id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 15096 Crash in garbage collection ts387@… Eric Pettersen "{{{ The following bug report has been submitted: Platform: macOS-14.4.1-arm64-arm-64bit ChimeraX Version: 1.7.1 (2024-01-23 01:58:08 UTC) Description Last time you used ChimeraX it crashed. Please describe steps that led to the crash here. Fatal Python error: Segmentation fault Current thread 0x00000001e8a4bac0 (most recent call first): Garbage-collecting File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/serialize.py"", line 81 in msgpack_deserialize File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/session.py"", line 721 in restore File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/session.py"", line 1017 in open File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core_formats/__init__.py"", line 37 in open File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/open_command/cmd.py"", 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""ReadOnly portion of Libraries: Total=1.5G resident=0K(0%) swapped_out_or_unallocated=1.5G(100%)\nWritable regions: Total=3.4G written=0K(0%) resident=0K(0%) swapped_out=0K(0%) unallocated=3.4G(100%)\n\n VIRTUAL REGION \nREGION TYPE SIZE COUNT (non-coalesced) \n=========== ======= ======= \nAccelerate framework 128K 1 \nActivity Tracing 256K 1 \nCG image 352K 16 \nColorSync 640K 30 \nCoreAnimation 784K 47 \nCoreGraphics 32K 2 \nCoreServices 16K 1 \nCoreUI image data 4512K 31 \nFoundation 16K 1 \nKernel Alloc Once 32K 1 \nMALLOC 2.7G 111 \nMALLOC guard page 384K 24 \nMach message 64K 3 \nOpenGL GLSL 384K 4 \nSTACK GUARD 448K 28 \nStack 157.6M 29 \nStack Guard 56.0M 1 \nVM_ALLOCATE 262.4M 170 \nVM_ALLOCATE (reserved) 288.0M 5 reserved VM address space (unallocated)\n__AUTH 2794K 416 \n__AUTH_CONST 32.8M 634 \n__CTF 824 1 \n__DATA 26.2M 808 \n__DATA_CONST 43.2M 820 \n__DATA_DIRTY 1877K 228 \n__FONT_DATA 2352 1 \n__GLSLBUILTINS 5174K 1 \n__LINKEDIT 562.0M 181 \n__OBJC_RO 71.7M 1 \n__OBJC_RW 2195K 1 \n__TEXT 982.7M 837 \ndyld private memory 736K 6 \nmapped file 989.9M 59 \nshared memory 3200K 28 \n=========== ======= ======= \nTOTAL 6.1G 4528 \nTOTAL, minus reserved VM space 5.9G 4528 \n"", ""legacyInfo"" : { ""threadTriggered"" : { ""name"" : ""CrBrowserMain"", ""queue"" : ""com.apple.main-thread"" } }, ""logWritingSignature"" : ""d0a848ccc482eab4ddb96f56eba01dde398c2892"", ""trialInfo"" : { ""rollouts"" : [ { ""rolloutId"" : ""64b21a7351cbb02ce3442e4e"", ""factorPackIds"" : { ""REMINDERS_GROCERY"" : ""65542c604a6560536bdb1d22"" }, ""deploymentId"" : 240000032 }, { ""rolloutId"" : ""652eff3d1bce5442b8d753c9"", ""factorPackIds"" : { }, ""deploymentId"" : 240000009 } ], ""experiments"" : [ ] } } ===== Log before crash start ===== Startup Messages --- warning | Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR bundle with that from NMRSTAR bundle UCSF ChimeraX version: 1.7.1 (2024-01-23) © 2016-2023 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open > /Users/tahashahid/Desktop/comp002_frame010-5_comb-3_modified_real_space_refined_000.cif Summary of feedback from opening /Users/tahashahid/Desktop/comp002_frame010-5_comb-3_modified_real_space_refined_000.cif --- warnings | Skipping chem_comp category: Missing column 'type' near line 329 Missing entity information. Treating each chain as a separate entity. Bad residue range for struct_conf ""12"" near line 154 Bad residue range for struct_conf ""13"" near line 155 Bad residue range for struct_conf ""14"" near line 156 Bad residue range for struct_conf ""15"" near line 157 Bad residue range for struct_conf ""16"" near line 158 14 messages similar to the above omitted Invalid residue range for struct_conf ""31"": invalid entity ""B"", near line 173 Invalid residue range for struct_conf ""32"": invalid entity ""B"", near line 174 Invalid residue range for struct_conf ""33"": invalid entity ""B"", near line 175 Invalid residue range for struct_conf ""34"": invalid entity ""B"", near line 176 Invalid residue range for struct_conf ""35"": invalid entity ""B"", near line 177 25 messages similar to the above omitted Bad residue range for struct_conf ""73"" near line 215 Bad residue range for struct_conf ""74"" near line 216 Bad residue range for struct_conf ""75"" near line 217 Bad residue range for struct_conf ""76"" near line 218 Bad residue range for struct_conf ""77"" near line 219 15 messages similar to the above omitted Invalid residue range for struct_conf ""93"": invalid entity ""D"", near line 235 Invalid residue range for struct_conf ""94"": invalid entity ""D"", near line 236 Invalid residue range for struct_conf ""95"": invalid entity ""D"", near line 237 Invalid residue range for struct_conf ""96"": invalid entity ""D"", near line 238 Invalid residue range for struct_conf ""97"": invalid entity ""D"", near line 239 25 messages similar to the above omitted Bad residue range for struct_conf ""134"" near line 276 Bad residue range for struct_conf ""135"" near line 277 Bad residue range for struct_conf ""136"" near line 278 Bad residue range for struct_conf ""137"" near line 279 Bad residue range for struct_conf ""138"" near line 280 15 messages similar to the above omitted Invalid residue range for struct_conf ""154"": invalid entity ""F"", near line 296 Invalid residue range for struct_conf ""155"": invalid entity ""F"", near line 297 Invalid residue range for struct_conf ""156"": invalid entity ""F"", near line 298 Invalid residue range for struct_conf ""157"": invalid entity ""F"", near line 299 Invalid residue range for struct_conf ""158"": invalid entity ""F"", near line 300 27 messages similar to the above omitted Atom H is not in the residue template for LYS /A:266 Atom H is not in the residue template for LYS /B:266 Atom H is not in the residue template for LYS /C:266 Atom H is not in the residue template for LYS /D:266 Atom H is not in the residue template for LYS /E:266 1 messages similar to the above omitted Missing or incomplete sequence information. Inferred polymer connectivity. Skipping chem_comp category: Missing column 'type' near line 36715 Chain information for comp002_frame010-5_comb-3_modified_real_space_refined_000.cif #1 --- Chain | Description A B C D E F | No description available S | No description available > hide atoms > show cartoons > color bychain > dssp #1 > save > /Users/tahashahid/Desktop/comp002_frame010-5_comb-3_modified_real_space_refined_000_dssp.cif > relModel #1 Not saving entity_poly_seq for non-authoritative sequences > close session > open /Users/tahashahid/Documents/Work/Modelling/LTAg-CGfork_ATP- > Mg/3DVA/cs_P18_J332_component_002/comp_002_frame_010_AF2_matchmaker_MDFFflexfit_ISOLDE-5_comb-3.cxs ===== Log before crash end ===== Log: UCSF ChimeraX version: 1.7.1 (2024-01-23) © 2016-2023 Regents of the University of California. All rights reserved. > open /Users/tahashahid/Documents/Work/Modelling/LTAg-CGfork_ATP- > Mg/3DVA/cs_P18_J332_component_002/comp_002_frame_010_AF2_matchmaker_MDFFflexfit_ISOLDE-5_comb-3.cxs Opened J332_component_002_frame_010.mrc as #1.1.1.1, grid size 128,128,128, pixel 1.67, shown at level 0.338, step 1, values float32 Opened J332_component_002_frame_010_emready.mrc as #1.1.1.2, grid size 213,213,213, pixel 1, shown at level 1.71, step 1, values float32 Restoring stepper: comp002_frame010-5_comb.pdb Log from Thu May 2 23:31:55 2024UCSF ChimeraX version: 1.7.1 (2024-01-23) © 2016-2023 Regents of the University of California. All rights reserved. > open /Users/tahashahid/Documents/Work/Modelling/LTAg-CGfork_ATP- > Mg/3DVA/cs_P18_J332_component_002/comp_002_frame_010_AF2_matchmaker_MDFFflexfit_ISOLDE-5_comb-2.cxs Opened J332_component_002_frame_010.mrc as #1.1.1.1, grid size 128,128,128, pixel 1.67, shown at level 0.338, step 1, values float32 Opened J332_component_002_frame_010_emready.mrc as #1.1.1.2, grid size 213,213,213, pixel 1, shown at level 3.3, step 1, values float32 Restoring stepper: comp002_frame010-5_comb.pdb Log from Tue Apr 30 01:03:15 2024UCSF ChimeraX version: 1.7.1 (2024-01-23) © 2016-2023 Regents of the University of California. All rights reserved. > open /Users/tahashahid/Documents/Work/Modelling/LTAg-CGfork_ATP- > Mg/3DVA/cs_P18_J332_component_002/comp_002_frame_010_AF2_matchmaker_MDFFflexfit_ISOLDE-5_comb-1.cxs > format session Opened J332_component_002_frame_010.mrc as #1.1.1.1, grid size 128,128,128, pixel 1.67, shown at level 0.903, step 1, values float32 Opened J332_component_002_frame_010_emready.mrc as #1.1.1.2, grid size 213,213,213, pixel 1, shown at level 2.82, step 1, values float32 Restoring stepper: comp002_frame010-5_comb.pdb Log from Tue Jan 23 18:55:59 2024UCSF ChimeraX version: 1.6.1 (2023-05-09) © 2016-2023 Regents of the University of California. All rights reserved. > open /Users/tahashahid/Documents/Work/Modelling/LTAg-CGfork_ATP- > Mg/3DVA/cs_P18_J332_component_002/comp_002_frame_010_AF2_matchmaker_MDFFflexfit_ISOLDE-5_comb-1.cxs Opened J332_component_002_frame_010.mrc as #1.1.1.1, grid size 128,128,128, pixel 1.67, shown at level 0.903, step 1, values float32 Opened J332_component_002_frame_010_emready.mrc as #1.1.1.2, grid size 213,213,213, pixel 1, shown at level 2.17, step 1, values float32 Restoring stepper: comp002_frame010-5_comb.pdb Log from Tue Jan 23 03:11:45 2024UCSF ChimeraX version: 1.6.1 (2023-05-09) © 2016-2023 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open /Users/tahashahid/Documents/Work/Modelling/LTAg-CGfork_ATP- > Mg/3DVA/cs_P18_J332_component_002/comp002_frame010-5_comb.pdb Chain information for comp002_frame010-5_comb.pdb #1 --- Chain | Description A B C D E F | No description available S | No description available > open /Users/tahashahid/Documents/Work/Processing/LTAg_ATP- > Mg_CGfork/cryosparc_P18_J332_component_002/J332_component_002_frame_010.mrc Opened J332_component_002_frame_010.mrc as #2, grid size 128,128,128, pixel 1.67, shown at level 0.731, step 1, values float32 > open /Users/tahashahid/Documents/Work/Processing/LTAg_ATP- > Mg_CGfork/cryosparc_P18_J332_component_002/J332_component_002_frame_010_emready.mrc Opened J332_component_002_frame_010_emready.mrc as #3, grid size 213,213,213, pixel 1, shown at level 4.66, step 1, values float32 > open /Users/tahashahid/Documents/Work/Modelling/LTAg-CGfork_ATP- > Mg/3DVA/cs_P18_J332_component_002/comp002_frame010-5.pdb Chain information for comp002_frame010-5.pdb #4 --- Chain | Description A B C D E F | No description available S | No description available > open /Users/tahashahid/Library/CloudStorage/OneDrive- > UniversityofLeicester/for_taha/Comp002_models/Comp002_Frame10_ssDNA_ISOLDE.pdb Chain information for Comp002_Frame10_ssDNA_ISOLDE.pdb #5 --- Chain | Description A B C D E F | No description available S | No description available > open /Users/tahashahid/Documents/Work/Modelling/LTAg-CGfork_ATP- > Mg/3DVA/cs_P18_J332_component_002/comp002_frame015-7_comb-1.pdb Chain information for comp002_frame015-7_comb-1.pdb #6 --- Chain | Description A B C D E F | No description available S | No description available > isolde start > set selectionWidth 4 > isolde set simFidelityMode Medium/Medium ISOLDE: setting sim fidelity mode to Medium/Medium nonbonded_cutoff_distance = 0.900000 use_gbsa = True gbsa_cutoff = 1.100000 > ui tool show ""Volume Viewer"" > ui tool show ""Ramachandran Plot"" ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... Chain information for comp002_frame010-5_comb.pdb --- Chain | Description 1.2/A 1.2/B 1.2/C 1.2/D 1.2/E 1.2/F | No description available 1.2/S | No description available > clipper associate #2 toModel #1 Opened J332_component_002_frame_010.mrc as #1.1.1.1, grid size 128,128,128, pixel 1.67, shown at step 1, values float32 > clipper associate #3 toModel #1 Opened J332_component_002_frame_010_emready.mrc as #1.1.1.2, grid size 213,213,213, pixel 1, shown at step 1, values float32 > select clear > select add #6 36101 atoms, 36482 bonds, 2192 residues, 1 model selected > select add #5 72202 atoms, 72964 bonds, 4384 residues, 2 models selected > select add #4 108270 atoms, 109411 bonds, 6575 residues, 3 models selected > color sel bychain > color sel byhetero > style sel stick Changed 108270 atom styles > hide HC > select clear > hide #6 models > hide #5 models > hide #4 models > select #1/S 257 atoms, 272 bonds, 8 residues, 1 model selected > isolde sim start #1.2/S ISOLDE: started sim > show #4 models > hide #4 models > volume #1.1.1.2 level 3.318 > select clear > volume #1.1.1.2 level 5.304 > show #4 models > hide #4 models > show #4 models > hide #4 models > volume #1.1.1.2 level 2.803 > isolde stepto #1.2/S:2 > select clear [Repeated 1 time(s)] > isolde sim stop Sim termination reason: None ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > select #1/S 257 atoms, 272 bonds, 8 residues, 1 model selected > save /Users/tahashahid/Documents/Work/Modelling/LTAg-CGfork_ATP- > Mg/3DVA/cs_P18_J332_component_002/comp_002_frame_010_AF2_matchmaker_MDFFflexfit_ISOLDE-5_comb.cxs > includeMaps true Taking snapshot of stepper: comp002_frame010-5_comb.pdb > select #1/A:509-517,454-460 297 atoms, 297 bonds, 16 residues, 1 model selected > isolde sim start #1.2/A:454-460,509-517 Loading residue template for ATP from internal database ISOLDE: started sim > select clear > volume #1.1.1.2 level 1.231 > volume #1.1.1.2 level 1.556 > show #5 models > hide #5 models > show #5 models > hide #5 models > qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep > 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false Overall mean Q-Score: 0.64 > view #!1.2/A:511 > view #!1.2/A:516 > volume #1.1.1.2 level 0.9317 > view #!1.2/A:516 > qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep > 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false Overall mean Q-Score: 0.64 > qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep > 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false Overall mean Q-Score: 0.64 > view #!1.2/A:516 > volume #1.1.1.2 level 3.028 > volume #1.1.1.2 level 4.7 > volume #1.1.1.2 level 3.427 > view #!1.2/A:349 > qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep > 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false Overall mean Q-Score: 0.64 > view #!1.2/A:349 > qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep > 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false Overall mean Q-Score: 0.64 > view #!1.2/A:349 > volume #1.1.1.2 level 4.75 > volume #1.1.1.2 level 4.7 > view #!1.2/A:517 > qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep > 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false Overall mean Q-Score: 0.64 > view #!1.2/A:517 > isolde sim stop discardTo start Sim termination reason: None reverting to start ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > select #1/A:509-517,454-460 297 atoms, 297 bonds, 16 residues, 1 model selected > isolde sim start #1.2/A:454-460,509-517 ISOLDE: started sim > qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep > 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false Overall mean Q-Score: 0.64 > qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep > 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false Overall mean Q-Score: 0.64 > volume #1.1.1.2 level 2.554 > volume #1.1.1.2 level 5.249 > qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep > 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false Overall mean Q-Score: 0.64 > select clear > volume #1.1.1.2 level 2.529 > volume #1.1.1.2 level 3.452 > volume #1.1.1.2 level 1.88 > volume #1.1.1.2 level 3.078 > select clear > volume #1.1.1.2 level 1.056 > view #!1.2/A:515 > qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep > 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false Overall mean Q-Score: 0.64 > volume #1.1.1.2 level 1.93 > select clear > qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep > 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false Overall mean Q-Score: 0.64 > view #!1.2/A:512 > volume #1.1.1.2 level 1.181 > view #!1.2/A:512 > volume #1.1.1.2 level 2.404 > volume #1.1.1.2 level 1.78 > qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep > 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false Overall mean Q-Score: 0.64 > view #!1.2/A:513 > volume #1.1.1.2 level 3.402 > show #4 models > hide #4 models > volume #1.1.1.2 level 1.581 > volume #1.1.1.2 level 0.782 > qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep > 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false Overall mean Q-Score: 0.64 > qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep > 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false Overall mean Q-Score: 0.64 > volume #1.1.1.2 level 2.579 > qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep > 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false Overall mean Q-Score: 0.64 > view #!1.2/A:514 > volume #1.1.1.2 level 1.156 > volume #1.1.1.2 level 0.5574 > qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep > 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false Overall mean Q-Score: 0.64 > view #!1.2/A:514 > view #!1.2/A:456 > show #6 models > volume #1.1.1.2 level 0.4327 > volume #1.1.1.2 level 2.529 > qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep > 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false Overall mean Q-Score: 0.64 > hide #6 models > qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep > 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false Overall mean Q-Score: 0.64 > view #!1.2/A:456 > volume #1.1.1.2 level 0.7071 > volume #1.1.1.2 level 0.2829 > show #6 models > hide #6 models > qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep > 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false Overall mean Q-Score: 0.64 > qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep > 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false Overall mean Q-Score: 0.64 > volume #1.1.1.2 level 2.154 > qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep > 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false Overall mean Q-Score: 0.64 > view #!1.2/A:456 > volume #1.1.1.2 level 0.7321 > volume #1.1.1.2 level 0.3578 > qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep > 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false Overall mean Q-Score: 0.64 > qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep > 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false Overall mean Q-Score: 0.64 > qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep > 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false Overall mean Q-Score: 0.64 > qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep > 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false Overall mean Q-Score: 0.64 > volume #1.1.1.2 level 1.805 > qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep > 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false Overall mean Q-Score: 0.64 > view #!1.2/A:516 > volume #1.1.1.2 level 0.7321 > qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep > 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false Overall mean Q-Score: 0.64 > isolde sim pause > isolde sim resume > qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep > 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false Overall mean Q-Score: 0.64 > volume #1.1.1.2 level 2.154 > select clear > isolde sim pause > isolde sim resume > isolde sim pause > isolde sim resume > isolde sim pause > isolde sim resume > volume #1.1.1.2 level 1.331 > show #4 models > hide #4 models > show #5 models > isolde sim pause > select clear > isolde sim resume > isolde sim pause > isolde sim resume > isolde sim pause > isolde sim resume > hide #5 models > show #4 models > select clear > view #!1.2/A:516 > qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep > 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false Overall mean Q-Score: 0.64 > view #!1.2/A:516 [Repeated 1 time(s)] > show #6 models > hide #4 models > view #!1.2/A:349 > volume #1.1.1.2 level 3.976 > select clear > qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep > 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false Overall mean Q-Score: 0.64 > volume #1.1.1.2 level 2.204 > qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep > 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false Overall mean Q-Score: 0.64 > qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep > 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false