![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 7 months ago
Closed 7 months ago
#17312 closed defect (duplicate)
Crash on Mac waking from sleep
| Reported by: | Owned by: | Tom Goddard | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Window Toolkit | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description (last modified by )
The following bug report has been submitted:
Platform: macOS-15.3.2-arm64-arm-64bit
ChimeraX Version: 1.8 (2024-06-10 23:15:52 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 0x00000002084d8840 (most recent call first):
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 315 in event_loop
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1003 in init
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1166 in
File "", line 88 in _run_code
File "", line 198 in _run_module_as_main
Extension modules: chimerax.arrays._arrays, numpy.core._multiarray_umath, numpy.core._multiarray_tests, numpy.linalg._umath_linalg, numpy.fft._pocketfft_internal, numpy.random._common, numpy.random.bit_generator, numpy.random._bounded_integers, numpy.random._mt19937, numpy.random.mtrand, numpy.random._philox, numpy.random._pcg64, numpy.random._sfc64, numpy.random._generator, chimerax.geometry._geometry, PyQt6.QtCore, PyQt6.QtGui, PyQt6.QtWidgets, PyQt6.QtNetwork, PyQt6.QtPrintSupport, PyQt6.QtWebChannel, PyQt6.QtWebEngineCore, PyQt6.QtWebEngineWidgets, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, chimerax.map._map, charset_normalizer.md, PIL._imaging, matplotlib._c_internal_utils, matplotlib._path, kiwisolver._cext, matplotlib._image, chimerax.pdb_lib._load_libs, chimerax.surface._surface, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, lz4._version, lz4.frame._frame, msgpack._cmsgpack, chimerax.core._serialize, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.pdb._pdbio, psutil._psutil_osx, psutil._psutil_posix, lxml._elementpath, lxml.etree, PIL._imagingmath (total: 61)
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{
"uptime" : 680000,
"procRole" : "Foreground",
"version" : 2,
"userID" : 502,
"deployVersion" : 210,
"modelCode" : "Mac14,7",
"coalitionID" : 4012,
"osVersion" : {
"train" : "macOS 15.3.2",
"build" : "24D81",
"releaseType" : "User"
},
"captureTime" : "2025-04-07 08:46:27.4151 -0500",
"codeSigningMonitor" : 1,
"incident" : "2BAF2AD0-1A91-4C0A-9BF2-7B135D30ACB0",
"pid" : 65518,
"translated" : false,
"cpuType" : "ARM-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2025-04-05 12:31:12.7862 -0500",
"procStartAbsTime" : 15728554660352,
"procExitAbsTime" : 16430490487582,
"procName" : "ChimeraX",
"procPath" : "\/Applications\/ChimeraX-1.8.app\/Contents\/MacOS\/ChimeraX",
"bundleInfo" : {"CFBundleShortVersionString":"1.8.0","CFBundleVersion":"1.8.0.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
"storeInfo" : {"deviceIdentifierForVendor":"039446C8-56F1-54A1-9531-85BD2E8F600D","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "3C03AB57-DF91-6538-731F-87145E7E925C",
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 4294967295,
"instructionByteStream" : {"beforePC":"fyMD1f17v6n9AwCRcuD\/l78DAJH9e8Go\/w9f1sADX9YQKYDSARAA1A==","atPC":"AwEAVH8jA9X9e7+p\/QMAkWfg\/5e\/AwCR\/XvBqP8PX9bAA1\/WcAqA0g=="},
"bootSessionUUID" : "A7275150-C5A5-48E1-A7F7-1369D27D4EB2",
"wakeTime" : 23,
"sleepWakeUUID" : "946F6B3D-8ECC-402E-A984-2F1361197C94",
"sip" : "enabled",
"vmRegionInfo" : "0x76530012f7b9 is not in any region. Bytes after previous region: 24527066822586 \n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n owned unmapped memory unmapped-unmapped [911.5M] rw-\/rw- SM=PRV owned physical footprint (unmapped)\n---> \n UNUSED SPACE AT END",
"exception" : {"codes":"0x0000000000000001, 0x0012f6530012f7b9","rawCodes":[1,5337385924753337],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x0012f6530012f7b9 -> 0x000076530012f7b9 (possible pointer authentication failure)"},
"termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":65518},
"ktriageinfo" : "VM - (arg = 0x3) mach_vm_allocate_kernel failed within call to vm_map_enter\nVM - (arg = 0x3) mach_vm_allocate_kernel failed within call to vm_map_enter\nVM - (arg = 0x3) mach_vm_allocate_kernel failed within call to vm_map_enter\nVM - (arg = 0x3) mach_vm_allocate_kernel failed within call to vm_map_enter\nVM - (arg = 0x3) mach_vm_allocate_kernel failed within call to vm_map_enter\n",
"vmregioninfo" : "0x76530012f7b9 is not in any region. Bytes after previous region: 24527066822586 \n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n owned unmapped memory unmapped-unmapped [911.5M] rw-\/rw- SM=PRV owned physical footprint (unmapped)\n---> \n UNUSED SPACE AT END",
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===== Log before crash start =====
UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
> open "/Users/kompa012/Desktop/NiP N protein article/Figures/Model
> mechanism.cxs"
Opened cryosparc_P78_J379_map_sharp.mrc as #5, grid size 540,540,540, pixel
0.885, shown at level 0.07, step 1, values float32
Opened cryosparc_P78_J377_009_volume_map.mrc as #4, grid size 540,540,540,
pixel 0.885, shown at level 0.045, step 1, values float32
Opened cryosparc_P78_J379_map_sharp_one.mrc as #12, grid size 540,540,540,
pixel 0.885, shown at level 0.07, step 1, values float32
Opened cryosparc_P78_J400_008_volume_map_sharp.mrc as #21, grid size
540,540,540, pixel 0.885, shown at level 0.045, step 1, values float32
Opened cryosparc_P78_J368_map_sharp_zflip.mrc as #22, grid size 360,360,360,
pixel 0.885, shown at level 0.005, step 1, values float32
Opened cryosparc_P78_J378_map_sharp.mrc as #23, grid size 540,540,540, pixel
1.18, shown at level 0.005, step 1, values float32
Opened cryosparc_P78_J365_009_volume_map_zflip.mrc as #24, grid size
360,360,360, pixel 0.885, shown at level 0.045, step 1, values float32
Opened cryosparc_P78_J376_007_volume_map.mrc as #25, grid size 540,540,540,
pixel 1.18, shown at level 0.06, step 1, values float32
Log from Fri Apr 4 01:16:01 2025UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
> open "/Users/kompa012/Desktop/NiP N protein article/Figures/prot
> comparison1.cxs"
Opened cryosparc_P78_J379_map_sharp.mrc as #5, grid size 540,540,540, pixel
0.885, shown at level 0.07, step 1, values float32
Opened cryosparc_P78_J377_009_volume_map.mrc as #4, grid size 540,540,540,
pixel 0.885, shown at level 0.045, step 1, values float32
Opened cryosparc_P78_J379_map_sharp_one.mrc as #12, grid size 540,540,540,
pixel 0.885, shown at level 0.07, step 1, values float32
Opened cryosparc_P78_J400_008_volume_map_sharp.mrc as #21, grid size
540,540,540, pixel 0.885, shown at level 0.045, step 1, values float32
Opened cryosparc_P78_J368_map_sharp_zflip.mrc as #22, grid size 360,360,360,
pixel 0.885, shown at level 0.005, step 1, values float32
Opened cryosparc_P78_J378_map_sharp.mrc as #23, grid size 540,540,540, pixel
1.18, shown at level 0.005, step 1, values float32
Opened cryosparc_P78_J365_009_volume_map_zflip.mrc as #24, grid size
360,360,360, pixel 0.885, shown at level 0.045, step 1, values float32
Opened cryosparc_P78_J376_007_volume_map.mrc as #25, grid size 540,540,540,
pixel 1.18, shown at level 0.06, step 1, values float32
Log from Mon Mar 31 09:45:10 2025UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
> set bgColor transparent
Log from Wed Mar 26 17:06:10 2025UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
> open "/Users/kompa012/Desktop/NiP N protein article/Figures/prot
> comparison.cxs"
Opened cryosparc_P78_J379_map_sharp.mrc as #5, grid size 540,540,540, pixel
0.885, shown at level 0.07, step 1, values float32
Opened cryosparc_P78_J377_009_volume_map.mrc as #4, grid size 540,540,540,
pixel 0.885, shown at level 0.044, step 1, values float32
Opened cryosparc_P78_J379_map_sharp_one.mrc as #12, grid size 540,540,540,
pixel 0.885, shown at level 0.07, step 1, values float32
Log from Mon Mar 24 20:26:22 2025UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
> open "/Users/kompa012/Desktop/NiP N protein article/Figures/dimer close
> aup.cxs" format session
Opened cryosparc_P78_J379_map_sharp.mrc as #5, grid size 540,540,540, pixel
0.885, shown at level 0.07, step 1, values float32
Opened cryosparc_P78_J377_009_volume_map.mrc as #4, grid size 540,540,540,
pixel 0.885, shown at level 0.044, step 1, values float32
Opened cryosparc_P78_J379_map_sharp_one.mrc as #12, grid size 540,540,540,
pixel 0.885, shown at level 0.07, step 1, values float32
Log from Fri Mar 21 14:45:12 2025UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
> set bgColor transparent
Log from Tue Mar 18 10:07:50 2025 Startup Messages
---
note | available bundle cache has not been initialized yet
UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open "/Users/kompa012/Desktop/NiP N protein article/7nt5_J377_intactmodel-
> coot-0_real_space_refined_030.pdb"
Chain information for 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb
#1
---
Chain | Description
D E F G H I J K L M N O P Q | No description available
Z | No description available
> open "/Users/kompa012/Desktop/NiP N protein article/pdb_extract_3032647.cif"
Summary of feedback from opening /Users/kompa012/Desktop/NiP N protein
article/pdb_extract_3032647.cif
---
warning | Missing or incomplete sequence information. Inferred polymer connectivity.
Chain information for pdb_extract_3032647.cif #2
---
Chain | Description
D E F G H I J K L M N O P Q | No description available
Z | No description available
> hide #1 models
> show #1 models
> hide #2 models
> show #2 models
> open 7nt5 fromDatabase pdb format mmcif
Summary of feedback from opening 7nt5 fetched from pdb
---
note | Fetching compressed mmCIF 7nt5 from http://files.rcsb.org/download/7nt5.cif
7nt5 title:
CryoEM structure of the Nipah virus nucleocapsid single helical turn assembly
[more info...]
Chain information for 7nt5 #3
---
Chain | Description | UniProt
A B C D E F G H I J K L M | Nucleoprotein | NCAP_NIPAV 1-532
N | RNA (78-MER) |
> open "/Users/kompa012/Desktop/NiP N protein article/NiV N
> protein/cryosparc_P78_J377_009_volume_map.mrc"
Opened cryosparc_P78_J377_009_volume_map.mrc as #4, grid size 540,540,540,
pixel 0.885, shown at level 0.0369, step 4, values float32
> volume #4 step 1
> hide #!3 models
> ui tool show "Hide Dust"
> surface dust #4 size 5.31
> select add #1
44996 atoms, 45905 bonds, 5656 residues, 1 model selected
> style sel stick
Changed 44996 atom styles
> hide #2 models
> select add #4
44996 atoms, 45905 bonds, 5656 residues, 3 models selected
> select subtract #1
2 models selected
> transparency #4.1 70
> volume #4 level 0.03
> volume #4 level 0.02
> volume #4 level 0.015
> volume #4 level 0.05
> ui mousemode right select
> select clear
> volume #4 level 0.06
> select add #1
44996 atoms, 45905 bonds, 5656 residues, 1 model selected
> show sel surfaces
> select subtract #1
15 models selected
> select add #1.15
1680 atoms, 84 residues, 1 model selected
> hide sel surfaces
> show sel cartoons
> select clear
> select add #1
44996 atoms, 45905 bonds, 5656 residues, 1 model selected
> color zone #4 near sel & #1 distance 5.31
> select clear
> hide #!1 models
> open "/Users/kompa012/Desktop/NiP N protein article/NiV N
> protein/cryosparc_P78_J379_map_sharp.mrc"
Opened cryosparc_P78_J379_map_sharp.mrc as #5, grid size 540,540,540, pixel
0.885, shown at level 0.000704, step 4, values float32
> volume #5 step 1
> volume #5 level 0.02408
> surface dust #5 size 5.31
> volume #5 level 0.06
> volume #4 level 0.025
> show #!5 models
> hide #!4 models
> show #!1 models
> select add #1
44996 atoms, 45905 bonds, 5656 residues, 1 model selected
> hide sel surfaces
> show sel atoms
> select clear
> select add #5
2 models selected
> transparency #5.1 80
> select clear
> volume #5 level 0.04
> transparency #1,5 60
> hide #!5 models
> select add #1
44996 atoms, 45905 bonds, 5656 residues, 1 model selected
> select subtract #1.10
41902 atoms, 42758 bonds, 5258 residues, 16 models selected
> select subtract #1.11
38808 atoms, 39611 bonds, 4860 residues, 15 models selected
> select subtract #1.15
37128 atoms, 37764 bonds, 4776 residues, 14 models selected
> hide sel atoms
> select subtract #1.9
34034 atoms, 34617 bonds, 4378 residues, 13 models selected
> select add #1.9
37128 atoms, 34617 bonds, 4776 residues, 12 models selected
> select add #1
44996 atoms, 45905 bonds, 5656 residues, 13 models selected
> select subtract #1
15 models selected
> select add #1.9
3094 atoms, 398 residues, 1 model selected
> show sel atoms
> select clear
Cell requested for row 3 is out of bounds for table with 20 rows! Resizing
table model.
