Starting phenix.real_space_refine
on Fri Dec  8 19:51:11 2023 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vlt_32026/12_2023/7vlt_32026_neut.pdb
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vlt_32026/12_2023/7vlt_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vlt_32026/12_2023/7vlt_32026.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vlt_32026/12_2023/7vlt_32026.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vlt_32026/12_2023/7vlt_32026_neut.pdb"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vlt_32026/12_2023/7vlt_32026_neut.pdb"
  }
  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

  Symmetric amino acids flipped
    None
  Time to flip residues: 0.05s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib"
  Total number of atoms: 9024
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 9024
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1151, 9024
          Unusual residues: {' MG': 2, 'ADP': 1, 'ATP': 1, 'ETJ': 1, 'Y01': 1}
          Classifications: {'peptide': 1145, 'undetermined': 6}
          Incomplete info: {'truncation_to_alanine': 26}
          Link IDs: {'PTRANS': 33, 'TRANS': 1111, None: 6}
            Not linked:
              pdbres="MET A1545 "
              pdbres="ETJ A2001 "
            Not linked:
              pdbres="ETJ A2001 "
              pdbres="Y01 A2002 "
            Not linked:
              pdbres="Y01 A2002 "
              pdbres="ADP A2003 "
            Not linked:
              pdbres="ADP A2003 "
              pdbres=" MG A2004 "
            Not linked:
              pdbres=" MG A2004 "
              pdbres=" MG A2005 "
            Not linked:
              pdbres=" MG A2005 "
              pdbres="ATP A2006 "
          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
  Time building chain proxies: 5.28, per 1000 atoms: 0.59
  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  - 3.50
        Amino acid           : False - 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: 3.82
  Conformation dependent library (CDL) restraints added in 1.7 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: 1.14
  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: 3.15

  Time building geometry restraints manager: 4.10 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:
       99.58 -   115.21: 5987
      115.21 -   130.84: 6491
      130.84 -   146.47: 46
      146.47 -   162.11: 0
      162.11 -   177.74: 1
  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 2.440
  ... (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:             0.460
  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:             0.000
  Extract box with map and model:          2.200
  Check model and map are aligned:         0.130
  Set scattering table:                    0.080
  Process input model:                     27.980
  Find NCS groups from input model:        0.230
  Set up NCS constraints:                  0.030
  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:2.980
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   34.090
-------------------------------------------------------------------------------
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 fitting.
    rotamer outliers: 21
    poor density    : 180
  time to evaluate  : 0.942 
Fit side-chains
  outliers start: 21
  outliers final: 8
  residues processed: 198
  average time/residue: 0.2868
  time to fit residues: 73.3799
Evaluate side-chains
  106 residues out of total 986 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 8
    poor density    : 98
  time to evaluate  : 0.996 
Switching outliers to nearest non-outliers
  outliers start: 8
  outliers final: 0
  residues processed: 8
  average time/residue: 0.1559
  time to fit residues: 3.2536
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 97 optimal weight:    0.0970
   chunk 87 optimal weight:    0.9980
   chunk 48 optimal weight:    0.6980
   chunk 29 optimal weight:    3.9990
   chunk 58 optimal weight:    0.7980
   chunk 46 optimal weight:    4.9990
   chunk 90 optimal weight:    7.9990
   chunk 34 optimal weight:    0.0980
   chunk 54 optimal weight:    7.9990
   chunk 67 optimal weight:    0.5980
   chunk 104 optimal weight:    2.9990
   overall best weight:    0.4578

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

Flipped N/Q/H residues before XYZ refinement:
A1097 ASN
A1259 ASN
A1379 HIS
A1444 ASN
A1504 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7992
moved from start:          0.2145

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= 0.171
  Angle     :  0.526   6.736  12525  Z= 0.264
  Chirality :  0.040   0.191   1496
  Planarity :  0.004   0.053   1529
  Dihedral  :  8.702 124.169   1364
  Min Nonbonded Distance : 1.990

