Opened 7 months ago

Last modified 7 months ago

#17319 closed defect

ChimeraX bug report submission — at Initial Version

Reported by: chimerax-bug-report@… Owned by:
Priority: normal Milestone:
Component: Window Toolkit Version:
Keywords: Cc:
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        macOS-15.1.1-arm64-arm-64bit
ChimeraX Version: 1.9rc202411082121 (2024-11-08 21:21:14 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Segmentation fault

Thread 0x000000034bfc7000 (most recent call first):
  File "/Applications/ChimeraX-1.9-rc2024.11.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 579 in _handle_results
  File "/Applications/ChimeraX-1.9-rc2024.11.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.9-rc2024.11.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.9-rc2024.11.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x000000034afbb000 (most recent call first):
  File "/Applications/ChimeraX-1.9-rc2024.11.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 531 in _handle_tasks
  File "/Applications/ChimeraX-1.9-rc2024.11.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.9-rc2024.11.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.9-rc2024.11.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x0000000349faf000 (most recent call first):
  File "/Applications/ChimeraX-1.9-rc2024.11.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/selectors.py", line 415 in select
  File "/Applications/ChimeraX-1.9-rc2024.11.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/connection.py", line 930 in wait
  File "/Applications/ChimeraX-1.9-rc2024.11.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 502 in _wait_for_updates
  File "/Applications/ChimeraX-1.9-rc2024.11.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 522 in _handle_workers
  File "/Applications/ChimeraX-1.9-rc2024.11.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.9-rc2024.11.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.9-rc2024.11.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x0000000348fa3000 (most recent call first):
  File "/Applications/ChimeraX-1.9-rc2024.11.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.9-rc2024.11.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.9-rc2024.11.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.9-rc2024.11.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x0000000347f97000 (most recent call first):
  File "/Applications/ChimeraX-1.9-rc2024.11.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.9-rc2024.11.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.9-rc2024.11.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.9-rc2024.11.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x0000000346f8b000 (most recent call first):
  File "/Applications/ChimeraX-1.9-rc2024.11.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.9-rc2024.11.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.9-rc2024.11.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.9-rc2024.11.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x0000000345f7f000 (most recent call first):
  File "/Applications/ChimeraX-1.9-rc2024.11.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.9-rc2024.11.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.9-rc2024.11.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.9-rc2024.11.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x0000000344f73000 (most recent call first):
  File "/Applications/ChimeraX-1.9-rc2024.11.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.9-rc2024.11.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.9-rc2024.11.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.9-rc2024.11.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x0000000343f67000 (most recent call first):
  File "/Applications/ChimeraX-1.9-rc2024.11.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.9-rc2024.11.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.9-rc2024.11.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.9-rc2024.11.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x0000000342f5b000 (most recent call first):
  File "/Applications/ChimeraX-1.9-rc2024.11.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.9-rc2024.11.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.9-rc2024.11.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.9-rc2024.11.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x0000000341f4f000 (most recent call first):
  File "/Applications/ChimeraX-1.9-rc2024.11.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.9-rc2024.11.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.9-rc2024.11.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.9-rc2024.11.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x0000000340f43000 (most recent call first):
  File "/Applications/ChimeraX-1.9-rc2024.11.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.9-rc2024.11.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.9-rc2024.11.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.9-rc2024.11.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x000000033ff37000 (most recent call first):
  File "/Applications/ChimeraX-1.9-rc2024.11.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.9-rc2024.11.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.9-rc2024.11.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.9-rc2024.11.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x000000033ef2b000 (most recent call first):
  File "/Applications/ChimeraX-1.9-rc2024.11.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.9-rc2024.11.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.9-rc2024.11.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.9-rc2024.11.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x000000033df1f000 (most recent call first):
  File "/Applications/ChimeraX-1.9-rc2024.11.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.9-rc2024.11.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.9-rc2024.11.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.9-rc2024.11.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x000000033cf13000 (most recent call first):
  File "/Applications/ChimeraX-1.9-rc2024.11.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.9-rc2024.11.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.9-rc2024.11.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.9-rc2024.11.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x000000033bf07000 (most recent call first):
  File "/Applications/ChimeraX-1.9-rc2024.11.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.9-rc2024.11.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.9-rc2024.11.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.9-rc2024.11.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Current thread 0x0000000203087ac0 (most recent call first):
  File "/Applications/ChimeraX-1.9-rc2024.11.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 330 in event_loop
  File "/Applications/ChimeraX-1.9-rc2024.11.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1054 in init
  File "/Applications/ChimeraX-1.9-rc2024.11.08.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1217 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, chimerax.surface._surface, charset_normalizer.md, requests.packages.charset_normalizer.md, requests.packages.chardet.md, PIL._imaging, kiwisolver._cext, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.pdb_lib._load_libs, openmm._openmm, openmm.app.internal.compiled, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, psutil._psutil_osx, psutil._psutil_posix, chimerax.pdb._pdbio, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, PIL._imagingmath, cython.cimports.libc.math, scipy._lib._ccallback_c, scipy.special._ufuncs_cxx, scipy.special._ufuncs, scipy.special._specfun, scipy.special._comb, scipy.linalg._fblas, scipy.linalg._flapack, scipy.linalg.cython_lapack, scipy.linalg._cythonized_array_utils, scipy.linalg._solve_toeplitz, scipy.linalg._decomp_lu_cython, scipy.linalg._matfuncs_sqrtm_triu, scipy.linalg.cython_blas, scipy.linalg._matfuncs_expm, scipy.linalg._decomp_update, scipy.sparse._sparsetools, _csparsetools, scipy.sparse._csparsetools, scipy.sparse.linalg._dsolve._superlu, scipy.sparse.linalg._eigen.arpack._arpack, scipy.sparse.linalg._propack._spropack, scipy.sparse.linalg._propack._dpropack, scipy.sparse.linalg._propack._cpropack, scipy.sparse.linalg._propack._zpropack, scipy.sparse.csgraph._tools, scipy.sparse.csgraph._shortest_path, scipy.sparse.csgraph._traversal, scipy.sparse.csgraph._min_spanning_tree, scipy.sparse.csgraph._flow, scipy.sparse.csgraph._matching, scipy.sparse.csgraph._reordering, scipy.special._ellip_harm_2, scipy.interpolate._fitpack, scipy.interpolate._dfitpack, scipy.optimize._group_columns, scipy._lib.messagestream, scipy.optimize._trlib._trlib, scipy.optimize._lbfgsb, _moduleTNC, scipy.optimize._moduleTNC, scipy.optimize._cobyla, scipy.optimize._slsqp, scipy.optimize._minpack, scipy.optimize._lsq.givens_elimination, scipy.optimize._zeros, scipy.optimize._highs.cython.src._highs_wrapper, scipy.optimize._highs._highs_wrapper, scipy.optimize._highs.cython.src._highs_constants, scipy.optimize._highs._highs_constants, scipy.linalg._interpolative, scipy.optimize._bglu_dense, scipy.optimize._lsap, scipy.spatial._ckdtree, scipy.spatial._qhull, scipy.spatial._voronoi, scipy.spatial._distance_wrap, scipy.spatial._hausdorff, scipy.spatial.transform._rotation, scipy.optimize._direct, scipy.interpolate._bspl, scipy.interpolate._ppoly, scipy.interpolate.interpnd, scipy.interpolate._rbfinterp_pythran, scipy.interpolate._rgi_cython, chimerax.atom_search.ast, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, chimerax.chem_group._chem_group, chimerax.alignment_algs._sw, chimerax.dssp._dssp, chimerax.alignment_algs._nw (total: 126)


{"app_name":"ChimeraX","timestamp":"2025-04-07 21:37:05.00 -0500","app_version":"1.9.0","slice_uuid":"17982d98-65bc-3327-8526-577ec996453c","build_version":"1.9.0.0","platform":1,"bundleID":"edu.ucsf.cgl.ChimeraX","share_with_app_devs":1,"is_first_party":0,"bug_type":"309","os_version":"macOS 15.1.1 (24B2091)","roots_installed":0,"name":"ChimeraX","incident_id":"400D8F0A-155A-49AB-B9FA-628DCB1CB5F3"}
{
  "uptime" : 170000,
  "procRole" : "Foreground",
  "version" : 2,
  "userID" : 501,
  "deployVersion" : 210,
  "modelCode" : "Mac16,8",
  "coalitionID" : 1998,
  "osVersion" : {
    "train" : "macOS 15.1.1",
    "build" : "24B2091",
    "releaseType" : "User"
  },
  "captureTime" : "2025-04-07 21:36:59.6193 -0500",
  "codeSigningMonitor" : 2,
  "incident" : "400D8F0A-155A-49AB-B9FA-628DCB1CB5F3",
  "pid" : 23914,
  "translated" : false,
  "cpuType" : "ARM-64",
  "roots_installed" : 0,
  "bug_type" : "309",
  "procLaunch" : "2025-04-07 09:30:14.2926 -0500",
  "procStartAbsTime" : 3229846140087,
  "procExitAbsTime" : 4148004828263,
  "procName" : "ChimeraX",
  "procPath" : "\/Applications\/ChimeraX-1.9-rc2024.11.08.app\/Contents\/MacOS\/ChimeraX",
  "bundleInfo" : {"CFBundleShortVersionString":"1.9.0","CFBundleVersion":"1.9.0.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
  "storeInfo" : {"deviceIdentifierForVendor":"748C12F4-D50B-50E7-A8AF-353B633C1F65","thirdParty":true},
  "parentProc" : "launchd",
  "parentPid" : 1,
  "coalitionName" : "edu.ucsf.cgl.ChimeraX",
  "crashReporterKey" : "7FA5FDF8-8D67-28A2-72D7-B9E65B3FCACD",
  "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" : "51D843D1-B804-467F-9D93-B2D566F293A4",
  "sleepWakeUUID" : "57D8BBC3-196A-48F9-9695-65F6A8E6B370",
  "sip" : "enabled",
  "vmRegionInfo" : "0x168 is not in any region.  Bytes before following region: 4375543448\n      REGION TYPE                    START - END         [ VSIZE] PRT\/MAX SHRMOD  REGION DETAIL\n      UNUSED SPACE AT START\n--->  \n      __TEXT                      104cd8000-104cdc000    [   16K] r-x\/r-x SM=COW  \/Applications\/ChimeraX-1.9-rc2024.11.08.app\/Contents\/MacOS\/ChimeraX",
  "exception" : {"codes":"0x0000000000000001, 0x0000000000000168","rawCodes":[1,360],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x0000000000000168"},
  "termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":23914},
  "vmregioninfo" : "0x168 is not in any region.  Bytes before following region: 4375543448\n      REGION TYPE                    START - END         [ VSIZE] PRT\/MAX SHRMOD  REGION DETAIL\n      UNUSED SPACE AT START\n--->  \n      __TEXT                      104cd8000-104cdc000    [   16K] r-x\/r-x SM=COW  \/Applications\/ChimeraX-1.9-rc2024.11.08.app\/Contents\/MacOS\/ChimeraX",
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    "path" : "\/System\/Library\/Frameworks\/Foundation.framework\/Versions\/C\/Foundation",
    "name" : "Foundation",
    "CFBundleVersion" : "3107"
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    "uuid" : "12c75024-0fbf-38d8-85c2-ab6bfe2b6862",
    "path" : "\/usr\/lib\/system\/libsystem_malloc.dylib",
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    "size" : 307200,
    "uuid" : "063693ad-6cf6-38e8-a3c4-149469771f75",
    "path" : "\/usr\/lib\/system\/libxpc.dylib",
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  "vmSummary" : "ReadOnly portion of Libraries: Total=1.9G resident=0K(0%) swapped_out_or_unallocated=1.9G(100%)\nWritable regions: Total=19.3G written=10.4M(0%) resident=10.4M(0%) swapped_out=0K(0%) unallocated=19.3G(100%)\n\n                                VIRTUAL   REGION \nREGION TYPE                        SIZE    COUNT (non-coalesced) \n===========                     =======  ======= \nAccelerate framework               384K        3 \nActivity Tracing                   256K        1 \nCG image                          3616K       52 \nColorSync                          688K       34 \nCoreAnimation                     3616K      192 \nCoreGraphics                        64K        4 \nCoreImage                           32K        1 \nCoreUI image data                 5216K       41 \nFoundation                          48K        2 \nKernel Alloc Once                   32K        1 \nMALLOC                            17.3G      603 \nMALLOC guard page                  288K       18 \nMach message                        64K        3 \nOpenCL                            29.5M      328 \nOpenCL (reserved)                 1808K       42         reserved VM address space (unallocated)\nOpenGL GLSL                        384K        4 \nSTACK GUARD                       2112K      132 \nStack                            506.4M      137 \nStack Guard                       56.0M        1 \nVM_ALLOCATE                      709.9M      687 \nVM_ALLOCATE (reserved)           736.0M       10         reserved VM address space (unallocated)\n__AUTH                            5030K      661 \n__AUTH_CONST                      69.6M      908 \n__CTF                               824        1 \n__DATA                            35.1M     1169 \n__DATA_CONST                      35.9M     1177 \n__DATA_DIRTY                      2763K      342 \n__FONT_DATA                        2352        1 \n__GLSLBUILTINS                    5174K        1 \n__INFO_FILTER                         8        1 \n__LINKEDIT                       630.5M      267 \n__OBJC_RW                         2355K        1 \n__TEXT                             1.3G     1197 \n__TPRO_CONST                       272K        2 \ndyld private memory                304K        3 \nmapped file                        1.0G      219 \nowned unmapped memory            102.5M        1 \npage table in kernel              10.4M        1 \nshared memory                     3696K       24 \n===========                     =======  ======= \nTOTAL                             22.5G     8272 \nTOTAL, minus reserved VM space    21.7G     8272 \n",
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}
===== Log before crash start =====
Startup Messages  
---  
note | available bundle cache has not been initialized yet  
  

> mousemode middleMode center

> cofr centerOfView

> alias cofron cofr centerofview showpivot true

> alias cofroff cofr centerofview showpivot false

> alias symclip cofr centerofview; clip near -$1 far $1 position cofr

> alias cootmode set bgColor black; surface cap false; surface style solid;
> lighting flat; graphics silhouettes false; style stick; ~rib; color
> ##num_residues gold; color byhet ; disp; ~disp @H*; style ions ball; style
> solvent ball; size ballscale 0.2; size stickradius 0.07; transparency 70;
> cofr centerofview; clip near -10 far 10 position cofr; color ##~num_residues
> cornflower blue

> alias cootmode_mesh set bgColor black; surface cap false; surface style
> mesh; lighting flat; graphics silhouettes false; style stick; ~rib; color
> ##num_residues gold; color byhet ; disp; ~disp @H*; style solvent ball;
> style ions ball; size ballscale 0.2; size stickradius 0.07; cofr
> centerofview; clip near -10 far 10 position cofr; color ##~num_residues
> #3d60ffff; transparency 50

> alias cootmode_off surface style solid; lighting soft; graphics silhouettes
> false; hide atoms; default_mol_display; transparency 0; symclip 40; color
> ##~num_residues grey; size stickradius 0.2;

> alias ca_and_sidechains ~rib $1; ~surf $1; ~disp $1; disp @CA&protein&$1;
> disp @P&nucleic&$1; style $1 stick; disp sidechain&$1; disp
> ~backbone&nucleic&$1; size stickradius 0.1; size pseudobondradius 0.1

> alias ca_trace ~rib $1; ~surf $1; ~disp $1; disp @CA&protein&$1; disp
> @P&nucleic&$1; style $1 stick; size stickradius 0.1; size pseudobondradius
> 0.1

> alias map_sphere_15 surface unzone ##~num_residues; sel; close #10000;
> marker #10000 position cofr; sel ~sel; surface zone ##~num_residues
> nearAtoms sel distance 15; close #10000

> alias map_unsphere surface unzone ##~num_residues

> alias default_mol_display ~disp; rib; rainbow chain palette Pastel1-5;
> lighting soft; color byhet

> alias hidemaps surface unzone ##~num_residues; sel; close #10000; marker
> #10000 position cofr; sel ~sel; surface zone ##~num_residues nearAtoms sel
> distance 0; close #10000

> alias showmaps surface unzone ##~num_residues

> alias licorice car style protein modeh default arrows f xsect oval width 1
> thick 1; style stick; size stickRadius 0.5; ~disp @H*; color byhet

> alias caps_off surface cap false

> alias caps_on surface cap true

> alias rock_movie cofr showpivot false; movie record supersample 3; rock y
> 40; wait 136; movie encode ~/Desktop/rock_movie.mp4 quality high; stop

> alias publication_figure save Figure.png format png supersample 3
> transparentBackground true width 3000 height 3000

> buttonpanel Shortcuts rows 3 columns 5

> buttonpanel Shortcuts add default_disp command default_mol_display

> buttonpanel Shortcuts add Hide_H command "~disp @H*"

> buttonpanel Shortcuts add Licorice command licorice

> buttonpanel Shortcuts add Ribbons command "preset ribbons"

> buttonpanel Shortcuts add RockMovie command rock_movie

> buttonpanel Shortcuts add SymClip10 command "symclip 10"

> buttonpanel Shortcuts add SymClip20 command "symclip 20"

> buttonpanel Shortcuts add map_sphere command map_sphere_15

> buttonpanel Shortcuts add map_unsphere command map_unsphere

> buttonpanel Shortcuts add PubFigure command publication_figure

> buttonpanel Shortcuts add coot_mode command cootmode

> buttonpanel Shortcuts add coot_mesh command cootmode_mesh

> buttonpanel Shortcuts add coot_off command cootmode_off

> buttonpanel Shortcuts add hidemaps command hidemaps

> buttonpanel Shortcuts add showmaps command showmaps

> ui tool show "Model Panel"

UCSF ChimeraX version: 1.9rc202411082121 (2024-11-08)  
© 2016-2024 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open "/Users/zhouling95/Documents/Academic/McLellan
> Lab/MPXV/P913_J108_DeepEMhancer_zflipped.mrc"

Opened P913_J108_DeepEMhancer_zflipped.mrc as #1, grid size 384,384,384, pixel
0.933, shown at level 0.000654, step 2, values float32  

> surface dust #1 size 9.33

> volume #1 step 1

> open "/Users/zhouling95/Documents/Academic/McLellan
> Lab/MPXV/OPG153/AF3_J108_zflip_086-coot-0.pdb"

Chain information for AF3_J108_zflip_086-coot-0.pdb #2  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
E | No description available  
  

> open "/Users/zhouling95/Documents/Academic/McLellan
> Lab/MPXV/OPG153/Phenix/RealSpaceRefine_91/AF3_J108_zflip_086-coot-0_real_space_refined_091.pdb"

Chain information for AF3_J108_zflip_086-coot-0_real_space_refined_091.pdb #3  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
E | No description available  
  

> style stick

Changed 12646 atom styles  

> volume #1 level 0.00727

> color byhetero

> volume #1 color #b2b2b278

> show cartoons

> color #2 #5b7beeff

> color #3 #eee92cff

> color byhetero

> volume #1 level 0.01058

> volume #1 level 0.01

> volume #1 level 0.0098

> volume #1 level 0.0093

> volume #1 level 0.009

> volume #1 level 0.005692

> volume #1 level 0.002384

> volume #1 level 0.0025

> volume #1 level 0.0028

> volume #1 level 0.0032

> volume #1 level 0.0035

> volume #1 level 0.0045

> volume #1 level 0.01112

> volume #1 level 0.01442

> volume #1 level 0.07066

> volume #1 level 0.01112

> open "/Users/zhouling95/Documents/Academic/McLellan
> Lab/MPXV/OPG153/AF3_J108_zflip_086-coot-1.pdb"

Chain information for AF3_J108_zflip_086-coot-1.pdb #4  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
E | No description available  
  

> style stick

Changed 18969 atom styles  

> color byhetero

> show cartoons

> view #4/E:94

> open "/Users/zhouling95/Documents/Academic/McLellan
> Lab/MPXV/OPG153/AF3_J108_zflip_086-coot-2.pdb"

Chain information for AF3_J108_zflip_086-coot-2.pdb #5  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
E | No description available  
  

> style stick

Changed 25292 atom styles  

> color byhetero

> close #4

> show cartoons

> close #2-3,5

> open "/Users/zhouling95/Documents/Academic/McLellan
> Lab/MPXV/OPG153/AF3_J108_zflip_086-coot-2.pdb"

Chain information for AF3_J108_zflip_086-coot-2.pdb #2  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
E | No description available  
  

> close #2

> open "/Users/zhouling95/Documents/Academic/McLellan
> Lab/MPXV/OPG153/Phenix/RealSpaceRefine_92/AF3_J108_zflip_086-coot-1_real_space_refined_092.pdb"

Chain information for AF3_J108_zflip_086-coot-1_real_space_refined_092.pdb #2  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
E | No description available  
  

> style stick

Changed 6323 atom styles  

> isolde start

> set selectionWidth 4

Done loading forcefield  

> isolde set simFidelityMode Medium/Medium

ISOLDE: setting sim fidelity mode to Medium/Medium  
nonbonded_cutoff_distance = 0.900000  
use_gbsa = True  
gbsa_cutoff = 1.100000  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 43 residues in model #2 to IUPAC-IUB
standards.  
Chain information for AF3_J108_zflip_086-coot-1_real_space_refined_092.pdb  
---  
Chain | Description  
2.2/A | No description available  
2.2/B | No description available  
2.2/C | No description available  
2.2/D | No description available  
2.2/E | No description available  
  

> clipper associate #1 toModel #2

Opened P913_J108_DeepEMhancer_zflipped.mrc as #2.1.1.1, grid size 384,384,384,
pixel 0.933, shown at step 1, values float32  

> ui tool show "Ramachandran Plot"

> addh

Summary of feedback from adding hydrogens to
AF3_J108_zflip_086-coot-1_real_space_refined_092.pdb #2.2  
---  
notes | No usable SEQRES records for AF3_J108_zflip_086-coot-1_real_space_refined_092.pdb (#2.2) chain A; guessing termini instead  
No usable SEQRES records for
AF3_J108_zflip_086-coot-1_real_space_refined_092.pdb (#2.2) chain B; guessing
termini instead  
No usable SEQRES records for
AF3_J108_zflip_086-coot-1_real_space_refined_092.pdb (#2.2) chain C; guessing
termini instead  
No usable SEQRES records for
AF3_J108_zflip_086-coot-1_real_space_refined_092.pdb (#2.2) chain D; guessing
termini instead  
No usable SEQRES records for
AF3_J108_zflip_086-coot-1_real_space_refined_092.pdb (#2.2) chain E; guessing
termini instead  
Chain-initial residues that are actual N termini: /A ASN 19, /B VAL 2, /C ILE
2, /D VAL 2, /E ALA 1  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini: /B VAL 111, /C LYS 107, /D SER
113, /E LYS 107  
Chain-final residues that are not actual C termini: /A ASN 364  
631 hydrogen bonds  
/A ASN 364 is not terminus, removing H atom from 'C'  
6131 hydrogens added  
  

> isolde sim start /E:95

ISOLDE: started sim  

> volume #2.1.1.1 level 0.04783

> isolde cisflip /E:95

> isolde sim stop

Sim termination reason: None  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 1 residues in model #2.2 to IUPAC-IUB
standards.  
ISOLDE: stopped sim  

> save "/Users/zhouling95/Documents/Academic/McLellan
> Lab/MPXV/OPG153/AF3_J108_zflip_092.pdb"

> isolde sim start /B:29

ISOLDE: started sim  

> isolde sim stop

Sim termination reason: None  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 1 residues in model #2.2 to IUPAC-IUB
standards.  
ISOLDE: stopped sim  

> ui tool show "Ramachandran Plot"

> isolde sim start /B:26-32

ISOLDE: started sim  

> isolde sim stop

Sim termination reason: None  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 1 residues in model #2.2 to IUPAC-IUB
standards.  
ISOLDE: stopped sim  

> select #2

12454 atoms, 12616 bonds, 796 residues, 21 models selected  

> isolde sim start /A-E

ISOLDE: started sim  

> isolde pepflip /A:108

> isolde pepflip /A:109

> isolde pepflip /B:98

> isolde sim stop

Sim termination reason: None  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 17 residues in model #2.2 to IUPAC-IUB
standards.  
ISOLDE: stopped sim  

> save "/Users/zhouling95/Documents/Academic/McLellan
> Lab/MPXV/OPG153/AF3_J108_zflip_092-isolde.pdb"

> close #2

> open "/Users/zhouling95/Documents/Academic/McLellan
> Lab/MPXV/OPG153/Phenix/RealSpaceRefine_94/AF3_J108_zflip_092_real_space_refined_094.pdb"

Chain information for AF3_J108_zflip_092_real_space_refined_094.pdb #1  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
E | No description available  
  

> open "/Users/zhouling95/Documents/Academic/McLellan
> Lab/MPXV/OPG153/Phenix/RealSpaceRefine_96/AF3_J108_zflip_092-isolde_real_space_refined_096.pdb"

Chain information for AF3_J108_zflip_092-isolde_real_space_refined_096.pdb #2  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
E | No description available  
  

> open "/Users/zhouling95/Documents/Academic/McLellan
> Lab/MPXV/OPG153/Phenix/RealSpaceRefine_97/AF3_J108_zflip_092-isolde_real_space_refined_097.pdb"

Chain information for AF3_J108_zflip_092-isolde_real_space_refined_097.pdb #3  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
E | No description available  
  

> style stick

Changed 37362 atom styles  

> show cartoons

> color byhetero

> color #1 #90b9eeff

> color #2 #eed15fff

> color #3 #ee8b93ff

> color byhetero

> hide eH

Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword  

> hide H

> open "/Users/zhouling95/Documents/Academic/McLellan
> Lab/MPXV/P913_J108_DeepEMhancer_zflipped.mrc"

Opened P913_J108_DeepEMhancer_zflipped.mrc as #4, grid size 384,384,384, pixel
0.933, shown at level 0.000654, step 2, values float32  