> ui tool show Contacts
> select add #1.15
1680 atoms, 84 residues, 1 model selected
> select add #1.10
4774 atoms, 482 residues, 2 models selected
> select add #1.11
7868 atoms, 880 residues, 3 models selected
> select add #1.9
10962 atoms, 1278 residues, 4 models selected
> contacts sel restrict both ignoreHiddenModels true log true
Allowed overlap: -0.4
H-bond overlap reduction: 0.4
Ignore contacts between atoms separated by 4 bonds or less
Detect intra-residue contacts: False
Detect intra-molecule contacts: True
5727 contacts
atom1 atom2 overlap distance
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L PRO 280 CD 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L ILE 374 CD1 0.708 3.052
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L PRO 280 CG 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L ILE 374 CD1 0.578 3.182
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N ALA 269 CB 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N ALA 265 O 0.504 2.796
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M ILE 374 CG1 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N ASN 285 ND2 0.444 3.076
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L PRO 280 CD 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L ILE 374 CG2 0.435 3.325
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N ARG 192 NH1 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/Z U 66 P 0.403 3.337
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M ALA 269 CB 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M ALA 265 O 0.401 2.899
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M ARG 192 NH1 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/Z U 60 P 0.397 3.343
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L ALA 269 CB 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L ALA 265 O 0.363 2.937
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N ARG 60 NH2 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N ASP 57 CG 0.325 3.195
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L ILE 374 CB 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L PRO 280 CG 0.323 3.437
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M ARG 36 NH1 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M GLU 124 CD 0.280 3.240
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L PRO 280 CD 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L ILE 374 CB 0.265 3.495
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N ARG 36 NH1 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N GLU 124 CD 0.261 3.259
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N ASP 137 CG 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N LYS 133 O 0.255 3.045
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M ASP 137 CG 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M LYS 133 O 0.238 3.062
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L ASP 137 CG 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L LYS 133 O 0.236 3.064
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L ARG 36 NH1 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L GLU 124 CD 0.234 3.286
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L LEU 284 O 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L GLN 288 NE2 0.232 2.428
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M LEU 284 O 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M GLN 288 NE2 0.228 2.432
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L ASN 349 ND2 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/Z U 51 N3 0.228 3.052
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L GLU 286 OE1 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L TYR 359 OH 0.222 2.258
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L TYR 359 OH 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L GLU 286 CD 0.220 3.120
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L GLU 50 OE1 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L ARG 154 NH1 0.217 2.443
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N PRO 280 CD 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N ILE 374 CG2 0.216 3.544
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N TRP 173 CD1 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N GLU 169 O 0.216 2.964
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N LYS 34 CA 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N GLU 98 O 0.214 3.086
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L ARG 192 NH1 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/Z U 54 P 0.213 3.527
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M TRP 173 CD1 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M GLU 169 O 0.211 2.969
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L GLN 376 NE2 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L ARG 278 CG 0.210 3.310
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N ASN 349 ND2 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/Z U 63 N3 0.208 3.072
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L ASP 103 CG 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L ALA 41 CB 0.205 3.555
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M ASP 290 CB 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M PHE 287 O 0.204 3.096
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M ILE 101 CD1 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M ARG 89 NH1 0.201 3.319
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N TYR 151 OH 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N ASP 57 CG 0.198 3.142
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L ILE 101 CD1 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L ARG 89 NH1 0.197 3.323
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L TRP 173 CD1 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L GLU 169 O 0.191 2.989
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N GLU 50 OE1 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N ARG 154 NH1 0.191 2.469
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M ASN 285 ND2 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L TYR 279 CD1 0.191 3.209
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M PRO 328 O 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M TRP 331 CB 0.189 3.111
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M ASP 157 CG 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M THR 160 OG1 0.187 3.153
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M PRO 280 CG 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M ILE 374 CD1 0.187 3.573
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M GLN 15 NE2 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L PHE 268 CE1 0.186 3.214
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N ASP 3 N 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L ARG 381 CD 0.185 3.335
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M SER 332 OG 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M LEU 329 O 0.179 2.301
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N GLN 15 NE2 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M PHE 268 CE1 0.178 3.222
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L GLU 276 OE1 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M ASN 292 ND2 0.177 2.483
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N GLU 233 OE1 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N LYS 229 O 0.176 2.664
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N LEU 31 CD1 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M ARG 48 NH1 0.176 3.344
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N ILE 318 CD1 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N ARG 20 NH2 0.176 3.344
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M ARG 12 NH1 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M GLN 15 NE2 0.174 3.106
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N GLU 315 O 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M GLU 250 CD 0.174 3.126
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N ILE 101 CD1 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N ARG 89 NH1 0.174 3.346
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M ARG 60 NH1 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M PRO 144 CD 0.173 3.347
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M GLU 50 OE1 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M ARG 154 NH1 0.173 2.487
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L VAL 227 O 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L MET 231 CG 0.172 3.128
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N LEU 329 O 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N SER 332 OG 0.171 2.309
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L SER 344 OG 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L ASP 342 CG 0.170 3.170
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M GLY 373 O 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L GLN 388 CG 0.170 3.130
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N ASP 157 CG 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N THR 160 OG1 0.169 3.171
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L PHE 11 CE2 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L GLN 15 NE2 0.166 3.234
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N VAL 227 O 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N MET 231 CG 0.165 3.135
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M PHE 11 CE2 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M GLN 15 NE2 0.165 3.235
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M VAL 227 O 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M MET 231 CG 0.162 3.138
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N PHE 11 CE2 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N GLN 15 NE2 0.160 3.240
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N SER 344 OG 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N ASP 342 CG 0.160 3.180
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M ILE 374 CG2 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N ASN 285 ND2 0.159 3.361
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M LEU 31 CD1 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L ARG 48 NH1 0.159 3.361
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M LEU 314 CD2 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M LYS 229 CG 0.159 3.601
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M GLU 233 OE2 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M ARG 307 NH2 0.158 2.502
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N ASP 57 OD2 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N TYR 151 OH 0.158 2.322
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N PRO 144 CD 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N ARG 60 NH1 0.155 3.365
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L ASP 290 CB 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L PHE 287 O 0.155 3.145
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N GLN 376 NE2 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N ARG 278 CG 0.155 3.365
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L ILE 168 CD1 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L THR 52 CG2 0.153 3.607
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M ASP 103 CG 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M ALA 41 CB 0.153 3.607
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L LEU 314 CD2 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L LYS 229 CG 0.153 3.607
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N ARG 368 CB 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N GLN 364 O 0.152 3.148
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L ARG 368 CB 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L GLN 364 O 0.150 3.150
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L SER 332 OG 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L LEU 329 O 0.150 2.330
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M ARG 48 NH1 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N LEU 31 CD2 0.149 3.371
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M GLU 315 OE2 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M ARG 228 NH1 0.149 2.511
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N ASP 290 CB 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N PHE 287 O 0.149 3.151
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/Z U 38 C5' 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/Z U 37 C2' 0.149 3.611
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M ILE 168 CD1 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M THR 52 CG2 0.148 3.612
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L PRO 328 O 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L TRP 331 CB 0.147 3.153
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L ALA 283 CB 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L PRO 280 O 0.147 3.153
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N LYS 229 CD 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N ASP 94 CG 0.143 3.617
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N LEU 314 CD2 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N LYS 229 CG 0.143 3.617
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M ARG 368 CB 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M GLN 364 O 0.143 3.157
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N MET 114 CG 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N MET 107 CA 0.141 3.619
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L LEU 392 CD2 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M LEU 284 CD2 0.141 3.619
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/Z U 44 C5' 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/Z U 43 C2' 0.141 3.619
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N LEU 128 O 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N ILE 131 CG2 0.140 3.160
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/Z U 72 C5' 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/Z U 71 C2' 0.139 3.621
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M SER 139 CB 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M ARG 60 NH1 0.138 3.382
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L ARG 60 NH1 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L PRO 144 CD 0.137 3.383
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M ILE 131 CG1 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M GLY 127 O 0.133 3.167
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L SER 139 CB 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L ARG 60 NH1 0.133 3.387
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L ASP 157 CG 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L THR 160 OG1 0.133 3.207
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L ILE 172 CG1 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L ILE 168 O 0.132 3.168
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L TYR 151 OH 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L ASP 57 CG 0.131 3.209
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M TYR 151 OH 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M ASP 57 CG 0.129 3.211
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M ILE 172 CG1 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M ILE 168 O 0.129 3.171
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M ASP 96 CG 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L GLY 246 CA 0.128 3.632
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M ARG 302 NH2 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N TYR 14 CB 0.127 3.393
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/Z U 49 C2' 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/Z U 50 C5' 0.127 3.633
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N ASN 285 ND2 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M TYR 279 CD1 0.126 3.274
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N ILE 172 CG1 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N ILE 168 O 0.125 3.175
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/Z U 61 C2' 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/Z U 62 C5' 0.125 3.635
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M SER 90 CB 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M ALA 86 O 0.125 3.175
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/Z U 13 C2' 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/Z U 14 C6 0.125 3.515
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L GLN 288 O 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L LEU 291 CB 0.124 3.176
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/Z U 32 C5' 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/Z U 31 C2' 0.124 3.636
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N ILE 168 CD1 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N THR 52 CG2 0.124 3.636
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N SER 90 CB 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N ALA 86 O 0.123 3.177
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N PRO 328 O 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N TRP 331 CB 0.123 3.177
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N MET 231 CE 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N ILE 77 CG1 0.122 3.638
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/Z U 41 C5' 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/Z U 40 C2' 0.121 3.639
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/Z U 26 C5' 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/Z U 25 C2' 0.120 3.640
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/Z U 55 C2' 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/Z U 56 C5' 0.120 3.640
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N ARG 136 NH2 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N TYR 151 OH 0.119 2.581
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N MET 107 CG 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N SER 106 O 0.119 3.181
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L MET 231 CE 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L ILE 77 CG1 0.118 3.642
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L ARG 48 NH1 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M LEU 31 CD2 0.118 3.402
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M ILE 131 CG2 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M SER 61 CB 0.118 3.642
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N ASP 96 CG 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M GLY 246 CA 0.116 3.644
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N ASN 285 ND2 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M TYR 279 CE1 0.116 3.284
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N GLN 288 O 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N LEU 291 CB 0.115 3.185
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M ILE 252 CG1 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M ALA 248 O 0.115 3.185
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M ASP 290 O 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M THR 293 CB 0.115 3.185
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M GLU 233 CG 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M LYS 229 O 0.114 3.186
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M GLY 105 CA 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M ARG 116 NH2 0.114 3.406
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M SER 344 OG 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M ASP 342 CG 0.113 3.227
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N SER 139 CB 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N ARG 60 NH1 0.113 3.407
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N GLY 105 CA 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N ARG 116 NH2 0.112 3.408
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L GLN 171 O 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L ILE 174 CG1 0.112 3.188
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/Z U 24 C5' 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/Z U 23 C2' 0.111 3.649
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L ALA 248 O 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L ILE 252 CG1 0.111 3.189
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N ARG 193 NH1 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N ARG 192 CB 0.111 3.409
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M MET 114 CA 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M ASN 109 ND2 0.111 3.409
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L TRP 173 CH2 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L MET 231 CB 0.108 3.532
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M ALA 393 CB 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M VAL 389 O 0.107 3.193
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N ILE 131 CD1 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N ALA 64 CB 0.107 3.653
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L TRP 331 CA 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L THR 270 CG2 0.107 3.653
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L ARG 20 NH2 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L ILE 318 CG1 0.107 3.413
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L GLU 98 O 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L LYS 34 CA 0.106 3.194
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L SER 366 OG 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L GLY 363 CA 0.106 3.234
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/Z U 58 C2' 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/Z U 59 C5' 0.106 3.654
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M PRO 280 CD 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M ILE 374 CG1 0.106 3.654
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L GLY 105 CA 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L ARG 116 NH2 0.106 3.414
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N ARG 228 CD 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N VAL 180 CG1 0.105 3.655
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M TRP 213 CZ3 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M ILE 172 CD1 0.105 3.535
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N LEU 132 CD2 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N ASP 57 CB 0.105 3.655
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N MET 311 CE 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N ILE 304 CD1 0.105 3.655
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L ARG 218 NH1 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L LEU 175 CD2 0.104 3.416
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M LEU 132 CB 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M ARG 136 NH1 0.103 3.417
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L PHE 230 CB 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L PHE 74 CE1 0.103 3.537
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M LEU 392 CD2 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N LEU 284 CD2 0.103 3.657
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N TRP 331 NE1 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N MET 335 CE 0.102 3.418
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M GLU 98 O 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M LYS 34 CA 0.102 3.198
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M MET 114 N 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M ASN 109 ND2 0.102 3.178
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L ILE 166 CG1 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L VAL 162 O 0.102 3.198
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M ASP 57 CG 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M LEU 53 O 0.102 3.198
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N ILE 101 CA 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N ILE 37 O 0.102 3.198
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L VAL 198 CG1 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L ALA 195 CA 0.101 3.659
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N GLN 171 O 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N ILE 174 CG1 0.101 3.199
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/Z U 5 O4' 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/Z U 4 C2' 0.101 3.239
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M TRP 331 CA 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M THR 270 CG2 0.100 3.660
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N VAL 108 CG2 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N MET 107 SD 0.100 3.550
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M THR 270 CG2 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M GLY 266 O 0.100 3.200
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L MET 114 CA 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L ASN 109 ND2 0.100 3.420
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L LEU 56 CD2 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L TRP 213 CZ2 0.099 3.541
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M LEU 329 CD2 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L ILE 341 CG2 0.098 3.662
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L LEU 291 CD2 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L LEU 275 CD2 0.098 3.662
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L ARG 368 CG 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L THR 340 CG2 0.098 3.662
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N ARG 228 NH1 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N VAL 180 CG1 0.098 3.422
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/Z U 68 C5' 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/Z U 67 C2' 0.097 3.663
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M ILE 59 CG1 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M ALA 72 CB 0.097 3.663
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M MET 231 CE 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M ILE 77 CG1 0.097 3.663
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M LYS 321 CD 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M ILE 318 CD1 0.096 3.664
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M ARG 218 CB 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M LEU 214 O 0.096 3.204
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L MET 107 CA 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L MET 114 CG 0.096 3.664
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L ILE 271 CG1 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L PHE 267 O 0.096 3.204
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/Z U 80 C2' 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/Z U 81 C6 0.096 3.544
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L VAL 113 CG1 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L VAL 104 CG1 0.096 3.664