Molprobity Statistics.
  All-atom Clashscore : 6.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.41 %
    Favored  : 98.59 %
  Rotamer:
    Outliers :  1.04 %
    Allowed  : 11.26 %
    Favored  : 87.70 %
  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:  2.00 (0.25), residues: 1133
  helix:  2.01 (0.19), residues: 752
  sheet:  0.58 (0.62), residues: 65
  loop : -0.13 (0.35), residues: 316

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.007   0.001   TRP A1055 
   HIS   0.009   0.001   HIS A1504 
   PHE   0.017   0.001   PHE A1142 
   TYR   0.014   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
  129 residues out of total 986 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 10
    poor density    : 119
  time to evaluate  : 0.924 
Fit side-chains
  outliers start: 10
  outliers final: 6
  residues processed: 127
  average time/residue: 0.2459
  time to fit residues: 42.3666
Evaluate side-chains
  106 residues out of total 986 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 6
    poor density    : 100
  time to evaluate  : 0.974 
Switching outliers to nearest non-outliers
  outliers start: 6
  outliers final: 0
  residues processed: 6
  average time/residue: 0.1475
  time to fit residues: 2.6568
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 58 optimal weight:    3.9990
   chunk 32 optimal weight:    0.4980
   chunk 86 optimal weight:    0.8980
   chunk 71 optimal weight:    0.7980
   chunk 28 optimal weight:    0.7980
   chunk 104 optimal weight:    2.9990
   chunk 113 optimal weight:    0.0060
   chunk 93 optimal weight:   10.0000
   chunk 103 optimal weight:    1.9990
   chunk 35 optimal weight:    1.9990
   chunk 83 optimal weight:    5.9990
   overall best weight:    0.5996

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

Flipped N/Q/H residues before XYZ refinement:
A 326 ASN
A 412 ASN
A 447 ASN
A1259 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8022
moved from start:          0.2697

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   9208  Z= 0.172
  Angle     :  0.498   6.484  12525  Z= 0.248
  Chirality :  0.039   0.184   1496
  Planarity :  0.004   0.052   1529
  Dihedral  :  8.288 124.120   1364
  Min Nonbonded Distance : 1.963

Molprobity Statistics.
  All-atom Clashscore : 6.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.32 %
    Favored  : 98.68 %
  Rotamer:
    Outliers :  1.56 %
    Allowed  : 12.51 %
    Favored  : 85.92 %
  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:  2.40 (0.25), residues: 1133
  helix:  2.35 (0.19), residues: 757
  sheet:  0.61 (0.63), residues: 65
  loop : -0.08 (0.35), residues: 311

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.005   0.001   TRP A 906 
   HIS   0.008   0.001   HIS A1504 
   PHE   0.012   0.001   PHE A1149 
   TYR   0.008   0.001   TYR A1250 
   ARG   0.003   0.000   ARG A 820 

*********************** 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
  123 residues out of total 986 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 15
    poor density    : 108
  time to evaluate  : 0.923 
Fit side-chains
  outliers start: 15
  outliers final: 10
  residues processed: 118
  average time/residue: 0.2549
  time to fit residues: 40.7748
Evaluate side-chains
  104 residues out of total 986 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 10
    poor density    : 94
  time to evaluate  : 1.062 
Switching outliers to nearest non-outliers
  outliers start: 10
  outliers final: 0
  residues processed: 10
  average time/residue: 0.0929
  time to fit residues: 3.1382
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 103 optimal weight:    1.9990
   chunk 78 optimal weight:    3.9990
   chunk 54 optimal weight:    6.9990
   chunk 11 optimal weight:    0.7980
   chunk 49 optimal weight:    2.9990
   chunk 70 optimal weight:    0.6980
   chunk 104 optimal weight:    2.9990
   chunk 111 optimal weight:    4.9990
   chunk 99 optimal weight:    0.7980
   chunk 29 optimal weight:    0.8980
   chunk 92 optimal weight:    7.9990
   overall best weight:    1.0382

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

Flipped N/Q/H residues before XYZ refinement:
A 260 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8068
moved from start:          0.2937