Overall mean Q-Score: 0.64 > qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep > 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false Overall mean Q-Score: 0.64 > hide #6 models > volume #1.1.1.2 level 3.677 > volume #1.1.1.2 level 1.381 > view #!1.2/A:506 > qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep > 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false Overall mean Q-Score: 0.64 > select clear > volume #1.1.1.2 level 1.955 > select clear > view #!1.2/A:499 > qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep > 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false Overall mean Q-Score: 0.64 > isolde sim stop Sim termination reason: None ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB standards. ISOLDE: stopped sim > save /Users/tahashahid/Documents/Work/Modelling/LTAg-CGfork_ATP- > Mg/3DVA/cs_P18_J332_component_002/comp_002_frame_010_AF2_matchmaker_MDFFflexfit_ISOLDE-5_comb-1.cxs > includeMaps true Taking snapshot of stepper: comp002_frame010-5_comb.pdb > select #1/A:509-517,454-460 297 atoms, 297 bonds, 16 residues, 1 model selected > isolde sim start #1.2/A:454-460,509-517 ISOLDE: started sim > view #!1.2/A:505 > select clear > show #6 models > view #!1.2/A:520 > qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep > 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false Overall mean Q-Score: 0.64 > qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep > 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false Overall mean Q-Score: 0.64 > volume #1.1.1.2 level 2.903 > isolde sim stop discardTo start Sim termination reason: None reverting to start ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > volume #1.1.1.2 level 1.895 > select #1/A:509-517,454-460 297 atoms, 297 bonds, 16 residues, 1 model selected > isolde sim start #1.2/A:454-460,509-517 ISOLDE: started sim > qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep > 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false Overall mean Q-Score: 0.64 > view #!1.2/A:507 > volume #1.1.1.2 level 3.816 > qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep > 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false Overall mean Q-Score: 0.64 > volume #1.1.1.2 level 1.995 > qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep > 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false Overall mean Q-Score: 0.64 > qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep > 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false Overall mean Q-Score: 0.64 > volume #1.1.1.2 level 2.793 > isolde sim stop discardTo start Sim termination reason: None reverting to start ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep > 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false Overall mean Q-Score: 0.64 > select #1/A:509-517,454-460 297 atoms, 297 bonds, 16 residues, 1 model selected > isolde sim start #1.2/A:454-460,509-517 ISOLDE: started sim > select clear > hide #6 models > volume #1.1.1.2 level 1.571 > volume #1.1.1.2 level 3.068 > qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep > 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false Overall mean Q-Score: 0.64 > volume #1.1.1.2 level 1.271 > volume #1.1.1.2 level 2.719 > volume #1.1.1.2 level 1.097 > select clear > qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep > 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false Overall mean Q-Score: 0.64 > qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep > 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false Overall mean Q-Score: 0.64 > volume #1.1.1.2 level 1.87 > qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep > 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false Overall mean Q-Score: 0.64 > qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep > 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false Overall mean Q-Score: 0.64 > volume #1.1.1.2 level 3.742 > volume #1.1.1.2 level 2.17 > volume #1.1.1.2 level 1.097 > qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep > 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false Overall mean Q-Score: 0.64 > isolde sim stop Sim termination reason: None ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > select #1/D:509-517,454-460 297 atoms, 297 bonds, 16 residues, 1 model selected > isolde sim start #1.2/D:454-460,509-517 ISOLDE: started sim > select clear > volume #1.1.1.2 level 1.865 > show #5 models > hide #5 models > show #6 models > qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep > 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false Overall mean Q-Score: 0.64 > view #!1.2/D:458 > volume #1.1.1.2 level 0.5757 > select clear > hide #6 models > show #6 models > qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep > 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false Overall mean Q-Score: 0.64 > qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep > 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false Overall mean Q-Score: 0.64 > isolde sim stop Sim termination reason: None ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB standards. ISOLDE: stopped sim > select #1/F:509-517,454-460 297 atoms, 297 bonds, 16 residues, 1 model selected > isolde sim start #1.2/F:454-460,509-517 ISOLDE: started sim > select clear > hide #6 models > volume #1.1.1.2 level 1.255 > show #6 models > hide #6 models > show #5 models > hide #5 models > show #4 models > hide #4 models > qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep > 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false Overall mean Q-Score: 0.64 > volume #1.1.1.2 level 3.294 > volume #1.1.1.2 level 2.129 > volume #1.1.1.2 level 1.304 > show #6 models > select clear > isolde sim resume [Repeated 1 time(s)] > hide #6 models > volume #1.1.1.2 level 3.367 > volume #1.1.1.2 level 1.547 > select clear [Repeated 1 time(s)] > qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep > 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false Overall mean Q-Score: 0.64 > qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep > 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false Overall mean Q-Score: 0.64 > qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep > 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false Overall mean Q-Score: 0.64 > qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep > 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false Overall mean Q-Score: 0.64 > volume #1.1.1.2 level 2.663 > view #!1.2/F:512 > volume #1.1.1.2 level 1.887 > select clear > qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep > 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false Overall mean Q-Score: 0.64 > volume #1.1.1.2 level 2.76 > qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep > 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false Overall mean Q-Score: 0.64 > volume #1.1.1.2 level 1.692 > show #4 models > volume #1.1.1.2 level 3.1 > view #!1.2/F:505 > qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep > 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false Overall mean Q-Score: 0.64 > qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep > 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false Overall mean Q-Score: 0.64 > qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep > 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false Overall mean Q-Score: 0.64 > volume #1.1.1.2 level 1.692 > hide #4 models > qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep > 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false Overall mean Q-Score: 0.64 > qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep > 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false Overall mean Q-Score: 0.64 > qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep > 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false Overall mean Q-Score: 0.64 > volume #1.1.1.2 level 0.9641 > qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep > 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false Overall mean Q-Score: 0.64 > volume #1.1.1.2 level 1.425 > volume #1.1.1.2 level 0.6728 > volume #1.1.1.2 level 1.984 > qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep > 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false Overall mean Q-Score: 0.64 > view #!1.2/F:514 > qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep > 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false Overall mean Q-Score: 0.64 > volume #1.1.1.2 level 1.085 > volume #1.1.1.2 level 0.5029 > view #!1.2/F:515 > qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep > 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false Overall mean Q-Score: 0.64 > qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep > 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false Overall mean Q-Score: 0.64 > isolde sim stop Sim termination reason: None ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > save /Users/tahashahid/Documents/Work/Modelling/LTAg-CGfork_ATP- > Mg/3DVA/cs_P18_J332_component_002/comp_002_frame_010_AF2_matchmaker_MDFFflexfit_ISOLDE-5_comb-1.cxs > includeMaps true Taking snapshot of stepper: comp002_frame010-5_comb.pdb > select #1/S 257 atoms, 272 bonds, 8 residues, 1 model selected > isolde sim start #1.2/S ISOLDE: started sim > volume #1.1.1.2 level 3.028 > show #4 models > volume #1.1.1.2 level 3.322 > select clear > qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep > 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false Overall mean Q-Score: 0.64 > view #!1.2/E:510 > volume #1.1.1.2 level 2.17 > isolde sim stop Sim termination reason: None ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > save /Users/tahashahid/Documents/Work/Modelling/LTAg-CGfork_ATP- > Mg/3DVA/cs_P18_J332_component_002/comp_002_frame_010_AF2_matchmaker_MDFFflexfit_ISOLDE-5_comb-1.cxs > includeMaps true Taking snapshot of stepper: comp002_frame010-5_comb.pdb ——— End of log from Tue Jan 23 03:11:45 2024 ——— opened ChimeraX session > ui tool show ""Volume Viewer"" > view #1/A:800 > hide #4 models > view #1/B:800 > volume #1.1.1.2 level 4.418 > volume #1.1.1.2 level 3.246 > isolde sim start #1.2/C:498 ISOLDE: started sim > qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep > 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false Overall mean Q-Score: 0.64 > view #!1.2/C:498 > qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep > 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false Overall mean Q-Score: 0.64 > qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep > 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false Overall mean Q-Score: 0.64 > isolde sim stop Sim termination reason: None ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > save /Users/tahashahid/Documents/Work/Modelling/LTAg-CGfork_ATP- > Mg/3DVA/cs_P18_J332_component_002/comp_002_frame_010_AF2_matchmaker_MDFFflexfit_ISOLDE-5_comb-1.cxs > includeMaps true Taking snapshot of stepper: comp002_frame010-5_comb.pdb > view #1/C:800 > volume #1.1.1.2 level 5.305 > isolde sim start #1.2/D:498 ISOLDE: started sim > select clear > volume #1.1.1.2 level 3.716 > qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep > 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false Overall mean Q-Score: 0.64 > qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep > 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false Overall mean Q-Score: 0.64 > qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep > 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false Overall mean Q-Score: 0.64 > view #!1.2/D:498 > volume #1.1.1.2 level 4.977 > qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep > 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false Overall mean Q-Score: 0.64 > volume #1.1.1.2 level 2.959 > qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep > 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false Overall mean Q-Score: 0.64 > qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep > 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false Overall mean Q-Score: 0.64 > isolde sim pause > isolde sim stop Sim termination reason: None ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB standards. ISOLDE: stopped sim > view #1/D:800 > volume #1.1.1.2 level 2.822 > save /Users/tahashahid/Documents/Work/Modelling/LTAg-CGfork_ATP- > Mg/3DVA/cs_P18_J332_component_002/comp_002_frame_010_AF2_matchmaker_MDFFflexfit_ISOLDE-5_comb-1.cxs > includeMaps true Taking snapshot of stepper: comp002_frame010-5_comb.pdb > view #!1.2/E:498 > isolde sim start #1.2/E:498 ISOLDE: started sim > isolde sim stop discardTo start Sim termination reason: None reverting to start ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > view #1/E:800 > isolde sim start #1.2/F:498 ISOLDE: started sim > isolde sim stop discardTo start Sim termination reason: None reverting to start ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > save /Users/tahashahid/Documents/Work/Modelling/LTAg-CGfork_ATP- > Mg/3DVA/cs_P18_J332_component_002/comp_002_frame_010_AF2_matchmaker_MDFFflexfit_ISOLDE-5_comb-1.cxs > includeMaps true Taking snapshot of stepper: comp002_frame010-5_comb.pdb ——— End of log from Tue Jan 23 18:55:59 2024 ——— opened ChimeraX session > select clear > select add #4 36068 atoms, 36447 bonds, 2191 residues, 1 model selected > ui tool show ""Change Chain IDs"" > select subtract #4 Nothing selected > close #6 > open /Users/tahashahid/Documents/Work/Modelling/LTAg-CGfork_ATP- > Mg/3DVA/cs_P18_J332_component_001/comp001_frame010-4_comb-2_Rsr/comp001_frame010-4_comb-2_modified_real_space_refined_000_dssp.cif Summary of feedback from opening /Users/tahashahid/Documents/Work/Modelling/LTAg-CGfork_ATP- Mg/3DVA/cs_P18_J332_component_001/comp001_frame010-4_comb-2_Rsr/comp001_frame010-4_comb-2_modified_real_space_refined_000_dssp.cif --- warnings | Unknown polymer entity '1' near line 194 Unknown polymer entity '2' near line 35954 Atom H is not in the residue template for LYS /A:266 Atom H is not in the residue template for LYS /B:266 Atom H is not in the residue template for LYS /C:266 Atom H is not in the residue template for LYS /D:266 Atom H is not in the residue template for LYS /E:266 1 messages similar to the above omitted Missing or incomplete sequence information. Inferred polymer connectivity. Chain information for comp001_frame010-4_comb-2_modified_real_space_refined_000_dssp.cif #2 --- Chain | Description A B C D E F | No description available S | No description available > select clear [Repeated 1 time(s)] > select add #2 36017 atoms, 36398 bonds, 2186 residues, 1 model selected > color sel bychain > color sel byhetero > style sel stick Changed 36017 atom styles > hide HC > isolde start > set selectionWidth 4 Done loading forcefield > isolde set simFidelityMode Medium/Medium ISOLDE: setting sim fidelity mode to Medium/Medium nonbonded_cutoff_distance = 0.900000 use_gbsa = True gbsa_cutoff = 1.100000 > ui tool show ""Ramachandran Plot"" > ui tool show ""Model-map Q-Score"" > ui tool show ""Volume Viewer"" > hide #2 models > select #1/S 257 atoms, 272 bonds, 8 residues, 1 model selected > isolde sim start #1.2/S ISOLDE: started sim > select clear > show #5 models > hide #5 models > show #2 models > hide #2 models > select clear > show #2 models > hide #2 models > show #5 models > select #1/S 257 atoms, 272 bonds, 8 residues, 1 model selected > hide #5 models > show #2 models > select clear > isolde sim stop Sim termination reason: None ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > select #1/S 257 atoms, 272 bonds, 8 residues, 1 model selected > select #1/B:426-433,473-474,527-529,800/C:418,540,498 291 atoms, 288 bonds, 17 residues, 1 model selected > isolde sim start #1.2/B:426-433,473-474,527-529,800/C:418,498,540 Loading residue template for ATP from internal database ISOLDE: started sim > hide #2 models > volume #1.1.1.2 level 4.376 > select clear > qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep > 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false Overall mean Q-Score: 0.64 > view #!1.2/C:540 > qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep > 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false Overall mean Q-Score: 0.64 > view #!1.2/C:540 > volume #1.1.1.2 level 2.695 > show #2 models > isolde sim stop Sim termination reason: None ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > select #1/C:426-433,473-474,527-529,800/D:418,540,498 291 atoms, 288 bonds, 17 residues, 1 model selected > isolde sim start #1.2/C:426-433,473-474,527-529,800/D:418,498,540 ISOLDE: started sim > qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep > 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false Overall mean Q-Score: 0.64 > select clear > hide #2 models > qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep > 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false Overall mean Q-Score: 0.64 > volume #1.1.1.2 level 5.619 > qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep > 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false Overall mean Q-Score: 0.64 > view #!1.2/C:425 > qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep > 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false Overall mean Q-Score: 0.64 > show #5 models > volume #1.1.1.2 level 2.362 > hide #5 models > show #2 models > volume #1.1.1.2 level 5.902 > hide #2 models > qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep > 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false Overall mean Q-Score: 0.64 > view #!1.2/C:433 > qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep > 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false Overall mean Q-Score: 0.64 > volume #1.1.1.2 level 2.952 > volume #1.1.1.2 level 5.26 > select clear [Repeated 1 time(s)] > show #5 models > hide #5 models > show #2 models > volume #1.1.1.2 level 2.567 > select clear > hide #2 models > qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep > 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false Overall mean Q-Score: 0.64 > view #!1.2/C:428 > qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep > 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false Overall mean Q-Score: 0.64 > volume #1.1.1.2 level 4.901 > volume #1.1.1.2 level 3.439 > qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep > 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false Overall mean Q-Score: 0.64 > view #!1.2/C:430 > view #!1.2/D:498 > show #2 models > select clear > isolde sim stop Sim termination reason: None ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB standards. ISOLDE: stopped sim > isolde sim start #1.2/B:471 ISOLDE: started sim > select clear > hide #2 models > isolde sim stop Sim termination reason: None ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > select #1/D:426-433,473-474,527-529,800/E:418,540,498 291 atoms, 288 bonds, 17 residues, 1 model selected > isolde sim start #1.2/D:426-433,473-474,527-529,800/E:418,498,540 ISOLDE: started sim > show #2 models > view #!1.2/E:540 > qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep > 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false Overall mean Q-Score: 0.64 > view #!1.2/E:540 > hide #2 models > volume #1.1.1.2 level 2.219 > qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep > 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false Overall mean Q-Score: 0.64 > show #5 models > hide #5 models > show #2 models > hide #2 models > volume #1.1.1.2 level 5.523 > show #2 models > volume #1.1.1.2 level 2.727 > volume #1.1.1.2 level 5.549 > volume #1.1.1.2 level 4.507 > select clear [Repeated 3 time(s)] > view #!1.2/D:430 [Repeated 1 time(s)] > qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep > 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false Overall mean Q-Score: 0.64 > qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep > 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false Overall mean Q-Score: 0.64 > view #!1.2/D:432 > view #!1.2/D:430 > qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep > 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false Overall mean Q-Score: 0.64 > hide #2 models > volume #1.1.1.2 level 2.6 > isolde sim pause > isolde sim resume > isolde sim pause > view #!1.2/E:498 > isolde sim stop Sim termination reason: None ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > select #1/E:426-433,473-474,527-529,800/F:418,540,498 