Starting phenix.real_space_refine
on Sat Aug 23 04:16:03 2025 by dcliebschner
===============================================================================

Processing files:
-------------------------------------------------------------------------------

  Found model, /net/cci-nas-00/data/ceres_data/7vlt_32026/08_2025/7vlt_32026_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7vlt_32026/08_2025/7vlt_32026.map

Processing PHIL parameters:
-------------------------------------------------------------------------------

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.1
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7vlt_32026/08_2025/7vlt_32026_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7vlt_32026/08_2025/7vlt_32026_neut.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7vlt_32026/08_2025/7vlt_32026.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7vlt_32026/08_2025/7vlt_32026.map"
  }
  resolution = 3.1
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


Starting job
===============================================================================
-------------------------------------------------------------------------------
Citation:
*********
Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams
PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography.
Acta Cryst. D74:531-544.

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.008 sd=   0.177
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 6
    Type Number    sf(0)   Gaussians
     P       5      5.49       5
     Mg      2      5.21       5
     S      46      5.16       5
     C    5849      2.51       5
     N    1495      2.21       5
     O    1627      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 9024
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 8908
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1145, 8908
          Classifications: {'peptide': 1145}
          Incomplete info: {'truncation_to_alanine': 26}
          Link IDs: {'PTRANS': 33, 'TRANS': 1111}
          Chain breaks: 5
          Unresolved non-hydrogen bonds: 100
          Unresolved non-hydrogen angles: 123
          Unresolved non-hydrogen dihedrals: 80
          Planarities with less than four sites: {'ASP:plan': 6, 'ASN:plan1': 1, 'ARG:plan': 3, 'GLU:plan': 8, 'TYR:plan': 1, 'GLN:plan1': 2}
          Unresolved non-hydrogen planarities: 83
    Chain: "A"
      Number of atoms: 116
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 6, 116
          Unusual residues: {' MG': 2, 'ADP': 1, 'ATP': 1, 'ETJ': 1, 'Y01': 1}
          Classifications: {'undetermined': 6}
          Link IDs: {None: 5}
  Time building chain proxies: 2.16, per 1000 atoms: 0.24
  Number of scatterers: 9024
  At special positions: 0
  Unit cell: (72.27, 90.666, 135.342, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S      46     16.00
     P       5     15.00
     Mg      2     11.99
     O    1627      8.00
     N    1495      7.00
     C    5849      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.99
  Conformation dependent library (CDL) restraints added in 250.5 milliseconds
  
  Enol-peptide restraints added in 953.7 nanoseconds
  

  2266 Ramachandran restraints generated.
    1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2158

  Finding SS restraints...
    Secondary structure from input PDB file:
      48 helices and 5 sheets defined
      72.1% alpha, 8.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.35
  Creating SS restraints...
    Processing helix  chain 'A' and resid 252 through 255
    Processing helix  chain 'A' and resid 256 through 278
      removed outlier: 3.681A  pdb=" N   HIS A 278 " --> pdb=" O   LYS A 274 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 284 through 312
      removed outlier: 5.957A  pdb=" N   ARG A 295 " --> pdb=" O   ARG A 291 " (cutoff:3.500A)
      Proline residue:  A 296  - end of helix
    Processing helix  chain 'A' and resid 312 through 327
      removed outlier: 3.992A  pdb=" N   LEU A 316 " --> pdb=" O   PHE A 312 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 347 through 395
    Processing helix  chain 'A' and resid 397 through 402
    Processing helix  chain 'A' and resid 406 through 427
      removed outlier: 3.599A  pdb=" N   GLU A 417 " --> pdb=" O   LEU A 413 " (cutoff:3.500A)
      removed outlier: 4.604A  pdb=" N   THR A 418 " --> pdb=" O   VAL A 414 " (cutoff:3.500A)
      removed outlier: 3.855A  pdb=" N   ASN A 419 " --> pdb=" O   ALA A 415 " (cutoff:3.500A)
      removed outlier: 3.501A  pdb=" N   LEU A 427 " --> pdb=" O   TRP A 423 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 429 through 450
      Proline residue:  A 435  - end of helix
      removed outlier: 3.541A  pdb=" N   ASN A 447 " --> pdb=" O   ILE A 443 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 451 through 462
      removed outlier: 3.999A  pdb=" N   VAL A 455 " --> pdb=" O   SER A 451 " (cutoff:3.500A)
      removed outlier: 3.963A  pdb=" N   GLY A 456 " --> pdb=" O   SER A 452 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 462 through 498
    Processing helix  chain 'A' and resid 498 through 506
    Processing helix  chain 'A' and resid 507 through 559
      Proline residue:  A 544  - end of helix
    Processing helix  chain 'A' and resid 564 through 584
      Proline residue:  A 581  - end of helix
      removed outlier: 4.152A  pdb=" N   LEU A 584 " --> pdb=" O   THR A 580 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 584 through 607
    Processing helix  chain 'A' and resid 706 through 715
    Processing helix  chain 'A' and resid 761 through 768
    Processing helix  chain 'A' and resid 773 through 784
    Processing helix  chain 'A' and resid 786 through 791
    Processing helix  chain 'A' and resid 809 through 824
    Processing helix  chain 'A' and resid 839 through 849
    Processing helix  chain 'A' and resid 853 through 859
      removed outlier: 3.684A  pdb=" N   ASP A 858 " --> pdb=" O   PHE A 854 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 868 through 874
      removed outlier: 4.022A  pdb=" N   THR A 873 " --> pdb=" O   GLN A 870 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 891 through 899
    Processing helix  chain 'A' and resid 899 through 911
    Processing helix  chain 'A' and resid 976 through 984
    Processing helix  chain 'A' and resid 988 through 1016
      removed outlier: 3.728A  pdb=" N   ASP A1008 " --> pdb=" O   ILE A1004 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1029 through 1073
      removed outlier: 4.000A  pdb=" N   VAL A1053 " --> pdb=" O   THR A1049 " (cutoff:3.500A)
      removed outlier: 4.157A  pdb=" N   GLU A1054 " --> pdb=" O   SER A1050 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1076 through 1083
      removed outlier: 3.730A  pdb=" N   PHE A1080 " --> pdb=" O   PRO A1076 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1084 through 1102
      removed outlier: 3.897A  pdb=" N   ILE A1088 " --> pdb=" O   PRO A1084 " (cutoff:3.500A)
      removed outlier: 4.000A  pdb=" N   ARG A1091 " --> pdb=" O   LEU A1087 " (cutoff:3.500A)
      removed outlier: 3.836A  pdb=" N   ASP A1095 " --> pdb=" O   ARG A1091 " (cutoff:3.500A)
      removed outlier: 4.341A  pdb=" N   THR A1096 " --> pdb=" O   PHE A1092 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1102 through 1128
    Processing helix  chain 'A' and resid 1130 through 1163
      removed outlier: 3.650A  pdb=" N   ALA A1134 " --> pdb=" O   VAL A1130 " (cutoff:3.500A)
      removed outlier: 3.645A  pdb=" N   ALA A1136 " --> pdb=" O   LEU A1132 " (cutoff:3.500A)
      Proline residue:  A1137  - end of helix
      removed outlier: 4.202A  pdb=" N   ASP A1155 " --> pdb=" O   VAL A1151 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1163 through 1176
      removed outlier: 3.894A  pdb=" N   LEU A1167 " --> pdb=" O   THR A1163 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1177 through 1185
    Processing helix  chain 'A' and resid 1186 through 1238
    Processing helix  chain 'A' and resid 1242 through 1280
      removed outlier: 4.435A  pdb=" N   ASN A1259 " --> pdb=" O   THR A1255 " (cutoff:3.500A)
      removed outlier: 4.934A  pdb=" N   TRP A1260 " --> pdb=" O   ASN A1256 " (cutoff:3.500A)
      removed outlier: 3.776A  pdb=" N   ALA A1274 " --> pdb=" O   VAL A1270 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1281 through 1284
      removed outlier: 3.665A  pdb=" N   MET A1284 " --> pdb=" O   PHE A1281 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 1281 through 1284'
    Processing helix  chain 'A' and resid 1347 through 1355
      removed outlier: 4.071A  pdb=" N   PHE A1355 " --> pdb=" O   LEU A1351 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1377 through 1383
    Processing helix  chain 'A' and resid 1399 through 1404
    Processing helix  chain 'A' and resid 1410 through 1421
    Processing helix  chain 'A' and resid 1423 through 1430
    Processing helix  chain 'A' and resid 1432 through 1435
    Processing helix  chain 'A' and resid 1439 through 1443
      removed outlier: 3.856A  pdb=" N   GLU A1443 " --> pdb=" O   GLU A1440 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1446 through 1462
      removed outlier: 4.261A  pdb=" N   ARG A1461 " --> pdb=" O   ARG A1457 " (cutoff:3.500A)
      removed outlier: 3.926A  pdb=" N   LYS A1462 " --> pdb=" O   ALA A1458 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1476 through 1491
      removed outlier: 3.694A  pdb=" N   ILE A1482 " --> pdb=" O   ALA A1478 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1504 through 1509
      removed outlier: 4.109A  pdb=" N   THR A1508 " --> pdb=" O   THR A1505 " (cutoff:3.500A)
      removed outlier: 3.746A  pdb=" N   ALA A1509 " --> pdb=" O   ILE A1506 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1525 through 1532
    Processing helix  chain 'A' and resid 1535 through 1545
    Processing sheet with id=AA1, first strand: chain 'A' and resid 682 through 692
      removed outlier: 6.317A  pdb=" N   THR A 683 " --> pdb=" O   SER A 676 " (cutoff:3.500A)
      removed outlier: 7.308A  pdb=" N   SER A 676 " --> pdb=" O   THR A 683 " (cutoff:3.500A)
      removed outlier: 6.909A  pdb=" N   SER A 685 " --> pdb=" O   TYR A 674 " (cutoff:3.500A)
      removed outlier: 6.645A  pdb=" N   TYR A 674 " --> pdb=" O   SER A 685 " (cutoff:3.500A)
      removed outlier: 5.716A  pdb=" N   ILE A 687 " --> pdb=" O   ASN A 672 " (cutoff:3.500A)
      removed outlier: 3.762A  pdb=" N   ILE A 668 " --> pdb=" O   ILE A 691 " (cutoff:3.500A)
      removed outlier: 6.705A  pdb=" N   VAL A 670 " --> pdb=" O   VAL A 725 " (cutoff:3.500A)
      removed outlier: 6.842A  pdb=" N   VAL A 725 " --> pdb=" O   VAL A 670 " (cutoff:3.500A)
      removed outlier: 6.908A  pdb=" N   ASN A 672 " --> pdb=" O   GLY A 723 " (cutoff:3.500A)
      removed outlier: 6.284A  pdb=" N   TYR A 674 " --> pdb=" O   LEU A 721 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 748 through 751
      removed outlier: 6.515A  pdb=" N   VAL A 829 " --> pdb=" O   VAL A 863 " (cutoff:3.500A)
      removed outlier: 7.633A  pdb=" N   VAL A 865 " --> pdb=" O   VAL A 829 " (cutoff:3.500A)
      removed outlier: 7.279A  pdb=" N   LEU A 831 " --> pdb=" O   VAL A 865 " (cutoff:3.500A)
      removed outlier: 6.477A  pdb=" N   THR A 697 " --> pdb=" O   LEU A 864 " (cutoff:3.500A)
      removed outlier: 6.400A  pdb=" N   LEU A 696 " --> pdb=" O   TRP A 877 " (cutoff:3.500A)
      removed outlier: 7.726A  pdb=" N   ILE A 879 " --> pdb=" O   LEU A 696 " (cutoff:3.500A)
      removed outlier: 6.221A  pdb=" N   MET A 698 " --> pdb=" O   ILE A 879 " (cutoff:3.500A)
      removed outlier: 7.575A  pdb=" N   MET A 881 " --> pdb=" O   MET A 698 " (cutoff:3.500A)
      removed outlier: 6.387A  pdb=" N   VAL A 700 " --> pdb=" O   MET A 881 " (cutoff:3.500A)
      removed outlier: 6.783A  pdb=" N   ILE A 878 " --> pdb=" O   GLU A 889 " (cutoff:3.500A)
      removed outlier: 4.471A  pdb=" N   GLU A 889 " --> pdb=" O   ILE A 878 " (cutoff:3.500A)
      removed outlier: 7.096A  pdb=" N   ALA A 880 " --> pdb=" O   LEU A 887 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 1325 through 1332
      removed outlier: 6.822A  pdb=" N   LYS A1326 " --> pdb=" O   CYS A1314 " (cutoff:3.500A)
      removed outlier: 6.619A  pdb=" N   CYS A1314 " --> pdb=" O   LYS A1326 " (cutoff:3.500A)
      removed outlier: 5.808A  pdb=" N   VAL A1328 " --> pdb=" O   ASP A1312 " (cutoff:3.500A)
      removed outlier: 4.125A  pdb=" N   LEU A1313 " --> pdb=" O   ASP A1363 " (cutoff:3.500A)
      removed outlier: 6.796A  pdb=" N   ASP A1363 " --> pdb=" O   LEU A1313 " (cutoff:3.500A)
      removed outlier: 6.900A  pdb=" N   VAL A1315 " --> pdb=" O   ILE A1361 " (cutoff:3.500A)
      removed outlier: 7.085A  pdb=" N   ILE A1361 " --> pdb=" O   VAL A1315 " (cutoff:3.500A)
      removed outlier: 3.582A  pdb=" N   ILE A1371 " --> pdb=" O   ILE A1368 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 1386 through 1388
      removed outlier: 6.789A  pdb=" N   SER A1386 " --> pdb=" O   ILE A1467 " (cutoff:3.500A)
      removed outlier: 7.653A  pdb=" N   ASP A1469 " --> pdb=" O   SER A1386 " (cutoff:3.500A)
      removed outlier: 6.423A  pdb=" N   ILE A1388 " --> pdb=" O   ASP A1469 " (cutoff:3.500A)
      removed outlier: 6.358A  pdb=" N   LEU A1466 " --> pdb=" O   VAL A1497 " (cutoff:3.500A)
      removed outlier: 7.259A  pdb=" N   ILE A1499 " --> pdb=" O   LEU A1466 " (cutoff:3.500A)
      removed outlier: 6.495A  pdb=" N   MET A1468 " --> pdb=" O   ILE A1499 " (cutoff:3.500A)
      removed outlier: 6.731A  pdb=" N   VAL A1338 " --> pdb=" O   THR A1498 " (cutoff:3.500A)
      removed outlier: 6.422A  pdb=" N   LYS A1337 " --> pdb=" O   LEU A1511 " (cutoff:3.500A)
      removed outlier: 7.847A  pdb=" N   ILE A1513 " --> pdb=" O   LYS A1337 " (cutoff:3.500A)
      removed outlier: 6.231A  pdb=" N   GLY A1339 " --> pdb=" O   ILE A1513 " (cutoff:3.500A)
      removed outlier: 7.594A  pdb=" N   MET A1515 " --> pdb=" O   GLY A1339 " (cutoff:3.500A)
      removed outlier: 6.696A  pdb=" N   CYS A1341 " --> pdb=" O   MET A1515 " (cutoff:3.500A)
      removed outlier: 6.865A  pdb=" N   VAL A1512 " --> pdb=" O   TYR A1523 " (cutoff:3.500A)
      removed outlier: 4.485A  pdb=" N   TYR A1523 " --> pdb=" O   VAL A1512 " (cutoff:3.500A)
      removed outlier: 7.056A  pdb=" N   VAL A1514 " --> pdb=" O   LEU A1521 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 1397 through 1398