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051   9208  Z= 0.222
  Angle     :  0.524   7.140  12525  Z= 0.258
  Chirality :  0.040   0.194   1496
  Planarity :  0.004   0.050   1529
  Dihedral  :  8.131 126.072   1364
  Min Nonbonded Distance : 1.929

Molprobity Statistics.
  All-atom Clashscore : 6.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.41 %
    Favored  : 98.59 %
  Rotamer:
    Outliers :  1.25 %
    Allowed  : 13.35 %
    Favored  : 85.40 %
  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:  2.36 (0.25), residues: 1133
  helix:  2.30 (0.19), residues: 758
  sheet:  0.69 (0.63), residues: 65
  loop : -0.09 (0.35), residues: 310

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.005   0.001   TRP A 677 
   HIS   0.007   0.001   HIS A1504 
   PHE   0.012   0.001   PHE A1149 
   TYR   0.012   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
  124 residues out of total 986 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 12
    poor density    : 112
  time to evaluate  : 0.978 
Fit side-chains
   revert: symmetry clash
  outliers start: 12
  outliers final: 10
  residues processed: 119
  average time/residue: 0.2575
  time to fit residues: 41.1815
Evaluate side-chains
  107 residues out of total 986 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 10
    poor density    : 97
  time to evaluate  : 1.053 
Switching outliers to nearest non-outliers
  outliers start: 10
  outliers final: 0
  residues processed: 10
  average time/residue: 0.1025
  time to fit residues: 3.3170
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 63 optimal weight:    3.9990
   chunk 1 optimal weight:    0.7980
   chunk 82 optimal weight:    0.6980
   chunk 45 optimal weight:    0.9990
   chunk 94 optimal weight:    7.9990
   chunk 76 optimal weight:    0.5980
   chunk 0 optimal weight:    3.9990
   chunk 56 optimal weight:    8.9990
   chunk 99 optimal weight:    3.9990
   chunk 28 optimal weight:    1.9990
   chunk 37 optimal weight:    0.8980
   overall best weight:    0.7982

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

Flipped N/Q/H residues before XYZ refinement:
A1259 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8056
moved from start:          0.3189

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= 0.192
  Angle     :  0.505   6.677  12525  Z= 0.250
  Chirality :  0.039   0.193   1496
  Planarity :  0.004   0.047   1529
  Dihedral  :  7.934 126.170   1364
  Min Nonbonded Distance : 1.945

Molprobity Statistics.
  All-atom Clashscore : 6.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.24 %
    Favored  : 98.76 %
  Rotamer:
    Outliers :  0.63 %
    Allowed  : 14.39 %
    Favored  : 84.98 %
  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:  2.45 (0.25), residues: 1133
  helix:  2.39 (0.19), residues: 758
  sheet:  0.77 (0.63), residues: 65
  loop : -0.10 (0.35), residues: 310

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.004   0.001   TRP A 727 
   HIS   0.008   0.001   HIS A1504 
   PHE   0.010   0.001   PHE A1149 
   TYR   0.012   0.001   TYR A1250 
   ARG   0.003   0.000   ARG A 820 

*********************** 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
  111 residues out of total 986 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 6
    poor density    : 105
  time to evaluate  : 0.906 
Fit side-chains
  outliers start: 6
  outliers final: 6
  residues processed: 108
  average time/residue: 0.2563
  time to fit residues: 37.5646
Evaluate side-chains
  104 residues out of total 986 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 6
    poor density    : 98
  time to evaluate  : 1.084 
Switching outliers to nearest non-outliers
  outliers start: 6
  outliers final: 0
  residues processed: 6
  average time/residue: 0.0996
  time to fit residues: 2.5160
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 100 optimal weight:    0.1980
   chunk 21 optimal weight:    1.9990
   chunk 65 optimal weight:    3.9990
   chunk 27 optimal weight:    0.9980
   chunk 111 optimal weight:    3.9990
   chunk 92 optimal weight:    6.9990
   chunk 51 optimal weight:    0.6980
   chunk 9 optimal weight:    0.9980
   chunk 36 optimal weight:    4.9990
   chunk 58 optimal weight:    8.9990
   chunk 107 optimal weight:    3.9990
   overall best weight:    0.9782

