O7 Wrong number of grandchild atoms for phi/psi acceptor /E NAG 3932 O7 Skipping possible acceptor with bad geometry: /I NAG 3932 O7 Wrong number of grandchild atoms for phi/psi acceptor /I NAG 3932 O7 10 messages similar to the above omitted 1974 hydrogen bonds /A VAL 505 is not terminus, removing H atom from 'C' /B ASP 664 is not terminus, removing H atom from 'C' /C SER 230 is not terminus, removing H atom from 'C' /D CYS 214 is not terminus, removing H atom from 'C' /E VAL 505 is not terminus, removing H atom from 'C' 7 messages similar to the above omitted 0 hydrogens added No template found for residue A3932 (NAG) Adding hydrogens Summary of feedback from adding hydrogens to VRC40-trimer- rsr40_real_space_refined-coot-0.pdb #1.1 --- warning | Skipped 15 atom(s) with bad connectivities; see log for details notes | No usable SEQRES records for VRC40-trimer-rsr40_real_space_refined- coot-0.pdb (#1.1) chain A; guessing termini instead No usable SEQRES records for VRC40-trimer-rsr40_real_space_refined-coot-0.pdb (#1.1) chain B; guessing termini instead No usable SEQRES records for VRC40-trimer-rsr40_real_space_refined-coot-0.pdb (#1.1) chain C; guessing termini instead No usable SEQRES records for VRC40-trimer-rsr40_real_space_refined-coot-0.pdb (#1.1) chain D; guessing termini instead No usable SEQRES records for VRC40-trimer-rsr40_real_space_refined-coot-0.pdb (#1.1) chain E; guessing termini instead 7 messages similar to the above omitted Chain-initial residues that are actual N termini: /C GLN 1, /D GLN 1, /G GLN 1, /H GLN 1, /K GLN 1, /L GLN 1 Chain-initial residues that are not actual N termini: /A ALA 32, /B ALA 512, /E ALA 32, /F ALA 512, /I ALA 32, /J ALA 512 Chain-final residues that are actual C termini: Chain-final residues that are not actual C termini: /A VAL 505, /B ASP 664, /C SER 230, /D CYS 214, /E VAL 505, /F ASP 664, /G SER 230, /H CYS 214, /I VAL 505, /J ASP 664, /K SER 230, /L CYS 214 Skipping possible acceptor with bad geometry: /A NAG 3932 O7 Wrong number of grandchild atoms for phi/psi acceptor /A NAG 3932 O7 Skipping possible acceptor with bad geometry: /E NAG 3932 O7 Wrong number of grandchild atoms for phi/psi acceptor /E NAG 3932 O7 Skipping possible acceptor with bad geometry: /A NAG 3932 O7 Wrong number of grandchild atoms for phi/psi acceptor /A NAG 3932 O7 Skipping possible acceptor with bad geometry: /E NAG 3932 O7 Wrong number of grandchild atoms for phi/psi acceptor /E NAG 3932 O7 Skipping possible acceptor with bad geometry: /I NAG 3932 O7 Wrong number of grandchild atoms for phi/psi acceptor /I NAG 3932 O7 10 messages similar to the above omitted 1974 hydrogen bonds /A VAL 505 is not terminus, removing H atom from 'C' /B ASP 664 is not terminus, removing H atom from 'C' /C SER 230 is not terminus, removing H atom from 'C' /D CYS 214 is not terminus, removing H atom from 'C' /E VAL 505 is not terminus, removing H atom from 'C' 7 messages similar to the above omitted 0 hydrogens added No template found for residue A3932 (NAG) Adding hydrogens Summary of feedback from adding hydrogens to VRC40-trimer- rsr40_real_space_refined-coot-0.pdb #1.1 --- warning | Skipped 15 atom(s) with bad connectivities; see log for details notes | No usable SEQRES records for VRC40-trimer-rsr40_real_space_refined- coot-0.pdb (#1.1) chain A; guessing termini instead No usable SEQRES records for VRC40-trimer-rsr40_real_space_refined-coot-0.pdb (#1.1) chain B; guessing termini instead No usable SEQRES records for VRC40-trimer-rsr40_real_space_refined-coot-0.pdb (#1.1) chain C; guessing termini instead No usable SEQRES records for VRC40-trimer-rsr40_real_space_refined-coot-0.pdb (#1.1) chain D; guessing termini instead No usable SEQRES records for VRC40-trimer-rsr40_real_space_refined-coot-0.pdb (#1.1) chain E; guessing termini instead 7 messages similar to the above omitted Chain-initial residues that are actual N termini: /C GLN 1, /D GLN 1, /G GLN 1, /H GLN 1, /K GLN 1, /L GLN 1 Chain-initial residues that are not actual N termini: /A ALA 32, /B ALA 512, /E ALA 32, /F ALA 512, /I ALA 32, /J ALA 512 Chain-final residues that are actual C termini: Chain-final residues that are not actual C termini: /A VAL 505, /B ASP 664, /C SER 230, /D CYS 214, /E VAL 505, /F ASP 664, /G SER 230, /H CYS 214, /I VAL 505, /J ASP 664, /K SER 230, /L CYS 214 Skipping possible acceptor with bad geometry: /A NAG 3932 O7 Wrong number of grandchild atoms for phi/psi acceptor /A NAG 3932 O7 Skipping possible acceptor with bad geometry: /E NAG 3932 O7 Wrong number of grandchild atoms for phi/psi acceptor /E NAG 3932 O7 Skipping possible acceptor with bad geometry: /A NAG 3932 O7 Wrong number of grandchild atoms for phi/psi acceptor /A NAG 3932 O7 Skipping possible acceptor with bad geometry: /E NAG 3932 O7 Wrong number of grandchild atoms for phi/psi acceptor /E NAG 3932 O7 Skipping possible acceptor with bad geometry: /I NAG 3932 O7 Wrong number of grandchild atoms for phi/psi acceptor /I NAG 3932 O7 10 messages similar to the above omitted 1974 hydrogen bonds /A VAL 505 is not terminus, removing H atom from 'C' /B ASP 664 is not terminus, removing H atom from 'C' /C SER 230 is not terminus, removing H atom from 'C' /D CYS 214 is not terminus, removing H atom from 'C' /E VAL 505 is not terminus, removing H atom from 'C' 7 messages similar to the above omitted 0 hydrogens added No template found for residue A3932 (NAG) Adding hydrogens Summary of feedback from adding hydrogens to VRC40-trimer- rsr40_real_space_refined-coot-0.pdb #1.1 --- warning | Skipped 15 atom(s) with bad connectivities; see log for details notes | No usable SEQRES records for VRC40-trimer-rsr40_real_space_refined- coot-0.pdb (#1.1) chain A; guessing termini instead No usable SEQRES records for VRC40-trimer-rsr40_real_space_refined-coot-0.pdb (#1.1) chain B; guessing termini instead No usable SEQRES records for VRC40-trimer-rsr40_real_space_refined-coot-0.pdb (#1.1) chain C; guessing termini instead No usable SEQRES records for VRC40-trimer-rsr40_real_space_refined-coot-0.pdb (#1.1) chain D; guessing termini instead No usable SEQRES records for VRC40-trimer-rsr40_real_space_refined-coot-0.pdb (#1.1) chain E; guessing termini instead 7 messages similar to the above omitted Chain-initial residues that are actual N termini: /C GLN 1, /D GLN 1, /G GLN 1, /H GLN 1, /K GLN 1, /L GLN 1 Chain-initial residues that are not actual N termini: /A ALA 32, /B ALA 512, /E ALA 32, /F ALA 512, /I ALA 32, /J ALA 512 Chain-final residues that are actual C termini: Chain-final residues that are not actual C termini: /A VAL 505, /B ASP 664, /C SER 230, /D CYS 214, /E VAL 505, /F ASP 664, /G SER 230, /H CYS 214, /I VAL 505, /J ASP 664, /K SER 230, /L CYS 214 Skipping possible acceptor with bad geometry: /A NAG 3932 O7 Wrong number of grandchild atoms for phi/psi acceptor /A NAG 3932 O7 Skipping possible acceptor with bad geometry: /E NAG 3932 O7 Wrong number of grandchild atoms for phi/psi acceptor /E NAG 3932 O7 Skipping possible acceptor with bad geometry: /A NAG 3932 O7 Wrong number of grandchild atoms for phi/psi acceptor /A NAG 3932 O7 Skipping possible acceptor with bad geometry: /I NAG 3932 O7 Wrong number of grandchild atoms for phi/psi acceptor /I NAG 3932 O7 Skipping possible acceptor with bad geometry: /E NAG 3932 O7 Wrong number of grandchild atoms for phi/psi acceptor /E NAG 3932 O7 10 messages similar to the above omitted 1974 hydrogen bonds /A VAL 505 is not terminus, removing H atom from 'C' /B ASP 664 is not terminus, removing H atom from 'C' /C SER 230 is not terminus, removing H atom from 'C' /D CYS 214 is not terminus, removing H atom from 'C' /E VAL 505 is not terminus, removing H atom from 'C' 7 messages similar to the above omitted 0 hydrogens added No template found for residue A3932 (NAG) Adding hydrogens Summary of feedback from adding hydrogens to VRC40-trimer- rsr40_real_space_refined-coot-0.pdb #1.1 --- warning | Skipped 15 atom(s) with bad connectivities; see log for details notes | No usable SEQRES records for VRC40-trimer-rsr40_real_space_refined- coot-0.pdb (#1.1) chain A; guessing termini instead No usable SEQRES records for VRC40-trimer-rsr40_real_space_refined-coot-0.pdb (#1.1) chain B; guessing termini instead No usable SEQRES records for VRC40-trimer-rsr40_real_space_refined-coot-0.pdb (#1.1) chain C; guessing termini instead No usable SEQRES records for VRC40-trimer-rsr40_real_space_refined-coot-0.pdb (#1.1) chain D; guessing termini instead No usable SEQRES records for VRC40-trimer-rsr40_real_space_refined-coot-0.pdb (#1.1) chain E; guessing termini instead 7 messages similar to the above omitted Chain-initial residues that are actual N termini: /C GLN 1, /D GLN 1, /G GLN 1, /H GLN 1, /K GLN 1, /L GLN 1 Chain-initial residues that are not actual N termini: /A ALA 32, /B ALA 512, /E ALA 32, /F ALA 512, /I ALA 32, /J ALA 512 Chain-final residues that are actual C termini: Chain-final residues that are not actual C termini: /A VAL 505, /B ASP 664, /C SER 230, /D CYS 214, /E VAL 505, /F ASP 664, /G SER 230, /H CYS 214, /I VAL 505, /J ASP 664, /K SER 230, /L CYS 214 Skipping possible acceptor with bad geometry: /A NAG 3932 O7 Wrong