291 atoms, 288 bonds, 17 residues, 1 model selected > isolde sim start #1.2/E:426-433,473-474,527-529,800/F:418,498,540 ISOLDE: started sim > show #2 models > qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep > 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false Overall mean Q-Score: 0.64 > view #!1.2/F:499 > volume #1.1.1.2 level 5.216 > volume #1.1.1.2 level 2.237 > volume #1.1.1.2 level 5.07 > volume #1.1.1.2 level 3.23 > hide #2 models > show #2 models > isolde sim stop Sim termination reason: None ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > isolde sim start #1.2/E:533 ISOLDE: started sim > select clear > isolde sim stop Sim termination reason: None ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > select clear > select #1/E,D:509-517,454-460 594 atoms, 594 bonds, 32 residues, 1 model selected > isolde sim start #1.2/D-E:454-460,509-517 ISOLDE: started sim > view #!1.2/E:514 > qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep > 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false Overall mean Q-Score: 0.64 > volume #1.1.1.2 level 2.217 > qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep > 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false Overall mean Q-Score: 0.64 > qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep > 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false Overall mean Q-Score: 0.64 > volume #1.1.1.2 level 3.645 > volume #1.1.1.2 level 1.723 > select clear > hide #2 models > show #2 models > select clear > qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep > 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false Overall mean Q-Score: 0.64 > hide #2 models > volume #1.1.1.2 level 1.36 > qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep > 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false Overall mean Q-Score: 0.64 > qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep > 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false Overall mean Q-Score: 0.64 > volume #1.1.1.2 level 4.814 > volume #1.1.1.2 level 1.412 > view #!1.2/E:517 > qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep > 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false Overall mean Q-Score: 0.64 > select clear > show #2 models > qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep > 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false Overall mean Q-Score: 0.64 > volume #1.1.1.2 level 4.97 > view #!1.2/E:349 [Repeated 1 time(s)] > qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep > 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false Overall mean Q-Score: 0.64 > view #!1.2/E:349 > volume #1.1.1.2 level 2.321 > hide #2 models > select clear > volume #1.1.1.2 level 4.866 > volume #1.1.1.2 level 1.749 > volume #1.1.1.2 level 5.23 > qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep > 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false Overall mean Q-Score: 0.64 > volume #1.1.1.2 level 2.477 > volume #1.1.1.2 level 0.7884 > volume #1.1.1.2 level 5.931 > volume #1.1.1.2 level 1.568 > volume #1.1.1.2 level 4.139 > volume #1.1.1.2 level 1.438 > view #!1.2/E:517 > qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep > 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false Overall mean Q-Score: 0.64 > volume #1.1.1.2 level 3.853 > volume #1.1.1.2 level 1.204 > volume #1.1.1.2 level 4.347 > volume #1.1.1.2 level 1.62 > qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep > 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false Overall mean Q-Score: 0.64 > view #!1.2/E:517 > view #!1.2/E:458 [Repeated 1 time(s)] > qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep > 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false Overall mean Q-Score: 0.64 > volume #1.1.1.2 level 4.373 > volume #1.1.1.2 level 2.217 > volume #1.1.1.2 level 0.9702 > select clear > volume #1.1.1.2 level 2.892 > volume #1.1.1.2 level 1.1 > view #!1.2/E:456 > view #!1.2/D:456 > qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep > 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false Overall mean Q-Score: 0.64 > volume #1.1.1.2 level 3.801 > volume #1.1.1.2 level 1.542 > view #!1.2/E:456 > qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep > 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false Overall mean Q-Score: 0.64 > qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep > 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false Overall mean Q-Score: 0.64 > qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep > 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false Overall mean Q-Score: 0.64 > view #!1.2/D:349 > qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep > 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false Overall mean Q-Score: 0.64 > show #2 models > view #!1.2/D:514 > qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep > 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false Overall mean Q-Score: 0.64 > qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep > 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false Overall mean Q-Score: 0.64 > volume #1.1.1.2 level 4.996 > volume #1.1.1.2 level 2.113 > hide #2 models > show #2 models > select clear > qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep > 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false Overall mean Q-Score: 0.64 > view #!1.2/D:512 > qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep > 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false Overall mean Q-Score: 0.64 > view #!1.2/D:454 [Repeated 1 time(s)] > qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep > 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false Overall mean Q-Score: 0.64 > view #!1.2/D:454 > isolde sim pause > isolde sim resume > view #!1.2/D:517 > select clear > view #!1.2/D:517 > qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep > 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false Overall mean Q-Score: 0.64 > isolde sim stop Sim termination reason: None ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > select #1/C,B:509-517,454-460 594 atoms, 594 bonds, 32 residues, 1 model selected > isolde sim start #1.2/B-C:454-460,509-517 ISOLDE: started sim > view #!1.2/C:513 > qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep > 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false Overall mean Q-Score: 0.64 > view #!1.2/C:514 > hide #2 models > select clear > qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep > 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false Overall mean Q-Score: 0.64 > view #!1.2/C:456 > qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep > 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false Overall mean Q-Score: 0.64 > volume #1.1.1.2 level 1.1 > qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep > 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false Overall mean Q-Score: 0.64 > volume #1.1.1.2 level 3.646 > show #2 models > qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep > 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false Overall mean Q-Score: 0.64 > volume #1.1.1.2 level 2.009 > volume #1.1.1.2 level 1.308 > volume #1.1.1.2 level 2.944 > volume #1.1.1.2 level 1.412 > select clear > hide #2 models > view #!1.2/C:515 > qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep > 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false Overall mean Q-Score: 0.64 > select clear [Repeated 1 time(s)] > volume #1.1.1.2 level 4.633 > volume #1.1.1.2 level 1.723 > view #!1.2/C:520 > qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep > 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false Overall mean Q-Score: 0.64 > select clear > qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep > 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false Overall mean Q-Score: 0.64 > qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep > 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false Overall mean Q-Score: 0.64 > isolde sim stop Sim termination reason: None ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > save /Users/tahashahid/Documents/Work/Modelling/LTAg-CGfork_ATP- > Mg/3DVA/cs_P18_J332_component_002/comp_002_frame_010_AF2_matchmaker_MDFFflexfit_ISOLDE-5_comb-2.cxs > includeMaps true Taking snapshot of stepper: comp002_frame010-5_comb.pdb > view #!1.2/C:265 > select #1/A-F:265 84 atoms, 78 bonds, 6 residues, 1 model selected > delete atoms (#!1.2 & sel) > delete bonds (#!1.2 & sel) > select #1/A-F:266 132 atoms, 126 bonds, 6 residues, 1 model selected > qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep > 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false Overall mean Q-Score: 0.64 > select #1/A-F:266 132 atoms, 126 bonds, 6 residues, 1 model selected > isolde sim start #1.2/A-F:266 ISOLDE: started sim > qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep > 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false Overall mean Q-Score: 0.64 > view #!1.2/B:266 > qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep > 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false Overall mean Q-Score: 0.64 > view #!1.2/C:266 > view #!1.2/D:266 > view #!1.2/E:266 > qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep > 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false Overall mean Q-Score: 0.64 > view #!1.2/F:266 > qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep > 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false Overall mean Q-Score: 0.64 > isolde sim stop Sim termination reason: None ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > save /Users/tahashahid/Documents/Work/Modelling/LTAg-CGfork_ATP- > Mg/3DVA/cs_P18_J332_component_002/comp_002_frame_010_AF2_matchmaker_MDFFflexfit_ISOLDE-5_comb-2.cxs > includeMaps true Taking snapshot of stepper: comp002_frame010-5_comb.pdb > clipper isolate #1 maskRadius 16 > select clear > volume #1.1.1.2 level 3.831 > hide ~@CA > select clear > hide #!1.2 models > show #!1.2 models > show ~HC > select #1/C,B:509-517,454-460 594 atoms, 594 bonds, 32 residues, 1 model selected > isolde sim start #1.2/B-C:454-460,509-517 ISOLDE: started sim > view #!1.2/C:512 > show #2 