    616 hydrogen bonds defined for protein.
    1815 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.47

  Time building geometry restraints manager: 1.18 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

  Histogram of bond lengths:
        1.16 -     1.29: 1415
        1.29 -     1.42: 2320
        1.42 -     1.55: 5391
        1.55 -     1.69: 8
        1.69 -     1.82: 74
  Bond restraints: 9208
  Sorted by residual:
  bond pdb=" C13 ETJ A2001 "
       pdb=" C15 ETJ A2001 "
    ideal  model  delta    sigma   weight residual
    1.424  1.286  0.138 2.00e-02 2.50e+03 4.74e+01
  bond pdb=" CAY Y01 A2002 "
       pdb=" OAW Y01 A2002 "
    ideal  model  delta    sigma   weight residual
    1.332  1.461 -0.129 2.00e-02 2.50e+03 4.17e+01
  bond pdb=" CAX Y01 A2002 "
       pdb=" OAH Y01 A2002 "
    ideal  model  delta    sigma   weight residual
    1.248  1.332 -0.084 2.00e-02 2.50e+03 1.77e+01
  bond pdb=" C3  ETJ A2001 "
       pdb=" C6  ETJ A2001 "
    ideal  model  delta    sigma   weight residual
    1.399  1.471 -0.072 2.00e-02 2.50e+03 1.30e+01
  bond pdb=" N   ETJ A2001 "
       pdb=" C7  ETJ A2001 "
    ideal  model  delta    sigma   weight residual
    1.357  1.319  0.038 2.00e-02 2.50e+03 3.66e+00
  ... (remaining 9203 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.78: 12307
        1.78 -     3.55: 166
        3.55 -     5.33: 35
        5.33 -     7.11: 13
        7.11 -     8.88: 4
  Bond angle restraints: 12525
  Sorted by residual:
  angle pdb=" C1' ATP A2006 "
        pdb=" C2' ATP A2006 "
        pdb=" C3' ATP A2006 "
      ideal   model   delta    sigma   weight residual
     101.56  105.39   -3.83 1.19e+00 7.05e-01 1.04e+01
  angle pdb=" C2' ATP A2006 "
        pdb=" C3' ATP A2006 "
        pdb=" C4' ATP A2006 "
      ideal   model   delta    sigma   weight residual
     102.49  105.56   -3.07 1.00e+00 1.00e+00 9.43e+00
  angle pdb=" CAM Y01 A2002 "
        pdb=" CAY Y01 A2002 "
        pdb=" OAW Y01 A2002 "
      ideal   model   delta    sigma   weight residual
     111.19  120.07   -8.88 3.00e+00 1.11e-01 8.77e+00
  angle pdb=" C1' ATP A2006 "
        pdb=" C2' ATP A2006 "
        pdb=" O2' ATP A2006 "
      ideal   model   delta    sigma   weight residual
     110.58  102.82    7.76 2.79e+00 1.28e-01 7.72e+00
  angle pdb=" CAJ Y01 A2002 "
        pdb=" CAO Y01 A2002 "
        pdb=" CBB Y01 A2002 "
      ideal   model   delta    sigma   weight residual
     115.08  106.90    8.18 3.00e+00 1.11e-01 7.44e+00
  ... (remaining 12520 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    27.36: 5366
       27.36 -    54.72: 162
       54.72 -    82.08: 15
       82.08 -   109.45: 2
      109.45 -   136.81: 1
  Dihedral angle restraints: 5546
    sinusoidal: 2214
      harmonic: 3332
  Sorted by residual:
  dihedral pdb=" O2A ADP A2003 "
           pdb=" O3A ADP A2003 "
           pdb=" PA  ADP A2003 "
           pdb=" PB  ADP A2003 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00   76.81 -136.81     1      2.00e+01 2.50e-03 4.15e+01
  dihedral pdb=" O1B ADP A2003 "
           pdb=" O3A ADP A2003 "
           pdb=" PB  ADP A2003 "
           pdb=" PA  ADP A2003 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00   31.44  -91.44     1      2.00e+01 2.50e-03 2.46e+01
  dihedral pdb=" CA  HIS A 278 "
           pdb=" C   HIS A 278 "
           pdb=" N   PRO A 279 "
           pdb=" CA  PRO A 279 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.87   17.13     0      5.00e+00 4.00e-02 1.17e+01
  ... (remaining 5543 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.050: 1255
       0.050 -    0.100: 190
       0.100 -    0.150: 44
       0.150 -    0.200: 4
       0.200 -    0.250: 3
  Chirality restraints: 1496
  Sorted by residual:
  chirality pdb=" C2' ATP A2006 "
            pdb=" C1' ATP A2006 "
            pdb=" C3' ATP A2006 "
            pdb=" O2' ATP A2006 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.68   -2.93    0.25 2.00e-01 2.50e+01 1.57e+00
  chirality pdb=" C3' ATP A2006 "
            pdb=" C2' ATP A2006 "
            pdb=" C4' ATP A2006 "
            pdb=" O3' ATP A2006 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.88    0.25 2.00e-01 2.50e+01 1.50e+00
  chirality pdb=" CBB Y01 A2002 "
            pdb=" CAC Y01 A2002 "
            pdb=" CAO Y01 A2002 "
            pdb=" CBE Y01 A2002 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.58    2.34    0.24 2.00e-01 2.50e+01 1.44e+00
  ... (remaining 1493 not shown)