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L ASN 285 CA 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L GLN 288 CG 0.096 3.664
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M ALA 195 CA 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M VAL 198 CG1 0.096 3.664
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L ALA 248 O 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L ILE 251 CG2 0.096 3.204
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/Z U 77 C5' 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/Z U 76 C2' 0.095 3.665
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M ILE 255 O 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M VAL 259 CG2 0.095 3.205
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L ILE 374 CG1 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M ASN 285 ND2 0.094 3.426
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/Z U 48 C5' 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/Z U 47 C2' 0.094 3.666
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M GLU 286 CG 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L ILE 341 CD1 0.094 3.666
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L TRP 331 NE1 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L MET 335 CE 0.093 3.427
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M LYS 196 NZ 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/Z U 61 C1' 0.093 3.427
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/Z U 26 O2' 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/Z U 27 C5' 0.093 3.247
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M PRO 112 CD 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M LEU 132 CD1 0.093 3.667
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/Z U 12 C5' 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/Z U 11 C2' 0.093 3.667
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N PHE 230 O 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N ILE 234 CG1 0.092 3.208
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N ILE 166 CG1 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N VAL 162 O 0.092 3.208
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L GLU 260 CG 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L GLY 256 O 0.092 3.208
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N ALA 248 O 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N ILE 252 CG1 0.092 3.208
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M GLN 200 NE2 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M ARG 202 CD 0.092 3.428
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M TRP 173 CH2 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M MET 231 CB 0.092 3.548
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L LEU 76 CD1 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L ILE 59 CD1 0.092 3.668
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N TRP 173 CH2 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N MET 231 CB 0.091 3.549
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N VAL 113 CG1 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N VAL 104 CG1 0.091 3.669
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L ILE 111 CD1 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L ARG 136 NH2 0.091 3.429
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L ARG 12 NH1 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L GLN 15 NE2 0.091 3.189
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L ILE 174 CG2 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L ALA 170 O 0.091 3.209
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N LEU 209 CD1 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N GLN 171 NE2 0.090 3.430
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/Z U 74 C5' 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/Z U 73 C2' 0.090 3.670
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N ILE 255 O 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N VAL 259 CG2 0.090 3.210
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M SER 289 CB 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L GLU 276 CB 0.090 3.670
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N ALA 393 CB 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N VAL 389 O 0.089 3.211
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L SER 63 OG 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L THR 134 OG1 0.089 2.431
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N ILE 176 CD1 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N MET 231 CB 0.089 3.671
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N THR 340 CB 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N ALA 367 CB 0.089 3.671
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/Z U 54 C5' 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/Z U 53 C2' 0.089 3.671
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N ILE 271 CG1 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N PHE 267 O 0.089 3.211
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N ALA 72 CB 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N ILE 59 CG1 0.088 3.672
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M ILE 236 CG1 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M VAL 232 O 0.088 3.212
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N ILE 174 CG2 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N ALA 170 O 0.088 3.212
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N ILE 236 CG1 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N VAL 232 O 0.088 3.212
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M GLN 376 NE2 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M ARG 278 CG 0.087 3.433
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M PHE 230 CB 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M PHE 74 CE1 0.087 3.553
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L THR 270 CG2 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L GLY 266 O 0.087 3.213
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N ALA 195 CA 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N VAL 198 CG1 0.087 3.673
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/Z U 29 C5' 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/Z U 28 C2' 0.087 3.673
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L ILE 131 CG1 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L GLY 127 O 0.087 3.213
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L ILE 131 CG2 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L SER 61 CB 0.086 3.674
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N ILE 111 CD1 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N ARG 136 NH2 0.086 3.434
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L TYR 301 CB 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L MET 298 O 0.086 3.214
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M ILE 111 CD1 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M ARG 136 NH2 0.086 3.434
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L VAL 180 CG2 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L LEU 313 CD2 0.086 3.674
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/Z U 78 C5' 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/Z U 77 C2' 0.086 3.674
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M PHE 287 O 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M LEU 291 CD1 0.086 3.214
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M LYS 229 CD 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M ASP 94 CG 0.086 3.674
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M ILE 166 CG1 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M VAL 162 O 0.086 3.214
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M GLY 85 CA 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M ILE 88 CG2 0.085 3.675
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M GLN 171 O 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M ILE 174 CG1 0.085 3.215
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M LEU 76 CD1 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M ILE 59 CD1 0.085 3.675
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/Z U 55 C1' 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L LYS 196 NZ 0.085 3.435
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M ALA 248 O 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M ILE 251 CG2 0.085 3.215
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N LEU 313 CD2 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N VAL 180 CG2 0.085 3.675
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L ILE 255 O 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L VAL 259 CG2 0.085 3.215
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L LEU 132 CB 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L ARG 136 NH1 0.084 3.436
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N THR 134 OG1 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N SER 63 OG 0.084 2.436
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/Z U 7 C2' 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/Z U 8 C6 0.084 3.556
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N ILE 131 CG1 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N SER 61 CB 0.084 3.676
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N LEU 76 CD1 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N ILE 59 CD1 0.084 3.676
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N PRO 280 O 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N ALA 283 CB 0.084 3.216
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/Z U 84 C5' 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/Z U 83 C2' 0.083 3.677
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N ALA 248 O 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N ILE 251 CG2 0.083 3.217
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/Z U 20 C5' 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/Z U 19 C2' 0.082 3.678
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M ILE 251 O 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M ILE 255 CG1 0.082 3.218
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L ALA 72 O 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L THR 75 CG2 0.082 3.218
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N LEU 47 CD1 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N THR 42 CG2 0.082 3.678
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/Z U 52 C2' 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/Z U 53 C5' 0.082 3.678
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N MET 79 CE 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N LEU 51 CB 0.082 3.678
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N TRP 331 CA 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N THR 270 CG2 0.081 3.679
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L ALA 72 CB 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L ILE 59 CG1 0.081 3.679
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M MET 107 CA 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M MET 114 CG 0.081 3.679
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M ILE 111 CG2 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M LEU 132 CD1 0.081 3.679
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L GLU 315 OE2 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L ARG 228 NH1 0.081 2.579
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L VAL 113 CG2 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L MET 107 CE 0.081 3.679
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N ILE 251 O 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N ILE 255 CG1 0.080 3.220
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N ALA 186 O 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N GLU 190 CD 0.080 3.220
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M ARG 89 CG 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M GLY 85 O 0.080 3.220
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/Z U 75 C6 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/Z U 74 C2' 0.080 3.560
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M ILE 172 CD1 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M MET 217 CG 0.080 3.680
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/Z U 47 C5' 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/Z U 46 C2' 0.080 3.680
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M TYR 301 CB 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M MET 298 O 0.080 3.220
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/Z U 6 C5' 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/Z U 5 C2' 0.079 3.681
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N VAL 113 CG2 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N LEU 51 CD2 0.079 3.681
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M ASN 285 CB 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L THR 277 O 0.079 3.221
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N SER 138 CB 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N PRO 62 CD 0.079 3.681
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M ALA 72 O 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M THR 75 CG2 0.079 3.221
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L ILE 101 CA 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L ILE 37 O 0.078 3.222
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N GLU 260 CG 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N GLY 256 O 0.078 3.222
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M VAL 58 CG2 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M PHE 54 O 0.078 3.222
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L ILE 255 CD1 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L TRP 173 CB 0.078 3.682
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N VAL 58 CG2 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N PHE 54 O 0.078 3.222
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N ILE 131 CD1 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N ALA 64 CA 0.078 3.682
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N PRO 112 CD 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N LEU 132 CD1 0.078 3.682
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M VAL 113 CG1 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M VAL 104 CG1 0.077 3.683
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N LYS 133 CG 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N MET 129 O 0.077 3.223
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N THR 270 CG2 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N GLY 266 O 0.077 3.223
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N GLY 85 CA 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N ILE 88 CG2 0.077 3.683
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N ALA 72 O 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N THR 75 CG2 0.076 3.224
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M SER 317 CB 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L SER 253 CB 0.076 3.684
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M SER 366 OG 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M GLY 363 CA 0.076 3.264
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L ARG 36 NH2 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L GLU 124 CD 0.076 3.444
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L ILE 97 CD1 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L ILE 35 CD1 0.076 3.684
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N GLU 50 CG 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N VAL 108 CG2 0.076 3.684
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L TRP 213 CZ3 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L ILE 172 CD1 0.076 3.564
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M VAL 259 CG1 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M LEU 313 CD1 0.076 3.684
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N LEU 329 CD2 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M ILE 341 CG2 0.076 3.684
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M MET 125 O 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M MET 129 CG 0.075 3.225
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M GLN 364 O 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M ARG 368 CG 0.075 3.225
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N TRP 213 CZ3 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N ILE 172 CD1 0.075 3.565
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N PRO 112 CB 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N LEU 132 CD1 0.075 3.685
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M VAL 165 O 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M GLU 169 CG 0.075 3.225
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M PHE 230 O 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M ILE 234 CG1 0.075 3.225
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L ILE 236 CG1 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L VAL 232 O 0.074 3.226
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/Z U 67 C1' 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N LYS 196 NZ 0.074 3.446
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M MET 311 CE 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M ILE 304 CD1 0.074 3.686
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N VAL 165 O 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N GLU 169 CG 0.074 3.226
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N GLU 315 CG 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N LEU 225 CD1 0.074 3.686
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L THR 143 CG2 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L TYR 151 CB 0.074 3.686
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L LEU 392 CD1 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M PRO 280 CB 0.073 3.687
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M LEU 56 CD2 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M TRP 213 CZ2 0.073 3.567
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L VAL 58 CG2 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L PHE 54 O 0.073 3.227
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N SER 138 OG 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N PRO 62 CD 0.072 3.268
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M ASN 285 ND2 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L ILE 374 CD1 0.072 3.448
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N SER 289 CB 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M GLU 276 CB 0.072 3.688
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L GLN 200 CG 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L LYS 196 O 0.072 3.228
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M LYS 178 NZ 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/Z U 58 P 0.071 3.669
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L GLU 356 CB 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L TYR 359 CD2 0.071 3.569
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L ILE 176 CD1 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L MET 231 CB 0.071 3.689
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N LEU 56 CD2 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N TRP 213 CZ2 0.071 3.569
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/Z U 23 C5' 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/Z U 22 C2' 0.071 3.689
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M ILE 255 CD1 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M TRP 173 CB 0.071 3.689
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/Z U 11 C5' 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/Z U 10 C2' 0.071 3.689
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L ARG 193 CG 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L SER 189 O 0.070 3.230
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L PRO 84 CB 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L VAL 39 CG1 0.070 3.690
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/Z U 66 C5' 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/Z U 65 C2' 0.070 3.690
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/Z U 74 C6 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/Z U 73 C2' 0.070 3.570
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N ARG 193 CG 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N SER 189 O 0.070 3.230
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L ALA 72 CA 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L THR 75 CG2 0.070 3.690
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L SER 366 CA 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L HIS 370 O 0.069 3.231
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L MET 125 O 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L MET 129 CG 0.069 3.231
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M GLU 260 CG 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M GLY 256 O 0.069 3.231
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L PRO 40 CA 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L VAL 104 CG2 0.069 3.691
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N ILE 97 CD1 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N ILE 35 CD1 0.069 3.691
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L MET 114 N 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L ASN 109 ND2 0.068 3.212
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L PRO 112 CD 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L LEU 132 CD1 0.068 3.692
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M LEU 51 CA 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M MET 107 CE 0.068 3.692
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N ILE 172 CG2 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N ILE 77 CD1 0.068 3.692
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L ARG 228 CD 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L VAL 180 CG1 0.068 3.692
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N LEU 56 CG 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N THR 52 O 0.067 3.233
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N TRP 331 CD1 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N THR 270 CG2 0.067 3.573
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L PRO 84 CA 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L SER 78 OG 0.067 3.273
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M ILE 271 CG1 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M PHE 267 O 0.067 3.233
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/Z U 11 O4' 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/Z U 10 C2' 0.067 3.273
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L LEU 51 CA 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L MET 107 CE 0.067 3.693
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L GLY 256 CA 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L VAL 259 CG2 0.066 3.694
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M ALA 72 CA 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M THR 75 CG2 0.066 3.694
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N GLU 286 CG 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M ILE 341 CD1 0.066 3.694
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M ARG 193 CG 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M SER 189 O 0.066 3.234
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N SER 366 OG 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N GLY 363 CA 0.065 3.275
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L SER 159 O 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L VAL 162 CG2 0.065 3.235
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M VAL 180 CG2 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M LEU 313 CD2 0.065 3.695
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L THR 293 CB 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L ASP 290 O 0.065 3.235
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M GLY 105 CA 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M ARG 116 NE 0.065 3.455
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M MET 231 CG 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M ILE 176 CD1 0.065 3.695
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M SER 159 O 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M VAL 162 CG2 0.065 3.235
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M PHE 11 CB 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M GLU 7 O 0.064 3.236
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L ASP 57 CG 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L LEU 53 O 0.064 3.236
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M ALA 281 CA 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L LEU 392 CD1 0.064 3.696
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M MET 79 CG 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M THR 75 O 0.064 3.236
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M VAL 337 CG2 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M TYR 279 CE2 0.064 3.576
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L PRO 40 CD 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L VAL 39 CG1 0.064 3.696
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N LEU 235 CG 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N TRP 173 CZ3 0.064 3.576
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L ILE 88 CG2 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L GLY 85 CA 0.064 3.696
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/Z U 71 O4' 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/Z U 70 C2' 0.064 3.276
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N PHE 206 CB 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N ASN 204 ND2 0.064 3.456
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M ARG 228 CD 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M VAL 180 CG1 0.064 3.696
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L ARG 89 CG 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L GLY 85 O 0.064 3.236
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L MET 217 CG 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L ILE 172 CD1 0.063 3.697
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L VAL 165 O 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L ILE 168 CG1 0.063 3.237
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M THR 340 CB 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M ALA 367 CB 0.063 3.697
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N MET 217 CG 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N ILE 172 CD1 0.063 3.697
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M ILE 174 CG2 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M ALA 170 O 0.062 3.238
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/Z U 14 C5' 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/Z U 13 C2' 0.062 3.698