number of grandchild atoms for phi/psi acceptor /A NAG 3932 O7 Skipping possible acceptor with bad geometry: /E NAG 3932 O7 Wrong number of grandchild atoms for phi/psi acceptor /E NAG 3932 O7 Skipping possible acceptor with bad geometry: /E NAG 3932 O7 Wrong number of grandchild atoms for phi/psi acceptor /E NAG 3932 O7 Skipping possible acceptor with bad geometry: /A NAG 3932 O7 Wrong number of grandchild atoms for phi/psi acceptor /A NAG 3932 O7 Skipping possible acceptor with bad geometry: /I NAG 3932 O7 Wrong number of grandchild atoms for phi/psi acceptor /I NAG 3932 O7 10 messages similar to the above omitted 1974 hydrogen bonds /A VAL 505 is not terminus, removing H atom from 'C' /B ASP 664 is not terminus, removing H atom from 'C' /C SER 230 is not terminus, removing H atom from 'C' /D CYS 214 is not terminus, removing H atom from 'C' /E VAL 505 is not terminus, removing H atom from 'C' 7 messages similar to the above omitted 0 hydrogens added No template found for residue A3932 (NAG) Adding hydrogens Summary of feedback from adding hydrogens to VRC40-trimer- rsr40_real_space_refined-coot-0.pdb #1.1 --- warning | Skipped 15 atom(s) with bad connectivities; see log for details notes | No usable SEQRES records for VRC40-trimer-rsr40_real_space_refined- coot-0.pdb (#1.1) chain A; guessing termini instead No usable SEQRES records for VRC40-trimer-rsr40_real_space_refined-coot-0.pdb (#1.1) chain B; guessing termini instead No usable SEQRES records for VRC40-trimer-rsr40_real_space_refined-coot-0.pdb (#1.1) chain C; guessing termini instead No usable SEQRES records for VRC40-trimer-rsr40_real_space_refined-coot-0.pdb (#1.1) chain D; guessing termini instead No usable SEQRES records for VRC40-trimer-rsr40_real_space_refined-coot-0.pdb (#1.1) chain E; guessing termini instead 7 messages similar to the above omitted Chain-initial residues that are actual N termini: /C GLN 1, /D GLN 1, /G GLN 1, /H GLN 1, /K GLN 1, /L GLN 1 Chain-initial residues that are not actual N termini: /A ALA 32, /B ALA 512, /E ALA 32, /F ALA 512, /I ALA 32, /J ALA 512 Chain-final residues that are actual C termini: Chain-final residues that are not actual C termini: /A VAL 505, /B ASP 664, /C SER 230, /D CYS 214, /E VAL 505, /F ASP 664, /G SER 230, /H CYS 214, /I VAL 505, /J ASP 664, /K SER 230, /L CYS 214 Skipping possible acceptor with bad geometry: /A NAG 3932 O7 Wrong number of grandchild atoms for phi/psi acceptor /A NAG 3932 O7 Skipping possible acceptor with bad geometry: /E NAG 3932 O7 Wrong number of grandchild atoms for phi/psi acceptor /E NAG 3932 O7 Skipping possible acceptor with bad geometry: /E NAG 3932 O7 Wrong number of grandchild atoms for phi/psi acceptor /E NAG 3932 O7 Skipping possible acceptor with bad geometry: /A NAG 3932 O7 Wrong number of grandchild atoms for phi/psi acceptor /A NAG 3932 O7 Skipping possible acceptor with bad geometry: /I NAG 3932 O7 Wrong number of grandchild atoms for phi/psi acceptor /I NAG 3932 O7 10 messages similar to the above omitted 1974 hydrogen bonds /A VAL 505 is not terminus, removing H atom from 'C' /B ASP 664 is not terminus, removing H atom from 'C' /C SER 230 is not terminus, removing H atom from 'C' /D CYS 214 is not terminus, removing H atom from 'C' /E VAL 505 is not terminus, removing H atom from 'C' 7 messages similar to the above omitted 0 hydrogens added No template found for residue A3932 (NAG) Adding hydrogens Summary of feedback from adding hydrogens to VRC40-trimer- rsr40_real_space_refined-coot-0.pdb #1.1 --- warning | Skipped 15 atom(s) with bad connectivities; see log for details notes | No usable SEQRES records for VRC40-trimer-rsr40_real_space_refined- coot-0.pdb (#1.1) chain A; guessing termini instead No usable SEQRES records for VRC40-trimer-rsr40_real_space_refined-coot-0.pdb (#1.1) chain B; guessing termini instead No usable SEQRES records for VRC40-trimer-rsr40_real_space_refined-coot-0.pdb (#1.1) chain C; guessing termini instead No usable SEQRES records for VRC40-trimer-rsr40_real_space_refined-coot-0.pdb (#1.1) chain D; guessing termini instead No usable SEQRES records for VRC40-trimer-rsr40_real_space_refined-coot-0.pdb (#1.1) chain E; guessing termini instead 7 messages similar to the above omitted Chain-initial residues that are actual N termini: /C GLN 1, /D GLN 1, /G GLN 1, /H GLN 1, /K GLN 1, /L GLN 1 Chain-initial residues that are not actual N termini: /A ALA 32, /B ALA 512, /E ALA 32, /F ALA 512, /I ALA 32, /J ALA 512 Chain-final residues that are actual C termini: Chain-final residues that are not actual C termini: /A VAL 505, /B ASP 664, /C SER 230, /D CYS 214, /E VAL 505, /F ASP 664, /G SER 230, /H CYS 214, /I VAL 505, /J ASP 664, /K SER 230, /L CYS 214 Skipping possible acceptor with bad geometry: /A NAG 3932 O7 Wrong number of grandchild atoms for phi/psi acceptor /A NAG 3932 O7 Skipping possible acceptor with bad geometry: /E NAG 3932 O7 Wrong number of grandchild atoms for phi/psi acceptor /E NAG 3932 O7 Skipping possible acceptor with bad geometry: /E NAG 3932 O7 Wrong number of grandchild atoms for phi/psi acceptor /E NAG 3932 O7 Skipping possible acceptor with bad geometry: /A NAG 3932 O7 Wrong number of grandchild atoms for phi/psi acceptor /A NAG 3932 O7 Skipping possible acceptor with bad geometry: /I NAG 3932 O7 Wrong number of grandchild atoms for phi/psi acceptor /I NAG 3932 O7 10 messages similar to the above omitted 1974 hydrogen bonds /A VAL 505 is not terminus, removing H atom from 'C' /B ASP 664 is not terminus, removing H atom from 'C' /C SER 230 is not terminus, removing H atom from 'C' /D CYS 214 is not terminus, removing H atom from 'C' /E VAL 505 is not terminus, removing H atom from 'C' 7 messages similar to the above omitted 0 hydrogens added No template found for residue A3932 (NAG) Adding hydrogens Summary of feedback from adding hydrogens to VRC40-trimer- rsr40_real_space_refined-coot-0.pdb #1.1 --- warning | Skipped 15 atom(s) with bad connectivities; see log for details notes | No usable SEQRES records for VRC40-trimer-rsr40_real_space_refined- coot-0.pdb (#1.1) chain A; guessing termini instead No usable SEQRES records for VRC40-trimer-rsr40_real_space_refined-coot-0.pdb (#1.1) chain B; guessing termini instead No usable SEQRES records for VRC40-trimer-rsr40_real_space_refined-coot-0.pdb (#1.1) chain C; guessing termini instead No usable SEQRES records for VRC40-trimer-rsr40_real_space_refined-coot-0.pdb (#1.1) chain D; guessing termini instead No usable SEQRES records for VRC40-trimer-rsr40_real_space_refined-coot-0.pdb (#1.1) chain E; guessing termini instead 7 messages similar to the above omitted Chain-initial residues that are actual N termini: /C GLN 1, /D GLN 1, /G GLN 1, /H GLN 1, /K GLN 1, /L GLN 1 Chain-initial residues that are not actual N termini: /A ALA 32, /B ALA 512, /E ALA 32, /F ALA 512, /I ALA 32, /J ALA 512 Chain-final residues that are actual C termini: Chain-final residues that are not actual C termini: /A VAL 505, /B ASP 664, /C SER 230, /D CYS 214, /E VAL 505, /F ASP 664, /G SER 230, /H CYS 214, /I VAL 505, /J ASP 664, /K SER 230, /L CYS 214 Skipping possible acceptor with bad geometry: /A NAG 3932 O7 Wrong number of grandchild atoms for phi/psi acceptor /A NAG 3932 O7 Skipping possible acceptor with bad geometry: /E NAG 3932 O7 Wrong number of grandchild atoms for phi/psi acceptor /E NAG 3932 O7 Skipping possible acceptor with bad geometry: /A NAG 3932 O7 Wrong number of grandchild atoms for phi/psi acceptor /A NAG 3932 O7 Skipping possible acceptor with bad geometry: /E NAG 3932 O7 Wrong number of grandchild atoms for phi/psi acceptor /E NAG 3932 O7 Skipping possible acceptor with bad geometry: /I NAG 3932 O7 Wrong number of grandchild atoms for phi/psi acceptor /I NAG 3932 O7 10 messages similar to the above omitted 1974 hydrogen bonds /A VAL 505 is not terminus, removing H atom from 'C' /B ASP 664 is not terminus, removing H atom from 'C' /C SER 230 is not terminus, removing H atom from 'C' /D CYS 214 is not terminus, removing H atom from 'C' /E VAL 505 is not terminus, removing H atom from 'C' 7 messages similar to the above omitted 0 hydrogens added No template found for residue A3932 (NAG) Adding hydrogens Summary of feedback from adding hydrogens to VRC40-trimer- rsr40_real_space_refined-coot-0.pdb #1.1 --- warning | Skipped 15 atom(s) with bad connectivities; see log for details notes | No usable SEQRES records for VRC40-trimer-rsr40_real_space_refined- coot-0.pdb (#1.1) chain A; guessing termini instead No usable SEQRES records for VRC40-trimer-rsr40_real_space_refined-coot-0.pdb (#1.1) chain B; guessing termini instead No usable SEQRES records for VRC40-trimer-rsr40_real_space_refined-coot-0.pdb (#1.1) chain C; guessing termini instead No usable SEQRES records for VRC40-trimer-rsr40_real_space_refined-coot-0.pdb (#1.1) chain D; guessing termini instead No usable SEQRES records for VRC40-trimer-rsr40_real_space_refined-coot-0.pdb (#1.1) chain E; guessing termini instead 7 messages similar to the above omitted Chain-initial residues that are actual N termini: /C GLN 1, /D GLN 1, /G GLN 1, /H GLN 1, /K GLN 1, /L GLN 1 Chain-initial residues that are not actual N termini: /A