  Planarity restraints: 1529
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE A 543 "   -0.044 5.00e-02 4.00e+02   6.59e-02 6.95e+00
        pdb=" N   PRO A 544 "    0.114 5.00e-02 4.00e+02
        pdb=" CA  PRO A 544 "   -0.034 5.00e-02 4.00e+02
        pdb=" CD  PRO A 544 "   -0.037 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY A 314 "    0.035 5.00e-02 4.00e+02   5.37e-02 4.62e+00
        pdb=" N   PRO A 315 "   -0.093 5.00e-02 4.00e+02
        pdb=" CA  PRO A 315 "    0.028 5.00e-02 4.00e+02
        pdb=" CD  PRO A 315 "    0.030 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU A 549 "   -0.010 2.00e-02 2.50e+03   2.04e-02 4.15e+00
        pdb=" C   LEU A 549 "    0.035 2.00e-02 2.50e+03
        pdb=" O   LEU A 549 "   -0.013 2.00e-02 2.50e+03
        pdb=" N   ALA A 550 "   -0.012 2.00e-02 2.50e+03
  ... (remaining 1526 not shown)

  Histogram of nonbonded interaction distances:
        1.96 -     2.55: 27
        2.55 -     3.14: 7510
        3.14 -     3.73: 14022
        3.73 -     4.31: 19822
        4.31 -     4.90: 33304
  Nonbonded interactions: 74685
  Sorted by model distance:
  nonbonded pdb=" OE1 GLN A 753 "
            pdb="MG    MG A2004 "
     model   vdw
     1.963 2.170
  nonbonded pdb=" O1B ADP A2003 "
            pdb="MG    MG A2005 "
     model   vdw
     2.075 2.170
  nonbonded pdb=" OG  SER A 708 "
            pdb="MG    MG A2004 "
     model   vdw
     2.196 2.170
  nonbonded pdb=" O2' ATP A2006 "
            pdb=" O3' ATP A2006 "
     model   vdw
     2.333 2.432
  nonbonded pdb=" OH  TYR A 674 "
            pdb=" OD1 ASN A 686 "
     model   vdw
     2.342 3.040
  ... (remaining 74680 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.420
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.010
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.090
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     8.870
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:1.240
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   10.740
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7997
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.138   9208  Z= 0.190
  Angle     :  0.604   8.884  12525  Z= 0.303
  Chirality :  0.041   0.250   1496
  Planarity :  0.004   0.066   1529
  Dihedral  : 13.021 136.807   3388
  Min Nonbonded Distance : 1.963

Molprobity Statistics.
  All-atom Clashscore : 3.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.94 %
    Favored  : 98.06 %
  Rotamer:
    Outliers :  2.19 %
    Allowed  :  4.17 %
    Favored  : 93.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.12 (0.24), residues: 1133
  helix:  0.54 (0.18), residues: 758
  sheet:  0.17 (0.59), residues: 65
  loop : -0.84 (0.34), residues: 310

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A1461 
 TYR   0.016   0.001   TYR A1250 
 PHE   0.011   0.001   PHE A1035 
 TRP   0.006   0.001   TRP A1415 
 HIS   0.005   0.001   HIS A1001 

Details of bonding type rmsd
  covalent geometry    : bond        0.00368 ( 9208)
  covalent geometry    : angle       0.60408 (12525)
  hydrogen bonds       : bond        0.13575 (  616)
  hydrogen bonds       : angle       6.05089 ( 1815)

*********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  2266 Ramachandran restraints generated.
    1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2266 Ramachandran restraints generated.
    1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  201 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 180
  time to evaluate  : 0.284 
Fit side-chains
REVERT: A  387 MET cc_start: 0.8508 (mtp) cc_final: 0.8255 (ttt)
REVERT: A  394 ARG cc_start: 0.8250 (mmm160) cc_final: 0.7481 (mtm110)
REVERT: A  412 ASN cc_start: 0.8184 (t0) cc_final: 0.7971 (t0)
REVERT: A  416 ILE cc_start: 0.8583 (OUTLIER) cc_final: 0.8380 (mt)
REVERT: A  486 THR cc_start: 0.8868 (m) cc_final: 0.7956 (p)
REVERT: A  500 LYS cc_start: 0.8657 (tttp) cc_final: 0.8359 (tttt)
REVERT: A  722 GLU cc_start: 0.7305 (tt0) cc_final: 0.6992 (mt-10)
REVERT: A  724 LYS cc_start: 0.7643 (mptt) cc_final: 0.7110 (mmmt)
REVERT: A  795 PHE cc_start: 0.8568 (m-80) cc_final: 0.8250 (m-80)
REVERT: A  817 CYS cc_start: 0.8226 (t) cc_final: 0.7873 (m)
REVERT: A  842 LEU cc_start: 0.8607 (mp) cc_final: 0.8326 (mt)
REVERT: A  848 GLN cc_start: 0.8115 (tp40) cc_final: 0.7712 (mm-40)
REVERT: A  888 ARG cc_start: 0.8041 (tpt170) cc_final: 0.7814 (tpt90)
REVERT: A  976 LYS cc_start: 0.7797 (mttp) cc_final: 0.7460 (tptp)
REVERT: A 1309 LYS cc_start: 0.8074 (mttt) cc_final: 0.7452 (mptt)
REVERT: A 1358 MET cc_start: 0.8643 (mmm) cc_final: 0.8151 (mmm)
REVERT: A 1430 LEU cc_start: 0.8961 (OUTLIER) cc_final: 0.8682 (mt)
REVERT: A 1468 MET cc_start: 0.8646 (mtm) cc_final: 0.8224 (mtp)
REVERT: A 1520 ILE cc_start: 0.8941 (mt) cc_final: 0.8714 (mt)
  outliers start: 21
  outliers final: 8
  residues processed: 198
  average time/residue: 0.1345
  time to fit residues: 34.2545
Evaluate side-chains
  115 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 105
  time to evaluate  : 0.209 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  381 ARG
Chi-restraints excluded: chain A residue  416 ILE
Chi-restraints excluded: chain A residue  428 CYS
Chi-restraints excluded: chain A residue  508 GLU
Chi-restraints excluded: chain A residue  543 ILE
Chi-restraints excluded: chain A residue  593 VAL
Chi-restraints excluded: chain A residue 1270 VAL
Chi-restraints excluded: chain A residue 1406 GLU
Chi-restraints excluded: chain A residue 1430 LEU
Chi-restraints excluded: chain A residue 1446 SER
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 108 optimal weight:    0.9990
   chunk 49 optimal weight:    0.9980
   chunk 97 optimal weight:    1.9990
   chunk 113 optimal weight:    0.5980
   chunk 53 optimal weight:    0.7980
   chunk 5 optimal weight:    2.9990
   chunk 33 optimal weight:    0.7980
   chunk 65 optimal weight:    2.9990
   chunk 62 optimal weight:    3.9990
   chunk 51 optimal weight:    4.9990
   chunk 100 optimal weight:    2.9990
   overall best weight:    0.8382

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A 326 ASN
A 841 HIS
A1259 ASN
A1379 HIS
A1444 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3775 r_free = 0.3775 target = 0.152813 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3431 r_free = 0.3431 target = 0.121759 restraints weight = 10384.546|
|-----------------------------------------------------------------------------|
r_work (start): 0.3391 rms_B_bonded: 1.85
r_work: 0.3257 rms_B_bonded: 2.58 restraints_weight: 0.5000
r_work: 0.3109 rms_B_bonded: 4.33 restraints_weight: 0.2500
r_work (final): 0.3109
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7986
moved from start:          0.1979

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   9208  Z= 0.147
  Angle     :  0.544   6.768  12525  Z= 0.273
  Chirality :  0.041   0.196   1496
  Planarity :  0.004   0.055   1529
  Dihedral  :  9.515 129.050   1384
  Min Nonbonded Distance : 1.959

Molprobity Statistics.
  All-atom Clashscore : 5.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.59 %
    Favored  : 98.41 %
  Rotamer:
    Outliers :  2.09 %
    Allowed  : 11.37 %
    Favored  : 86.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.83 (0.25), residues: 1133
  helix:  1.86 (0.19), residues: 753
  sheet:  0.53 (0.62), residues: 65
  loop : -0.14 (0.35), residues: 315

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 774 
 TYR   0.012   0.001   TYR A1523 
 PHE   0.014   0.001   PHE A1142 
 TRP   0.008   0.001   TRP A1055 
 HIS   0.009   0.001   HIS A1504 

Details of bonding type rmsd
  covalent geometry    : bond        0.00329 ( 9208)
  covalent geometry    : angle       0.54427 (12525)
  hydrogen bonds       : bond        0.05355 (  616)
  hydrogen bonds       : angle       4.30700 ( 1815)