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L GLN 364 O 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L ARG 368 CG 0.062 3.238
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L GLY 274 CA 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L THR 270 O 0.062 3.238
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/Z U 58 C6 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M LEU 348 CD1 0.062 3.578
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M THR 134 CG2 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M ARG 130 O 0.062 3.238
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M ILE 97 CD1 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M ILE 35 CD1 0.062 3.698
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L ILE 111 CG2 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L LEU 132 CD1 0.061 3.699
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/Z U 53 O4' 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/Z U 52 C2' 0.061 3.279
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M LEU 235 CG 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M TRP 173 CZ3 0.061 3.579
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N TYR 327 OH 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N PHE 267 CA 0.061 3.279
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M TRP 331 NE1 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M MET 335 CE 0.061 3.459
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M TYR 197 CD2 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M ARG 193 O 0.061 3.119
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M LYS 133 CG 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M MET 129 O 0.061 3.239
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M ALA 186 O 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M GLU 190 CD 0.061 3.239
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N ASP 96 OD1 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M GLY 246 CA 0.060 3.240
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N SER 317 CB 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M SER 253 CB 0.060 3.700
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/Z U 59 O4' 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/Z U 58 C2' 0.060 3.280
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N ARG 89 CG 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N GLY 85 O 0.060 3.240
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N ASP 57 CG 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N LEU 53 O 0.060 3.240
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N ILE 255 CD1 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N TRP 173 CB 0.060 3.700
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M ARG 193 NH1 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M ARG 192 CB 0.060 3.460
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/Z U 42 C5' 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/Z U 41 C2' 0.060 3.700
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M THR 75 CB 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M PHE 38 O 0.060 3.240
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/Z U 35 C5' 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/Z U 34 C2' 0.060 3.700
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N LEU 128 CB 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N PRO 112 CB 0.060 3.700
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/Z U 60 C5' 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/Z U 59 C2' 0.060 3.700
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M ALA 265 CB 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/Z U 57 OP1 0.060 3.240
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N ILE 176 CG2 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N TRP 173 O 0.059 3.241
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L VAL 165 O 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L GLU 169 CG 0.059 3.241
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M LEU 132 CD2 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M ASP 57 CB 0.059 3.701
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L LEU 313 CD1 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L VAL 259 CG1 0.059 3.701
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M ILE 77 CG2 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M MET 231 CE 0.058 3.702
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N ILE 77 CG1 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N ALA 73 O 0.058 3.242
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L THR 340 CB 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L ALA 367 CB 0.058 3.702
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L SER 44 O 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L ARG 48 CG 0.058 3.242
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N VAL 232 CG2 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N ARG 228 O 0.057 3.243
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/Z U 12 O4' 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/Z U 11 C2' 0.057 3.283
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L ILE 77 CG1 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L ALA 73 O 0.057 3.243
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L THR 340 CB 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L VAL 337 O 0.057 3.243
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L LEU 314 CB 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L TYR 310 O 0.056 3.244
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L ARG 130 O 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L THR 134 CG2 0.056 3.244
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N ARG 307 CD 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N LEU 314 CD1 0.056 3.704
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N LEU 47 CD2 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N THR 42 CG2 0.056 3.704
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N GLY 256 CA 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N VAL 259 CG2 0.055 3.705
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/Z U 35 O4' 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/Z U 34 C2' 0.055 3.285
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/Z U 68 N3 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N GLN 199 NE2 0.055 3.225
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N SER 138 CB 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N PRO 62 CG 0.055 3.705
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N MET 125 O 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N MET 129 CG 0.055 3.245
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M VAL 165 O 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M ILE 168 CG1 0.055 3.245
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/Z U 66 O4' 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/Z U 65 C2' 0.055 3.285
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N ALA 281 CA 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M LEU 392 CD1 0.054 3.706
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L LEU 175 CD1 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L MET 217 CG 0.054 3.706
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L MET 311 CE 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L ILE 304 CD1 0.054 3.706
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/Z U 9 C6 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/Z U 8 C2' 0.054 3.586
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N GLN 364 O 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N ARG 368 CG 0.054 3.246
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M PRO 84 CB 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M VAL 39 CG1 0.054 3.706
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N TYR 327 CD2 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N ILE 294 CD1 0.054 3.586
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M GLU 315 CG 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M LEU 225 CD1 0.054 3.706
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/Z U 64 C2' 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/Z U 65 O4' 0.054 3.286
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L SER 296 O 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L LEU 299 CG 0.053 3.247
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/Z U 61 OP2 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M TYR 258 OH 0.053 2.427
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N ALA 135 CB 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N SER 61 CB 0.053 3.707
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M ARG 36 CG 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M VAL 100 CG1 0.053 3.707
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M LEU 291 CB 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N ILE 4 CD1 0.053 3.707
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L SER 78 OG 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L PRO 84 CB 0.053 3.287
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N LYS 321 CB 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N ILE 318 O 0.053 3.247
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M ALA 64 CA 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M ILE 131 CD1 0.053 3.707
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N LYS 120 CB 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N ARG 117 CB 0.053 3.707
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/Z U 17 C5' 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/Z U 16 C2' 0.052 3.708
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/Z U 79 O2' 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/Z U 80 C5' 0.052 3.288
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M TYR 327 OH 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M PHE 267 CA 0.052 3.288
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L LEU 56 CG 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L THR 52 O 0.051 3.249
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/Z U 30 C5' 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/Z U 29 C2' 0.051 3.709
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M THR 75 CG2 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M ALA 55 CB 0.051 3.709
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M ILE 176 CG2 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M TRP 173 O 0.051 3.249
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N SER 61 OG 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N ILE 131 CG1 0.051 3.289
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M VAL 113 CG2 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M MET 107 CE 0.051 3.709
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L ILE 176 CG2 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L TRP 173 O 0.050 3.250
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M SER 366 CA 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M HIS 370 O 0.050 3.250
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M TYR 279 CD2 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M THR 277 CG2 0.050 3.590
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/Z U 83 C5' 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/Z U 82 C2' 0.050 3.710
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L LEU 209 CD1 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L GLN 171 NE2 0.050 3.470
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N LEU 51 CD2 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N MET 107 CE 0.050 3.710
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M ILE 255 CD1 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M ILE 174 CG2 0.049 3.711
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L LYS 133 CG 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L MET 129 O 0.049 3.251
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N LYS 69 CE 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N ALA 64 CB 0.049 3.711
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N PHE 273 O 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N THR 277 CG2 0.049 3.251
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M LYS 120 CB 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M ARG 117 CB 0.049 3.711
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L GLU 276 CG 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L ILE 271 O 0.048 3.252
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N THR 320 CG2 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M ASP 254 CG 0.048 3.712
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M GLU 50 CG 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M MET 107 CE 0.048 3.712
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L ILE 172 CG2 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L ILE 77 CD1 0.048 3.712
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N VAL 238 CG2 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N ILE 234 O 0.048 3.252
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N LEU 175 CG 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N GLN 171 O 0.047 3.253
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M LEU 355 CD1 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M SER 332 CB 0.047 3.713
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L PHE 230 O 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L ILE 234 CG1 0.047 3.253
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N LYS 239 CB 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N LEU 235 O 0.047 3.253
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M PRO 40 CD 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M VAL 39 CG1 0.047 3.713
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M ASP 96 OD1 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L GLY 246 CA 0.046 3.254
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M PHE 273 O 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M THR 277 CG2 0.046 3.254
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N GLN 200 NE2 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N ARG 202 CD 0.046 3.474
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M GLY 85 O 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M ILE 88 CG2 0.046 3.254
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M ILE 97 CA 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M THR 33 O 0.046 3.254
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N PHE 74 CE2 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N ILE 35 CD1 0.046 3.594
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N LEU 18 CB 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N TYR 14 O 0.045 3.255
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N ILE 4 CD1 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M LEU 275 CD1 0.045 3.715
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L GLU 50 CG 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L MET 107 CE 0.045 3.715
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L LEU 132 CD2 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L ASP 57 CB 0.045 3.715
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/Z U 54 O4' 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/Z U 53 C2' 0.045 3.295
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L PHE 267 CB 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L TYR 327 OH 0.045 3.295
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L LEU 18 CB 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L TYR 14 O 0.045 3.255
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N LEU 76 CG 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N ALA 55 CB 0.044 3.716
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L LEU 384 CB 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/L GLN 388 OE1 0.044 3.256
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N TYR 197 CD2 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N ARG 193 O 0.044 3.136
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N VAL 238 CG1 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/N ILE 234 O 0.044 3.256
7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M VAL 396 CG2 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/M LEU 392 O 0.044 3.256
[deleted to fit within ticket limits]
> select subtract #26
28 atoms, 28 bonds, 3 residues, 6 models selected
> select add #27
3826 atoms, 3812 bonds, 503 residues, 2 models selected
> select subtract #27.1
3431 atoms, 3416 bonds, 454 residues, 16 models selected
> select subtract #27.2
3270 atoms, 3256 bonds, 431 residues, 15 models selected
> hide sel cartoons
> select add #27
3826 atoms, 3812 bonds, 503 residues, 14 models selected
> select subtract #27
28 atoms, 28 bonds, 3 residues, 15 models selected
> select add #26
14779 atoms, 15057 bonds, 5 pseudobonds, 1842 residues, 3 models selected
> coulombic sel
Using Amber 20 recommended default charges and atom types for standard
residues
Coulombic values for 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb_K
SES surface #1.8: minimum, -15.77, mean -0.30, maximum 13.72
Coulombic values for 9cgi_A SES surface #26.2: minimum, -21.89, mean -1.27,
maximum 23.84
Coulombic values for 9cgi_B SES surface #26.3: minimum, -17.78, mean -3.16,
maximum 11.29
Coulombic values for 9cgi_C SES surface #26.4: minimum, -16.72, mean -3.70,
maximum 11.33
Coulombic values for 9cgi_D SES surface #26.5: minimum, -17.18, mean -2.14,
maximum 10.58
Coulombic values for 9cgi_E SES surface #26.6: minimum, -17.72, mean -2.81,
maximum 11.54
To also show corresponding color key, enter the above coulombic command and
add key true
> select subtract #26
28 atoms, 28 bonds, 3 residues, 6 models selected
> select add #1
44999 atoms, 45909 bonds, 47 pseudobonds, 5656 residues, 2 models selected
> show sel cartoons
> ui mousemode right select
> select clear
> hide #!5 models
> select add #26
14751 atoms, 15029 bonds, 5 pseudobonds, 1839 residues, 2 models selected
> ui mousemode right "translate selected models"
> view matrix models #26,1,0,0,-1.1886,0,1,0,17.558,0,0,1,8.777
> ui mousemode right "rotate selected models"
> view matrix models
> #26,0.9949,-0.094514,0.035185,8.5037,0.031255,-0.042748,-0.9986,390.05,0.095886,0.99461,-0.039576,34.591
> view matrix models
> #26,-0.41206,0.33602,-0.84693,360.82,-0.81363,-0.55409,0.17602,384.01,-0.41013,0.76163,0.50172,51.686
> view matrix models
> #26,-0.20045,0.1588,-0.96675,378.15,0.4724,-0.84882,-0.23738,293.61,-0.85829,-0.50427,0.095133,424.02
> view matrix models
> #26,0.32994,0.27052,-0.90441,254.68,0.66956,-0.74243,0.022195,188.56,-0.66546,-0.61288,-0.42608,514.95
> view matrix models
> #26,0.97015,0.24011,-0.033876,-26.819,0.24057,-0.93552,0.25872,247.3,0.03043,-0.25915,-0.96536,444.2
> view matrix models
> #26,0.96087,0.25429,-0.10988,-12.186,0.27518,-0.92175,0.27324,235.92,-0.031804,-0.29278,-0.95565,458.89
> view matrix models
> #26,-0.091514,-0.9932,-0.071913,374.78,-0.77748,0.02614,0.62837,188.77,-0.62222,0.11341,-0.77458,457.26
> view matrix models
> #26,-0.92508,-0.33598,-0.17703,429.66,-0.37951,0.80099,0.46302,23.814,-0.013766,0.49551,-0.86849,307.36
> view matrix models
> #26,-0.54535,-0.78706,-0.28833,462.14,-0.83645,0.48869,0.24805,199.12,-0.05433,0.37645,-0.92484,345.82
> hide sel surfaces
> view matrix models
> #26,-0.8066,0.33689,-0.48569,358.9,0.15804,0.91468,0.37199,-73.672,0.56957,0.22329,-0.79103,234.18
> show sel surfaces
> view matrix models
> #26,-0.45304,0.73558,-0.50366,235.11,0.78479,0.59709,0.16612,-85.793,0.42292,-0.32001,-0.84778,362.03
> view matrix models
> #26,-0.42771,0.73503,-0.52612,235.4,0.78958,0.58714,0.1784,-87.425,0.44004,-0.33911,-0.83149,359.02
> view matrix models
> #26,-0.53356,0.73211,-0.42347,233.37,0.76521,0.63113,0.12699,-80.263,0.36024,-0.25628,-0.89697,372.01
> view matrix models
> #26,-0.64662,0.48872,-0.58569,326.7,0.28647,0.86719,0.40734,-95.201,0.70697,0.095611,-0.70075,213.41
> view matrix models
> #26,-0.74162,0.42068,-0.52252,341.57,0.25646,0.89756,0.35863,-85.248,0.61986,0.13196,-0.77353,237.05
> view matrix models
> #26,-0.3342,-0.77748,-0.53276,474.15,-0.87787,0.46249,-0.12424,282.39,0.343,0.42618,-0.83709,248.55
> ui mousemode right "translate selected models"
> view matrix models
> #26,-0.3342,-0.77748,-0.53276,469.14,-0.87787,0.46249,-0.12424,271.49,0.343,0.42618,-0.83709,252.11
> view matrix models
> #26,-0.3342,-0.77748,-0.53276,462.55,-0.87787,0.46249,-0.12424,268.16,0.343,0.42618,-0.83709,252.09
> ui mousemode right "rotate selected models"
> view matrix models
> #26,-0.064152,-0.94938,-0.30751,398.88,-0.83172,-0.11942,0.5422,222.37,-0.55148,0.29055,-0.78195,418.58
> view matrix models
> #26,-0.70823,-0.19994,-0.67708,459.8,-0.32067,0.94552,0.056216,54.026,0.62895,0.25693,-0.73376,210.03
> view matrix models
> #26,-0.2232,0.40519,-0.88657,317.86,0.62828,0.75519,0.18697,-104.68,0.74528,-0.51528,-0.42313,255.39
> ui mousemode right "translate selected models"
> view matrix models
> #26,-0.2232,0.40519,-0.88657,292.6,0.62828,0.75519,0.18697,-105.78,0.74528,-0.51528,-0.42313,272.1
> ui mousemode right "rotate selected models"
> view matrix models
> #26,-0.56416,0.70946,-0.42236,206.56,0.64949,0.065482,-0.75755,197.81,-0.50979,-0.70169,-0.49773,536.08
> ui mousemode right "translate selected models"
> view matrix models
> #26,-0.56416,0.70946,-0.42236,218.03,0.64949,0.065482,-0.75755,195.45,-0.50979,-0.70169,-0.49773,533.06
> ui mousemode right "rotate selected models"
> view matrix models
> #26,-0.88295,0.46108,0.088372,211.15,-0.46329,-0.82528,-0.32292,449.77,-0.075962,-0.32607,0.94229,101.97
> ui mousemode right "translate selected models"
> view matrix models
> #26,-0.88295,0.46108,0.088372,240.01,-0.46329,-0.82528,-0.32292,403.92,-0.075962,-0.32607,0.94229,190.96
> view matrix models
> #26,-0.88295,0.46108,0.088372,247.52,-0.46329,-0.82528,-0.32292,432.94,-0.075962,-0.32607,0.94229,204.75
> view matrix models
> #26,-0.88295,0.46108,0.088372,251.15,-0.46329,-0.82528,-0.32292,431.56,-0.075962,-0.32607,0.94229,207.9
> view matrix models
> #26,-0.88295,0.46108,0.088372,249.13,-0.46329,-0.82528,-0.32292,436.72,-0.075962,-0.32607,0.94229,208.06
> ui mousemode right "rotate selected models"
> view matrix models
> #26,-0.92302,0.38037,0.057922,275.72,-0.37782,-0.86759,-0.32332,429,-0.072728,-0.32031,0.94452,206.09
> ui mousemode right "move picked models"
> ui mousemode right "translate selected models"
> view matrix models
> #26,-0.92302,0.38037,0.057922,272.94,-0.37782,-0.86759,-0.32332,432.28,-0.072728,-0.32031,0.94452,206.3
> view matrix models
> #26,-0.92302,0.38037,0.057922,273.18,-0.37782,-0.86759,-0.32332,428.72,-0.072728,-0.32031,0.94452,204.54
> ui tool show Matchmaker
> matchmaker #27/A to #26/C pairing ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 9cgi, chain C (#26) with 7pno, chain A (#27), sequence alignment
score = 264.9
RMSD between 47 pruned atom pairs is 0.588 angstroms; (across all 49 pairs:
0.738)
> ui mousemode right select
> select clear
> select add #26
14751 atoms, 15029 bonds, 5 pseudobonds, 1839 residues, 2 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #26,-0.96833,0.24704,0.036201,307.69,-0.24321,-0.90047,-0.36057,418.41,-0.056477,-0.35795,0.93203,210.53
> ui mousemode right "translate selected models"
> view matrix models
> #26,-0.96833,0.24704,0.036201,299.47,-0.24321,-0.90047,-0.36057,418.25,-0.056477,-0.35795,0.93203,208.56
> ui tool show Matchmaker
> matchmaker #27/A to #26/C pairing ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 9cgi, chain C (#26) with 7pno, chain A (#27), sequence alignment
score = 264.9
RMSD between 47 pruned atom pairs is 0.588 angstroms; (across all 49 pairs:
0.738)
> ui mousemode right select
> select clear
> lighting flat
> ui tool show Matchmaker
> matchmaker #28/A to #1/Q pairing ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb, chain Q
(#1) with 4co6, chain A (#28), sequence alignment score = 1659
RMSD between 199 pruned atom pairs is 0.774 angstroms; (across all 330 pairs:
4.755)
> select add #27
3798 atoms, 3784 bonds, 500 residues, 1 model selected
> select subtract #27
14 models selected
> select add #28
7640 atoms, 7651 bonds, 10 pseudobonds, 1078 residues, 2 models selected
> ui mousemode right "translate selected models"
> view matrix models
> #28,0.85468,-0.4086,0.32028,165.24,-0.41357,-0.16294,0.89577,131.61,-0.31383,-0.89805,-0.30824,398.15
> view matrix models
> #28,0.85468,-0.4086,0.32028,212.71,-0.41357,-0.16294,0.89577,99.285,-0.31383,-0.89805,-0.30824,361.28
> view matrix models
> #28,0.85468,-0.4086,0.32028,206.29,-0.41357,-0.16294,0.89577,64.963,-0.31383,-0.89805,-0.30824,396.62
> ui mousemode right "rotate selected models"
> view matrix models
> #28,0.85664,-0.41291,0.30932,206.88,-0.40524,-0.16747,0.89874,64.538,-0.3193,-0.89524,-0.31079,396.94
> view matrix models
> #28,0.84646,-0.39223,0.36008,204.16,-0.44398,-0.14666,0.88395,66.574,-0.2939,-0.9081,-0.29828,395.43
> view matrix models
> #28,0.85216,-0.40332,0.33342,205.58,-0.42359,-0.15753,0.89205,65.483,-0.30726,-0.9014,-0.30508,396.24
> view matrix models
> #28,-0.59605,-0.58709,-0.54777,317.37,-0.65222,0.7519,-0.096164,112.18,0.46833,0.29995,-0.83108,370.51
> ui mousemode right select
> select clear
> ui mousemode right "rotate selected models"
> select add #27
3798 atoms, 3784 bonds, 500 residues, 1 model selected
> select add #28
11438 atoms, 11435 bonds, 10 pseudobonds, 1578 residues, 17 models selected
> select subtract #27
7640 atoms, 7651 bonds, 10 pseudobonds, 1078 residues, 22 models selected
> view matrix models
> #28,-0.59854,-0.60076,-0.52994,316.75,-0.63906,0.75698,-0.13636,113.73,0.48307,0.25705,-0.837,371.01
> view matrix models
> #28,0.96383,-0.25551,-0.075756,220.53,-0.13769,-0.23406,-0.96242,156.2,0.22818,0.93805,-0.26077,337.63
> ui mousemode right "translate selected models"
> view matrix models
> #28,0.96383,-0.25551,-0.075756,228.41,-0.13769,-0.23406,-0.96242,177.36,0.22818,0.93805,-0.26077,323.87
> view matrix models
> #28,0.96383,-0.25551,-0.075756,235.45,-0.13769,-0.23406,-0.96242,167.73,0.22818,0.93805,-0.26077,328.82
> view matrix models
> #28,0.96383,-0.25551,-0.075756,225.93,-0.13769,-0.23406,-0.96242,148.47,0.22818,0.93805,-0.26077,307.49
> ui mousemode right select
> select clear
> show #!5 models
> hide #!5 models
> select add #28
7640 atoms, 7651 bonds, 10 pseudobonds, 1078 residues, 2 models selected
> select subtract #28
6 models selected
> select add #28.4
1439 atoms, 200 residues, 1 model selected
> select subtract #28.4
1 model selected
> select add #28.5
317 atoms, 40 residues, 1 model selected
> show sel surfaces
> select clear
> save "/Users/kompa012/Desktop/NiP N protein article/Figures/mechanism 1.png"
> width 3000 height 2374 supersample 3 transparentBackground true
> turn y 90
> turn y -90
> turn y -120
> turn y 120
[Repeated 1 time(s)]
> turn x 30
> save "/Users/kompa012/Desktop/NiP N protein article/Figures/mechanism 2.png"
> width 3000 height 2374 supersample 3 transparentBackground true
> open 4co6 fromDatabase pdb format mmcif
4co6 title:
Crystal structure of the Nipah virus RNA free nucleoprotein- phosphoprotein
complex [more info...]