ALA 32, /B ALA 512, /E ALA 32, /F ALA 512, /I ALA 32, /J ALA 512 Chain-final residues that are actual C termini: Chain-final residues that are not actual C termini: /A VAL 505, /B ASP 664, /C SER 230, /D CYS 214, /E VAL 505, /F ASP 664, /G SER 230, /H CYS 214, /I VAL 505, /J ASP 664, /K SER 230, /L CYS 214 Skipping possible acceptor with bad geometry: /A NAG 3932 O7 Wrong number of grandchild atoms for phi/psi acceptor /A NAG 3932 O7 Skipping possible acceptor with bad geometry: /E NAG 3932 O7 Wrong number of grandchild atoms for phi/psi acceptor /E NAG 3932 O7 Skipping possible acceptor with bad geometry: /A NAG 3932 O7 Wrong number of grandchild atoms for phi/psi acceptor /A NAG 3932 O7 Skipping possible acceptor with bad geometry: /E NAG 3932 O7 Wrong number of grandchild atoms for phi/psi acceptor /E NAG 3932 O7 Skipping possible acceptor with bad geometry: /I NAG 3932 O7 Wrong number of grandchild atoms for phi/psi acceptor /I NAG 3932 O7 10 messages similar to the above omitted 1974 hydrogen bonds /A VAL 505 is not terminus, removing H atom from 'C' /B ASP 664 is not terminus, removing H atom from 'C' /C SER 230 is not terminus, removing H atom from 'C' /D CYS 214 is not terminus, removing H atom from 'C' /E VAL 505 is not terminus, removing H atom from 'C' 7 messages similar to the above omitted 0 hydrogens added No template found for residue A3932 (NAG) Adding hydrogens Summary of feedback from adding hydrogens to VRC40-trimer- rsr40_real_space_refined-coot-0.pdb #1.1 --- warning | Skipped 15 atom(s) with bad connectivities; see log for details notes | No usable SEQRES records for VRC40-trimer-rsr40_real_space_refined- coot-0.pdb (#1.1) chain A; guessing termini instead No usable SEQRES records for VRC40-trimer-rsr40_real_space_refined-coot-0.pdb (#1.1) chain B; guessing termini instead No usable SEQRES records for VRC40-trimer-rsr40_real_space_refined-coot-0.pdb (#1.1) chain C; guessing termini instead No usable SEQRES records for VRC40-trimer-rsr40_real_space_refined-coot-0.pdb (#1.1) chain D; guessing termini instead No usable SEQRES records for VRC40-trimer-rsr40_real_space_refined-coot-0.pdb (#1.1) chain E; guessing termini instead 7 messages similar to the above omitted Chain-initial residues that are actual N termini: /C GLN 1, /D GLN 1, /G GLN 1, /H GLN 1, /K GLN 1, /L GLN 1 Chain-initial residues that are not actual N termini: /A ALA 32, /B ALA 512, /E ALA 32, /F ALA 512, /I ALA 32, /J ALA 512 Chain-final residues that are actual C termini: Chain-final residues that are not actual C termini: /A VAL 505, /B ASP 664, /C SER 230, /D CYS 214, /E VAL 505, /F ASP 664, /G SER 230, /H CYS 214, /I VAL 505, /J ASP 664, /K SER 230, /L CYS 214 Skipping possible acceptor with bad geometry: /A NAG 3932 O7 Wrong number of grandchild atoms for phi/psi acceptor /A NAG 3932 O7 Skipping possible acceptor with bad geometry: /A NAG 3932 O7 Wrong number of grandchild atoms for phi/psi acceptor /A NAG 3932 O7 Skipping possible acceptor with bad geometry: /E NAG 3932 O7 Wrong number of grandchild atoms for phi/psi acceptor /E NAG 3932 O7 Skipping possible acceptor with bad geometry: /E NAG 3932 O7 Wrong number of grandchild atoms for phi/psi acceptor /E NAG 3932 O7 Skipping possible acceptor with bad geometry: /I NAG 3932 O7 Wrong number of grandchild atoms for phi/psi acceptor /I NAG 3932 O7 10 messages similar to the above omitted 1974 hydrogen bonds /A VAL 505 is not terminus, removing H atom from 'C' /B ASP 664 is not terminus, removing H atom from 'C' /C SER 230 is not terminus, removing H atom from 'C' /D CYS 214 is not terminus, removing H atom from 'C' /E VAL 505 is not terminus, removing H atom from 'C' 7 messages similar to the above omitted 0 hydrogens added No template found for residue A3932 (NAG) Adding hydrogens Summary of feedback from adding hydrogens to VRC40-trimer- rsr40_real_space_refined-coot-0.pdb #1.1 --- warning | Skipped 15 atom(s) with bad connectivities; see log for details notes | No usable SEQRES records for VRC40-trimer-rsr40_real_space_refined- coot-0.pdb (#1.1) chain A; guessing termini instead No usable SEQRES records for VRC40-trimer-rsr40_real_space_refined-coot-0.pdb (#1.1) chain B; guessing termini instead No usable SEQRES records for VRC40-trimer-rsr40_real_space_refined-coot-0.pdb (#1.1) chain C; guessing termini instead No usable SEQRES records for VRC40-trimer-rsr40_real_space_refined-coot-0.pdb (#1.1) chain D; guessing termini instead No usable SEQRES records for VRC40-trimer-rsr40_real_space_refined-coot-0.pdb (#1.1) chain E; guessing termini instead 7 messages similar to the above omitted Chain-initial residues that are actual N termini: /C GLN 1, /D GLN 1, /G GLN 1, /H GLN 1, /K GLN 1, /L GLN 1 Chain-initial residues that are not actual N termini: /A ALA 32, /B ALA 512, /E ALA 32, /F ALA 512, /I ALA 32, /J ALA 512 Chain-final residues that are actual C termini: Chain-final residues that are not actual C termini: /A VAL 505, /B ASP 664, /C SER 230, /D CYS 214, /E VAL 505, /F ASP 664, /G SER 230, /H CYS 214, /I VAL 505, /J ASP 664, /K SER 230, /L CYS 214 Skipping possible acceptor with bad geometry: /A NAG 3932 O7 Wrong number of grandchild atoms for phi/psi acceptor /A NAG 3932 O7 Skipping possible acceptor with bad geometry: /E NAG 3932 O7 Wrong number of grandchild atoms for phi/psi acceptor /E NAG 3932 O7 Skipping possible acceptor with bad geometry: /E NAG 3932 O7 Wrong number of grandchild atoms for phi/psi acceptor /E NAG 3932 O7 Skipping possible acceptor with bad geometry: /A NAG 3932 O7 Wrong number of grandchild atoms for phi/psi acceptor /A NAG 3932 O7 Skipping possible acceptor with bad geometry: /I NAG 3932 O7 Wrong number of grandchild atoms for phi/psi acceptor /I NAG 3932 O7 10 messages similar to the above omitted 1974 hydrogen bonds /A VAL 505 is not terminus, removing H atom from 'C' /B ASP 664 is not terminus, removing H atom from 'C' /C SER 230 is not terminus, removing H atom from 'C' /D CYS 214 is not terminus, removing H atom from 'C' /E VAL 505 is not terminus, removing H atom from 'C' 7 messages similar to the above omitted 0 hydrogens added No template found for residue A3932 (NAG) Adding hydrogens Summary of feedback from adding hydrogens to VRC40-trimer- rsr40_real_space_refined-coot-0.pdb #1.1 --- warning | Skipped 15 atom(s) with bad connectivities; see log for details notes | No usable SEQRES records for VRC40-trimer-rsr40_real_space_refined- coot-0.pdb (#1.1) chain A; guessing termini instead No usable SEQRES records for VRC40-trimer-rsr40_real_space_refined-coot-0.pdb (#1.1) chain B; guessing termini instead No usable SEQRES records for VRC40-trimer-rsr40_real_space_refined-coot-0.pdb (#1.1) chain C; guessing termini instead No usable SEQRES records for VRC40-trimer-rsr40_real_space_refined-coot-0.pdb (#1.1) chain D; guessing termini instead No usable SEQRES records for VRC40-trimer-rsr40_real_space_refined-coot-0.pdb (#1.1) chain E; guessing termini instead 7 messages similar to the above omitted Chain-initial residues that are actual N termini: /C GLN 1, /D GLN 1, /G GLN 1, /H GLN 1, /K GLN 1, /L GLN 1 Chain-initial residues that are not actual N termini: /A ALA 32, /B ALA 512, /E ALA 32, /F ALA 512, /I ALA 32, /J ALA 512 Chain-final residues that are actual C termini: Chain-final residues that are not actual C termini: /A VAL 505, /B ASP 664, /C SER 230, /D CYS 214, /E VAL 505, /F ASP 664, /G SER 230, /H CYS 214, /I VAL 505, /J ASP 664, /K SER 230, /L CYS 214 Skipping possible acceptor with bad geometry: /A NAG 3932 O7 Wrong number of grandchild atoms for phi/psi acceptor /A NAG 3932 O7 Skipping possible acceptor with bad geometry: /E NAG 3932 O7 Wrong number of grandchild atoms for phi/psi acceptor /E NAG 3932 O7 Skipping possible acceptor with bad geometry: /E NAG 3932 O7 Wrong number of grandchild atoms for phi/psi acceptor /E NAG 3932 O7 Skipping possible acceptor with bad geometry: /A NAG 3932 O7 Wrong number of grandchild atoms for phi/psi acceptor /A NAG 3932 O7 Skipping possible acceptor with bad geometry: /I NAG 3932 O7 Wrong number of grandchild atoms for phi/psi acceptor /I NAG 3932 O7 10 messages similar to the above omitted 1974 hydrogen bonds /A VAL 505 is not terminus, removing H atom from 'C' /B ASP 664 is not terminus, removing H atom from 'C' /C SER 230 is not terminus, removing H atom from 'C' /D CYS 214 is not terminus, removing H atom from 'C' /E VAL 505 is not terminus, removing H atom from 'C' 7 messages similar to the above omitted 0 hydrogens added No template found for residue A3932 (NAG) Adding hydrogens Summary of feedback from adding hydrogens to VRC40-trimer- rsr40_real_space_refined-coot-0.pdb #1.1 --- warning | Skipped 15 atom(s) with bad connectivities; see log for details notes | No usable SEQRES records for VRC40-trimer-rsr40_real_space_refined- coot-0.pdb (#1.1) chain A; guessing termini instead No usable SEQRES records for VRC40-trimer-rsr40_real_space_refined-coot-0.pdb (#1.1) chain B; guessing termini instead No usable SEQRES records for VRC40-trimer-rsr40_real_space_refined-coot-0.pdb (#1.1) chain C; guessing termini instead No usable SEQRES records for VRC40-trimer-rsr40_real_space_refined-coot-0.pdb (#1.1) chain D; guessing termini instead No usable SEQRES records for VRC40-trimer-rsr40_real_space_refined-coot-0.pdb (#1.1) chain E; guessing termini instead 7 messages similar to the above omitted Chain-initial residues that are actual N termini: /C GLN 1, /D GLN 1, /G GLN 1, /H GLN 1, /K GLN 1, /L GLN 1 Chain-initial residues that are not actual N termini: /A ALA 32, /B ALA 512, /E ALA 32, /F ALA 512, /I ALA 32, /J ALA 512 Chain-final residues that are actual C termini: Chain-final residues that are not actual C termini: /A VAL 505, /B ASP 664, /C SER 230, /D CYS 214, /E VAL 505, /F ASP 664, /G SER 230, /H CYS 214, /I VAL 505, /J ASP 664, /K SER 230, /L CYS 214 Skipping possible acceptor with bad geometry: /A NAG 3932 O7 Wrong number of grandchild atoms for phi/psi acceptor /A NAG 3932 O7 Skipping possible acceptor with bad geometry: /E NAG 3932 O7 Wrong number of grandchild atoms for phi/psi acceptor /E NAG 3932 O7 Skipping possible acceptor with bad geometry: /A NAG 3932 O7 Wrong number of grandchild atoms for phi/psi acceptor /A NAG 3932 O7 Skipping possible acceptor with bad geometry: /E NAG 3932 O7 Wrong number of grandchild atoms for phi/psi acceptor /E NAG 3932 O7 Skipping possible acceptor with bad geometry: /I NAG 3932 O7 Wrong number of grandchild atoms for phi/psi acceptor /I NAG 3932 O7 10 messages similar to the above omitted 1974 hydrogen bonds /A VAL 505 is not terminus, removing H atom from 'C' /B ASP 664 is not terminus, removing H atom from 'C' /C SER 230 is not terminus, removing H atom from 'C' /D CYS 214 is not terminus, removing H atom from 'C' /E VAL 505 is not terminus, removing H atom from 'C' 7 messages similar to the above omitted 0 hydrogens added No template found for residue A3932 (NAG) Adding hydrogens Summary of feedback from adding hydrogens to VRC40-trimer- rsr40_real_space_refined-coot-0.pdb #1.1 --- warning | Skipped 15 atom(s) with bad connectivities; see log for details notes | No usable SEQRES records for VRC40-trimer-rsr40_real_space_refined- coot-0.pdb (#1.1) chain A; guessing termini instead No usable SEQRES records for VRC40-trimer-rsr40_real_space_refined-coot-0.pdb (#1.1) chain B; guessing termini instead No usable SEQRES records for VRC40-trimer-rsr40_real_space_refined-coot-0.pdb (#1.1) chain C; guessing termini instead No usable SEQRES records for VRC40-trimer-rsr40_real_space_refined-coot-0.pdb (#1.1) chain D; guessing termini instead No usable SEQRES records for VRC40-trimer-rsr40_real_space_refined-coot-0.pdb (#1.1) chain E; guessing termini instead 7 messages similar to the above omitted Chain-initial residues that are actual N termini: /C GLN 1, /D GLN 1, /G GLN 1, /H GLN 1, /K GLN 1, /L GLN 1 Chain-initial residues that are not actual N termini: /A ALA 32, /B ALA 512, /E ALA 32, /F ALA 512, /I ALA 32, /J ALA 512 Chain-final residues that are actual C termini: Chain-final residues that are not actual C termini: /A VAL 505, /B ASP 664, /C SER 230, /D CYS 214, /E VAL 505, /F ASP 664, /G SER 230, /H CYS 214, /I VAL 505, /J ASP 664, /K SER 230, /L CYS 214 Skipping possible acceptor with bad geometry: /A NAG 3932 O7 Wrong number of grandchild atoms for phi/psi acceptor /A NAG 3932 O7 Skipping possible acceptor with bad geometry: /E NAG 3932 O7 Wrong number of grandchild atoms for phi/psi acceptor /E NAG 3932 O7 Skipping possible acceptor with bad geometry: /A NAG 3932 O7 Wrong number of grandchild atoms for phi/psi acceptor /A NAG 3932 O7 Skipping possible acceptor with bad geometry: /E NAG 3932 O7 Wrong number of grandchild atoms for phi/psi acceptor /E NAG 3932 O7 Skipping possible acceptor with bad geometry: /I NAG 3932 O7 Wrong number of grandchild atoms for phi/psi acceptor /I NAG 3932 O7 10 messages similar to the above omitted 1974 hydrogen bonds /A VAL 505 is not terminus, removing H atom from 'C' /B ASP 664 is not terminus, removing H atom from 'C' /C SER 230 is not terminus, removing H atom from 'C' /D CYS 214 is not terminus, removing H atom from 'C' /E VAL 505 is not terminus, removing H atom from 'C' 7 messages similar to the above omitted 0 hydrogens added No template found for residue A3932 (NAG) Adding hydrogens Summary of feedback from adding hydrogens to VRC40-trimer- rsr40_real_space_refined-coot-0.pdb #1.1 --- warning | Skipped 15 atom(s) with bad connectivities; see log for details notes | No usable SEQRES records for VRC40-trimer-rsr40_real_space_refined- coot-0.pdb (#1.1) chain A; guessing termini instead No usable SEQRES records for VRC40-trimer-rsr40_real_space_refined-coot-0.pdb (#1.1) chain B; guessing termini instead No usable SEQRES records for VRC40-trimer-rsr40_real_space_refined-coot-0.pdb (#1.1) chain C; guessing termini instead No usable SEQRES records for VRC40-trimer-rsr40_real_space_refined-coot-0.pdb (#1.1) chain D; guessing termini instead No usable SEQRES records for VRC40-trimer-rsr40_real_space_refined-coot-0.pdb (#1.1) chain E; guessing termini instead 7 messages similar to the above omitted Chain-initial residues that are actual N termini: /C GLN 1, /D GLN 1, /G GLN 1, /H GLN 1, /K GLN 1, /L GLN 1 Chain-initial residues that are not actual N termini: /A ALA 32, /B ALA 512, /E ALA 32, /F ALA 512, /I ALA 32, /J ALA 512 Chain-final residues that are actual C termini: Chain-final residues that are not actual C termini: /A VAL 505, /B ASP 664, /C SER 230, /D CYS 214, /E VAL 505, /F ASP 664, /G SER 230, /H CYS 214, /I VAL 505, /J ASP 664, /K SER 230, /L CYS 214 Skipping possible acceptor with bad geometry: /A NAG 3932 O7 Wrong number of grandchild atoms for phi/psi acceptor /A NAG 3932 O7 Skipping possible acceptor with bad geometry: /E NAG 3932 O7 Wrong number of grandchild atoms for phi/psi acceptor /E NAG 3932 O7 Skipping possible acceptor with bad geometry: /A NAG 3932 O7 Wrong number of grandchild atoms for phi/psi acceptor /A NAG 3932 O7 Skipping possible acceptor with bad geometry: /E NAG 3932 O7 Wrong number of grandchild atoms for phi/psi acceptor /E NAG 3932 O7 Skipping possible acceptor with bad geometry: /I NAG 3932 O7 Wrong number of grandchild atoms for phi/psi acceptor /I NAG 3932 O7 10 messages similar to the above omitted 1974 hydrogen bonds /A VAL 505 is not terminus, removing H atom from 'C' /B ASP 664 is not terminus, removing H atom from 'C' /C SER 230 is not terminus, removing H atom from 'C' /D CYS 214 is not terminus, removing H atom from 'C' /E VAL 505 is not terminus, removing H atom from 'C' 7 messages similar to the above omitted 0 hydrogens added No template found for residue A3932 (NAG) Adding hydrogens Summary of feedback from adding hydrogens to VRC40-trimer- rsr40_real_space_refined-coot-0.pdb #1.1 --- warning | Skipped 15 atom(s) with bad connectivities; see log for details notes | No usable SEQRES records for VRC40-trimer-rsr40_real_space_refined- coot-0.pdb (#1.1) chain A; guessing termini instead No usable SEQRES records for VRC40-trimer-rsr40_real_space_refined-coot-0.pdb (#1.1) chain B; guessing termini instead No usable SEQRES records for VRC40-trimer-rsr40_real_space_refined-coot-0.pdb (#1.1) chain C; guessing termini instead No usable SEQRES records for VRC40-trimer-rsr40_real_space_refined-coot-0.pdb (#1.1) chain D; guessing termini instead No usable SEQRES records for VRC40-trimer-rsr40_real_space_refined-coot-0.pdb (#1.1) chain E; guessing termini instead 7 messages similar to the above omitted Chain-initial residues that are actual N termini: /C GLN 1, /D GLN 1, /G GLN 1, /H GLN 1, /K GLN 1, /L GLN 1 Chain-initial residues that are not actual N termini: /A ALA 32, /B ALA 512, /E ALA 32, /F ALA 512, /I ALA 32, /J ALA 512 Chain-final residues that are actual C termini: Chain-final residues that are not actual C termini: /A VAL 505, /B ASP 664, /C SER 230, /D CYS 214, /E VAL 505, /F ASP 664, /G SER 230, /H CYS 214, /I VAL 505, /J ASP 664, /K SER 230, /L CYS 214 Skipping possible acceptor with bad geometry: /A NAG 3932 O7 Wrong number of grandchild atoms for phi/psi acceptor /A NAG 3932 O7 Skipping possible acceptor with bad geometry: /E NAG 3932 O7 Wrong number of grandchild atoms for phi/psi acceptor /E NAG 3932 O7 Skipping possible acceptor with bad geometry: /A NAG 3932 O7 Wrong number of grandchild atoms for phi/psi acceptor /A NAG 3932 O7 Skipping possible acceptor with bad geometry: /E NAG 3932 O7 Wrong number of grandchild atoms for phi/psi acceptor /E NAG 3932 O7 Skipping possible acceptor with bad geometry: /I NAG 3932 O7 Wrong number of grandchild atoms for phi/psi acceptor /I NAG 3932 O7 10 messages similar to the above omitted 1974 hydrogen bonds /A VAL 505 is not terminus, removing H atom from 'C' /B ASP 664 is not terminus, removing H atom from 'C' /C SER 230 is not terminus, removing H atom from 'C' /D CYS 214 is not terminus, removing H atom from 'C' /E VAL 505 is not terminus, removing H atom from 'C' 7 messages similar to the above omitted 0 hydrogens added No template found for residue A3932 (NAG) Adding hydrogens Summary of feedback from adding hydrogens to VRC40-trimer- rsr40_real_space_refined-coot-0.pdb #1.1 --- warning | Skipped 15 atom(s) with bad connectivities; see log for details notes | No usable SEQRES records for