Starting phenix.real_space_refine
on Tue May 13 00:14:41 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9aso_43821/05_2025/9aso_43821.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9aso_43821/05_2025/9aso_43821.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.9
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9aso_43821/05_2025/9aso_43821.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9aso_43821/05_2025/9aso_43821.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9aso_43821/05_2025/9aso_43821.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9aso_43821/05_2025/9aso_43821.cif"
  }
  resolution = 2.9
  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=  -0.000 sd=   0.010
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: 7
    Type Number    sf(0)   Gaussians
     Ca      2      9.91       5
     Zn      2      6.06       5
     P      71      5.49       5
     S      52      5.16       5
     C    5709      2.51       5
     N    1652      2.21       5
     O    1938      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 9 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 9426
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 7497
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 916, 7497
          Classifications: {'peptide': 916}
          Link IDs: {'PTRANS': 52, 'TRANS': 863}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 220
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 26, 220
          Classifications: {'peptide': 26}
          Link IDs: {'PTRANS': 1, 'TRANS': 24}
    Chain: "C"
      Number of atoms: 203
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 24, 203
          Classifications: {'peptide': 24}
          Link IDs: {'PTRANS': 1, 'TRANS': 22}
    Chain: "E"
      Number of atoms: 1500
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 71, 1500
          Classifications: {'RNA': 71}
          Modifications used: {'rna2p_pur': 3, 'rna2p_pyr': 2, 'rna3p_pur': 28, 'rna3p_pyr': 38}
          Link IDs: {'rna2p': 4, 'rna3p': 66}
          Chain breaks: 1
    Chain: "A"
      Number of atoms: 4
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 4
          Unusual residues: {' CA': 2, ' ZN': 2}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}
    Chain: "E"
      Number of atoms: 2
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 2
          Classifications: {'water': 2}
          Link IDs: {None: 1}

List of CYS excluded from plausible disulfide bonds:
  (reason: may participate in coordination)
  ATOM    961  SG  CYS A 561      51.073  71.653 120.870  1.00172.12           S
  ATOM   1919  SG  CYS A 676      53.071  68.480 120.056  1.00178.36           S
  ATOM    769  SG  CYS A 536      62.414  49.991 102.297  1.00181.72           S
  ATOM    784  SG  CYS A 538      63.025  49.510  98.508  1.00190.39           S

  Time building chain proxies: 7.02, per 1000 atoms: 0.74
  Number of scatterers: 9426
  At special positions: 0
  Unit cell: (82.176, 98.44, 158.36, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 7
    Type Number    sf(0)
     Zn      2     29.99
     Ca      2     19.99
     S      52     16.00
     P      71     15.00
     O    1938      8.00
     N    1652      7.00
     C    5709      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: 2.38
  Conformation dependent library (CDL) restraints added in 1.0 seconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN A1401 "
        pdb="ZN    ZN A1401 " - pdb=" NE2 HIS A 609 "
        pdb="ZN    ZN A1401 " - pdb=" NE2 HIS A 680 "
        pdb="ZN    ZN A1401 " - pdb=" SG  CYS A 676 "
        pdb="ZN    ZN A1401 " - pdb=" SG  CYS A 561 "
      pdb="  ZN A1402 "
        pdb="ZN    ZN A1402 " - pdb=" NE2 HIS A1026 "
        pdb="ZN    ZN A1402 " - pdb=" NE2 HIS A 549 "
        pdb="ZN    ZN A1402 " - pdb=" SG  CYS A 536 "
        pdb="ZN    ZN A1402 " - pdb=" SG  CYS A 538 "
      Number of angles added : 4


