Starting phenix.real_space_refine
on Sun Dec 29 02:47:59 2024 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7vlt_32026/12_2024/7vlt_32026_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7vlt_32026/12_2024/7vlt_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_32026/12_2024/7vlt_32026.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7vlt_32026/12_2024/7vlt_32026.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7vlt_32026/12_2024/7vlt_32026_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7vlt_32026/12_2024/7vlt_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-5532/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: 5.77, per 1000 atoms: 0.64
  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: 2.58
  Conformation dependent library (CDL) restraints added in 2.0 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: 1.09
  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: 3.59

  Time building geometry restraints manager: 2.92 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:             0.330
  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:          0.280
  Check model and map are aligned:         0.070
  Set scattering table:                    0.070
  Process input model:                     24.710
  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:             0.000
  Load rotamer database and sin/cos tables:3.110
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   28.720
-------------------------------------------------------------------------------
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  : 0.978 
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: 0.2864
  time to fit residues: 73.1789
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  : 0.932 
-------------------------------------------------------------------------------
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

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8017
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  : 0.939 
Fit side-chains
REVERT: A  273 LYS cc_start: 0.7521 (mtpp) cc_final: 0.7313 (ttpp)
REVERT: A  412 ASN cc_start: 0.8532 (t0) cc_final: 0.7753 (m-40)
REVERT: A  447 ASN cc_start: 0.8213 (m110) cc_final: 0.7976 (t0)
REVERT: A  486 THR cc_start: 0.8868 (m) cc_final: 0.7982 (p)
REVERT: A  573 SER cc_start: 0.8541 (t) cc_final: 0.8186 (m)
REVERT: A  722 GLU cc_start: 0.7158 (tt0) cc_final: 0.6883 (mt-10)
REVERT: A  724 LYS cc_start: 0.7807 (mptt) cc_final: 0.7288 (mtpp)
REVERT: A  764 GLU cc_start: 0.8350 (mm-30) cc_final: 0.7776 (mt-10)
REVERT: A  795 PHE cc_start: 0.8445 (m-80) cc_final: 0.8214 (m-80)
REVERT: A  817 CYS cc_start: 0.8341 (t) cc_final: 0.7957 (m)
REVERT: A  847 MET cc_start: 0.8754 (tpp) cc_final: 0.8361 (tpt)
REVERT: A  910 MET cc_start: 0.7553 (mtp) cc_final: 0.7301 (mtp)
REVERT: A  976 LYS cc_start: 0.7791 (mttp) cc_final: 0.7462 (tptp)
REVERT: A 1158 GLU cc_start: 0.7922 (mt-10) cc_final: 0.7444 (tp30)
REVERT: A 1161 ASP cc_start: 0.7579 (m-30) cc_final: 0.7296 (m-30)
REVERT: A 1270 VAL cc_start: 0.8721 (OUTLIER) cc_final: 0.8510 (t)
REVERT: A 1309 LYS cc_start: 0.8124 (mttt) cc_final: 0.7317 (mppt)
REVERT: A 1426 MET cc_start: 0.7420 (tmm) cc_final: 0.7025 (ttt)
REVERT: A 1468 MET cc_start: 0.8808 (mtm) cc_final: 0.8515 (mtp)
  outliers start: 17
  outliers final: 11
  residues processed: 135
  average time/residue: 0.2798
  time to fit residues: 51.3454
Evaluate side-chains
  118 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 106
  time to evaluate  : 1.068 
-------------------------------------------------------------------------------
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 1270 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 57 optimal weight:    2.9990
   chunk 32 optimal weight:    0.9990
   chunk 86 optimal weight:    0.6980
   chunk 70 optimal weight:    0.7980
   chunk 28 optimal weight:    0.9980
   chunk 103 optimal weight:    0.0470
   chunk 112 optimal weight:    5.9990
   chunk 92 optimal weight:    0.0270
   chunk 102 optimal weight:    0.8980
   chunk 35 optimal weight:    0.4980
   chunk 83 optimal weight:    0.9990
   overall best weight:    0.4136

-------------------------------------------------------------------------------
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
A1259 ASN
A1379 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8002
moved from start:          0.2449

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.041   9208  Z= 0.155
  Angle     :  0.490   6.328  12525  Z= 0.244
  Chirality :  0.039   0.194   1496
  Planarity :  0.004   0.053   1529
  Dihedral  :  8.866 128.611   1376
  Min Nonbonded Distance : 2.002

