Starting phenix.real_space_refine
on Fri Feb 14 02:05:12 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7vlt_32026/02_2025/7vlt_32026_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7vlt_32026/02_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 {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7vlt_32026/02_2025/7vlt_32026.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7vlt_32026/02_2025/7vlt_32026.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7vlt_32026/02_2025/7vlt_32026_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7vlt_32026/02_2025/7vlt_32026_neut.cif"
  }
  resolution = 3.1
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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-filer2/raid1/xp/phenix/phenix-dev-5592/modules/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: {'GLN:plan1': 2, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 6, 'GLU:plan': 8, 'ARG:plan': 3}
          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: 5.92, per 1000 atoms: 0.66
  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: 2.64
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  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: 1.10
  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: 3.56

  Time building geometry restraints manager: 2.89 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:             0.530
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.310
  Check model and map are aligned:         0.060
  Set scattering table:                    0.080
  Process input model:                     24.890
  Find NCS groups from input model:        0.100
  Set up NCS constraints:                  0.040
  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:2.970
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   29.000
-------------------------------------------------------------------------------
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= 0.241
  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 : 3.24
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  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
 TRP   0.006   0.001   TRP A1415 
 HIS   0.005   0.001   HIS A1001 
 PHE   0.011   0.001   PHE A1035 
 TYR   0.016   0.001   TYR A1250 
 ARG   0.003   0.000   ARG A1461 

*********************** 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  : 1.045 
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: 0.2835
  time to fit residues: 72.5631
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  : 0.892 
-------------------------------------------------------------------------------
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 96 optimal weight:    8.9990
   chunk 86 optimal weight:    0.9990
   chunk 47 optimal weight:    3.9990
   chunk 29 optimal weight:    0.5980
   chunk 58 optimal weight:    0.0050
   chunk 46 optimal weight:    5.9990
   chunk 89 optimal weight:    5.9990
   chunk 34 optimal weight:    0.8980
   chunk 54 optimal weight:    0.9980
   chunk 66 optimal weight:    0.3980
   chunk 103 optimal weight:    3.9990
   overall best weight:    0.5794

-------------------------------------------------------------------------------
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
A1402 ASN
A1444 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3791 r_free = 0.3791 target = 0.154453 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3455 r_free = 0.3455 target = 0.123682 restraints weight = 10248.403|
|-----------------------------------------------------------------------------|
r_work (start): 0.3437 rms_B_bonded: 1.84
r_work: 0.3304 rms_B_bonded: 2.58 restraints_weight: 0.5000
r_work: 0.3154 rms_B_bonded: 4.35 restraints_weight: 0.2500
r_work (final): 0.3154
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7956
moved from start:          0.1920

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   9208  Z= 0.180
  Angle     :  0.530   6.882  12525  Z= 0.267
  Chirality :  0.040   0.193   1496
  Planarity :  0.004   0.053   1529
  Dihedral  :  9.519 127.914   1384
  Min Nonbonded Distance : 1.981

Molprobity Statistics.
  All-atom Clashscore : 5.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.50 %
    Favored  : 98.50 %
  Rotamer:
    Outliers :  1.77 %
    Allowed  : 11.16 %
    Favored  : 87.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.91 (0.25), residues: 1133
  helix:  1.93 (0.19), residues: 753
  sheet:  0.51 (0.62), residues: 65
  loop : -0.13 (0.35), residues: 315

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A1055 
 HIS   0.009   0.001   HIS A1504 
 PHE   0.013   0.001   PHE A1142 
 TYR   0.013   0.001   TYR A1523 
 ARG   0.004   0.000   ARG A 774 

*********************** 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
  137 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 120
  time to evaluate  : 1.029 
Fit side-chains
REVERT: A  273 LYS cc_start: 0.7486 (mtpp) cc_final: 0.7244 (ttpp)
REVERT: A  412 ASN cc_start: 0.8412 (t0) cc_final: 0.7557 (m-40)
REVERT: A  447 ASN cc_start: 0.8305 (m110) cc_final: 0.7956 (t0)
REVERT: A  486 THR cc_start: 0.8687 (m) cc_final: 0.7832 (p)
REVERT: A  573 SER cc_start: 0.8490 (t) cc_final: 0.8162 (m)
REVERT: A  722 GLU cc_start: 0.7225 (tt0) cc_final: 0.6953 (mt-10)
REVERT: A  724 LYS cc_start: 0.7927 (mptt) cc_final: 0.7335 (mtpp)
REVERT: A  764 GLU cc_start: 0.8191 (mm-30) cc_final: 0.7588 (mt-10)
REVERT: A  795 PHE cc_start: 0.8560 (m-80) cc_final: 0.8334 (m-80)
REVERT: A  817 CYS cc_start: 0.8233 (t) cc_final: 0.7775 (m)
REVERT: A  847 MET cc_start: 0.8592 (tpp) cc_final: 0.8238 (tpt)
REVERT: A  910 MET cc_start: 0.7279 (mtp) cc_final: 0.7040 (mtp)
REVERT: A  976 LYS cc_start: 0.7676 (mttp) cc_final: 0.7382 (tptp)
REVERT: A 1158 GLU cc_start: 0.7631 (mt-10) cc_final: 0.7054 (tp30)
REVERT: A 1161 ASP cc_start: 0.7500 (m-30) cc_final: 0.7193 (m-30)
REVERT: A 1309 LYS cc_start: 0.8031 (mttt) cc_final: 0.7149 (mppt)
REVERT: A 1426 MET cc_start: 0.7481 (tmm) cc_final: 0.7145 (ttt)
REVERT: A 1468 MET cc_start: 0.8724 (mtm) cc_final: 0.8423 (mtp)
  outliers start: 17
  outliers final: 11
  residues processed: 135
  average time/residue: 0.2584
  time to fit residues: 46.9940
Evaluate side-chains
  117 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 106
  time to evaluate  : 1.026 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  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 87 optimal weight:    2.9990
   chunk 17 optimal weight:    4.9990
   chunk 96 optimal weight:    8.9990
   chunk 41 optimal weight:    4.9990
   chunk 50 optimal weight:    2.9990
   chunk 27 optimal weight:    0.6980
   chunk 51 optimal weight:    0.5980
   chunk 111 optimal weight:    1.9990
   chunk 93 optimal weight:   10.0000
   chunk 0 optimal weight:    5.9990
   chunk 21 optimal weight:    0.7980
   overall best weight:    1.4184