  1916 Ramachandran restraints generated.
    958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1842

  Finding SS restraints...
    Secondary structure from input PDB file:
      42 helices and 6 sheets defined
      56.1% alpha, 11.6% beta
      17 base pairs and 45 stacking pairs defined.
    Time for finding SS restraints: 3.32
  Creating SS restraints...
    Processing helix  chain 'A' and resid 438 through 452
      removed outlier: 3.538A  pdb=" N   ARG A 442 " --> pdb=" O   THR A 438 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 454 through 463
      removed outlier: 3.629A  pdb=" N   ALA A 462 " --> pdb=" O   LYS A 458 " (cutoff:3.500A)
      removed outlier: 3.976A  pdb=" N   ARG A 463 " --> pdb=" O   ALA A 459 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 503 through 512
      removed outlier: 3.559A  pdb=" N   GLU A 507 " --> pdb=" O   ASP A 503 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 541 through 545
      removed outlier: 3.698A  pdb=" N   THR A 545 " --> pdb=" O   ALA A 542 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 641 through 656
      removed outlier: 3.527A  pdb=" N   ILE A 656 " --> pdb=" O   LEU A 652 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 698 through 709
      removed outlier: 3.574A  pdb=" N   ILE A 702 " --> pdb=" O   SER A 698 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 718 through 725
    Processing helix  chain 'A' and resid 726 through 738
      removed outlier: 3.524A  pdb=" N   GLU A 736 " --> pdb=" O   LYS A 732 " (cutoff:3.500A)
      removed outlier: 3.680A  pdb=" N   CYS A 737 " --> pdb=" O   TYR A 733 " (cutoff:3.500A)
      removed outlier: 3.690A  pdb=" N   LYS A 738 " --> pdb=" O   ALA A 734 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 783 through 786
    Processing helix  chain 'A' and resid 787 through 806
      removed outlier: 3.644A  pdb=" N   ASN A 806 " --> pdb=" O   HIS A 802 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 811 through 830
      removed outlier: 3.786A  pdb=" N   GLN A 816 " --> pdb=" O   GLN A 812 " (cutoff:3.500A)
      removed outlier: 3.961A  pdb=" N   LYS A 817 " --> pdb=" O   THR A 813 " (cutoff:3.500A)
      removed outlier: 3.784A  pdb=" N   LEU A 818 " --> pdb=" O   ASP A 814 " (cutoff:3.500A)
      removed outlier: 3.732A  pdb=" N   ALA A 819 " --> pdb=" O   LYS A 815 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 854 through 861
    Processing helix  chain 'A' and resid 862 through 884
      removed outlier: 3.734A  pdb=" N   LEU A 866 " --> pdb=" O   MET A 862 " (cutoff:3.500A)
      removed outlier: 4.620A  pdb=" N   MET A 877 " --> pdb=" O   HIS A 873 " (cutoff:3.500A)
      removed outlier: 5.118A  pdb=" N   HIS A 878 " --> pdb=" O   GLN A 874 " (cutoff:3.500A)
      removed outlier: 4.190A  pdb=" N   LEU A 879 " --> pdb=" O   CYS A 875 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 889 through 897
      removed outlier: 3.616A  pdb=" N   LEU A 893 " --> pdb=" O   ASP A 889 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 909 through 921
    Processing helix  chain 'A' and resid 929 through 934
      removed outlier: 3.594A  pdb=" N   VAL A 932 " --> pdb=" O   ASP A 929 " (cutoff:3.500A)
      removed outlier: 4.128A  pdb=" N   HIS A 933 " --> pdb=" O   ARG A 930 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 941 through 950
      removed outlier: 3.752A  pdb=" N   ILE A 946 " --> pdb=" O   ILE A 942 " (cutoff:3.500A)
      removed outlier: 3.639A  pdb=" N   ASN A 947 " --> pdb=" O   ASN A 943 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 965 through 988
      removed outlier: 3.670A  pdb=" N   PHE A 970 " --> pdb=" O   GLU A 966 " (cutoff:3.500A)
      removed outlier: 3.712A  pdb=" N   LEU A 971 " --> pdb=" O   ARG A 967 " (cutoff:3.500A)
      removed outlier: 3.885A  pdb=" N   ALA A 974 " --> pdb=" O   PHE A 970 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 992 through 1004
    Processing helix  chain 'A' and resid 1005 through 1017
      removed outlier: 3.768A  pdb=" N   LEU A1016 " --> pdb=" O   LEU A1012 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1018 through 1021
    Processing helix  chain 'A' and resid 1027 through 1031
      removed outlier: 4.024A  pdb=" N   LEU A1030 " --> pdb=" O   GLY A1027 " (cutoff:3.500A)
      removed outlier: 3.656A  pdb=" N   CYS A1031 " --> pdb=" O   PRO A1028 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 1027 through 1031'
    Processing helix  chain 'A' and resid 1032 through 1055
    Processing helix  chain 'A' and resid 1056 through 1069
      removed outlier: 3.573A  pdb=" N   ALA A1060 " --> pdb=" O   SER A1056 " (cutoff:3.500A)
      removed outlier: 3.690A  pdb=" N   PHE A1069 " --> pdb=" O   GLY A1065 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1071 through 1079
    Processing helix  chain 'A' and resid 1084 through 1090
      removed outlier: 3.919A  pdb=" N   GLU A1090 " --> pdb=" O   LEU A1086 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1094 through 1100
      removed outlier: 4.220A  pdb=" N   GLU A1099 " --> pdb=" O   GLN A1096 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1101 through 1115
      removed outlier: 3.672A  pdb=" N   THR A1108 " --> pdb=" O   LEU A1104 " (cutoff:3.500A)
      removed outlier: 4.247A  pdb=" N   GLU A1109 " --> pdb=" O   GLN A1105 " (cutoff:3.500A)
      removed outlier: 4.021A  pdb=" N   PHE A1110 " --> pdb=" O   LYS A1106 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1120 through 1128
      removed outlier: 4.057A  pdb=" N   LEU A1124 " --> pdb=" O   HIS A1120 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1143 through 1166
      removed outlier: 3.714A  pdb=" N   GLU A1147 " --> pdb=" O   ASN A1143 " (cutoff:3.500A)
      removed outlier: 4.241A  pdb=" N   PHE A1148 " --> pdb=" O   GLN A1144 " (cutoff:3.500A)
      removed outlier: 4.086A  pdb=" N   LEU A1149 " --> pdb=" O   ARG A1145 " (cutoff:3.500A)
      removed outlier: 3.998A  pdb=" N   SER A1152 " --> pdb=" O   PHE A1148 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1170 through 1182
    Processing helix  chain 'A' and resid 1183 through 1195
      removed outlier: 3.571A  pdb=" N   ALA A1188 " --> pdb=" O   ASN A1184 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1203 through 1208
      removed outlier: 4.232A  pdb=" N   LYS A1207 " --> pdb=" O   ASN A1203 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1213 through 1232
    Processing helix  chain 'A' and resid 1234 through 1245
    Processing helix  chain 'A' and resid 1248 through 1256
    Processing helix  chain 'A' and resid 1260 through 1271
      removed outlier: 3.584A  pdb=" N   THR A1271 " --> pdb=" O   GLN A1267 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1316 through 1332
    Processing helix  chain 'A' and resid 1334 through 1348
      removed outlier: 3.573A  pdb=" N   ALA A1338 " --> pdb=" O   PHE A1334 " (cutoff:3.500A)
      removed outlier: 3.732A  pdb=" N   LYS A1347 " --> pdb=" O   PHE A1343 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1348 through 1358
    Processing helix  chain 'B' and resid 728 through 749
      removed outlier: 3.808A  pdb=" N   LEU B 732 " --> pdb=" O   ASN B 728 " (cutoff:3.500A)
      removed outlier: 3.857A  pdb=" N   GLN B 736 " --> pdb=" O   LEU B 732 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 728 through 749
    Processing sheet with id=AA1, first strand: chain 'A' and resid 413 through 415
      removed outlier: 6.484A  pdb=" N   ARG A 414 " --> pdb=" O   VAL A 696 " (cutoff:3.500A)
      removed outlier: 4.059A  pdb=" N   GLY A 603 " --> pdb=" O   ARG A 684 " (cutoff:3.500A)
      removed outlier: 6.390A  pdb=" N   VAL A 686 " --> pdb=" O   PHE A 601 " (cutoff:3.500A)
      removed outlier: 5.698A  pdb=" N   PHE A 601 " --> pdb=" O   VAL A 686 " (cutoff:3.500A)
      removed outlier: 9.348A  pdb=" N   PHE A 688 " --> pdb=" O   TYR A 599 " (cutoff:3.500A)
      removed outlier: 9.671A  pdb=" N   TYR A 599 " --> pdb=" O   PHE A 688 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 413 through 415
      removed outlier: 6.484A  pdb=" N   ARG A 414 " --> pdb=" O   VAL A 696 " (cutoff:3.500A)
      removed outlier: 4.059A  pdb=" N   GLY A 603 " --> pdb=" O   ARG A 684 " (cutoff:3.500A)
      removed outlier: 6.390A  pdb=" N   VAL A 686 " --> pdb=" O   PHE A 601 " (cutoff:3.500A)
      removed outlier: 5.698A  pdb=" N   PHE A 601 " --> pdb=" O   VAL A 686 " (cutoff:3.500A)
      removed outlier: 9.348A  pdb=" N   PHE A 688 " --> pdb=" O   TYR A 599 " (cutoff:3.500A)
      removed outlier: 9.671A  pdb=" N   TYR A 599 " --> pdb=" O   PHE A 688 " (cutoff:3.500A)
      removed outlier: 11.962A  pdb=" N   GLU A 602 " --> pdb=" O   VAL A 578 " (cutoff:3.500A)
      removed outlier: 7.565A  pdb=" N   VAL A 578 " --> pdb=" O   GLU A 602 " (cutoff:3.500A)
      removed outlier: 4.661A  pdb=" N   PHE A 604 " --> pdb=" O   ILE A 576 " (cutoff:3.500A)
      removed outlier: 4.059A  pdb=" N   CYS A 618 " --> pdb=" O   ILE A 629 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 422 through 423
    Processing sheet with id=AA4, first strand: chain 'A' and resid 711 through 712
      removed outlier: 3.815A  pdb=" N   LYS A 711 " --> pdb=" O   LYS A 849 " (cutoff:3.500A)
      removed outlier: 3.546A  pdb=" N   THR A 850 " --> pdb=" O   ILE A 741 " (cutoff:3.500A)
      removed outlier: 4.850A  pdb=" N   ILE A 741 " --> pdb=" O   THR A 850 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 756 through 758
      removed outlier: 3.558A  pdb=" N   GLN A 756 " --> pdb=" O   VAL A 773 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 1283 through 1290
      removed outlier: 6.901A  pdb=" N   THR A1299 " --> pdb=" O   LEU A1287 " (cutoff:3.500A)
      removed outlier: 4.666A  pdb=" N   THR A1289 " --> pdb=" O   THR A1297 " (cutoff:3.500A)
      removed outlier: 6.358A  pdb=" N   THR A1297 " --> pdb=" O   THR A1289 " (cutoff:3.500A)
      removed outlier: 4.066A  pdb=" N   GLY A1310 " --> pdb=" O   VAL A1302 " (cutoff:3.500A)