Molprobity Statistics.
  All-atom Clashscore : 5.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.50 %
    Favored  : 98.50 %
  Rotamer:
    Outliers :  1.88 %
    Allowed  : 12.51 %
    Favored  : 85.61 %
  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:  2.44 (0.25), residues: 1133
  helix:  2.37 (0.19), residues: 758
  sheet:  0.49 (0.62), residues: 65
  loop : -0.02 (0.35), residues: 310

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A 979 
 HIS   0.017   0.001   HIS A1379 
 PHE   0.012   0.001   PHE A1149 
 TYR   0.007   0.001   TYR A1250 
 ARG   0.006   0.000   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
  129 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 111
  time to evaluate  : 1.003 
Fit side-chains
REVERT: A  273 LYS cc_start: 0.7728 (mtpp) cc_final: 0.7480 (ttpp)
REVERT: A  412 ASN cc_start: 0.8566 (t0) cc_final: 0.8327 (t0)
REVERT: A  724 LYS cc_start: 0.7875 (mptt) cc_final: 0.7382 (mtpp)
REVERT: A  763 GLU cc_start: 0.8080 (tt0) cc_final: 0.7802 (tt0)
REVERT: A  764 GLU cc_start: 0.8220 (mm-30) cc_final: 0.7570 (mt-10)
REVERT: A  817 CYS cc_start: 0.8426 (t) cc_final: 0.8080 (m)
REVERT: A  847 MET cc_start: 0.8720 (tpp) cc_final: 0.8317 (tpt)
REVERT: A  898 LYS cc_start: 0.8256 (mmtp) cc_final: 0.7860 (mmtm)
REVERT: A  910 MET cc_start: 0.7397 (mtp) cc_final: 0.6897 (mtp)
REVERT: A  976 LYS cc_start: 0.7804 (mttp) cc_final: 0.7489 (tptp)
REVERT: A 1158 GLU cc_start: 0.7865 (mt-10) cc_final: 0.7583 (tp30)
REVERT: A 1254 ILE cc_start: 0.8772 (mt) cc_final: 0.8401 (tp)
REVERT: A 1309 LYS cc_start: 0.8004 (mttt) cc_final: 0.7169 (mppt)
REVERT: A 1311 HIS cc_start: 0.6920 (m90) cc_final: 0.6712 (m170)
REVERT: A 1358 MET cc_start: 0.8814 (mmm) cc_final: 0.8308 (mmm)
REVERT: A 1468 MET cc_start: 0.8897 (mtm) cc_final: 0.8524 (mtp)
  outliers start: 18
  outliers final: 11
  residues processed: 124
  average time/residue: 0.2363
  time to fit residues: 40.1991
Evaluate side-chains
  109 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 98
  time to evaluate  : 0.890 
-------------------------------------------------------------------------------
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  508 GLU
Chi-restraints excluded: chain A residue  543 ILE
Chi-restraints excluded: chain A residue  781 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 1259 ASN
Chi-restraints excluded: chain A residue 1277 LYS
Chi-restraints excluded: chain A residue 1379 HIS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 102 optimal weight:    3.9990
   chunk 77 optimal weight:    4.9990
   chunk 53 optimal weight:    2.9990
   chunk 11 optimal weight:    0.7980
   chunk 49 optimal weight:    0.8980
   chunk 69 optimal weight:    2.9990
   chunk 104 optimal weight:    0.7980
   chunk 110 optimal weight:    6.9990
   chunk 54 optimal weight:    0.9990
   chunk 98 optimal weight:    0.9990
   chunk 29 optimal weight:    3.9990
   overall best weight:    0.8984

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

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

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8051
moved from start:          0.2674

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   9208  Z= 0.205
  Angle     :  0.509   6.604  12525  Z= 0.251
  Chirality :  0.040   0.190   1496
  Planarity :  0.004   0.051   1529
  Dihedral  :  8.599 132.285   1369
  Min Nonbonded Distance : 1.943

Molprobity Statistics.
  All-atom Clashscore : 5.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.50 %
    Favored  : 98.50 %
  Rotamer:
    Outliers :  2.50 %
    Allowed  : 12.41 %
    Favored  : 85.09 %
  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:  2.42 (0.25), residues: 1133
  helix:  2.36 (0.19), residues: 758
  sheet:  0.83 (0.69), residues: 59
  loop : -0.08 (0.34), residues: 316

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A 677 
 HIS   0.008   0.001   HIS A1379 
 PHE   0.010   0.001   PHE A1149 
 TYR   0.009   0.001   TYR A1250 
 ARG   0.004   0.000   ARG A 820 