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8072
moved from start:          0.3331

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   9208  Z= 0.215
  Angle     :  0.521   7.195  12525  Z= 0.255
  Chirality :  0.040   0.192   1496
  Planarity :  0.004   0.047   1529
  Dihedral  :  7.872 126.543   1364
  Min Nonbonded Distance : 1.927

Molprobity Statistics.
  All-atom Clashscore : 7.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.24 %
    Favored  : 98.76 %
  Rotamer:
    Outliers :  1.04 %
    Allowed  : 15.12 %
    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:  2.42 (0.25), residues: 1133
  helix:  2.36 (0.19), residues: 760
  sheet:  1.00 (0.67), residues: 59
  loop : -0.16 (0.34), residues: 314

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.005   0.001   TRP A 677 
   HIS   0.008   0.001   HIS A1504 
   PHE   0.009   0.001   PHE A1149 
   TYR   0.012   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
  111 residues out of total 986 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 10
    poor density    : 101
  time to evaluate  : 0.916 
Fit side-chains
  outliers start: 10
  outliers final: 8
  residues processed: 106
  average time/residue: 0.2519
  time to fit residues: 36.1187
Evaluate side-chains
  105 residues out of total 986 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 8
    poor density    : 97
  time to evaluate  : 0.894 
Switching outliers to nearest non-outliers
  outliers start: 8
  outliers final: 0
  residues processed: 8
  average time/residue: 0.0881
  time to fit residues: 2.6071
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 12 optimal weight:    1.9990
   chunk 63 optimal weight:    0.9990
   chunk 81 optimal weight:    0.9980
   chunk 62 optimal weight:    0.1980
   chunk 93 optimal weight:    8.9990
   chunk 110 optimal weight:    0.9980
   chunk 69 optimal weight:    1.9990
   chunk 67 optimal weight:    0.6980
   chunk 51 optimal weight:    0.9980
   chunk 68 optimal weight:    0.6980
   chunk 44 optimal weight:    4.9990
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
A1451 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8049
moved from start:          0.3455

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     :  0.498   6.389  12525  Z= 0.247
  Chirality :  0.039   0.191   1496
  Planarity :  0.003   0.046   1529
  Dihedral  :  7.759 125.816   1364
  Min Nonbonded Distance : 1.957

Molprobity Statistics.
  All-atom Clashscore : 7.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.32 %
    Favored  : 98.68 %
  Rotamer:
    Outliers :  0.52 %
    Allowed  : 15.43 %
    Favored  : 84.05 %
  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:  2.47 (0.19), residues: 760
  sheet:  1.04 (0.68), residues: 59
  loop : -0.15 (0.34), residues: 314

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.004   0.001   TRP A 432 
   HIS   0.009   0.001   HIS A1504 
   PHE   0.008   0.001   PHE A1149 
   TYR   0.012   0.001   TYR A1250 
   ARG   0.002   0.000   ARG A 820 

*********************** 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
  111 residues out of total 986 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 5
    poor density    : 106
  time to evaluate  : 0.968 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 5
  outliers final: 4
  residues processed: 109
  average time/residue: 0.2632
  time to fit residues: 38.7845
Evaluate side-chains
  104 residues out of total 986 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 4
    poor density    : 100
  time to evaluate  : 1.054 
Switching outliers to nearest non-outliers
  outliers start: 4
  outliers final: 0
  residues processed: 4
  average time/residue: 0.1043
  time to fit residues: 2.1953
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 66 optimal weight:    5.9990
   chunk 33 optimal weight:    0.7980
   chunk 21 optimal weight:    1.9990
   chunk 70 optimal weight:    0.5980
   chunk 75 optimal weight:    3.9990
   chunk 54 optimal weight:    5.9990
   chunk 10 optimal weight:    3.9990
   chunk 87 optimal weight:    1.9990
   chunk 100 optimal weight:    2.9990
   chunk 106 optimal weight:    0.8980
   chunk 96 optimal weight:    1.9990
   overall best weight:    1.2584