Chain information for 4co6 #29
---
Chain | Description | UniProt
A B C | NUCLEOPROTEIN | NCAP_NIPAV 32-383
D E F | PHOSPHOPROTEIN | PHOSP_NIPAV 1-50
Non-standard residues in 4co6 #29
---
BR — bromide ion
CL — chloride ion
4co6 mmCIF Assemblies
---
1| software_defined_assembly
2| software_defined_assembly
3| software_defined_assembly
10 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
Cell requested for row 27 is out of bounds for table with 35 rows! Resizing
table model.
> open 4co6 fromDatabase pdb format mmcif
4co6 title:
Crystal structure of the Nipah virus RNA free nucleoprotein- phosphoprotein
complex [more info...]
Chain information for 4co6 #30
---
Chain | Description | UniProt
A B C | NUCLEOPROTEIN | NCAP_NIPAV 32-383
D E F | PHOSPHOPROTEIN | PHOSP_NIPAV 1-50
Non-standard residues in 4co6 #30
---
BR — bromide ion
CL — chloride ion
4co6 mmCIF Assemblies
---
1| software_defined_assembly
2| software_defined_assembly
3| software_defined_assembly
10 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> open 4co6 fromDatabase pdb format mmcif
4co6 title:
Crystal structure of the Nipah virus RNA free nucleoprotein- phosphoprotein
complex [more info...]
Chain information for 4co6 #31
---
Chain | Description | UniProt
A B C | NUCLEOPROTEIN | NCAP_NIPAV 32-383
D E F | PHOSPHOPROTEIN | PHOSP_NIPAV 1-50
Non-standard residues in 4co6 #31
---
BR — bromide ion
CL — chloride ion
4co6 mmCIF Assemblies
---
1| software_defined_assembly
2| software_defined_assembly
3| software_defined_assembly
10 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> select add #29
7640 atoms, 7651 bonds, 10 pseudobonds, 1078 residues, 2 models selected
> select add #30
15280 atoms, 15302 bonds, 20 pseudobonds, 2156 residues, 4 models selected
> select add #31
22920 atoms, 22953 bonds, 30 pseudobonds, 3234 residues, 6 models selected
> hide sel atoms
> show sel cartoons
> show sel surfaces
> hide sel surfaces
> select subtract #29
15280 atoms, 15302 bonds, 20 pseudobonds, 2156 residues, 22 models selected
> select subtract #30
7640 atoms, 7651 bonds, 10 pseudobonds, 1078 residues, 14 models selected
> select subtract #31.2
5046 atoms, 5009 bonds, 8 pseudobonds, 748 residues, 8 models selected
> select subtract #31.5
4729 atoms, 4690 bonds, 8 pseudobonds, 708 residues, 7 models selected
> hide sel cartoons
> select add #31
7640 atoms, 7651 bonds, 10 pseudobonds, 1078 residues, 6 models selected
> select subtract #31
6 models selected
> select add #30
7640 atoms, 7651 bonds, 10 pseudobonds, 1078 residues, 2 models selected
> select subtract #30.2
5046 atoms, 5009 bonds, 8 pseudobonds, 748 residues, 8 models selected
> select subtract #30.5
4729 atoms, 4690 bonds, 8 pseudobonds, 708 residues, 7 models selected
> hide sel cartoons
> select add #30
7640 atoms, 7651 bonds, 10 pseudobonds, 1078 residues, 6 models selected
> select subtract #30
6 models selected
> select add #29
7640 atoms, 7651 bonds, 10 pseudobonds, 1078 residues, 2 models selected
> select subtract #29.2
5046 atoms, 5009 bonds, 8 pseudobonds, 748 residues, 8 models selected
> select subtract #29.5
4729 atoms, 4690 bonds, 8 pseudobonds, 708 residues, 7 models selected
> hide sel cartoons
> ui tool show Matchmaker
> matchmaker #29/A to #28/A pairing ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 4co6, chain A (#28) with 4co6, chain A (#29), sequence alignment
score = 1787.5
RMSD between 330 pruned atom pairs is 0.000 angstroms; (across all 330 pairs:
0.000)
> ui tool show Matchmaker
> matchmaker #30/A to #28/A pairing ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 4co6, chain A (#28) with 4co6, chain A (#30), sequence alignment
score = 1787.5
RMSD between 330 pruned atom pairs is 0.000 angstroms; (across all 330 pairs:
0.000)
> matchmaker #31/A to #28/A pairing ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 4co6, chain A (#28) with 4co6, chain A (#31), sequence alignment
score = 1787.5
RMSD between 330 pruned atom pairs is 0.000 angstroms; (across all 330 pairs:
0.000)
> matchmaker #31/A to #28/A pairing ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 4co6, chain A (#28) with 4co6, chain A (#31), sequence alignment
score = 1787.5
RMSD between 330 pruned atom pairs is 0.000 angstroms; (across all 330 pairs:
0.000)
> select add #29
7640 atoms, 7651 bonds, 10 pseudobonds, 1078 residues, 6 models selected
> select subtract #29
6 models selected
> select add #29
7640 atoms, 7651 bonds, 10 pseudobonds, 1078 residues, 2 models selected
> ui mousemode right "translate selected models"
> view matrix models
> #29,0.96383,-0.25551,-0.075756,266.78,-0.13769,-0.23406,-0.96242,165.83,0.22818,0.93805,-0.26077,354.3
> select add #30
15280 atoms, 15302 bonds, 20 pseudobonds, 2156 residues, 10 models selected
> select subtract #29
7640 atoms, 7651 bonds, 10 pseudobonds, 1078 residues, 14 models selected
> view matrix models
> #30,0.96383,-0.25551,-0.075756,248.66,-0.13769,-0.23406,-0.96242,215.56,0.22818,0.93805,-0.26077,389.22
> select add #31
15280 atoms, 15302 bonds, 20 pseudobonds, 2156 residues, 10 models selected
> select subtract #30
7640 atoms, 7651 bonds, 10 pseudobonds, 1078 residues, 14 models selected
> view matrix models
> #31,0.96383,-0.25551,-0.075756,187.3,-0.13769,-0.23406,-0.96242,137.29,0.22818,0.93805,-0.26077,268.29
> view matrix models
> #31,0.96383,-0.25551,-0.075756,130.59,-0.13769,-0.23406,-0.96242,109.92,0.22818,0.93805,-0.26077,305.01
> view matrix models
> #31,0.96383,-0.25551,-0.075756,124.86,-0.13769,-0.23406,-0.96242,93.081,0.22818,0.93805,-0.26077,295.75
> select add #30
15280 atoms, 15302 bonds, 20 pseudobonds, 2156 residues, 10 models selected
> select subtract #31
7640 atoms, 7651 bonds, 10 pseudobonds, 1078 residues, 14 models selected
> view matrix models
> #30,0.96383,-0.25551,-0.075756,173.42,-0.13769,-0.23406,-0.96242,79.32,0.22818,0.93805,-0.26077,377.28
> select add #29
15280 atoms, 15302 bonds, 20 pseudobonds, 2156 residues, 10 models selected
> select subtract #30
7640 atoms, 7651 bonds, 10 pseudobonds, 1078 residues, 14 models selected
> view matrix models
> #29,0.96383,-0.25551,-0.075756,255.93,-0.13769,-0.23406,-0.96242,151.48,0.22818,0.93805,-0.26077,396.42
> select subtract #29
6 models selected
> seelct #28 /d
Unknown command: seelct #28 /d
> seelct #28 d
Unknown command: seelct #28 d
> select #29/d
319 atoms, 319 bonds, 42 residues, 1 model selected
> show sel surfaces
> select #30/d
319 atoms, 319 bonds, 42 residues, 1 model selected
> show sel surfaces
> select #31/d
319 atoms, 319 bonds, 42 residues, 1 model selected
> show sel cartoons
> show sel surfaces
> ui mousemode right select
> select clear
> save "/Users/kompa012/Desktop/NiP N protein article/Figures/mechanism 1.png"
> width 3000 height 2374 supersample 3 transparentBackground true
> turn y 120
> turn x 30
> save "/Users/kompa012/Desktop/NiP N protein article/Figures/mechanism 2.png"
> width 3000 height 2374 supersample 3 transparentBackground true
> save "/Users/kompa012/Desktop/NiP N protein article/Figures/Model
> mechanism.cxs"
——— End of log from Fri Apr 4 01:16:01 2025 ———
opened ChimeraX session
> select #31/a:3-31
Nothing selected
> select #31/a:3
Nothing selected
> select #31 /a :3
Nothing selected
> select #31 /a
2642 atoms, 2642 bonds, 2 pseudobonds, 378 residues, 2 models selected
> select #28,29,30,31 /a
10568 atoms, 10568 bonds, 8 pseudobonds, 1512 residues, 8 models selected
> select #28,29,30,31 /a :3
Nothing selected
> select #28,29,30,31 /a :4
Nothing selected
> select #28,29,30,31 /A :5
Nothing selected
> select #28,29,30,31 /A :34
36 atoms, 32 bonds, 4 residues, 4 models selected
> ui tool show "Show Sequence Viewer"
> sequence chain #31/A
Alignment identifier is 31/A
> select #28,29,30,31 /A :32-260
6856 atoms, 6956 bonds, 8 pseudobonds, 876 residues, 8 models selected
> ui tool show "Color Actions"
> color (#!28-31 & sel) #86dde2ff
> select #28,29,30,31 /A :261-369
3460 atoms, 3544 bonds, 436 residues, 4 models selected
> color (#!28-31 & sel) #d6b3c4ff
> select #28,29,30,31 /A :370-371
60 atoms, 60 bonds, 8 residues, 4 models selected
> color (#!28-31 & sel) #b1bf9eff
> select #27 /b
161 atoms, 160 bonds, 23 residues, 1 model selected
> select #27 /b :900
Nothing selected
> select add #31
7640 atoms, 7651 bonds, 10 pseudobonds, 1078 residues, 2 models selected
> select add #27
11438 atoms, 11435 bonds, 10 pseudobonds, 1578 residues, 9 models selected
> select subtract #31
3798 atoms, 3784 bonds, 500 residues, 21 models selected
> select add #26
18549 atoms, 18813 bonds, 5 pseudobonds, 2339 residues, 17 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #26,-0.98169,0.17801,-0.067753,334.4,-0.13878,-0.91214,-0.38566,406.93,-0.13045,-0.3692,0.92015,225.84,#27,0.78712,-0.45681,0.41444,167.1,-0.13234,-0.78136,-0.60989,158.53,0.60243,0.42521,-0.67548,340.1
> view matrix models
> #26,-0.98533,0.15754,-0.065556,338,-0.12027,-0.91371,-0.38816,404.49,-0.12105,-0.37458,0.91926,225.29,#27,0.79058,-0.46675,0.39639,167.34,-0.1492,-0.77463,-0.61457,158.72,0.5939,0.42673,-0.68204,340.26
> view matrix models
> #26,-0.97738,0.21135,0.0079217,312.75,-0.15714,-0.70059,-0.69605,437.61,-0.14156,-0.68155,0.71795,320.98,#27,0.82658,-0.38407,0.4114,167.46,-0.28026,-0.91478,-0.29091,152.66,0.48807,0.12516,-0.86378,341.98
> ui mousemode right "translate selected models"
> view matrix models
> #26,-0.97738,0.21135,0.0079217,308.9,-0.15714,-0.70059,-0.69605,435.59,-0.14156,-0.68155,0.71795,321.13,#27,0.82658,-0.38407,0.4114,163.61,-0.28026,-0.91478,-0.29091,150.65,0.48807,0.12516,-0.86378,342.13
> view matrix models
> #26,-0.97738,0.21135,0.0079217,307.27,-0.15714,-0.70059,-0.69605,434.71,-0.14156,-0.68155,0.71795,321.04,#27,0.82658,-0.38407,0.4114,161.98,-0.28026,-0.91478,-0.29091,149.76,0.48807,0.12516,-0.86378,342.05
> view matrix models
> #26,-0.97738,0.21135,0.0079217,306.89,-0.15714,-0.70059,-0.69605,433.23,-0.14156,-0.68155,0.71795,322.02,#27,0.82658,-0.38407,0.4114,161.61,-0.28026,-0.91478,-0.29091,148.28,0.48807,0.12516,-0.86378,343.03
> ui mousemode right "rotate selected models"
> view matrix models
> #26,-0.96061,0.23302,-0.15143,332.68,-0.21622,-0.969,-0.11951,371.4,-0.17458,-0.082061,0.98122,174.31,#27,0.72548,-0.48068,0.49257,160,0.076903,-0.65459,-0.75206,156.48,0.68393,0.58349,-0.43793,337.82
> ui mousemode right "translate selected models"
> view matrix models
> #26,-0.96061,0.23302,-0.15143,328.89,-0.21622,-0.969,-0.11951,383.3,-0.17458,-0.082061,0.98122,172.32,#27,0.72548,-0.48068,0.49257,156.21,0.076903,-0.65459,-0.75206,168.37,0.68393,0.58349,-0.43793,335.83
> ui mousemode right "rotate selected models"
> view matrix models
> #26,-0.89931,0.42408,-0.10672,277.36,-0.41366,-0.90413,-0.10697,403.86,-0.14186,-0.052056,0.98852,160.2,#27,0.70644,-0.32696,0.62772,154.98,0.25077,-0.71374,-0.65398,165.34,0.66185,0.61942,-0.42223,335.91
> ui mousemode right "translate selected models"
> view matrix models
> #26,-0.89931,0.42408,-0.10672,279.76,-0.41366,-0.90413,-0.10697,408.57,-0.14186,-0.052056,0.98852,160.17,#27,0.70644,-0.32696,0.62772,157.38,0.25077,-0.71374,-0.65398,170.05,0.66185,0.61942,-0.42223,335.88
> view matrix models
> #26,-0.89931,0.42408,-0.10672,279.39,-0.41366,-0.90413,-0.10697,406.06,-0.14186,-0.052056,0.98852,161.2,#27,0.70644,-0.32696,0.62772,157,0.25077,-0.71374,-0.65398,167.54,0.66185,0.61942,-0.42223,336.91
> view matrix models
> #26,-0.89931,0.42408,-0.10672,275.97,-0.41366,-0.90413,-0.10697,417.73,-0.14186,-0.052056,0.98852,155.23,#27,0.70644,-0.32696,0.62772,153.59,0.25077,-0.71374,-0.65398,179.21,0.66185,0.61942,-0.42223,330.94
> ui mousemode right "rotate selected models"
> view matrix models
> #26,-0.81438,0.55189,-0.17946,254.92,-0.56104,-0.82779,0.00028938,408.15,-0.14839,0.10092,0.98377,131.66,#27,0.60046,-0.27636,0.75039,152.47,0.43568,-0.67381,-0.59679,177.11,0.67055,0.68527,-0.28419,328.81
> ui mousemode right "translate selected models"
> view matrix models
> #26,-0.81438,0.55189,-0.17946,253.08,-0.56104,-0.82779,0.00028938,403.24,-0.14839,0.10092,0.98377,141.15,#27,0.60046,-0.27636,0.75039,150.63,0.43568,-0.67381,-0.59679,172.2,0.67055,0.68527,-0.28419,338.3
> view matrix models
> #26,-0.81438,0.55189,-0.17946,264.85,-0.56104,-0.82779,0.00028938,399.04,-0.14839,0.10092,0.98377,146.15,#27,0.60046,-0.27636,0.75039,162.4,0.43568,-0.67381,-0.59679,168,0.67055,0.68527,-0.28419,343.31
> ui mousemode right "rotate selected models"
> view matrix models
> #26,-0.84969,0.47946,-0.21942,291.23,-0.49086,-0.87123,-0.0029264,394.99,-0.19257,0.10522,0.97563,154.65,#27,0.60502,-0.35735,0.71151,162.61,0.37378,-0.66156,-0.6501,169.44,0.70302,0.65927,-0.26669,342.62
> ui mousemode right "translate selected models"
> view matrix models
> #26,-0.84969,0.47946,-0.21942,291.42,-0.49086,-0.87123,-0.0029264,394.43,-0.19257,0.10522,0.97563,161.56,#27,0.60502,-0.35735,0.71151,162.8,0.37378,-0.66156,-0.6501,168.89,0.70302,0.65927,-0.26669,349.53
> ui mousemode right select
Drag select of 9cgi_A SES surface, 73 of 1141544 triangles
> select clear
> select add #31