*********************** 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
  134 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 110
  time to evaluate  : 0.916 
Fit side-chains
REVERT: A  273 LYS cc_start: 0.7811 (mtpp) cc_final: 0.7572 (ttpp)
REVERT: A  412 ASN cc_start: 0.8557 (t0) cc_final: 0.8333 (t0)
REVERT: A  724 LYS cc_start: 0.7933 (mptt) cc_final: 0.7426 (mtpp)
REVERT: A  763 GLU cc_start: 0.8108 (tt0) cc_final: 0.7809 (tt0)
REVERT: A  764 GLU cc_start: 0.8265 (mm-30) cc_final: 0.7593 (mt-10)
REVERT: A  795 PHE cc_start: 0.8394 (m-80) cc_final: 0.8192 (m-80)
REVERT: A  817 CYS cc_start: 0.8581 (t) cc_final: 0.8239 (m)
REVERT: A  898 LYS cc_start: 0.8404 (mmtp) cc_final: 0.7944 (mmtm)
REVERT: A  910 MET cc_start: 0.7483 (mtp) cc_final: 0.6995 (mtp)
REVERT: A  976 LYS cc_start: 0.7731 (mttp) cc_final: 0.7440 (tptp)
REVERT: A 1161 ASP cc_start: 0.7552 (m-30) cc_final: 0.7290 (m-30)
REVERT: A 1254 ILE cc_start: 0.8861 (mt) cc_final: 0.8480 (tp)
REVERT: A 1309 LYS cc_start: 0.8089 (mttt) cc_final: 0.7222 (mppt)
REVERT: A 1358 MET cc_start: 0.8852 (mmm) cc_final: 0.8368 (mmm)
REVERT: A 1468 MET cc_start: 0.8903 (mtm) cc_final: 0.8527 (mtp)
  outliers start: 24
  outliers final: 20
  residues processed: 127
  average time/residue: 0.2386
  time to fit residues: 41.6209
Evaluate side-chains
  118 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 98
  time to evaluate  : 1.042 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  375 GLU
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  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 1277 LYS
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=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 91 optimal weight:   10.0000
   chunk 62 optimal weight:    0.0670
   chunk 1 optimal weight:    2.9990
   chunk 82 optimal weight:    0.8980
   chunk 45 optimal weight:    4.9990
   chunk 94 optimal weight:    6.9990
   chunk 76 optimal weight:    2.9990
   chunk 0 optimal weight:    4.9990
   chunk 56 optimal weight:    2.9990
   chunk 98 optimal weight:    0.9980
   chunk 27 optimal weight:    0.8980
   overall best weight:    1.1720

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

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8091
moved from start:          0.2949

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048   9208  Z= 0.244
  Angle     :  0.536   7.265  12525  Z= 0.264
  Chirality :  0.041   0.199   1496
  Planarity :  0.004   0.049   1529
  Dihedral  :  8.437 141.600   1369
  Min Nonbonded Distance : 1.916

Molprobity Statistics.
  All-atom Clashscore : 5.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.32 %
    Favored  : 98.68 %
  Rotamer:
    Outliers :  2.50 %
    Allowed  : 13.76 %
    Favored  : 83.73 %
  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:  2.28 (0.25), residues: 1133
  helix:  2.25 (0.19), residues: 758
  sheet:  0.75 (0.69), residues: 59
  loop : -0.13 (0.34), residues: 316

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A1260 
 HIS   0.008   0.001   HIS A1504 
 PHE   0.012   0.001   PHE A1362 
 TYR   0.013   0.001   TYR A 532 
 ARG   0.004   0.000   ARG A 774 