> surface dust #4 size 9.33

> volume #4 step 1

> volume #4 level 0.00727

> volume #4 color #b2b2b26e

> volume #4 color #d5d5d56e

> lighting simple

> hide #3 models

> hide #2 models

> color #1 bychain

> color #1 byhetero

> open "/Users/zhouling95/Documents/Academic/McLellan
> Lab/MPXV/OPG153/Phenix/RealSpaceRefine_98/AF3_J108_zflip_092_real_space_refined_094_real_space_refined_098.pdb"

Chain information for
AF3_J108_zflip_092_real_space_refined_094_real_space_refined_098.pdb #5  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
E | No description available  
  

> color #5 #6758eeff

> style #1,5 stick

Changed 24908 atom styles  

> color #1,5 byhetero

> hide H

> show #1,5 atoms

> show #1,5 cartoons

> hide H

> color #5 #6aa2eaff

> color #1,5 byhetero

> volume #4 level 0.003962

> open "/Users/zhouling95/Documents/Academic/McLellan
> Lab/MPXV/OPG153/AF3_J108_zflip_098-coot-2.pdb"

Chain information for AF3_J108_zflip_098-coot-2.pdb #6  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
E | No description available  
  

> style #1,5-6 stick

Changed 31231 atom styles  

> color #6 #5aee37ff

> style #1,5-6 stick

Changed 31231 atom styles  

> color #1,5-6 byhetero

> show #1,5-6 cartoons

> close #5

> close #3

> close #2

> close #1

> isolde start

> set selectionWidth 4

Done loading forcefield  

> isolde set simFidelityMode Medium/Medium

ISOLDE: setting sim fidelity mode to Medium/Medium  
nonbonded_cutoff_distance = 0.900000  
use_gbsa = True  
gbsa_cutoff = 1.100000  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 37 residues in model #6 to IUPAC-IUB
standards.  
Chain information for AF3_J108_zflip_098-coot-2.pdb  
---  
Chain | Description  
1.2/A | No description available  
1.2/B | No description available  
1.2/C | No description available  
1.2/D | No description available  
1.2/E | No description available  
  

> clipper associate #4 toModel #1

Opened P913_J108_DeepEMhancer_zflipped.mrc as #1.1.1.1, grid size 384,384,384,
pixel 0.933, shown at step 1, values float32  

> volume #1.1.1.1 level 0.02206

> addh

Summary of feedback from adding hydrogens to AF3_J108_zflip_098-coot-2.pdb
#1.2  
---  
notes | No usable SEQRES records for AF3_J108_zflip_098-coot-2.pdb (#1.2) chain A; guessing termini instead  
No usable SEQRES records for AF3_J108_zflip_098-coot-2.pdb (#1.2) chain B;
guessing termini instead  
No usable SEQRES records for AF3_J108_zflip_098-coot-2.pdb (#1.2) chain C;
guessing termini instead  
No usable SEQRES records for AF3_J108_zflip_098-coot-2.pdb (#1.2) chain D;
guessing termini instead  
No usable SEQRES records for AF3_J108_zflip_098-coot-2.pdb (#1.2) chain E;
guessing termini instead  
Chain-initial residues that are actual N termini: /A ASN 19, /B VAL 2, /C ILE
2, /D VAL 2, /E ALA 1  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini: /B VAL 111, /C LYS 107, /D SER
113, /E LYS 107  
Chain-final residues that are not actual C termini: /A ASN 364  
621 hydrogen bonds  
/A ASN 364 is not terminus, removing H atom from 'C'  
6131 hydrogens added  
  

> ui tool show "Ramachandran Plot"

> select #1

12454 atoms, 12616 bonds, 796 residues, 16 models selected  

> isolde sim start /A-E

ISOLDE: started sim  

> isolde pepflip /A:108

> isolde pepflip /A:109

> isolde pepflip /B:26

> isolde pepflip /E:69

> isolde pepflip /E:68

> isolde pepflip /E:69

> isolde pepflip /E:67

> isolde pepflip /B:41

Unable to flip peptide bond after 50 rounds. Giving up.  

> isolde pepflip /B:98

> isolde sim stop

Sim termination reason: None  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 16 residues in model #1.2 to IUPAC-IUB
standards.  
ISOLDE: stopped sim  

> save "/Users/zhouling95/Documents/Academic/McLellan
> Lab/MPXV/OPG153/AF3_J108_zflip_098-coot-2-isolde.pdb"

> close #1

> open "/Users/zhouling95/Documents/Academic/McLellan
> Lab/MPXV/OPG153/Phenix/RealSpaceRefine_102/AF3_J108_zflip_098-coot-2_real_space_refined_102.pdb"

Chain information for AF3_J108_zflip_098-coot-2_real_space_refined_102.pdb #1  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
E | No description available  
  

> show atoms

> style stick

Changed 6323 atom styles  

> show cartoons

> open "/Users/zhouling95/Documents/Academic/McLellan
> Lab/MPXV/OPG153/Phenix/RealSpaceRefine_98/AF3_J108_zflip_092_real_space_refined_094_real_space_refined_098.pdb"

Chain information for
AF3_J108_zflip_092_real_space_refined_094_real_space_refined_098.pdb #2  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
E | No description available  
  

> show atoms

> style stick

Changed 18777 atom styles  

> show cartoons

> color #2 #3037eeff

> color byhetero

> hide H

> open "/Users/zhouling95/Documents/Academic/McLellan
> Lab/MPXV/P913_J108_DeepEMhancer_zflipped.mrc"

Opened P913_J108_DeepEMhancer_zflipped.mrc as #3, grid size 384,384,384, pixel
0.933, shown at level 0.000654, step 2, values float32  

> surface dust #3 size 9.33

> volume #3 step 1

> volume #3 level 0.01058

> lighting simple

> volume #3 color #b2b2b244

> volume #3 color #b2b2b245

> volume #3 level 0.00727

> open "/Users/zhouling95/Documents/Academic/McLellan
> Lab/MPXV/OPG153/Phenix/RealSpaceRefine_103/AF3_J108_zflip_098-coot-2-isolde_real_space_refined_103.pdb"

Chain information for
AF3_J108_zflip_098-coot-2-isolde_real_space_refined_103.pdb #4  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
E | No description available  
  

> style stick

Changed 31231 atom styles  

> hide H

> color #4 #eee737ff

> color #4 #eecc60ff

> color #4 #eea4aaff

> color byhetero

> hide H

> color #4 #e9de3fff

> hide H

> color byhetero

> show cartoons

> open "/Users/zhouling95/Documents/Academic/McLellan
> Lab/MPXV/OPG153/AF3_J108_zflip_103-coot-0.pdb"

Chain information for AF3_J108_zflip_103-coot-0.pdb #5  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
E | No description available  
  

> style stick

Changed 37554 atom styles  

> color byhetero

> show cartoons

> color #5 #25eedcff

> show atoms

> color byhetero

> hide H

> show cartoons

> hide #4 models

> open "/Users/zhouling95/Documents/Academic/McLellan
> Lab/MPXV/OPG153/Phenix/RealSpaceRefine_106/AF3_J108_zflip_103-coot-0_real_space_refined_106.pdb"

Chain information for AF3_J108_zflip_103-coot-0_real_space_refined_106.pdb #6  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
E | No description available  
  

> show #1-2,5-6 atoms

> show #1-2,5-6 cartoons

> style #1-2,5-6 stick

Changed 31423 atom styles  

> hide H

> hide #1 models

> hide #2 models

> color #5-6 byhetero

> open "/Users/zhouling95/Documents/Academic/McLellan
> Lab/MPXV/OPG153/Phenix/RealSpaceRefine_107/AF3_J108_zflip_103-coot-0_real_space_refined_107.pdb"

Chain information for AF3_J108_zflip_103-coot-0_real_space_refined_107.pdb #7  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
E | No description available  
  

> style #5-7 stick

Changed 18969 atom styles  

> show #5-7 cartoons

> color #7 #5c6eeeff

> color #5-7 byhetero

> close #7

> close #6

> close #4

> close #2

> close #5

> close #1

> open "/Users/zhouling95/Documents/Academic/McLellan
> Lab/MPXV/OPG153/Phenix/RealSpaceRefine_114/AF3_J108_zflip_112-coot-2_real_space_refined_114.pdb"

Chain information for AF3_J108_zflip_112-coot-2_real_space_refined_114.pdb #1  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
E | No description available  
  

> style stick

Changed 6323 atom styles  

> show cartoons

> color byhetero

> open "/Users/zhouling95/Documents/Academic/McLellan
> Lab/MPXV/OPG153/Phenix/RealSpaceRefine_48/AF3_del_J108_zflip_047_real_space_refined_048.pdb"

Chain information for AF3_del_J108_zflip_047_real_space_refined_048.pdb #2  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
E | No description available  
  

> color #2 #3f60eeff

> style stick

Changed 18777 atom styles  

> show cartoons

> color byhetero

> hide H

> open "/Users/zhouling95/Documents/Academic/McLellan
> Lab/MPXV/OPG153/AF3_J108_zflip_114-coot-0.pdb"

Chain information for AF3_J108_zflip_114-coot-0.pdb #4  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
E | No description available  
  

> style stick

Changed 25100 atom styles  

> color byhetero

> color #4 #ee874fff

> color byhetero

> show cartoons

> hide #2 models

> show #2 models

> hide #4 models

> show #4 models

> hide #1 models

> show #1 models

> open "/Users/zhouling95/Documents/Academic/McLellan
> Lab/MPXV/OPG153/Phenix/RealSpaceRefine_119/AF3_J108_zflip_114-coot-0_real_space_refined_119.pdb"

Chain information for AF3_J108_zflip_114-coot-0_real_space_refined_119.pdb #5  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
E | No description available  
  

> style stick

Changed 31423 atom styles  

> show cartoons

> color byhetero

> color #5 #ebee3bff

> color byhetero

> hide #4 models

> hide #2 models

> isolde start

> set selectionWidth 4

Done loading forcefield  

> isolde set simFidelityMode Medium/Medium

ISOLDE: setting sim fidelity mode to Medium/Medium  
nonbonded_cutoff_distance = 0.900000  
use_gbsa = True  
gbsa_cutoff = 1.100000  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 39 residues in model #5 to IUPAC-IUB
standards.  
Chain information for AF3_J108_zflip_114-coot-0_real_space_refined_119.pdb  
---  
Chain | Description  
5.2/A | No description available  
5.2/B | No description available  
5.2/C | No description available  
5.2/D | No description available  
5.2/E | No description available  
  

> clipper associate #3 toModel #5

Opened P913_J108_DeepEMhancer_zflipped.mrc as #5.1.1.1, grid size 384,384,384,
pixel 0.933, shown at step 1, values float32  

> ui tool show "Ramachandran Plot"

> close #5

> close #4

> open "/Users/zhouling95/Documents/Academic/McLellan
> Lab/MPXV/OPG153/Phenix/RealSpaceRefine_119/AF3_J108_zflip_114-coot-0_real_space_refined_119.pdb"

Chain information for AF3_J108_zflip_114-coot-0_real_space_refined_119.pdb #3  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
E | No description available  
  

> style #1,3 stick

Changed 12646 atom styles  

> show #1,3 cartoons

> open "/Users/zhouling95/Documents/Academic/McLellan
> Lab/MPXV/P913_J108_DeepEMhancer_zflipped.mrc"

Opened P913_J108_DeepEMhancer_zflipped.mrc as #4, grid size 384,384,384, pixel
0.933, shown at level 0.000654, step 2, values float32  

> surface dust #4 size 9.33

> volume #4 step 1

> volume #4 level 0.01058

> ui tool show "Model-map Q-Score"

> style #3 stick

Changed 6323 atom styles  

> color #3 byhetero

> transparency #4 60

> qscore #3 toVolume #4 useGui false pointsPerShell 8 shellRadiusStep 0.100
> maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false

Overall mean Q-Score: 0.67  

> close #1-3#4

> open "/Users/zhouling95/Documents/Academic/McLellan
> Lab/MPXV/OPG153/Phenix/RealSpaceRefine_119/AF3_J108_zflip_114-coot-0_real_space_refined_119.pdb"

Chain information for AF3_J108_zflip_114-coot-0_real_space_refined_119.pdb #1  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
E | No description available  
  

> open "/Users/zhouling95/Documents/Academic/McLellan
> Lab/MPXV/P913_J108_DeepEMhancer_zflipped.mrc"

Opened P913_J108_DeepEMhancer_zflipped.mrc as #2, grid size 384,384,384, pixel
0.933, shown at level 0.000654, step 2, values float32  

> style stick

Changed 6323 atom styles  

> surface dust #2 size 9.33

> volume #2 step 1

> volume #2 level 0.0006542

> volume #2 level 0.006858

> color byhetero

> volume #2 level 0.003756

> volume #2 color #b2b2b25f

> volume #2 color #b2b2b25e

> show cartoons

> volume #2 color #b2b2b2

> open "/Users/zhouling95/Documents/Academic/McLellan
> Lab/MPXV/OPG153/Phenix/RealSpaceRefine_48/AF3_del_J108_zflip_047_real_space_refined_048.pdb"

Chain information for AF3_del_J108_zflip_047_real_space_refined_048.pdb #3  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
E | No description available  
  

> style stick

Changed 18777 atom styles  

> hide H

> color #3 #5939eeff

> color #3 #58b5eeff

> color byhetero

> volume #2 color #b2b2b26a

> volume #2 color #b2b2b26b

> show cartoons

> surface dust #2 size 9.33

> open "/Users/zhouling95/Documents/Academic/McLellan
> Lab/MPXV/OPG153/AF3_J108_zflip_119-coot-1.pdb"

Chain information for AF3_J108_zflip_119-coot-1.pdb #4  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
E | No description available  
  

> style stick

Changed 25100 atom styles  

> color #4 #deee25ff

> show cartoons

> volume #2 level 0.00996

> lighting simple

> color byhetero

> hide #1 models

> show #1 models

> show cartoons

> open
> /Users/zhouling95/Library/Containers/net.whatsapp.WhatsApp/Data/tmp/documents/FE326F4C-6797-4A8B-B80E-480FCEF94D36/153G-02M12-Kabat_fit-
> coot-20.pdb

Summary of feedback from opening
/Users/zhouling95/Library/Containers/net.whatsapp.WhatsApp/Data/tmp/documents/FE326F4C-6797-4A8B-B80E-480FCEF94D36/153G-02M12-Kabat_fit-
coot-20.pdb  
---  
warning | Cannot find LINK/SSBOND residue CYS (25 )  
  
Chain information for 153G-02M12-Kabat_fit-coot-20.pdb #5  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
  

> mmaker #5 to #1

Computing secondary structure  
Parameters  
---  
Chain pairing | bb  
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 AF3_J108_zflip_114-coot-0_real_space_refined_119.pdb, chain A (#1)
with 153G-02M12-Kabat_fit-coot-20.pdb, chain A (#5), sequence alignment score
= 1728.3  
RMSD between 343 pruned atom pairs is 0.547 angstroms; (across all 345 pairs:
0.574)  
  

> show atoms

> hide H

> open "/Users/zhouling95/Documents/Academic/McLellan
> Lab/MPXV/OPG153/AF3_J108_zflip_119-coot-3.pdb"

Chain information for AF3_J108_zflip_119-coot-3.pdb #6  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
E | No description available  
  

> style stick

Changed 36030 atom styles  

> show cartoons

> color #6 #35ee59ff

> hide #5 models

> dssp

Computing secondary structure  

> hide #4 models

> show #4 models

> hide #4 models

> hide #6 models

> show #6 models

> select add #6

6323 atoms, 6485 bonds, 796 residues, 1 model selected  

> select subtract #6

Nothing selected  

> select add #6

6323 atoms, 6485 bonds, 796 residues, 1 model selected  

> select subtract #6

Nothing selected  

> show #1,3,6 atoms

> hide H

> hide #3 models

> show #3 models

> hide #3 models

> show #3 models

> dssp

Computing secondary structure  

> show #5 models

> hide #5 models

> show #5 models

> close #3-6

> close #1

> open "/Users/zhouling95/Documents/Academic/McLellan
> Lab/MPXV/OPG153/AF3_J108_zflip_131-coot-1.pdb"

Chain information for AF3_J108_zflip_131-coot-1.pdb #1  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
E | No description available  
  

> style stick

Changed 6323 atom styles  

> show cartoons

> color byhetero

> isolde start

> set selectionWidth 4

Done loading forcefield  

> isolde set simFidelityMode Medium/Medium

ISOLDE: setting sim fidelity mode to Medium/Medium  
nonbonded_cutoff_distance = 0.900000  
use_gbsa = True  
gbsa_cutoff = 1.100000  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 37 residues in model #1 to IUPAC-IUB
standards.  
Chain information for AF3_J108_zflip_131-coot-1.pdb  
---  
Chain | Description  
1.2/A | No description available  
1.2/B | No description available  
1.2/C | No description available  
1.2/D | No description available  
1.2/E | No description available  
  

> clipper associate #2 toModel #1

Opened P913_J108_DeepEMhancer_zflipped.mrc as #1.1.1.1, grid size 384,384,384,
pixel 0.933, shown at step 1, values float32  

> ui tool show "Ramachandran Plot"

> addh

Summary of feedback from adding hydrogens to AF3_J108_zflip_131-coot-1.pdb
#1.2  
---  
notes | No usable SEQRES records for AF3_J108_zflip_131-coot-1.pdb (#1.2) chain A; guessing termini instead  
No usable SEQRES records for AF3_J108_zflip_131-coot-1.pdb (#1.2) chain B;
guessing termini instead  
No usable SEQRES records for AF3_J108_zflip_131-coot-1.pdb (#1.2) chain C;
guessing termini instead  
No usable SEQRES records for AF3_J108_zflip_131-coot-1.pdb (#1.2) chain D;
guessing termini instead  
No usable SEQRES records for AF3_J108_zflip_131-coot-1.pdb (#1.2) chain E;
guessing termini instead  
Chain-initial residues that are actual N termini: /A ASN 19, /B VAL 2, /C ILE
2, /D VAL 2, /E ALA 1  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini: /B VAL 111, /C LYS 107, /D SER
113, /E LYS 107  
Chain-final residues that are not actual C termini: /A ASN 364  
619 hydrogen bonds  
/A ASN 364 is not terminus, removing H atom from 'C'  
6131 hydrogens added  
  

> volume #1.1.1.1 level 0.01511

> select #1/A:328

19 atoms, 18 bonds, 1 residue, 1 model selected  

> view #1/A:328

> isolde sim start /A:328

ISOLDE: started sim  

> isolde sim stop

Sim termination reason: None  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 2 residues in model #1.2 to IUPAC-IUB
standards.  
ISOLDE: stopped sim  

> isolde sim start /A:329

ISOLDE: started sim  

> isolde sim stop

Sim termination reason: None  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> save "/Users/zhouling95/Documents/Academic/McLellan
> Lab/MPXV/OPG153/AF3_J108_zflip_131-coot-1-isolde.pdb"

> close #1

> open "/Users/zhouling95/Documents/Academic/McLellan
> Lab/MPXV/OPG153/Phenix/RealSpaceRefine_141/AF3_J108_zflip_131-coot-1_real_space_refined_141.pdb"

Chain information for AF3_J108_zflip_131-coot-1_real_space_refined_141.pdb #1  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
E | No description available  
  

> open "/Users/zhouling95/Documents/Academic/McLellan
> Lab/MPXV/P913_J108_DeepEMhancer_zflipped.mrc"

Opened P913_J108_DeepEMhancer_zflipped.mrc as #2, grid size 384,384,384, pixel
0.933, shown at level 0.000654, step 2, values float32  

> style stick

Changed 6323 atom styles  

> volume #2 step 1

> volume #2 level 0.01616

> surface dust #2 size 9.33

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 41 residues in model #1 to IUPAC-IUB
standards.  
Chain information for AF3_J108_zflip_131-coot-1_real_space_refined_141.pdb  
---  
Chain | Description  
1.2/A | No description available  
1.2/B | No description available  
1.2/C | No description available  
1.2/D | No description available  
1.2/E | No description available  
  

> clipper associate #2 toModel #1

Opened P913_J108_DeepEMhancer_zflipped.mrc as #1.1.1.1, grid size 384,384,384,
pixel 0.933, shown at step 1, values float32  

> addh

Summary of feedback from adding hydrogens to
AF3_J108_zflip_131-coot-1_real_space_refined_141.pdb #1.2  
---  
notes | No usable SEQRES records for AF3_J108_zflip_131-coot-1_real_space_refined_141.pdb (#1.2) chain A; guessing termini instead  
No usable SEQRES records for
AF3_J108_zflip_131-coot-1_real_space_refined_141.pdb (#1.2) chain B; guessing
termini instead  
No usable SEQRES records for
AF3_J108_zflip_131-coot-1_real_space_refined_141.pdb (#1.2) chain C; guessing
termini instead  
No usable SEQRES records for
AF3_J108_zflip_131-coot-1_real_space_refined_141.pdb (#1.2) chain D; guessing
termini instead  
No usable SEQRES records for
AF3_J108_zflip_131-coot-1_real_space_refined_141.pdb (#1.2) chain E; guessing
termini instead  
Chain-initial residues that are actual N termini: /A ASN 19, /B VAL 2, /C ILE
2, /D VAL 2, /E ALA 1  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini: /B VAL 111, /C LYS 107, /D SER
113, /E LYS 107  
Chain-final residues that are not actual C termini: /A ASN 364  
616 hydrogen bonds  
/A ASN 364 is not terminus, removing H atom from 'C'  
6131 hydrogens added  
  

> ui tool show "Ramachandran Plot"