-------------------------------------------------------------------------------
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

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3732 r_free = 0.3732 target = 0.149089 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3376 r_free = 0.3376 target = 0.117512 restraints weight = 10604.786|
|-----------------------------------------------------------------------------|
r_work (start): 0.3335 rms_B_bonded: 1.88
r_work: 0.3198 rms_B_bonded: 2.61 restraints_weight: 0.5000
r_work: 0.3048 rms_B_bonded: 4.38 restraints_weight: 0.2500
r_work (final): 0.3048
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8054
moved from start:          0.2573

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.054   9208  Z= 0.280
  Angle     :  0.572   8.070  12525  Z= 0.282
  Chirality :  0.042   0.205   1496
  Planarity :  0.004   0.056   1529
  Dihedral  :  9.120 138.607   1375
  Min Nonbonded Distance : 1.920

Molprobity Statistics.
  All-atom Clashscore : 6.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.59 %
    Favored  : 98.41 %
  Rotamer:
    Outliers :  2.71 %
    Allowed  : 11.99 %
    Favored  : 85.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.99 (0.25), residues: 1133
  helix:  2.01 (0.19), residues: 756
  sheet:  0.50 (0.66), residues: 59
  loop : -0.15 (0.34), residues: 318

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 423 
 HIS   0.019   0.002   HIS A1379 
 PHE   0.014   0.002   PHE A1149 
 TYR   0.012   0.002   TYR A 484 
 ARG   0.005   0.001   ARG A 888 

*********************** 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
  142 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 116
  time to evaluate  : 0.971 
Fit side-chains
REVERT: A  273 LYS cc_start: 0.7886 (mtpp) cc_final: 0.7597 (ttpp)
REVERT: A  447 ASN cc_start: 0.8303 (m110) cc_final: 0.8102 (t0)
REVERT: A  591 PHE cc_start: 0.8852 (m-80) cc_final: 0.8511 (m-10)
REVERT: A  724 LYS cc_start: 0.7999 (mptt) cc_final: 0.7336 (mtpp)
REVERT: A  795 PHE cc_start: 0.8590 (m-80) cc_final: 0.8146 (m-80)
REVERT: A  797 ASP cc_start: 0.8023 (t70) cc_final: 0.7638 (t0)
REVERT: A  817 CYS cc_start: 0.8528 (t) cc_final: 0.8108 (m)
REVERT: A  888 ARG cc_start: 0.7948 (tpt90) cc_final: 0.7729 (ttm-80)
REVERT: A  898 LYS cc_start: 0.8157 (mmtp) cc_final: 0.7754 (mmtm)
REVERT: A  910 MET cc_start: 0.7346 (mtp) cc_final: 0.7093 (mtp)
REVERT: A  976 LYS cc_start: 0.7723 (mttp) cc_final: 0.7443 (tptp)
REVERT: A 1158 GLU cc_start: 0.7591 (mt-10) cc_final: 0.7294 (tp30)
REVERT: A 1192 GLN cc_start: 0.7743 (tp40) cc_final: 0.7333 (mt0)
REVERT: A 1254 ILE cc_start: 0.8799 (OUTLIER) cc_final: 0.8450 (tp)
REVERT: A 1309 LYS cc_start: 0.8091 (mttt) cc_final: 0.7216 (mptt)
REVERT: A 1311 HIS cc_start: 0.7004 (m90) cc_final: 0.6714 (m170)
REVERT: A 1468 MET cc_start: 0.8815 (mtm) cc_final: 0.8393 (mtp)
  outliers start: 26
  outliers final: 22
  residues processed: 133
  average time/residue: 0.2424
  time to fit residues: 43.6425
Evaluate side-chains
  121 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 98
  time to evaluate  : 0.984 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  326 ASN
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  578 LEU
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  842 LEU
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 1254 ILE
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
Chi-restraints excluded: chain A residue 1536 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 6 optimal weight:    0.9980
   chunk 98 optimal weight:    0.8980
   chunk 67 optimal weight:    2.9990
   chunk 81 optimal weight:    0.8980
   chunk 34 optimal weight:    0.8980
   chunk 87 optimal weight:    0.9990
   chunk 7 optimal weight:    2.9990
   chunk 112 optimal weight:    3.9990
   chunk 113 optimal weight:    5.9990
   chunk 86 optimal weight:    0.7980
   chunk 4 optimal weight:    0.9980
   overall best weight:    0.8980