*********************** 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
  137 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 113
  time to evaluate  : 1.075 
Fit side-chains
REVERT: A  273 LYS cc_start: 0.7858 (mtpp) cc_final: 0.7624 (ttpp)
REVERT: A  412 ASN cc_start: 0.8642 (t0) cc_final: 0.8416 (t0)
REVERT: A  591 PHE cc_start: 0.8945 (m-80) cc_final: 0.8630 (m-10)
REVERT: A  705 CYS cc_start: 0.8084 (m) cc_final: 0.7873 (p)
REVERT: A  724 LYS cc_start: 0.7982 (mptt) cc_final: 0.7400 (mtpp)
REVERT: A  774 ARG cc_start: 0.8189 (ttm-80) cc_final: 0.7942 (tpp-160)
REVERT: A  795 PHE cc_start: 0.8476 (m-80) cc_final: 0.8100 (m-80)
REVERT: A  797 ASP cc_start: 0.8083 (t70) cc_final: 0.7730 (t0)
REVERT: A  817 CYS cc_start: 0.8686 (t) cc_final: 0.8378 (m)
REVERT: A  898 LYS cc_start: 0.8362 (mmtp) cc_final: 0.7947 (mmtm)
REVERT: A  910 MET cc_start: 0.7560 (mtp) cc_final: 0.7355 (mtp)
REVERT: A  976 LYS cc_start: 0.7752 (mttp) cc_final: 0.7481 (tptp)
REVERT: A 1073 ILE cc_start: 0.8764 (tt) cc_final: 0.8410 (tt)
REVERT: A 1157 GLN cc_start: 0.8228 (tp40) cc_final: 0.8015 (mm-40)
REVERT: A 1161 ASP cc_start: 0.7649 (m-30) cc_final: 0.7324 (m-30)
REVERT: A 1254 ILE cc_start: 0.8914 (mt) cc_final: 0.8572 (tp)
REVERT: A 1309 LYS cc_start: 0.8209 (mttt) cc_final: 0.7188 (mptt)
REVERT: A 1468 MET cc_start: 0.8890 (mtm) cc_final: 0.8466 (mtp)
  outliers start: 24
  outliers final: 22
  residues processed: 128
  average time/residue: 0.2539
  time to fit residues: 44.0158
Evaluate side-chains
  121 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 99
  time to evaluate  : 1.023 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  375 GLU
Chi-restraints excluded: chain A residue  387 MET
Chi-restraints excluded: chain A residue  405 MET
Chi-restraints excluded: chain A residue  434 MET
Chi-restraints excluded: chain A residue  508 GLU
Chi-restraints excluded: chain A residue  534 SER
Chi-restraints excluded: chain A residue  543 ILE
Chi-restraints excluded: chain A residue  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 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 37 optimal weight:    0.9980
   chunk 99 optimal weight:    0.9980
   chunk 21 optimal weight:    0.9990
   chunk 64 optimal weight:    0.9990
   chunk 27 optimal weight:    1.9990
   chunk 110 optimal weight:    6.9990
   chunk 91 optimal weight:    9.9990
   chunk 51 optimal weight:    0.9980
   chunk 9 optimal weight:    0.9990
   chunk 36 optimal weight:    2.9990
   chunk 57 optimal weight:    8.9990
   overall best weight:    0.9984

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

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8081
moved from start:          0.3099

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   9208  Z= 0.219
  Angle     :  0.523   6.922  12525  Z= 0.257
  Chirality :  0.040   0.199   1496
  Planarity :  0.004   0.048   1529
  Dihedral  :  8.335 145.873   1369
  Min Nonbonded Distance : 1.934

Molprobity Statistics.
  All-atom Clashscore : 5.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.24 %
    Favored  : 98.76 %
  Rotamer:
    Outliers :  3.13 %
    Allowed  : 13.56 %
    Favored  : 83.32 %
  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:  0.61 (0.67), residues: 59
  loop : -0.15 (0.34), residues: 316

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A1260 
 HIS   0.009   0.001   HIS A1379 
 PHE   0.009   0.001   PHE A1149 
 TYR   0.016   0.001   TYR A1250 
 ARG   0.003   0.000   ARG A 820 

*********************** 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
  139 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 109
  time to evaluate  : 1.004 
Fit side-chains
REVERT: A  273 LYS cc_start: 0.7849 (mtpp) cc_final: 0.7625 (ttpp)
REVERT: A  387 MET cc_start: 0.8723 (OUTLIER) cc_final: 0.8308 (mtt)
REVERT: A  591 PHE cc_start: 0.8950 (m-80) cc_final: 0.8644 (m-10)
REVERT: A  690 ARG cc_start: 0.7970 (ptt-90) cc_final: 0.7559 (ptm160)
REVERT: A  705 CYS cc_start: 0.8109 (m) cc_final: 0.7814 (p)
REVERT: A  724 LYS cc_start: 0.7984 (mptt) cc_final: 0.7364 (mtpp)
REVERT: A  795 PHE cc_start: 0.8462 (m-80) cc_final: 0.8032 (m-80)
REVERT: A  797 ASP cc_start: 0.8057 (t70) cc_final: 0.7742 (t0)
REVERT: A  817 CYS cc_start: 0.8681 (t) cc_final: 0.8375 (m)
REVERT: A  910 MET cc_start: 0.7550 (mtp) cc_final: 0.7344 (mtp)
REVERT: A  976 LYS cc_start: 0.7757 (mttp) cc_final: 0.7479 (tptp)
REVERT: A 1161 ASP cc_start: 0.7628 (m-30) cc_final: 0.7405 (m-30)
REVERT: A 1254 ILE cc_start: 0.8910 (mt) cc_final: 0.8556 (tp)
REVERT: A 1309 LYS cc_start: 0.8227 (mttt) cc_final: 0.7416 (mptt)
REVERT: A 1416 GLU cc_start: 0.8067 (tp30) cc_final: 0.7668 (tt0)
REVERT: A 1468 MET cc_start: 0.8871 (mtm) cc_final: 0.8440 (mtp)
  outliers start: 30
  outliers final: 24
  residues processed: 129
  average time/residue: 0.2297
  time to fit residues: 40.5815
Evaluate side-chains
  129 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 104
  time to evaluate  : 0.944 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  375 GLU
Chi-restraints excluded: chain A residue  387 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  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 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 106 optimal weight:    3.9990
   chunk 12 optimal weight:    0.9990
   chunk 62 optimal weight:    0.0770
   chunk 80 optimal weight:    1.9990
   chunk 92 optimal weight:    2.9990
   chunk 61 optimal weight:    0.7980
   chunk 109 optimal weight:    1.9990
   chunk 68 optimal weight:    0.9980
   chunk 66 optimal weight:    5.9990
   chunk 50 optimal weight:    0.2980
   chunk 67 optimal weight:    1.9990
   overall best weight:    0.6340