> isolde sim start /A-E

ISOLDE: started sim  

> volume #1.1.1.1 level 0.01837

> isolde pepflip /A:320

> volume #1.1.1.1 level 0.005965

> isolde pepflip /A:108

> isolde pepflip /E:69

> isolde sim stop discardTo start

Sim termination reason: None  
reverting to start  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  
Computing secondary structure  
s1:
NVASITAFKSMIDETWDKKIEANTCISRKHRNIIHEVIRDFMKAYPKMDENRKSPLGAPMQWLTQYYILKNEYHKTMLAYDDGSLNTKFKTLNIYMITNVGQYILYIVFCIISGKNHDGTPYIYDSEITSNDKNLINDRIKYACKQILHGQLTMALRIRNKFMFIGSPMYLWFNVNGSHVYHEIYDRNVGFHNKEIGRLLYAFMYYLSISGRFLNDLALLKFTYLGESWTFSLSVPEYILYGLGYSVFDTIEKFSNDAILVYIRTNNRNGYDYAEFNKKGIVKVTEDKPDNDKRIHAIRLINYSSDVQHIHFGFRNTLIIDNECTSIQSSAENATDTGHHQDSKIN  
s2:
NVASITAFKSMIDETWDKKIEANTCISRKHRNIIHEVIRDFMKAYPKMDENRKSPLGAPMQWLTQYYILKNEYHKTMLAYDDGSLNTKFKTLNIYMITNVGQYILYIVFCIISGKNHDGTPYIYDSEITSNDKNLINDRIKYACKQILHGQLTMALRIRNKFMFIGSPMYLWFNVNGSHVYHEIYDRNVGFHNKEIGRLLYAFMYYLSISGRFLNDLALLKFTYLGESWTFSLSVPEYILYGLGYSVFDTIEKFSNDAILVYIRTNNRNGYDYAEFNKKGIVKVTEDKPDNDKRIHAIRLINYSSDVQHIHFGFRNTLIIDNECTSIQSSAENATDTGHHQDSKIN  
s1:
NVASITAFKSMIDETWDKKIEANTCISRKHRNIIHEVIRDFMKAYPKMDENRKSPLGAPMQWLTQYYILKNEYHKTMLAYDDGSLNTKFKTLNIYMITNVGQYILYIVFCIIS..GKNHDGTPYIYDSEITSNDKNLINDRIKYACKQILHGQLTMALR........IRNKFMFIGSPMYLWFNVNGSHVYHEIYDRNVGFHNKEIGRLLYAFMYYLSISGRFLNDLALLKFTYLGESWTFSLSVPEYILYGLGYSVFDTIEKFSNDAILVYIRTNNRNGYDYAEFNKKGIVKVTEDKPDNDKRIHAIRLINYSSDVQHIHFGFRNTLIIDNECTSIQSSAENATDTGHHQDSKIN  
s2:
...........................................................................VQLQESGPGLVKPSETLSLTCTVSGGSISNYYWSWIRQPPGKGLEWIGYIYYIGTTNYNPSL.KSRVTISVD.TSKNQFSLKLSSVTAADTAVYYCARHTDSRAWYYFDYWGQGTLVTV..................................................................................................................................................................  
s1:
NVASITAFKSMIDETWDKKIEANTCISRKHRNIIHEVIRDFMKAYPKMDENRKSPLGAPMQWLTQYYILKNEYHKTMLAYDDGSLNTKFKTLNIYMITNVGQYILYIVFCIISGKNHDGTPYIYDSEITSNDKNLINDRIKYACKQILHGQLTMALRIRNKFMFIG.SPMYLWFNVNGSHVYHEIYDRNVGFHNKEIGRLLYAFMYYLSISGRFLNDLALLKFTYLG.ESWTFSLSVPEYILYGLGYSVFDTIEKFSNDAILVYIRTNNRNGYDYAEFNKKGIVKVTEDKPDNDKRIHAIRLINYSSDVQHIHFGFRNTLIIDNECTSIQSSAENATDTGHHQDSKIN  
s2:
..........................................................................................................................IQMTQSPSSVSASVGDRVTITCRA.SQGISSWLAWYQQK...PGKAPKLLMY..DASDLQSGVPSR...FSGSGSGT.....DFTLTISSLQPEDFATYYCQQANSFPWTFGQGTKVEIK..........................................................................................................  
s1:
NVASITAFKSMIDETWDKKIEANTCISRKHRNIIHEVIRDFMKAYPKMDENRKSPLGAPMQWLTQYYILKNEYHKTMLAYDDGSLNTKFKTLNIYMITNVGQYILYIVFCIISGKNHDGTPYIYDSEITSNDKNLINDRIKYACKQILHGQLTMALRIRNKFMFIGSPMYLWFNVNGSHVYHEIYDRNVGFHNKEIGRLLYAFMYYLSISGRFLNDLALLKFTYLGESWTFSLSVPEYILYGLGYSVFDTIEKFSNDAILVYIRTNNRNGYDYAEFNKKGIVKVTED..KPDNDKRIHAIRLINYSSDVQHIHFGFRNTLIIDNECTSIQSSAENATDTGHHQDSKIN  
s2:
...........................................................................................................................................................................................................VQLVQSGGGVVQPGRSLRLSCAASGFTFSSHGMHWVRQAPGKG.LEWVAVISYDGSNEHYGDSVKGRFTISRDNSKNTLSLQMNSLRAEDTAVYYCARPFSYGAGYYFDSWGQGALVTVSS........................  
s1:
NVASITAFKSMIDETWDKKIEANTCISRKHRNIIHEVIRDFMKAYPKMDENRKSPLGAPMQWLTQYYILKNEYHKTMLAYDDGSLNTKFKTLNIYMITNVGQYILYIVFCIISGKNHDGTPYIYDSEITSNDKNLINDRIKYACKQILHGQLTMALRIRNKFMFIGSPMYLWFNVN.....GSHVYHEIYDRNVGFHNKEIGRLLYAFMYYLSI..SG...RFLNDLALLKFTYLGESWTFSLSVPEYILYGLGYSVFDTIEKFSNDAILVYIRTNNRNGYDYAEFNKKGIVKVTEDKPDNDKRIHAIRLINYSSDVQHIHFGFRNTLIIDNECTSIQSSAENATDTGHHQDSKIN  
s2:
................................................................................................................................................................AIQMTQSPSSLSASVGDRVTITCRASQNI.DSYLNWYQQKPGEAPKLLMYAASSLQSGVPSRFSGSGSGTDFTLIIS....SLQREDFATYYCQQS.YSTPPTFGQGTKLEIK...................................................................................  
s1:
...........................................................................VQLQESGPGLVKPSETLSLTCTVSGGSISNYYWSWIRQPPGKGLEWIGYIYYIGTTNYNPSL.KSRVTISVD.TSKNQFSLKLSSVTAADTAVYYCARHTDSRAWYYFDYWGQGTLVTV..................................................................................................................................................................  
s2:
NVASITAFKSMIDETWDKKIEANTCISRKHRNIIHEVIRDFMKAYPKMDENRKSPLGAPMQWLTQYYILKNEYHKTMLAYDDGSLNTKFKTLNIYMITNVGQYILYIVFCIIS..GKNHDGTPYIYDSEITSNDKNLINDRIKYACKQILHGQLTMALR........IRNKFMFIGSPMYLWFNVNGSHVYHEIYDRNVGFHNKEIGRLLYAFMYYLSISGRFLNDLALLKFTYLGESWTFSLSVPEYILYGLGYSVFDTIEKFSNDAILVYIRTNNRNGYDYAEFNKKGIVKVTEDKPDNDKRIHAIRLINYSSDVQHIHFGFRNTLIIDNECTSIQSSAENATDTGHHQDSKIN  
s1:
VQLQESGPGLVKPSETLSLTCTVSGGSISNYYWSWIRQPPGKGLEWIGYIYYIGTTNYNPSLKSRVTISVDTSKNQFSLKLSSVTAADTAVYYCARHTDSRAWYYFDYWGQGTLVTV  
s2:
VQLQESGPGLVKPSETLSLTCTVSGGSISNYYWSWIRQPPGKGLEWIGYIYYIGTTNYNPSLKSRVTISVDTSKNQFSLKLSSVTAADTAVYYCARHTDSRAWYYFDYWGQGTLVTV  
s1:
VQLQESGPGLVKPS..ETLSLTCTVSGGSISNYYWSWIRQPPGKGLEWIGYIYYIGTTNYNPSLKSRVTISVDTSKNQFSLKLSSVTAADTAVYYCARHTDSRAWYYFDYWGQGTLVTV.  
s2:
IQMTQS.PSSVSASVGDRVTITCRASQG.ISS.WLAWYQQKPGKAPKLLMY....DASDLQSGVPSR..FSGSGSGTDFTLTISSLQPEDFATYYCQQ.ANSFPWTF....GQGTKVEIK  
s1:
VQLQESGPGLVKPSETLSLTCTVSGGSISNYYWSWIRQPPGKGLEWIGYIYYIGT.TNYNPSLKSRVTISVDTSKNQFSLKLSSVTAADTAVYYCARHTDSRAWYYFDYWGQGTLVTV..  
s2:
VQLVQSGGGVVQPGRSLRLSCAASGFTFSSHGMHWVRQAPGKGLEWVAVISYDGSNEHYGDSVKGRFTISRDNSKNTLSLQMNSLRAEDTAVYYCARPFSYGAGYYFDSWGQGALVTVSS  
s1:
.VQLQESGPGL.VKPSETLSLTCTVSGGSISNYYWSWIRQPPGKGLEWIGYIYYIGTTNYNPSLKSRVTISVDTSKNQFSLKLSSVTAADTAVYYCARHTDSRAWYYFDYWGQGTLVTV.  
s2:
AIQMTQSPSSLSASVGDRVTITCRASQNIDS..YLNWYQQKPGEAPKLLMY....AASSLQSGVPSR..FSGSGSGTDFTLIISSLQREDFATYYCQQSYSTPPTF.....GQGTKLEIK  
s1:
..........................................................................................................................IQMTQSPSSVSASVGDRVTITCRA.SQGISSWLAWYQQK...PGKAPKLLMY..DASDLQSGVPSR...FSGSGSGT.....DFTLTISSLQPEDFATYYCQQANSFPWTFGQGTKVEIK..........................................................................................................  
s2:
NVASITAFKSMIDETWDKKIEANTCISRKHRNIIHEVIRDFMKAYPKMDENRKSPLGAPMQWLTQYYILKNEYHKTMLAYDDGSLNTKFKTLNIYMITNVGQYILYIVFCIISGKNHDGTPYIYDSEITSNDKNLINDRIKYACKQILHGQLTMALRIRNKFMFIG.SPMYLWFNVNGSHVYHEIYDRNVGFHNKEIGRLLYAFMYYLSISGRFLNDLALLKFTYLG.ESWTFSLSVPEYILYGLGYSVFDTIEKFSNDAILVYIRTNNRNGYDYAEFNKKGIVKVTEDKPDNDKRIHAIRLINYSSDVQHIHFGFRNTLIIDNECTSIQSSAENATDTGHHQDSKIN  
s1:
IQMTQS.PSSVSASVGDRVTITCRASQG.ISS.WLAWYQQKPGKAPKLLMY....DASDLQSGVPSR..FSGSGSGTDFTLTISSLQPEDFATYYCQQ.ANSFPWTF....GQGTKVEIK  
s2:
VQLQESGPGLVKPS..ETLSLTCTVSGGSISNYYWSWIRQPPGKGLEWIGYIYYIGTTNYNPSLKSRVTISVDTSKNQFSLKLSSVTAADTAVYYCARHTDSRAWYYFDYWGQGTLVTV.  
s1:
IQMTQSPSSVSASVGDRVTITCRASQGISSWLAWYQQKPGKAPKLLMYDASDLQSGVPSRFSGSGSGTDFTLTISSLQPEDFATYYCQQANSFPWTFGQGTKVEIK  
s2:
IQMTQSPSSVSASVGDRVTITCRASQGISSWLAWYQQKPGKAPKLLMYDASDLQSGVPSRFSGSGSGTDFTLTISSLQPEDFATYYCQQANSFPWTFGQGTKVEIK  
s1:
IQMTQSPSSVSASVGDRVTITCRASQGI...SSWLAWYQQKPGKA...PKLLMYDASDLQSG..VPSRFSGSGSGTDFTLTI..SSLQPEDFATYYCQQANSFPW.....TFGQGTKVEIK.  
s2:
VQLVQSGGGVV.QPGRSLRLSCAAS.GFTFSSHGMHWVRQAPGKGLEWVAVISYDGSNEHYGDSVKGRFTISRDNSKNTLSLQMNSLRAEDTAVYYCARPFSYGAGYYFDSWGQGALVTVSS  
s1:
.IQMTQSPSSVSASVGDRVTITCRASQGISSWLAWYQQKPGKAPKLLMYDASDLQSGVPSRFSGSGSGTDFTLTISSLQPEDFATYYCQQANSFPWTFGQGTKVEIK  
s2:
AIQMTQSPSSLSASVGDRVTITCRASQNIDSYLNWYQQKPGEAPKLLMYAASSLQSGVPSRFSGSGSGTDFTLIISSLQREDFATYYCQQSYSTPPTFGQGTKLEIK  
s1:
...........................................................................................................................................................................................................VQLVQSGGGVVQPGRSLRLSCAASGFTFSSHGMHWVRQAPGKG.LEWVAVISYDGSNEHYGDSVKGRFTISRDNSKNTLSLQMNSLRAEDTAVYYCARPFSYGAGYYFDSWGQGALVTVSS........................  
s2:
NVASITAFKSMIDETWDKKIEANTCISRKHRNIIHEVIRDFMKAYPKMDENRKSPLGAPMQWLTQYYILKNEYHKTMLAYDDGSLNTKFKTLNIYMITNVGQYILYIVFCIISGKNHDGTPYIYDSEITSNDKNLINDRIKYACKQILHGQLTMALRIRNKFMFIGSPMYLWFNVNGSHVYHEIYDRNVGFHNKEIGRLLYAFMYYLSISGRFLNDLALLKFTYLGESWTFSLSVPEYILYGLGYSVFDTIEKFSNDAILVYIRTNNRNGYDYAEFNKKGIVKVTED..KPDNDKRIHAIRLINYSSDVQHIHFGFRNTLIIDNECTSIQSSAENATDTGHHQDSKIN  
s1:
VQLVQSGGGVVQPGRSLRLSCAASGFTFSSHGMHWVRQAPGKGLEWVAVISYDGSNEHYGDSVKGRFTISRDNSKNTLSLQMNSLRAEDTAVYYCARPFSYGAGYYFDSWGQGALVTVSS  
s2:
VQLQESGPGLVKPSETLSLTCTVSGGSISNYYWSWIRQPPGKGLEWIGYIYYIGT.TNYNPSLKSRVTISVDTSKNQFSLKLSSVTAADTAVYYCARHTDSRAWYYFDYWGQGTLVTV..  
s1:
VQLVQSGGGVV.QPGRSLRLSCAAS.GFTFSSHGMHWVRQAPGKGLEWVAVISYDGSNEHYGDSVKGRFTISRDNSKNTLSLQMNSLRAEDTAVYYCARPFSYGAGYYFDSWGQGALVTVSS  
s2:
IQMTQSPSSVSASVGDRVTITCRASQGI...SSWLAWYQQKPGKA...PKLLMYDASDLQSG..VPSRFSGSGSGTDFTLTI..SSLQPEDFATYYCQQANSFPW.....TFGQGTKVEIK.  
s1:
VQLVQSGGGVVQPGRSLRLSCAASGFTFSSHGMHWVRQAPGKGLEWVAVISYDGSNEHYGDSVKGRFTISRDNSKNTLSLQMNSLRAEDTAVYYCARPFSYGAGYYFDSWGQGALVTVSS  
s2:
VQLVQSGGGVVQPGRSLRLSCAASGFTFSSHGMHWVRQAPGKGLEWVAVISYDGSNEHYGDSVKGRFTISRDNSKNTLSLQMNSLRAEDTAVYYCARPFSYGAGYYFDSWGQGALVTVSS  
s1:
.VQLVQSGGGVV.QPGRSLRLSCAASGFTFSSHGMHWVRQAPGKGLEWVAVISYDGSNEHYGDSVKGRFTISRDNSKNTLSLQMNSLRAEDTAVYYCARPFSYGAGYYFDSWGQGALVTVSS  
s2:
AIQMTQSPSSLSASVGDRVTITCRASQ.NIDSY.LNWYQQKPG...EAPKLLMYAASSLQSG..VPSRFSGSGSGTDFTLII..SSLQREDFATYYCQQSYSTP.....PTFGQGTKLEIK.  
s1:
................................................................................................................................................................AIQMTQSPSSLSASVGDRVTITCRASQNI.DSYLNWYQQKPGEAPKLLMYAASSLQSGVPSRFSGSGSGTDFTLIIS....SLQREDFATYYCQQS.YSTPPTFGQGTKLEIK...................................................................................  
s2:
NVASITAFKSMIDETWDKKIEANTCISRKHRNIIHEVIRDFMKAYPKMDENRKSPLGAPMQWLTQYYILKNEYHKTMLAYDDGSLNTKFKTLNIYMITNVGQYILYIVFCIISGKNHDGTPYIYDSEITSNDKNLINDRIKYACKQILHGQLTMALRIRNKFMFIGSPMYLWFNVN.....GSHVYHEIYDRNVGFHNKEIGRLLYAFMYYLSI..SG...RFLNDLALLKFTYLGESWTFSLSVPEYILYGLGYSVFDTIEKFSNDAILVYIRTNNRNGYDYAEFNKKGIVKVTEDKPDNDKRIHAIRLINYSSDVQHIHFGFRNTLIIDNECTSIQSSAENATDTGHHQDSKIN  
s1:
AIQMTQSPSSLSASVGDRVTITCRASQNIDS..YLNWYQQKPGEAPKLLMY....AASSLQSGVPSR..FSGSGSGTDFTLIISSLQREDFATYYCQQSYSTPPTF.....GQGTKLEIK  
s2:
.VQLQESGPGL.VKPSETLSLTCTVSGGSISNYYWSWIRQPPGKGLEWIGYIYYIGTTNYNPSLKSRVTISVDTSKNQFSLKLSSVTAADTAVYYCARHTDSRAWYYFDYWGQGTLVTV.  
s1:
AIQMTQSPSSLSASVGDRVTITCRASQNIDSYLNWYQQKPGEAPKLLMYAASSLQSGVPSRFSGSGSGTDFTLIISSLQREDFATYYCQQSYSTPPTFGQGTKLEIK  
s2:
.IQMTQSPSSVSASVGDRVTITCRASQGISSWLAWYQQKPGKAPKLLMYDASDLQSGVPSRFSGSGSGTDFTLTISSLQPEDFATYYCQQANSFPWTFGQGTKVEIK  
s1:
AIQMTQSPSSLSASVGDRVTITCRASQ.NIDSY.LNWYQQKPG...EAPKLLMYAASSLQSG..VPSRFSGSGSGTDFTLII..SSLQREDFATYYCQQSYSTP.....PTFGQGTKLEIK.  
s2:
.VQLVQSGGGVV.QPGRSLRLSCAASGFTFSSHGMHWVRQAPGKGLEWVAVISYDGSNEHYGDSVKGRFTISRDNSKNTLSLQMNSLRAEDTAVYYCARPFSYGAGYYFDSWGQGALVTVSS  
s1:
AIQMTQSPSSLSASVGDRVTITCRASQNIDSYLNWYQQKPGEAPKLLMYAASSLQSGVPSRFSGSGSGTDFTLIISSLQREDFATYYCQQSYSTPPTFGQGTKLEIK  
s2:
AIQMTQSPSSLSASVGDRVTITCRASQNIDSYLNWYQQKPGEAPKLLMYAASSLQSGVPSRFSGSGSGTDFTLIISSLQREDFATYYCQQSYSTPPTFGQGTKLEIK  

"Adjust for PAE" is checked in the distance restraint options, but the
reference model has no PAE matrix assigned. This option has been ignored.  

> isolde restrain distances "#1.2/A","#1.2/B","#1.2/C","#1.2/D","#1.2/E"
> templateAtoms "#1.2/A","#1.2/B","#1.2/C","#1.2/D","#1.2/E" perChain false
> adjustForConfidence false useCoordinateAlignment false kappa 4.40 fallOff
> 2.50 groupName "Reference Distance Restraints"

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  

> isolde restrain torsions #1.2/A templateResidues #1.2/A adjustForConfidence
> false sidechains true springConstant 250.00 alpha 0.20

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  

> isolde restrain torsions #1.2/B templateResidues #1.2/B adjustForConfidence
> false sidechains true springConstant 250.00 alpha 0.20

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  

> isolde restrain torsions #1.2/C templateResidues #1.2/C adjustForConfidence
> false sidechains true springConstant 250.00 alpha 0.20

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  

> isolde restrain torsions #1.2/D templateResidues #1.2/D adjustForConfidence
> false sidechains true springConstant 250.00 alpha 0.20

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  

> isolde restrain torsions #1.2/E templateResidues #1.2/E adjustForConfidence
> false sidechains true springConstant 250.00 alpha 0.20

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  

> isolde sim start /A:107

ISOLDE: started sim  

> isolde sim stop

Sim termination reason: None  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> ; #1

Incomplete command: sequence  

> select #1

12454 atoms, 12616 bonds, 796 residues, 21 models selected  

> isolde sim start /A-E

ISOLDE: started sim  

> isolde sim stop

Sim termination reason: None  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 2 residues in model #1.2 to IUPAC-IUB
standards.  
ISOLDE: stopped sim  

> save "/Users/zhouling95/Documents/Academic/McLellan
> Lab/MPXV/OPG153/AF3_J108_zflip_141-isolde.pdb"

> close #1

> open "/Users/zhouling95/Documents/Academic/McLellan
> Lab/MPXV/P913_J108_DeepEMhancer_zflipped.mrc"

Opened P913_J108_DeepEMhancer_zflipped.mrc as #1, grid size 384,384,384, pixel
0.933, shown at level 0.000654, step 2, values float32  

> open "/Users/zhouling95/Documents/Academic/McLellan
> Lab/MPXV/OPG153/Phenix/RealSpaceRefine_145/AF3_J108_zflip_141-isolde_real_space_refined_145.pdb"

Chain information for AF3_J108_zflip_141-isolde_real_space_refined_145.pdb #2  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
E | No description available  
  

> color byhetero

> style stick

Changed 12454 atom styles  

> volume #1 step 1

> volume #1 color #b2b2b26b

> surface dust #1 size 9.33

> hide H

> show cartoons

> volume #1 level 0.01616

> volume #1 level 0.00996

> color bychain

> color byhetero

> open
> /Users/zhouling95/Library/Containers/net.whatsapp.WhatsApp/Data/tmp/documents/0F160952-8339-44A6-A51F-F6112F38230F/153G-02M12-Kabat_fit-
> coot-20.pdb

Summary of feedback from opening
/Users/zhouling95/Library/Containers/net.whatsapp.WhatsApp/Data/tmp/documents/0F160952-8339-44A6-A51F-F6112F38230F/153G-02M12-Kabat_fit-
coot-20.pdb  
---  
warning | Cannot find LINK/SSBOND residue CYS (25 )  
  
Chain information for 153G-02M12-Kabat_fit-coot-20.pdb #3  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
  

> mmaker #3 to #2

Computing secondary structure  
Parameters  
---  
Chain pairing | bb  
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 AF3_J108_zflip_141-isolde_real_space_refined_145.pdb, chain A (#2)
with 153G-02M12-Kabat_fit-coot-20.pdb, chain A (#3), sequence alignment score
= 1739.7  
RMSD between 343 pruned atom pairs is 0.537 angstroms; (across all 345 pairs:
0.567)  
  

> show atoms

> hide H

> hide #3 models

> show #3 models

> open "/Users/zhouling95/Documents/Academic/McLellan
> Lab/MPXV/OPG153/AF3_J108_zflip_141-isolde_real_space_refined_145-coot-0.pdb"

Chain information for
AF3_J108_zflip_141-isolde_real_space_refined_145-coot-0.pdb #4  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
E | No description available  
  

> show atoms

> style stick

Changed 23384 atom styles  

> show cartoons

> hide H

> color #4 #4fee55ff

> color byhetero

> hide #4 models

> show #4 models

> hide #4 models

> show #4 models

> hide #4 models

> show #4 models

> close #4

> open "/Users/zhouling95/Documents/Academic/McLellan
> Lab/MPXV/OPG153/Phenix/RealSpaceRefine_145/AF3_J108_zflip_141-isolde_real_space_refined_145-pm.pdb"

Chain information for AF3_J108_zflip_141-isolde_real_space_refined_145-pm.pdb
#4  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
E | No description available  
  

> style stick

Changed 29515 atom styles  

> color byhetero

> show cartoons

Computing secondary structure  

> hide H

> hide #3 models

> hide #2 models

> show #2 models

> hide #2 models

> show #2 models

> hide #4 models

> show #4 models

> hide #4 models

> show #4 models

> hide #2 models

> show #!1 models

> show #2 models

> hide #4 models

> volume #1 level 0.0006542

> volume #1 level 0.006858

> dssp

Computing secondary structure  

> volume #1 level 0.003756

> ui tool show "Model-map Q-Score"

> style #2 stick

Changed 12454 atom styles  

> color #2 byhetero

> transparency #1 60

> qscore #2 toVolume #1 useGui false pointsPerShell 8 shellRadiusStep 0.100
> maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false

Overall mean Q-Score: 0.68  

> volume #1 level 0.01616

> ui tool show "Show Sequence Viewer"

> sequence chain #4/A

Alignment identifier is 4/A  

> select #4/A:19

16 atoms, 15 bonds, 1 residue, 1 model selected  

> select #4/A

5649 atoms, 5718 bonds, 346 residues, 1 model selected  

> ui tool show "Show Sequence Viewer"

> sequence chain #4/D

Alignment identifier is 4/D  

> select #4/D:113

12 atoms, 11 bonds, 1 residue, 1 model selected  

> select #4/D

1784 atoms, 1807 bonds, 120 residues, 1 model selected  

> ui tool show "Show Sequence Viewer"

> sequence chain #4/E

Alignment identifier is 4/E  

> select #4/E:107

23 atoms, 22 bonds, 1 residue, 1 model selected  

> select #4/E

1610 atoms, 1627 bonds, 107 residues, 1 model selected  

> ui tool show "Show Sequence Viewer"

> sequence chain #4/B

Alignment identifier is 4/B  

> select #4/B:110-111

31 atoms, 30 bonds, 2 residues, 1 model selected  

> select #4/B

1823 atoms, 1851 bonds, 117 residues, 1 model selected  

> ui tool show "Show Sequence Viewer"

> sequence chain #4/C

Alignment identifier is 4/C  

> select #4/C:2

21 atoms, 20 bonds, 1 residue, 1 model selected  

> select #4/C

1588 atoms, 1608 bonds, 106 residues, 1 model selected  

> ui tool show "Show Sequence Viewer"

> sequence chain #4/D

Alignment identifier is 4/D  

> ui tool show "Show Sequence Viewer"

> sequence chain #4/E

Alignment identifier is 4/E  

> ui tool show "Show Sequence Viewer"

> sequence chain #4/D

Destroying pre-existing alignment with identifier 4/D  
Alignment identifier is 4/D  

> ui tool show "Show Sequence Viewer"

> sequence chain #4/E

Destroying pre-existing alignment with identifier 4/E  
Alignment identifier is 4/E  

> select
> #4/D:3-7,10-12,18-25,34-39,45-51,57-59,67-72,77-82,88-98,100A-103,107-111

1086 atoms, 1093 bonds, 67 residues, 1 model selected  

> select #4/E:4-7,10-12,19-25,33-38,45-48,62-66,71-75,85-90,103-105

699 atoms, 697 bonds, 43 residues, 1 model selected  

> ui tool show "Show Sequence Viewer"

> sequence chain #4/B

Alignment identifier is 4/B  

> ui tool show "Show Sequence Viewer"

> sequence chain #4/C

Alignment identifier is 4/C  

> select #4/B:3-6,18-25,33-39,46-52,57-59,67-72,77-82,88-95,100D-103,107-109

948 atoms, 956 bonds, 56 residues, 1 model selected  

> show #3 models

> show #4 models

> hide #4 models

> hide #3 models

> hide #!1 models

> show #!1 models

> close #2

> close #1

> open "/Users/zhouling95/Documents/Academic/McLellan
> Lab/MPXV/OPG153/Phenix/RealSpaceRefine_145/AF3_J108_zflip_141-isolde_real_space_refined_145.pdb"

Chain information for AF3_J108_zflip_141-isolde_real_space_refined_145.pdb #1  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
E | No description available  
  

> open "/Users/zhouling95/Documents/Academic/McLellan
> Lab/MPXV/P913_J108_DeepEMhancer_zflipped.mrc"

Opened P913_J108_DeepEMhancer_zflipped.mrc as #2, grid size 384,384,384, pixel
0.933, shown at level 0.000654, step 2, values float32  

> style #1 stick

Changed 12454 atom styles  

> surface dust #2 size 9.33

> volume #2 step 1

> volume #2 level 0.01306

> color #1 byhetero

> hide H

> volume #2 color #b2b2b270

> isolde start

> set selectionWidth 4

Done loading forcefield  

> isolde set simFidelityMode Medium/Medium

ISOLDE: setting sim fidelity mode to Medium/Medium  
nonbonded_cutoff_distance = 0.900000  
use_gbsa = True  
gbsa_cutoff = 1.100000  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 42 residues in model #1 to IUPAC-IUB
standards.  
Chain information for AF3_J108_zflip_141-isolde_real_space_refined_145.pdb  
---  
Chain | Description  
1.2/A | No description available  
1.2/B | No description available  
1.2/C | No description available  
1.2/D | No description available  
1.2/E | No description available  
  

> close #1.2

Deleting atomic symmetry model...  
Deleting atomic symmetry model...  