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

Flipped N/Q/H residues before XYZ refinement:
A 807 ASN
A 841 HIS
A1259 ASN
A1379 HIS
A1451 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3748 r_free = 0.3748 target = 0.150601 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3399 r_free = 0.3399 target = 0.119411 restraints weight = 10520.215|
|-----------------------------------------------------------------------------|
r_work (start): 0.3357 rms_B_bonded: 1.87
r_work: 0.3222 rms_B_bonded: 2.61 restraints_weight: 0.5000
r_work: 0.3072 rms_B_bonded: 4.39 restraints_weight: 0.2500
r_work (final): 0.3072
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8023
moved from start:          0.2770

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= 0.207
  Angle     :  0.524   6.967  12525  Z= 0.258
  Chirality :  0.040   0.207   1496
  Planarity :  0.004   0.052   1529
  Dihedral  :  8.938 139.969   1373
  Min Nonbonded Distance : 1.940

Molprobity Statistics.
  All-atom Clashscore : 5.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.41 %
    Favored  : 98.59 %
  Rotamer:
    Outliers :  2.61 %
    Allowed  : 13.56 %
    Favored  : 83.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.14 (0.25), residues: 1133
  helix:  2.14 (0.19), residues: 758
  sheet:  0.52 (0.66), residues: 59
  loop : -0.14 (0.34), residues: 316

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 727 
 HIS   0.007   0.001   HIS A1504 
 PHE   0.013   0.001   PHE A1362 
 TYR   0.015   0.001   TYR A1250 
 ARG   0.003   0.000   ARG A 888 

*********************** 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
  137 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 112
  time to evaluate  : 0.987 
Fit side-chains
REVERT: A  273 LYS cc_start: 0.7758 (mtpp) cc_final: 0.7501 (ttpp)
REVERT: A  412 ASN cc_start: 0.8415 (t0) cc_final: 0.8188 (t0)
REVERT: A  591 PHE cc_start: 0.8836 (m-80) cc_final: 0.8501 (m-10)
REVERT: A  690 ARG cc_start: 0.8065 (ptt-90) cc_final: 0.7656 (ptm160)
REVERT: A  724 LYS cc_start: 0.8078 (mptt) cc_final: 0.7354 (mtpp)
REVERT: A  795 PHE cc_start: 0.8569 (m-80) cc_final: 0.8189 (m-80)
REVERT: A  797 ASP cc_start: 0.7996 (t70) cc_final: 0.7624 (t0)
REVERT: A  817 CYS cc_start: 0.8588 (t) cc_final: 0.8204 (m)
REVERT: A  888 ARG cc_start: 0.7918 (tpt90) cc_final: 0.7628 (ttm-80)
REVERT: A  898 LYS cc_start: 0.8133 (mmtp) cc_final: 0.7772 (mmtm)
REVERT: A  910 MET cc_start: 0.7303 (mtp) cc_final: 0.6821 (mtp)
REVERT: A  976 LYS cc_start: 0.7712 (mttp) cc_final: 0.7437 (tptp)
REVERT: A 1161 ASP cc_start: 0.7625 (m-30) cc_final: 0.7366 (m-30)
REVERT: A 1254 ILE cc_start: 0.8762 (mt) cc_final: 0.8435 (tp)
REVERT: A 1309 LYS cc_start: 0.8118 (mttt) cc_final: 0.7021 (mptt)
REVERT: A 1468 MET cc_start: 0.8812 (mtm) cc_final: 0.8375 (mtp)
  outliers start: 25
  outliers final: 19
  residues processed: 130
  average time/residue: 0.2455
  time to fit residues: 43.4331
Evaluate side-chains
  119 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 100
  time to evaluate  : 0.974 
-------------------------------------------------------------------------------
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  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  836 SER
Chi-restraints excluded: chain A residue  842 LEU
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 1430 LEU
Chi-restraints excluded: chain A residue 1463 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 18 optimal weight:    0.8980
   chunk 11 optimal weight:    0.7980
   chunk 97 optimal weight:    4.9990
   chunk 22 optimal weight:    0.6980
   chunk 42 optimal weight:    2.9990
   chunk 61 optimal weight:    0.7980
   chunk 91 optimal weight:   10.0000
   chunk 52 optimal weight:    4.9990
   chunk 65 optimal weight:    2.9990
   chunk 55 optimal weight:    0.5980
   chunk 44 optimal weight:    3.9990
   overall best weight:    0.7580

-------------------------------------------------------------------------------
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
A1379 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3727 r_free = 0.3727 target = 0.149128 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3381 r_free = 0.3381 target = 0.118196 restraints weight = 10507.465|
|-----------------------------------------------------------------------------|
r_work (start): 0.3369 rms_B_bonded: 1.87
r_work: 0.3233 rms_B_bonded: 2.61 restraints_weight: 0.5000
r_work: 0.3082 rms_B_bonded: 4.42 restraints_weight: 0.2500
r_work (final): 0.3082
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8000
moved from start:          0.3051

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= 0.186
  Angle     :  0.501   6.528  12525  Z= 0.248
  Chirality :  0.039   0.199   1496
  Planarity :  0.004   0.049   1529
  Dihedral  :  8.612 144.163   1373
  Min Nonbonded Distance : 1.961