*********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  2266 Ramachandran restraints generated.
    1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2266 Ramachandran restraints generated.
    1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  143 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 123
  time to evaluate  : 0.350 
Fit side-chains
REVERT: A  273 LYS cc_start: 0.7517 (mtpp) cc_final: 0.7278 (ttpp)
REVERT: A  447 ASN cc_start: 0.8311 (m110) cc_final: 0.7975 (t0)
REVERT: A  486 THR cc_start: 0.8732 (m) cc_final: 0.7887 (p)
REVERT: A  573 SER cc_start: 0.8374 (t) cc_final: 0.7990 (m)
REVERT: A  722 GLU cc_start: 0.7230 (tt0) cc_final: 0.6965 (mt-10)
REVERT: A  724 LYS cc_start: 0.7938 (mptt) cc_final: 0.7341 (mtpp)
REVERT: A  764 GLU cc_start: 0.8197 (mm-30) cc_final: 0.7592 (mt-10)
REVERT: A  795 PHE cc_start: 0.8579 (m-80) cc_final: 0.8293 (m-80)
REVERT: A  817 CYS cc_start: 0.8398 (t) cc_final: 0.7934 (m)
REVERT: A  847 MET cc_start: 0.8574 (tpp) cc_final: 0.8210 (tpt)
REVERT: A  910 MET cc_start: 0.7342 (mtp) cc_final: 0.7109 (mtp)
REVERT: A  976 LYS cc_start: 0.7653 (mttp) cc_final: 0.7375 (tptp)
REVERT: A 1158 GLU cc_start: 0.7630 (mt-10) cc_final: 0.7074 (tp30)
REVERT: A 1309 LYS cc_start: 0.8063 (mttt) cc_final: 0.7133 (mppt)
REVERT: A 1358 MET cc_start: 0.8755 (mmm) cc_final: 0.8389 (mtp)
REVERT: A 1468 MET cc_start: 0.8730 (mtm) cc_final: 0.8436 (mtp)
  outliers start: 20
  outliers final: 13
  residues processed: 139
  average time/residue: 0.1126
  time to fit residues: 21.1877
Evaluate side-chains
  120 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 107
  time to evaluate  : 0.356 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  326 ASN
Chi-restraints excluded: chain A residue  381 ARG
Chi-restraints excluded: chain A residue  508 GLU
Chi-restraints excluded: chain A residue  543 ILE
Chi-restraints excluded: chain A residue  580 THR
Chi-restraints excluded: chain A residue  593 VAL
Chi-restraints excluded: chain A residue  781 THR
Chi-restraints excluded: chain A residue  836 SER
Chi-restraints excluded: chain A residue  993 MET
Chi-restraints excluded: chain A residue 1140 VAL
Chi-restraints excluded: chain A residue 1277 LYS
Chi-restraints excluded: chain A residue 1379 HIS
Chi-restraints excluded: chain A residue 1446 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 72 optimal weight:    0.5980
   chunk 39 optimal weight:    0.9980
   chunk 10 optimal weight:    3.9990
   chunk 14 optimal weight:    2.9990
   chunk 13 optimal weight:    0.9980
   chunk 9 optimal weight:    0.9990
   chunk 31 optimal weight:    0.9980
   chunk 88 optimal weight:    4.9990
   chunk 54 optimal weight:    0.6980
   chunk 56 optimal weight:    8.9990
   chunk 8 optimal weight:    0.7980
   overall best weight:    0.8180

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A 260 ASN
A 326 ASN
A 841 HIS
A1259 ASN
A1379 HIS
A1402 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3767 r_free = 0.3767 target = 0.152076 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3423 r_free = 0.3423 target = 0.121012 restraints weight = 10337.863|
|-----------------------------------------------------------------------------|
r_work (start): 0.3381 rms_B_bonded: 1.86
r_work: 0.3249 rms_B_bonded: 2.58 restraints_weight: 0.5000
r_work: 0.3100 rms_B_bonded: 4.34 restraints_weight: 0.2500
r_work (final): 0.3100
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7995
moved from start:          0.2459

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   9208  Z= 0.138
  Angle     :  0.521   6.631  12525  Z= 0.259
  Chirality :  0.040   0.200   1496
  Planarity :  0.004   0.053   1529
  Dihedral  :  9.010 132.560   1375
  Min Nonbonded Distance : 1.954

Molprobity Statistics.
  All-atom Clashscore : 5.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.59 %
    Favored  : 98.41 %
  Rotamer:
    Outliers :  2.09 %
    Allowed  : 13.14 %
    Favored  : 84.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.19 (0.25), residues: 1133
  helix:  2.15 (0.19), residues: 758
  sheet:  0.56 (0.63), residues: 65
  loop : -0.07 (0.35), residues: 310

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 888 
 TYR   0.008   0.001   TYR A1250 
 PHE   0.012   0.001   PHE A1149 
 TRP   0.005   0.001   TRP A 677 
 HIS   0.015   0.001   HIS A1379 

Details of bonding type rmsd
  covalent geometry    : bond        0.00314 ( 9208)
  covalent geometry    : angle       0.52085 (12525)
  hydrogen bonds       : bond        0.05061 (  616)
  hydrogen bonds       : angle       4.11689 ( 1815)

*********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  2266 Ramachandran restraints generated.
    1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2266 Ramachandran restraints generated.
    1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 109
  time to evaluate  : 0.354 
Fit side-chains
REVERT: A  273 LYS cc_start: 0.7727 (mtpp) cc_final: 0.7450 (ttpp)
REVERT: A  412 ASN cc_start: 0.8169 (t0) cc_final: 0.7895 (t0)
REVERT: A  447 ASN cc_start: 0.8411 (m110) cc_final: 0.8109 (t0)
REVERT: A  724 LYS cc_start: 0.8024 (mptt) cc_final: 0.7451 (mtpp)
REVERT: A  764 GLU cc_start: 0.8107 (mm-30) cc_final: 0.7500 (mt-10)
REVERT: A  795 PHE cc_start: 0.8546 (m-80) cc_final: 0.8270 (m-80)
REVERT: A  817 CYS cc_start: 0.8537 (t) cc_final: 0.8119 (m)
REVERT: A  847 MET cc_start: 0.8545 (tpp) cc_final: 0.8198 (tpt)
REVERT: A  848 GLN cc_start: 0.8124 (tp40) cc_final: 0.7621 (mm-40)
REVERT: A  888 ARG cc_start: 0.7922 (tpt90) cc_final: 0.7704 (ttm-80)
REVERT: A  898 LYS cc_start: 0.8167 (mmtp) cc_final: 0.7757 (mmtm)
REVERT: A  910 MET cc_start: 0.7193 (mtp) cc_final: 0.6718 (mtp)
REVERT: A  976 LYS cc_start: 0.7658 (mttp) cc_final: 0.7393 (tptp)
REVERT: A 1158 GLU cc_start: 0.7591 (mt-10) cc_final: 0.7279 (tp30)
REVERT: A 1254 ILE cc_start: 0.8754 (mt) cc_final: 0.8398 (tp)
REVERT: A 1309 LYS cc_start: 0.7981 (mttt) cc_final: 0.7015 (mppt)
REVERT: A 1311 HIS cc_start: 0.6973 (m90) cc_final: 0.6699 (m170)
REVERT: A 1358 MET cc_start: 0.8789 (mmm) cc_final: 0.8381 (mtp)
REVERT: A 1468 MET cc_start: 0.8810 (mtm) cc_final: 0.8401 (mtp)
  outliers start: 20
  outliers final: 16
  residues processed: 122
  average time/residue: 0.1178
  time to fit residues: 19.3794
Evaluate side-chains
  117 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 101
  time to evaluate  : 0.338 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  375 GLU
Chi-restraints excluded: chain A residue  381 ARG
Chi-restraints excluded: chain A residue  434 MET
Chi-restraints excluded: chain A residue  508 GLU
Chi-restraints excluded: chain A residue  543 ILE
Chi-restraints excluded: chain A residue  580 THR
Chi-restraints excluded: chain A residue  586 SER
Chi-restraints excluded: chain A residue  781 THR
Chi-restraints excluded: chain A residue  836 SER
Chi-restraints excluded: chain A residue  993 MET
Chi-restraints excluded: chain A residue 1140 VAL
Chi-restraints excluded: chain A residue 1227 VAL
Chi-restraints excluded: chain A residue 1259 ASN
Chi-restraints excluded: chain A residue 1277 LYS
Chi-restraints excluded: chain A residue 1379 HIS
Chi-restraints excluded: chain A residue 1463 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 89 optimal weight:    4.9990
   chunk 72 optimal weight:    0.9990
   chunk 85 optimal weight:    1.9990
   chunk 25 optimal weight:    1.9990
   chunk 59 optimal weight:    4.9990
   chunk 45 optimal weight:    4.9990
   chunk 8 optimal weight:    5.9990
   chunk 60 optimal weight:    0.7980
   chunk 58 optimal weight:    3.9990
   chunk 46 optimal weight:    1.9990
   chunk 4 optimal weight:    0.8980
   overall best weight:    1.3386

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A 841 HIS
A1259 ASN
A1379 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3754 r_free = 0.3754 target = 0.150935 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3386 r_free = 0.3386 target = 0.118459 restraints weight = 10544.785|
|-----------------------------------------------------------------------------|
r_work (start): 0.3338 rms_B_bonded: 1.94
r_work: 0.3201 rms_B_bonded: 2.67 restraints_weight: 0.5000
r_work: 0.3048 rms_B_bonded: 4.48 restraints_weight: 0.2500
r_work (final): 0.3048
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8041
moved from start:          0.2699

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.051   9208  Z= 0.175
  Angle     :  0.549   7.592  12525  Z= 0.270
  Chirality :  0.041   0.205   1496
  Planarity :  0.004   0.051   1529
  Dihedral  :  8.978 138.075   1373
  Min Nonbonded Distance : 1.910

Molprobity Statistics.
  All-atom Clashscore : 5.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.59 %
    Favored  : 98.41 %
  Rotamer:
    Outliers :  2.82 %
    Allowed  : 13.03 %
    Favored  : 84.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.15 (0.25), residues: 1133
  helix:  2.13 (0.19), residues: 756
  sheet:  0.70 (0.67), residues: 59
  loop : -0.12 (0.34), residues: 318