> open "/Users/zhouling95/Documents/Academic/McLellan
> Lab/MPXV/OPG153/Phenix/RealSpaceRefine_145/AF3_J108_zflip_141-isolde_real_space_refined_145.pdb"

Chain information for AF3_J108_zflip_141-isolde_real_space_refined_145.pdb #5  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
E | No description available  
  

> style #5 stick

Changed 12454 atom styles  

> show #5 cartoons

> hide H

> color #5 byhetero

> select #5:Cys

122 atoms, 115 bonds, 12 residues, 1 model selected  

> ui tool show "Side View"

> select #5:Pro

378 atoms, 380 bonds, 27 residues, 1 model selected  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 42 residues in model #5 to IUPAC-IUB
standards.  
Chain information for AF3_J108_zflip_141-isolde_real_space_refined_145.pdb  
---  
Chain | Description  
5.2/A | No description available  
5.2/B | No description available  
5.2/C | No description available  
5.2/D | No description available  
5.2/E | No description available  
  
Deleting atomic symmetry model...  

> select #5/C:8,95

28 atoms, 28 bonds, 2 residues, 1 model selected  

> view #5/C:8,95

> close #5

Deleting atomic symmetry model...  

> open "/Users/zhouling95/Documents/Academic/McLellan
> Lab/MPXV/OPG153/Phenix/RealSpaceRefine_145/AF3_J108_zflip_141-isolde_real_space_refined_145.pdb"

Chain information for AF3_J108_zflip_141-isolde_real_space_refined_145.pdb #5  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
E | No description available  
  

> style #5 stick

Changed 12454 atom styles  

> show #5 cartoons

> color #5 byhetero

> hide H

> volume #2 level 0.006858

> close #5

Deleting atomic symmetry model...  

> open "/Users/zhouling95/Documents/Academic/McLellan
> Lab/MPXV/OPG153/Phenix/RealSpaceRefine_145/AF3_J108_zflip_141-isolde_real_space_refined_145.pdb"

Chain information for AF3_J108_zflip_141-isolde_real_space_refined_145.pdb #5  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
E | No description available  
  

> style #5 stick

Changed 12454 atom styles  

> show #5 cartoons

> color #5 byhetero

> hide H

> open "/Users/zhouling95/Documents/Academic/McLellan
> Lab/MPXV/OPG153/AF3_J108_zflip_145-coot-0.pdb"

Chain information for AF3_J108_zflip_145-coot-0.pdb #6  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
E | No description available  
  

> style #5-6 stick

Changed 18777 atom styles  

> show #5-6 cartoons

> color #5-6 byhetero

> volume #2 level 0.0004824

> volume #2 level 0.01005

> volume #2 level 0.006858

> open "/Users/zhouling95/Documents/Academic/McLellan
> Lab/MPXV/OPG153/AF3_J108_zflip_145-coot-2.pdb"

Chain information for AF3_J108_zflip_145-coot-2.pdb #7  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
E | No description available  
  

> style #5-7 stick

Changed 25100 atom styles  

> show #5-7 cartoons

> color #7 #446feeff

> color #5-7 byhetero

> close #6

Deleting atomic symmetry model...  

> close #4

Deleting atomic symmetry model...  

> open "/Users/zhouling95/Documents/Academic/McLellan
> Lab/MPXV/OPG153/Phenix/RealSpaceRefine_149/AF3_J108_zflip_145-coot-0_real_space_refined_149.pdb"

Chain information for AF3_J108_zflip_145-coot-0_real_space_refined_149.pdb #4  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
E | No description available  
  

> style #4-5,7 stick

Changed 25100 atom styles  

> color #4-5,7 byhetero

> color #4 #e0ee1dff

> color #4-5,7 byhetero

> show #4-5,7 cartoons

> hide #5 models

> open "/Users/zhouling95/Documents/Academic/McLellan
> Lab/MPXV/OPG153/Phenix/RealSpaceRefine_152/AF3_J108_zflip_145-coot-2_real_space_refined_152.pdb"

Chain information for AF3_J108_zflip_145-coot-2_real_space_refined_152.pdb #6  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
E | No description available  
  

> style #4,6-7 stick

Changed 18969 atom styles  

> show #4,6-7 cartoons

> color #4,6-7 byhetero

> color #6 #21ee18ff

> color #4,6-7 byhetero

> open "/Users/zhouling95/Documents/Academic/McLellan
> Lab/MPXV/OPG153/Phenix/RealSpaceRefine_153/AF3_J108_zflip_145-coot-2_real_space_refined_153.pdb"

Chain information for AF3_J108_zflip_145-coot-2_real_space_refined_153.pdb #8  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
E | No description available  
  

> show #4,6-8 atoms

> style #4,6-8 stick

Changed 25292 atom styles  

> show #4,6-8 cartoons

> open "/Users/zhouling95/Documents/Academic/McLellan
> Lab/MPXV/OPG153/AF3_J108_zflip_153-coot-0.pdb"

Chain information for AF3_J108_zflip_153-coot-0.pdb #9  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
E | No description available  
  

> style #4,6-9 stick

Changed 31615 atom styles  

> close #8

Deleting atomic symmetry model...  

> close #7

Deleting atomic symmetry model...  

> close #4-6

Deleting atomic symmetry model...  

> close #3

Deleting atomic symmetry model...  

> close #1

Deleting atomic symmetry model...  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 43 residues in model #9 to IUPAC-IUB
standards.  
Chain information for AF3_J108_zflip_153-coot-0.pdb  
---  
Chain | Description  
1.2/A | No description available  
1.2/B | No description available  
1.2/C | No description available  
1.2/D | No description available  
1.2/E | No description available  
  

> clipper associate #2 toModel #1

Opened P913_J108_DeepEMhancer_zflipped.mrc as #1.1.1.1, grid size 384,384,384,
pixel 0.933, shown at step 1, values float32  

> addh

Summary of feedback from adding hydrogens to AF3_J108_zflip_153-coot-0.pdb
#1.2  
---  
notes | No usable SEQRES records for AF3_J108_zflip_153-coot-0.pdb (#1.2) chain A; guessing termini instead  
No usable SEQRES records for AF3_J108_zflip_153-coot-0.pdb (#1.2) chain B;
guessing termini instead  
No usable SEQRES records for AF3_J108_zflip_153-coot-0.pdb (#1.2) chain C;
guessing termini instead  
No usable SEQRES records for AF3_J108_zflip_153-coot-0.pdb (#1.2) chain D;
guessing termini instead  
No usable SEQRES records for AF3_J108_zflip_153-coot-0.pdb (#1.2) chain E;
guessing termini instead  
Chain-initial residues that are actual N termini: /A ASN 19, /B VAL 2, /C ILE
2, /D VAL 2, /E ALA 1  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini: /B VAL 111, /C LYS 107, /D SER
113, /E LYS 107  
Chain-final residues that are not actual C termini: /A ASN 364  
652 hydrogen bonds  
/A ASN 364 is not terminus, removing H atom from 'C'  
6131 hydrogens added  
  

> volume #1.1.1.1 level 0.05947

Computing secondary structure  
s1:
NVASITAFKSMIDETWDKKIEANTCISRKHRNIIHEVIRDFMKAYPKMDENRKSPLGAPMQWLTQYYILKNEYHKTMLAYDDGSLNTKFKTLNIYMITNVGQYILYIVFCIISGKNHDGTPYIYDSEITSNDKNLINDRIKYACKQILHGQLTMALRIRNKFMFIGSPMYLWFNVNGSHVYHEIYDRNVGFHNKEIGRLLYAFMYYLSISGRFLNDLALLKFTYLGESWTFSLSVPEYILYGLGYSVFDTIEKFSNDAILVYIRTNNRNGYDYAEFNKKGIVKVTEDKPDNDKRIHAIRLINYSSDVQHIHFGFRNTLIIDNECTSIQSSAENATDTGHHQDSKIN  
s2:
NVASITAFKSMIDETWDKKIEANTCISRKHRNIIHEVIRDFMKAYPKMDENRKSPLGAPMQWLTQYYILKNEYHKTMLAYDDGSLNTKFKTLNIYMITNVGQYILYIVFCIISGKNHDGTPYIYDSEITSNDKNLINDRIKYACKQILHGQLTMALRIRNKFMFIGSPMYLWFNVNGSHVYHEIYDRNVGFHNKEIGRLLYAFMYYLSISGRFLNDLALLKFTYLGESWTFSLSVPEYILYGLGYSVFDTIEKFSNDAILVYIRTNNRNGYDYAEFNKKGIVKVTEDKPDNDKRIHAIRLINYSSDVQHIHFGFRNTLIIDNECTSIQSSAENATDTGHHQDSKIN  
s1:
NVASITAFKSMIDETWDKKIEANTCISRKHRNIIHEVIRDFMKAYPKMDENRKSPLGAPMQWLTQYYILKNEYHKTMLAYDDGSLNTKFKTLNIYMITNVGQYILYIVFCIIS..GKNHDGTPYIYDSEITSNDKNLINDRIKYACKQILHGQLTMALR........IRNKFMFIGSPMYLWFNVNGSHVYHEIYDRNVGFHNKEIGRLLYAFMYYLSISGRFLNDLALLKFTYLGESWTFSLSVPEYILYGLGYSVFDTIEKFSNDAILVYIRTNNRNGYDYAEFNKKGIVKVTEDKPDNDKRIHAIRLINYSSDVQHIHFGFRNTLIIDNECTSIQSSAENATDTGHHQDSKIN  
s2:
...........................................................................VQLQESGPGLVKPSETLSLTCTVSGGSISNYYWSWIRQPPGKGLEWIGYIYYIGTTNYNPSL.KSRVTISVD.TSKNQFSLKLSSVTAADTAVYYCARHTDSRAWYYFDYWGQGTLVTV..................................................................................................................................................................  
s1:
NVASITAFKSMIDETWDKKIEANTCISRKHRNIIHEVIRDFMKAYPKMDENRKSPLGAPMQWLTQYYILKNEYHKTMLAYDDGSLNTKFKTLNIYMITNVGQYILYIVFCIISGKNHDGTPYIYDSEITSNDKNLINDRIKYACKQILHGQLTMALRIRNKFMFIG.SPMYLWFNVNGSHVYHEIYDRNVGFHNKEIGRLLYAFMYYLSISGRFLNDLALLKFTYLG.ESWTFSLSVPEYILYGLGYSVFDTIEKFSNDAILVYIRTNNRNGYDYAEFNKKGIVKVTEDKPDNDKRIHAIRLINYSSDVQHIHFGFRNTLIIDNECTSIQSSAENATDTGHHQDSKIN  
s2:
..........................................................................................................................IQMTQSPSSVSASVGDRVTITCRA.SQGISSWLAWYQQK...PGKAPKLLMY..DASDLQSGVPSR...FSGSGSGT.....DFTLTISSLQPEDFATYYCQQANSFPWTFGQGTKVEIK..........................................................................................................  
s1:
NVASITAFKSMIDETWDKKIEANTCISRKHRNIIHEVIRDFMKAYPKMDENRKSPLGAPMQWLTQYYILKNEYHKTMLAYDDGSLNTKFKTLNIYMITNVGQYILYIVFCIISGKNHDGTPYIYDSEITSNDKNLINDRIKYACKQILHGQLTMALRIRNKFMFIGSPMYLWFNVNGSHVYHEIYDRNVGFHNKEIGRLLYAFMYYLSISGRFLNDLALLKFTYLGESWTFSLSVPEYILYGLGYSVFDTIEKFSNDAILVYIRTNNRNGYDYAEFNKKGIVKVTED..KPDNDKRIHAIRLINYSSDVQHIHFGFRNTLIIDNECTSIQSSAENATDTGHHQDSKIN  
s2:
...........................................................................................................................................................................................................VQLVQSGGGVVQPGRSLRLSCAASGFTFSSHGMHWVRQAPGKG.LEWVAVISYDGSNEHYGDSVKGRFTISRDNSKNTLSLQMNSLRAEDTAVYYCARPFSYGAGYYFDSWGQGALVTVSS........................  
s1:
NVASITAFKSMIDETWDKKIEANTCISRKHRNIIHEVIRDFMKAYPKMDENRKSPLGAPMQWLTQYYILKNEYHKTMLAYDDGSLNTKFKTLNIYMITNVGQYILYIVFCIISGKNHDGTPYIYDSEITSNDKNLINDRIKYACKQILHGQLTMALRIRNKFMFIGSPMYLWFNVN.....GSHVYHEIYDRNVGFHNKEIGRLLYAFMYYLSI..SG...RFLNDLALLKFTYLGESWTFSLSVPEYILYGLGYSVFDTIEKFSNDAILVYIRTNNRNGYDYAEFNKKGIVKVTEDKPDNDKRIHAIRLINYSSDVQHIHFGFRNTLIIDNECTSIQSSAENATDTGHHQDSKIN  
s2:
................................................................................................................................................................AIQMTQSPSSLSASVGDRVTITCRASQNI.DSYLNWYQQKPGEAPKLLMYAASSLQSGVPSRFSGSGSGTDFTLIIS....SLQREDFATYYCQQS.YSTPPTFGQGTKLEIK...................................................................................  
s1:
...........................................................................VQLQESGPGLVKPSETLSLTCTVSGGSISNYYWSWIRQPPGKGLEWIGYIYYIGTTNYNPSL.KSRVTISVD.TSKNQFSLKLSSVTAADTAVYYCARHTDSRAWYYFDYWGQGTLVTV..................................................................................................................................................................  
s2:
NVASITAFKSMIDETWDKKIEANTCISRKHRNIIHEVIRDFMKAYPKMDENRKSPLGAPMQWLTQYYILKNEYHKTMLAYDDGSLNTKFKTLNIYMITNVGQYILYIVFCIIS..GKNHDGTPYIYDSEITSNDKNLINDRIKYACKQILHGQLTMALR........IRNKFMFIGSPMYLWFNVNGSHVYHEIYDRNVGFHNKEIGRLLYAFMYYLSISGRFLNDLALLKFTYLGESWTFSLSVPEYILYGLGYSVFDTIEKFSNDAILVYIRTNNRNGYDYAEFNKKGIVKVTEDKPDNDKRIHAIRLINYSSDVQHIHFGFRNTLIIDNECTSIQSSAENATDTGHHQDSKIN  
s1:
VQLQESGPGLVKPSETLSLTCTVSGGSISNYYWSWIRQPPGKGLEWIGYIYYIGTTNYNPSLKSRVTISVDTSKNQFSLKLSSVTAADTAVYYCARHTDSRAWYYFDYWGQGTLVTV  
s2:
VQLQESGPGLVKPSETLSLTCTVSGGSISNYYWSWIRQPPGKGLEWIGYIYYIGTTNYNPSLKSRVTISVDTSKNQFSLKLSSVTAADTAVYYCARHTDSRAWYYFDYWGQGTLVTV  
s1:
VQLQESGPGLVKPS..ETLSLTCTVSGGSISNYYWSWIRQPPGKGLEWIGYIYYIGTTNYNPSLKSRVTISVDTSKNQFSLKLSSVTAADTAVYYCARHTDSRAWYYFDYWGQGTLVTV.  
s2:
IQMTQS.PSSVSASVGDRVTITCRASQG.ISS.WLAWYQQKPGKAPKLLMY....DASDLQSGVPSR..FSGSGSGTDFTLTISSLQPEDFATYYCQQ.ANSFPWTF....GQGTKVEIK  
s1:
VQLQESGPGLVKPSETLSLTCTVSGGSISNYYWSWIRQPPGKGLEWIGYIYYIGT.TNYNPSLKSRVTISVDTSKNQFSLKLSSVTAADTAVYYCARHTDSRAWYYFDYWGQGTLVTV..  
s2:
VQLVQSGGGVVQPGRSLRLSCAASGFTFSSHGMHWVRQAPGKGLEWVAVISYDGSNEHYGDSVKGRFTISRDNSKNTLSLQMNSLRAEDTAVYYCARPFSYGAGYYFDSWGQGALVTVSS  
s1:
.VQLQESGPGL.VKPSETLSLTCTVSGGSISNYYWSWIRQPPGKGLEWIGYIYYIGTTNYNPSLKSRVTISVDTSKNQFSLKLSSVTAADTAVYYCARHTDSRAWYYFDYWGQGTLVTV.  
s2:
AIQMTQSPSSLSASVGDRVTITCRASQNIDS..YLNWYQQKPGEAPKLLMY....AASSLQSGVPSR..FSGSGSGTDFTLIISSLQREDFATYYCQQSYSTPPTF.....GQGTKLEIK  
s1:
..........................................................................................................................IQMTQSPSSVSASVGDRVTITCRA.SQGISSWLAWYQQK...PGKAPKLLMY..DASDLQSGVPSR...FSGSGSGT.....DFTLTISSLQPEDFATYYCQQANSFPWTFGQGTKVEIK..........................................................................................................  
s2:
NVASITAFKSMIDETWDKKIEANTCISRKHRNIIHEVIRDFMKAYPKMDENRKSPLGAPMQWLTQYYILKNEYHKTMLAYDDGSLNTKFKTLNIYMITNVGQYILYIVFCIISGKNHDGTPYIYDSEITSNDKNLINDRIKYACKQILHGQLTMALRIRNKFMFIG.SPMYLWFNVNGSHVYHEIYDRNVGFHNKEIGRLLYAFMYYLSISGRFLNDLALLKFTYLG.ESWTFSLSVPEYILYGLGYSVFDTIEKFSNDAILVYIRTNNRNGYDYAEFNKKGIVKVTEDKPDNDKRIHAIRLINYSSDVQHIHFGFRNTLIIDNECTSIQSSAENATDTGHHQDSKIN  
s1:
IQMTQS.PSSVSASVGDRVTITCRASQG.ISS.WLAWYQQKPGKAPKLLMY....DASDLQSGVPSR..FSGSGSGTDFTLTISSLQPEDFATYYCQQ.ANSFPWTF....GQGTKVEIK  
s2:
VQLQESGPGLVKPS..ETLSLTCTVSGGSISNYYWSWIRQPPGKGLEWIGYIYYIGTTNYNPSLKSRVTISVDTSKNQFSLKLSSVTAADTAVYYCARHTDSRAWYYFDYWGQGTLVTV.  
s1:
IQMTQSPSSVSASVGDRVTITCRASQGISSWLAWYQQKPGKAPKLLMYDASDLQSGVPSRFSGSGSGTDFTLTISSLQPEDFATYYCQQANSFPWTFGQGTKVEIK  
s2:
IQMTQSPSSVSASVGDRVTITCRASQGISSWLAWYQQKPGKAPKLLMYDASDLQSGVPSRFSGSGSGTDFTLTISSLQPEDFATYYCQQANSFPWTFGQGTKVEIK  
s1:
IQMTQSPSSVSASVGDRVTITCRASQGI...SSWLAWYQQKPGKA...PKLLMYDASDLQSG..VPSRFSGSGSGTDFTLTI..SSLQPEDFATYYCQQANSFPW.....TFGQGTKVEIK.  
s2:
VQLVQSGGGVV.QPGRSLRLSCAAS.GFTFSSHGMHWVRQAPGKGLEWVAVISYDGSNEHYGDSVKGRFTISRDNSKNTLSLQMNSLRAEDTAVYYCARPFSYGAGYYFDSWGQGALVTVSS  
s1:
.IQMTQSPSSVSASVGDRVTITCRASQGISSWLAWYQQKPGKAPKLLMYDASDLQSGVPSRFSGSGSGTDFTLTISSLQPEDFATYYCQQANSFPWTFGQGTKVEIK  
s2:
AIQMTQSPSSLSASVGDRVTITCRASQNIDSYLNWYQQKPGEAPKLLMYAASSLQSGVPSRFSGSGSGTDFTLIISSLQREDFATYYCQQSYSTPPTFGQGTKLEIK  
s1:
...........................................................................................................................................................................................................VQLVQSGGGVVQPGRSLRLSCAASGFTFSSHGMHWVRQAPGKG.LEWVAVISYDGSNEHYGDSVKGRFTISRDNSKNTLSLQMNSLRAEDTAVYYCARPFSYGAGYYFDSWGQGALVTVSS........................  
s2:
NVASITAFKSMIDETWDKKIEANTCISRKHRNIIHEVIRDFMKAYPKMDENRKSPLGAPMQWLTQYYILKNEYHKTMLAYDDGSLNTKFKTLNIYMITNVGQYILYIVFCIISGKNHDGTPYIYDSEITSNDKNLINDRIKYACKQILHGQLTMALRIRNKFMFIGSPMYLWFNVNGSHVYHEIYDRNVGFHNKEIGRLLYAFMYYLSISGRFLNDLALLKFTYLGESWTFSLSVPEYILYGLGYSVFDTIEKFSNDAILVYIRTNNRNGYDYAEFNKKGIVKVTED..KPDNDKRIHAIRLINYSSDVQHIHFGFRNTLIIDNECTSIQSSAENATDTGHHQDSKIN  
s1:
VQLVQSGGGVVQPGRSLRLSCAASGFTFSSHGMHWVRQAPGKGLEWVAVISYDGSNEHYGDSVKGRFTISRDNSKNTLSLQMNSLRAEDTAVYYCARPFSYGAGYYFDSWGQGALVTVSS  
s2:
VQLQESGPGLVKPSETLSLTCTVSGGSISNYYWSWIRQPPGKGLEWIGYIYYIGT.TNYNPSLKSRVTISVDTSKNQFSLKLSSVTAADTAVYYCARHTDSRAWYYFDYWGQGTLVTV..  
s1:
VQLVQSGGGVV.QPGRSLRLSCAAS.GFTFSSHGMHWVRQAPGKGLEWVAVISYDGSNEHYGDSVKGRFTISRDNSKNTLSLQMNSLRAEDTAVYYCARPFSYGAGYYFDSWGQGALVTVSS  
s2:
IQMTQSPSSVSASVGDRVTITCRASQGI...SSWLAWYQQKPGKA...PKLLMYDASDLQSG..VPSRFSGSGSGTDFTLTI..SSLQPEDFATYYCQQANSFPW.....TFGQGTKVEIK.  
s1:
VQLVQSGGGVVQPGRSLRLSCAASGFTFSSHGMHWVRQAPGKGLEWVAVISYDGSNEHYGDSVKGRFTISRDNSKNTLSLQMNSLRAEDTAVYYCARPFSYGAGYYFDSWGQGALVTVSS  
s2:
VQLVQSGGGVVQPGRSLRLSCAASGFTFSSHGMHWVRQAPGKGLEWVAVISYDGSNEHYGDSVKGRFTISRDNSKNTLSLQMNSLRAEDTAVYYCARPFSYGAGYYFDSWGQGALVTVSS  
s1:
.VQLVQSGGGVV.QPGRSLRLSCAASGFTFSSHGMHWVRQAPGKGLEWVAVISYDGSNEHYGDSVKGRFTISRDNSKNTLSLQMNSLRAEDTAVYYCARPFSYGAGYYFDSWGQGALVTVSS  
s2:
AIQMTQSPSSLSASVGDRVTITCRASQ.NIDSY.LNWYQQKPG...EAPKLLMYAASSLQSG..VPSRFSGSGSGTDFTLII..SSLQREDFATYYCQQSYSTP.....PTFGQGTKLEIK.  
s1:
................................................................................................................................................................AIQMTQSPSSLSASVGDRVTITCRASQNI.DSYLNWYQQKPGEAPKLLMYAASSLQSGVPSRFSGSGSGTDFTLIIS....SLQREDFATYYCQQS.YSTPPTFGQGTKLEIK...................................................................................  
s2:
NVASITAFKSMIDETWDKKIEANTCISRKHRNIIHEVIRDFMKAYPKMDENRKSPLGAPMQWLTQYYILKNEYHKTMLAYDDGSLNTKFKTLNIYMITNVGQYILYIVFCIISGKNHDGTPYIYDSEITSNDKNLINDRIKYACKQILHGQLTMALRIRNKFMFIGSPMYLWFNVN.....GSHVYHEIYDRNVGFHNKEIGRLLYAFMYYLSI..SG...RFLNDLALLKFTYLGESWTFSLSVPEYILYGLGYSVFDTIEKFSNDAILVYIRTNNRNGYDYAEFNKKGIVKVTEDKPDNDKRIHAIRLINYSSDVQHIHFGFRNTLIIDNECTSIQSSAENATDTGHHQDSKIN  
s1:
AIQMTQSPSSLSASVGDRVTITCRASQNIDS..YLNWYQQKPGEAPKLLMY....AASSLQSGVPSR..FSGSGSGTDFTLIISSLQREDFATYYCQQSYSTPPTF.....GQGTKLEIK  
s2:
.VQLQESGPGL.VKPSETLSLTCTVSGGSISNYYWSWIRQPPGKGLEWIGYIYYIGTTNYNPSLKSRVTISVDTSKNQFSLKLSSVTAADTAVYYCARHTDSRAWYYFDYWGQGTLVTV.  
s1:
AIQMTQSPSSLSASVGDRVTITCRASQNIDSYLNWYQQKPGEAPKLLMYAASSLQSGVPSRFSGSGSGTDFTLIISSLQREDFATYYCQQSYSTPPTFGQGTKLEIK  
s2:
.IQMTQSPSSVSASVGDRVTITCRASQGISSWLAWYQQKPGKAPKLLMYDASDLQSGVPSRFSGSGSGTDFTLTISSLQPEDFATYYCQQANSFPWTFGQGTKVEIK  
s1:
AIQMTQSPSSLSASVGDRVTITCRASQ.NIDSY.LNWYQQKPG...EAPKLLMYAASSLQSG..VPSRFSGSGSGTDFTLII..SSLQREDFATYYCQQSYSTP.....PTFGQGTKLEIK.  
s2:
.VQLVQSGGGVV.QPGRSLRLSCAASGFTFSSHGMHWVRQAPGKGLEWVAVISYDGSNEHYGDSVKGRFTISRDNSKNTLSLQMNSLRAEDTAVYYCARPFSYGAGYYFDSWGQGALVTVSS  
s1:
AIQMTQSPSSLSASVGDRVTITCRASQNIDSYLNWYQQKPGEAPKLLMYAASSLQSGVPSRFSGSGSGTDFTLIISSLQREDFATYYCQQSYSTPPTFGQGTKLEIK  
s2:
AIQMTQSPSSLSASVGDRVTITCRASQNIDSYLNWYQQKPGEAPKLLMYAASSLQSGVPSRFSGSGSGTDFTLIISSLQREDFATYYCQQSYSTPPTFGQGTKLEIK  

"Adjust for PAE" is checked in the distance restraint options, but the
reference model has no PAE matrix assigned. This option has been ignored.  