Molprobity Statistics.
  All-atom Clashscore : 5.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.24 %
    Favored  : 98.76 %
  Rotamer:
    Outliers :  2.61 %
    Allowed  : 13.56 %
    Favored  : 83.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.35 (0.25), residues: 1133
  helix:  2.33 (0.19), residues: 758
  sheet:  0.66 (0.68), residues: 59
  loop : -0.17 (0.34), residues: 316

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP A 677 
 HIS   0.008   0.001   HIS A1504 
 PHE   0.010   0.001   PHE A1149 
 TYR   0.010   0.001   TYR A1250 
 ARG   0.003   0.000   ARG A 888 

*********************** 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: 25
    poor density    : 110
  time to evaluate  : 0.947 
Fit side-chains
REVERT: A  273 LYS cc_start: 0.7782 (mtpp) cc_final: 0.7537 (ttpp)
REVERT: A  690 ARG cc_start: 0.8025 (ptt-90) cc_final: 0.7611 (ptm160)
REVERT: A  724 LYS cc_start: 0.7969 (mptt) cc_final: 0.7356 (mtpp)
REVERT: A  795 PHE cc_start: 0.8538 (m-80) cc_final: 0.8304 (m-80)
REVERT: A  797 ASP cc_start: 0.8090 (t70) cc_final: 0.7703 (t0)
REVERT: A  817 CYS cc_start: 0.8519 (t) cc_final: 0.8231 (m)
REVERT: A  889 GLU cc_start: 0.7447 (OUTLIER) cc_final: 0.6973 (tt0)
REVERT: A  898 LYS cc_start: 0.8235 (mmtp) cc_final: 0.7860 (mmtm)
REVERT: A  976 LYS cc_start: 0.7640 (mttp) cc_final: 0.7377 (tptp)
REVERT: A 1073 ILE cc_start: 0.8689 (tt) cc_final: 0.8312 (tt)
REVERT: A 1254 ILE cc_start: 0.8762 (mt) cc_final: 0.8451 (tp)
REVERT: A 1284 MET cc_start: 0.8306 (ttp) cc_final: 0.8049 (ttp)
REVERT: A 1309 LYS cc_start: 0.8124 (mttt) cc_final: 0.7031 (mptt)
REVERT: A 1358 MET cc_start: 0.8705 (mmm) cc_final: 0.8413 (tpp)
REVERT: A 1468 MET cc_start: 0.8773 (mtm) cc_final: 0.8295 (mtp)
  outliers start: 25
  outliers final: 23
  residues processed: 126
  average time/residue: 0.2479
  time to fit residues: 42.2444
Evaluate side-chains
  125 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 101
  time to evaluate  : 0.986 
-------------------------------------------------------------------------------
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  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  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 1430 LEU
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 45 optimal weight:    0.6980
   chunk 72 optimal weight:    0.5980
   chunk 99 optimal weight:    0.6980
   chunk 64 optimal weight:    0.9980
   chunk 106 optimal weight:    0.8980
   chunk 39 optimal weight:    2.9990
   chunk 12 optimal weight:    0.7980
   chunk 26 optimal weight:    0.6980
   chunk 85 optimal weight:    0.9980
   chunk 71 optimal weight:    0.7980
   chunk 86 optimal weight:    0.9980
   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
A1379 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3759 r_free = 0.3759 target = 0.151756 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3416 r_free = 0.3416 target = 0.121057 restraints weight = 10502.649|
|-----------------------------------------------------------------------------|
r_work (start): 0.3374 rms_B_bonded: 1.88
r_work: 0.3237 rms_B_bonded: 2.63 restraints_weight: 0.5000
r_work: 0.3089 rms_B_bonded: 4.41 restraints_weight: 0.2500
r_work (final): 0.3089
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8005
moved from start:          0.3186

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= 0.181
  Angle     :  0.495   6.606  12525  Z= 0.245
  Chirality :  0.039   0.194   1496
  Planarity :  0.004   0.048   1529
  Dihedral  :  8.494 147.653   1373
  Min Nonbonded Distance : 1.959

Molprobity Statistics.
  All-atom Clashscore : 5.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.24 %
    Favored  : 98.76 %
  Rotamer:
    Outliers :  2.92 %
    Allowed  : 14.39 %
    Favored  : 82.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.49 (0.25), residues: 1133
  helix:  2.46 (0.19), residues: 758
  sheet:  0.60 (0.67), residues: 59
  loop : -0.14 (0.34), residues: 316

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP A1055 
 HIS   0.008   0.001   HIS A1504 
 PHE   0.008   0.001   PHE A1149 
 TYR   0.013   0.001   TYR A1250 
 ARG   0.004   0.000   ARG A 774 