    387 hydrogen bonds defined for protein.
    1122 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      43 hydrogen bonds
      86 hydrogen bond angles
      0 basepair planarities
      17 basepair parallelities
      45 stacking parallelities
  Total time for adding SS restraints: 3.58

  Time building geometry restraints manager: 2.82 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2811
        1.34 -     1.46: 1975
        1.46 -     1.58: 4774
        1.58 -     1.70: 140
        1.70 -     1.82: 84
  Bond restraints: 9784
  Sorted by residual:
  bond pdb=" O5'   C E  24 "
       pdb=" C5'   C E  24 "
    ideal  model  delta    sigma   weight residual
    1.420  1.449 -0.029 1.50e-02 4.44e+03 3.72e+00
  bond pdb=" O5'   C E  22 "
       pdb=" C5'   C E  22 "
    ideal  model  delta    sigma   weight residual
    1.420  1.449 -0.029 1.50e-02 4.44e+03 3.62e+00
  bond pdb=" O5'   A E  19 "
       pdb=" C5'   A E  19 "
    ideal  model  delta    sigma   weight residual
    1.420  1.448 -0.028 1.50e-02 4.44e+03 3.58e+00
  bond pdb=" O5'   U E  20 "
       pdb=" C5'   U E  20 "
    ideal  model  delta    sigma   weight residual
    1.420  1.448 -0.028 1.50e-02 4.44e+03 3.54e+00
  bond pdb=" O5'   C E  25 "
       pdb=" C5'   C E  25 "
    ideal  model  delta    sigma   weight residual
    1.420  1.447 -0.027 1.50e-02 4.44e+03 3.34e+00
  ... (remaining 9779 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.37: 13400
        2.37 -     4.73: 123
        4.73 -     7.10: 23
        7.10 -     9.47: 6
        9.47 -    11.83: 6
  Bond angle restraints: 13558
  Sorted by residual:
  angle pdb=" C3'   C E  22 "
        pdb=" O3'   C E  22 "
        pdb=" P     U E  23 "
      ideal   model   delta    sigma   weight residual
     120.20  108.37   11.83 1.50e+00 4.44e-01 6.22e+01
  angle pdb=" C3'   G E  21 "
        pdb=" O3'   G E  21 "
        pdb=" P     C E  22 "
      ideal   model   delta    sigma   weight residual
     120.20  108.49   11.71 1.50e+00 4.44e-01 6.10e+01
  angle pdb=" C3'   C E  24 "
        pdb=" O3'   C E  24 "
        pdb=" P     C E  25 "
      ideal   model   delta    sigma   weight residual
     120.20  109.27   10.93 1.50e+00 4.44e-01 5.31e+01
  angle pdb=" C3'   U E  20 "
        pdb=" O3'   U E  20 "
        pdb=" P     G E  21 "
      ideal   model   delta    sigma   weight residual
     120.20  109.49   10.71 1.50e+00 4.44e-01 5.10e+01
  angle pdb=" C3'   A E  19 "
        pdb=" O3'   A E  19 "
        pdb=" P     U E  20 "
      ideal   model   delta    sigma   weight residual
     120.20  109.50   10.70 1.50e+00 4.44e-01 5.09e+01
  ... (remaining 13553 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    25.42: 5548
       25.42 -    50.84: 368
       50.84 -    76.25: 139
       76.25 -   101.67: 1
      101.67 -   127.09: 1
  Dihedral angle restraints: 6057
    sinusoidal: 3220
      harmonic: 2837
  Sorted by residual:
  dihedral pdb=" O4'   C E  22 "
           pdb=" C1'   C E  22 "
           pdb=" N1    C E  22 "
           pdb=" C2    C E  22 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -160.00  -32.91 -127.09     1      1.50e+01 4.44e-03 6.84e+01
  dihedral pdb=" O4'   A E  90 "
           pdb=" C1'   A E  90 "
           pdb=" N9    A E  90 "
           pdb=" C4    A E  90 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -90.00  -22.97  -67.03     1      2.00e+01 2.50e-03 1.46e+01
  dihedral pdb=" CA  MET A 935 "
           pdb=" C   MET A 935 "
           pdb=" N   HIS A 936 "
           pdb=" CA  HIS A 936 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -162.33  -17.67     0      5.00e+00 4.00e-02 1.25e+01
  ... (remaining 6054 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.081: 1438
       0.081 -    0.161: 79
       0.161 -    0.242: 5
       0.242 -    0.322: 0
       0.322 -    0.403: 7
  Chirality restraints: 1529
  Sorted by residual:
  chirality pdb=" P     A E  19 "
            pdb=" OP1   A E  19 "
            pdb=" OP2   A E  19 "
            pdb=" O5'   A E  19 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.41   -2.81   -0.40 2.00e-01 2.50e+01 4.06e+00
  chirality pdb=" P     U E  20 "
            pdb=" OP1   U E  20 "
            pdb=" OP2   U E  20 "
            pdb=" O5'   U E  20 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.41   -2.79   -0.38 2.00e-01 2.50e+01 3.59e+00
  chirality pdb=" P     U E  23 "
            pdb=" OP1   U E  23 "
            pdb=" OP2   U E  23 "
            pdb=" O5'   U E  23 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.41   -2.79   -0.38 2.00e-01 2.50e+01 3.55e+00
  ... (remaining 1526 not shown)