> isolde restrain distances "#1.2/A","#1.2/B","#1.2/C","#1.2/D","#1.2/E"
> templateAtoms "#1.2/A","#1.2/B","#1.2/C","#1.2/D","#1.2/E" perChain false
> adjustForConfidence false useCoordinateAlignment false kappa 4.40 fallOff
> 2.50 groupName "Reference Distance Restraints"

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  

> isolde restrain torsions #1.2/A templateResidues #1.2/A adjustForConfidence
> false sidechains true springConstant 250.00 alpha 0.20

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  

> isolde restrain torsions #1.2/B templateResidues #1.2/B adjustForConfidence
> false sidechains true springConstant 250.00 alpha 0.20

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  

> isolde restrain torsions #1.2/C templateResidues #1.2/C adjustForConfidence
> false sidechains true springConstant 250.00 alpha 0.20

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  

> isolde restrain torsions #1.2/D templateResidues #1.2/D adjustForConfidence
> false sidechains true springConstant 250.00 alpha 0.20

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  

> isolde restrain torsions #1.2/E templateResidues #1.2/E adjustForConfidence
> false sidechains true springConstant 250.00 alpha 0.20

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  

> ui tool show "Ramachandran Plot"

> select #1

12454 atoms, 12616 bonds, 796 residues, 17 models selected  

> isolde sim start /A-E

ISOLDE: started sim  

> isolde sim stop

Sim termination reason: None  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 5 residues in model #1.2 to IUPAC-IUB
standards.  
ISOLDE: stopped sim  

> save "/Users/zhouling95/Documents/Academic/McLellan
> Lab/MPXV/OPG153/AF3_J108_zflip_153-coot-0-isolde.pdb"

> close #1

> open "/Users/zhouling95/Documents/Academic/McLellan
> Lab/MPXV/P913_J108_DeepEMhancer_zflipped.mrc"

Opened P913_J108_DeepEMhancer_zflipped.mrc as #1, grid size 384,384,384, pixel
0.933, shown at level 0.000654, step 2, values float32  

> surface dust #1 size 9.33

> volume #1 step 1

> volume #1 level 0.01022

> open "/Users/zhouling95/Documents/Academic/McLellan
> Lab/MPXV/OPG153/Phenix/RealSpaceRefine_154/AF3_J108_zflip_141-isolde_real_space_refined_145_real_space_refined_154.pdb"

Chain information for
AF3_J108_zflip_141-isolde_real_space_refined_145_real_space_refined_154.pdb #2  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
E | No description available  
  

> style stick

Changed 12454 atom styles  

> show cartoons

> color bychain

> color byhetero

> hide H

> volume #1 level 0.00703

> open "/Users/zhouling95/Documents/Academic/McLellan
> Lab/MPXV/OPG153/Phenix/RealSpaceRefine_153/AF3_J108_zflip_145-coot-2_real_space_refined_153.pdb"

Chain information for AF3_J108_zflip_145-coot-2_real_space_refined_153.pdb #3  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
E | No description available  
  

> style stick

Changed 18777 atom styles  

> hide #2 models

> color #3 byhetero

> show #2 models

> open "/Users/zhouling95/Documents/Academic/McLellan
> Lab/MPXV/OPG153/Phenix/RealSpaceRefine_155/AF3_J108_zflip_153-coot-0-isolde_real_space_refined_155.pdb"

Chain information for
AF3_J108_zflip_153-coot-0-isolde_real_space_refined_155.pdb #4  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
E | No description available  
  

> style stick

Changed 31231 atom styles  

> color byhetero

> hide H

> hide #4 models

> show #4 models

> hide #4 models

> hide #2 models

> select add #2

12454 atoms, 12616 bonds, 796 residues, 1 model selected  

> show #4 models

> hide #4 models

> volume #1 color #b2b2b270

> show #3 cartoons

> show #4 models

> show #3-4 cartoons

> color #4 #6b73eeff

> color #3-4 byhetero

> open "/Users/zhouling95/Documents/Academic/McLellan
> Lab/MPXV/OPG153/Phenix/RealSpaceRefine_156/AF3_J108_zflip_153-coot-0-isolde_real_space_refined_156.pdb"

Chain information for
AF3_J108_zflip_153-coot-0-isolde_real_space_refined_156.pdb #5  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
E | No description available  
  

> style #3-5 stick

Changed 31231 atom styles  

> show #3-5 cartoons

> color #5 #eeea42ff

> color #3-5 byhetero

> hide H

> hide #4 models

> hide #!1 models

> show #!1 models

> select subtract #2

Nothing selected  

> hide #5 models

> open "/Users/zhouling95/Documents/Academic/McLellan
> Lab/MPXV/OPG153/AF3_J108_zflip_153-coot-0-isolde.pdb"

Chain information for AF3_J108_zflip_153-coot-0-isolde.pdb #6  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
E | No description available  
  

> close #6

> open "/Users/zhouling95/Documents/Academic/McLellan
> Lab/MPXV/OPG153/Phenix/RealSpaceRefine_145/AF3_J108_zflip_141-isolde_real_space_refined_145.pdb"

Chain information for AF3_J108_zflip_141-isolde_real_space_refined_145.pdb #6  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
E | No description available  
  

> style #3,6 stick

Changed 18777 atom styles  

> show #3,6 cartoons

> color #6 #4f6aeeff

> color #6 #49d3eeff

> color #3,6 byhetero

> hide H

> hide #6 models

> select #3/B:31

8 atoms, 7 bonds, 1 residue, 1 model selected  

> volume #1 level 0.01978

> volume #1 level 0.003842

> select #3/D:64

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select #3/64

Nothing selected  

> select #3:64

33 atoms, 29 bonds, 5 residues, 1 model selected  

> volume #1 level 0.01659

> volume #1 level 0.01022

> volume #1 level 0.003842

> volume #1 level 0.01341

> select #3/B:31

8 atoms, 7 bonds, 1 residue, 1 model selected  

> view #3/B:31

> volume #1 level 0.01978

> open "/Users/zhouling95/Documents/Academic/McLellan
> Lab/MPXV/OPG153/AF3_J108_zflip_153-coot-1.pdb"

Chain information for AF3_J108_zflip_153-coot-1.pdb #7  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
E | No description available  
  

> style sel stick

Changed 8 atom styles  

> show sel cartoons

> select add #7

6331 atoms, 6492 bonds, 797 residues, 2 models selected  

> style sel stick

Changed 6331 atom styles  

> show sel cartoons

> color sel byhetero

> select subtract #7

8 atoms, 7 bonds, 1 residue, 1 model selected  

> volume #1 level 0.003842

> volume #1 level 0.01022

> ui tool show "Show Sequence Viewer"

> sequence chain #7/A

Alignment identifier is 7/A  

> select #3/A:asn

232 atoms, 204 bonds, 29 residues, 1 model selected  

> select #7/A:asn

232 atoms, 204 bonds, 29 residues, 1 model selected  

> select #7/A:194,320,351

24 atoms, 21 bonds, 3 residues, 1 model selected  

> close #2-7

> open "/Users/zhouling95/Documents/Academic/McLellan
> Lab/MPXV/OPG153/Phenix/RealSpaceRefine_158/AF3_J108_zflip_153-coot-1_real_space_refined_158.pdb"

Chain information for AF3_J108_zflip_153-coot-1_real_space_refined_158.pdb #2  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
E | No description available  
  

> isolde start

> set selectionWidth 4

Done loading forcefield  

> isolde set simFidelityMode Medium/Medium

ISOLDE: setting sim fidelity mode to Medium/Medium  
nonbonded_cutoff_distance = 0.900000  
use_gbsa = True  
gbsa_cutoff = 1.100000  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 41 residues in model #2 to IUPAC-IUB
standards.  
Chain information for AF3_J108_zflip_153-coot-1_real_space_refined_158.pdb  
---  
Chain | Description  
2.2/A | No description available  
2.2/B | No description available  
2.2/C | No description available  
2.2/D | No description available  
2.2/E | No description available  
  

> clipper associate #1 toModel #2

Opened P913_J108_DeepEMhancer_zflipped.mrc as #2.1.1.1, grid size 384,384,384,
pixel 0.933, shown at step 1, values float32  

> addh

Summary of feedback from adding hydrogens to
AF3_J108_zflip_153-coot-1_real_space_refined_158.pdb #2.2  
---  
notes | No usable SEQRES records for AF3_J108_zflip_153-coot-1_real_space_refined_158.pdb (#2.2) chain A; guessing termini instead  
No usable SEQRES records for
AF3_J108_zflip_153-coot-1_real_space_refined_158.pdb (#2.2) chain B; guessing
termini instead  
No usable SEQRES records for
AF3_J108_zflip_153-coot-1_real_space_refined_158.pdb (#2.2) chain C; guessing
termini instead  
No usable SEQRES records for
AF3_J108_zflip_153-coot-1_real_space_refined_158.pdb (#2.2) chain D; guessing
termini instead  
No usable SEQRES records for
AF3_J108_zflip_153-coot-1_real_space_refined_158.pdb (#2.2) chain E; guessing
termini instead  
Chain-initial residues that are actual N termini: /A ASN 19, /B VAL 2, /C ILE
2, /D VAL 2, /E ALA 1  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini: /B VAL 111, /C LYS 107, /D SER
113, /E LYS 107  
Chain-final residues that are not actual C termini: /A ASN 364  
656 hydrogen bonds  
/A ASN 364 is not terminus, removing H atom from 'C'  
6131 hydrogens added  
  

> volume #2.1.1.1 level 0.02859

Computing secondary structure  
s1:
NVASITAFKSMIDETWDKKIEANTCISRKHRNIIHEVIRDFMKAYPKMDENRKSPLGAPMQWLTQYYILKNEYHKTMLAYDDGSLNTKFKTLNIYMITNVGQYILYIVFCIISGKNHDGTPYIYDSEITSNDKNLINDRIKYACKQILHGQLTMALRIRNKFMFIGSPMYLWFNVNGSHVYHEIYDRNVGFHNKEIGRLLYAFMYYLSISGRFLNDLALLKFTYLGESWTFSLSVPEYILYGLGYSVFDTIEKFSNDAILVYIRTNNRNGYDYAEFNKKGIVKVTEDKPDNDKRIHAIRLINYSSDVQHIHFGFRNTLIIDNECTSIQSSAENATDTGHHQDSKIN  
s2:
NVASITAFKSMIDETWDKKIEANTCISRKHRNIIHEVIRDFMKAYPKMDENRKSPLGAPMQWLTQYYILKNEYHKTMLAYDDGSLNTKFKTLNIYMITNVGQYILYIVFCIISGKNHDGTPYIYDSEITSNDKNLINDRIKYACKQILHGQLTMALRIRNKFMFIGSPMYLWFNVNGSHVYHEIYDRNVGFHNKEIGRLLYAFMYYLSISGRFLNDLALLKFTYLGESWTFSLSVPEYILYGLGYSVFDTIEKFSNDAILVYIRTNNRNGYDYAEFNKKGIVKVTEDKPDNDKRIHAIRLINYSSDVQHIHFGFRNTLIIDNECTSIQSSAENATDTGHHQDSKIN  
s1:
NVASITAFKSMIDETWDKKIEANTCISRKHRNIIHEVIRDFMKAYPKMDENRKSPLGAPMQWLTQYYILKNEYHKTMLAYDDGSLNTKFKTLNIYMITNVGQYILYIVFCIIS..GKNHDGTPYIYDSEITSNDKNLINDRIKYACKQILHGQLTMALR........IRNKFMFIGSPMYLWFNVNGSHVYHEIYDRNVGFHNKEIGRLLYAFMYYLSISGRFLNDLALLKFTYLGESWTFSLSVPEYILYGLGYSVFDTIEKFSNDAILVYIRTNNRNGYDYAEFNKKGIVKVTEDKPDNDKRIHAIRLINYSSDVQHIHFGFRNTLIIDNECTSIQSSAENATDTGHHQDSKIN  
s2:
...........................................................................VQLQESGPGLVKPSETLSLTCTVSGGSISNYYWSWIRQPPGKGLEWIGYIYYIGTTNYNPSL.KSRVTISVD.TSKNQFSLKLSSVTAADTAVYYCARHTDSRAWYYFDYWGQGTLVTV..................................................................................................................................................................  
s1:
NVASITAFKSMIDETWDKKIEANTCISRKHRNIIHEVIRDFMKAYPKMDENRKSPLGAPMQWLTQYYILKNEYHKTMLAYDDGSLNTKFKTLNIYMITNVGQYILYIVFCIISGKNHDGTPYIYDSEITSNDKNLINDRIKYACKQILHGQLTMALRIRNKFMFIG.SPMYLWFNVNGSHVYHEIYDRNVGFHNKEIGRLLYAFMYYLSISGRFLNDLALLKFTYLG.ESWTFSLSVPEYILYGLGYSVFDTIEKFSNDAILVYIRTNNRNGYDYAEFNKKGIVKVTEDKPDNDKRIHAIRLINYSSDVQHIHFGFRNTLIIDNECTSIQSSAENATDTGHHQDSKIN  
s2:
..........................................................................................................................IQMTQSPSSVSASVGDRVTITCRA.SQGISSWLAWYQQK...PGKAPKLLMY..DASDLQSGVPSR...FSGSGSGT.....DFTLTISSLQPEDFATYYCQQANSFPWTFGQGTKVEIK..........................................................................................................  
s1:
NVASITAFKSMIDETWDKKIEANTCISRKHRNIIHEVIRDFMKAYPKMDENRKSPLGAPMQWLTQYYILKNEYHKTMLAYDDGSLNTKFKTLNIYMITNVGQYILYIVFCIISGKNHDGTPYIYDSEITSNDKNLINDRIKYACKQILHGQLTMALRIRNKFMFIGSPMYLWFNVNGSHVYHEIYDRNVGFHNKEIGRLLYAFMYYLSISGRFLNDLALLKFTYLGESWTFSLSVPEYILYGLGYSVFDTIEKFSNDAILVYIRTNNRNGYDYAEFNKKGIVKVTED..KPDNDKRIHAIRLINYSSDVQHIHFGFRNTLIIDNECTSIQSSAENATDTGHHQDSKIN  
s2:
...........................................................................................................................................................................................................VQLVQSGGGVVQPGRSLRLSCAASGFTFSSHGMHWVRQAPGKG.LEWVAVISYDGSNEHYGDSVKGRFTISRDNSKNTLSLQMNSLRAEDTAVYYCARPFSYGAGYYFDSWGQGALVTVSS........................  
s1:
NVASITAFKSMIDETWDKKIEANTCISRKHRNIIHEVIRDFMKAYPKMDENRKSPLGAPMQWLTQYYILKNEYHKTMLAYDDGSLNTKFKTLNIYMITNVGQYILYIVFCIISGKNHDGTPYIYDSEITSNDKNLINDRIKYACKQILHGQLTMALRIRNKFMFIGSPMYLWFNVN.....GSHVYHEIYDRNVGFHNKEIGRLLYAFMYYLSI..SG...RFLNDLALLKFTYLGESWTFSLSVPEYILYGLGYSVFDTIEKFSNDAILVYIRTNNRNGYDYAEFNKKGIVKVTEDKPDNDKRIHAIRLINYSSDVQHIHFGFRNTLIIDNECTSIQSSAENATDTGHHQDSKIN  
s2:
................................................................................................................................................................AIQMTQSPSSLSASVGDRVTITCRASQNI.DSYLNWYQQKPGEAPKLLMYAASSLQSGVPSRFSGSGSGTDFTLIIS....SLQREDFATYYCQQS.YSTPPTFGQGTKLEIK...................................................................................  
s1:
...........................................................................VQLQESGPGLVKPSETLSLTCTVSGGSISNYYWSWIRQPPGKGLEWIGYIYYIGTTNYNPSL.KSRVTISVD.TSKNQFSLKLSSVTAADTAVYYCARHTDSRAWYYFDYWGQGTLVTV..................................................................................................................................................................  
s2:
NVASITAFKSMIDETWDKKIEANTCISRKHRNIIHEVIRDFMKAYPKMDENRKSPLGAPMQWLTQYYILKNEYHKTMLAYDDGSLNTKFKTLNIYMITNVGQYILYIVFCIIS..GKNHDGTPYIYDSEITSNDKNLINDRIKYACKQILHGQLTMALR........IRNKFMFIGSPMYLWFNVNGSHVYHEIYDRNVGFHNKEIGRLLYAFMYYLSISGRFLNDLALLKFTYLGESWTFSLSVPEYILYGLGYSVFDTIEKFSNDAILVYIRTNNRNGYDYAEFNKKGIVKVTEDKPDNDKRIHAIRLINYSSDVQHIHFGFRNTLIIDNECTSIQSSAENATDTGHHQDSKIN  
s1:
VQLQESGPGLVKPSETLSLTCTVSGGSISNYYWSWIRQPPGKGLEWIGYIYYIGTTNYNPSLKSRVTISVDTSKNQFSLKLSSVTAADTAVYYCARHTDSRAWYYFDYWGQGTLVTV  
s2:
VQLQESGPGLVKPSETLSLTCTVSGGSISNYYWSWIRQPPGKGLEWIGYIYYIGTTNYNPSLKSRVTISVDTSKNQFSLKLSSVTAADTAVYYCARHTDSRAWYYFDYWGQGTLVTV  
s1:
VQLQESGPGLVKPS..ETLSLTCTVSGGSISNYYWSWIRQPPGKGLEWIGYIYYIGTTNYNPSLKSRVTISVDTSKNQFSLKLSSVTAADTAVYYCARHTDSRAWYYFDYWGQGTLVTV.  
s2:
IQMTQS.PSSVSASVGDRVTITCRASQG.ISS.WLAWYQQKPGKAPKLLMY....DASDLQSGVPSR..FSGSGSGTDFTLTISSLQPEDFATYYCQQ.ANSFPWTF....GQGTKVEIK  
s1:
VQLQESGPGLVKPSETLSLTCTVSGGSISNYYWSWIRQPPGKGLEWIGYIYYIGT.TNYNPSLKSRVTISVDTSKNQFSLKLSSVTAADTAVYYCARHTDSRAWYYFDYWGQGTLVTV..  
s2:
VQLVQSGGGVVQPGRSLRLSCAASGFTFSSHGMHWVRQAPGKGLEWVAVISYDGSNEHYGDSVKGRFTISRDNSKNTLSLQMNSLRAEDTAVYYCARPFSYGAGYYFDSWGQGALVTVSS  
s1:
.VQLQESGPGL.VKPSETLSLTCTVSGGSISNYYWSWIRQPPGKGLEWIGYIYYIGTTNYNPSLKSRVTISVDTSKNQFSLKLSSVTAADTAVYYCARHTDSRAWYYFDYWGQGTLVTV.  
s2:
AIQMTQSPSSLSASVGDRVTITCRASQNIDS..YLNWYQQKPGEAPKLLMY....AASSLQSGVPSR..FSGSGSGTDFTLIISSLQREDFATYYCQQSYSTPPTF.....GQGTKLEIK  
s1:
..........................................................................................................................IQMTQSPSSVSASVGDRVTITCRA.SQGISSWLAWYQQK...PGKAPKLLMY..DASDLQSGVPSR...FSGSGSGT.....DFTLTISSLQPEDFATYYCQQANSFPWTFGQGTKVEIK..........................................................................................................  
s2:
NVASITAFKSMIDETWDKKIEANTCISRKHRNIIHEVIRDFMKAYPKMDENRKSPLGAPMQWLTQYYILKNEYHKTMLAYDDGSLNTKFKTLNIYMITNVGQYILYIVFCIISGKNHDGTPYIYDSEITSNDKNLINDRIKYACKQILHGQLTMALRIRNKFMFIG.SPMYLWFNVNGSHVYHEIYDRNVGFHNKEIGRLLYAFMYYLSISGRFLNDLALLKFTYLG.ESWTFSLSVPEYILYGLGYSVFDTIEKFSNDAILVYIRTNNRNGYDYAEFNKKGIVKVTEDKPDNDKRIHAIRLINYSSDVQHIHFGFRNTLIIDNECTSIQSSAENATDTGHHQDSKIN  
s1:
IQMTQS.PSSVSASVGDRVTITCRASQG.ISS.WLAWYQQKPGKAPKLLMY....DASDLQSGVPSR..FSGSGSGTDFTLTISSLQPEDFATYYCQQ.ANSFPWTF....GQGTKVEIK  
s2:
VQLQESGPGLVKPS..ETLSLTCTVSGGSISNYYWSWIRQPPGKGLEWIGYIYYIGTTNYNPSLKSRVTISVDTSKNQFSLKLSSVTAADTAVYYCARHTDSRAWYYFDYWGQGTLVTV.  
s1:
IQMTQSPSSVSASVGDRVTITCRASQGISSWLAWYQQKPGKAPKLLMYDASDLQSGVPSRFSGSGSGTDFTLTISSLQPEDFATYYCQQANSFPWTFGQGTKVEIK  
s2:
IQMTQSPSSVSASVGDRVTITCRASQGISSWLAWYQQKPGKAPKLLMYDASDLQSGVPSRFSGSGSGTDFTLTISSLQPEDFATYYCQQANSFPWTFGQGTKVEIK  
s1:
IQMTQSPSSVSASVGDRVTITCRASQGI...SSWLAWYQQKPGKA...PKLLMYDASDLQSG..VPSRFSGSGSGTDFTLTI..SSLQPEDFATYYCQQANSFPW.....TFGQGTKVEIK.  
s2:
VQLVQSGGGVV.QPGRSLRLSCAAS.GFTFSSHGMHWVRQAPGKGLEWVAVISYDGSNEHYGDSVKGRFTISRDNSKNTLSLQMNSLRAEDTAVYYCARPFSYGAGYYFDSWGQGALVTVSS  
s1:
.IQMTQSPSSVSASVGDRVTITCRASQGISSWLAWYQQKPGKAPKLLMYDASDLQSGVPSRFSGSGSGTDFTLTISSLQPEDFATYYCQQANSFPWTFGQGTKVEIK  
s2:
AIQMTQSPSSLSASVGDRVTITCRASQNIDSYLNWYQQKPGEAPKLLMYAASSLQSGVPSRFSGSGSGTDFTLIISSLQREDFATYYCQQSYSTPPTFGQGTKLEIK  
s1:
...........................................................................................................................................................................................................VQLVQSGGGVVQPGRSLRLSCAASGFTFSSHGMHWVRQAPGKG.LEWVAVISYDGSNEHYGDSVKGRFTISRDNSKNTLSLQMNSLRAEDTAVYYCARPFSYGAGYYFDSWGQGALVTVSS........................  
s2:
NVASITAFKSMIDETWDKKIEANTCISRKHRNIIHEVIRDFMKAYPKMDENRKSPLGAPMQWLTQYYILKNEYHKTMLAYDDGSLNTKFKTLNIYMITNVGQYILYIVFCIISGKNHDGTPYIYDSEITSNDKNLINDRIKYACKQILHGQLTMALRIRNKFMFIGSPMYLWFNVNGSHVYHEIYDRNVGFHNKEIGRLLYAFMYYLSISGRFLNDLALLKFTYLGESWTFSLSVPEYILYGLGYSVFDTIEKFSNDAILVYIRTNNRNGYDYAEFNKKGIVKVTED..KPDNDKRIHAIRLINYSSDVQHIHFGFRNTLIIDNECTSIQSSAENATDTGHHQDSKIN  
s1:
VQLVQSGGGVVQPGRSLRLSCAASGFTFSSHGMHWVRQAPGKGLEWVAVISYDGSNEHYGDSVKGRFTISRDNSKNTLSLQMNSLRAEDTAVYYCARPFSYGAGYYFDSWGQGALVTVSS  
s2:
VQLQESGPGLVKPSETLSLTCTVSGGSISNYYWSWIRQPPGKGLEWIGYIYYIGT.TNYNPSLKSRVTISVDTSKNQFSLKLSSVTAADTAVYYCARHTDSRAWYYFDYWGQGTLVTV..  
s1:
VQLVQSGGGVV.QPGRSLRLSCAAS.GFTFSSHGMHWVRQAPGKGLEWVAVISYDGSNEHYGDSVKGRFTISRDNSKNTLSLQMNSLRAEDTAVYYCARPFSYGAGYYFDSWGQGALVTVSS  
s2:
IQMTQSPSSVSASVGDRVTITCRASQGI...SSWLAWYQQKPGKA...PKLLMYDASDLQSG..VPSRFSGSGSGTDFTLTI..SSLQPEDFATYYCQQANSFPW.....TFGQGTKVEIK.  
s1:
VQLVQSGGGVVQPGRSLRLSCAASGFTFSSHGMHWVRQAPGKGLEWVAVISYDGSNEHYGDSVKGRFTISRDNSKNTLSLQMNSLRAEDTAVYYCARPFSYGAGYYFDSWGQGALVTVSS  
s2:
VQLVQSGGGVVQPGRSLRLSCAASGFTFSSHGMHWVRQAPGKGLEWVAVISYDGSNEHYGDSVKGRFTISRDNSKNTLSLQMNSLRAEDTAVYYCARPFSYGAGYYFDSWGQGALVTVSS  
s1:
.VQLVQSGGGVV.QPGRSLRLSCAASGFTFSSHGMHWVRQAPGKGLEWVAVISYDGSNEHYGDSVKGRFTISRDNSKNTLSLQMNSLRAEDTAVYYCARPFSYGAGYYFDSWGQGALVTVSS  
s2:
AIQMTQSPSSLSASVGDRVTITCRASQ.NIDSY.LNWYQQKPG...EAPKLLMYAASSLQSG..VPSRFSGSGSGTDFTLII..SSLQREDFATYYCQQSYSTP.....PTFGQGTKLEIK.  
s1:
................................................................................................................................................................AIQMTQSPSSLSASVGDRVTITCRASQNI.DSYLNWYQQKPGEAPKLLMYAASSLQSGVPSRFSGSGSGTDFTLIIS....SLQREDFATYYCQQS.YSTPPTFGQGTKLEIK...................................................................................  
s2:
NVASITAFKSMIDETWDKKIEANTCISRKHRNIIHEVIRDFMKAYPKMDENRKSPLGAPMQWLTQYYILKNEYHKTMLAYDDGSLNTKFKTLNIYMITNVGQYILYIVFCIISGKNHDGTPYIYDSEITSNDKNLINDRIKYACKQILHGQLTMALRIRNKFMFIGSPMYLWFNVN.....GSHVYHEIYDRNVGFHNKEIGRLLYAFMYYLSI..SG...RFLNDLALLKFTYLGESWTFSLSVPEYILYGLGYSVFDTIEKFSNDAILVYIRTNNRNGYDYAEFNKKGIVKVTEDKPDNDKRIHAIRLINYSSDVQHIHFGFRNTLIIDNECTSIQSSAENATDTGHHQDSKIN  
s1:
AIQMTQSPSSLSASVGDRVTITCRASQNIDS..YLNWYQQKPGEAPKLLMY....AASSLQSGVPSR..FSGSGSGTDFTLIISSLQREDFATYYCQQSYSTPPTF.....GQGTKLEIK  
s2:
.VQLQESGPGL.VKPSETLSLTCTVSGGSISNYYWSWIRQPPGKGLEWIGYIYYIGTTNYNPSLKSRVTISVDTSKNQFSLKLSSVTAADTAVYYCARHTDSRAWYYFDYWGQGTLVTV.  
s1:
AIQMTQSPSSLSASVGDRVTITCRASQNIDSYLNWYQQKPGEAPKLLMYAASSLQSGVPSRFSGSGSGTDFTLIISSLQREDFATYYCQQSYSTPPTFGQGTKLEIK  
s2:
.IQMTQSPSSVSASVGDRVTITCRASQGISSWLAWYQQKPGKAPKLLMYDASDLQSGVPSRFSGSGSGTDFTLTISSLQPEDFATYYCQQANSFPWTFGQGTKVEIK  
s1:
AIQMTQSPSSLSASVGDRVTITCRASQ.NIDSY.LNWYQQKPG...EAPKLLMYAASSLQSG..VPSRFSGSGSGTDFTLII..SSLQREDFATYYCQQSYSTP.....PTFGQGTKLEIK.  
s2:
.VQLVQSGGGVV.QPGRSLRLSCAASGFTFSSHGMHWVRQAPGKGLEWVAVISYDGSNEHYGDSVKGRFTISRDNSKNTLSLQMNSLRAEDTAVYYCARPFSYGAGYYFDSWGQGALVTVSS  
s1:
AIQMTQSPSSLSASVGDRVTITCRASQNIDSYLNWYQQKPGEAPKLLMYAASSLQSGVPSRFSGSGSGTDFTLIISSLQREDFATYYCQQSYSTPPTFGQGTKLEIK  
s2:
AIQMTQSPSSLSASVGDRVTITCRASQNIDSYLNWYQQKPGEAPKLLMYAASSLQSGVPSRFSGSGSGTDFTLIISSLQREDFATYYCQQSYSTPPTFGQGTKLEIK  

"Adjust for PAE" is checked in the distance restraint options, but the
reference model has no PAE matrix assigned. This option has been ignored.  