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 820 
 TYR   0.016   0.001   TYR A1250 
 PHE   0.013   0.001   PHE A1362 
 TRP   0.006   0.001   TRP A 727 
 HIS   0.008   0.001   HIS A1379 

Details of bonding type rmsd
  covalent geometry    : bond        0.00420 ( 9208)
  covalent geometry    : angle       0.54940 (12525)
  hydrogen bonds       : bond        0.05355 (  616)
  hydrogen bonds       : angle       4.12398 ( 1815)

*********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  2266 Ramachandran restraints generated.
    1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2266 Ramachandran restraints generated.
    1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 105
  time to evaluate  : 0.376 
Fit side-chains
REVERT: A  273 LYS cc_start: 0.7756 (mtpp) cc_final: 0.7479 (ttpp)
REVERT: A  412 ASN cc_start: 0.8206 (t0) cc_final: 0.7948 (t0)
REVERT: A  447 ASN cc_start: 0.8350 (m110) cc_final: 0.8135 (t0)
REVERT: A  591 PHE cc_start: 0.8854 (m-80) cc_final: 0.8502 (m-10)
REVERT: A  690 ARG cc_start: 0.8115 (ptt-90) cc_final: 0.7664 (ptm160)
REVERT: A  724 LYS cc_start: 0.8080 (mptt) cc_final: 0.7363 (mtpp)
REVERT: A  795 PHE cc_start: 0.8590 (m-80) cc_final: 0.8122 (m-80)
REVERT: A  797 ASP cc_start: 0.8011 (t70) cc_final: 0.7612 (t0)
REVERT: A  817 CYS cc_start: 0.8517 (t) cc_final: 0.8091 (m)
REVERT: A  888 ARG cc_start: 0.7971 (tpt90) cc_final: 0.7640 (ttm-80)
REVERT: A  898 LYS cc_start: 0.8123 (mmtp) cc_final: 0.7753 (mmtm)
REVERT: A  910 MET cc_start: 0.7281 (mtp) cc_final: 0.6805 (mtp)
REVERT: A  976 LYS cc_start: 0.7626 (mttp) cc_final: 0.7377 (tptp)
REVERT: A 1158 GLU cc_start: 0.7533 (mt-10) cc_final: 0.7305 (tp30)
REVERT: A 1161 ASP cc_start: 0.7634 (m-30) cc_final: 0.7332 (m-30)
REVERT: A 1254 ILE cc_start: 0.8794 (mt) cc_final: 0.8467 (tp)
REVERT: A 1309 LYS cc_start: 0.8092 (mttt) cc_final: 0.6999 (mptt)
REVERT: A 1358 MET cc_start: 0.8725 (mmm) cc_final: 0.8512 (mtp)
REVERT: A 1416 GLU cc_start: 0.7808 (tp30) cc_final: 0.7604 (tp30)
REVERT: A 1468 MET cc_start: 0.8809 (mtm) cc_final: 0.8405 (mtp)
  outliers start: 27
  outliers final: 22
  residues processed: 124
  average time/residue: 0.1205
  time to fit residues: 20.1873
Evaluate side-chains
  119 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 97
  time to evaluate  : 0.352 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  375 GLU
Chi-restraints excluded: chain A residue  381 ARG
Chi-restraints excluded: chain A residue  405 MET
Chi-restraints excluded: chain A residue  434 MET
Chi-restraints excluded: chain A residue  508 GLU
Chi-restraints excluded: chain A residue  514 SER
Chi-restraints excluded: chain A residue  534 SER
Chi-restraints excluded: chain A residue  543 ILE
Chi-restraints excluded: chain A residue  580 THR
Chi-restraints excluded: chain A residue  586 SER
Chi-restraints excluded: chain A residue  781 THR
Chi-restraints excluded: chain A residue  799 THR
Chi-restraints excluded: chain A residue  836 SER
Chi-restraints excluded: chain A residue  983 THR
Chi-restraints excluded: chain A residue  993 MET
Chi-restraints excluded: chain A residue 1140 VAL
Chi-restraints excluded: chain A residue 1227 VAL
Chi-restraints excluded: chain A residue 1277 LYS
Chi-restraints excluded: chain A residue 1379 HIS
Chi-restraints excluded: chain A residue 1437 THR
Chi-restraints excluded: chain A residue 1463 SER
Chi-restraints excluded: chain A residue 1536 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 83 optimal weight:    2.9990
   chunk 108 optimal weight:    0.7980
   chunk 59 optimal weight:    0.8980
   chunk 54 optimal weight:    1.9990
   chunk 74 optimal weight:    0.7980
   chunk 27 optimal weight:    2.9990
   chunk 67 optimal weight:    0.7980
   chunk 105 optimal weight:    1.9990
   chunk 90 optimal weight:    0.8980
   chunk 49 optimal weight:    2.9990
   chunk 95 optimal weight:    1.9990
   overall best weight:    0.8380

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A 841 HIS
A1379 HIS
A1451 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3751 r_free = 0.3751 target = 0.150857 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3401 r_free = 0.3401 target = 0.119629 restraints weight = 10548.135|
|-----------------------------------------------------------------------------|
r_work (start): 0.3362 rms_B_bonded: 1.88
r_work: 0.3226 rms_B_bonded: 2.62 restraints_weight: 0.5000
r_work: 0.3079 rms_B_bonded: 4.39 restraints_weight: 0.2500
r_work (final): 0.3079
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8019
moved from start:          0.2930

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   9208  Z= 0.135
  Angle     :  0.509   6.704  12525  Z= 0.252
  Chirality :  0.040   0.202   1496
  Planarity :  0.004   0.048   1529
  Dihedral  :  8.720 141.556   1373
  Min Nonbonded Distance : 1.949

Molprobity Statistics.
  All-atom Clashscore : 6.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.41 %
    Favored  : 98.59 %
  Rotamer:
    Outliers :  2.50 %
    Allowed  : 14.49 %
    Favored  : 83.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.33 (0.25), residues: 1133
  helix:  2.28 (0.19), residues: 758
  sheet:  0.84 (0.69), residues: 59
  loop : -0.13 (0.34), residues: 316

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 888 
 TYR   0.010   0.001   TYR A 532 
 PHE   0.010   0.001   PHE A1149 
 TRP   0.006   0.001   TRP A1260 
 HIS   0.009   0.001   HIS A1379 

Details of bonding type rmsd
  covalent geometry    : bond        0.00308 ( 9208)
  covalent geometry    : angle       0.50893 (12525)
  hydrogen bonds       : bond        0.04926 (  616)
  hydrogen bonds       : angle       4.00040 ( 1815)

*********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  2266 Ramachandran restraints generated.
    1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2266 Ramachandran restraints generated.
    1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 111
  time to evaluate  : 0.366 
Fit side-chains
REVERT: A  273 LYS cc_start: 0.7802 (mtpp) cc_final: 0.7538 (ttpp)
REVERT: A  591 PHE cc_start: 0.8826 (m-80) cc_final: 0.8492 (m-10)
REVERT: A  690 ARG cc_start: 0.8048 (ptt-90) cc_final: 0.7587 (ptm160)
REVERT: A  724 LYS cc_start: 0.8071 (mptt) cc_final: 0.7387 (mtpp)
REVERT: A  795 PHE cc_start: 0.8548 (m-80) cc_final: 0.8278 (m-80)
REVERT: A  797 ASP cc_start: 0.8097 (t70) cc_final: 0.7700 (t0)
REVERT: A  817 CYS cc_start: 0.8576 (t) cc_final: 0.8200 (m)
REVERT: A  888 ARG cc_start: 0.7952 (tpt90) cc_final: 0.7694 (ttm-80)
REVERT: A  889 GLU cc_start: 0.7534 (OUTLIER) cc_final: 0.7026 (tt0)
REVERT: A  898 LYS cc_start: 0.8253 (mmtp) cc_final: 0.7867 (mmtm)
REVERT: A  910 MET cc_start: 0.7302 (mtp) cc_final: 0.6830 (mtp)
REVERT: A  976 LYS cc_start: 0.7641 (mttp) cc_final: 0.7384 (tptp)
REVERT: A 1254 ILE cc_start: 0.8786 (mt) cc_final: 0.8468 (tp)
REVERT: A 1309 LYS cc_start: 0.8121 (mttt) cc_final: 0.7023 (mptt)
REVERT: A 1358 MET cc_start: 0.8715 (mmm) cc_final: 0.8438 (mtp)
REVERT: A 1468 MET cc_start: 0.8828 (mtm) cc_final: 0.8392 (mtp)
  outliers start: 24
  outliers final: 19
  residues processed: 126
  average time/residue: 0.1228
  time to fit residues: 20.6300
Evaluate side-chains
  119 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 99
  time to evaluate  : 0.346 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  375 GLU
Chi-restraints excluded: chain A residue  381 ARG
Chi-restraints excluded: chain A residue  434 MET
Chi-restraints excluded: chain A residue  508 GLU
Chi-restraints excluded: chain A residue  534 SER
Chi-restraints excluded: chain A residue  543 ILE
Chi-restraints excluded: chain A residue  580 THR
Chi-restraints excluded: chain A residue  586 SER
Chi-restraints excluded: chain A residue  781 THR
Chi-restraints excluded: chain A residue  799 THR
Chi-restraints excluded: chain A residue  836 SER
Chi-restraints excluded: chain A residue  889 GLU
Chi-restraints excluded: chain A residue  987 PHE
Chi-restraints excluded: chain A residue  993 MET
Chi-restraints excluded: chain A residue 1140 VAL
Chi-restraints excluded: chain A residue 1227 VAL
Chi-restraints excluded: chain A residue 1277 LYS
Chi-restraints excluded: chain A residue 1379 HIS
Chi-restraints excluded: chain A residue 1463 SER
Chi-restraints excluded: chain A residue 1536 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 12 optimal weight:    1.9990
   chunk 52 optimal weight:    0.3980
   chunk 50 optimal weight:    0.6980
   chunk 87 optimal weight:    1.9990
   chunk 96 optimal weight:   10.0000
   chunk 72 optimal weight:    4.9990
   chunk 6 optimal weight:    0.7980
   chunk 41 optimal weight:    1.9990
   chunk 99 optimal weight:    1.9990
   chunk 101 optimal weight:    0.8980
   chunk 40 optimal weight:    0.8980
   overall best weight:    0.7380