VRC40-trimer-rsr40_real_space_refined- coot-0.pdb (#1.1) chain A; guessing termini instead No usable SEQRES records for VRC40-trimer-rsr40_real_space_refined-coot-0.pdb (#1.1) chain B; guessing termini instead No usable SEQRES records for VRC40-trimer-rsr40_real_space_refined-coot-0.pdb (#1.1) chain C; guessing termini instead No usable SEQRES records for VRC40-trimer-rsr40_real_space_refined-coot-0.pdb (#1.1) chain D; guessing termini instead No usable SEQRES records for VRC40-trimer-rsr40_real_space_refined-coot-0.pdb (#1.1) chain E; guessing termini instead 7 messages similar to the above omitted Chain-initial residues that are actual N termini: /C GLN 1, /D GLN 1, /G GLN 1, /H GLN 1, /K GLN 1, /L GLN 1 Chain-initial residues that are not actual N termini: /A ALA 32, /B ALA 512, /E ALA 32, /F ALA 512, /I ALA 32, /J ALA 512 Chain-final residues that are actual C termini: Chain-final residues that are not actual C termini: /A VAL 505, /B ASP 664, /C SER 230, /D CYS 214, /E VAL 505, /F ASP 664, /G SER 230, /H CYS 214, /I VAL 505, /J ASP 664, /K SER 230, /L CYS 214 Skipping possible acceptor with bad geometry: /A NAG 3932 O7 Wrong number of grandchild atoms for phi/psi acceptor /A NAG 3932 O7 Skipping possible acceptor with bad geometry: /E NAG 3932 O7 Wrong number of grandchild atoms for phi/psi acceptor /E NAG 3932 O7 Skipping possible acceptor with bad geometry: /E NAG 3932 O7 Wrong number of grandchild atoms for phi/psi acceptor /E NAG 3932 O7 Skipping possible acceptor with bad geometry: /A NAG 3932 O7 Wrong number of grandchild atoms for phi/psi acceptor /A NAG 3932 O7 Skipping possible acceptor with bad geometry: /I NAG 3932 O7 Wrong number of grandchild atoms for phi/psi acceptor /I NAG 3932 O7 10 messages similar to the above omitted 1974 hydrogen bonds /A VAL 505 is not terminus, removing H atom from 'C' /B ASP 664 is not terminus, removing H atom from 'C' /C SER 230 is not terminus, removing H atom from 'C' /D CYS 214 is not terminus, removing H atom from 'C' /E VAL 505 is not terminus, removing H atom from 'C' 7 messages similar to the above omitted 0 hydrogens added No template found for residue A3932 (NAG) Adding hydrogens Summary of feedback from adding hydrogens to VRC40-trimer- rsr40_real_space_refined-coot-0.pdb #1.1 --- warning | Skipped 15 atom(s) with bad connectivities; see log for details notes | No usable SEQRES records for VRC40-trimer-rsr40_real_space_refined- coot-0.pdb (#1.1) chain A; guessing termini instead No usable SEQRES records for VRC40-trimer-rsr40_real_space_refined-coot-0.pdb (#1.1) chain B; guessing termini instead No usable SEQRES records for VRC40-trimer-rsr40_real_space_refined-coot-0.pdb (#1.1) chain C; guessing termini instead No usable SEQRES records for VRC40-trimer-rsr40_real_space_refined-coot-0.pdb (#1.1) chain D; guessing termini instead No usable SEQRES records for VRC40-trimer-rsr40_real_space_refined-coot-0.pdb (#1.1) chain E; guessing termini instead 7 messages similar to the above omitted Chain-initial residues that are actual N termini: /C GLN 1, /D GLN 1, /G GLN 1, /H GLN 1, /K GLN 1, /L GLN 1 Chain-initial residues that are not actual N termini: /A ALA 32, /B ALA 512, /E ALA 32, /F ALA 512, /I ALA 32, /J ALA 512 Chain-final residues that are actual C termini: Chain-final residues that are not actual C termini: /A VAL 505, /B ASP 664, /C SER 230, /D CYS 214, /E VAL 505, /F ASP 664, /G SER 230, /H CYS 214, /I VAL 505, /J ASP 664, /K SER 230, /L CYS 214 Skipping possible acceptor with bad geometry: /A NAG 3932 O7 Wrong number of grandchild atoms for phi/psi acceptor /A NAG 3932 O7 Skipping possible acceptor with bad geometry: /A NAG 3932 O7 Wrong number of grandchild atoms for phi/psi acceptor /A NAG 3932 O7 Skipping possible acceptor with bad geometry: /E NAG 3932 O7 Wrong number of grandchild atoms for phi/psi acceptor /E NAG 3932 O7 Skipping possible acceptor with bad geometry: /E NAG 3932 O7 Wrong number of grandchild atoms for phi/psi acceptor /E NAG 3932 O7 Skipping possible acceptor with bad geometry: /I NAG 3932 O7 Wrong number of grandchild atoms for phi/psi acceptor /I NAG 3932 O7 10 messages similar to the above omitted 1974 hydrogen bonds /A VAL 505 is not terminus, removing H atom from 'C' /B ASP 664 is not terminus, removing H atom from 'C' /C SER 230 is not terminus, removing H atom from 'C' /D CYS 214 is not terminus, removing H atom from 'C' /E VAL 505 is not terminus, removing H atom from 'C' 7 messages similar to the above omitted 0 hydrogens added No template found for residue A3932 (NAG) Adding hydrogens Summary of feedback from adding hydrogens to VRC40-trimer- rsr40_real_space_refined-coot-0.pdb #1.1 --- warning | Skipped 15 atom(s) with bad connectivities; see log for details notes | No usable SEQRES records for VRC40-trimer-rsr40_real_space_refined- coot-0.pdb (#1.1) chain A; guessing termini instead No usable SEQRES records for VRC40-trimer-rsr40_real_space_refined-coot-0.pdb (#1.1) chain B; guessing termini instead No usable SEQRES records for VRC40-trimer-rsr40_real_space_refined-coot-0.pdb (#1.1) chain C; guessing termini instead No usable SEQRES records for VRC40-trimer-rsr40_real_space_refined-coot-0.pdb (#1.1) chain D; guessing termini instead No usable SEQRES records for VRC40-trimer-rsr40_real_space_refined-coot-0.pdb (#1.1) chain E; guessing termini instead 7 messages similar to the above omitted Chain-initial residues that are actual N termini: /C GLN 1, /D GLN 1, /G GLN 1, /H GLN 1, /K GLN 1, /L GLN 1 Chain-initial residues that are not actual N termini: /A ALA 32, /B ALA 512, /E ALA 32, /F ALA 512, /I ALA 32, /J ALA 512 Chain-final residues that are actual C termini: Chain-final residues that are not actual C termini: /A VAL 505, /B ASP 664, /C SER 230, /D CYS 214, /E VAL 505, /F ASP 664, /G SER 230, /H CYS 214, /I VAL 505, /J ASP 664, /K SER 230, /L CYS 214 Skipping possible acceptor with bad geometry: /A NAG 3932 O7 Wrong number of grandchild atoms for phi/psi acceptor /A NAG 3932 O7 Skipping possible acceptor with bad geometry: /E NAG 3932 O7 Wrong number of grandchild atoms for phi/psi acceptor /E NAG 3932 O7 Skipping possible acceptor with bad geometry: /E NAG 3932 O7 Wrong number of grandchild atoms for phi/psi acceptor /E NAG 3932 O7 Skipping possible acceptor with bad geometry: /I NAG 3932 O7 Wrong number of grandchild atoms for phi/psi acceptor /I NAG 3932 O7 Skipping possible acceptor with bad geometry: /A NAG 3932 O7 Wrong number of grandchild atoms for phi/psi acceptor /A NAG 3932 O7 10 messages similar to the above omitted 1974 hydrogen bonds /A VAL 505 is not terminus, removing H atom from 'C' /B ASP 664 is not terminus, removing H atom from 'C' /C SER 230 is not terminus, removing H atom from 'C' /D CYS 214 is not terminus, removing H atom from 'C' /E VAL 505 is not terminus, removing H atom from 'C' 7 messages similar to the above omitted 0 hydrogens added No template found for residue A3932 (NAG) Adding hydrogens Summary of feedback from adding hydrogens to VRC40-trimer- rsr40_real_space_refined-coot-0.pdb #1.1 --- warning | Skipped 15 atom(s) with bad connectivities; see log for details notes | No usable SEQRES records for VRC40-trimer-rsr40_real_space_refined- coot-0.pdb (#1.1) chain A; guessing termini instead No usable SEQRES records for VRC40-trimer-rsr40_real_space_refined-coot-0.pdb (#1.1) chain B; guessing termini instead No usable SEQRES records for VRC40-trimer-rsr40_real_space_refined-coot-0.pdb (#1.1) chain C; guessing termini instead No usable SEQRES records for VRC40-trimer-rsr40_real_space_refined-coot-0.pdb (#1.1) chain D; guessing termini instead No usable SEQRES records for VRC40-trimer-rsr40_real_space_refined-coot-0.pdb (#1.1) chain E; guessing termini instead 7 messages similar to the above omitted Chain-initial residues that are actual N termini: /C GLN 1, /D GLN 1, /G GLN 1, /H GLN 1, /K GLN 1, /L GLN 1 Chain-initial residues that are not actual N termini: /A ALA 32, /B ALA 512, /E ALA 32, /F ALA 512, /I ALA 32, /J ALA 512 Chain-final residues that are actual C termini: Chain-final residues that are not actual C termini: /A VAL 505, /B ASP 664, /C SER 230, /D CYS 214, /E VAL 505, /F ASP 664, /G SER 230, /H CYS 214, /I VAL 505, /J ASP 664, /K SER 230, /L CYS 214 Skipping possible acceptor with bad geometry: /A NAG 3932 O7 Wrong number of grandchild atoms for phi/psi acceptor /A NAG 3932 O7 Skipping possible acceptor with bad geometry: /E NAG 3932 O7 Wrong number of grandchild atoms for phi/psi acceptor /E NAG 3932 O7 Skipping possible acceptor with bad geometry: /A NAG 3932 O7 Wrong number of grandchild atoms for phi/psi acceptor /A NAG 3932 O7 Skipping possible acceptor with bad geometry: /E NAG 3932 O7 Wrong number of grandchild atoms for phi/psi acceptor /E NAG 3932 O7 Skipping possible acceptor with bad geometry: /I NAG 3932 O7 Wrong number of grandchild atoms for phi/psi acceptor /I NAG 3932 O7 10 messages similar to the above omitted 1974 hydrogen bonds /A VAL 505 is not terminus, removing H atom from 'C' /B ASP 664 is not terminus, removing H atom from 'C' /C SER 230 is not terminus, removing H atom from 'C' /D CYS 214 is not terminus, removing H atom from 'C' /E VAL 505 is not