7640 atoms, 7651 bonds, 10 pseudobonds, 1078 residues, 2 models selected
> ui mousemode right "translate selected models"
> view matrix models
> #31,0.96383,-0.25551,-0.075756,108.1,-0.13769,-0.23406,-0.96242,91.973,0.22818,0.93805,-0.26077,293.09
> view matrix models
> #31,0.96383,-0.25551,-0.075756,98.757,-0.13769,-0.23406,-0.96242,88.128,0.22818,0.93805,-0.26077,293.9
> select add #30
15280 atoms, 15302 bonds, 20 pseudobonds, 2156 residues, 10 models selected
> select subtract #31
7640 atoms, 7651 bonds, 10 pseudobonds, 1078 residues, 14 models selected
> select add #29
15280 atoms, 15302 bonds, 20 pseudobonds, 2156 residues, 10 models selected
> select subtract #30
7640 atoms, 7651 bonds, 10 pseudobonds, 1078 residues, 14 models selected
> select add #28
15280 atoms, 15302 bonds, 20 pseudobonds, 2156 residues, 10 models selected
> select subtract #29
7640 atoms, 7651 bonds, 10 pseudobonds, 1078 residues, 14 models selected
> view matrix models
> #28,0.96383,-0.25551,-0.075756,248.12,-0.13769,-0.23406,-0.96242,162.23,0.22818,0.93805,-0.26077,302.26
> ui mousemode right select
> select clear
> save "/Users/kompa012/Desktop/NiP N protein article/Figures/mechanism 1.png"
> width 3000 height 2359 supersample 3 transparentBackground true
> turn y 120
> turn y -120
> select add #31
7640 atoms, 7651 bonds, 10 pseudobonds, 1078 residues, 2 models selected
> select add #30
15280 atoms, 15302 bonds, 20 pseudobonds, 2156 residues, 10 models selected
Drag select of 4co6_D SES surface, 20 of 56036 triangles, 56 residues
> ui mousemode right "translate selected models"
> select add #30
8070 atoms, 7651 bonds, 10 pseudobonds, 1134 residues, 4 models selected
> select add #31
15280 atoms, 15302 bonds, 20 pseudobonds, 2156 residues, 11 models selected
> select subtract #31
7640 atoms, 7651 bonds, 10 pseudobonds, 1078 residues, 14 models selected
> view matrix models
> #30,0.96383,-0.25551,-0.075756,104.68,-0.13769,-0.23406,-0.96242,72.142,0.22818,0.93805,-0.26077,368.25
> select add #31
15280 atoms, 15302 bonds, 20 pseudobonds, 2156 residues, 10 models selected
> select subtract #30
7640 atoms, 7651 bonds, 10 pseudobonds, 1078 residues, 14 models selected
> view matrix models
> #31,0.96383,-0.25551,-0.075756,86.058,-0.13769,-0.23406,-0.96242,104.92,0.22818,0.93805,-0.26077,279.35
> select add #29
15280 atoms, 15302 bonds, 20 pseudobonds, 2156 residues, 10 models selected
> select add #28
22920 atoms, 22953 bonds, 30 pseudobonds, 3234 residues, 18 models selected
> select subtract #31
15280 atoms, 15302 bonds, 20 pseudobonds, 2156 residues, 22 models selected
> view matrix models
> #28,0.96383,-0.25551,-0.075756,257.58,-0.13769,-0.23406,-0.96242,165.34,0.22818,0.93805,-0.26077,302,#29,0.96383,-0.25551,-0.075756,265.4,-0.13769,-0.23406,-0.96242,154.59,0.22818,0.93805,-0.26077,396.16
> turn y 120
> select subtract #29
7640 atoms, 7651 bonds, 10 pseudobonds, 1078 residues, 14 models selected
> select subtract #28
6 models selected
> select add #28
7640 atoms, 7651 bonds, 10 pseudobonds, 1078 residues, 2 models selected
> view matrix models
> #28,0.96383,-0.25551,-0.075756,253.14,-0.13769,-0.23406,-0.96242,182.51,0.22818,0.93805,-0.26077,459.68
> turn y -120
> view matrix models
> #28,0.96383,-0.25551,-0.075756,168.58,-0.13769,-0.23406,-0.96242,136.8,0.22818,0.93805,-0.26077,474.81
> turn y 120
> turn y -120
> ui mousemode right select
> select clear
> save "/Users/kompa012/Desktop/NiP N protein article/Figures/mechanism 1.png"
> width 3000 height 2359 supersample 3 transparentBackground true
> turn y 120
> save "/Users/kompa012/Desktop/NiP N protein article/Figures/mechanism 2.png"
> width 3000 height 2359 supersample 3 transparentBackground true
> turn x 30
> turn x -30
> turn y -120
> ui tool show "Side View"
> select #31/d
319 atoms, 319 bonds, 42 residues, 1 model selected
> color (#!31 & sel) #e2ffb7ff
> select clear
> lighting full
> lighting soft
> turn y 120
> turn y -120
> lighting shadows true intensity 0.5
> lighting shadows false
> lighting shadows true
> lighting shadows false
> turn y 120
> turn y -120
> save "/Users/kompa012/Desktop/NiP N protein article/Figures/mechanism 1.png"
> width 3000 height 2359 supersample 3 transparentBackground true
> turn y 120
> save "/Users/kompa012/Desktop/NiP N protein article/Figures/mechanism 2.png"
> width 3000 height 2359 supersample 3 transparentBackground true
> turn y -120
> save "/Users/kompa012/Desktop/NiP N protein article/Figures/mechanism 1.png"
> width 3000 height 2359 supersample 3 transparentBackground true
> save "/Users/kompa012/Desktop/NiP N protein article/Figures/Model
> mechanism.cxs"
> open "/Users/kompa012/Desktop/NiP N protein article/Figures/prot comparison
> hel.cxs" format session
Opened cryosparc_P78_J379_map_sharp.mrc as #5, grid size 540,540,540, pixel
0.885, shown at level 0.07, step 1, values float32
Opened cryosparc_P78_J377_009_volume_map.mrc as #4, grid size 540,540,540,
pixel 0.885, shown at level 0.044, step 1, values float32
Opened cryosparc_P78_J379_map_sharp_one.mrc as #12, grid size 540,540,540,
pixel 0.885, shown at level 0.07, step 1, values float32
Opened cryosparc_P78_J400_008_volume_map_sharp.mrc as #21, grid size
540,540,540, pixel 0.885, shown at level 0.03, step 1, values float32
opened ChimeraX session
> open "/Users/kompa012/Desktop/NiP N protein article/Figures/prot
> comparison1.cxs" format session
Opened cryosparc_P78_J379_map_sharp.mrc as #5, grid size 540,540,540, pixel
0.885, shown at level 0.07, step 1, values float32
Opened cryosparc_P78_J377_009_volume_map.mrc as #4, grid size 540,540,540,
pixel 0.885, shown at level 0.045, step 1, values float32
Opened cryosparc_P78_J379_map_sharp_one.mrc as #12, grid size 540,540,540,
pixel 0.885, shown at level 0.07, step 1, values float32
Opened cryosparc_P78_J400_008_volume_map_sharp.mrc as #21, grid size
540,540,540, pixel 0.885, shown at level 0.045, step 1, values float32
Opened cryosparc_P78_J368_map_sharp_zflip.mrc as #22, grid size 360,360,360,
pixel 0.885, shown at level 0.005, step 1, values float32
Opened cryosparc_P78_J378_map_sharp.mrc as #23, grid size 540,540,540, pixel
1.18, shown at level 0.005, step 1, values float32
Opened cryosparc_P78_J365_009_volume_map_zflip.mrc as #24, grid size
360,360,360, pixel 0.885, shown at level 0.045, step 1, values float32
Opened cryosparc_P78_J376_007_volume_map.mrc as #25, grid size 540,540,540,
pixel 1.18, shown at level 0.06, step 1, values float32
opened ChimeraX session
> show #!11 models
> show #!4 models
> select add #4
28 atoms, 28 bonds, 3 residues, 3 models selected
> volume #4 level 0.07
> volume #4 level 0.03
> transparency (#!1 & sel) 80
> select subtract #4
28 atoms, 28 bonds, 3 residues, 1 model selected
> select add #4
28 atoms, 28 bonds, 3 residues, 3 models selected
> ui mousemode right select
> select clear
> select add #4
2 models selected
> transparency #4.1 70
> select add #1
44999 atoms, 45909 bonds, 47 pseudobonds, 5656 residues, 4 models selected
> select add #6
44999 atoms, 45909 bonds, 51 pseudobonds, 5656 residues, 20 models selected
> show sel cartoons
> open "/Users/kompa012/Desktop/NiP N protein article/Figures/prot comparison
> hel.cxs"
Opened cryosparc_P78_J379_map_sharp.mrc as #5, grid size 540,540,540, pixel
0.885, shown at level 0.07, step 1, values float32
Opened cryosparc_P78_J377_009_volume_map.mrc as #4, grid size 540,540,540,
pixel 0.885, shown at level 0.044, step 1, values float32
Opened cryosparc_P78_J379_map_sharp_one.mrc as #12, grid size 540,540,540,
pixel 0.885, shown at level 0.07, step 1, values float32
Opened cryosparc_P78_J400_008_volume_map_sharp.mrc as #21, grid size
540,540,540, pixel 0.885, shown at level 0.03, step 1, values float32
opened ChimeraX session
> show #!4 models
> hide #!5 models
> show #!12 models
> hide #!12 models
> show #!12 models
> show sel cartoons
> select add #12
11 atoms, 10 bonds, 1 residue, 3 models selected
> select subtract #12
11 atoms, 10 bonds, 1 residue, 1 model selected
> open "/Users/kompa012/Desktop/NiP N protein article/Figures/Model
> mechanism.cxs"
Opened cryosparc_P78_J379_map_sharp.mrc as #5, grid size 540,540,540, pixel
0.885, shown at level 0.07, step 1, values float32
Opened cryosparc_P78_J377_009_volume_map.mrc as #4, grid size 540,540,540,
pixel 0.885, shown at level 0.045, step 1, values float32
Opened cryosparc_P78_J379_map_sharp_one.mrc as #12, grid size 540,540,540,
pixel 0.885, shown at level 0.07, step 1, values float32
Opened cryosparc_P78_J400_008_volume_map_sharp.mrc as #21, grid size
540,540,540, pixel 0.885, shown at level 0.045, step 1, values float32
Opened cryosparc_P78_J368_map_sharp_zflip.mrc as #22, grid size 360,360,360,
pixel 0.885, shown at level 0.005, step 1, values float32
Opened cryosparc_P78_J378_map_sharp.mrc as #23, grid size 540,540,540, pixel
1.18, shown at level 0.005, step 1, values float32
Opened cryosparc_P78_J365_009_volume_map_zflip.mrc as #24, grid size
360,360,360, pixel 0.885, shown at level 0.045, step 1, values float32
Opened cryosparc_P78_J376_007_volume_map.mrc as #25, grid size 540,540,540,
pixel 1.18, shown at level 0.06, step 1, values float32
opened ChimeraX session
> show #!4 models
> show #!11 models
> select add #4
2 models selected
> transparency #4.1 70
> hide #!1 models
> select add #11
3094 atoms, 3147 bonds, 398 residues, 3 models selected
> show sel cartoons
> show #!1 models
> hide #!31 models
> hide #!30 models
> hide #!29 models
> hide #!28 models
> hide #!26 models
> hide #!27 models
> hide #!4 models
> select clear
> ui mousemode right select
> select clear
> select #1/d,f,q
9282 atoms, 9441 bonds, 1 pseudobond, 1194 residues, 2 models selected
> select add #1
44999 atoms, 45909 bonds, 47 pseudobonds, 5656 residues, 5 models selected
> select subtract #1.1
41905 atoms, 42762 bonds, 46 pseudobonds, 5258 residues, 17 models selected
> select subtract #1.2
38811 atoms, 39615 bonds, 43 pseudobonds, 4860 residues, 16 models selected
> select subtract #1.14
35717 atoms, 36468 bonds, 43 pseudobonds, 4462 residues, 15 models selected
> select subtract #1.15
34034 atoms, 34617 bonds, 18 pseudobonds, 4378 residues, 14 models selected
> select add #1.15
35717 atoms, 34617 bonds, 18 pseudobonds, 4462 residues, 13 models selected
> hide sel cartoons
> hide sel atoms
> hide sel surfaces
> select #11:3-30
211 atoms, 213 bonds, 28 residues, 1 model selected
> color (#!11 & sel) #f8f0acff
> select #11:3-31
219 atoms, 221 bonds, 29 residues, 1 model selected
> select #11:32-260
1791 atoms, 1818 bonds, 229 residues, 1 model selected
> color (#!11 & sel) #79c7ccff
> select #11:261-369
865 atoms, 886 bonds, 109 residues, 1 model selected
> color (#!11 & sel) #cfacbdff
> select #11:370-400
219 atoms, 219 bonds, 31 residues, 1 model selected
> color (#!11 & sel) #abb999ff
> select clear
> show #!4 models
> volume #4 level 0.03
> volume #4 level 0.04
> volume #4 level 0.0375
> hide #!11 models
> hide #!1 models
> save "/Users/kompa012/Desktop/NiP N protein article/Figures/Figure 5S.cxs"
> show #!1 models
> hide #!1 models
> show #!1 models
> show #!11 models
> hide #!11 models
> hide #!1 models
> save "/Users/kompa012/Desktop/NiP N protein article/Figures/layers
> interaction map 720.png" width 3000 height 2355 supersample 3
> transparentBackground true
> show #!1 models
> show #!11 models
> save "/Users/kompa012/Desktop/NiP N protein article/Figures/layers
> interaction map 720 prot.png" width 3000 height 2355 supersample 3
> transparentBackground true
> save "/Users/kompa012/Desktop/NiP N protein article/Figures/layers
> interaction map 720 prot zoom.png" width 3000 height 2355 supersample 3
> transparentBackground true
> select add #4
2 models selected
> transparency #4.1 90
> transparency #4.1 80
> select clear
> save "/Users/kompa012/Desktop/NiP N protein article/Figures/layers
> interaction map 720 prot.png" width 3000 height 2352 supersample 3
> transparentBackground true
> hide #!1 models
> hide #!11 models
> save "/Users/kompa012/Desktop/NiP N protein article/Figures/layers
> interaction map 720.png" width 3000 height 2352 supersample 3
> transparentBackground true
> show #!1 models
> show #!11 models
> save "/Users/kompa012/Desktop/NiP N protein article/Figures/layers
> interaction map 720 prot zoom.png" width 3000 height 2352 supersample 3
> transparentBackground true
> hide #!4 models
> select #1/d:158
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/d:158
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/d:154
11 atoms, 10 bonds, 1 residue, 1 model selected
> hide #!11 models
> hide #!1 models
> show #!26 models
> hide #!26 models
> show #!20 models
> show #!19 models
> show #!18 models
> show #!17 models
> show #!16 models
> show #!15 models
> show #!14 models
> show #!13 models
> show #!1 models
> select add #1
44999 atoms, 45909 bonds, 47 pseudobonds, 5656 residues, 3 models selected
> select subtract #1
15 models selected
> select add #1
44999 atoms, 45909 bonds, 47 pseudobonds, 5656 residues, 2 models selected
> hide sel cartoons