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A 447 ASN
A 841 HIS
A1259 ASN
A1379 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3750 r_free = 0.3750 target = 0.150814 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3405 r_free = 0.3405 target = 0.120061 restraints weight = 10610.661|
|-----------------------------------------------------------------------------|
r_work (start): 0.3367 rms_B_bonded: 1.88
r_work: 0.3229 rms_B_bonded: 2.63 restraints_weight: 0.5000
r_work: 0.3081 rms_B_bonded: 4.41 restraints_weight: 0.2500
r_work (final): 0.3081
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8012
moved from start:          0.3113

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   9208  Z= 0.128
  Angle     :  0.502   6.581  12525  Z= 0.248
  Chirality :  0.039   0.197   1496
  Planarity :  0.004   0.048   1529
  Dihedral  :  8.559 144.728   1373
  Min Nonbonded Distance : 1.955

Molprobity Statistics.
  All-atom Clashscore : 6.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.41 %
    Favored  : 98.59 %
  Rotamer:
    Outliers :  3.02 %
    Allowed  : 14.08 %
    Favored  : 82.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.44 (0.25), residues: 1133
  helix:  2.40 (0.19), residues: 758
  sheet:  0.80 (0.68), residues: 59
  loop : -0.15 (0.34), residues: 316

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 774 
 TYR   0.014   0.001   TYR A1250 
 PHE   0.009   0.001   PHE A1149 
 TRP   0.004   0.001   TRP A1055 
 HIS   0.008   0.001   HIS A1504 

Details of bonding type rmsd
  covalent geometry    : bond        0.00290 ( 9208)
  covalent geometry    : angle       0.50235 (12525)
  hydrogen bonds       : bond        0.04766 (  616)
  hydrogen bonds       : angle       3.92663 ( 1815)

*********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  2266 Ramachandran restraints generated.
    1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2266 Ramachandran restraints generated.
    1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 101
  time to evaluate  : 0.363 
Fit side-chains
REVERT: A  273 LYS cc_start: 0.7767 (mtpp) cc_final: 0.7525 (ttpp)
REVERT: A  387 MET cc_start: 0.8645 (ttt) cc_final: 0.8369 (mtp)
REVERT: A  690 ARG cc_start: 0.8022 (ptt-90) cc_final: 0.7617 (ptm160)
REVERT: A  724 LYS cc_start: 0.8001 (mptt) cc_final: 0.7392 (mtpp)
REVERT: A  795 PHE cc_start: 0.8522 (m-80) cc_final: 0.8269 (m-80)
REVERT: A  797 ASP cc_start: 0.8092 (t70) cc_final: 0.7700 (t0)
REVERT: A  817 CYS cc_start: 0.8504 (t) cc_final: 0.8255 (m)
REVERT: A  888 ARG cc_start: 0.8010 (tpt90) cc_final: 0.7807 (ttm-80)
REVERT: A  889 GLU cc_start: 0.7522 (OUTLIER) cc_final: 0.7031 (tt0)
REVERT: A  898 LYS cc_start: 0.8252 (mmtp) cc_final: 0.7855 (mmtm)
REVERT: A  976 LYS cc_start: 0.7662 (mttp) cc_final: 0.7397 (tptp)
REVERT: A 1073 ILE cc_start: 0.8700 (tt) cc_final: 0.8332 (tt)
REVERT: A 1254 ILE cc_start: 0.8849 (mt) cc_final: 0.8587 (tp)
REVERT: A 1309 LYS cc_start: 0.8133 (mttt) cc_final: 0.7040 (mptt)
REVERT: A 1358 MET cc_start: 0.8706 (mmm) cc_final: 0.8391 (mtp)
REVERT: A 1416 GLU cc_start: 0.7795 (tp30) cc_final: 0.7500 (tt0)
REVERT: A 1468 MET cc_start: 0.8791 (mtm) cc_final: 0.8326 (mtp)
  outliers start: 29
  outliers final: 26
  residues processed: 121
  average time/residue: 0.1203
  time to fit residues: 19.5880
Evaluate side-chains
  126 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 99
  time to evaluate  : 0.349 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  284 SER
Chi-restraints excluded: chain A residue  375 GLU
Chi-restraints excluded: chain A residue  381 ARG
Chi-restraints excluded: chain A residue  434 MET
Chi-restraints excluded: chain A residue  508 GLU
Chi-restraints excluded: chain A residue  534 SER
Chi-restraints excluded: chain A residue  543 ILE
Chi-restraints excluded: chain A residue  563 LEU
Chi-restraints excluded: chain A residue  580 THR
Chi-restraints excluded: chain A residue  586 SER
Chi-restraints excluded: chain A residue  593 VAL
Chi-restraints excluded: chain A residue  781 THR
Chi-restraints excluded: chain A residue  799 THR
Chi-restraints excluded: chain A residue  836 SER
Chi-restraints excluded: chain A residue  842 LEU
Chi-restraints excluded: chain A residue  889 GLU
Chi-restraints excluded: chain A residue  987 PHE
Chi-restraints excluded: chain A residue  993 MET
Chi-restraints excluded: chain A residue 1005 VAL
Chi-restraints excluded: chain A residue 1140 VAL
Chi-restraints excluded: chain A residue 1227 VAL
Chi-restraints excluded: chain A residue 1259 ASN
Chi-restraints excluded: chain A residue 1275 VAL
Chi-restraints excluded: chain A residue 1277 LYS
Chi-restraints excluded: chain A residue 1321 LEU
Chi-restraints excluded: chain A residue 1463 SER
Chi-restraints excluded: chain A residue 1536 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 86 optimal weight:    2.9990
   chunk 71 optimal weight:    0.6980
   chunk 51 optimal weight:    0.9980
   chunk 62 optimal weight:    0.9980
   chunk 88 optimal weight:    4.9990
   chunk 43 optimal weight:    2.9990
   chunk 12 optimal weight:    1.9990
   chunk 61 optimal weight:    0.9980
   chunk 108 optimal weight:    2.9990
   chunk 22 optimal weight:    0.8980
   chunk 27 optimal weight:    2.9990
   overall best weight:    0.9180

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A 841 HIS
A1259 ASN
A1379 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3754 r_free = 0.3754 target = 0.150979 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3408 r_free = 0.3408 target = 0.120291 restraints weight = 10695.620|
|-----------------------------------------------------------------------------|
r_work (start): 0.3383 rms_B_bonded: 1.88
r_work: 0.3243 rms_B_bonded: 2.65 restraints_weight: 0.5000
r_work: 0.3095 rms_B_bonded: 4.44 restraints_weight: 0.2500
r_work (final): 0.3095
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8018
moved from start:          0.3188

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   9208  Z= 0.139
  Angle     :  0.516   7.345  12525  Z= 0.254
  Chirality :  0.040   0.194   1496
  Planarity :  0.004   0.047   1529
  Dihedral  :  8.539 151.594   1373
  Min Nonbonded Distance : 1.937

Molprobity Statistics.
  All-atom Clashscore : 6.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.15 %
    Favored  : 98.85 %
  Rotamer:
    Outliers :  3.23 %
    Allowed  : 14.29 %
    Favored  : 82.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.42 (0.25), residues: 1133
  helix:  2.39 (0.19), residues: 760
  sheet:  0.64 (0.67), residues: 59
  loop : -0.17 (0.34), residues: 314

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 774 
 TYR   0.013   0.001   TYR A1250 
 PHE   0.008   0.001   PHE A 469 
 TRP   0.006   0.001   TRP A1260 
 HIS   0.008   0.001   HIS A1504 

Details of bonding type rmsd
  covalent geometry    : bond        0.00324 ( 9208)
  covalent geometry    : angle       0.51589 (12525)
  hydrogen bonds       : bond        0.04862 (  616)
  hydrogen bonds       : angle       3.92696 ( 1815)