terminus, removing H atom from 'C' 7 messages similar to the above omitted 0 hydrogens added No template found for residue A3932 (NAG) Adding hydrogens Summary of feedback from adding hydrogens to VRC40-trimer- rsr40_real_space_refined-coot-0.pdb #1.1 --- warning | Skipped 15 atom(s) with bad connectivities; see log for details notes | No usable SEQRES records for VRC40-trimer-rsr40_real_space_refined- coot-0.pdb (#1.1) chain A; guessing termini instead No usable SEQRES records for VRC40-trimer-rsr40_real_space_refined-coot-0.pdb (#1.1) chain B; guessing termini instead No usable SEQRES records for VRC40-trimer-rsr40_real_space_refined-coot-0.pdb (#1.1) chain C; guessing termini instead No usable SEQRES records for VRC40-trimer-rsr40_real_space_refined-coot-0.pdb (#1.1) chain D; guessing termini instead No usable SEQRES records for VRC40-trimer-rsr40_real_space_refined-coot-0.pdb (#1.1) chain E; guessing termini instead 7 messages similar to the above omitted Chain-initial residues that are actual N termini: /C GLN 1, /D GLN 1, /G GLN 1, /H GLN 1, /K GLN 1, /L GLN 1 Chain-initial residues that are not actual N termini: /A ALA 32, /B ALA 512, /E ALA 32, /F ALA 512, /I ALA 32, /J ALA 512 Chain-final residues that are actual C termini: Chain-final residues that are not actual C termini: /A VAL 505, /B ASP 664, /C SER 230, /D CYS 214, /E VAL 505, /F ASP 664, /G SER 230, /H CYS 214, /I VAL 505, /J ASP 664, /K SER 230, /L CYS 214 Skipping possible acceptor with bad geometry: /A NAG 3932 O7 Wrong number of grandchild atoms for phi/psi acceptor /A NAG 3932 O7 Skipping possible acceptor with bad geometry: /E NAG 3932 O7 Wrong number of grandchild atoms for phi/psi acceptor /E NAG 3932 O7 Skipping possible acceptor with bad geometry: /E NAG 3932 O7 Wrong number of grandchild atoms for phi/psi acceptor /E NAG 3932 O7 Skipping possible acceptor with bad geometry: /A NAG 3932 O7 Wrong number of grandchild atoms for phi/psi acceptor /A NAG 3932 O7 Skipping possible acceptor with bad geometry: /I NAG 3932 O7 Wrong number of grandchild atoms for phi/psi acceptor /I NAG 3932 O7 10 messages similar to the above omitted 1974 hydrogen bonds /A VAL 505 is not terminus, removing H atom from 'C' /B ASP 664 is not terminus, removing H atom from 'C' /C SER 230 is not terminus, removing H atom from 'C' /D CYS 214 is not terminus, removing H atom from 'C' /E VAL 505 is not terminus, removing H atom from 'C' 7 messages similar to the above omitted 0 hydrogens added No template found for residue A3932 (NAG) Adding hydrogens Summary of feedback from adding hydrogens to VRC40-trimer- rsr40_real_space_refined-coot-0.pdb #1.1 --- warning | Skipped 15 atom(s) with bad connectivities; see log for details notes | No usable SEQRES records for VRC40-trimer-rsr40_real_space_refined- coot-0.pdb (#1.1) chain A; guessing termini instead No usable SEQRES records for VRC40-trimer-rsr40_real_space_refined-coot-0.pdb (#1.1) chain B; guessing termini instead No usable SEQRES records for VRC40-trimer-rsr40_real_space_refined-coot-0.pdb (#1.1) chain C; guessing termini instead No usable SEQRES records for VRC40-trimer-rsr40_real_space_refined-coot-0.pdb (#1.1) chain D; guessing termini instead No usable SEQRES records for VRC40-trimer-rsr40_real_space_refined-coot-0.pdb (#1.1) chain E; guessing termini instead 7 messages similar to the above omitted Chain-initial residues that are actual N termini: /C GLN 1, /D GLN 1, /G GLN 1, /H GLN 1, /K GLN 1, /L GLN 1 Chain-initial residues that are not actual N termini: /A ALA 32, /B ALA 512, /E ALA 32, /F ALA 512, /I ALA 32, /J ALA 512 Chain-final residues that are actual C termini: Chain-final residues that are not actual C termini: /A VAL 505, /B ASP 664, /C SER 230, /D CYS 214, /E VAL 505, /F ASP 664, /G SER 230, /H CYS 214, /I VAL 505, /J ASP 664, /K SER 230, /L CYS 214 Skipping possible acceptor with bad geometry: /A NAG 3932 O7 Wrong number of grandchild atoms for phi/psi acceptor /A NAG 3932 O7 Skipping possible acceptor with bad geometry: /E NAG 3932 O7 Wrong number of grandchild atoms for phi/psi acceptor /E NAG 3932 O7 Skipping possible acceptor with bad geometry: /A NAG 3932 O7 Wrong number of grandchild atoms for phi/psi acceptor /A NAG 3932 O7 Skipping possible acceptor with bad geometry: /E NAG 3932 O7 Wrong number of grandchild atoms for phi/psi acceptor /E NAG 3932 O7 Skipping possible acceptor with bad geometry: /I NAG 3932 O7 Wrong number of grandchild atoms for phi/psi acceptor /I NAG 3932 O7 10 messages similar to the above omitted 1974 hydrogen bonds /A VAL 505 is not terminus, removing H atom from 'C' /B ASP 664 is not terminus, removing H atom from 'C' /C SER 230 is not terminus, removing H atom from 'C' /D CYS 214 is not terminus, removing H atom from 'C' /E VAL 505 is not terminus, removing H atom from 'C' 7 messages similar to the above omitted 0 hydrogens added No template found for residue A3932 (NAG) Adding hydrogens Summary of feedback from adding hydrogens to VRC40-trimer- rsr40_real_space_refined-coot-0.pdb #1.1 --- warning | Skipped 15 atom(s) with bad connectivities; see log for details notes | No usable SEQRES records for VRC40-trimer-rsr40_real_space_refined- coot-0.pdb (#1.1) chain A; guessing termini instead No usable SEQRES records for VRC40-trimer-rsr40_real_space_refined-coot-0.pdb (#1.1) chain B; guessing termini instead No usable SEQRES records for VRC40-trimer-rsr40_real_space_refined-coot-0.pdb (#1.1) chain C; guessing termini instead No usable SEQRES records for VRC40-trimer-rsr40_real_space_refined-coot-0.pdb (#1.1) chain D; guessing termini instead No usable SEQRES records for VRC40-trimer-rsr40_real_space_refined-coot-0.pdb (#1.1) chain E; guessing termini instead 7 messages similar to the above omitted Chain-initial residues that are actual N termini: /C GLN 1, /D GLN 1, /G GLN 1, /H GLN 1, /K GLN 1, /L GLN 1 Chain-initial residues that are not actual N termini: /A ALA 32, /B ALA 512, /E ALA 32, /F ALA 512, /I ALA 32, /J ALA 512 Chain-final residues that are actual C termini: Chain-final residues that are not actual C termini: /A VAL 505, /B ASP 664, /C SER 230, /D CYS 214, /E VAL 505, /F ASP 664, /G SER 230, /H CYS 214, /I VAL 505, /J ASP 664, /K SER 230, /L CYS 214 Skipping possible acceptor with bad geometry: /A NAG 3932 O7 Wrong number of grandchild atoms for phi/psi acceptor /A NAG 3932 O7 Skipping possible acceptor with bad geometry: /A NAG 3932 O7 Wrong number of grandchild atoms for phi/psi acceptor /A NAG 3932 O7 Skipping possible acceptor with bad geometry: /E NAG 3932 O7 Wrong number of grandchild atoms for phi/psi acceptor /E NAG 3932 O7 Skipping possible acceptor with bad geometry: /E NAG 3932 O7 Wrong number of grandchild atoms for phi/psi acceptor /E NAG 3932 O7 Skipping possible acceptor with bad geometry: /I NAG 3932 O7 Wrong number of grandchild atoms for phi/psi acceptor /I NAG 3932 O7 10 messages similar to the above omitted 1974 hydrogen bonds /A VAL 505 is not terminus, removing H atom from 'C' /B ASP 664 is not terminus, removing H atom from 'C' /C SER 230 is not terminus, removing H atom from 'C' /D CYS 214 is not terminus, removing H atom from 'C' /E VAL 505 is not terminus, removing H atom from 'C' 7 messages similar to the above omitted 0 hydrogens added No template found for residue A3932 (NAG) Adding hydrogens Summary of feedback from adding hydrogens to VRC40-trimer- rsr40_real_space_refined-coot-0.pdb #1.1 --- warning | Skipped 15 atom(s) with bad connectivities; see log for details notes | No usable SEQRES records for VRC40-trimer-rsr40_real_space_refined- coot-0.pdb (#1.1) chain A; guessing termini instead No usable SEQRES records for VRC40-trimer-rsr40_real_space_refined-coot-0.pdb (#1.1) chain B; guessing termini instead No usable SEQRES records for VRC40-trimer-rsr40_real_space_refined-coot-0.pdb (#1.1) chain C; guessing termini instead No usable SEQRES records for VRC40-trimer-rsr40_real_space_refined-coot-0.pdb (#1.1) chain D; guessing termini instead No usable SEQRES records for VRC40-trimer-rsr40_real_space_refined-coot-0.pdb (#1.1) chain E; guessing termini instead 7 messages similar to the above omitted Chain-initial residues that are actual N termini: /C GLN 1, /D GLN 1, /G GLN 1, /H GLN 1, /K GLN 1, /L GLN 1 Chain-initial residues that are not actual N termini: /A ALA 32, /B ALA 512, /E ALA 32, /F ALA 512, /I ALA 32, /J ALA 512 Chain-final residues that are actual C termini: Chain-final residues that are not actual C termini: /A VAL 505, /B ASP 664, /C SER 230, /D CYS 214, /E VAL 505, /F ASP 664, /G SER 230, /H CYS 214, /I VAL 505, /J ASP 664, /K SER 230, /L CYS 214 Skipping possible acceptor with bad geometry: /A NAG 3932 O7 Wrong number of grandchild atoms for phi/psi acceptor /A NAG 3932 O7 Skipping possible acceptor with bad geometry: /E NAG 3932 O7 Wrong number of grandchild atoms for phi/psi acceptor /E NAG 3932 O7 Skipping possible acceptor with bad geometry: /A NAG 3932 O7 Wrong number of grandchild atoms for phi/psi acceptor /A NAG 3932 O7 Skipping possible acceptor with bad geometry: /E NAG 3932 O7 Wrong number of grandchild atoms for phi/psi acceptor /E NAG 3932 O7 Skipping possible acceptor with bad geometry: /I NAG 3932 O7 Wrong number of grandchild atoms for phi/psi acceptor /I NAG 3932 O7 10 messages similar to the above omitted 1974 hydrogen bonds /A VAL 505 is not terminus, removing H atom from 'C' /B ASP 664 is not terminus, removing H atom from 'C' /C SER 230 is not terminus, removing H atom from 'C' /D CYS 214 is not terminus, removing H atom from 'C' /E VAL 505 is not terminus, removing H atom from 'C' 7 messages similar to the above omitted 0 hydrogens added No template found for residue A3932 (NAG) Adding hydrogens Summary of feedback from adding hydrogens to VRC40-trimer- rsr40_real_space_refined-coot-0.pdb #1.1 --- warning | Skipped 15 atom(s) with bad connectivities; see log for details notes | No usable SEQRES records for VRC40-trimer-rsr40_real_space_refined- coot-0.pdb (#1.1) chain A; guessing termini instead No usable SEQRES records for VRC40-trimer-rsr40_real_space_refined-coot-0.pdb (#1.1) chain B; guessing termini instead No usable SEQRES records for VRC40-trimer-rsr40_real_space_refined-coot-0.pdb (#1.1) chain C; guessing termini instead No usable SEQRES records for VRC40-trimer-rsr40_real_space_refined-coot-0.pdb (#1.1) chain D; guessing termini instead No usable SEQRES records for VRC40-trimer-rsr40_real_space_refined-coot-0.pdb (#1.1) chain E; guessing termini instead 7 messages similar to the above omitted Chain-initial residues that are actual N termini: /C GLN 1, /D GLN 1, /G GLN 1, /H GLN 1, /K GLN 1, /L GLN 1 Chain-initial residues that are not actual N termini: /A ALA 32, /B ALA 512, /E ALA 32, /F ALA 512, /I ALA 32, /J ALA 512 Chain-final residues that are actual C termini: Chain-final residues that are not actual C termini: /A VAL 505, /B ASP 664, /C SER 230, /D CYS 214, /E VAL 505, /F ASP 664, /G SER 230, /H CYS 214, /I VAL 505, /J ASP 664, /K SER 230, /L CYS 214 Skipping possible acceptor with bad geometry: /A NAG 3932 O7 Wrong number of grandchild atoms for phi/psi acceptor /A NAG 3932 O7 Skipping possible acceptor with bad geometry: /E NAG 3932 O7 Wrong number of grandchild atoms for phi/psi acceptor /E NAG 3932 O7 Skipping possible acceptor with bad geometry: /A NAG 3932 O7 Wrong number of grandchild atoms for phi/psi acceptor /A NAG 3932 O7 Skipping possible acceptor with bad geometry: /E NAG 3932 O7 Wrong number of grandchild atoms for phi/psi acceptor /E NAG 3932 O7 Skipping possible acceptor with bad geometry: /I NAG 3932 O7 Wrong number of grandchild atoms for phi/psi acceptor /I NAG 3932 O7 10 messages similar to the above omitted 1974 hydrogen bonds /A VAL 505 is not terminus, removing H atom from 'C' /B ASP 664 is not terminus, removing H atom from 'C' /C SER 230 is not terminus, removing H atom from 'C' /D CYS 214 is not terminus, removing H atom from 'C' /E VAL 505 is not terminus, removing H atom from 'C' 7 messages similar to the above omitted 0 hydrogens added No template found for residue A3932 (NAG) Adding hydrogens Summary of feedback from adding hydrogens to VRC40-trimer- rsr40_real_space_refined-coot-0.pdb #1.1 --- warning | Skipped 15 atom(s) with bad connectivities; see log for details notes | No usable SEQRES records for VRC40-trimer-rsr40_real_space_refined- coot-0.pdb (#1.1) chain A; guessing termini instead No usable SEQRES records for VRC40-trimer-rsr40_real_space_refined-coot-0.pdb (#1.1) chain B; guessing termini instead No usable SEQRES records for VRC40-trimer-rsr40_real_space_refined-coot-0.pdb (#1.1) chain C; guessing termini instead No usable SEQRES records for VRC40-trimer-rsr40_real_space_refined-coot-0.pdb (#1.1) chain D; guessing termini instead No usable SEQRES records for VRC40-trimer-rsr40_real_space_refined-coot-0.pdb (#1.1) chain E; guessing termini instead 7 messages similar to the above omitted Chain-initial residues that are actual N termini: /C GLN 1, /D GLN 1, /G GLN 1, /H GLN 1, /K GLN 1, /L GLN 1 Chain-initial residues that are not actual N termini: /A ALA 32, /B ALA 512, /E ALA 32, /F ALA 512, /I ALA 32, /J ALA 512 Chain-final residues that are actual C termini: Chain-final residues that are not actual C termini: /A VAL 505, /B ASP 664, /C SER 230, /D CYS 214, /E VAL 505, /F ASP 664, /G SER 230, /H CYS 214, /I VAL 505, /J ASP 664, /K SER 230, /L CYS 214 Skipping possible acceptor with bad geometry: /A NAG 3932 O7 Wrong number of grandchild atoms for phi/psi acceptor /A NAG 3932 O7 Skipping possible acceptor with bad geometry: /A NAG 3932 O7 Wrong number of grandchild atoms for phi/psi acceptor /A NAG 3932 O7 Skipping possible acceptor with bad geometry: /E NAG 3932 O7 Wrong number of grandchild atoms for phi/psi acceptor /E NAG 3932 O7 Skipping possible acceptor with bad geometry: /E NAG 3932 O7 Wrong number of grandchild atoms for phi/psi acceptor /E NAG 3932 O7 Skipping possible acceptor with bad geometry: /I NAG 3932 O7 Wrong number of grandchild atoms for phi/psi acceptor /I NAG 3932 O7 10 messages similar to the above omitted 1974 hydrogen bonds /A VAL 505 is not terminus, removing H atom from 'C' /B ASP 664 is not terminus, removing H atom from 'C' /C SER 230 is not terminus, removing H atom from 'C' /D CYS 214 is not terminus, removing H atom from 'C' /E VAL 505 is not terminus, removing H atom from 'C' 7 messages similar to the above omitted 0 hydrogens added No template found for residue A3932 (NAG) Adding hydrogens Summary of feedback from adding hydrogens to VRC40-trimer- rsr40_real_space_refined-coot-0.pdb #1.1 --- warning | Skipped 15 atom(s) with bad connectivities; see log for details notes | No usable SEQRES records for VRC40-trimer-rsr40_real_space_refined- coot-0.pdb (#1.1) chain A; guessing termini instead No usable SEQRES records for VRC40-trimer-rsr40_real_space_refined-coot-0.pdb (#1.1) chain B; guessing termini instead No usable SEQRES records for VRC40-trimer-rsr40_real_space_refined-coot-0.pdb (#1.1) chain C; guessing termini instead No usable SEQRES records for VRC40-trimer-rsr40_real_space_refined-coot-0.pdb (#1.1) chain D; guessing termini instead No usable SEQRES records for VRC40-trimer-rsr40_real_space_refined-coot-0.pdb (#1.1) chain E; guessing termini instead 7 messages similar to the above omitted Chain-initial residues that are actual N termini: /C GLN 1, /D GLN 1, /G GLN 1, /H GLN 1, /K GLN 1, /L GLN 1 Chain-initial residues that are not actual N termini: /A ALA 32, /B ALA 512, /E ALA 32, /F ALA 512, /I ALA 32, /J ALA 512 Chain-final residues that are actual C termini: Chain-final residues that are not actual C termini: /A VAL 505, /B ASP 664, /C SER 230, /D CYS 214, /E VAL 505, /F ASP 664, /G SER 230, /H CYS 214, /I VAL 505, /J ASP 664, /K SER 230, /L CYS 214 Skipping possible acceptor with bad geometry: /A NAG 3932 O7 Wrong number of grandchild atoms for phi/psi acceptor /A NAG 3932 O7 Skipping possible acceptor with bad geometry: /E NAG 3932 O7 Wrong number of grandchild atoms for phi/psi acceptor /E NAG 3932 O7 Skipping possible acceptor with bad geometry: /A NAG 3932 O7 Wrong number of grandchild atoms for phi/psi acceptor /A NAG 3932 O7 Skipping possible acceptor with bad geometry: /E NAG 3932 O7 Wrong number of grandchild atoms for phi/psi acceptor /E NAG 3932 O7 Skipping possible acceptor with bad geometry: /I NAG 3932 O7 Wrong number of grandchild atoms for phi/psi acceptor /I NAG 3932 O7 10 messages similar to the above omitted 1974 hydrogen bonds /A VAL 505 is not terminus, removing H atom from 'C' /B ASP 664 is not terminus, removing H atom from 'C' /C SER 230 is not terminus, removing H atom from 'C' /D CYS 214 is not terminus, removing H atom from 'C' /E VAL 505 is not terminus, removing H atom from 'C' 7 messages similar to the above omitted 0 hydrogens added No template found for residue A3932 (NAG) Excluding residue > clipper associate #2 toModel #1 > clipper associate #2 toModel #1 > show #!1.1 target m > show #!1.1 target m > hide #!1.1 target m > show #!1.1 target m > select #1 51607 atoms, 52256 bonds, 18 models selected > toolshed show ISOLDE > set selectionWidth 4 Done loading forcefield > clipper associate #2 toModel #1 > clipper associate #2 toModel #1 > hide #!1.2 models > close #1.2 > open "/Users/km503/Documents/VRC40/higher > resolution/cryosparc_P4_J12_008_volume_map_sharp_local-zflip.mrc" Opened cryosparc_P4_J12_008_volume_map_sharp_local-zflip.mrc, grid size 320,320,320, pixel 1.08, shown at level 0.667, step 2, values float32 > clipper associate #2 toModel #1 > addh Summary of feedback from adding hydrogens to VRC40-trimer- rsr40_real_space_refined-coot-0.pdb #1.1 --- warning | Skipped 15 atom(s) with bad connectivities; see log for details notes | No usable SEQRES records for VRC40-trimer-rsr40_real_space_refined- coot-0.pdb (#1.1) chain A; guessing termini instead No usable SEQRES records for VRC40-trimer-rsr40_real_space_refined-coot-0.pdb (#1.1) chain B; guessing termini instead No usable SEQRES records for VRC40-trimer-rsr40_real_space_refined-coot-0.pdb (#1.1) chain C; guessing termini instead No usable SEQRES records for VRC40-trimer-rsr40_real_space_refined-coot-0.pdb (#1.1) chain D; guessing termini instead No usable SEQRES records for VRC40-trimer-rsr40_real_space_refined-coot-0.pdb (#1.1) chain E; guessing termini instead 7 messages similar to