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

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

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8054
moved from start:          0.3237

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= 0.173
  Angle     :  0.497   6.862  12525  Z= 0.246
  Chirality :  0.039   0.195   1496
  Planarity :  0.004   0.047   1529
  Dihedral  :  8.195 148.620   1369
  Min Nonbonded Distance : 1.974

Molprobity Statistics.
  All-atom Clashscore : 6.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.15 %
    Favored  : 98.85 %
  Rotamer:
    Outliers :  2.71 %
    Allowed  : 14.49 %
    Favored  : 82.79 %
  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:  2.51 (0.19), residues: 758
  sheet:  0.58 (0.67), residues: 59
  loop : -0.15 (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   0.011   0.001   TYR A1250 
 ARG   0.005   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
  134 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 108
  time to evaluate  : 0.959 
Fit side-chains
REVERT: A  273 LYS cc_start: 0.7853 (mtpp) cc_final: 0.7649 (ttpp)
REVERT: A  387 MET cc_start: 0.8627 (OUTLIER) cc_final: 0.8411 (mtp)
REVERT: A  690 ARG cc_start: 0.7974 (ptt-90) cc_final: 0.7546 (ptm160)
REVERT: A  724 LYS cc_start: 0.7865 (mptt) cc_final: 0.7326 (mtpp)
REVERT: A  774 ARG cc_start: 0.8152 (ttm-80) cc_final: 0.7661 (tpp-160)
REVERT: A  795 PHE cc_start: 0.8389 (m-80) cc_final: 0.8113 (m-80)
REVERT: A  797 ASP cc_start: 0.8022 (t70) cc_final: 0.7709 (t0)
REVERT: A  889 GLU cc_start: 0.7328 (OUTLIER) cc_final: 0.7054 (tt0)
REVERT: A  976 LYS cc_start: 0.7788 (mttp) cc_final: 0.7516 (tptp)
REVERT: A 1073 ILE cc_start: 0.8626 (tt) cc_final: 0.8310 (tt)
REVERT: A 1161 ASP cc_start: 0.7596 (m-30) cc_final: 0.7379 (m-30)
REVERT: A 1254 ILE cc_start: 0.8942 (mt) cc_final: 0.8648 (tp)
REVERT: A 1309 LYS cc_start: 0.8212 (mttt) cc_final: 0.7407 (mptt)
REVERT: A 1416 GLU cc_start: 0.8096 (tp30) cc_final: 0.7825 (tt0)
REVERT: A 1468 MET cc_start: 0.8879 (mtm) cc_final: 0.8337 (mtp)
  outliers start: 26
  outliers final: 22
  residues processed: 124
  average time/residue: 0.2403
  time to fit residues: 40.7137
Evaluate side-chains
  130 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 106
  time to evaluate  : 1.147 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  375 GLU
Chi-restraints excluded: chain A residue  387 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 1259 ASN
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 43 optimal weight:    2.9990
   chunk 65 optimal weight:    2.9990
   chunk 33 optimal weight:    0.7980
   chunk 21 optimal weight:    0.7980
   chunk 69 optimal weight:    2.9990
   chunk 74 optimal weight:    0.7980
   chunk 54 optimal weight:    0.9990
   chunk 10 optimal weight:    3.9990
   chunk 86 optimal weight:    0.7980
   chunk 99 optimal weight:    0.5980
   chunk 105 optimal weight:    0.8980
   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 841 HIS
A1379 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8062
moved from start:          0.3287