> select #1/k
3094 atoms, 3147 bonds, 398 residues, 1 model selected
> show sel cartoons
> select #1/q
3094 atoms, 3147 bonds, 398 residues, 1 model selected
> show sel cartoons
> hide sel cartoons
> select #1/z
1683 atoms, 1851 bonds, 84 residues, 1 model selected
> show sel cartoons
> hide sel cartoons
> select #1/z
1683 atoms, 1851 bonds, 84 residues, 1 model selected
> 43-49
Unknown command: 43-49
> show sel cartoons
> hide sel cartoons
> select #1/z:43-49
140 atoms, 153 bonds, 7 residues, 1 model selected
> show sel cartoons
> show #!9 models
> show #!8 models
> show #!7 models
> hide #!7 models
> show #!10 models
> hide #!13 models
> select clear
> hide #!20 models
> hide #!19 models
> hide #!18 models
> hide #!17 models
> hide #!16 models
> hide #!15 models
> hide #!14 models
> hide #!10 models
> hide #!9 models
> hide #!8 models
> save "/Users/kompa012/Desktop/NiP N protein article/Figures/NiV prot.png"
> width 3000 height 2352 supersample 3 transparentBackground true
> show #!7 models
> hide #!7 models
> show #!8 models
> hide #!1 models
> save "/Users/kompa012/Desktop/NiP N protein article/Figures/Sendai.png"
> width 3000 height 2352 supersample 3 transparentBackground true
> show #!9 models
> hide #!8 models
> save "/Users/kompa012/Desktop/NiP N protein article/Figures/Ebola top.png"
> width 3000 height 2352 supersample 3 transparentBackground true
> show #!10 models
> hide #!9 models
> save "/Users/kompa012/Desktop/NiP N protein article/Figures/Measles.png"
> width 3000 height 2352 supersample 3 transparentBackground true
> show #!14 models
> hide #!10 models
> save "/Users/kompa012/Desktop/NiP N protein article/Figures/HMPV top.png"
> width 3000 height 2352 supersample 3 transparentBackground true
> show #!15 models
> hide #!14 models
> show #!14 models
> hide #!14 models
> save "/Users/kompa012/Desktop/NiP N protein article/Figures/HPIV3.png" width
> 3000 height 2352 supersample 3 transparentBackground true
> show #!16 models
> hide #!15 models
> save "/Users/kompa012/Desktop/NiP N protein article/Figures/HPIV5.png" width
> 3000 height 2352 supersample 3 transparentBackground true
> show #!17 models
> hide #!16 models
> save "/Users/kompa012/Desktop/NiP N protein article/Figures/MuV top.png"
> width 3000 height 2352 supersample 3 transparentBackground true
> show #!18 models
> hide #!17 models
> save "/Users/kompa012/Desktop/NiP N protein article/Figures/NDV top.png"
> width 3000 height 2352 supersample 3 transparentBackground true
> show #!19 models
> hide #!18 models
> save "/Users/kompa012/Desktop/NiP N protein article/Figures/HEV top.png"
> width 3000 height 2352 supersample 3 transparentBackground true
> show #!20 models
> hide #!19 models
> save "/Users/kompa012/Desktop/NiP N protein article/Figures/RSV.png" width
> 3000 height 2352 supersample 3 transparentBackground true
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!20 models
> select #1/k:178,192,193,199,258
52 atoms, 49 bonds, 5 residues, 1 model selected
> show sel atoms
> select #1/z:43-49
140 atoms, 153 bonds, 7 residues, 1 model selected
> show sel cartoons
> show sel atoms
> hide sel cartoons
> select clear
> ui mousemode right distance
> distance #1/K:178@NZ #1/Z:46@OP1
Distance between 7nt5_J377_intactmodel-coot-0_real_space_refined_030.pdb #1/K
LYS 178 NZ and /Z U 46 OP1: 3.049Å
> show #!6 models
> ~distance #1/Z:45@OP1 #1/K:265@N
> show #!8 models
> select add #8.2
120 atoms, 6 residues, 1 model selected
> show sel atoms
> hide sel cartoons
> ui mousemode right select
> select clear
> select #8/A:180
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> hide #!1 models
> select #8/A:260
12 atoms, 12 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel ball
Changed 12 atom styles
> select #8/A:180
9 atoms, 8 bonds, 1 residue, 1 model selected
> style sel ball
Changed 9 atom styles
> select #8/A:194
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel ball
Changed 8 atom styles
> show #!1 models
> hide #!8 models
> show #!8 models
> hide #!1 models
> select #8/A:195
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel sphere
Changed 11 atom styles
> style sel ball
Changed 11 atom styles
> ui mousemode right distance
> select add #8.2
131 atoms, 10 bonds, 7 residues, 2 models selected
> select subtract #8.1
120 atoms, 6 residues, 3 models selected
> style sel ball
Changed 120 atom styles
> select subtract #8.2
1 model selected
> show #!1 models
> hide #!1 models
> distance #8/A:180@NZ #8/B:4@OP1
Distance between 6m7d sendai #8/A LYS 180 NZ and /B U 4 OP1: 2.942Å
> distance #8/B:5@OP2 #8/A:180@NZ
Distance between 6m7d sendai #8/B U 5 OP2 and /A LYS 180 NZ: 2.958Å
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> distance #8/A:194@ND2 #8/B:6@OP2
Distance between 6m7d sendai #8/A ASN 194 ND2 and /B U 6 OP2: 2.579Å
> show #!1 models
> hide #!1 models
> distance #8/A:195@NH2 #8/B:6@OP2
Distance between 6m7d sendai #8/A ARG 195 NH2 and /B U 6 OP2: 2.706Å
> show #!1 models
> hide #!6 models
> show #!6 models
> hide #!8 models
> show #!8 models
> hide #!1 models
> ui mousemode right select
> select #8/A:201
9 atoms, 8 bonds, 1 residue, 1 model selected
> style sel ball
Changed 9 atom styles
> show sel atoms
> show #!1 models
> hide #!1 models
> hide #!8 models
> show #!1 models
> save "/Users/kompa012/Desktop/NiP N protein article/Figures/NiV DNA zoom
> prot.png" width 3000 height 2352 supersample 3 transparentBackground true
> hide #!1 models
> show #!8 models
> save "/Users/kompa012/Desktop/NiP N protein article/Figures/Sendai DNA zoom
> prot.png" width 3000 height 2352 supersample 3 transparentBackground true
> save "/Users/kompa012/Desktop/NiP N protein article/Figures/figure 4 prot
> compar.cxs"
> select clear
> show #!9 models
> hide #!8 models
Cell requested for row 0 is out of bounds for table with 33 rows! Resizing
table model.
> show #!1 models
> hide #!9 models
> show #!9 models
> hide #!1 models
> select #9/A:181
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #9/A:182
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> select #9/A:181
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> hide sel atoms
> select #9/A:182
9 atoms, 8 bonds, 1 residue, 1 model selected
> style sel ball
Changed 9 atom styles
> show #!1 models
> hide #!1 models
> select #9/A:174
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel ball
Changed 11 atom styles
> show #!1 models
> hide #!1 models
> select #9/A:175
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel ball
Changed 9 atom styles
> show #!1 models
> hide #!1 models
> show #!1 models
> close #2
> close #7
> hide #!9 models
> show #!9 models
> hide #!9 models
> hide #!1 models
> show #!1 models
> show #!9 models
> hide #!1 models
> select #9/A:238
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel ball
Changed 9 atom styles
> show #!1 models
> hide #!9 models
> show #!9 models
> hide #!1 models
> select #9/A:160
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel ball
Changed 9 atom styles
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!1 models
> select clear
> save "/Users/kompa012/Desktop/NiP N protein article/Figures/EBOLA DNA zoom
> prot.png" width 3000 height 2352 supersample 3 transparentBackground true
> show #!10 models
> hide #!9 models
> select add #10.3
120 atoms, 6 residues, 1 model selected
> show sel atoms
> hide sel cartoons
> style sel ball
Changed 120 atom styles
> select add #10
3073 atoms, 3136 bonds, 2 pseudobonds, 383 residues, 3 models selected
> select subtract #10
2 models selected
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> select #10/B:200
7 atoms, 6 bonds, 1 residue, 1 model selected
> show sel atoms
> hide sel atoms
> show #!1 models
> hide #!1 models
> select #10/B:201
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel ball
Changed 9 atom styles
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> select #10/B:180
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel ball
Changed 9 atom styles
> show #!1 models
> hide #!1 models
> ui mousemode right distance
> distance #10/B:180@NZ #10/R:10@OP1
Distance between 4uft Measles #10/B LYS 180 NZ and /R C 10 OP1: 3.676Å
> distance #10/R:11@OP2 #10/B:180@NZ
Distance between 4uft Measles #10/R C 11 OP2 and /B LYS 180 NZ: 4.476Å
> ~distance #10/R:11@OP2 #10/B:180@NZ
> show #!1 models
> hide #!1 models
> ui mousemode right select
> select #10/B:260
12 atoms, 12 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel ball
Changed 12 atom styles
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!10 models
> show #!10 models
> hide #!1 models
> select #10/B:194
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel ball
Changed 11 atom styles
> select #10/B:195
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel ball
Changed 11 atom styles
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!10 models
> show #!10 models
> hide #!1 models
> ui mousemode right distance
> distance #10/B:194@NH2 #10/R:12@OP2
Distance between 4uft Measles #10/B ARG 194 NH2 and /R C 12 OP2: 5.503Å
> distance #10/B:194@NH1 #10/R:12@OP2
Distance between 4uft Measles #10/B ARG 194 NH1 and /R C 12 OP2: 3.413Å
> ~distance #10/B:194@NH2 #10/R:12@OP2
> distance #10/B:195@NH2 #10/R:11@OP1
Distance between 4uft Measles #10/B ARG 195 NH2 and /R C 11 OP1: 7.347Å
> ~distance #10/B:195@NH2 #10/R:11@OP1
> distance #10/B:195@NH1 #10/R:11@OP1
Distance between 4uft Measles #10/B ARG 195 NH1 and /R C 11 OP1: 6.955Å
> ~distance #10/B:195@NH1 #10/R:11@OP1
> show #!1 models
> hide #!1 models
> ui mousemode right select
> select clear
> save "/Users/kompa012/Desktop/NiP N protein article/Figures/measls DNA zoom
> prot.png" width 3000 height 2352 supersample 3 transparentBackground true
> show #!14 models
> hide #!10 models
> select add #14.5
280 atoms, 14 residues, 1 model selected
> hide sel cartoons
> show sel atoms
> style sel ball
Changed 280 atom styles
> select add #14
6056 atoms, 6171 bonds, 758 residues, 2 models selected
> color (#!14 & sel) byhetero
> select subtract #14
5 models selected
> show #!1 models
> hide #!1 models
> select #14/C:171
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel ball
Changed 9 atom styles
> show #!1 models
> hide #!1 models
> ui mousemode right distance
> distance #10/B:195@NH1 #14/C:171@NZ
Distance between 4uft Measles #10/B ARG 195 NH1 and 8pds HMPV #14/C LYS 171
NZ: 7.647Å
> distance #14/E:69@OP2 #14/C:171@NZ
Distance between 8pds HMPV #14/E C 69 OP2 and /C LYS 171 NZ: 3.023Å
> distance #14/E:68@OP1 #14/C:171@NZ
Distance between 8pds HMPV #14/E C 68 OP1 and /C LYS 171 NZ: 3.361Å
> ui mousemode right select
> select clear
> show #!1 models
> hide #!1 models
> select #14/C:250
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel ball
Changed 9 atom styles
> show #!1 models
> hide #!14 models
> show #!14 models
> hide #!1 models
> select #14/E:71@OP2
1 atom, 1 residue, 1 model selected
> select #14/C:250@NE2
1 atom, 1 residue, 1 model selected
> ui mousemode right distance
> distance #14/E:71@OP2 #14/C:250@NE2
Distance between 8pds HMPV #14/E C 71 OP2 and /C GLN 250 NE2: 6.013Å
> ~distance #14/E:71@OP2 #14/C:250@NE2
> distance #14/E:70@OP1 #14/C:250@NE2
Distance between 8pds HMPV #14/E C 70 OP1 and /C GLN 250 NE2: 9.537Å
> ~distance #14/E:70@OP1 #14/C:250@NE2
> show #!1 models
> hide #!1 models
> ui mousemode right select
> select #14/C:185
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #14/C:186
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel ball
Changed 11 atom styles
> select #14/C:185
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel ball
Changed 11 atom styles
> ui mousemode right distance
> distance #14/E:70@OP2 #14/C:185@NH1
Distance between 8pds HMPV #14/E C 70 OP2 and /C ARG 185 NH1: 5.093Å
> distance #14/C:185@NH2 #14/E:70@OP2
Distance between 8pds HMPV #14/C ARG 185 NH2 and /E C 70 OP2: 3.124Å
> ~distance #14/E:70@OP2 #14/C:185@NH1
> distance #14/C:186@NE #14/E:71@OP2
Distance between 8pds HMPV #14/C ARG 186 NE and /E C 71 OP2: 2.827Å
> ui mousemode right select
> select clear
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> save "/Users/kompa012/Desktop/NiP N protein article/Figures/HMPV DNA zoom
> prot.png" width 3000 height 2352 supersample 3 transparentBackground true
> show #!15 models
> hide #!14 models
> select add #15.3
169 atoms, 23 residues, 1 model selected
> select add #15.2
2654 atoms, 351 residues, 2 models selected
> select subtract #15.3
2485 atoms, 328 residues, 3 models selected
> select add #15.3
2654 atoms, 351 residues, 2 models selected
> select subtract #15.2
169 atoms, 23 residues, 3 models selected
> hide sel cartoons
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> select #15/A:200
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel ball
Changed 9 atom styles
> show #!1 models
> hide #!1 models
> select #15/A:194
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel ball
Changed 11 atom styles
> select #15/A:193
7 atoms, 6 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel ball
Changed 7 atom styles