  Planarity restraints: 1497
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CG  GLU C 745 "   -0.012 2.00e-02 2.50e+03   2.44e-02 5.94e+00
        pdb=" CD  GLU C 745 "    0.042 2.00e-02 2.50e+03
        pdb=" OE1 GLU C 745 "   -0.015 2.00e-02 2.50e+03
        pdb=" OE2 GLU C 745 "   -0.015 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CG  GLU C 744 "   -0.010 2.00e-02 2.50e+03   2.05e-02 4.21e+00
        pdb=" CD  GLU C 744 "    0.035 2.00e-02 2.50e+03
        pdb=" OE1 GLU C 744 "   -0.013 2.00e-02 2.50e+03
        pdb=" OE2 GLU C 744 "   -0.013 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CG  GLU B 737 "   -0.009 2.00e-02 2.50e+03   1.90e-02 3.60e+00
        pdb=" CD  GLU B 737 "    0.033 2.00e-02 2.50e+03
        pdb=" OE1 GLU B 737 "   -0.012 2.00e-02 2.50e+03
        pdb=" OE2 GLU B 737 "   -0.012 2.00e-02 2.50e+03
  ... (remaining 1494 not shown)

  Histogram of nonbonded interaction distances:
        2.28 -     2.80: 2334
        2.80 -     3.33: 8160
        3.33 -     3.85: 15244
        3.85 -     4.38: 17752
        4.38 -     4.90: 29543
  Nonbonded interactions: 73033
  Sorted by model distance:
  nonbonded pdb=" N   ASP A 955 "
            pdb=" OD1 ASP A 955 "
     model   vdw
     2.281 3.120
  nonbonded pdb=" OP1   U E  31 "
            pdb=" O   HOH E 201 "
     model   vdw
     2.319 3.040
  nonbonded pdb=" OE2 GLU A1147 "
            pdb="CA    CA A1403 "
     model   vdw
     2.356 2.510
  nonbonded pdb=" NH2 ARG A1213 "
            pdb=" OP2   U E  89 "
     model   vdw
     2.380 3.120
  nonbonded pdb=" NH1 ARG A1095 "
            pdb=" O   PHE A1118 "
     model   vdw
     2.395 3.120
  ... (remaining 73028 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'B' and resid 726 through 749)
  selection = chain 'C'
}

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:             6.010
  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:          0.370
  Check model and map are aligned:         0.070
  Set scattering table:                    0.080
  Process input model:                     30.310
  Find NCS groups from input model:        0.110
  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:             0.010
  Load rotamer database and sin/cos tables:10.640
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   47.640
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6371
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      :  0.003   0.039   9792  Z= 0.142
  Angle     :  0.603  11.832  13562  Z= 0.324
  Chirality :  0.045   0.403   1529
  Planarity :  0.003   0.031   1497
  Dihedral  : 17.619 127.090   4215
  Min Nonbonded Distance : 2.281

Molprobity Statistics.
  All-atom Clashscore : 3.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.57 %
    Favored  : 98.43 %
  Rotamer:
    Outliers :  1.04 %
    Allowed  : 14.06 %
    Favored  : 84.91 %
  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:  1.28 (0.27), residues: 958
  helix:  2.01 (0.24), residues: 480
  sheet:  0.63 (0.50), residues: 92
  loop : -0.57 (0.29), residues: 386

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.032   0.001   TRP A1357 
 HIS   0.004   0.001   HIS A 873 
 PHE   0.011   0.001   PHE A 970 
 TYR   0.006   0.001   TYR A1229 
 ARG   0.007   0.000   ARG C 746 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.18157 (  423)
  hydrogen bonds       : angle       5.28085 ( 1208)
  metal coordination   : bond        0.01014 (    8)
  metal coordination   : angle       2.11452 (    4)
  covalent geometry    : bond        0.00288 ( 9784)
  covalent geometry    : angle       0.60209 (13558)

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

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

  1916 Ramachandran restraints generated.
    958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1916 Ramachandran restraints generated.
    958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  64 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 55
  time to evaluate  : 1.052 
Fit side-chains
   revert: symmetry clash
  outliers start: 9
  outliers final: 9
  residues processed: 63
  average time/residue: 1.7163
  time to fit residues: 114.6431
Evaluate side-chains
  64 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 55
  time to evaluate  : 1.011 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  632 ILE
Chi-restraints excluded: chain A residue  875 CYS
Chi-restraints excluded: chain A residue  955 ASP
Chi-restraints excluded: chain A residue 1035 ASP
Chi-restraints excluded: chain A residue 1048 ILE
Chi-restraints excluded: chain A residue 1198 GLU
Chi-restraints excluded: chain A residue 1274 THR
Chi-restraints excluded: chain A residue 1283 LEU
Chi-restraints excluded: chain C residue  731 ILE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 86 optimal weight:    2.9990
   chunk 77 optimal weight:    0.0060
   chunk 42 optimal weight:    0.3980
   chunk 26 optimal weight:    2.9990
   chunk 52 optimal weight:    3.9990
   chunk 41 optimal weight:    0.7980
   chunk 79 optimal weight:    0.5980
   chunk 30 optimal weight:    0.0020
   chunk 48 optimal weight:    0.9980
   chunk 59 optimal weight:    4.9990
   chunk 92 optimal weight:    4.9990
   overall best weight:    0.3604

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

Flipped N/Q/H residues before XYZ refinement:
A1340 GLN
C 730 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3578 r_free = 0.3578 target = 0.072095 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3031 r_free = 0.3031 target = 0.049953 restraints weight = 28063.277|
|-----------------------------------------------------------------------------|
r_work (start): 0.3013 rms_B_bonded: 2.95
r_work: 0.2848 rms_B_bonded: 3.98 restraints_weight: 0.5000
r_work (final): 0.2848
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8652
moved from start:          0.0834

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   9792  Z= 0.100
  Angle     :  0.487   6.621  13562  Z= 0.247
  Chirality :  0.035   0.143   1529
  Planarity :  0.003   0.032   1497
  Dihedral  : 17.855 109.784   2191
  Min Nonbonded Distance : 2.366

Molprobity Statistics.
  All-atom Clashscore : 2.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.57 %
    Favored  : 98.43 %
  Rotamer:
    Outliers :  1.27 %
    Allowed  : 13.02 %
    Favored  : 85.71 %
  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:  1.51 (0.27), residues: 958
  helix:  2.13 (0.24), residues: 495
  sheet:  0.62 (0.48), residues: 102
  loop : -0.47 (0.31), residues: 361

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A1357 
 HIS   0.005   0.001   HIS C 730 
 PHE   0.011   0.001   PHE A1148 
 TYR   0.006   0.001   TYR A 705 
 ARG   0.005   0.000   ARG C 746 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04427 (  423)
  hydrogen bonds       : angle       3.62823 ( 1208)
  metal coordination   : bond        0.01106 (    8)
  metal coordination   : angle       2.09275 (    4)
  covalent geometry    : bond        0.00206 ( 9784)
  covalent geometry    : angle       0.48578 (13558)