models > hide #2 models > volume #1.1.1.2 level 2.013 > volume #1.1.1.2 level 1.337 > volume #1.1.1.2 level 2.61 > qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep > 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false Overall mean Q-Score: 0.64 > qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep > 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false Overall mean Q-Score: 0.64 > qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep > 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false Overall mean Q-Score: 0.64 > qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep > 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false Overall mean Q-Score: 0.64 > qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep > 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false Overall mean Q-Score: 0.64 > select clear > show #2 models > volume #1.1.1.2 level 0.8958 > hide #2 models > volume #1.1.1.2 level 2.662 > volume #1.1.1.2 level 1.727 > qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep > 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false Overall mean Q-Score: 0.65 > view #!1.2/B:512 > show #2 models > hide #2 models > qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep > 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false Overall mean Q-Score: 0.64 > view #!1.2/B:511 > qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep > 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false Overall mean Q-Score: 0.64 > volume #1.1.1.2 level 0.5321 > show #2 models > hide #2 models > show #2 models > volume #1.1.1.2 level 2.87 > volume #1.1.1.2 level 0.8958 > volume #1.1.1.2 level 3.364 > volume #1.1.1.2 level 1.259 > select clear > view #!1.2/B:456 > qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep > 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false Overall mean Q-Score: 0.64 > view #!1.2/B:456 [Repeated 1 time(s)] > qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep > 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false Overall mean Q-Score: 0.64 > qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep > 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false Overall mean Q-Score: 0.65 > qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep > 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false Overall mean Q-Score: 0.64 > qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep > 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false Overall mean Q-Score: 0.64 > view #!1.2/B:456 > hide #2 models > qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep > 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false Overall mean Q-Score: 0.65 > volume #1.1.1.2 level 3.286 > view #!1.2/B:489 > qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep > 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false Overall mean Q-Score: 0.64 > qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep > 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false Overall mean Q-Score: 0.64 > volume #1.1.1.2 level 1.156 > volume #1.1.1.2 level 2.818 > isolde sim pause > isolde sim stop Sim termination reason: None ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: Corrected atom nomenclature of 2 residues in model #1.2 to IUPAC-IUB standards. ISOLDE: stopped sim > isolde sim start #1.2/D:473 ISOLDE: started sim > select clear > isolde sim pause > isolde sim stop Sim termination reason: None ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > select #1/A:509-517,454-460 297 atoms, 297 bonds, 16 residues, 1 model selected > isolde sim start #1.2/A:454-460,509-517 ISOLDE: started sim > view #!1.2/A:513 > volume #1.1.1.2 level 1.538 > view #!1.2/A:455 > qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep > 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false Overall mean Q-Score: 0.65 > show #5 models > select clear > volume #1.1.1.2 level 3.445 > volume #1.1.1.2 level 1.982 > view #!1.2/A:457 > qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep > 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false Overall mean Q-Score: 0.65 > qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep > 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false Overall mean Q-Score: 0.65 > volume #1.1.1.2 level 0.5448 > qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep > 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false Overall mean Q-Score: 0.65 > view #!1.2/A:514 > qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep > 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false Overall mean Q-Score: 0.65 > volume #1.1.1.2 level 2.295 > view #!1.2/A:506 [Repeated 1 time(s)] > qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep > 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false Overall mean Q-Score: 0.65 > volume #1.1.1.2 level 0.4402 > select clear > volume #1.1.1.2 level 3.079 > hide #5 models > select clear > isolde sim pause > isolde sim resume > isolde sim pause > isolde sim resume > isolde sim pause > isolde sim stop Sim termination reason: None ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: Corrected atom nomenclature of 2 residues in model #1.2 to IUPAC-IUB standards. ISOLDE: stopped sim > save /Users/tahashahid/Documents/Work/Modelling/LTAg-CGfork_ATP- > Mg/3DVA/cs_P18_J332_component_002/comp_002_frame_010_AF2_matchmaker_MDFFflexfit_ISOLDE-5_comb-2.cxs > includeMaps true Taking snapshot of stepper: comp002_frame010-5_comb.pdb > view #1/F:509-517,454-460 > select #1/F:509-517,454-460 297 atoms, 297 bonds, 16 residues, 1 model selected > isolde sim start #1.2/F:454-460,509-517 ISOLDE: started sim > select clear > volume #1.1.1.2 level 1.376 > qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep > 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false Overall mean Q-Score: 0.65 > qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep > 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false Overall mean Q-Score: 0.65 > isolde sim stop discardTo start Sim termination reason: None reverting to start ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > save /Users/tahashahid/Documents/Work/Modelling/LTAg-CGfork_ATP- > Mg/3DVA/cs_P18_J332_component_002/comp_002_frame_010_AF2_matchmaker_MDFFflexfit_ISOLDE-5_comb-2.cxs > includeMaps true Taking snapshot of stepper: comp002_frame010-5_comb.pdb > select #1/F:509-517,454-460 297 atoms, 297 bonds, 16 residues, 1 model selected > isolde sim start #1.2/F:454-460,509-517 ISOLDE: started sim > select clear [Repeated 1 time(s)] > volume #1.1.1.2 level 1.198 > show #5 models > hide #5 models > show #2 models > qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep > 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false Overall mean Q-Score: 0.64 > view #!1.2/F:456 > hide #2 models > qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep > 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false Overall mean Q-Score: 0.64 > select clear > qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep > 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false Overall mean Q-Score: 0.64 > qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep > 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false Overall mean Q-Score: 0.65 > qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep > 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false Overall mean Q-Score: 0.64 > view #!1.2/F:456 [Repeated 1 time(s)] > qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep > 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false Overall mean Q-Score: 0.64 > qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep > 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false Overall mean Q-Score: 0.64 > qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep > 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false Overall mean Q-Score: 0.64 > qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep > 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false Overall mean Q-Score: 0.64 > qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep > 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false Overall mean Q-Score: 0.64 > view #!1.2/F:456 > volume #1.1.1.2 level 3.893 > select clear > view #!1.2/F:456 > volume #1.1.1.2 level 1.173 > show #5 models > hide #5 models > hide #1.3 models > show #2 models > show #1.3 models > select clear > qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep > 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false Overall mean Q-Score: 0.65 > view #!1.2/F:510 > qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep > 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false Overall mean Q-Score: 0.65 > select clear > volume #1.1.1.2 level 2.291 > volume #1.1.1.2 level 1.224 > select clear > view #!1.2/F:520 > qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep > 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false Overall mean Q-Score: 0.64 > volume #1.1.1.2 level 3.308 > view #!1.2/F:507 > qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep > 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false Overall mean Q-Score: 0.64 > qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep > 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false Overall mean Q-Score: 0.65 > hide #2 models > qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep > 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false Overall mean Q-Score: 0.65 > view #!1.2/F:507 > view #!1.2/F:505 > qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep > 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false Overall mean Q-Score: 0.65 > view #!1.2/F:505 > qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep > 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false Overall mean Q-Score: 0.65 > volume #1.1.1.2 level 1.453 > volume #1.1.1.2 level 3.003 > select clear > isolde sim stop Sim termination reason: None ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB standards. ISOLDE: stopped sim > select #1/F:426-433,473-474,527-529,800/A:418,540,498 291 atoms, 288 bonds, 17 residues, 1 model selected > isolde sim start #1.2/A:418,498,540/F:426-433,473-474,527-529,800 ISOLDE: started