the above omitted Chain-initial residues that are actual N termini: /C GLN 1, /D GLN 1, /G GLN 1, /H GLN 1, /K GLN 1, /L GLN 1 Chain-initial residues that are not actual N termini: /A ALA 32, /B ALA 512, /E ALA 32, /F ALA 512, /I ALA 32, /J ALA 512 Chain-final residues that are actual C termini: Chain-final residues that are not actual C termini: /A VAL 505, /B ASP 664, /C SER 230, /D CYS 214, /E VAL 505, /F ASP 664, /G SER 230, /H CYS 214, /I VAL 505, /J ASP 664, /K SER 230, /L CYS 214 Skipping possible acceptor with bad geometry: /A NAG 3932 O7 Wrong number of grandchild atoms for phi/psi acceptor /A NAG 3932 O7 Skipping possible acceptor with bad geometry: /A NAG 3932 O7 Wrong number of grandchild atoms for phi/psi acceptor /A NAG 3932 O7 Skipping possible acceptor with bad geometry: /E NAG 3932 O7 Wrong number of grandchild atoms for phi/psi acceptor /E NAG 3932 O7 Skipping possible acceptor with bad geometry: /E NAG 3932 O7 Wrong number of grandchild atoms for phi/psi acceptor /E NAG 3932 O7 Skipping possible acceptor with bad geometry: /I NAG 3932 O7 Wrong number of grandchild atoms for phi/psi acceptor /I NAG 3932 O7 10 messages similar to the above omitted 1977 hydrogen bonds /A VAL 505 is not terminus, removing H atom from 'C' /B ASP 664 is not terminus, removing H atom from 'C' /C SER 230 is not terminus, removing H atom from 'C' /D CYS 214 is not terminus, removing H atom from 'C' /E VAL 505 is not terminus, removing H atom from 'C' 7 messages similar to the above omitted 0 hydrogens added > hide HC > isolde restrain ligands #1 QWidget::repaint: Recursive repaint detected > select #1 51607 atoms, 52256 bonds, 18 models selected > isolde sim start sel No template found for residue A3943 (NAG) Excluding residue No template found for residue A3944 (NAG) Excluding residue No template found for residue A3961 (NAG) Excluding residue No template found for residue A3964 (NAG) Excluding residue No template found for residue A3969 (MAN) Excluding residue No template found for residue E3932 (NAG) Excluding residue No template found for residue E3943 (NAG) Excluding residue No template found for residue E3944 (NAG) Excluding residue No template found for residue E3961 (NAG) Excluding residue No template found for residue E3964 (NAG) Excluding residue No template found for residue E3969 (MAN) Excluding residue No template found for residue I3932 (NAG) Excluding residue No template found for residue I3943 (NAG) Excluding residue No template found for residue I3944 (NAG) Excluding residue No template found for residue I3961 (NAG) Excluding residue No template found for residue I3964 (NAG) Excluding residue No template found for residue I3969 (MAN) Excluding residue > select #1 51607 atoms, 52256 bonds, 18 models selected > isolde sim start sel Simulation already running! > select clear No rotamer preview selected! Ignoring command. No rotamer preview selected! Ignoring command. Traceback (most recent call last): File "/private/var/folders/xv/05d2bhc950b8q5xxkg5j9c25qc0nm9/T/AppTranslocation/7849F4B9-F847-4719-B2BB-F74924045DFA/d/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/triggerset.py", line 130, in invoke return self._func(self._name, data) File "/Users/km503/Library/Application Support/ChimeraX/0.91/site- packages/chimerax/isolde/openmm/openmm_interface.py", line 1686, in _push_coords_to_sim self.thread_handler.coords = self._pending_coords File "/Users/km503/Library/Application Support/ChimeraX/0.91/site- packages/chimerax/isolde/openmm/openmm_interface.py", line 309, in coords f(self._c_pointer, n, pointer(coords)) File "/private/var/folders/xv/05d2bhc950b8q5xxkg5j9c25qc0nm9/T/AppTranslocation/7849F4B9-F847-4719-B2BB-F74924045DFA/d/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/molc.py", line 320, in pointer cty = numpy_type_to_ctype[a.dtype.type] AttributeError: 'NoneType' object has no attribute 'dtype' Error processing trigger "coord update": AttributeError: 'NoneType' object has no attribute 'dtype' File "/private/var/folders/xv/05d2bhc950b8q5xxkg5j9c25qc0nm9/T/AppTranslocation/7849F4B9-F847-4719-B2BB-F74924045DFA/d/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/molc.py", line 320, in pointer cty = numpy_type_to_ctype[a.dtype.type] See log for complete Python traceback. Traceback (most recent call last): File "/private/var/folders/xv/05d2bhc950b8q5xxkg5j9c25qc0nm9/T/AppTranslocation/7849F4B9-F847-4719-B2BB-F74924045DFA/d/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/triggerset.py", line 130, in invoke return self._func(self._name, data) File "/Users/km503/Library/Application Support/ChimeraX/0.91/site- packages/chimerax/isolde/openmm/openmm_interface.py", line 1686, in _push_coords_to_sim self.thread_handler.coords = self._pending_coords File "/Users/km503/Library/Application Support/ChimeraX/0.91/site- packages/chimerax/isolde/openmm/openmm_interface.py", line 309, in coords f(self._c_pointer, n, pointer(coords)) File "/private/var/folders/xv/05d2bhc950b8q5xxkg5j9c25qc0nm9/T/AppTranslocation/7849F4B9-F847-4719-B2BB-F74924045DFA/d/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/molc.py", line 320, in pointer cty = numpy_type_to_ctype[a.dtype.type] AttributeError: 'NoneType' object has no attribute 'dtype' Error processing trigger "coord update": AttributeError: 'NoneType' object has no attribute 'dtype' File "/private/var/folders/xv/05d2bhc950b8q5xxkg5j9c25qc0nm9/T/AppTranslocation/7849F4B9-F847-4719-B2BB-F74924045DFA/d/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/molc.py", line 320, in pointer cty = numpy_type_to_ctype[a.dtype.type] See log for complete Python traceback. Traceback (most recent call last): File "/private/var/folders/xv/05d2bhc950b8q5xxkg5j9c25qc0nm9/T/AppTranslocation/7849F4B9-F847-4719-B2BB-F74924045DFA/d/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/triggerset.py", line 130, in invoke return self._func(self._name, data) File "/Users/km503/Library/Application Support/ChimeraX/0.91/site- packages/chimerax/isolde/openmm/openmm_interface.py", line 1686, in _push_coords_to_sim self.thread_handler.coords = self._pending_coords File "/Users/km503/Library/Application Support/ChimeraX/0.91/site- packages/chimerax/isolde/openmm/openmm_interface.py", line 309, in coords f(self._c_pointer, n, pointer(coords)) File "/private/var/folders/xv/05d2bhc950b8q5xxkg5j9c25qc0nm9/T/AppTranslocation/7849F4B9-F847-4719-B2BB-F74924045DFA/d/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/molc.py", line 320, in pointer cty = numpy_type_to_ctype[a.dtype.type] AttributeError: 'NoneType' object has no attribute 'dtype' Error processing trigger "coord update": AttributeError: 'NoneType' object has no attribute 'dtype' File "/private/var/folders/xv/05d2bhc950b8q5xxkg5j9c25qc0nm9/T/AppTranslocation/7849F4B9-F847-4719-B2BB-F74924045DFA/d/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/molc.py", line 320, in pointer cty = numpy_type_to_ctype[a.dtype.type] See log for complete Python traceback. Traceback (most recent call last): File "/private/var/folders/xv/05d2bhc950b8q5xxkg5j9c25qc0nm9/T/AppTranslocation/7849F4B9-F847-4719-B2BB-F74924045DFA/d/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/triggerset.py", line 130, in invoke return self._func(self._name, data) File "/Users/km503/Library/Application Support/ChimeraX/0.91/site- packages/chimerax/isolde/openmm/openmm_interface.py", line 1686, in _push_coords_to_sim self.thread_handler.coords = self._pending_coords File "/Users/km503/Library/Application Support/ChimeraX/0.91/site- packages/chimerax/isolde/openmm/openmm_interface.py", line 309, in coords f(self._c_pointer, n, pointer(coords)) File "/private/var/folders/xv/05d2bhc950b8q5xxkg5j9c25qc0nm9/T/AppTranslocation/7849F4B9-F847-4719-B2BB-F74924045DFA/d/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/molc.py", line 320, in pointer cty = numpy_type_to_ctype[a.dtype.type] AttributeError: 'NoneType' object has no attribute 'dtype' Error processing trigger "coord update": AttributeError: 'NoneType' object has no attribute 'dtype' File "/private/var/folders/xv/05d2bhc950b8q5xxkg5j9c25qc0nm9/T/AppTranslocation/7849F4B9-F847-4719-B2BB-F74924045DFA/d/ChimeraX-0.91.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/molc.py", line 320, in pointer cty = numpy_type_to_ctype[a.dtype.type] See log for complete Python traceback. OpenGL version: 4.1 ATI-3.5.5 OpenGL renderer: AMD Radeon Pro 5500M OpenGL Engine OpenGL vendor: ATI Technologies Inc.
Change History (3)
comment:1 by , 6 years ago
| Component: | Unassigned → Third Party |
|---|---|
| Description: | modified (diff) |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → isolde.openmm.openmm_interface: 'coords' is None |
| Version: | → 0.91 |
comment:2 by , 6 years ago
comment:3 by , 6 years ago
| Resolution: | → fixed |
|---|---|
| Status: | assigned → closed |
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Thanks for reporting this! I can see the underlying bug and will get it fixed for the next release. For now, you should be able to avoid it if you make sure to do more than one "coordinate changing" thing at a time while paused (that is, press play before doing anything else).