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= 0.187
  Angle     :  0.499   6.533  12525  Z= 0.247
  Chirality :  0.039   0.191   1496
  Planarity :  0.004   0.046   1529
  Dihedral  :  8.178 152.637   1366
  Min Nonbonded Distance : 1.952

Molprobity Statistics.
  All-atom Clashscore : 6.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.24 %
    Favored  : 98.76 %
  Rotamer:
    Outliers :  2.92 %
    Allowed  : 14.29 %
    Favored  : 82.79 %
  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:  2.55 (0.25), residues: 1133
  helix:  2.50 (0.19), residues: 761
  sheet:  0.55 (0.67), residues: 59
  loop : -0.13 (0.34), residues: 313

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP A1055 
 HIS   0.009   0.001   HIS A1504 
 PHE   0.011   0.001   PHE A1362 
 TYR   0.015   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
  132 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 104
  time to evaluate  : 1.026 
Fit side-chains
REVERT: A  387 MET cc_start: 0.8650 (OUTLIER) cc_final: 0.8423 (mtp)
REVERT: A  690 ARG cc_start: 0.7975 (ptt-90) cc_final: 0.7548 (ptm160)
REVERT: A  724 LYS cc_start: 0.7864 (mptt) cc_final: 0.7302 (mtpp)
REVERT: A  774 ARG cc_start: 0.8135 (ttm-80) cc_final: 0.7699 (tpp-160)
REVERT: A  795 PHE cc_start: 0.8394 (m-80) cc_final: 0.8069 (m-80)
REVERT: A  797 ASP cc_start: 0.8061 (t70) cc_final: 0.7754 (t0)
REVERT: A  889 GLU cc_start: 0.7325 (OUTLIER) cc_final: 0.7055 (tt0)
REVERT: A  910 MET cc_start: 0.7442 (mtp) cc_final: 0.6975 (mtp)
REVERT: A  976 LYS cc_start: 0.7784 (mttp) cc_final: 0.7501 (tptp)
REVERT: A 1073 ILE cc_start: 0.8622 (tt) cc_final: 0.8292 (tt)
REVERT: A 1254 ILE cc_start: 0.8958 (mt) cc_final: 0.8658 (tp)
REVERT: A 1309 LYS cc_start: 0.8225 (mttt) cc_final: 0.7417 (mptt)
REVERT: A 1416 GLU cc_start: 0.8100 (tp30) cc_final: 0.7832 (tt0)
REVERT: A 1468 MET cc_start: 0.8870 (mtm) cc_final: 0.8329 (mtp)
  outliers start: 28
  outliers final: 25
  residues processed: 121
  average time/residue: 0.2405
  time to fit residues: 39.9676
Evaluate side-chains
  128 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 101
  time to evaluate  : 1.075 
-------------------------------------------------------------------------------
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  387 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  808 LEU
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 96 optimal weight:    7.9990
   chunk 102 optimal weight:    0.7980
   chunk 105 optimal weight:    0.9980
   chunk 61 optimal weight:    0.6980
   chunk 44 optimal weight:    1.9990
   chunk 80 optimal weight:    1.9990
   chunk 31 optimal weight:    0.7980
   chunk 92 optimal weight:    1.9990
   chunk 67 optimal weight:    0.6980
   chunk 108 optimal weight:    2.9990
   chunk 66 optimal weight:    1.9990
   overall best weight:    0.7980

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

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

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8063
moved from start:          0.3348

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= 0.191
  Angle     :  0.504   7.267  12525  Z= 0.248
  Chirality :  0.039   0.190   1496
  Planarity :  0.004   0.046   1529
  Dihedral  :  8.209 158.193   1366
  Min Nonbonded Distance : 1.949