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

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

  1916 Ramachandran restraints generated.
    958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1916 Ramachandran restraints generated.
    958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  66 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 55
  time to evaluate  : 0.955 
Fit side-chains
   revert: symmetry clash
REVERT: A 1355 MET cc_start: 0.7805 (ttm) cc_final: 0.7546 (ttp)
REVERT: C  734 LYS cc_start: 0.8849 (mtpp) cc_final: 0.8627 (mtmt)
  outliers start: 11
  outliers final: 3
  residues processed: 63
  average time/residue: 1.5934
  time to fit residues: 106.5692
Evaluate side-chains
  56 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 53
  time to evaluate  : 1.001 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  933 HIS
Chi-restraints excluded: chain A residue 1048 ILE
Chi-restraints excluded: chain A residue 1283 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 19 optimal weight:    0.0170
   chunk 57 optimal weight:    0.0970
   chunk 17 optimal weight:    0.6980
   chunk 42 optimal weight:    0.9990
   chunk 1 optimal weight:    2.9990
   chunk 65 optimal weight:    1.9990
   chunk 48 optimal weight:    2.9990
   chunk 24 optimal weight:    0.0770
   chunk 61 optimal weight:    2.9990
   chunk 13 optimal weight:    1.9990
   chunk 41 optimal weight:    0.9990
   overall best weight:    0.3776

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

Flipped N/Q/H residues before XYZ refinement:
A1340 GLN
C 730 HIS
C 736 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3576 r_free = 0.3576 target = 0.072185 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3039 r_free = 0.3039 target = 0.050109 restraints weight = 28349.295|
|-----------------------------------------------------------------------------|
r_work (start): 0.3014 rms_B_bonded: 3.01
r_work: 0.2843 rms_B_bonded: 4.02 restraints_weight: 0.5000
r_work (final): 0.2843
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8650
moved from start:          0.1031

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031   9792  Z= 0.093
  Angle     :  0.467   6.032  13562  Z= 0.237
  Chirality :  0.034   0.147   1529
  Planarity :  0.003   0.032   1497
  Dihedral  : 17.738 101.806   2178
  Min Nonbonded Distance : 2.361

Molprobity Statistics.
  All-atom Clashscore : 2.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.77 %
    Favored  : 98.23 %
  Rotamer:
    Outliers :  0.69 %
    Allowed  : 14.52 %
    Favored  : 84.79 %
  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:  1.64 (0.27), residues: 958
  helix:  2.27 (0.24), residues: 495
  sheet:  0.63 (0.48), residues: 102
  loop : -0.45 (0.31), residues: 361

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP A1357 
 HIS   0.006   0.001   HIS C 730 
 PHE   0.010   0.001   PHE A1148 
 TYR   0.006   0.001   TYR A1229 
 ARG   0.009   0.000   ARG C 746 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03862 (  423)
  hydrogen bonds       : angle       3.42010 ( 1208)
  metal coordination   : bond        0.00973 (    8)
  metal coordination   : angle       2.07083 (    4)
  covalent geometry    : bond        0.00199 ( 9784)
  covalent geometry    : angle       0.46562 (13558)

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

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

  1916 Ramachandran restraints generated.
    958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1916 Ramachandran restraints generated.
    958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  60 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 54
  time to evaluate  : 1.041 
Fit side-chains
   revert: symmetry clash
REVERT: A 1355 MET cc_start: 0.7862 (ttm) cc_final: 0.7553 (ttp)
  outliers start: 6
  outliers final: 1
  residues processed: 58
  average time/residue: 1.7584
  time to fit residues: 108.1013
Evaluate side-chains
  53 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 52
  time to evaluate  : 0.946 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  933 HIS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 14 optimal weight:    1.9990
   chunk 42 optimal weight:    2.9990
   chunk 75 optimal weight:    3.9990
   chunk 74 optimal weight:    0.9990
   chunk 101 optimal weight:    4.9990
   chunk 4 optimal weight:    3.9990
   chunk 19 optimal weight:    0.0170
   chunk 5 optimal weight:    7.9990
   chunk 29 optimal weight:    1.9990
   chunk 92 optimal weight:    5.9990
   chunk 46 optimal weight:    2.9990
   overall best weight:    1.6026

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

Flipped N/Q/H residues before XYZ refinement:
A 724 GLN
A 936 HIS
C 730 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3507 r_free = 0.3507 target = 0.069071 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2944 r_free = 0.2944 target = 0.046738 restraints weight = 28136.558|
|-----------------------------------------------------------------------------|
r_work (start): 0.2919 rms_B_bonded: 2.99
r_work: 0.2741 rms_B_bonded: 4.00 restraints_weight: 0.5000
r_work (final): 0.2741
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8772
moved from start:          0.1205

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.043   9792  Z= 0.197
  Angle     :  0.550   6.693  13562  Z= 0.282
  Chirality :  0.038   0.175   1529
  Planarity :  0.004   0.036   1497
  Dihedral  : 17.744  95.371   2174
  Min Nonbonded Distance : 2.434

Molprobity Statistics.
  All-atom Clashscore : 3.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.30 %
    Favored  : 97.70 %
  Rotamer:
    Outliers :  1.04 %
    Allowed  : 14.06 %
    Favored  : 84.91 %
  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:  1.41 (0.28), residues: 958
  helix:  2.09 (0.24), residues: 494
  sheet:  0.37 (0.49), residues: 103
  loop : -0.50 (0.31), residues: 361

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP A1357 
 HIS   0.006   0.001   HIS C 730 
 PHE   0.011   0.001   PHE A1148 
 TYR   0.013   0.001   TYR A1332 
 ARG   0.007   0.000   ARG C 746 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06136 (  423)
  hydrogen bonds       : angle       3.73256 ( 1208)
  metal coordination   : bond        0.01556 (    8)
  metal coordination   : angle       3.91376 (    4)
  covalent geometry    : bond        0.00464 ( 9784)
  covalent geometry    : angle       0.54640 (13558)

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

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

  1916 Ramachandran restraints generated.
    958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1916 Ramachandran restraints generated.
    958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  62 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 53
  time to evaluate  : 1.020 
Fit side-chains
   revert: symmetry clash
REVERT: A  877 MET cc_start: 0.8844 (mpp) cc_final: 0.8575 (mmt)
REVERT: A 1355 MET cc_start: 0.7898 (ttm) cc_final: 0.7553 (ttp)
REVERT: C  737 GLU cc_start: 0.8588 (pm20) cc_final: 0.8368 (pm20)
  outliers start: 9
  outliers final: 3
  residues processed: 60
  average time/residue: 1.6762
  time to fit residues: 106.7198
Evaluate side-chains
  55 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 52
  time to evaluate  : 0.983 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  672 SER
Chi-restraints excluded: chain A residue  933 HIS
Chi-restraints excluded: chain A residue 1048 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 67 optimal weight:    1.9990
   chunk 72 optimal weight:    3.9990
   chunk 37 optimal weight:    3.9990
   chunk 71 optimal weight:    0.9980
   chunk 46 optimal weight:    3.9990
   chunk 90 optimal weight:    3.9990
   chunk 22 optimal weight:    0.8980
   chunk 3 optimal weight:    0.9990
   chunk 95 optimal weight:    6.9990
   chunk 28 optimal weight:    1.9990
   chunk 52 optimal weight:    0.4980
   overall best weight:    1.0784