> isolde restrain distances "#2.2/A","#2.2/B","#2.2/C","#2.2/D","#2.2/E"
> templateAtoms "#2.2/A","#2.2/B","#2.2/C","#2.2/D","#2.2/E" perChain false
> adjustForConfidence false useCoordinateAlignment false kappa 3.30 fallOff
> 2.90 groupName "Reference Distance Restraints"

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  

> isolde restrain torsions #2.2/A templateResidues #2.2/A adjustForConfidence
> false sidechains true springConstant 145.00 alpha 0.20

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  

> isolde restrain torsions #2.2/B templateResidues #2.2/B adjustForConfidence
> false sidechains true springConstant 145.00 alpha 0.20

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  

> isolde restrain torsions #2.2/C templateResidues #2.2/C adjustForConfidence
> false sidechains true springConstant 145.00 alpha 0.20

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  

> isolde restrain torsions #2.2/D templateResidues #2.2/D adjustForConfidence
> false sidechains true springConstant 145.00 alpha 0.20

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  

> isolde restrain torsions #2.2/E templateResidues #2.2/E adjustForConfidence
> false sidechains true springConstant 145.00 alpha 0.20

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  

> ui tool show "Ramachandran Plot"

> select #1

Nothing selected  

> select #2

12454 atoms, 12616 bonds, 796 residues, 17 models selected  

> isolde sim start /A-E

ISOLDE: started sim  

> isolde pepflip /B:32

> isolde pepflip /B:41

Unable to flip peptide bond after 50 rounds. Giving up.  

> isolde sim stop

Sim termination reason: None  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 5 residues in model #2.2 to IUPAC-IUB
standards.  
ISOLDE: stopped sim  

> save "/Users/zhouling95/Documents/Academic/McLellan
> Lab/MPXV/OPG153/AF3_J108_zflip_158-isolde.pdb"

> close #2

> open "/Users/zhouling95/Documents/Academic/McLellan
> Lab/MPXV/OPG153/Phenix/RealSpaceRefine_164/AF3_J108_zflip_141-isolde_real_space_refined_145_real_space_refined_164.pdb"

Chain information for
AF3_J108_zflip_141-isolde_real_space_refined_145_real_space_refined_164.pdb #1  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
E | No description available  
  

> open "/Users/zhouling95/Documents/Academic/McLellan
> Lab/MPXV/P913_J108_DeepEMhancer_zflipped.mrc"

Opened P913_J108_DeepEMhancer_zflipped.mrc as #2, grid size 384,384,384, pixel
0.933, shown at level 0.000654, step 2, values float32  

> style stick

Changed 12454 atom styles  

> show cartoons

> volume #2 step 1

> surface dust #2 size 9.33

> volume #2 level 0.01022

> color byhetero

> hide H

> volume #2 color #b2b2b27c

> volume #2 color #b2b2b27d

> volume #2 level 0.00703

> volume #2 level 0.003842

> open "/Users/zhouling95/Documents/Academic/McLellan
> Lab/MPXV/OPG153/AF3_J108_zflip_158-isolde.pdb"

Chain information for AF3_J108_zflip_158-isolde.pdb #3  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
E | No description available  
  

> style stick

Changed 24908 atom styles  

> color byhetero

> show cartoons

> color #3 #6a75ffff

> color byhetero

> hide H

> volume #2 level 0.0006542

> volume #2 level -0.005722

> volume #2 level 0.00703

> volume #2 level 0.01659

> volume #2 level 0.003842

> volume #2 level 0.0006542

> volume #2 level 0.00703

> lighting simple

> close #3

> close #1

> open "/Users/zhouling95/Documents/Academic/McLellan
> Lab/MPXV/OPG153/Phenix/RealSpaceRefine_170/AF3_J108_zflip_168-coot-0_real_space_refined_170.pdb"

Chain information for AF3_J108_zflip_168-coot-0_real_space_refined_170.pdb #1  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
E | No description available  
  

> isolde start

> set selectionWidth 4

Done loading forcefield  

> isolde set simFidelityMode Medium/Medium

ISOLDE: setting sim fidelity mode to Medium/Medium  
nonbonded_cutoff_distance = 0.900000  
use_gbsa = True  
gbsa_cutoff = 1.100000  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 38 residues in model #1 to IUPAC-IUB
standards.  
Chain information for AF3_J108_zflip_168-coot-0_real_space_refined_170.pdb  
---  
Chain | Description  
1.2/A | No description available  
1.2/B | No description available  
1.2/C | No description available  
1.2/D | No description available  
1.2/E | No description available  
  

> clipper associate #2 toModel #1

Opened P913_J108_DeepEMhancer_zflipped.mrc as #1.1.1.1, grid size 384,384,384,
pixel 0.933, shown at step 1, values float32  

> addh

Summary of feedback from adding hydrogens to
AF3_J108_zflip_168-coot-0_real_space_refined_170.pdb #1.2  
---  
notes | No usable SEQRES records for AF3_J108_zflip_168-coot-0_real_space_refined_170.pdb (#1.2) chain A; guessing termini instead  
No usable SEQRES records for
AF3_J108_zflip_168-coot-0_real_space_refined_170.pdb (#1.2) chain B; guessing
termini instead  
No usable SEQRES records for
AF3_J108_zflip_168-coot-0_real_space_refined_170.pdb (#1.2) chain C; guessing
termini instead  
No usable SEQRES records for
AF3_J108_zflip_168-coot-0_real_space_refined_170.pdb (#1.2) chain D; guessing
termini instead  
No usable SEQRES records for
AF3_J108_zflip_168-coot-0_real_space_refined_170.pdb (#1.2) chain E; guessing
termini instead  
Chain-initial residues that are actual N termini: /A ASN 19, /B VAL 2, /C ILE
2, /D VAL 2, /E ALA 1  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini: /B VAL 111, /C LYS 107, /D SER
113, /E LYS 107  
Chain-final residues that are not actual C termini: /A ASN 364  
640 hydrogen bonds  
/A ASN 364 is not terminus, removing H atom from 'C'  
6131 hydrogens added  
  
Computing secondary structure  
s1:
NVASITAFKSMIDETWDKKIEANTCISRKHRNIIHEVIRDFMKAYPKMDENRKSPLGAPMQWLTQYYILKNEYHKTMLAYDDGSLNTKFKTLNIYMITNVGQYILYIVFCIISGKNHDGTPYIYDSEITSNDKNLINDRIKYACKQILHGQLTMALRIRNKFMFIGSPMYLWFNVNGSHVYHEIYDRNVGFHNKEIGRLLYAFMYYLSISGRFLNDLALLKFTYLGESWTFSLSVPEYILYGLGYSVFDTIEKFSNDAILVYIRTNNRNGYDYAEFNKKGIVKVTEDKPDNDKRIHAIRLINYSSDVQHIHFGFRNTLIIDNECTSIQSSAENATDTGHHQDSKIN  
s2:
NVASITAFKSMIDETWDKKIEANTCISRKHRNIIHEVIRDFMKAYPKMDENRKSPLGAPMQWLTQYYILKNEYHKTMLAYDDGSLNTKFKTLNIYMITNVGQYILYIVFCIISGKNHDGTPYIYDSEITSNDKNLINDRIKYACKQILHGQLTMALRIRNKFMFIGSPMYLWFNVNGSHVYHEIYDRNVGFHNKEIGRLLYAFMYYLSISGRFLNDLALLKFTYLGESWTFSLSVPEYILYGLGYSVFDTIEKFSNDAILVYIRTNNRNGYDYAEFNKKGIVKVTEDKPDNDKRIHAIRLINYSSDVQHIHFGFRNTLIIDNECTSIQSSAENATDTGHHQDSKIN  
s1:
NVASITAFKSMIDETWDKKIEANTCISRKHRNIIHEVIRDFMKAYPKMDENRKSPLGAPMQWLTQYYILKNEYHKTMLAYDDGSLNTKFKTLNIYMITNVGQYILYIVFCIIS..GKNHDGTPYIYDSEITSNDKNLINDRIKYACKQILHGQLTMALR........IRNKFMFIGSPMYLWFNVNGSHVYHEIYDRNVGFHNKEIGRLLYAFMYYLSISGRFLNDLALLKFTYLGESWTFSLSVPEYILYGLGYSVFDTIEKFSNDAILVYIRTNNRNGYDYAEFNKKGIVKVTEDKPDNDKRIHAIRLINYSSDVQHIHFGFRNTLIIDNECTSIQSSAENATDTGHHQDSKIN  
s2:
...........................................................................VQLQESGPGLVKPSETLSLTCTVSGGSISNYYWSWIRQPPGKGLEWIGYIYYIGTTNYNPSL.KSRVTISVD.TSKNQFSLKLSSVTAADTAVYYCARHTDSRAWYYFDYWGQGTLVTV..................................................................................................................................................................  
s1:
NVASITAFKSMIDETWDKKIEANTCISRKHRNIIHEVIRDFMKAYPKMDENRKSPLGAPMQWLTQYYILKNEYHKTMLAYDDGSLNTKFKTLNIYMITNVGQYILYIVFCIISGKNHDGTPYIYDSEITSNDKNLINDRIKYACKQILHGQLTMALRIRNKFMFIG.SPMYLWFNVNGSHVYHEIYDRNVGFHNKEIGRLLYAFMYYLSISGRFLNDLALLKFTYLG.ESWTFSLSVPEYILYGLGYSVFDTIEKFSNDAILVYIRTNNRNGYDYAEFNKKGIVKVTEDKPDNDKRIHAIRLINYSSDVQHIHFGFRNTLIIDNECTSIQSSAENATDTGHHQDSKIN  
s2:
..........................................................................................................................IQMTQSPSSVSASVGDRVTITCRA.SQGISSWLAWYQQK...PGKAPKLLMY..DASDLQSGVPSR...FSGSGSGT.....DFTLTISSLQPEDFATYYCQQANSFPWTFGQGTKVEIK..........................................................................................................  
s1:
NVASITAFKSMIDETWDKKIEANTCISRKHRNIIHEVIRDFMKAYPKMDENRKSPLGAPMQWLTQYYILKNEYHKTMLAYDDGSLNTKFKTLNIYMITNVGQYILYIVFCIISGKNHDGTPYIYDSEITSNDKNLINDRIKYACKQILHGQLTMALRIRNKFMFIGSPMYLWFNVNGSHVYHEIYDRNVGFHNKEIGRLLYAFMYYLSISGRFLNDLALLKFTYLGESWTFSLSVPEYILYGLGYSVFDTIEKFSNDAILVYIRTNNRNGYDYAEFNKKGIVKVTED..KPDNDKRIHAIRLINYSSDVQHIHFGFRNTLIIDNECTSIQSSAENATDTGHHQDSKIN  
s2:
...........................................................................................................................................................................................................VQLVQSGGGVVQPGRSLRLSCAASGFTFSSHGMHWVRQAPGKG.LEWVAVISYDGSNEHYGDSVKGRFTISRDNSKNTLSLQMNSLRAEDTAVYYCARPFSYGAGYYFDSWGQGALVTVSS........................  
s1:
NVASITAFKSMIDETWDKKIEANTCISRKHRNIIHEVIRDFMKAYPKMDENRKSPLGAPMQWLTQYYILKNEYHKTMLAYDDGSLNTKFKTLNIYMITNVGQYILYIVFCIISGKNHDGTPYIYDSEITSNDKNLINDRIKYACKQILHGQLTMALRIRNKFMFIGSPMYLWFNVN.....GSHVYHEIYDRNVGFHNKEIGRLLYAFMYYLSI..SG...RFLNDLALLKFTYLGESWTFSLSVPEYILYGLGYSVFDTIEKFSNDAILVYIRTNNRNGYDYAEFNKKGIVKVTEDKPDNDKRIHAIRLINYSSDVQHIHFGFRNTLIIDNECTSIQSSAENATDTGHHQDSKIN  
s2:
................................................................................................................................................................AIQMTQSPSSLSASVGDRVTITCRASQNI.DSYLNWYQQKPGEAPKLLMYAASSLQSGVPSRFSGSGSGTDFTLIIS....SLQREDFATYYCQQS.YSTPPTFGQGTKLEIK...................................................................................  
s1:
...........................................................................VQLQESGPGLVKPSETLSLTCTVSGGSISNYYWSWIRQPPGKGLEWIGYIYYIGTTNYNPSL.KSRVTISVD.TSKNQFSLKLSSVTAADTAVYYCARHTDSRAWYYFDYWGQGTLVTV..................................................................................................................................................................  
s2:
NVASITAFKSMIDETWDKKIEANTCISRKHRNIIHEVIRDFMKAYPKMDENRKSPLGAPMQWLTQYYILKNEYHKTMLAYDDGSLNTKFKTLNIYMITNVGQYILYIVFCIIS..GKNHDGTPYIYDSEITSNDKNLINDRIKYACKQILHGQLTMALR........IRNKFMFIGSPMYLWFNVNGSHVYHEIYDRNVGFHNKEIGRLLYAFMYYLSISGRFLNDLALLKFTYLGESWTFSLSVPEYILYGLGYSVFDTIEKFSNDAILVYIRTNNRNGYDYAEFNKKGIVKVTEDKPDNDKRIHAIRLINYSSDVQHIHFGFRNTLIIDNECTSIQSSAENATDTGHHQDSKIN  
s1:
VQLQESGPGLVKPSETLSLTCTVSGGSISNYYWSWIRQPPGKGLEWIGYIYYIGTTNYNPSLKSRVTISVDTSKNQFSLKLSSVTAADTAVYYCARHTDSRAWYYFDYWGQGTLVTV  
s2:
VQLQESGPGLVKPSETLSLTCTVSGGSISNYYWSWIRQPPGKGLEWIGYIYYIGTTNYNPSLKSRVTISVDTSKNQFSLKLSSVTAADTAVYYCARHTDSRAWYYFDYWGQGTLVTV  
s1:
VQLQESGPGLVKPS..ETLSLTCTVSGGSISNYYWSWIRQPPGKGLEWIGYIYYIGTTNYNPSLKSRVTISVDTSKNQFSLKLSSVTAADTAVYYCARHTDSRAWYYFDYWGQGTLVTV.  
s2:
IQMTQS.PSSVSASVGDRVTITCRASQG.ISS.WLAWYQQKPGKAPKLLMY....DASDLQSGVPSR..FSGSGSGTDFTLTISSLQPEDFATYYCQQ.ANSFPWTF....GQGTKVEIK  
s1:
VQLQESGPGLVKPSETLSLTCTVSGGSISNYYWSWIRQPPGKGLEWIGYIYYIGT.TNYNPSLKSRVTISVDTSKNQFSLKLSSVTAADTAVYYCARHTDSRAWYYFDYWGQGTLVTV..  
s2:
VQLVQSGGGVVQPGRSLRLSCAASGFTFSSHGMHWVRQAPGKGLEWVAVISYDGSNEHYGDSVKGRFTISRDNSKNTLSLQMNSLRAEDTAVYYCARPFSYGAGYYFDSWGQGALVTVSS  
s1:
.VQLQESGPGL.VKPSETLSLTCTVSGGSISNYYWSWIRQPPGKGLEWIGYIYYIGTTNYNPSLKSRVTISVDTSKNQFSLKLSSVTAADTAVYYCARHTDSRAWYYFDYWGQGTLVTV.  
s2:
AIQMTQSPSSLSASVGDRVTITCRASQNIDS..YLNWYQQKPGEAPKLLMY....AASSLQSGVPSR..FSGSGSGTDFTLIISSLQREDFATYYCQQSYSTPPTF.....GQGTKLEIK  
s1:
..........................................................................................................................IQMTQSPSSVSASVGDRVTITCRA.SQGISSWLAWYQQK...PGKAPKLLMY..DASDLQSGVPSR...FSGSGSGT.....DFTLTISSLQPEDFATYYCQQANSFPWTFGQGTKVEIK..........................................................................................................  
s2:
NVASITAFKSMIDETWDKKIEANTCISRKHRNIIHEVIRDFMKAYPKMDENRKSPLGAPMQWLTQYYILKNEYHKTMLAYDDGSLNTKFKTLNIYMITNVGQYILYIVFCIISGKNHDGTPYIYDSEITSNDKNLINDRIKYACKQILHGQLTMALRIRNKFMFIG.SPMYLWFNVNGSHVYHEIYDRNVGFHNKEIGRLLYAFMYYLSISGRFLNDLALLKFTYLG.ESWTFSLSVPEYILYGLGYSVFDTIEKFSNDAILVYIRTNNRNGYDYAEFNKKGIVKVTEDKPDNDKRIHAIRLINYSSDVQHIHFGFRNTLIIDNECTSIQSSAENATDTGHHQDSKIN  
s1:
IQMTQS.PSSVSASVGDRVTITCRASQG.ISS.WLAWYQQKPGKAPKLLMY....DASDLQSGVPSR..FSGSGSGTDFTLTISSLQPEDFATYYCQQ.ANSFPWTF....GQGTKVEIK  
s2:
VQLQESGPGLVKPS..ETLSLTCTVSGGSISNYYWSWIRQPPGKGLEWIGYIYYIGTTNYNPSLKSRVTISVDTSKNQFSLKLSSVTAADTAVYYCARHTDSRAWYYFDYWGQGTLVTV.  
s1:
IQMTQSPSSVSASVGDRVTITCRASQGISSWLAWYQQKPGKAPKLLMYDASDLQSGVPSRFSGSGSGTDFTLTISSLQPEDFATYYCQQANSFPWTFGQGTKVEIK  
s2:
IQMTQSPSSVSASVGDRVTITCRASQGISSWLAWYQQKPGKAPKLLMYDASDLQSGVPSRFSGSGSGTDFTLTISSLQPEDFATYYCQQANSFPWTFGQGTKVEIK  
s1:
IQMTQSPSSVSASVGDRVTITCRASQGI...SSWLAWYQQKPGKA...PKLLMYDASDLQSG..VPSRFSGSGSGTDFTLTI..SSLQPEDFATYYCQQANSFPW.....TFGQGTKVEIK.  
s2:
VQLVQSGGGVV.QPGRSLRLSCAAS.GFTFSSHGMHWVRQAPGKGLEWVAVISYDGSNEHYGDSVKGRFTISRDNSKNTLSLQMNSLRAEDTAVYYCARPFSYGAGYYFDSWGQGALVTVSS  
s1:
.IQMTQSPSSVSASVGDRVTITCRASQGISSWLAWYQQKPGKAPKLLMYDASDLQSGVPSRFSGSGSGTDFTLTISSLQPEDFATYYCQQANSFPWTFGQGTKVEIK  
s2:
AIQMTQSPSSLSASVGDRVTITCRASQNIDSYLNWYQQKPGEAPKLLMYAASSLQSGVPSRFSGSGSGTDFTLIISSLQREDFATYYCQQSYSTPPTFGQGTKLEIK  
s1:
...........................................................................................................................................................................................................VQLVQSGGGVVQPGRSLRLSCAASGFTFSSHGMHWVRQAPGKG.LEWVAVISYDGSNEHYGDSVKGRFTISRDNSKNTLSLQMNSLRAEDTAVYYCARPFSYGAGYYFDSWGQGALVTVSS........................  
s2:
NVASITAFKSMIDETWDKKIEANTCISRKHRNIIHEVIRDFMKAYPKMDENRKSPLGAPMQWLTQYYILKNEYHKTMLAYDDGSLNTKFKTLNIYMITNVGQYILYIVFCIISGKNHDGTPYIYDSEITSNDKNLINDRIKYACKQILHGQLTMALRIRNKFMFIGSPMYLWFNVNGSHVYHEIYDRNVGFHNKEIGRLLYAFMYYLSISGRFLNDLALLKFTYLGESWTFSLSVPEYILYGLGYSVFDTIEKFSNDAILVYIRTNNRNGYDYAEFNKKGIVKVTED..KPDNDKRIHAIRLINYSSDVQHIHFGFRNTLIIDNECTSIQSSAENATDTGHHQDSKIN  
s1:
VQLVQSGGGVVQPGRSLRLSCAASGFTFSSHGMHWVRQAPGKGLEWVAVISYDGSNEHYGDSVKGRFTISRDNSKNTLSLQMNSLRAEDTAVYYCARPFSYGAGYYFDSWGQGALVTVSS  
s2:
VQLQESGPGLVKPSETLSLTCTVSGGSISNYYWSWIRQPPGKGLEWIGYIYYIGT.TNYNPSLKSRVTISVDTSKNQFSLKLSSVTAADTAVYYCARHTDSRAWYYFDYWGQGTLVTV..  
s1:
VQLVQSGGGVV.QPGRSLRLSCAAS.GFTFSSHGMHWVRQAPGKGLEWVAVISYDGSNEHYGDSVKGRFTISRDNSKNTLSLQMNSLRAEDTAVYYCARPFSYGAGYYFDSWGQGALVTVSS  
s2:
IQMTQSPSSVSASVGDRVTITCRASQGI...SSWLAWYQQKPGKA...PKLLMYDASDLQSG..VPSRFSGSGSGTDFTLTI..SSLQPEDFATYYCQQANSFPW.....TFGQGTKVEIK.  
s1:
VQLVQSGGGVVQPGRSLRLSCAASGFTFSSHGMHWVRQAPGKGLEWVAVISYDGSNEHYGDSVKGRFTISRDNSKNTLSLQMNSLRAEDTAVYYCARPFSYGAGYYFDSWGQGALVTVSS  
s2:
VQLVQSGGGVVQPGRSLRLSCAASGFTFSSHGMHWVRQAPGKGLEWVAVISYDGSNEHYGDSVKGRFTISRDNSKNTLSLQMNSLRAEDTAVYYCARPFSYGAGYYFDSWGQGALVTVSS  
s1:
.VQLVQSGGGVV.QPGRSLRLSCAASGFTFSSHGMHWVRQAPGKGLEWVAVISYDGSNEHYGDSVKGRFTISRDNSKNTLSLQMNSLRAEDTAVYYCARPFSYGAGYYFDSWGQGALVTVSS  
s2:
AIQMTQSPSSLSASVGDRVTITCRASQ.NIDSY.LNWYQQKPG...EAPKLLMYAASSLQSG..VPSRFSGSGSGTDFTLII..SSLQREDFATYYCQQSYSTP.....PTFGQGTKLEIK.  
s1:
................................................................................................................................................................AIQMTQSPSSLSASVGDRVTITCRASQNI.DSYLNWYQQKPGEAPKLLMYAASSLQSGVPSRFSGSGSGTDFTLIIS....SLQREDFATYYCQQS.YSTPPTFGQGTKLEIK...................................................................................  
s2:
NVASITAFKSMIDETWDKKIEANTCISRKHRNIIHEVIRDFMKAYPKMDENRKSPLGAPMQWLTQYYILKNEYHKTMLAYDDGSLNTKFKTLNIYMITNVGQYILYIVFCIISGKNHDGTPYIYDSEITSNDKNLINDRIKYACKQILHGQLTMALRIRNKFMFIGSPMYLWFNVN.....GSHVYHEIYDRNVGFHNKEIGRLLYAFMYYLSI..SG...RFLNDLALLKFTYLGESWTFSLSVPEYILYGLGYSVFDTIEKFSNDAILVYIRTNNRNGYDYAEFNKKGIVKVTEDKPDNDKRIHAIRLINYSSDVQHIHFGFRNTLIIDNECTSIQSSAENATDTGHHQDSKIN  
s1:
AIQMTQSPSSLSASVGDRVTITCRASQNIDS..YLNWYQQKPGEAPKLLMY....AASSLQSGVPSR..FSGSGSGTDFTLIISSLQREDFATYYCQQSYSTPPTF.....GQGTKLEIK  
s2:
.VQLQESGPGL.VKPSETLSLTCTVSGGSISNYYWSWIRQPPGKGLEWIGYIYYIGTTNYNPSLKSRVTISVDTSKNQFSLKLSSVTAADTAVYYCARHTDSRAWYYFDYWGQGTLVTV.  
s1:
AIQMTQSPSSLSASVGDRVTITCRASQNIDSYLNWYQQKPGEAPKLLMYAASSLQSGVPSRFSGSGSGTDFTLIISSLQREDFATYYCQQSYSTPPTFGQGTKLEIK  
s2:
.IQMTQSPSSVSASVGDRVTITCRASQGISSWLAWYQQKPGKAPKLLMYDASDLQSGVPSRFSGSGSGTDFTLTISSLQPEDFATYYCQQANSFPWTFGQGTKVEIK  
s1:
AIQMTQSPSSLSASVGDRVTITCRASQ.NIDSY.LNWYQQKPG...EAPKLLMYAASSLQSG..VPSRFSGSGSGTDFTLII..SSLQREDFATYYCQQSYSTP.....PTFGQGTKLEIK.  
s2:
.VQLVQSGGGVV.QPGRSLRLSCAASGFTFSSHGMHWVRQAPGKGLEWVAVISYDGSNEHYGDSVKGRFTISRDNSKNTLSLQMNSLRAEDTAVYYCARPFSYGAGYYFDSWGQGALVTVSS  
s1:
AIQMTQSPSSLSASVGDRVTITCRASQNIDSYLNWYQQKPGEAPKLLMYAASSLQSGVPSRFSGSGSGTDFTLIISSLQREDFATYYCQQSYSTPPTFGQGTKLEIK  
s2:
AIQMTQSPSSLSASVGDRVTITCRASQNIDSYLNWYQQKPGEAPKLLMYAASSLQSGVPSRFSGSGSGTDFTLIISSLQREDFATYYCQQSYSTPPTFGQGTKLEIK  

"Adjust for PAE" is checked in the distance restraint options, but the
reference model has no PAE matrix assigned. This option has been ignored.  