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

Flipped N/Q/H residues before XYZ refinement:
A1259 ASN
A1402 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8090
moved from start:          0.3528

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045   9208  Z= 0.253
  Angle     :  0.544   7.567  12525  Z= 0.267
  Chirality :  0.041   0.196   1496
  Planarity :  0.004   0.046   1529
  Dihedral  :  7.861 127.352   1364
  Min Nonbonded Distance : 1.909

Molprobity Statistics.
  All-atom Clashscore : 7.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.41 %
    Favored  : 98.59 %
  Rotamer:
    Outliers :  0.94 %
    Allowed  : 15.33 %
    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:  2.33 (0.25), residues: 1133
  helix:  2.31 (0.19), residues: 760
  sheet:  0.87 (0.67), residues: 59
  loop : -0.22 (0.34), residues: 314

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.006   0.001   TRP A 906 
   HIS   0.009   0.001   HIS A1504 
   PHE   0.009   0.001   PHE A 569 
   TYR   0.013   0.001   TYR A1250 
   ARG   0.003   0.000   ARG A 820 

*********************** 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
  110 residues out of total 986 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 9
    poor density    : 101
  time to evaluate  : 0.848 
Fit side-chains
   revert: symmetry clash
  outliers start: 9
  outliers final: 6
  residues processed: 104
  average time/residue: 0.2725
  time to fit residues: 37.9974
Evaluate side-chains
  105 residues out of total 986 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 6
    poor density    : 99
  time to evaluate  : 1.003 
Switching outliers to nearest non-outliers
  outliers start: 6
  outliers final: 0
  residues processed: 6
  average time/residue: 0.0986
  time to fit residues: 2.4590
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 103 optimal weight:    0.9980
   chunk 106 optimal weight:    0.8980
   chunk 62 optimal weight:    0.9990
   chunk 44 optimal weight:    2.9990
   chunk 81 optimal weight:    0.9990
   chunk 31 optimal weight:    0.9980
   chunk 93 optimal weight:    8.9990
   chunk 97 optimal weight:    1.9990
   chunk 102 optimal weight:    0.4980
   chunk 67 optimal weight:    0.9980
   chunk 109 optimal weight:    0.9980
   overall best weight:    0.8780

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

Flipped N/Q/H residues before XYZ refinement:
A1484 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8068
moved from start:          0.3610

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= 0.199
  Angle     :  0.510   6.835  12525  Z= 0.251
  Chirality :  0.039   0.193   1496
  Planarity :  0.004   0.046   1529
  Dihedral  :  7.780 127.494   1364
  Min Nonbonded Distance : 1.944

Molprobity Statistics.
  All-atom Clashscore : 7.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.24 %
    Favored  : 98.76 %
  Rotamer:
    Outliers :  0.52 %
    Allowed  : 15.85 %
    Favored  : 83.63 %
  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:  2.46 (0.25), residues: 1133
  helix:  2.42 (0.19), residues: 760
  sheet:  0.92 (0.68), residues: 59
  loop : -0.20 (0.34), residues: 314

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.004   0.001   TRP A1055 
   HIS   0.010   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 381 

*********************** 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
  106 residues out of total 986 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 5
    poor density    : 101
  time to evaluate  : 1.138 
Fit side-chains
   revert: symmetry clash
  outliers start: 5
  outliers final: 3
  residues processed: 103
  average time/residue: 0.2724
  time to fit residues: 37.8222
Evaluate side-chains
  103 residues out of total 986 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 3
    poor density    : 100
  time to evaluate  : 1.012 
Switching outliers to nearest non-outliers
  outliers start: 3
  outliers final: 0
  residues processed: 3
  average time/residue: 0.0918
  time to fit residues: 1.9132
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 66 optimal weight:    5.9990
   chunk 51 optimal weight:    6.9990
   chunk 75 optimal weight:    3.9990
   chunk 114 optimal weight:    5.9990
   chunk 105 optimal weight:    0.6980
   chunk 91 optimal weight:    0.8980
   chunk 9 optimal weight:    0.8980
   chunk 70 optimal weight:    0.6980
   chunk 55 optimal weight:    4.9990
   chunk 72 optimal weight:    4.9990
   chunk 97 optimal weight:    0.6980
   overall best weight:    0.7780