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

Flipped N/Q/H residues before XYZ refinement:
C 730 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3524 r_free = 0.3524 target = 0.069818 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2968 r_free = 0.2968 target = 0.047599 restraints weight = 28159.998|
|-----------------------------------------------------------------------------|
r_work (start): 0.2943 rms_B_bonded: 2.98
r_work: 0.2765 rms_B_bonded: 4.03 restraints_weight: 0.5000
r_work (final): 0.2765
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8734
moved from start:          0.1219

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   9792  Z= 0.139
  Angle     :  0.500   6.264  13562  Z= 0.256
  Chirality :  0.037   0.165   1529
  Planarity :  0.004   0.036   1497
  Dihedral  : 17.723  88.239   2174
  Min Nonbonded Distance : 2.376

Molprobity Statistics.
  All-atom Clashscore : 2.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.09 %
    Favored  : 97.91 %
  Rotamer:
    Outliers :  1.38 %
    Allowed  : 14.06 %
    Favored  : 84.56 %
  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:  1.41 (0.28), residues: 958
  helix:  2.08 (0.24), residues: 494
  sheet:  0.36 (0.49), residues: 103
  loop : -0.49 (0.32), residues: 361

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP A1357 
 HIS   0.005   0.001   HIS C 730 
 PHE   0.012   0.001   PHE A 970 
 TYR   0.008   0.001   TYR A1332 
 ARG   0.005   0.000   ARG C 741 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04873 (  423)
  hydrogen bonds       : angle       3.55730 ( 1208)
  metal coordination   : bond        0.01398 (    8)
  metal coordination   : angle       3.03219 (    4)
  covalent geometry    : bond        0.00321 ( 9784)
  covalent geometry    : angle       0.49772 (13558)

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

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

  1916 Ramachandran restraints generated.
    958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1916 Ramachandran restraints generated.
    958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  65 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 53
  time to evaluate  : 0.938 
Fit side-chains
   revert: symmetry clash
REVERT: A 1355 MET cc_start: 0.7883 (ttm) cc_final: 0.7558 (ttp)
  outliers start: 12
  outliers final: 3
  residues processed: 62
  average time/residue: 1.5572
  time to fit residues: 102.8380
Evaluate side-chains
  55 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 52
  time to evaluate  : 1.123 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  804 LEU
Chi-restraints excluded: chain A residue  933 HIS
Chi-restraints excluded: chain A residue 1048 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 62 optimal weight:    0.6980
   chunk 96 optimal weight:    3.9990
   chunk 15 optimal weight:    0.5980
   chunk 60 optimal weight:    2.9990
   chunk 81 optimal weight:    2.9990
   chunk 14 optimal weight:    0.5980
   chunk 11 optimal weight:    1.9990
   chunk 80 optimal weight:    0.9990
   chunk 101 optimal weight:    3.9990
   chunk 82 optimal weight:    0.8980
   chunk 99 optimal weight:   10.0000
   overall best weight:    0.7582

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

Flipped N/Q/H residues before XYZ refinement:
C 730 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3536 r_free = 0.3536 target = 0.070338 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2990 r_free = 0.2990 target = 0.048281 restraints weight = 28242.586|
|-----------------------------------------------------------------------------|
r_work (start): 0.2964 rms_B_bonded: 2.97
r_work: 0.2788 rms_B_bonded: 4.03 restraints_weight: 0.5000
r_work (final): 0.2788
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8727
moved from start:          0.1311

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   9792  Z= 0.116
  Angle     :  0.494   7.501  13562  Z= 0.251
  Chirality :  0.035   0.146   1529
  Planarity :  0.003   0.036   1497
  Dihedral  : 17.475  88.035   2174
  Min Nonbonded Distance : 2.352

Molprobity Statistics.
  All-atom Clashscore : 2.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.30 %
    Favored  : 97.70 %
  Rotamer:
    Outliers :  0.92 %
    Allowed  : 14.98 %
    Favored  : 84.10 %
  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:  1.47 (0.28), residues: 958
  helix:  2.14 (0.24), residues: 494
  sheet:  0.38 (0.49), residues: 103
  loop : -0.49 (0.32), residues: 361

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP A1357 
 HIS   0.005   0.001   HIS C 730 
 PHE   0.012   0.001   PHE A1148 
 TYR   0.007   0.001   TYR A 705 
 ARG   0.006   0.000   ARG C 741 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04326 (  423)
  hydrogen bonds       : angle       3.45765 ( 1208)
  metal coordination   : bond        0.01281 (    8)
  metal coordination   : angle       2.69280 (    4)
  covalent geometry    : bond        0.00264 ( 9784)
  covalent geometry    : angle       0.49205 (13558)

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

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

  1916 Ramachandran restraints generated.
    958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1916 Ramachandran restraints generated.
    958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  61 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 53
  time to evaluate  : 0.967 
Fit side-chains
   revert: symmetry clash
REVERT: A 1355 MET cc_start: 0.7921 (ttm) cc_final: 0.7583 (ttp)
REVERT: C  734 LYS cc_start: 0.8853 (mtpp) cc_final: 0.8587 (mtmt)
  outliers start: 8
  outliers final: 3
  residues processed: 59
  average time/residue: 1.8009
  time to fit residues: 112.2822
Evaluate side-chains
  55 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 52
  time to evaluate  : 1.059 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  672 SER
Chi-restraints excluded: chain A residue  933 HIS
Chi-restraints excluded: chain A residue 1048 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 10 optimal weight:    1.9990
   chunk 33 optimal weight:    1.9990
   chunk 94 optimal weight:    1.9990
   chunk 23 optimal weight:    1.9990
   chunk 46 optimal weight:    2.9990
   chunk 50 optimal weight:    1.9990
   chunk 65 optimal weight:    2.9990
   chunk 14 optimal weight:    0.8980
   chunk 45 optimal weight:    3.9990
   chunk 54 optimal weight:    0.0270
   chunk 12 optimal weight:    0.2980
   overall best weight:    1.0442

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

Flipped N/Q/H residues before XYZ refinement:
C 730 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3523 r_free = 0.3523 target = 0.069783 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2967 r_free = 0.2967 target = 0.047537 restraints weight = 28359.159|
|-----------------------------------------------------------------------------|
r_work (start): 0.2943 rms_B_bonded: 2.99
r_work: 0.2765 rms_B_bonded: 4.03 restraints_weight: 0.5000
r_work (final): 0.2765
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8750
moved from start:          0.1360