> isolde restrain distances "#1.2/A","#1.2/B","#1.2/C","#1.2/D","#1.2/E"
> templateAtoms "#1.2/A","#1.2/B","#1.2/C","#1.2/D","#1.2/E" perChain false
> adjustForConfidence false useCoordinateAlignment false kappa 4.40 fallOff
> 2.50 groupName "Reference Distance Restraints"

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  

> isolde restrain torsions #1.2/A templateResidues #1.2/A adjustForConfidence
> false sidechains true springConstant 250.00 alpha 0.20

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  

> isolde restrain torsions #1.2/B templateResidues #1.2/B adjustForConfidence
> false sidechains true springConstant 250.00 alpha 0.20

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  

> isolde restrain torsions #1.2/C templateResidues #1.2/C adjustForConfidence
> false sidechains true springConstant 250.00 alpha 0.20

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  

> isolde restrain torsions #1.2/D templateResidues #1.2/D adjustForConfidence
> false sidechains true springConstant 250.00 alpha 0.20

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  

> isolde restrain torsions #1.2/E templateResidues #1.2/E adjustForConfidence
> false sidechains true springConstant 250.00 alpha 0.20

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  

> ui tool show "Ramachandran Plot"

> isolde sim start /A-E

ISOLDE: started sim  

> volume #1.1.1.1 level 0.03426

> isolde pepflip /B:32

> isolde pepflip /B:31

> isolde sim stop discardTo start

Sim termination reason: None  
reverting to start  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> isolde sim start /B:32

ISOLDE: started sim  

> isolde pepflip /B:32

> isolde sim stop discardTo start

Sim termination reason: None  
reverting to start  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> select #1

12454 atoms, 12616 bonds, 796 residues, 21 models selected  

> isolde sim start /A-E

ISOLDE: started sim  

> isolde sim stop

Sim termination reason: None  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 3 residues in model #1.2 to IUPAC-IUB
standards.  
ISOLDE: stopped sim  

"Adjust for PAE" is checked in the distance restraint options, but the
reference model has no PAE matrix assigned. This option has been ignored.  

> isolde restrain distances "#1.2/A","#1.2/B","#1.2/C","#1.2/D","#1.2/E"
> templateAtoms "#1.2/A","#1.2/B","#1.2/C","#1.2/D","#1.2/E" perChain false
> adjustForConfidence false useCoordinateAlignment false kappa 2.40 fallOff
> 2.50 groupName "Reference Distance Restraints"

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  

> isolde restrain torsions #1.2/A templateResidues #1.2/A adjustForConfidence
> false sidechains true springConstant 130.00 alpha 0.20

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  

> isolde restrain torsions #1.2/B templateResidues #1.2/B adjustForConfidence
> false sidechains true springConstant 130.00 alpha 0.20

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  

> isolde restrain torsions #1.2/C templateResidues #1.2/C adjustForConfidence
> false sidechains true springConstant 130.00 alpha 0.20

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  

> isolde restrain torsions #1.2/D templateResidues #1.2/D adjustForConfidence
> false sidechains true springConstant 130.00 alpha 0.20

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  

> isolde restrain torsions #1.2/E templateResidues #1.2/E adjustForConfidence
> false sidechains true springConstant 130.00 alpha 0.20

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  

> isolde sim start /A-E

ISOLDE: started sim  

> isolde pepflip /B:32

> isolde pepflip /B:31

> isolde sim stop discardTo start

Sim termination reason: None  
reverting to start  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> save "/Users/zhouling95/Documents/Academic/McLellan
> Lab/MPXV/OPG153/AF3_J108_zflip_168-coot-0_170-isolde.pdb"

> close #1.2.5

> isolde sim start /B:32

ISOLDE: started sim  

> isolde pepflip /B:32

> isolde sim stop

Sim termination reason: None  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> save "/Users/zhouling95/Documents/Academic/McLellan
> Lab/MPXV/OPG153/AF3_J108_zflip_168-coot-0_170-isolde-1.pdb"

> open "/Users/zhouling95/Documents/Academic/McLellan
> Lab/MPXV/OPG153/Phenix/RealSpaceRefine_174/AF3_J108_zflip_168-coot-0_170-isolde-1_real_space_refined_174.pdb"

Chain information for
AF3_J108_zflip_168-coot-0_170-isolde-1_real_space_refined_174.pdb #2  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
E | No description available  
  

> close #1

> open "/Users/zhouling95/Documents/Academic/McLellan
> Lab/MPXV/P913_J108_DeepEMhancer_zflipped.mrc"

Opened P913_J108_DeepEMhancer_zflipped.mrc as #1, grid size 384,384,384, pixel
0.933, shown at level 0.000654, step 2, values float32  

> style stick

Changed 12454 atom styles  

> volume #1 step 1

> volume #1 level 0.01022

> surface dust #1 size 9.33

> color byhetero

> hide H

> volume #1 color #b2b2b273

> show cartoons

> volume #1 level 0.003842

> open "/Users/zhouling95/Documents/Academic/McLellan
> Lab/MPXV/OPG153/Phenix/RealSpaceRefine_170/AF3_J108_zflip_168-coot-0_real_space_refined_170.pdb"

Chain information for AF3_J108_zflip_168-coot-0_real_space_refined_170.pdb #3  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
E | No description available  
  

> show atoms

> style stick

Changed 18777 atom styles  

> show cartoons

> color #3 #556deeff

> color byhetero

> hide H

> volume #1 level 0.01022

> volume #1 level 0.00703

> open
> /Users/zhouling95/Library/Containers/net.whatsapp.WhatsApp/Data/tmp/documents/394357D8-FE34-479D-853C-C1932E3CC4B7/153G-02M12-Kabat_fit-
> coot-20.pdb

Summary of feedback from opening
/Users/zhouling95/Library/Containers/net.whatsapp.WhatsApp/Data/tmp/documents/394357D8-FE34-479D-853C-C1932E3CC4B7/153G-02M12-Kabat_fit-
coot-20.pdb  
---  
warning | Cannot find LINK/SSBOND residue CYS (25 )  
  
Chain information for 153G-02M12-Kabat_fit-coot-20.pdb #4  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
  

> mmaker #4 to #3

Computing secondary structure  
Parameters  
---  
Chain pairing | bb  
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 AF3_J108_zflip_168-coot-0_real_space_refined_170.pdb, chain A (#3)
with 153G-02M12-Kabat_fit-coot-20.pdb, chain A (#4), sequence alignment score
= 1751.1  
RMSD between 343 pruned atom pairs is 0.537 angstroms; (across all 345 pairs:
0.567)  
  

> show atoms

> hide H

> hide #2 models

> hide #4 models

> open "/Users/zhouling95/Documents/Academic/McLellan
> Lab/MPXV/OPG153/Phenix/RealSpaceRefine_176/AF3_J108_zflip_170-coot-0_real_space_refined_176.pdb"

Chain information for AF3_J108_zflip_170-coot-0_real_space_refined_176.pdb #5  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
E | No description available  
  

> color #5 #d2ee5eff

> style #3,5 stick

Changed 12646 atom styles  

> show #3,5 cartoons

> color #3,5 byhetero

> select #3/B:27

4 atoms, 3 bonds, 1 residue, 1 model selected  

> open "/Users/zhouling95/Documents/Academic/McLellan
> Lab/MPXV/OPG153/AF3_J108_zflip_170-coot-0.pdb"

Chain information for AF3_J108_zflip_170-coot-0.pdb #6  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
E | No description available  
  

> style sel stick

Changed 4 atom styles  

> show sel cartoons

> select add #6

6327 atoms, 6488 bonds, 797 residues, 2 models selected  

> select add #3

12646 atoms, 12970 bonds, 1592 residues, 2 models selected  

> select subtract #3

6323 atoms, 6485 bonds, 796 residues, 1 model selected  

> style sel stick

Changed 6323 atom styles  

> show sel cartoons

> color sel byhetero

> select subtract #6

Nothing selected  

> hide #6 models

> open "/Users/zhouling95/Documents/Academic/McLellan
> Lab/MPXV/OPG153/AF3_J108_zflip_170-coot-1.pdb"

Chain information for AF3_J108_zflip_170-coot-1.pdb #7  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
E | No description available  
  

> style #3,5,7 stick

Changed 18969 atom styles  

> show #3,5,7 cartoons

> color #3,5,7 byhetero

> open "/Users/zhouling95/Documents/Academic/McLellan
> Lab/MPXV/OPG153/AF3_J108_zflip_170-coot-2.pdb"

Chain information for AF3_J108_zflip_170-coot-2.pdb #8  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
E | No description available  
  

> style #3,5,7-8 stick

Changed 25292 atom styles  

> show #3,5,7-8 cartoons

> hide #7 models

> color #3,5,8 byhetero

> color #8 #4eee38ff

> color #3,5,8 byhetero

> volume #1 level 0.003842

> close #2-7

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 33 residues in model #8 to IUPAC-IUB
standards.  
Chain information for AF3_J108_zflip_170-coot-2.pdb  
---  
Chain | Description  
2.2/A | No description available  
2.2/B | No description available  
2.2/C | No description available  
2.2/D | No description available  
2.2/E | No description available  
  

> clipper associate #1 toModel #2

Opened P913_J108_DeepEMhancer_zflipped.mrc as #2.1.1.1, grid size 384,384,384,
pixel 0.933, shown at step 1, values float32  

> volume #2.1.1.1 level 0.03537

Computing secondary structure  
s1:
NVASITAFKSMIDETWDKKIEANTCISRKHRNIIHEVIRDFMKAYPKMDENRKSPLGAPMQWLTQYYILKNEYHKTMLAYDDGSLNTKFKTLNIYMITNVGQYILYIVFCIISGKNHDGTPYIYDSEITSNDKNLINDRIKYACKQILHGQLTMALRIRNKFMFIGSPMYLWFNVNGSHVYHEIYDRNVGFHNKEIGRLLYAFMYYLSISGRFLNDLALLKFTYLGESWTFSLSVPEYILYGLGYSVFDTIEKFSNDAILVYIRTNNRNGYDYAEFNKKGIVKVTEDKPDNDKRIHAIRLINYSSDVQHIHFGFRNTLIIDNECTSIQSSAENATDTGHHQDSKIN  
s2:
NVASITAFKSMIDETWDKKIEANTCISRKHRNIIHEVIRDFMKAYPKMDENRKSPLGAPMQWLTQYYILKNEYHKTMLAYDDGSLNTKFKTLNIYMITNVGQYILYIVFCIISGKNHDGTPYIYDSEITSNDKNLINDRIKYACKQILHGQLTMALRIRNKFMFIGSPMYLWFNVNGSHVYHEIYDRNVGFHNKEIGRLLYAFMYYLSISGRFLNDLALLKFTYLGESWTFSLSVPEYILYGLGYSVFDTIEKFSNDAILVYIRTNNRNGYDYAEFNKKGIVKVTEDKPDNDKRIHAIRLINYSSDVQHIHFGFRNTLIIDNECTSIQSSAENATDTGHHQDSKIN  
s1:
NVASITAFKSMIDETWDKKIEANTCISRKHRNIIHEVIRDFMKAYPKMDENRKSPLGAPMQWLT.QYYILKNEYHKTMLAYDDGSLNTKFKTLNIYMITNVGQYILYIVFCIISGKNHDGTPYIYDSEITSNDKNLINDRIKYACKQILHGQLTMALRIRNKFMFIGSPMYLWFNVNGSHVYHEIYDRNVGFHNKEIGRLLYAFMYYLSISGRFLNDLALLKFTYLGESWTFSLSVPEYILYGLGYSVFDTIEKFSNDAILVYIRTNNRNGYDYAEFNKKGIVKVTEDKPDNDKRIHAIRLINYSSDVQHIHFGFRNTLIIDNECTSIQSSAENATDTGHHQDSKIN  
s2:
.........VQLQESGPGLVKPSETLSLTCTVS.GGSISNYYWSWIRQ......PPGKGLEWIGYIYYIGTTNYNPSLKSRVTISVDTSKNQFSLKL.SSVTAADTAVYYCARHTDSRAWYYFDYWGQGTLVTV.....................................................................................................................................................................................................................  
s1:
NVASITAFKSMIDETWDKKIEANTCISRKHRNIIHEVIRDFMKAYPKMDENRKSPLGAPMQWLTQYYILKNEYHKTMLAYDDGSLNTKFKTLNIYMITNVGQYILYIVFCIISGKNHDGTPYIYDSEITSNDKNLINDRIKYACKQILHGQLTMALRIRNKFMFIG.SPMYLWFNVNGSHVYHEIYDRNVGFHNKEIGRLLYAFMYYLSISGRFLNDLALLKFTYLG.ESWTFSLSVPEYILYGLGYSVFDTIEKFSNDAILVYIRTNNRNGYDYAEFNKKGIVKVTEDKPDNDKRIHAIRLINYSSDVQHIHFGFRNTLIIDNECTSIQSSAENATDTGHHQDSKIN  
s2:
..........................................................................................................................IQMTQSPSSVSASVGDRVTITCRA.SQGISSWLAWYQQK...PGKAPKLLMY..DASDLQSGVPSR...FSGSGSGT.....DFTLTISSLQPEDFATYYCQQANSFPWTFGQGTKVEIK..........................................................................................................  
s1:
NVASITAFKSMIDETWDKKIEANTCISRKHRNIIHEVIRDFMKAYPKMDENRKSPLGAPMQWLTQYYILKNEYHKTMLAYDDGSLNTKFKTLNIYMITNVGQYILYIVFCIISGKNHDGTPYIYDSEITSNDKNLINDRIKYACKQILHGQLTMALRIRNKFMFIGSPMYLWFNVNGSHVYHEIYDRNVGFHNKEIGRLLYAFMYYLSISGRFLNDLALLKFTYLGESWTFSLSVPEYILYGLGYSVFDTIEKFSNDAILVYIRTNNRNGYDYAEFNKKGIVKVTED..KPDNDKRIHAIRLINYSSDVQHIHFGFRNTLIIDNECTSIQSSAENATDTGHHQDSKIN  
s2:
...........................................................................................................................................................................................................VQLVQSGGGVVQPGRSLRLSCAASGFTFSSHGMHWVRQAPGKG.LEWVAVISYDGSNEHYGDSVKGRFTISRDNSKNTLSLQMNSLRAEDTAVYYCARPFSYGAGYYFDSWGQGALVTVSS........................  
s1:
NVASITAFKSMIDETWDKKIEANTCISRKHRNIIHEVIRDFMKAYPKMDENRKSPLGAPMQWLTQYYILKNEYHKTMLAYDDGSLNTKFKTLNIYMITNVGQYILYIVFCIISGKNHDGTPYIYDSEITSNDKNLINDRIKYACKQILHGQLTMALRIRNKFMFIGSPMYLWFNVN.....GSHVYHEIYDRNVGFHNKEIGRLLYAFMYYLSI..SG...RFLNDLALLKFTYLGESWTFSLSVPEYILYGLGYSVFDTIEKFSNDAILVYIRTNNRNGYDYAEFNKKGIVKVTEDKPDNDKRIHAIRLINYSSDVQHIHFGFRNTLIIDNECTSIQSSAENATDTGHHQDSKIN  
s2:
................................................................................................................................................................AIQMTQSPSSLSASVGDRVTITCRASQNI.DSYLNWYQQKPGEAPKLLMYAASSLQSGVPSRFSGSGSGTDFTLIIS....SLQREDFATYYCQQS.YSTPPTFGQGTKLEIK...................................................................................  
s1:
.........VQLQESGPGLVKPSETLSLTCTVS.GGSISNYYWSWIRQ......PPGKGLEWIGYIYYIGTTNYNPSLKSRVTISVDTSKNQFSLKL.SSVTAADTAVYYCARHTDSRAWYYFDYWGQGTLVTV.....................................................................................................................................................................................................................  
s2:
NVASITAFKSMIDETWDKKIEANTCISRKHRNIIHEVIRDFMKAYPKMDENRKSPLGAPMQWLT.QYYILKNEYHKTMLAYDDGSLNTKFKTLNIYMITNVGQYILYIVFCIISGKNHDGTPYIYDSEITSNDKNLINDRIKYACKQILHGQLTMALRIRNKFMFIGSPMYLWFNVNGSHVYHEIYDRNVGFHNKEIGRLLYAFMYYLSISGRFLNDLALLKFTYLGESWTFSLSVPEYILYGLGYSVFDTIEKFSNDAILVYIRTNNRNGYDYAEFNKKGIVKVTEDKPDNDKRIHAIRLINYSSDVQHIHFGFRNTLIIDNECTSIQSSAENATDTGHHQDSKIN  
s1:
VQLQESGPGLVKPSETLSLTCTVSGGSISNYYWSWIRQPPGKGLEWIGYIYYIGTTNYNPSLKSRVTISVDTSKNQFSLKLSSVTAADTAVYYCARHTDSRAWYYFDYWGQGTLVTV  
s2:
VQLQESGPGLVKPSETLSLTCTVSGGSISNYYWSWIRQPPGKGLEWIGYIYYIGTTNYNPSLKSRVTISVDTSKNQFSLKLSSVTAADTAVYYCARHTDSRAWYYFDYWGQGTLVTV  
s1:
VQLQESGPGLVKPS..ETLSLTCTVSGGSISNYYWSWIRQPPGKGLEWIGYIYYIGTTNYNPSLKSRVTISVDTSKNQFSLKLSSVTAADTAVYYCARHTDSRAWYYFDYWGQGTLVTV.  
s2:
IQMTQS.PSSVSASVGDRVTITCRASQG.ISS.WLAWYQQKPGKAPKLLMY....DASDLQSGVPSR..FSGSGSGTDFTLTISSLQPEDFATYYCQQ.ANSFPWTF....GQGTKVEIK  
s1:
VQLQESGPGLVKPSETLSLTCTVSGGSISNYYWSWIRQPPGKGLEWIGYIYYIGT.TNYNPSLKSRVTISVDTSKNQFSLKLSSVTAADTAVYYCARHTDSRAWYYFDYWGQGTLVTV..  
s2:
VQLVQSGGGVVQPGRSLRLSCAASGFTFSSHGMHWVRQAPGKGLEWVAVISYDGSNEHYGDSVKGRFTISRDNSKNTLSLQMNSLRAEDTAVYYCARPFSYGAGYYFDSWGQGALVTVSS  
s1:
.VQLQESGPGL.VKPSETLSLTCTVSGGSISNYYWSWIRQPPGKGLEWIGYIYYIGTTNYNPSLKSRVTISVDTSKNQFSLKLSSVTAADTAVYYCARHTDSRAWYYFDYWGQGTLVTV.  
s2:
AIQMTQSPSSLSASVGDRVTITCRASQNIDS..YLNWYQQKPGEAPKLLMY....AASSLQSGVPSR..FSGSGSGTDFTLIISSLQREDFATYYCQQSYSTPPTF.....GQGTKLEIK  
s1:
..........................................................................................................................IQMTQSPSSVSASVGDRVTITCRA.SQGISSWLAWYQQK...PGKAPKLLMY..DASDLQSGVPSR...FSGSGSGT.....DFTLTISSLQPEDFATYYCQQANSFPWTFGQGTKVEIK..........................................................................................................  
s2:
NVASITAFKSMIDETWDKKIEANTCISRKHRNIIHEVIRDFMKAYPKMDENRKSPLGAPMQWLTQYYILKNEYHKTMLAYDDGSLNTKFKTLNIYMITNVGQYILYIVFCIISGKNHDGTPYIYDSEITSNDKNLINDRIKYACKQILHGQLTMALRIRNKFMFIG.SPMYLWFNVNGSHVYHEIYDRNVGFHNKEIGRLLYAFMYYLSISGRFLNDLALLKFTYLG.ESWTFSLSVPEYILYGLGYSVFDTIEKFSNDAILVYIRTNNRNGYDYAEFNKKGIVKVTEDKPDNDKRIHAIRLINYSSDVQHIHFGFRNTLIIDNECTSIQSSAENATDTGHHQDSKIN  
s1:
IQMTQS.PSSVSASVGDRVTITCRASQG.ISS.WLAWYQQKPGKAPKLLMY....DASDLQSGVPSR..FSGSGSGTDFTLTISSLQPEDFATYYCQQ.ANSFPWTF....GQGTKVEIK  
s2:
VQLQESGPGLVKPS..ETLSLTCTVSGGSISNYYWSWIRQPPGKGLEWIGYIYYIGTTNYNPSLKSRVTISVDTSKNQFSLKLSSVTAADTAVYYCARHTDSRAWYYFDYWGQGTLVTV.  
s1:
IQMTQSPSSVSASVGDRVTITCRASQGISSWLAWYQQKPGKAPKLLMYDASDLQSGVPSRFSGSGSGTDFTLTISSLQPEDFATYYCQQANSFPWTFGQGTKVEIK  
s2:
IQMTQSPSSVSASVGDRVTITCRASQGISSWLAWYQQKPGKAPKLLMYDASDLQSGVPSRFSGSGSGTDFTLTISSLQPEDFATYYCQQANSFPWTFGQGTKVEIK  
s1:
IQMTQSPSSVSASVGDRVTITCRASQGI...SSWLAWYQQKPGKA...PKLLMYDASDLQSG..VPSRFSGSGSGTDFTLTI..SSLQPEDFATYYCQQANSFPW.....TFGQGTKVEIK.  
s2:
VQLVQSGGGVV.QPGRSLRLSCAAS.GFTFSSHGMHWVRQAPGKGLEWVAVISYDGSNEHYGDSVKGRFTISRDNSKNTLSLQMNSLRAEDTAVYYCARPFSYGAGYYFDSWGQGALVTVSS  
s1:
.IQMTQSPSSVSASVGDRVTITCRASQGISSWLAWYQQKPGKAPKLLMYDASDLQSGVPSRFSGSGSGTDFTLTISSLQPEDFATYYCQQANSFPWTFGQGTKVEIK  
s2:
AIQMTQSPSSLSASVGDRVTITCRASQNIDSYLNWYQQKPGEAPKLLMYAASSLQSGVPSRFSGSGSGTDFTLIISSLQREDFATYYCQQSYSTPPTFGQGTKLEIK  
s1:
...........................................................................................................................................................................................................VQLVQSGGGVVQPGRSLRLSCAASGFTFSSHGMHWVRQAPGKG.LEWVAVISYDGSNEHYGDSVKGRFTISRDNSKNTLSLQMNSLRAEDTAVYYCARPFSYGAGYYFDSWGQGALVTVSS........................  
s2:
NVASITAFKSMIDETWDKKIEANTCISRKHRNIIHEVIRDFMKAYPKMDENRKSPLGAPMQWLTQYYILKNEYHKTMLAYDDGSLNTKFKTLNIYMITNVGQYILYIVFCIISGKNHDGTPYIYDSEITSNDKNLINDRIKYACKQILHGQLTMALRIRNKFMFIGSPMYLWFNVNGSHVYHEIYDRNVGFHNKEIGRLLYAFMYYLSISGRFLNDLALLKFTYLGESWTFSLSVPEYILYGLGYSVFDTIEKFSNDAILVYIRTNNRNGYDYAEFNKKGIVKVTED..KPDNDKRIHAIRLINYSSDVQHIHFGFRNTLIIDNECTSIQSSAENATDTGHHQDSKIN  
s1:
VQLVQSGGGVVQPGRSLRLSCAASGFTFSSHGMHWVRQAPGKGLEWVAVISYDGSNEHYGDSVKGRFTISRDNSKNTLSLQMNSLRAEDTAVYYCARPFSYGAGYYFDSWGQGALVTVSS  
s2:
VQLQESGPGLVKPSETLSLTCTVSGGSISNYYWSWIRQPPGKGLEWIGYIYYIGT.TNYNPSLKSRVTISVDTSKNQFSLKLSSVTAADTAVYYCARHTDSRAWYYFDYWGQGTLVTV..  
s1:
VQLVQSGGGVV.QPGRSLRLSCAAS.GFTFSSHGMHWVRQAPGKGLEWVAVISYDGSNEHYGDSVKGRFTISRDNSKNTLSLQMNSLRAEDTAVYYCARPFSYGAGYYFDSWGQGALVTVSS  
s2:
IQMTQSPSSVSASVGDRVTITCRASQGI...SSWLAWYQQKPGKA...PKLLMYDASDLQSG..VPSRFSGSGSGTDFTLTI..SSLQPEDFATYYCQQANSFPW.....TFGQGTKVEIK.  
s1:
VQLVQSGGGVVQPGRSLRLSCAASGFTFSSHGMHWVRQAPGKGLEWVAVISYDGSNEHYGDSVKGRFTISRDNSKNTLSLQMNSLRAEDTAVYYCARPFSYGAGYYFDSWGQGALVTVSS  
s2:
VQLVQSGGGVVQPGRSLRLSCAASGFTFSSHGMHWVRQAPGKGLEWVAVISYDGSNEHYGDSVKGRFTISRDNSKNTLSLQMNSLRAEDTAVYYCARPFSYGAGYYFDSWGQGALVTVSS  
s1:
.VQLVQSGGGVV.QPGRSLRLSCAASGFTFSSHGMHWVRQAPGKGLEWVAVISYDGSNEHYGDSVKGRFTISRDNSKNTLSLQMNSLRAEDTAVYYCARPFSYGAGYYFDSWGQGALVTVSS  
s2:
AIQMTQSPSSLSASVGDRVTITCRASQ.NIDSY.LNWYQQKPG...EAPKLLMYAASSLQSG..VPSRFSGSGSGTDFTLII..SSLQREDFATYYCQQSYSTP.....PTFGQGTKLEIK.  
s1:
................................................................................................................................................................AIQMTQSPSSLSASVGDRVTITCRASQNI.DSYLNWYQQKPGEAPKLLMYAASSLQSGVPSRFSGSGSGTDFTLIIS....SLQREDFATYYCQQS.YSTPPTFGQGTKLEIK...................................................................................  
s2:
NVASITAFKSMIDETWDKKIEANTCISRKHRNIIHEVIRDFMKAYPKMDENRKSPLGAPMQWLTQYYILKNEYHKTMLAYDDGSLNTKFKTLNIYMITNVGQYILYIVFCIISGKNHDGTPYIYDSEITSNDKNLINDRIKYACKQILHGQLTMALRIRNKFMFIGSPMYLWFNVN.....GSHVYHEIYDRNVGFHNKEIGRLLYAFMYYLSI..SG...RFLNDLALLKFTYLGESWTFSLSVPEYILYGLGYSVFDTIEKFSNDAILVYIRTNNRNGYDYAEFNKKGIVKVTEDKPDNDKRIHAIRLINYSSDVQHIHFGFRNTLIIDNECTSIQSSAENATDTGHHQDSKIN  
s1:
AIQMTQSPSSLSASVGDRVTITCRASQNIDS..YLNWYQQKPGEAPKLLMY....AASSLQSGVPSR..FSGSGSGTDFTLIISSLQREDFATYYCQQSYSTPPTF.....GQGTKLEIK  
s2:
.VQLQESGPGL.VKPSETLSLTCTVSGGSISNYYWSWIRQPPGKGLEWIGYIYYIGTTNYNPSLKSRVTISVDTSKNQFSLKLSSVTAADTAVYYCARHTDSRAWYYFDYWGQGTLVTV.  
s1:
AIQMTQSPSSLSASVGDRVTITCRASQNIDSYLNWYQQKPGEAPKLLMYAASSLQSGVPSRFSGSGSGTDFTLIISSLQREDFATYYCQQSYSTPPTFGQGTKLEIK  
s2:
.IQMTQSPSSVSASVGDRVTITCRASQGISSWLAWYQQKPGKAPKLLMYDASDLQSGVPSRFSGSGSGTDFTLTISSLQPEDFATYYCQQANSFPWTFGQGTKVEIK  
s1:
AIQMTQSPSSLSASVGDRVTITCRASQ.NIDSY.LNWYQQKPG...EAPKLLMYAASSLQSG..VPSRFSGSGSGTDFTLII..SSLQREDFATYYCQQSYSTP.....PTFGQGTKLEIK.  
s2:
.VQLVQSGGGVV.QPGRSLRLSCAASGFTFSSHGMHWVRQAPGKGLEWVAVISYDGSNEHYGDSVKGRFTISRDNSKNTLSLQMNSLRAEDTAVYYCARPFSYGAGYYFDSWGQGALVTVSS  
s1:
AIQMTQSPSSLSASVGDRVTITCRASQNIDSYLNWYQQKPGEAPKLLMYAASSLQSGVPSRFSGSGSGTDFTLIISSLQREDFATYYCQQSYSTPPTFGQGTKLEIK  
s2:
AIQMTQSPSSLSASVGDRVTITCRASQNIDSYLNWYQQKPGEAPKLLMYAASSLQSGVPSRFSGSGSGTDFTLIISSLQREDFATYYCQQSYSTPPTFGQGTKLEIK  