*********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  2266 Ramachandran restraints generated.
    1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2266 Ramachandran restraints generated.
    1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 104
  time to evaluate  : 0.320 
Fit side-chains
REVERT: A  273 LYS cc_start: 0.7812 (mtpp) cc_final: 0.7561 (ttpp)
REVERT: A  387 MET cc_start: 0.8660 (OUTLIER) cc_final: 0.8342 (mtt)
REVERT: A  591 PHE cc_start: 0.8843 (m-80) cc_final: 0.8527 (m-10)
REVERT: A  690 ARG cc_start: 0.8025 (ptt-90) cc_final: 0.7608 (ptm160)
REVERT: A  724 LYS cc_start: 0.8130 (mptt) cc_final: 0.7517 (mtpp)
REVERT: A  795 PHE cc_start: 0.8520 (m-80) cc_final: 0.8238 (m-80)
REVERT: A  797 ASP cc_start: 0.8119 (t70) cc_final: 0.7750 (t0)
REVERT: A  817 CYS cc_start: 0.8527 (t) cc_final: 0.8273 (m)
REVERT: A  888 ARG cc_start: 0.8018 (tpt90) cc_final: 0.7803 (ttm-80)
REVERT: A  889 GLU cc_start: 0.7502 (OUTLIER) cc_final: 0.7011 (tt0)
REVERT: A  898 LYS cc_start: 0.8226 (mmtp) cc_final: 0.7837 (mmtm)
REVERT: A  910 MET cc_start: 0.7225 (mtp) cc_final: 0.6941 (mtp)
REVERT: A  976 LYS cc_start: 0.7705 (mttp) cc_final: 0.7430 (tptp)
REVERT: A 1073 ILE cc_start: 0.8709 (tt) cc_final: 0.8325 (tt)
REVERT: A 1161 ASP cc_start: 0.7671 (m-30) cc_final: 0.7418 (m-30)
REVERT: A 1254 ILE cc_start: 0.8793 (mt) cc_final: 0.8463 (tp)
REVERT: A 1309 LYS cc_start: 0.8147 (mttt) cc_final: 0.7242 (mptt)
REVERT: A 1358 MET cc_start: 0.8708 (mmm) cc_final: 0.8386 (mtp)
REVERT: A 1416 GLU cc_start: 0.7791 (tp30) cc_final: 0.7491 (tt0)
REVERT: A 1468 MET cc_start: 0.8787 (mtm) cc_final: 0.8312 (mtp)
REVERT: A 1517 ARG cc_start: 0.8503 (mtp85) cc_final: 0.8288 (mtp85)
  outliers start: 31
  outliers final: 28
  residues processed: 124
  average time/residue: 0.1158
  time to fit residues: 19.3283
Evaluate side-chains
  131 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 101
  time to evaluate  : 0.344 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  284 SER
Chi-restraints excluded: chain A residue  375 GLU
Chi-restraints excluded: chain A residue  381 ARG
Chi-restraints excluded: chain A residue  387 MET
Chi-restraints excluded: chain A residue  405 MET
Chi-restraints excluded: chain A residue  434 MET
Chi-restraints excluded: chain A residue  508 GLU
Chi-restraints excluded: chain A residue  534 SER
Chi-restraints excluded: chain A residue  543 ILE
Chi-restraints excluded: chain A residue  563 LEU
Chi-restraints excluded: chain A residue  580 THR
Chi-restraints excluded: chain A residue  593 VAL
Chi-restraints excluded: chain A residue  781 THR
Chi-restraints excluded: chain A residue  799 THR
Chi-restraints excluded: chain A residue  836 SER
Chi-restraints excluded: chain A residue  842 LEU
Chi-restraints excluded: chain A residue  889 GLU
Chi-restraints excluded: chain A residue  987 PHE
Chi-restraints excluded: chain A residue  993 MET
Chi-restraints excluded: chain A residue 1005 VAL
Chi-restraints excluded: chain A residue 1140 VAL
Chi-restraints excluded: chain A residue 1227 VAL
Chi-restraints excluded: chain A residue 1255 THR
Chi-restraints excluded: chain A residue 1259 ASN
Chi-restraints excluded: chain A residue 1275 VAL
Chi-restraints excluded: chain A residue 1277 LYS
Chi-restraints excluded: chain A residue 1321 LEU
Chi-restraints excluded: chain A residue 1379 HIS
Chi-restraints excluded: chain A residue 1463 SER
Chi-restraints excluded: chain A residue 1536 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 113 optimal weight:    6.9990
   chunk 44 optimal weight:    1.9990
   chunk 3 optimal weight:    0.6980
   chunk 14 optimal weight:    3.9990
   chunk 2 optimal weight:    1.9990
   chunk 30 optimal weight:    0.9980
   chunk 97 optimal weight:    0.7980
   chunk 96 optimal weight:    6.9990
   chunk 60 optimal weight:    2.9990
   chunk 80 optimal weight:    2.9990
   chunk 69 optimal weight:    0.6980
   overall best weight:    1.0382

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A 841 HIS
A1259 ASN
A1379 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3736 r_free = 0.3736 target = 0.149576 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3386 r_free = 0.3386 target = 0.118741 restraints weight = 10648.400|
|-----------------------------------------------------------------------------|
r_work (start): 0.3347 rms_B_bonded: 1.89
r_work: 0.3210 rms_B_bonded: 2.63 restraints_weight: 0.5000
r_work: 0.3061 rms_B_bonded: 4.41 restraints_weight: 0.2500
r_work (final): 0.3061
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8025
moved from start:          0.3235

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   9208  Z= 0.148
  Angle     :  0.522   7.026  12525  Z= 0.257
  Chirality :  0.040   0.194   1496
  Planarity :  0.004   0.046   1529
  Dihedral  :  8.584 159.067   1373
  Min Nonbonded Distance : 1.929

Molprobity Statistics.
  All-atom Clashscore : 6.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.32 %
    Favored  : 98.68 %
  Rotamer:
    Outliers :  3.23 %
    Allowed  : 14.60 %
    Favored  : 82.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.39 (0.25), residues: 1133
  helix:  2.38 (0.19), residues: 760
  sheet:  0.58 (0.67), residues: 59
  loop : -0.18 (0.34), residues: 314

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 774 
 TYR   0.014   0.001   TYR A1250 
 PHE   0.008   0.001   PHE A 469 
 TRP   0.004   0.001   TRP A1302 
 HIS   0.009   0.001   HIS A1504 

Details of bonding type rmsd
  covalent geometry    : bond        0.00349 ( 9208)
  covalent geometry    : angle       0.52233 (12525)
  hydrogen bonds       : bond        0.04927 (  616)
  hydrogen bonds       : angle       3.94465 ( 1815)

*********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  2266 Ramachandran restraints generated.
    1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2266 Ramachandran restraints generated.
    1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 104
  time to evaluate  : 0.412 
Fit side-chains
   revert: symmetry clash
REVERT: A  273 LYS cc_start: 0.7844 (mtpp) cc_final: 0.7629 (ttpp)
REVERT: A  387 MET cc_start: 0.8679 (OUTLIER) cc_final: 0.8376 (mtt)
REVERT: A  591 PHE cc_start: 0.8849 (m-80) cc_final: 0.8530 (m-10)
REVERT: A  690 ARG cc_start: 0.8098 (ptt-90) cc_final: 0.7658 (ptm160)
REVERT: A  724 LYS cc_start: 0.8139 (mptt) cc_final: 0.7521 (mtpp)
REVERT: A  795 PHE cc_start: 0.8548 (m-80) cc_final: 0.8235 (m-80)
REVERT: A  797 ASP cc_start: 0.8138 (t70) cc_final: 0.7788 (t0)
REVERT: A  817 CYS cc_start: 0.8572 (t) cc_final: 0.8234 (m)
REVERT: A  888 ARG cc_start: 0.8003 (tpt90) cc_final: 0.7798 (ttm-80)
REVERT: A  889 GLU cc_start: 0.7548 (OUTLIER) cc_final: 0.7069 (tt0)
REVERT: A  898 LYS cc_start: 0.8246 (mmtp) cc_final: 0.7857 (mmtm)
REVERT: A  910 MET cc_start: 0.7300 (mtp) cc_final: 0.7026 (mtp)
REVERT: A  976 LYS cc_start: 0.7701 (mttp) cc_final: 0.7415 (tptp)
REVERT: A 1073 ILE cc_start: 0.8739 (tt) cc_final: 0.8347 (tt)
REVERT: A 1161 ASP cc_start: 0.7674 (m-30) cc_final: 0.7440 (m-30)
REVERT: A 1254 ILE cc_start: 0.8794 (mt) cc_final: 0.8460 (tp)
REVERT: A 1358 MET cc_start: 0.8704 (mmm) cc_final: 0.8389 (mtp)
REVERT: A 1416 GLU cc_start: 0.7800 (tp30) cc_final: 0.7504 (tt0)
REVERT: A 1468 MET cc_start: 0.8783 (mtm) cc_final: 0.8304 (mtp)
REVERT: A 1517 ARG cc_start: 0.8524 (mtp85) cc_final: 0.8296 (mtp85)
  outliers start: 31
  outliers final: 27
  residues processed: 124
  average time/residue: 0.1224
  time to fit residues: 20.4208
Evaluate side-chains
  133 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 104
  time to evaluate  : 0.358 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  284 SER
Chi-restraints excluded: chain A residue  375 GLU
Chi-restraints excluded: chain A residue  381 ARG
Chi-restraints excluded: chain A residue  387 MET
Chi-restraints excluded: chain A residue  405 MET
Chi-restraints excluded: chain A residue  434 MET
Chi-restraints excluded: chain A residue  534 SER
Chi-restraints excluded: chain A residue  543 ILE
Chi-restraints excluded: chain A residue  563 LEU
Chi-restraints excluded: chain A residue  580 THR
Chi-restraints excluded: chain A residue  586 SER
Chi-restraints excluded: chain A residue  593 VAL
Chi-restraints excluded: chain A residue  781 THR
Chi-restraints excluded: chain A residue  799 THR
Chi-restraints excluded: chain A residue  836 SER
Chi-restraints excluded: chain A residue  842 LEU
Chi-restraints excluded: chain A residue  889 GLU
Chi-restraints excluded: chain A residue  987 PHE
Chi-restraints excluded: chain A residue  993 MET
Chi-restraints excluded: chain A residue 1140 VAL
Chi-restraints excluded: chain A residue 1227 VAL
Chi-restraints excluded: chain A residue 1255 THR
Chi-restraints excluded: chain A residue 1259 ASN
Chi-restraints excluded: chain A residue 1275 VAL
Chi-restraints excluded: chain A residue 1277 LYS
Chi-restraints excluded: chain A residue 1321 LEU
Chi-restraints excluded: chain A residue 1379 HIS
Chi-restraints excluded: chain A residue 1463 SER
Chi-restraints excluded: chain A residue 1536 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 8 optimal weight:    0.7980
   chunk 1 optimal weight:    1.9990
   chunk 29 optimal weight:    2.9990
   chunk 17 optimal weight:    0.4980
   chunk 16 optimal weight:    0.8980
   chunk 30 optimal weight:    5.9990
   chunk 38 optimal weight:    6.9990
   chunk 63 optimal weight:    0.6980
   chunk 11 optimal weight:    0.6980
   chunk 27 optimal weight:    2.9990
   chunk 32 optimal weight:    0.7980
   overall best weight:    0.6980

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A 841 HIS
A1259 ASN
A1379 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3751 r_free = 0.3751 target = 0.151018 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3406 r_free = 0.3406 target = 0.120338 restraints weight = 10637.928|
|-----------------------------------------------------------------------------|
r_work (start): 0.3367 rms_B_bonded: 1.88
r_work: 0.3229 rms_B_bonded: 2.63 restraints_weight: 0.5000
r_work: 0.3081 rms_B_bonded: 4.41 restraints_weight: 0.2500
r_work (final): 0.3081
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8013
moved from start:          0.3299