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   9792  Z= 0.140
  Angle     :  0.516   7.259  13562  Z= 0.262
  Chirality :  0.036   0.151   1529
  Planarity :  0.004   0.035   1497
  Dihedral  : 17.442  87.807   2174
  Min Nonbonded Distance : 2.381

Molprobity Statistics.
  All-atom Clashscore : 3.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.51 %
    Favored  : 97.49 %
  Rotamer:
    Outliers :  0.92 %
    Allowed  : 15.32 %
    Favored  : 83.76 %
  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:  1.42 (0.28), residues: 958
  helix:  2.11 (0.24), residues: 494
  sheet:  0.29 (0.49), residues: 103
  loop : -0.49 (0.32), residues: 361

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.001   TRP A1357 
 HIS   0.005   0.001   HIS C 730 
 PHE   0.012   0.001   PHE A1148 
 TYR   0.009   0.001   TYR A1332 
 ARG   0.007   0.000   ARG C 746 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04861 (  423)
  hydrogen bonds       : angle       3.51571 ( 1208)
  metal coordination   : bond        0.01417 (    8)
  metal coordination   : angle       3.15362 (    4)
  covalent geometry    : bond        0.00327 ( 9784)
  covalent geometry    : angle       0.51308 (13558)

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

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

  1916 Ramachandran restraints generated.
    958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1916 Ramachandran restraints generated.
    958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  61 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 53
  time to evaluate  : 1.025 
Fit side-chains
   revert: symmetry clash
REVERT: A 1355 MET cc_start: 0.7891 (ttm) cc_final: 0.7557 (ttp)
REVERT: C  734 LYS cc_start: 0.8880 (mtpp) cc_final: 0.8629 (mtmt)
  outliers start: 8
  outliers final: 3
  residues processed: 60
  average time/residue: 1.7024
  time to fit residues: 108.5506
Evaluate side-chains
  55 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 52
  time to evaluate  : 0.968 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  875 CYS
Chi-restraints excluded: chain A residue  933 HIS
Chi-restraints excluded: chain A residue 1048 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 79 optimal weight:    1.9990
   chunk 50 optimal weight:    0.8980
   chunk 35 optimal weight:    1.9990
   chunk 91 optimal weight:    0.9990
   chunk 31 optimal weight:    3.9990
   chunk 82 optimal weight:    0.8980
   chunk 3 optimal weight:    1.9990
   chunk 88 optimal weight:    0.8980
   chunk 45 optimal weight:    3.9990
   chunk 26 optimal weight:    0.4980
   chunk 85 optimal weight:    4.9990
   overall best weight:    0.8382

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

Flipped N/Q/H residues before XYZ refinement:
C 730 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3540 r_free = 0.3540 target = 0.070426 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.2980 r_free = 0.2980 target = 0.048125 restraints weight = 28572.038|
|-----------------------------------------------------------------------------|
r_work (start): 0.2961 rms_B_bonded: 2.98
r_work: 0.2792 rms_B_bonded: 3.99 restraints_weight: 0.5000
r_work (final): 0.2792
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8715
moved from start:          0.1440

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   9792  Z= 0.122
  Angle     :  0.508   7.979  13562  Z= 0.258
  Chirality :  0.036   0.146   1529
  Planarity :  0.004   0.035   1497
  Dihedral  : 17.423  88.133   2174
  Min Nonbonded Distance : 2.364

Molprobity Statistics.
  All-atom Clashscore : 3.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.30 %
    Favored  : 97.70 %
  Rotamer:
    Outliers :  0.69 %
    Allowed  : 15.67 %
    Favored  : 83.64 %
  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:  1.48 (0.28), residues: 958
  helix:  2.16 (0.24), residues: 494
  sheet:  0.33 (0.49), residues: 103
  loop : -0.48 (0.32), residues: 361

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A1357 
 HIS   0.006   0.001   HIS C 730 
 PHE   0.012   0.001   PHE A1148 
 TYR   0.007   0.001   TYR A1332 
 ARG   0.007   0.000   ARG C 741 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04426 (  423)
  hydrogen bonds       : angle       3.43609 ( 1208)
  metal coordination   : bond        0.01291 (    8)
  metal coordination   : angle       2.79907 (    4)
  covalent geometry    : bond        0.00281 ( 9784)
  covalent geometry    : angle       0.50596 (13558)

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

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

  1916 Ramachandran restraints generated.
    958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1916 Ramachandran restraints generated.
    958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  58 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 52
  time to evaluate  : 1.102 
Fit side-chains
   revert: symmetry clash
REVERT: A 1355 MET cc_start: 0.7895 (ttm) cc_final: 0.7576 (ttp)
REVERT: C  734 LYS cc_start: 0.8878 (mtpp) cc_final: 0.8647 (mtmt)
  outliers start: 6
  outliers final: 3
  residues processed: 56
  average time/residue: 1.8228
  time to fit residues: 108.2409
Evaluate side-chains
  55 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 52
  time to evaluate  : 1.001 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  875 CYS
Chi-restraints excluded: chain A residue  933 HIS
Chi-restraints excluded: chain A residue 1048 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 72 optimal weight:    0.5980
   chunk 25 optimal weight:    3.9990
   chunk 90 optimal weight:    3.9990
   chunk 27 optimal weight:    0.0870
   chunk 52 optimal weight:    0.4980
   chunk 78 optimal weight:    2.9990
   chunk 96 optimal weight:    3.9990
   chunk 68 optimal weight:    1.9990
   chunk 4 optimal weight:    3.9990
   chunk 9 optimal weight:    2.9990
   chunk 55 optimal weight:    2.9990
   overall best weight:    1.2362

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

Flipped N/Q/H residues before XYZ refinement:
C 730 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3514 r_free = 0.3514 target = 0.069352 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2956 r_free = 0.2956 target = 0.047160 restraints weight = 28214.663|
|-----------------------------------------------------------------------------|
r_work (start): 0.2932 rms_B_bonded: 2.97
r_work: 0.2756 rms_B_bonded: 4.00 restraints_weight: 0.5000
r_work (final): 0.2756
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8764
moved from start:          0.1489

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   9792  Z= 0.159
  Angle     :  0.545   8.560  13562  Z= 0.276
  Chirality :  0.037   0.159   1529
  Planarity :  0.004   0.035   1497
  Dihedral  : 17.424  87.277   2174
  Min Nonbonded Distance : 2.393

Molprobity Statistics.
  All-atom Clashscore : 3.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.61 %
    Favored  : 97.39 %
  Rotamer:
    Outliers :  0.81 %
    Allowed  : 15.78 %
    Favored  : 83.41 %
  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:  1.41 (0.28), residues: 958
  helix:  2.09 (0.24), residues: 494
  sheet:  0.28 (0.47), residues: 108
  loop : -0.47 (0.32), residues: 356