*********************** 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: 28
    poor density    : 102
  time to evaluate  : 0.942 
Fit side-chains
REVERT: A  273 LYS cc_start: 0.7780 (mtpp) cc_final: 0.7544 (ttpp)
REVERT: A  387 MET cc_start: 0.8606 (ttt) cc_final: 0.8309 (mtp)
REVERT: A  690 ARG cc_start: 0.8038 (ptt-90) cc_final: 0.7617 (ptm160)
REVERT: A  724 LYS cc_start: 0.7988 (mptt) cc_final: 0.7389 (mtpp)
REVERT: A  795 PHE cc_start: 0.8509 (m-80) cc_final: 0.8294 (m-80)
REVERT: A  797 ASP cc_start: 0.8086 (t70) cc_final: 0.7709 (t0)
REVERT: A  817 CYS cc_start: 0.8487 (t) cc_final: 0.8250 (m)
REVERT: A  889 GLU cc_start: 0.7257 (OUTLIER) cc_final: 0.6948 (tt0)
REVERT: A  898 LYS cc_start: 0.8276 (mmtp) cc_final: 0.7866 (mmtm)
REVERT: A  910 MET cc_start: 0.7260 (mtp) cc_final: 0.6966 (mtp)
REVERT: A  976 LYS cc_start: 0.7697 (mttp) cc_final: 0.7426 (tptp)
REVERT: A 1073 ILE cc_start: 0.8683 (tt) cc_final: 0.8297 (tt)
REVERT: A 1254 ILE cc_start: 0.8844 (mt) cc_final: 0.8572 (tp)
REVERT: A 1309 LYS cc_start: 0.8133 (mttt) cc_final: 0.7041 (mptt)
REVERT: A 1358 MET cc_start: 0.8758 (mmm) cc_final: 0.8476 (tpp)
REVERT: A 1468 MET cc_start: 0.8795 (mtm) cc_final: 0.8311 (mtp)
  outliers start: 28
  outliers final: 23
  residues processed: 121
  average time/residue: 0.2379
  time to fit residues: 39.4424
Evaluate side-chains
  122 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 98
  time to evaluate  : 1.107 
-------------------------------------------------------------------------------
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  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 1275 VAL
Chi-restraints excluded: chain A residue 1277 LYS
Chi-restraints excluded: chain A residue 1379 HIS
Chi-restraints excluded: chain A residue 1430 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 58 optimal weight:    1.9990
   chunk 6 optimal weight:    0.6980
   chunk 48 optimal weight:    0.7980
   chunk 13 optimal weight:    2.9990
   chunk 62 optimal weight:    0.0020
   chunk 7 optimal weight:    4.9990
   chunk 71 optimal weight:    0.9980
   chunk 94 optimal weight:    7.9990
   chunk 91 optimal weight:   10.0000
   chunk 90 optimal weight:    9.9990
   chunk 22 optimal weight:    0.5980
   overall best weight:    0.6188

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

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3772 r_free = 0.3772 target = 0.152665 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3434 r_free = 0.3434 target = 0.122312 restraints weight = 10594.617|
|-----------------------------------------------------------------------------|
r_work (start): 0.3409 rms_B_bonded: 1.86
r_work: 0.3271 rms_B_bonded: 2.63 restraints_weight: 0.5000
r_work: 0.3124 rms_B_bonded: 4.41 restraints_weight: 0.2500
r_work (final): 0.3124
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7992
moved from start:          0.3283

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   9208  Z= 0.169
  Angle     :  0.493   7.042  12525  Z= 0.242
  Chirality :  0.039   0.192   1496
  Planarity :  0.004   0.046   1529
  Dihedral  :  8.391 151.637   1373
  Min Nonbonded Distance : 1.969

Molprobity Statistics.
  All-atom Clashscore : 5.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.97 %
    Favored  : 99.03 %
  Rotamer:
    Outliers :  2.82 %
    Allowed  : 14.91 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.58 (0.25), residues: 1133
  helix:  2.53 (0.19), residues: 760
  sheet:  0.55 (0.66), residues: 59
  loop : -0.11 (0.34), residues: 314

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP A1055 
 HIS   0.009   0.001   HIS A1504 
 PHE   0.008   0.001   PHE A1149 
 TYR   0.012   0.001   TYR A1250 
 ARG   0.004   0.000   ARG A 774 

*********************** 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: 27
    poor density    : 108
  time to evaluate  : 0.934 
Fit side-chains
   revert: symmetry clash
REVERT: A  273 LYS cc_start: 0.7784 (mtpp) cc_final: 0.7555 (ttpp)
REVERT: A  387 MET cc_start: 0.8691 (ttt) cc_final: 0.8379 (mtp)
REVERT: A  413 LEU cc_start: 0.8307 (OUTLIER) cc_final: 0.8106 (mp)
REVERT: A  690 ARG cc_start: 0.8021 (ptt-90) cc_final: 0.7603 (ptm160)
REVERT: A  724 LYS cc_start: 0.8117 (mptt) cc_final: 0.7517 (mtpp)
REVERT: A  774 ARG cc_start: 0.8123 (ttm-80) cc_final: 0.7635 (tpp-160)
REVERT: A  795 PHE cc_start: 0.8544 (m-80) cc_final: 0.8321 (m-80)
REVERT: A  797 ASP cc_start: 0.8071 (t70) cc_final: 0.7705 (t0)
REVERT: A  817 CYS cc_start: 0.8475 (t) cc_final: 0.8246 (m)
REVERT: A  889 GLU cc_start: 0.7245 (OUTLIER) cc_final: 0.6938 (tt0)
REVERT: A  898 LYS cc_start: 0.8257 (mmtp) cc_final: 0.7854 (mmtm)
REVERT: A  910 MET cc_start: 0.7246 (mtp) cc_final: 0.6970 (mtp)
REVERT: A  976 LYS cc_start: 0.7662 (mttp) cc_final: 0.7404 (tptp)
REVERT: A 1073 ILE cc_start: 0.8664 (tt) cc_final: 0.8285 (tt)
REVERT: A 1254 ILE cc_start: 0.8834 (mt) cc_final: 0.8564 (tp)
REVERT: A 1309 LYS cc_start: 0.8134 (mttt) cc_final: 0.7235 (mptt)
REVERT: A 1358 MET cc_start: 0.8757 (mmm) cc_final: 0.8489 (tpp)
REVERT: A 1468 MET cc_start: 0.8790 (mtm) cc_final: 0.8223 (mtp)
  outliers start: 27
  outliers final: 24
  residues processed: 127
  average time/residue: 0.2410
  time to fit residues: 42.0162
Evaluate side-chains
  132 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 106
  time to evaluate  : 0.937 
-------------------------------------------------------------------------------
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  413 LEU
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 1275 VAL
Chi-restraints excluded: chain A residue 1277 LYS
Chi-restraints excluded: chain A residue 1379 HIS
Chi-restraints excluded: chain A residue 1430 LEU
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 6 optimal weight:    0.9990
   chunk 27 optimal weight:    2.9990
   chunk 106 optimal weight:    0.8980
   chunk 37 optimal weight:    0.7980
   chunk 12 optimal weight:    1.9990
   chunk 108 optimal weight:    3.9990
   chunk 60 optimal weight:    2.9990
   chunk 85 optimal weight:    0.6980
   chunk 81 optimal weight:    0.7980
   chunk 96 optimal weight:    3.9990
   chunk 26 optimal weight:    0.9990
   overall best weight:    0.8382