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   9208  Z= 0.126
  Angle     :  0.503   6.813  12525  Z= 0.248
  Chirality :  0.039   0.195   1496
  Planarity :  0.004   0.046   1529
  Dihedral  :  8.534 163.511   1370
  Min Nonbonded Distance : 1.961

Molprobity Statistics.
  All-atom Clashscore : 6.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.06 %
    Favored  : 98.94 %
  Rotamer:
    Outliers :  2.92 %
    Allowed  : 14.81 %
    Favored  : 82.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.54 (0.25), residues: 1133
  helix:  2.49 (0.19), residues: 761
  sheet:  0.55 (0.67), residues: 59
  loop : -0.11 (0.34), residues: 313

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 774 
 TYR   0.012   0.001   TYR A1250 
 PHE   0.007   0.001   PHE A 469 
 TRP   0.004   0.001   TRP A1055 
 HIS   0.009   0.001   HIS A1504 

Details of bonding type rmsd
  covalent geometry    : bond        0.00285 ( 9208)
  covalent geometry    : angle       0.50326 (12525)
  hydrogen bonds       : bond        0.04703 (  616)
  hydrogen bonds       : angle       3.88409 ( 1815)

*********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  2266 Ramachandran restraints generated.
    1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2266 Ramachandran restraints generated.
    1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 109
  time to evaluate  : 0.373 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  273 LYS cc_start: 0.7763 (mtpp) cc_final: 0.7560 (ttpp)
REVERT: A  387 MET cc_start: 0.8662 (ttt) cc_final: 0.8414 (mtp)
REVERT: A  690 ARG cc_start: 0.8092 (ptt-90) cc_final: 0.7662 (ptm160)
REVERT: A  702 GLN cc_start: 0.8513 (pt0) cc_final: 0.8216 (mt0)
REVERT: A  724 LYS cc_start: 0.8133 (mptt) cc_final: 0.7532 (mtpp)
REVERT: A  774 ARG cc_start: 0.8128 (ttm-80) cc_final: 0.7654 (tpp-160)
REVERT: A  795 PHE cc_start: 0.8537 (m-80) cc_final: 0.8268 (m-80)
REVERT: A  797 ASP cc_start: 0.8105 (t70) cc_final: 0.7763 (t0)
REVERT: A  817 CYS cc_start: 0.8516 (t) cc_final: 0.8273 (m)
REVERT: A  889 GLU cc_start: 0.7532 (OUTLIER) cc_final: 0.7061 (tt0)
REVERT: A  898 LYS cc_start: 0.8239 (mmtp) cc_final: 0.7853 (mmtm)
REVERT: A  910 MET cc_start: 0.7266 (mtp) cc_final: 0.6994 (mtp)
REVERT: A  976 LYS cc_start: 0.7662 (mttp) cc_final: 0.7397 (tptp)
REVERT: A 1073 ILE cc_start: 0.8698 (tt) cc_final: 0.8312 (tt)
REVERT: A 1254 ILE cc_start: 0.8853 (mt) cc_final: 0.8576 (tp)
REVERT: A 1284 MET cc_start: 0.8525 (ttp) cc_final: 0.8302 (ttp)
REVERT: A 1358 MET cc_start: 0.8698 (mmm) cc_final: 0.8349 (mtp)
REVERT: A 1416 GLU cc_start: 0.7802 (tp30) cc_final: 0.7510 (tt0)
REVERT: A 1468 MET cc_start: 0.8791 (mtm) cc_final: 0.8310 (mtp)
REVERT: A 1517 ARG cc_start: 0.8570 (mtp85) cc_final: 0.8352 (mtp85)
  outliers start: 28
  outliers final: 27
  residues processed: 127
  average time/residue: 0.1209
  time to fit residues: 20.6075
Evaluate side-chains
  130 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 102
  time to evaluate  : 0.421 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  284 SER
Chi-restraints excluded: chain A residue  375 GLU
Chi-restraints excluded: chain A residue  381 ARG
Chi-restraints excluded: chain A residue  405 MET
Chi-restraints excluded: chain A residue  434 MET
Chi-restraints excluded: chain A residue  534 SER
Chi-restraints excluded: chain A residue  543 ILE
Chi-restraints excluded: chain A residue  563 LEU
Chi-restraints excluded: chain A residue  580 THR
Chi-restraints excluded: chain A residue  586 SER
Chi-restraints excluded: chain A residue  593 VAL
Chi-restraints excluded: chain A residue  781 THR
Chi-restraints excluded: chain A residue  799 THR
Chi-restraints excluded: chain A residue  836 SER
Chi-restraints excluded: chain A residue  842 LEU
Chi-restraints excluded: chain A residue  889 GLU
Chi-restraints excluded: chain A residue  987 PHE
Chi-restraints excluded: chain A residue  993 MET
Chi-restraints excluded: chain A residue 1140 VAL
Chi-restraints excluded: chain A residue 1227 VAL
Chi-restraints excluded: chain A residue 1255 THR
Chi-restraints excluded: chain A residue 1259 ASN
Chi-restraints excluded: chain A residue 1275 VAL
Chi-restraints excluded: chain A residue 1277 LYS
Chi-restraints excluded: chain A residue 1321 LEU
Chi-restraints excluded: chain A residue 1379 HIS
Chi-restraints excluded: chain A residue 1463 SER
Chi-restraints excluded: chain A residue 1536 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Traceback (most recent call last):
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py", line 9, in <module>
    run_program(real_space_refine.Program)
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/iotbx/cli_parser.py", line 999, in run_program
    task.run()
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/programs/real_space_refine.py", line 206, in run
    self.rsr_result = rsr_wrappers.run_real_space_refine(
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__
    self._refined = macro_cycle_real_space.run(
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__
    self.caller(self.refine_xyz)
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller
    func()
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz
    self.minimization_no_ncs()
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs
    ro = mmtbx.refinement.real_space.individual_sites.easy(
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__
    self.weight = mmtbx.refinement.real_space.weight.run(
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__
    ro.refine(
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine
    real_space_result = refinery(
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__
    refiner.refine(
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine
    self.refined = maptbx.real_space_refinement_simple.lbfgs(
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__
    O.minimizer = scitbx.lbfgs.run(
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run
    return run_c_plus_plus(
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus
    f, g = target_evaluator.compute_functional_and_gradients()
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients
    gr_e = O.geometry_restraints_manager.energies_sites(
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1588, in energies_sites
    pair_proxies = self.pair_proxies(
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1491, in pair_proxies
    check_bonded_distance_cutoff(sites_frac=sites_frac)
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1372, in check_bonded_distance_cutoff
    raise RuntimeError(msg)
RuntimeError: Bond distance > max_reasonable_bond_distance: 62.3439 > 50:
  distance: 27 - 43:  12.760
  distance: 31 - 51:  21.296
  distance: 35 - 59:  32.537
  distance: 39 - 43:  12.968
  distance: 40 - 66:  25.111
  distance: 43 - 44:  29.161
  distance: 44 - 45:  22.624
  distance: 44 - 47:  30.649
  distance: 45 - 46:  10.795
  distance: 45 - 51:  17.001
  distance: 46 - 71:  45.113
  distance: 47 - 48:   3.325
  distance: 48 - 49:  34.259
  distance: 51 - 52:  30.004
  distance: 52 - 53:  41.786
  distance: 52 - 55:  44.473
  distance: 53 - 59:  27.871
  distance: 55 - 56:  14.950
  distance: 56 - 57:   8.117
  distance: 56 - 58:  11.476
  distance: 59 - 60:  31.582
  distance: 60 - 61:  47.279
  distance: 60 - 63:   8.869
  distance: 61 - 62:  23.997
  distance: 61 - 66:  11.295
  distance: 66 - 67:   4.286
  distance: 67 - 68:  29.655
  distance: 67 - 70:   9.151
  distance: 68 - 69:  11.571
  distance: 68 - 71:  16.801
  distance: 71 - 72:   4.246
  distance: 72 - 73:  10.724
  distance: 72 - 75:  17.180
  distance: 73 - 74:  31.117
  distance: 74 - 103:  19.578
  distance: 75 - 76:  14.273
  distance: 75 - 77:   3.207
  distance: 79 - 80:  11.250
  distance: 80 - 81:  15.070
  distance: 80 - 83:   7.848
  distance: 81 - 82:  31.048
  distance: 82 - 112:  34.133
  distance: 83 - 84:  13.066
  distance: 84 - 85:  31.847
  distance: 85 - 86:  17.632
  distance: 85 - 87:   8.027
  distance: 88 - 89:  24.025
  distance: 89 - 90:  11.402
  distance: 89 - 92:  17.279
  distance: 90 - 91:  15.168
  distance: 90 - 95:   8.243
  distance: 91 - 120:  17.267
  distance: 92 - 93:  10.299
  distance: 92 - 94:  21.547
  distance: 95 - 96:  28.693
  distance: 96 - 97:  19.454
  distance: 96 - 99:  17.240
  distance: 97 - 98:  14.849
  distance: 97 - 103:  27.662
  distance: 98 - 127:  28.598
  distance: 99 - 100:  27.958
  distance: 100 - 101:  20.462
  distance: 100 - 102:  29.202
  distance: 103 - 104:  29.537
  distance: 104 - 105:  34.480
  distance: 104 - 107:  24.357
  distance: 105 - 106:   5.937
  distance: 105 - 112:  10.374
  distance: 106 - 141:  36.304
  distance: 107 - 108:  17.051
  distance: 108 - 109:   5.610
  distance: 109 - 111:   9.251
  distance: 112 - 113:   3.271
  distance: 113 - 114:  15.250
  distance: 113 - 116:   3.260
  distance: 114 - 115:  38.812
  distance: 114 - 120:  26.089
  distance: 115 - 149:  32.279
  distance: 117 - 119:  23.117