Molprobity Statistics.
  All-atom Clashscore : 6.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.06 %
    Favored  : 98.94 %
  Rotamer:
    Outliers :  2.92 %
    Allowed  : 14.18 %
    Favored  : 82.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  2.53 (0.25), residues: 1133
  helix:  2.50 (0.19), residues: 758
  sheet:  0.57 (0.67), 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   0.009   0.001   HIS A1504 
 PHE   0.010   0.001   PHE A1362 
 TYR   0.014   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  : 0.979 
Fit side-chains
REVERT: A  387 MET cc_start: 0.8657 (OUTLIER) cc_final: 0.8430 (mtp)
REVERT: A  690 ARG cc_start: 0.7972 (ptt-90) cc_final: 0.7548 (ptm160)
REVERT: A  724 LYS cc_start: 0.7866 (mptt) cc_final: 0.7304 (mtpp)
REVERT: A  774 ARG cc_start: 0.8134 (ttm-80) cc_final: 0.7706 (tpp-160)
REVERT: A  795 PHE cc_start: 0.8399 (m-80) cc_final: 0.8070 (m-80)
REVERT: A  797 ASP cc_start: 0.8155 (t70) cc_final: 0.7806 (t0)
REVERT: A  889 GLU cc_start: 0.7315 (OUTLIER) cc_final: 0.7039 (tt0)
REVERT: A  910 MET cc_start: 0.7457 (mtp) cc_final: 0.7173 (mtp)
REVERT: A  976 LYS cc_start: 0.7781 (mttp) cc_final: 0.7498 (tptp)
REVERT: A 1073 ILE cc_start: 0.8616 (tt) cc_final: 0.8287 (tt)
REVERT: A 1254 ILE cc_start: 0.8959 (mt) cc_final: 0.8657 (tp)
REVERT: A 1309 LYS cc_start: 0.8241 (mttt) cc_final: 0.7430 (mptt)
REVERT: A 1406 GLU cc_start: 0.7563 (mp0) cc_final: 0.7038 (mp0)
REVERT: A 1416 GLU cc_start: 0.8101 (tp30) cc_final: 0.7837 (tt0)
REVERT: A 1468 MET cc_start: 0.8869 (mtm) cc_final: 0.8382 (mtp)
  outliers start: 28
  outliers final: 26
  residues processed: 125
  average time/residue: 0.2342
  time to fit residues: 40.1256
Evaluate side-chains
  131 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 103
  time to evaluate  : 0.978 
-------------------------------------------------------------------------------
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  387 MET
Chi-restraints excluded: chain A residue  405 MET
Chi-restraints excluded: chain A residue  434 MET
Chi-restraints excluded: chain A residue  534 SER
Chi-restraints excluded: chain A residue  543 ILE
Chi-restraints excluded: chain A residue  563 LEU
Chi-restraints excluded: chain A residue  580 THR
Chi-restraints excluded: chain A residue  586 SER
Chi-restraints excluded: chain A residue  593 VAL
Chi-restraints excluded: chain A residue  781 THR
Chi-restraints excluded: chain A residue  799 THR
Chi-restraints excluded: chain A residue  836 SER
Chi-restraints excluded: chain A residue  842 LEU
Chi-restraints excluded: chain A residue  889 GLU
Chi-restraints excluded: chain A residue  987 PHE
Chi-restraints excluded: chain A residue  993 MET
Chi-restraints excluded: chain A residue 1140 VAL
Chi-restraints excluded: chain A residue 1227 VAL
Chi-restraints excluded: chain A residue 1255 THR
Chi-restraints excluded: chain A residue 1259 ASN
Chi-restraints excluded: chain A residue 1275 VAL
Chi-restraints excluded: chain A residue 1277 LYS
Chi-restraints excluded: chain A residue 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 51 optimal weight:    0.8980
   chunk 75 optimal weight:    4.9990
   chunk 113 optimal weight:    7.9990
   chunk 104 optimal weight:    1.9990
   chunk 90 optimal weight:   10.0000
   chunk 9 optimal weight:    0.9990
   chunk 69 optimal weight:    0.7980
   chunk 55 optimal weight:    0.6980
   chunk 71 optimal weight:    0.6980
   chunk 96 optimal weight:    2.9990
   chunk 27 optimal weight:    2.9990
   overall best weight:    0.8182

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

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8063
moved from start:          0.3378

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= 0.194
  Angle     :  0.508   7.042  12525  Z= 0.251
  Chirality :  0.039   0.188   1496
  Planarity :  0.004   0.046   1529
  Dihedral  :  8.256 161.966   1366
  Min Nonbonded Distance : 1.948

Molprobity Statistics.
  All-atom Clashscore : 6.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.15 %
    Favored  : 98.85 %
  Rotamer:
    Outliers :  3.02 %
    Allowed  : 13.97 %
    Favored  : 83.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  2.53 (0.25), residues: 1133
  helix:  2.51 (0.19), residues: 758
  sheet:  0.50 (0.67), residues: 59
  loop : -0.16 (0.34), residues: 316