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

Flipped N/Q/H residues before XYZ refinement:
A1379 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3764 r_free = 0.3764 target = 0.152005 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3422 r_free = 0.3422 target = 0.121448 restraints weight = 10589.892|
|-----------------------------------------------------------------------------|
r_work (start): 0.3369 rms_B_bonded: 1.88
r_work: 0.3233 rms_B_bonded: 2.62 restraints_weight: 0.5000
r_work: 0.3084 rms_B_bonded: 4.41 restraints_weight: 0.2500
r_work (final): 0.3084
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8009
moved from start:          0.3325

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= 0.194
  Angle     :  0.503   6.741  12525  Z= 0.247
  Chirality :  0.039   0.188   1496
  Planarity :  0.004   0.046   1529
  Dihedral  :  8.395 157.875   1370
  Min Nonbonded Distance : 1.943

Molprobity Statistics.
  All-atom Clashscore : 5.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.41 %
    Favored  : 98.59 %
  Rotamer:
    Outliers :  3.13 %
    Allowed  : 14.49 %
    Favored  : 82.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.54 (0.25), residues: 1133
  helix:  2.49 (0.19), residues: 761
  sheet:  0.51 (0.66), residues: 59
  loop : -0.11 (0.34), residues: 313

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP A1302 
 HIS   0.009   0.001   HIS A1504 
 PHE   0.008   0.001   PHE A 469 
 TYR   0.013   0.001   TYR A1250 
 ARG   0.004   0.000   ARG A 774 

*********************** 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
  136 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 106
  time to evaluate  : 0.999 
Fit side-chains
   revert: symmetry clash
REVERT: A  273 LYS cc_start: 0.7737 (mtpp) cc_final: 0.7525 (ttpp)
REVERT: A  387 MET cc_start: 0.8629 (ttt) cc_final: 0.8341 (mtp)
REVERT: A  690 ARG cc_start: 0.8024 (ptt-90) cc_final: 0.7606 (ptm160)
REVERT: A  702 GLN cc_start: 0.8424 (pt0) cc_final: 0.8108 (mt0)
REVERT: A  724 LYS cc_start: 0.8119 (mptt) cc_final: 0.7520 (mtpp)
REVERT: A  774 ARG cc_start: 0.8096 (ttm-80) cc_final: 0.7648 (tpp-160)
REVERT: A  795 PHE cc_start: 0.8554 (m-80) cc_final: 0.8302 (m-80)
REVERT: A  797 ASP cc_start: 0.8209 (t70) cc_final: 0.7794 (t0)
REVERT: A  817 CYS cc_start: 0.8496 (t) cc_final: 0.8266 (m)
REVERT: A  889 GLU cc_start: 0.7238 (OUTLIER) cc_final: 0.6947 (tt0)
REVERT: A  898 LYS cc_start: 0.8236 (mmtp) cc_final: 0.7846 (mmtm)
REVERT: A  910 MET cc_start: 0.7266 (mtp) cc_final: 0.6975 (mtp)
REVERT: A  976 LYS cc_start: 0.7668 (mttp) cc_final: 0.7421 (tptp)
REVERT: A 1073 ILE cc_start: 0.8698 (tt) cc_final: 0.8309 (tt)
REVERT: A 1254 ILE cc_start: 0.8858 (mt) cc_final: 0.8572 (tp)
REVERT: A 1309 LYS cc_start: 0.8164 (mttt) cc_final: 0.7259 (mptt)
REVERT: A 1358 MET cc_start: 0.8649 (mmm) cc_final: 0.8394 (tpp)
REVERT: A 1468 MET cc_start: 0.8778 (mtm) cc_final: 0.8272 (mtp)
  outliers start: 30
  outliers final: 25
  residues processed: 127
  average time/residue: 0.2399
  time to fit residues: 41.7186
Evaluate side-chains
  129 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 103
  time to evaluate  : 1.051 
-------------------------------------------------------------------------------
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  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 1275 VAL
Chi-restraints excluded: chain A residue 1277 LYS
Chi-restraints excluded: chain A residue 1379 HIS
Chi-restraints excluded: chain A residue 1430 LEU
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 52 optimal weight:    0.7980
   chunk 54 optimal weight:    0.9980
   chunk 29 optimal weight:    2.9990
   chunk 98 optimal weight:    0.6980
   chunk 12 optimal weight:    0.9980
   chunk 75 optimal weight:    4.9990
   chunk 66 optimal weight:    3.9990
   chunk 92 optimal weight:    2.9990
   chunk 82 optimal weight:    0.6980
   chunk 53 optimal weight:    0.8980
   chunk 14 optimal weight:    0.9990
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
A1379 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3763 r_free = 0.3763 target = 0.152065 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3419 r_free = 0.3419 target = 0.121102 restraints weight = 10491.535|
|-----------------------------------------------------------------------------|
r_work (start): 0.3367 rms_B_bonded: 1.89
r_work: 0.3231 rms_B_bonded: 2.63 restraints_weight: 0.5000
r_work: 0.3084 rms_B_bonded: 4.40 restraints_weight: 0.2500
r_work (final): 0.3084
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8010
moved from start:          0.3374