> show #!1 models
> hide #!1 models
> select #15/A:179
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel ball
Changed 9 atom styles
> show #!1 models
> hide #!1 models
> select #15/A:259
12 atoms, 12 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel ball
Changed 12 atom styles
> show #!1 models
> hide #!1 models
> select clear
> save "/Users/kompa012/Desktop/NiP N protein article/Figures/HIPV3 DNA zoom
> prot.png" width 3000 height 2352 supersample 3 transparentBackground true
> show #!16 models
> hide #!15 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> select #16/G:180
9 atoms, 8 bonds, 1 residue, 1 model selected
> select add #16.16
1569 atoms, 8 bonds, 79 residues, 2 models selected
> show sel atoms
> select subtract #16.9
1560 atoms, 78 residues, 3 models selected
> select add #16.9
4695 atoms, 473 residues, 2 models selected
> color (#!16 & sel) byhetero
> style sel ball
Changed 4695 atom styles
> select clear
> show #!1 models
> hide #!1 models
> select #16/G:201
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> select #16/G:202
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> select #16/G:201
9 atoms, 8 bonds, 1 residue, 1 model selected
> hide sel cartoons
> show sel cartoons
> hide sel atoms
> select #16/G:200
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> hide sel atoms
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> select #16/G:201
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #16/G:202
9 atoms, 8 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #16/G:201
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> ui mousemode right distance
> distance #16/G:201@CG #16/N:58@O4
Distance between 4xjn HPIV5 #16/G GLN 201 CG and /N U 58 O4: 3.301Å
> ~distance #16/G:201@CG #16/N:58@O4
> hide sel atoms
> ui mousemode right select
> select #16/G:197
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> select #16/G:198
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> select #16/G:260
12 atoms, 12 bonds, 1 residue, 1 model selected
> show sel atoms
> ui mousemode right distance
> distance #16/G:260@OH #16/N:58@OP2
Distance between 4xjn HPIV5 #16/G TYR 260 OH and /N U 58 OP2: 2.890Å
> distance #16/G:198@NZ #16/N:58@OP2
Distance between 4xjn HPIV5 #16/G LYS 198 NZ and /N U 58 OP2: 5.422Å
> ~distance #16/G:198@NZ #16/N:58@OP2
> distance #16/G:198@NZ #16/N:58@O4'
Distance between 4xjn HPIV5 #16/G LYS 198 NZ and /N U 58 O4': 3.863Å
> ui mousemode right select
> select #16/G:197
9 atoms, 8 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #16/G:202
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> ui mousemode right distance
> distance #16/G:202@NE2 #16/N:58@O4
Distance between 4xjn HPIV5 #16/G GLN 202 NE2 and /N U 58 O4: 6.730Å
> ~distance #16/G:202@NE2 #16/N:58@O4
> ~distance #16/G:198@NZ #16/N:58@O4'
> ui mousemode right select
> select #16/G:202
9 atoms, 8 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #16/G:198
9 atoms, 8 bonds, 1 residue, 1 model selected
> hide sel cartoons
> show sel cartoons
> hide sel atoms
> select #16/G:201
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> ui tool show Rotamers
Populating font family aliases took 241 ms. Replace uses of missing font
family "Times" with one that exists to avoid this cost.
> swapaa interactive sel GLN rotLib Dunbrack
4xjn HPIV5 #16/G GLN 201: phi -72.1, psi -30.6 trans
Changed 648 bond radii
> ui mousemode right distance
> distance #16.17.2/A:1@OE1 #!16/N:58@O4
Distance between rotamer 2 #16.17.2/A GLN 1 OE1 and 4xjn HPIV5 #!16/N U 58 O4:
1.656Å
> distance #!16/N:58@O4 #16.17.58/A:1@NE2
Distance between 4xjn HPIV5 #!16/N U 58 O4 and rotamer 58 #16.17.58/A GLN 1
NE2: 2.287Å
> ui mousemode right select
> select clear
> select #16/G:194
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> ui mousemode right distance
> ~distance #10/B:194@NH1 #10/R:12@OP2
> distance #16/G:194@NZ #16/N:57@OP2
Distance between 4xjn HPIV5 #16/G LYS 194 NZ and /N U 57 OP2: 3.935Å
> ui mousemode right select
> select #16/G:195
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> ui mousemode right distance
> distance #16/N:56@OP1 #16/G:195@NH1
Distance between 4xjn HPIV5 #16/N U 56 OP1 and /G ARG 195 NH1: 6.862Å
> ~distance #16/N:56@OP1 #16/G:195@NH1
> distance #16/G:195@NH2 #16/N:57@OP2
Distance between 4xjn HPIV5 #16/G ARG 195 NH2 and /N U 57 OP2: 3.089Å
> ui mousemode right select
> select clear
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> save "/Users/kompa012/Desktop/NiP N protein article/Figures/HIPV5 DNA zoom
> prot.png" width 3000 height 2352 supersample 3 transparentBackground true
> show #!17 models
> hide #!16 models
> select add #17.2
120 atoms, 6 residues, 1 model selected
> hide sel cartoons
> show sel atoms
> style sel ball
Changed 120 atom styles
> select add #17
3088 atoms, 3161 bonds, 380 residues, 2 models selected
> select subtract #17
2 models selected
> show #!1 models
> hide #!1 models
> select #17/A:201
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel ball
Changed 9 atom styles
> select #17/A:260
12 atoms, 12 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel ball
Changed 12 atom styles
> select #17/A:194
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel ball
Changed 11 atom styles
> select #17/A:195
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel ball
Changed 11 atom styles
> select clear
> select #17/A:180
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel ball
Changed 9 atom styles
> ui mousemode right distance
> distance #17/B:23@OP1 #17/A:180@NZ
Distance between 7ewq MuV #17/B U 23 OP1 and /A LYS 180 NZ: 2.721Å
> distance #17/A:194@CZ #17/B:25@OP2
Distance between 7ewq MuV #17/A ARG 194 CZ and /B U 25 OP2: 4.234Å
> distance #17/A:195@NH1 #17/B:25@OP2
Distance between 7ewq MuV #17/A ARG 195 NH1 and /B U 25 OP2: 3.763Å
> distance #17/A:194@NH2 #17/B:24@OP1
Distance between 7ewq MuV #17/A ARG 194 NH2 and /B U 24 OP1: 2.864Å
> ~distance #17/A:194@CZ #17/B:25@OP2
> ui mousemode right select
> select clear
> save "/Users/kompa012/Desktop/NiP N protein article/Figures/MUV DNA zoom
> prot.png" width 3000 height 2352 supersample 3 transparentBackground true
> show #!18 models
> hide #!17 models
> select add #18.3
120 atoms, 6 residues, 1 model selected
> show sel atoms
> hide sel cartoons
> style sel ball
Changed 120 atom styles
> select clear
> select #18/A:199
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel ball
Changed 9 atom styles
> select #18/A:258
12 atoms, 12 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel ball
Changed 12 atom styles
> select #18/A:193
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel ball
Changed 11 atom styles
> select #18/A:192
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel ball
Changed 11 atom styles
> select #18/A:178
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel ball
Changed 9 atom styles
> save "/Users/kompa012/Desktop/NiP N protein article/Figures/figure 4 prot
> compar.cxs"
===== Log before crash end =====
Log:
Startup Messages
---
note | available bundle cache has not been initialized yet
UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
OpenGL version: 4.1 Metal - 89.3
OpenGL renderer: Apple M2
OpenGL vendor: Apple
Python: 3.11.4
Locale: UTF-8
Qt version: PyQt6 6.6.1, Qt 6.6.1
Qt runtime version: 6.6.3
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: Mac14,7
Model Number: Z16S0005DLL/A
Chip: Apple M2
Total Number of Cores: 8 (4 performance and 4 efficiency)
Memory: 16 GB
System Firmware Version: 11881.81.4
OS Loader Version: 11881.81.4
Software:
System Software Overview:
System Version: macOS 15.3.2 (24D81)
Kernel Version: Darwin 24.3.0
Time since boot: 24 days, 9 hours, 31 minutes
Graphics/Displays:
Apple M2:
Chipset Model: Apple M2
Type: GPU
Bus: Built-In
Total Number of Cores: 10
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
PHL 272P7VU:
Resolution: 3840 x 2160 (2160p/4K UHD 1 - Ultra High Definition)
UI Looks like: 1920 x 1080 @ 60.00Hz
Main Display: Yes
Mirror: Off
Online: Yes
Rotation: Supported
Color LCD:
Display Type: Built-In Retina LCD
Resolution: 2560 x 1600 Retina
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
Installed Packages:
alabaster: 0.7.16
appdirs: 1.4.4
appnope: 0.1.4
asttokens: 2.4.1
Babel: 2.15.0
beautifulsoup4: 4.12.3
blockdiag: 3.0.0
blosc2: 2.0.0
build: 1.2.1
certifi: 2023.11.17
cftime: 1.6.4
charset-normalizer: 3.3.2
ChimeraX-AddCharge: 1.5.17
ChimeraX-AddH: 2.2.6
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.5
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.12.7
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.1.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.57.1
ChimeraX-AtomicLibrary: 14.0.6
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.4.6
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.12.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.2.7
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.4
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.4
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.2.4
ChimeraX-ColorActions: 1.0.5
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.6
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.8
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.3
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2.4
ChimeraX-DiffPlot: 1.0
ChimeraX-DistMonitor: 1.4.2
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-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-Label: 1.1.10
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.1.6
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.2
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: 2.1.3
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.7.1
ChimeraX-MedicalToolbar: 1.0.3
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.14.1
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.17
ChimeraX-ModelPanel: 1.5
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: 1.2
ChimeraX-NMRSTAR: 1.0.2
ChimeraX-NRRD: 1.2
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.13.5
ChimeraX-PDB: 2.7.5
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: 1.1.1
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.4.1
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-Segmentations: 3.0.15
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.11.2
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.1.1
ChimeraX-ShowSequences: 1.0.3
ChimeraX-SideView: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.16.5
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.2.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.5
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: 1.39.1
ChimeraX-uniprot: 2.3
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.4.3
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: 1.1.4
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.2
contourpy: 1.2.1
cxservices: 1.2.2
cycler: 0.12.1
Cython: 3.0.10
debugpy: 1.8.1
decorator: 5.1.1
docutils: 0.20.1
executing: 2.0.1
filelock: 3.13.4
fonttools: 4.53.0
funcparserlib: 2.0.0a0
glfw: 2.7.0
grako: 3.16.5
h5py: 3.11.0
html2text: 2024.2.26
idna: 3.7
ihm: 1.0
imagecodecs: 2024.1.1
imagesize: 1.4.1
ipykernel: 6.29.2
ipython: 8.21.0
ipywidgets: 8.1.3
jedi: 0.19.1
jinja2: 3.1.4
jupyter-client: 8.6.0
jupyter-core: 5.7.2
jupyterlab-widgets: 3.0.11
kiwisolver: 1.4.5
line-profiler: 4.1.2
lxml: 5.2.1
lz4: 4.3.3
MarkupSafe: 2.1.5
matplotlib: 3.8.4
matplotlib-inline: 0.1.7
msgpack: 1.0.8
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.10.0
numpy: 1.26.4
openvr: 1.26.701
packaging: 23.2
ParmEd: 4.2.2
parso: 0.8.4
pep517: 0.13.1
pexpect: 4.9.0
pillow: 10.3.0
pip: 24.0
pkginfo: 1.10.0
platformdirs: 4.2.2
prompt-toolkit: 3.0.47
psutil: 5.9.8
ptyprocess: 0.7.0
pure-eval: 0.2.2
py-cpuinfo: 9.0.0
pycollada: 0.8
pydicom: 2.4.4
pygments: 2.17.2
pynmrstar: 3.3.4
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.3401
pyparsing: 3.1.2
pyproject-hooks: 1.1.0
PyQt6-commercial: 6.6.1
PyQt6-Qt6: 6.6.3
PyQt6-sip: 13.6.0
PyQt6-WebEngine-commercial: 6.6.0
PyQt6-WebEngine-Qt6: 6.6.3
python-dateutil: 2.9.0.post0
pytz: 2024.1
pyzmq: 26.0.3
qtconsole: 5.5.1
QtPy: 2.4.1
RandomWords: 0.4.0
requests: 2.31.0
scipy: 1.13.0
setuptools: 69.5.1
setuptools-scm: 8.0.4
sfftk-rw: 0.8.1
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.5
sphinx: 7.2.6
sphinx-autodoc-typehints: 2.0.1
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: 0.6.3
tables: 3.8.0
tcia-utils: 1.5.1
tifffile: 2024.1.30
tinyarray: 1.2.4
tornado: 6.4.1
traitlets: 5.14.2
typing-extensions: 4.12.2
tzdata: 2024.1
urllib3: 2.2.1
wcwidth: 0.2.13
webcolors: 1.13
wheel: 0.43.0
wheel-filename: 1.4.1
widgetsnbextension: 4.0.11
Change History (2)
comment:1 by , 7 months ago
| Component: | Unassigned → Window Toolkit |
|---|---|
| Description: | modified (diff) |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Crash on Mac waking from sleep |
comment:2 by , 7 months ago
| Resolution: | → duplicate |
|---|---|
| Status: | assigned → closed |
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