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.001   TRP A1357 
 HIS   0.006   0.001   HIS C 730 
 PHE   0.012   0.001   PHE A1148 
 TYR   0.010   0.001   TYR A1332 
 ARG   0.006   0.000   ARG C 741 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05191 (  423)
  hydrogen bonds       : angle       3.53379 ( 1208)
  metal coordination   : bond        0.01480 (    8)
  metal coordination   : angle       3.44997 (    4)
  covalent geometry    : bond        0.00375 ( 9784)
  covalent geometry    : angle       0.54150 (13558)

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

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

  1916 Ramachandran restraints generated.
    958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1916 Ramachandran restraints generated.
    958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  59 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 52
  time to evaluate  : 0.982 
Fit side-chains
   revert: symmetry clash
REVERT: A 1355 MET cc_start: 0.7889 (ttm) cc_final: 0.7577 (ttp)
  outliers start: 7
  outliers final: 3
  residues processed: 57
  average time/residue: 1.7085
  time to fit residues: 103.2354
Evaluate side-chains
  55 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 52
  time to evaluate  : 1.049 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  875 CYS
Chi-restraints excluded: chain A residue  933 HIS
Chi-restraints excluded: chain A residue 1048 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 19 optimal weight:    0.0870
   chunk 62 optimal weight:    0.9980
   chunk 34 optimal weight:    2.9990
   chunk 46 optimal weight:    4.9990
   chunk 70 optimal weight:    2.9990
   chunk 66 optimal weight:    3.9990
   chunk 41 optimal weight:    0.5980
   chunk 84 optimal weight:    0.0470
   chunk 80 optimal weight:    0.6980
   chunk 56 optimal weight:    0.9980
   chunk 45 optimal weight:    0.3980
   overall best weight:    0.3656

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

Flipped N/Q/H residues before XYZ refinement:
C 730 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3570 r_free = 0.3570 target = 0.071760 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3022 r_free = 0.3022 target = 0.049657 restraints weight = 28489.879|
|-----------------------------------------------------------------------------|
r_work (start): 0.3004 rms_B_bonded: 2.97
r_work: 0.2839 rms_B_bonded: 4.00 restraints_weight: 0.5000
r_work (final): 0.2839
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8667
moved from start:          0.1585

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.042   9792  Z= 0.096
  Angle     :  0.499   9.146  13562  Z= 0.252
  Chirality :  0.034   0.132   1529
  Planarity :  0.003   0.034   1497
  Dihedral  : 17.348  87.897   2174
  Min Nonbonded Distance : 2.320

Molprobity Statistics.
  All-atom Clashscore : 2.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.98 %
    Favored  : 98.02 %
  Rotamer:
    Outliers :  0.46 %
    Allowed  : 16.36 %
    Favored  : 83.18 %
  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:  1.58 (0.28), residues: 958
  helix:  2.23 (0.24), residues: 494
  sheet:  0.43 (0.47), residues: 108
  loop : -0.44 (0.32), residues: 356

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP A1357 
 HIS   0.005   0.001   HIS C 730 
 PHE   0.012   0.001   PHE A1148 
 TYR   0.006   0.001   TYR A1229 
 ARG   0.007   0.000   ARG C 741 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03460 (  423)
  hydrogen bonds       : angle       3.31614 ( 1208)
  metal coordination   : bond        0.01058 (    8)
  metal coordination   : angle       2.20887 (    4)
  covalent geometry    : bond        0.00214 ( 9784)
  covalent geometry    : angle       0.49795 (13558)

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

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

  1916 Ramachandran restraints generated.
    958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1916 Ramachandran restraints generated.
    958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  57 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 53
  time to evaluate  : 1.102 
Fit side-chains
   revert: symmetry clash
REVERT: A 1355 MET cc_start: 0.7842 (ttm) cc_final: 0.7534 (ttp)
REVERT: C  734 LYS cc_start: 0.8870 (mtpp) cc_final: 0.8642 (mtmt)
  outliers start: 4
  outliers final: 3
  residues processed: 56
  average time/residue: 1.7982
  time to fit residues: 106.5784
Evaluate side-chains
  55 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 52
  time to evaluate  : 0.939 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  875 CYS
Chi-restraints excluded: chain A residue  933 HIS
Chi-restraints excluded: chain A residue 1048 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 1 optimal weight:    2.9990
   chunk 27 optimal weight:    2.9990
   chunk 34 optimal weight:    2.9990
   chunk 50 optimal weight:    2.9990
   chunk 37 optimal weight:    3.9990
   chunk 49 optimal weight:    3.9990
   chunk 73 optimal weight:    0.9990
   chunk 10 optimal weight:    2.9990
   chunk 55 optimal weight:    2.9990
   chunk 67 optimal weight:    0.8980
   chunk 99 optimal weight:   10.0000
   overall best weight:    2.1788

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

Flipped N/Q/H residues before XYZ refinement:
C 730 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3502 r_free = 0.3502 target = 0.068634 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2926 r_free = 0.2926 target = 0.046188 restraints weight = 28343.228|
|-----------------------------------------------------------------------------|
r_work (start): 0.2908 rms_B_bonded: 2.96
r_work: 0.2736 rms_B_bonded: 3.96 restraints_weight: 0.5000
r_work (final): 0.2736
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8773
moved from start:          0.1658

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.052   9792  Z= 0.248
  Angle     :  0.609   9.161  13562  Z= 0.309
  Chirality :  0.040   0.185   1529
  Planarity :  0.004   0.035   1497
  Dihedral  : 17.390  86.000   2174
  Min Nonbonded Distance : 2.432

Molprobity Statistics.
  All-atom Clashscore : 3.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.71 %
    Favored  : 97.29 %
  Rotamer:
    Outliers :  0.81 %
    Allowed  : 16.01 %
    Favored  : 83.18 %
  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:  1.28 (0.28), residues: 958
  helix:  2.02 (0.24), residues: 493
  sheet:  0.18 (0.48), residues: 103
  loop : -0.58 (0.32), residues: 362

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP A1357 
 HIS   0.007   0.002   HIS C 730 
 PHE   0.012   0.001   PHE A1148 
 TYR   0.013   0.001   TYR A1332 
 ARG   0.007   0.000   ARG C 741 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06315 (  423)
  hydrogen bonds       : angle       3.69338 ( 1208)
  metal coordination   : bond        0.01582 (    8)
  metal coordination   : angle       4.33599 (    4)
  covalent geometry    : bond        0.00593 ( 9784)
  covalent geometry    : angle       0.60424 (13558)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5363.45 seconds
wall clock time: 93 minutes 40.77 seconds (5620.77 seconds total)