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8060
moved from start:          0.3670

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   9208  Z= 0.190
  Angle     :  0.509   6.636  12525  Z= 0.252
  Chirality :  0.039   0.190   1496
  Planarity :  0.004   0.046   1529
  Dihedral  :  7.711 127.195   1364
  Min Nonbonded Distance : 1.950

Molprobity Statistics.
  All-atom Clashscore : 7.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.32 %
    Favored  : 98.68 %
  Rotamer:
    Outliers :  0.10 %
    Allowed  : 15.85 %
    Favored  : 84.05 %
  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:  2.52 (0.25), residues: 1133
  helix:  2.46 (0.19), residues: 760
  sheet:  0.94 (0.68), residues: 59
  loop : -0.17 (0.34), residues: 314

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.004   0.001   TRP A 677 
   HIS   0.010   0.001   HIS A1504 
   PHE   0.008   0.001   PHE A 469 
   TYR   0.013   0.001   TYR A1331 
   ARG   0.004   0.000   ARG A 381 

********************** 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
  105 residues out of total 986 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 104
  time to evaluate  : 1.165 
Fit side-chains
  outliers start: 1
  outliers final: 1
  residues processed: 104
  average time/residue: 0.2757
  time to fit residues: 38.4868
Evaluate side-chains
  101 residues out of total 986 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 100
  time to evaluate  : 1.020 
Switching outliers to nearest non-outliers
  outliers start: 1
  outliers final: 0
  residues processed: 1
  average time/residue: 0.1069
  time to fit residues: 1.5994
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 27 optimal weight:    2.9990
   chunk 84 optimal weight:    0.7980
   chunk 13 optimal weight:    0.5980
   chunk 25 optimal weight:    1.9990
   chunk 91 optimal weight:    6.9990
   chunk 38 optimal weight:    7.9990
   chunk 93 optimal weight:    8.9990
   chunk 11 optimal weight:    0.9980
   chunk 16 optimal weight:    0.0370
   chunk 80 optimal weight:    0.7980
   chunk 5 optimal weight:    0.6980
   overall best weight:    0.5858

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

Flipped N/Q/H residues before XYZ refinement:
A1259 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3778 r_free = 0.3778 target = 0.153546 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3444 r_free = 0.3444 target = 0.123271 restraints weight = 10413.869|
|-----------------------------------------------------------------------------|
r_work (start): 0.3422 rms_B_bonded: 1.89
r_work: 0.3283 rms_B_bonded: 2.65 restraints_weight: 0.5000
r_work: 0.3133 rms_B_bonded: 4.47 restraints_weight: 0.2500
r_work (final): 0.3133
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8002
moved from start:          0.3772

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   9208  Z= 0.166
  Angle     :  0.498   6.448  12525  Z= 0.247
  Chirality :  0.039   0.187   1496
  Planarity :  0.003   0.045   1529
  Dihedral  :  7.584 125.910   1364
  Min Nonbonded Distance : 1.977

Molprobity Statistics.
  All-atom Clashscore : 7.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.41 %
    Favored  : 98.59 %
  Rotamer:
    Outliers :  0.31 %
    Allowed  : 16.06 %
    Favored  : 83.63 %
  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:  2.64 (0.25), residues: 1133
  helix:  2.56 (0.19), residues: 760
  sheet:  1.00 (0.68), residues: 59
  loop : -0.16 (0.34), residues: 314

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.005   0.001   TRP A1214 
   HIS   0.010   0.001   HIS A1504 
   PHE   0.007   0.001   PHE A 469 
   TYR   0.015   0.001   TYR A1331 
   ARG   0.004   0.000   ARG A 381 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1991.40 seconds
wall clock time: 36 minutes 54.46 seconds (2214.46 seconds total)