sim > show #5 models > hide #5 models > show #2 models > select clear > hide #2 models > volume #1.1.1.2 level 4.765 > open /Users/tahashahid/Documents/Work/Modelling/LTAg-CGfork_ATP- > Mg/3DVA/cs_P18_J332_component_000/comp000_frame010_MDFF_ISOLDE-5_comb-5_Rsr/comp000_frame010_5_comb-5_modified_real_space_refined_000_dssp.cif Summary of feedback from opening /Users/tahashahid/Documents/Work/Modelling/LTAg-CGfork_ATP- Mg/3DVA/cs_P18_J332_component_000/comp000_frame010_MDFF_ISOLDE-5_comb-5_Rsr/comp000_frame010_5_comb-5_modified_real_space_refined_000_dssp.cif --- warnings | Unknown polymer entity '1' near line 194 Unknown polymer entity '2' near line 35954 Atom H is not in the residue template for LYS /A:266 Atom H is not in the residue template for LYS /B:266 Atom H is not in the residue template for LYS /C:266 Atom H is not in the residue template for LYS /D:266 Atom H is not in the residue template for LYS /E:266 1 messages similar to the above omitted Missing or incomplete sequence information. Inferred polymer connectivity. Chain information for comp000_frame010_5_comb-5_modified_real_space_refined_000_dssp.cif #3 --- Chain | Description A B C D E F | No description available S | No description available > select clear > hide #3 models > select add #3 36017 atoms, 36398 bonds, 2186 residues, 1 model selected > show #3 models > color sel bychain > color sel byhetero > style sel stick Changed 36017 atom styles > hide HC > volume #1.1.1.2 level 2.881 > select clear > view #!1.2/F:474 > qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep > 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false Overall mean Q-Score: 0.65 > qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep > 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false Overall mean Q-Score: 0.65 > hide #3 models > show #2 models > hide #2 models > isolde pepflip #1.2/F:474 > select clear > isolde pepflip #1.2/F:474 > show #3 models > show #2 models > hide #2 models > hide #3 models > show #3 models > view #!1.2/F:428 > volume #1.1.1.2 level 1.902 > hide #3 models > volume #1.1.1.2 level 4.398 > volume #1.1.1.2 level 2.905 > volume #1.1.1.2 level 4.374 > volume #1.1.1.2 level 3.762 > show #3 models > hide #3 models > show #2 models > hide #2 models > volume #1.1.1.2 level 2.783 > show #2 models > volume #1.1.1.2 level 3.884 > qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep > 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false Overall mean Q-Score: 0.65 > hide #2 models > volume #1.1.1.2 level 3.297 > select clear [Repeated 2 time(s)] > show #2 models > show #3 models > select clear > hide #3 models > hide #2 models > show #2 models > hide #2 models > select clear > show #2 models > show #3 models > hide #3 models > hide #2 models > select clear > show #2 models > hide #2 models > volume #1.1.1.2 level 1.461 > volume #1.1.1.2 level 2.832 > qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep > 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false Overall mean Q-Score: 0.65 > view #!1.2/A:535 > volume #1.1.1.2 level 0.9228 > volume #1.1.1.2 level 2.098 > qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep > 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false Overall mean Q-Score: 0.65 > select clear > qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep > 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false Overall mean Q-Score: 0.65 > qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep > 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false Overall mean Q-Score: 0.65 > view #!1.2/A:535 > volume #1.1.1.2 level 3.713 > volume #1.1.1.2 level 1.633 > select clear > view #!1.2/A:416 [Repeated 2 time(s)] > qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep > 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false Overall mean Q-Score: 0.65 > qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep > 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false Overall mean Q-Score: 0.65 > volume #1.1.1.2 level 3.223 > view #!1.2/A:418 > isolde sim pause > isolde sim resume > volume #1.1.1.2 level 1.388 > show #2 models > hide #2 models > qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep > 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false Overall mean Q-Score: 0.65 > view #!1.2/A:535 > select clear > qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep > 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false Overall mean Q-Score: 0.65 > qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep > 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false Overall mean Q-Score: 0.65 > view #!1.2/A:535 [Repeated 1 time(s)] > qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep > 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false Overall mean Q-Score: 0.65 > qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep > 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false Overall mean Q-Score: 0.65 > select clear > isolde sim pause > isolde sim stop Sim termination reason: None ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: Corrected atom nomenclature of 2 residues in model #1.2 to IUPAC-IUB standards. ISOLDE: stopped sim > select #1/A:426-433,473-474,527-529,800/B:418,540,498 291 atoms, 288 bonds, 17 residues, 1 model selected > isolde sim start #1.2/A:426-433,473-474,527-529,800/B:418,498,540 ISOLDE: started sim > volume #1.1.1.2 level 3.604 > show #2 models > hide #2 models > volume #1.1.1.2 level 1.886 > show #2 models > hide #2 models > show #2 models > volume #1.1.1.2 level 4.476 > volume #1.1.1.2 level 3.53 > view #!1.2/A:430 > qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep > 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false Overall mean Q-Score: 0.65 > view #!1.2/A:430 > volume #1.1.1.2 level 2.459 > hide #2 models > volume #1.1.1.2 level 0.5161 > volume #1.1.1.2 level 1.985 > show #2 models > volume #1.1.1.2 level 4.7 > volume #1.1.1.2 level 3.43 > qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep > 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false Overall mean Q-Score: 0.65 > qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep > 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false Overall mean Q-Score: 0.65 > volume #1.1.1.2 level 1.487 > hide #2 models > show #2 models > select clear > qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep > 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false Overall mean Q-Score: 0.65 > view #!1.2/A:474 > hide #2 models > show #2 models > hide #2 models > show #3 models > hide #3 models > qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep > 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false Overall mean Q-Score: 0.65 > volume #1.1.1.2 level 4.252 > volume #1.1.1.2 level 0.8897 > volume #1.1.1.2 level 1.587 > show #2 models > hide #2 models > show #3 models > hide #3 models > qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep > 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false Overall mean Q-Score: 0.65 > qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep > 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false Overall mean Q-Score: 0.65 > volume #1.1.1.1 level 0.3377 > qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep > 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false Overall mean Q-Score: 0.65 > view #!1.2/A:548 > qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep > 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false Overall mean Q-Score: 0.65 > select clear > view #!1.2/A:548 [Repeated 1 time(s)] > qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep > 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false Overall mean Q-Score: 0.65 > view #!1.2/A:530 > view #!1.2/A:529 > qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep > 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false Overall mean Q-Score: 0.65 > select clear [Repeated 1 time(s)] > isolde sim pause > isolde sim resume > isolde sim stop Sim termination reason: None ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: Corrected atom nomenclature of 3 residues in model #1.2 to IUPAC-IUB standards. ISOLDE: stopped sim > volume #1.1.1.2 level 3.657 > show #2 models > hide #2 models > show #2 models > show #3 models > volume #1.1.1.2 level 1.845 > isolde sim start #1.2/B:480 ISOLDE: started sim > select clear > hide #3 models > hide #2 models > volume #1.1.1.2 level 4.592 > isolde pepflip #1.2/B:480 > volume #1.1.1.2 level 2.351 > volume #1.1.1.2 level 1.652 > isolde pepflip #1.2/B:479 > isolde pepflip #1.2/B:480 > volume #1.1.1.2 level 3.074 > isolde sim stop discardTo start Sim termination reason: None reverting to start ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > select #1/B:475-490 210 atoms, 210 bonds, 16 residues, 1 model selected > isolde sim start #1.2/B:475-490 ISOLDE: started sim > select clear [Repeated 1 time(s)] > isolde pepflip #1.2/B:480 > volume #1.1.1.2 level 1.68 > volume #1.1.1.2 level 1.132 > qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep > 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false Overall mean Q-Score: 0.65 > view #!1.2/B:483 [Repeated 1 time(s)] > qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep > 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false Overall mean Q-Score: 0.65 > qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep > 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false Overall mean Q-Score: 0.65 > view #!1.2/B:483 > show #2 models > hide #2 models > show #3 models > hide #3 models > volume #1.1.1.2 level 3.422 > volume #1.1.1.2 level 1.231 > volume #1.1.1.2 level 3.323 > volume #1.1.1.2 level 1.754 > volume #1.1.1.2 level 3.846 > volume #1.1.1.2 level 1.754 > volume #1.1.1.2 level 0.7584 > qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep > 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false Overall mean Q-Score: 0.65 > view #!1.2/B:483 [Repeated 3 time(s)] > qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep > 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false Overall mean Q-Score: 0.65 > view #!1.2/B:483 > qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep > 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false