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP A1055 
 HIS   0.010   0.001   HIS A1504 
 PHE   0.010   0.001   PHE A1362 
 TYR   0.014   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
  134 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 105
  time to evaluate  : 1.054 
Fit side-chains
   revert: symmetry clash
REVERT: A  387 MET cc_start: 0.8661 (OUTLIER) cc_final: 0.8432 (mtp)
REVERT: A  690 ARG cc_start: 0.7971 (ptt-90) cc_final: 0.7546 (ptm160)
REVERT: A  724 LYS cc_start: 0.7839 (mptt) cc_final: 0.7309 (mtpp)
REVERT: A  774 ARG cc_start: 0.8135 (ttm-80) cc_final: 0.7708 (tpp-160)
REVERT: A  795 PHE cc_start: 0.8403 (m-80) cc_final: 0.8040 (m-80)
REVERT: A  797 ASP cc_start: 0.8155 (t70) cc_final: 0.7816 (t0)
REVERT: A  889 GLU cc_start: 0.7228 (OUTLIER) cc_final: 0.6951 (tt0)
REVERT: A  910 MET cc_start: 0.7466 (mtp) cc_final: 0.6988 (mtp)
REVERT: A  976 LYS cc_start: 0.7779 (mttp) cc_final: 0.7496 (tptp)
REVERT: A 1073 ILE cc_start: 0.8618 (tt) cc_final: 0.8288 (tt)
REVERT: A 1254 ILE cc_start: 0.8959 (mt) cc_final: 0.8658 (tp)
REVERT: A 1309 LYS cc_start: 0.8256 (mttt) cc_final: 0.7441 (mptt)
REVERT: A 1406 GLU cc_start: 0.7534 (mp0) cc_final: 0.7049 (mp0)
REVERT: A 1416 GLU cc_start: 0.8105 (tp30) cc_final: 0.7839 (tt0)
REVERT: A 1468 MET cc_start: 0.8869 (mtm) cc_final: 0.8385 (mtp)
  outliers start: 29
  outliers final: 26
  residues processed: 122
  average time/residue: 0.2467
  time to fit residues: 41.6904
Evaluate side-chains
  133 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 105
  time to evaluate  : 1.015 
-------------------------------------------------------------------------------
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  387 MET
Chi-restraints excluded: chain A residue  405 MET
Chi-restraints excluded: chain A residue  434 MET
Chi-restraints excluded: chain A residue  534 SER
Chi-restraints excluded: chain A residue  543 ILE
Chi-restraints excluded: chain A residue  563 LEU
Chi-restraints excluded: chain A residue  580 THR
Chi-restraints excluded: chain A residue  586 SER
Chi-restraints excluded: chain A residue  593 VAL
Chi-restraints excluded: chain A residue  781 THR
Chi-restraints excluded: chain A residue  799 THR
Chi-restraints excluded: chain A residue  808 LEU
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 83 optimal weight:    3.9990
   chunk 13 optimal weight:    2.9990
   chunk 25 optimal weight:    0.9980
   chunk 90 optimal weight:    0.6980
   chunk 37 optimal weight:    0.9990
   chunk 93 optimal weight:    0.6980
   chunk 11 optimal weight:    0.6980
   chunk 16 optimal weight:    0.5980
   chunk 79 optimal weight:    1.9990
   chunk 5 optimal weight:    0.9980
   chunk 65 optimal weight:    2.9990
   overall best weight:    0.7380

-------------------------------------------------------------------------------
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 = 0.3759 r_free = 0.3759 target = 0.151580 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3414 r_free = 0.3414 target = 0.120782 restraints weight = 10411.164|
|-----------------------------------------------------------------------------|
r_work (start): 0.3374 rms_B_bonded: 1.88
r_work: 0.3240 rms_B_bonded: 2.61 restraints_weight: 0.5000
r_work: 0.3088 rms_B_bonded: 4.43 restraints_weight: 0.2500
r_work (final): 0.3088
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8000
moved from start:          0.3429

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= 0.185
  Angle     :  0.504   8.035  12525  Z= 0.249
  Chirality :  0.039   0.188   1496
  Planarity :  0.004   0.046   1529
  Dihedral  :  8.253 164.935   1366
  Min Nonbonded Distance : 1.957

Molprobity Statistics.
  All-atom Clashscore : 6.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.15 %
    Favored  : 98.85 %
  Rotamer:
    Outliers :  2.82 %
    Allowed  : 13.97 %
    Favored  : 83.21 %
  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:  2.56 (0.25), residues: 1133
  helix:  2.54 (0.19), residues: 758
  sheet:  0.41 (0.66), residues: 59
  loop : -0.15 (0.34), residues: 316

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP A1055 
 HIS   0.010   0.001   HIS A1504 
 PHE   0.015   0.001   PHE A1540 
 TYR   0.014   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: 2046.40 seconds
wall clock time: 38 minutes 14.78 seconds (2294.78 seconds total)