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   9208  Z= 0.192
  Angle     :  0.501   6.670  12525  Z= 0.246
  Chirality :  0.039   0.187   1496
  Planarity :  0.004   0.045   1529
  Dihedral  :  8.451 163.491   1370
  Min Nonbonded Distance : 1.949

Molprobity Statistics.
  All-atom Clashscore : 5.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.24 %
    Favored  : 98.76 %
  Rotamer:
    Outliers :  2.92 %
    Allowed  : 14.49 %
    Favored  : 82.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.54 (0.25), residues: 1133
  helix:  2.48 (0.19), residues: 762
  sheet:  0.43 (0.66), residues: 59
  loop : -0.09 (0.34), residues: 312

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP A1302 
 HIS   0.009   0.001   HIS A1504 
 PHE   0.008   0.001   PHE A 469 
 TYR   0.012   0.001   TYR A1250 
 ARG   0.004   0.000   ARG A 774 

*********************** 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
  136 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 108
  time to evaluate  : 0.924 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  273 LYS cc_start: 0.7766 (mtpp) cc_final: 0.7562 (ttpp)
REVERT: A  387 MET cc_start: 0.8621 (ttt) cc_final: 0.8344 (mtp)
REVERT: A  690 ARG cc_start: 0.8020 (ptt-90) cc_final: 0.7613 (ptm160)
REVERT: A  702 GLN cc_start: 0.8437 (pt0) cc_final: 0.8156 (mt0)
REVERT: A  724 LYS cc_start: 0.8101 (mptt) cc_final: 0.7530 (mtpp)
REVERT: A  774 ARG cc_start: 0.8099 (ttm-80) cc_final: 0.7664 (tpp-160)
REVERT: A  795 PHE cc_start: 0.8484 (m-80) cc_final: 0.8208 (m-80)
REVERT: A  797 ASP cc_start: 0.8261 (t70) cc_final: 0.7843 (t0)
REVERT: A  817 CYS cc_start: 0.8499 (t) cc_final: 0.8274 (m)
REVERT: A  889 GLU cc_start: 0.7218 (OUTLIER) cc_final: 0.6932 (tt0)
REVERT: A  976 LYS cc_start: 0.7667 (mttp) cc_final: 0.7414 (tptp)
REVERT: A 1073 ILE cc_start: 0.8692 (tt) cc_final: 0.8303 (tt)
REVERT: A 1254 ILE cc_start: 0.8867 (mt) cc_final: 0.8578 (tp)
REVERT: A 1358 MET cc_start: 0.8647 (mmm) cc_final: 0.8401 (tpp)
REVERT: A 1468 MET cc_start: 0.8786 (mtm) cc_final: 0.8230 (mtp)
  outliers start: 28
  outliers final: 26
  residues processed: 127
  average time/residue: 0.2391
  time to fit residues: 41.1445
Evaluate side-chains
  129 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 102
  time to evaluate  : 1.011 
-------------------------------------------------------------------------------
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 1275 VAL
Chi-restraints excluded: chain A residue 1277 LYS
Chi-restraints excluded: chain A residue 1379 HIS
Chi-restraints excluded: chain A residue 1430 LEU
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
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 11 optimal weight:    0.9980
   chunk 97 optimal weight:    0.9990
   chunk 61 optimal weight:    0.6980
   chunk 42 optimal weight:    3.9990
   chunk 37 optimal weight:    0.9980
   chunk 28 optimal weight:    0.6980
   chunk 44 optimal weight:    0.7980
   chunk 9 optimal weight:    0.7980
   chunk 69 optimal weight:    0.5980
   chunk 75 optimal weight:    3.9990
   chunk 24 optimal weight:    0.9980
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
A1379 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3756 r_free = 0.3756 target = 0.151354 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3412 r_free = 0.3412 target = 0.120664 restraints weight = 10599.424|
|-----------------------------------------------------------------------------|
r_work (start): 0.3375 rms_B_bonded: 1.89
r_work: 0.3238 rms_B_bonded: 2.63 restraints_weight: 0.5000
r_work: 0.3089 rms_B_bonded: 4.43 restraints_weight: 0.2500
r_work (final): 0.3089
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8004
moved from start:          0.3461