"Adjust for PAE" is checked in the distance restraint options, but the
reference model has no PAE matrix assigned. This option has been ignored.  

> isolde restrain distances "#2.2/A","#2.2/B","#2.2/C","#2.2/D","#2.2/E"
> templateAtoms "#2.2/A","#2.2/B","#2.2/C","#2.2/D","#2.2/E" perChain false
> adjustForConfidence false useCoordinateAlignment false kappa 2.10 fallOff
> 2.50 groupName "Reference Distance Restraints"

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  

> isolde restrain torsions #2.2/A templateResidues #2.2/A adjustForConfidence
> false sidechains true springConstant 130.00 alpha 0.20

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  

> isolde restrain torsions #2.2/B templateResidues #2.2/B adjustForConfidence
> false sidechains true springConstant 130.00 alpha 0.20

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  

> isolde restrain torsions #2.2/C templateResidues #2.2/C adjustForConfidence
> false sidechains true springConstant 130.00 alpha 0.20

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  

> isolde restrain torsions #2.2/D templateResidues #2.2/D adjustForConfidence
> false sidechains true springConstant 130.00 alpha 0.20

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  

> isolde restrain torsions #2.2/E templateResidues #2.2/E adjustForConfidence
> false sidechains true springConstant 130.00 alpha 0.20

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  

> addh

Summary of feedback from adding hydrogens to AF3_J108_zflip_170-coot-2.pdb
#2.2  
---  
notes | No usable SEQRES records for AF3_J108_zflip_170-coot-2.pdb (#2.2) chain A; guessing termini instead  
No usable SEQRES records for AF3_J108_zflip_170-coot-2.pdb (#2.2) chain B;
guessing termini instead  
No usable SEQRES records for AF3_J108_zflip_170-coot-2.pdb (#2.2) chain C;
guessing termini instead  
No usable SEQRES records for AF3_J108_zflip_170-coot-2.pdb (#2.2) chain D;
guessing termini instead  
No usable SEQRES records for AF3_J108_zflip_170-coot-2.pdb (#2.2) chain E;
guessing termini instead  
Chain-initial residues that are actual N termini: /A ASN 19, /B VAL 2, /C ILE
2, /D VAL 2, /E ALA 1  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini: /B VAL 111, /C LYS 107, /D SER
113, /E LYS 107  
Chain-final residues that are not actual C termini: /A ASN 364  
646 hydrogen bonds  
/A ASN 364 is not terminus, removing H atom from 'C'  
6131 hydrogens added  
  

> ui tool show "Ramachandran Plot"

> isolde sim start /A-E

ISOLDE: started sim  

> isolde sim stop discardTo start

Sim termination reason: None  
reverting to start  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

"Adjust for PAE" is checked in the distance restraint options, but the
reference model has no PAE matrix assigned. This option has been ignored.  

> isolde restrain distances "#2.2/A","#2.2/B","#2.2/C","#2.2/D","#2.2/E"
> templateAtoms "#2.2/A","#2.2/B","#2.2/C","#2.2/D","#2.2/E" perChain false
> adjustForConfidence false useCoordinateAlignment false kappa 2.10 fallOff
> 2.50 groupName "Reference Distance Restraints"

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  

> isolde restrain torsions #2.2/A templateResidues #2.2/A adjustForConfidence
> false sidechains true springConstant 130.00 alpha 0.20

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  

> isolde restrain torsions #2.2/B templateResidues #2.2/B adjustForConfidence
> false sidechains true springConstant 130.00 alpha 0.20

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  

> isolde restrain torsions #2.2/C templateResidues #2.2/C adjustForConfidence
> false sidechains true springConstant 130.00 alpha 0.20

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  

> isolde restrain torsions #2.2/D templateResidues #2.2/D adjustForConfidence
> false sidechains true springConstant 130.00 alpha 0.20

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  

> isolde restrain torsions #2.2/E templateResidues #2.2/E adjustForConfidence
> false sidechains true springConstant 130.00 alpha 0.20

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  

"Adjust for PAE" is checked in the distance restraint options, but the
reference model has no PAE matrix assigned. This option has been ignored.  

> isolde restrain distances "#2.2/A","#2.2/B","#2.2/C","#2.2/D","#2.2/E"
> templateAtoms "#2.2/A","#2.2/B","#2.2/C","#2.2/D","#2.2/E" perChain false
> adjustForConfidence false useCoordinateAlignment false kappa 2.10 fallOff
> 2.50 groupName "Reference Distance Restraints"

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  

> isolde restrain torsions #2.2/A templateResidues #2.2/A adjustForConfidence
> false sidechains true springConstant 130.00 alpha 0.20

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  

> isolde restrain torsions #2.2/B templateResidues #2.2/B adjustForConfidence
> false sidechains true springConstant 130.00 alpha 0.20

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  

> isolde restrain torsions #2.2/C templateResidues #2.2/C adjustForConfidence
> false sidechains true springConstant 130.00 alpha 0.20

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  

> isolde restrain torsions #2.2/D templateResidues #2.2/D adjustForConfidence
> false sidechains true springConstant 130.00 alpha 0.20

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  

> isolde restrain torsions #2.2/E templateResidues #2.2/E adjustForConfidence
> false sidechains true springConstant 130.00 alpha 0.20

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  

> isolde sim start /A-E

ISOLDE: started sim  

> isolde pepflip /B:31

> isolde sim stop discardTo start

Sim termination reason: None  
reverting to start  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> isolde sim start /B:28

ISOLDE: started sim  

> isolde sim stop discardTo start

Sim termination reason: None  
reverting to start  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> isolde sim start /B:25-31

ISOLDE: started sim  

> isolde sim stop discardTo start

Sim termination reason: None  
reverting to start  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> isolde sim start /B:28

ISOLDE: started sim  

> isolde sim stop

Sim termination reason: None  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> save "/Users/zhouling95/Documents/Academic/McLellan
> Lab/MPXV/OPG153/AF3_J108_zflip_170-coot-2-isolde.pdb"

> close #2

> open "/Users/zhouling95/Documents/Academic/McLellan
> Lab/MPXV/OPG153/Phenix/RealSpaceRefine_178/AF3_J108_zflip_170-coot-2_real_space_refined_178.pdb"

Chain information for AF3_J108_zflip_170-coot-2_real_space_refined_178.pdb #1  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
E | No description available  
  

> open "/Users/zhouling95/Documents/Academic/McLellan
> Lab/MPXV/OPG153/Phenix/RealSpaceRefine_170/AF3_J108_zflip_168-coot-0_real_space_refined_170.pdb"

Chain information for AF3_J108_zflip_168-coot-0_real_space_refined_170.pdb #2  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
E | No description available  
  

> show atoms

> show cartoons

> style stick

Changed 12646 atom styles  

> color byhetero

> color #2 #7775eeff

> color #2 #53eebaff

> color #1 #cdee5bff

> color #1 #eece74ff

> color byhetero

> open "/Users/zhouling95/Documents/Academic/McLellan
> Lab/MPXV/P913_J108_DeepEMhancer_zflipped.mrc"

Opened P913_J108_DeepEMhancer_zflipped.mrc as #3, grid size 384,384,384, pixel
0.933, shown at level 0.000654, step 2, values float32  

> surface dust #3 size 9.33

> volume #3 step 1

> volume #3 level 0.003842

> volume #3 color #b2b2b267

> volume #3 color #b2b2b266

> lighting simple

> open "/Users/zhouling95/Documents/Academic/McLellan
> Lab/MPXV/OPG153/Phenix/RealSpaceRefine_180/AF3_J108_zflip_170-coot-2_real_space_refined_178_real_space_refined_180.pdb"

Chain information for
AF3_J108_zflip_170-coot-2_real_space_refined_178_real_space_refined_180.pdb #4  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
E | No description available  
  

> show atoms

> style stick

Changed 18969 atom styles  

> show cartoons

> color byhetero

> hide #2 models

> show #2 models


===== Log before crash end =====

Log:
Startup Messages  
---  
note | available bundle cache has not been initialized yet  
  

> mousemode middleMode center

> cofr centerOfView

> alias cofron cofr centerofview showpivot true

> alias cofroff cofr centerofview showpivot false

> alias symclip cofr centerofview; clip near -$1 far $1 position cofr

> alias cootmode set bgColor black; surface cap false; surface style solid;
> lighting flat; graphics silhouettes false; style stick; ~rib; color
> ##num_residues gold; color byhet ; disp; ~disp @H*; style ions ball; style
> solvent ball; size ballscale 0.2; size stickradius 0.07; transparency 70;
> cofr centerofview; clip near -10 far 10 position cofr; color ##~num_residues
> cornflower blue

> alias cootmode_mesh set bgColor black; surface cap false; surface style
> mesh; lighting flat; graphics silhouettes false; style stick; ~rib; color
> ##num_residues gold; color byhet ; disp; ~disp @H*; style solvent ball;
> style ions ball; size ballscale 0.2; size stickradius 0.07; cofr
> centerofview; clip near -10 far 10 position cofr; color ##~num_residues
> #3d60ffff; transparency 50

> alias cootmode_off surface style solid; lighting soft; graphics silhouettes
> false; hide atoms; default_mol_display; transparency 0; symclip 40; color
> ##~num_residues grey; size stickradius 0.2;

> alias ca_and_sidechains ~rib $1; ~surf $1; ~disp $1; disp @CA&protein&$1;
> disp @P&nucleic&$1; style $1 stick; disp sidechain&$1; disp
> ~backbone&nucleic&$1; size stickradius 0.1; size pseudobondradius 0.1

> alias ca_trace ~rib $1; ~surf $1; ~disp $1; disp @CA&protein&$1; disp
> @P&nucleic&$1; style $1 stick; size stickradius 0.1; size pseudobondradius
> 0.1

> alias map_sphere_15 surface unzone ##~num_residues; sel; close #10000;
> marker #10000 position cofr; sel ~sel; surface zone ##~num_residues
> nearAtoms sel distance 15; close #10000

> alias map_unsphere surface unzone ##~num_residues

> alias default_mol_display ~disp; rib; rainbow chain palette Pastel1-5;
> lighting soft; color byhet

> alias hidemaps surface unzone ##~num_residues; sel; close #10000; marker
> #10000 position cofr; sel ~sel; surface zone ##~num_residues nearAtoms sel
> distance 0; close #10000

> alias showmaps surface unzone ##~num_residues

> alias licorice car style protein modeh default arrows f xsect oval width 1
> thick 1; style stick; size stickRadius 0.5; ~disp @H*; color byhet

> alias caps_off surface cap false

> alias caps_on surface cap true

> alias rock_movie cofr showpivot false; movie record supersample 3; rock y
> 40; wait 136; movie encode ~/Desktop/rock_movie.mp4 quality high; stop

> alias publication_figure save Figure.png format png supersample 3
> transparentBackground true width 3000 height 3000

> buttonpanel Shortcuts rows 3 columns 5

> buttonpanel Shortcuts add default_disp command default_mol_display

> buttonpanel Shortcuts add Hide_H command "~disp @H*"

> buttonpanel Shortcuts add Licorice command licorice

> buttonpanel Shortcuts add Ribbons command "preset ribbons"

> buttonpanel Shortcuts add RockMovie command rock_movie

> buttonpanel Shortcuts add SymClip10 command "symclip 10"

> buttonpanel Shortcuts add SymClip20 command "symclip 20"

> buttonpanel Shortcuts add map_sphere command map_sphere_15

> buttonpanel Shortcuts add map_unsphere command map_unsphere

> buttonpanel Shortcuts add PubFigure command publication_figure

> buttonpanel Shortcuts add coot_mode command cootmode

> buttonpanel Shortcuts add coot_mesh command cootmode_mesh

> buttonpanel Shortcuts add coot_off command cootmode_off

> buttonpanel Shortcuts add hidemaps command hidemaps

> buttonpanel Shortcuts add showmaps command showmaps

> ui tool show "Model Panel"

UCSF ChimeraX version: 1.9rc202411082121 (2024-11-08)  
© 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 M4 Pro
OpenGL vendor: Apple

Python: 3.11.4
Locale: UTF-8
Qt version: PyQt6 6.7.1, Qt 6.7.1
Qt runtime version: 6.7.3
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: Mac16,8
      Model Number: MX2J3LL/A
      Chip: Apple M4 Pro
      Total Number of Cores: 14 (10 performance and 4 efficiency)
      Memory: 24 GB
      System Firmware Version: 11881.41.5
      OS Loader Version: 11881.41.5

Software:

    System Software Overview:

      System Version: macOS 15.1.1 (24B2091)
      Kernel Version: Darwin 24.1.0
      Time since boot: 4 days, 11 hours, 6 minutes

Graphics/Displays:

    Apple M4 Pro:

      Chipset Model: Apple M4 Pro
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 20
      Vendor: Apple (0x106b)
      Metal Support: Metal 3
      Displays:
        Color LCD:
          Display Type: Built-in Liquid Retina XDR Display
          Resolution: 3024 x 1964 Retina
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: No
          Connection Type: Internal
        U32J59x:
          Resolution: 4096 x 2304
          UI Looks like: 2048 x 1152 @ 30.00Hz
          Mirror: Off
          Online: Yes
          Rotation: Supported


Installed Packages:
    alabaster: 1.0.0
    appdirs: 1.4.4
    appnope: 0.1.4
    asttokens: 2.4.1
    auditwheel: 6.1.0
    autocommand: 2.2.2
    babel: 2.16.0
    backports.tarfile: 1.2.0
    beautifulsoup4: 4.12.3
    blockdiag: 3.0.0
    blosc2: 2.7.1
    build: 1.2.1
    certifi: 2023.11.17
    cftime: 1.6.4.post1
    charset-normalizer: 3.4.0
    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: 2.16.1
    ChimeraX-AlphaFold: 1.0.1
    ChimeraX-AltlocExplorer: 1.1.2
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.58.7
    ChimeraX-AtomicLibrary: 14.1.11
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.4
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.4.7
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.13
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.4.0
    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: 2.3
    ChimeraX-Clipper: 0.23.0
    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: 1.9rc202411082121
    ChimeraX-CoreFormats: 1.2
    ChimeraX-coulombic: 1.4.4
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.3
    ChimeraX-Dicom: 1.2.5
    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: 1.4.1
    ChimeraX-Hbonds: 2.5
    ChimeraX-Help: 1.3
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.3
    ChimeraX-ISOLDE: 1.8.dev0
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-IUPAC: 1.0
    ChimeraX-KVFinder: 1.2.1
    ChimeraX-Label: 1.1.11
    ChimeraX-ListInfo: 1.2.2
    ChimeraX-Log: 1.2
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.9.1
    ChimeraX-Map: 1.3
    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: 2.1.6
    ChimeraX-MCopy: 1.0
    ChimeraX-MDcrds: 2.7.2
    ChimeraX-MedicalToolbar: 1.1
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.14.2
    ChimeraX-MMTF: 2.2
    ChimeraX-ModelArchive: 1.0
    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-MutationScores: 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: 1.14
    ChimeraX-OrthoPick: 1.0.1
    ChimeraX-PDB: 2.7.6
    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: 1.1.2
    ChimeraX-PubChem: 2.2
    ChimeraX-QScore: 1.1
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.6.1
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.3.1
    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: 3.2.6
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.14
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.2.0
    ChimeraX-ShowSequences: 1.0.3
    ChimeraX-SideView: 1.0.1
    ChimeraX-SimilarStructures: 1.0.1
    ChimeraX-Smiles: 2.1.2
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.18.1
    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: 1.2.3
    ChimeraX-ToolshedUtils: 1.2.4
    ChimeraX-Topography: 1.0
    ChimeraX-ToQuest: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.41
    ChimeraX-Umap: 1.0
    ChimeraX-uniprot: 2.3.1
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.4.4
    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: 1.3.0
    cxservices: 1.2.3
    cycler: 0.12.1
    Cython: 3.0.10
    debugpy: 1.8.8
    decorator: 5.1.1
    docutils: 0.21.2
    executing: 2.1.0
    filelock: 3.15.4
    fonttools: 4.54.1
    funcparserlib: 2.0.0a0
    glfw: 2.7.0
    grako: 3.16.5
    h5py: 3.12.1
    html2text: 2024.2.26
    idna: 3.10
    ihm: 1.3
    imagecodecs: 2024.6.1
    imagesize: 1.4.1
    importlib_metadata: 8.0.0
    importlib_resources: 6.4.0
    inflect: 7.3.1
    ipykernel: 6.29.5
    ipython: 8.26.0
    ipywidgets: 8.1.5
    jaraco.context: 5.3.0
    jaraco.functools: 4.0.1
    jaraco.text: 3.12.1
    jedi: 0.19.1
    Jinja2: 3.1.4
    jupyter_client: 8.6.2
    jupyter_core: 5.7.2
    jupyterlab_widgets: 3.0.13
    kiwisolver: 1.4.7
    line_profiler: 4.1.3
    lxml: 5.2.2
    lz4: 4.3.3
    MarkupSafe: 3.0.2
    matplotlib: 3.9.2
    matplotlib-inline: 0.1.7
    more-itertools: 10.3.0
    msgpack: 1.0.8
    ndindex: 1.9.2
    nest-asyncio: 1.6.0
    netCDF4: 1.6.5
    networkx: 3.3
    nibabel: 5.2.0
    nptyping: 2.5.0
    numexpr: 2.10.1
    numpy: 1.26.4
    openvr: 1.26.701
    ordered-set: 4.1.0
    packaging: 23.2
    packaging: 24.1
    ParmEd: 4.2.2
    parso: 0.8.4
    pep517: 0.13.1
    pexpect: 4.9.0
    pillow: 10.4.0
    pip: 24.2
    pkginfo: 1.11.1
    platformdirs: 4.3.6
    platformdirs: 4.2.2
    prompt_toolkit: 3.0.48
    psutil: 6.0.0
    ptyprocess: 0.7.0
    pure_eval: 0.2.3
    py-cpuinfo: 9.0.0
    pycollada: 0.8
    pydicom: 2.4.4
    pyelftools: 0.31
    Pygments: 2.18.0
    pynmrstar: 3.3.4
    pynrrd: 1.0.0
    PyOpenGL: 3.1.7
    PyOpenGL-accelerate: 3.1.7
    pyopenxr: 1.0.3401
    pyparsing: 3.2.0
    pyproject_hooks: 1.2.0
    PyQt6-commercial: 6.7.1
    PyQt6-Qt6: 6.7.3
    PyQt6-WebEngine-commercial: 6.7.0
    PyQt6-WebEngine-Qt6: 6.7.3
    PyQt6-WebEngineSubwheel-Qt6: 6.7.3
    PyQt6_sip: 13.8.0
    python-dateutil: 2.9.0.post0
    pytz: 2024.2
    pyzmq: 26.2.0
    qtconsole: 5.5.2
    QtPy: 2.4.2
    qtshim: 1.0
    RandomWords: 0.4.0
    requests: 2.32.3
    scipy: 1.14.0
    setuptools: 72.1.0
    sfftk-rw: 0.8.1
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.6
    Sphinx: 8.0.2
    sphinx-autodoc-typehints: 2.2.3
    sphinxcontrib-applehelp: 2.0.0
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 2.0.0
    sphinxcontrib-htmlhelp: 2.1.0
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 2.0.0
    sphinxcontrib-serializinghtml: 2.0.0
    stack-data: 0.6.3
    superqt: 0.6.3
    tables: 3.10.1
    tcia_utils: 1.5.1
    tifffile: 2024.7.24
    tinyarray: 1.2.4
    tomli: 2.0.1
    tornado: 6.4.1
    traitlets: 5.14.3
    typeguard: 4.3.0
    typing_extensions: 4.12.2
    typing_extensions: 4.12.2
    tzdata: 2024.2
    urllib3: 2.2.3
    wcwidth: 0.2.13
    webcolors: 24.6.0
    wheel: 0.43.0
    wheel: 0.43.0
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.13
    zipp: 3.19.2

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