Overall mean Q-Score: 0.65 > volume #1.1.1.2 level 3.298 > isolde sim pause > isolde sim resume > isolde sim pause > isolde sim resume > isolde sim pause > isolde sim stop Sim termination reason: None ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB standards. ISOLDE: stopped sim > select clear > isolde sim start #1.2/E:427 ISOLDE: started sim > isolde sim stop Sim termination reason: None ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > isolde sim start #1.2/F:427 ISOLDE: started sim > isolde sim pause > isolde sim resume > isolde sim pause > isolde sim resume > isolde sim pause > isolde sim stop Sim termination reason: None ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > save /Users/tahashahid/Documents/Work/Modelling/LTAg-CGfork_ATP- > Mg/3DVA/cs_P18_J332_component_002/comp_002_frame_010_AF2_matchmaker_MDFFflexfit_ISOLDE-5_comb-2.cxs > includeMaps true Taking snapshot of stepper: comp002_frame010-5_comb.pdb ——— End of log from Tue Apr 30 01:03:15 2024 ——— opened ChimeraX session > isode start Unknown command: isode start > isolde start > set selectionWidth 4 Done loading forcefield > isolde set simFidelityMode Medium/Medium ISOLDE: setting sim fidelity mode to Medium/Medium nonbonded_cutoff_distance = 0.900000 use_gbsa = True gbsa_cutoff = 1.100000 > ui tool show ""Volume Viewer"" > ui tool show ""Ramachandran Plot"" > ui tool show ""Model-map Q-Score"" > qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep > 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false Overall mean Q-Score: 0.65 > view #!1.2/S:8 > select #1.2/S 257 atoms, 272 bonds, 8 residues, 1 model selected > isolde sim start #1.2/S ISOLDE: started sim > select clear > isolde stepto #1.2/D:456 > volume #1.1.1.2 level 1.706 > qscore #1.2 toVolume #1.1.1.2 useGui false pointsPerShell 8 shellRadiusStep > 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false Overall mean Q-Score: 0.65 > isolde sim stop Sim termination reason: None ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > select #1/S 257 atoms, 272 bonds, 8 residues, 1 model selected > select #1/S 257 atoms, 272 bonds, 8 residues, 1 model selected > isolde sim start #1.2/S ISOLDE: started sim > select #1/S:7 32 atoms, 33 bonds, 1 residue, 1 model selected > isolde sim stop Sim termination reason: None ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > save /Users/tahashahid/Documents/Work/Modelling/LTAg-CGfork_ATP- > Mg/3DVA/cs_P18_J332_component_002/comp_002_frame_010_AF2_matchmaker_MDFFflexfit_ISOLDE-5_comb-3.cxs > includeMaps true Taking snapshot of stepper: comp002_frame010-5_comb.pdb ——— End of log from Thu May 2 23:31:55 2024 ——— opened ChimeraX session OpenGL version: 4.1 Metal - 88 OpenGL renderer: Apple M3 Pro OpenGL vendor: Apple Python: 3.11.2 Locale: UTF-8 Qt version: PyQt6 6.3.1, Qt 6.3.1 Qt runtime version: 6.3.2 Qt platform: cocoa Hardware: Hardware Overview: Model Name: MacBook Pro Model Identifier: Mac15,7 Model Number: MRW13B/A Chip: Apple M3 Pro Total Number of Cores: 12 (6 performance and 6 efficiency) Memory: 18 GB System Firmware Version: 10151.101.3 OS Loader Version: 10151.101.3 Software: System Software Overview: System Version: macOS 14.4.1 (23E224) Kernel Version: Darwin 23.4.0 Time since boot: 14 days, 23 hours, 5 minutes Graphics/Displays: Apple M3 Pro: Chipset Model: Apple M3 Pro Type: GPU Bus: Built-In Total Number of Cores: 18 Vendor: Apple (0x106b) Metal Support: Metal 3 Displays: Color LCD: Display Type: Built-in Liquid Retina XDR Display Resolution: 3456 x 2234 Retina Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: Yes Connection Type: Internal Installed Packages: alabaster: 0.7.16 appdirs: 1.4.4 appnope: 0.1.3 asttokens: 2.4.1 Babel: 2.14.0 backcall: 0.2.0 beautifulsoup4: 4.11.2 blockdiag: 3.0.0 blosc2: 2.0.0 build: 0.10.0 certifi: 2022.12.7 cftime: 1.6.3 charset-normalizer: 3.3.2 ChimeraX-AddCharge: 1.5.13 ChimeraX-AddH: 2.2.5 ChimeraX-AlignmentAlgorithms: 2.0.1 ChimeraX-AlignmentHdrs: 3.4.1 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 2.12.2 ChimeraX-AlphaFold: 1.0 ChimeraX-AltlocExplorer: 1.1.1 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.49.1 ChimeraX-AtomicLibrary: 12.1.5 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.3.2 ChimeraX-BasicActions: 1.1.2 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 2.1.2 ChimeraX-BondRot: 2.0.4 ChimeraX-BugReporter: 1.0.1 ChimeraX-BuildStructure: 2.10.5 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.2.2 ChimeraX-ButtonPanel: 1.0.1 ChimeraX-CageBuilder: 1.0.1 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.3.2 ChimeraX-ChangeChains: 1.1 ChimeraX-CheckWaters: 1.3.2 ChimeraX-ChemGroup: 2.0.1 ChimeraX-Clashes: 2.2.4 ChimeraX-Clipper: 0.22.4 ChimeraX-ColorActions: 1.0.3 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.5 ChimeraX-CommandLine: 1.2.5 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.7.1 ChimeraX-CoreFormats: 1.2 ChimeraX-coulombic: 1.4.2 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0.1 ChimeraX-DataFormats: 1.2.3 ChimeraX-Dicom: 1.2 ChimeraX-DistMonitor: 1.4 ChimeraX-DockPrep: 1.1.3 ChimeraX-Dssp: 2.0 ChimeraX-EMDB-SFF: 1.0 ChimeraX-ESMFold: 1.0 ChimeraX-FileHistory: 1.0.1 ChimeraX-FunctionKey: 1.0.1 ChimeraX-Geometry: 1.3 ChimeraX-gltf: 1.0 ChimeraX-Graphics: 1.1.1 ChimeraX-Hbonds: 2.4 ChimeraX-Help: 1.2.2 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.1 ChimeraX-ImageFormats: 1.2 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0.1 ChimeraX-ISOLDE: 1.7.1 ChimeraX-ItemsInspection: 1.0.1 ChimeraX-IUPAC: 1.0 ChimeraX-Label: 1.1.8 ChimeraX-ListInfo: 1.2.2 ChimeraX-Log: 1.1.6 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.9.1 ChimeraX-Map: 1.1.4 ChimeraX-MapData: 2.0 ChimeraX-MapEraser: 1.0.1 ChimeraX-MapFilter: 2.0.1 ChimeraX-MapFit: 2.0 ChimeraX-MapSeries: 2.1.1 ChimeraX-Markers: 1.0.1 ChimeraX-Mask: 1.0.2 ChimeraX-MatchMaker: 2.1.2 ChimeraX-MCopy: 1.0 ChimeraX-MDcrds: 2.6.1 ChimeraX-MedicalToolbar: 1.0.2 ChimeraX-Meeting: 1.0.1 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.12.1 ChimeraX-MMTF: 2.2 ChimeraX-Modeller: 1.5.14 ChimeraX-ModelPanel: 1.4 ChimeraX-ModelSeries: 1.0.1 ChimeraX-Mol2: 2.0.3 ChimeraX-Mole: 1.0 ChimeraX-Morph: 1.0.2 ChimeraX-MouseModes: 1.2 ChimeraX-Movie: 1.0 ChimeraX-Neuron: 1.0 ChimeraX-Nifti: 1.1 ChimeraX-NRRD: 1.1 ChimeraX-Nucleotides: 2.0.3 ChimeraX-OpenCommand: 1.13.1 ChimeraX-PDB: 2.7.3 ChimeraX-PDBBio: 1.0.1 ChimeraX-PDBLibrary: 1.0.4 ChimeraX-PDBMatrices: 1.0 ChimeraX-PickBlobs: 1.0.1 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.1 ChimeraX-PubChem: 2.1 ChimeraX-QScore: 1.1 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1.2 ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.1 ChimeraX-RenumberResidues: 1.1 ChimeraX-ResidueFit: 1.0.1 ChimeraX-RestServer: 1.2 ChimeraX-RNALayout: 1.0 ChimeraX-RotamerLibMgr: 4.0 ChimeraX-RotamerLibsDunbrack: 2.0 ChimeraX-RotamerLibsDynameomics: 2.0 ChimeraX-RotamerLibsRichardson: 2.0 ChimeraX-SaveCommand: 1.5.1 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0.2 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0.1 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.11 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0.1 ChimeraX-Shortcuts: 1.1.1 ChimeraX-ShowSequences: 1.0.2 ChimeraX-SideView: 1.0.1 ChimeraX-Smiles: 2.1.2 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.12.4 ChimeraX-STL: 1.0.1 ChimeraX-Storm: 1.0 ChimeraX-StructMeasure: 1.1.2 ChimeraX-Struts: 1.0.1 ChimeraX-Surface: 1.0.1 ChimeraX-SwapAA: 2.0.1 ChimeraX-SwapRes: 2.2.2 ChimeraX-TapeMeasure: 1.0 ChimeraX-TaskManager: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.1.2 ChimeraX-ToolshedUtils: 1.2.4 ChimeraX-Topography: 1.0 ChimeraX-ToQuest: 1.0 ChimeraX-Tug: 1.0.1 ChimeraX-UI: 1.33.3 ChimeraX-uniprot: 2.3 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDockX: 1.3.2 ChimeraX-VIPERdb: 1.0 ChimeraX-Vive: 1.1 ChimeraX-VolumeMenu: 1.0.1 ChimeraX-vrml: 1.0 ChimeraX-VTK: 1.0 ChimeraX-WavefrontOBJ: 1.0 ChimeraX-WebCam: 1.0.2 ChimeraX-WebServices: 1.1.3 ChimeraX-Zone: 1.0.1 colorama: 0.4.6 comm: 0.2.1 contourpy: 1.2.0 cxservices: 1.2.2 cycler: 0.12.1 Cython: 0.29.33 debugpy: 1.8.0 decorator: 5.1.1 docutils: 0.19 executing: 2.0.1 filelock: 3.9.0 fonttools: 4.47.2 funcparserlib: 2.0.0a0 glfw: 2.6.4 grako: 3.16.5 h5py: 3.10.0 html2text: 2020.1.16 idna: 3.6 ihm: 0.38 imagecodecs: 2023.9.18 imagesize: 1.4.1 ipykernel: 6.23.2 ipython: 8.14.0 ipython-genutils: 0.2.0 ipywidgets: 8.1.1 jedi: 0.18.2 Jinja2: 3.1.2 jupyter-client: 8.2.0 jupyter-core: 5.7.1 jupyterlab-widgets: 3.0.9 kiwisolver: 1.4.5 line-profiler: 4.0.2 lxml: 4.9.2 lz4: 4.3.2 MarkupSafe: 2.1.4 matplotlib: 3.7.2 matplotlib-inline: 0.1.6 msgpack: 1.0.4 nest-asyncio: 1.6.0 netCDF4: 1.6.2 networkx: 3.1 nibabel: 5.0.1 nptyping: 2.5.0 numexpr: 2.8.8 numpy: 1.25.1 openvr: 1.23.701 packaging: 21.3 ParmEd: 3.4.3 parso: 0.8.3 pep517: 0.13.0 pexpect: 4.9.0 pickleshare: 0.7.5 pillow: 10.2.0 pip: 23.0 pkginfo: 1.9.6 platformdirs: 4.1.0 prompt-toolkit: 3.0.43 psutil: 5.9.5 ptyprocess: 0.7.0 pure-eval: 0.2.2 py-cpuinfo: 9.0.0 pycollada: 0.7.2 pydicom: 2.3.0 Pygments: 2.16.1 pynrrd: 1.0.0 PyOpenGL: 3.1.7 PyOpenGL-accelerate: 3.1.7 pyopenxr: 1.0.2801 pyparsing: 3.0.9 pyproject-hooks: 1.0.0 PyQt6-commercial: 6.3.1 PyQt6-Qt6: 6.3.2 PyQt6-sip: 13.4.0 PyQt6-WebEngine-commercial: 6.3.1 PyQt6-WebEngine-Qt6: 6.3.2 python-dateutil: 2.8.2 pytz: 2023.3.post1 pyzmq: 25.1.2 qtconsole: 5.4.3 QtPy: 2.4.1 RandomWords: 0.4.0 requests: 2.31.0 scipy: 1.11.1 setuptools: 67.4.0 setuptools-scm: 7.0.5 sfftk-rw: 0.7.3 six: 1.16.0 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 soupsieve: 2.5 sphinx: 6.1.3 sphinx-autodoc-typehints: 1.22 sphinxcontrib-applehelp: 1.0.8 sphinxcontrib-blockdiag: 3.0.0 sphinxcontrib-devhelp: 1.0.6 sphinxcontrib-htmlhelp: 2.0.5 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 1.0.7 sphinxcontrib-serializinghtml: 1.1.10 stack-data: 0.6.3 superqt: 0.5.0 tables: 3.8.0 tcia-utils: 1.5.1 tifffile: 2023.7.18 tinyarray: 1.2.4 tomli: 2.0.1 tornado: 6.4 traitlets: 5.9.0 typing-extensions: 4.9.0 tzdata: 2023.4 urllib3: 2.1.0 wcwidth: 0.2.13 webcolors: 1.12 wheel: 0.38.4 wheel-filename: 1.4.1 widgetsnbextension: 4.0.9 }}} " defect closed normal Core duplicate Tom Goddard all ChimeraX