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= 0.182
  Angle     :  0.499   6.624  12525  Z= 0.246
  Chirality :  0.039   0.188   1496
  Planarity :  0.004   0.045   1529
  Dihedral  :  8.486 166.086   1370
  Min Nonbonded Distance : 1.961

Molprobity Statistics.
  All-atom Clashscore : 5.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.97 %
    Favored  : 99.03 %
  Rotamer:
    Outliers :  2.82 %
    Allowed  : 14.81 %
    Favored  : 82.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.57 (0.25), residues: 1133
  helix:  2.52 (0.19), residues: 762
  sheet:  0.40 (0.66), residues: 59
  loop : -0.09 (0.34), residues: 312

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP A1302 
 HIS   0.010   0.001   HIS A1504 
 PHE   0.008   0.001   PHE A 469 
 TYR   0.012   0.001   TYR A1250 
 ARG   0.004   0.000   ARG A 774 

********************** REFINEMENT MACRO_CYCLE 10 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
  138 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 111
  time to evaluate  : 1.015 
Fit side-chains
   revert: symmetry clash
REVERT: A  273 LYS cc_start: 0.7768 (mtpp) cc_final: 0.7561 (ttpp)
REVERT: A  387 MET cc_start: 0.8728 (ttt) cc_final: 0.8449 (mtp)
REVERT: A  690 ARG cc_start: 0.8015 (ptt-90) cc_final: 0.7598 (ptm160)
REVERT: A  724 LYS cc_start: 0.8101 (mptt) cc_final: 0.7526 (mtpp)
REVERT: A  774 ARG cc_start: 0.8097 (ttm-80) cc_final: 0.7674 (tpp-160)
REVERT: A  795 PHE cc_start: 0.8471 (m-80) cc_final: 0.8192 (m-80)
REVERT: A  797 ASP cc_start: 0.8261 (t70) cc_final: 0.7854 (t0)
REVERT: A  817 CYS cc_start: 0.8491 (t) cc_final: 0.8275 (m)
REVERT: A  889 GLU cc_start: 0.7046 (OUTLIER) cc_final: 0.6736 (tt0)
REVERT: A  976 LYS cc_start: 0.7667 (mttp) cc_final: 0.7415 (tptp)
REVERT: A 1073 ILE cc_start: 0.8659 (tt) cc_final: 0.8274 (tt)
REVERT: A 1254 ILE cc_start: 0.8856 (mt) cc_final: 0.8575 (tp)
REVERT: A 1329 LYS cc_start: 0.8406 (ptmt) cc_final: 0.7104 (mtpp)
REVERT: A 1358 MET cc_start: 0.8649 (mmm) cc_final: 0.8408 (tpp)
REVERT: A 1468 MET cc_start: 0.8722 (mtm) cc_final: 0.8155 (mtp)
  outliers start: 27
  outliers final: 26
  residues processed: 129
  average time/residue: 0.2794
  time to fit residues: 49.7758
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  : 1.044 
-------------------------------------------------------------------------------
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 1275 VAL
Chi-restraints excluded: chain A residue 1277 LYS
Chi-restraints excluded: chain A residue 1379 HIS
Chi-restraints excluded: chain A residue 1430 LEU
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
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 10 optimal weight:    3.9990
   chunk 14 optimal weight:    0.8980
   chunk 4 optimal weight:    0.0970
   chunk 58 optimal weight:    6.9990
   chunk 3 optimal weight:    1.9990
   chunk 66 optimal weight:    1.9990
   chunk 70 optimal weight:    0.6980
   chunk 20 optimal weight:    0.3980
   chunk 33 optimal weight:    0.8980
   chunk 47 optimal weight:    3.9990
   chunk 78 optimal weight:    2.9990
   overall best weight:    0.5978

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

Flipped N/Q/H residues before XYZ refinement:
A1379 HIS
A1504 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3767 r_free = 0.3767 target = 0.152265 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3425 r_free = 0.3425 target = 0.121719 restraints weight = 10581.186|
|-----------------------------------------------------------------------------|
r_work (start): 0.3387 rms_B_bonded: 1.88
r_work: 0.3251 rms_B_bonded: 2.62 restraints_weight: 0.5000
r_work: 0.3104 rms_B_bonded: 4.41 restraints_weight: 0.2500
r_work (final): 0.3104
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7992
moved from start:          0.3520

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= 0.170
  Angle     :  0.500   8.023  12525  Z= 0.246
  Chirality :  0.039   0.187   1496
  Planarity :  0.004   0.045   1529
  Dihedral  :  8.418 166.439   1370
  Min Nonbonded Distance : 1.974

Molprobity Statistics.
  All-atom Clashscore : 5.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.97 %
    Favored  : 99.03 %
  Rotamer:
    Outliers :  2.82 %
    Allowed  : 14.81 %
    Favored  : 82.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.62 (0.25), residues: 1133
  helix:  2.55 (0.19), residues: 763
  sheet:  0.41 (0.66), residues: 59
  loop : -0.08 (0.35), residues: 311

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP A1214 
 HIS   0.010   0.001   HIS A1504 
 PHE   0.015   0.001   PHE A1540 
 TYR   0.013   0.001   TYR A1250 
 ARG   0.004   0.000   ARG A 774 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4728.92 seconds
wall clock time: 84 minutes 24.99 seconds (5064.99 seconds total)