Starting phenix.real_space_refine
on Sat Aug 23 03:46:17 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9aso_43821/08_2025/9aso_43821.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9aso_43821/08_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 {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9aso_43821/08_2025/9aso_43821.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9aso_43821/08_2025/9aso_43821.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9aso_43821/08_2025/9aso_43821.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9aso_43821/08_2025/9aso_43821.map"
  }
  resolution = 2.9
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 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): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 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: 2.08, per 1000 atoms: 0.22
  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: 0.84
  Conformation dependent library (CDL) restraints added in 233.3 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  
  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: 0.97
  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: 1.76

  Time building geometry restraints manager: 1.10 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:             5.100
  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:          0.180
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     10.440
  Find NCS groups from input model:        0.050
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:5.780
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   21.620
-------------------------------------------------------------------------------
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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.28 (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
 ARG   0.007   0.000   ARG C 746 
 TYR   0.006   0.001   TYR A1229 
 PHE   0.011   0.001   PHE A 970 
 TRP   0.032   0.001   TRP A1357 
 HIS   0.004   0.001   HIS A 873 

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

*********************** 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  : 0.229 
Fit side-chains
   revert: symmetry clash
  outliers start: 9
  outliers final: 9
  residues processed: 63
  average time/residue: 0.7299
  time to fit residues: 48.6247
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  : 0.344 
-------------------------------------------------------------------------------
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 49 optimal weight:    3.9990
   chunk 97 optimal weight:    7.9990
   chunk 53 optimal weight:    2.9990
   chunk 5 optimal weight:    4.9990
   chunk 33 optimal weight:    0.0050
   chunk 65 optimal weight:    1.9990
   chunk 62 optimal weight:    1.9990
   chunk 51 optimal weight:    5.9990
   chunk 100 optimal weight:    3.9990
   chunk 38 optimal weight:    0.8980
   chunk 61 optimal weight:    0.8980
   overall best weight:    1.1598

-------------------------------------------------------------------------------
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 = 0.3536 r_free = 0.3536 target = 0.070234 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.2970 r_free = 0.2970 target = 0.047821 restraints weight = 28189.904|
|-----------------------------------------------------------------------------|
r_work (start): 0.2952 rms_B_bonded: 2.96
r_work: 0.2782 rms_B_bonded: 3.98 restraints_weight: 0.5000
r_work (final): 0.2782
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8723
moved from start:          0.0808

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   9792  Z= 0.157
  Angle     :  0.525   6.416  13562  Z= 0.269
  Chirality :  0.037   0.156   1529
  Planarity :  0.004   0.033   1497
  Dihedral  : 17.902 111.252   2191
  Min Nonbonded Distance : 2.385

Molprobity Statistics.
  All-atom Clashscore : 2.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.98 %
    Favored  : 98.02 %
  Rotamer:
    Outliers :  1.38 %
    Allowed  : 13.25 %
    Favored  : 85.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.41 (0.27), residues: 958
  helix:  2.05 (0.24), residues: 495
  sheet:  0.49 (0.47), residues: 102
  loop : -0.50 (0.31), residues: 361

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG C 746 
 TYR   0.009   0.001   TYR A1332 
 PHE   0.011   0.001   PHE A1148 
 TRP   0.013   0.001   TRP A1357 
 HIS   0.005   0.001   HIS C 730 

Details of bonding type rmsd
  covalent geometry    : bond        0.00355 ( 9784)
  covalent geometry    : angle       0.52200 (13558)
  hydrogen bonds       : bond        0.05601 (  423)
  hydrogen bonds       : angle       3.78219 ( 1208)
  metal coordination   : bond        0.01386 (    8)
  metal coordination   : angle       3.19418 (    4)

*********************** 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
  65 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 53
  time to evaluate  : 0.355 
Fit side-chains
   revert: symmetry clash
REVERT: A 1355 MET cc_start: 0.7866 (ttm) cc_final: 0.7574 (ttp)
  outliers start: 12
  outliers final: 2
  residues processed: 61
  average time/residue: 0.8127
  time to fit residues: 52.2528
Evaluate side-chains
  54 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 52
  time to evaluate  : 0.358 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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 78 optimal weight:    2.9990
   chunk 45 optimal weight:    0.5980
   chunk 58 optimal weight:    1.9990
   chunk 41 optimal weight:    0.8980
   chunk 84 optimal weight:    0.5980
   chunk 7 optimal weight:    0.0670
   chunk 10 optimal weight:    1.9990
   chunk 25 optimal weight:    3.9990
   chunk 75 optimal weight:    2.9990
   chunk 85 optimal weight:    0.8980
   chunk 94 optimal weight:    3.9990
   overall best weight:    0.6118

-------------------------------------------------------------------------------
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 = 0.3547 r_free = 0.3547 target = 0.070863 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3004 r_free = 0.3004 target = 0.048820 restraints weight = 28253.106|
|-----------------------------------------------------------------------------|
r_work (start): 0.2978 rms_B_bonded: 2.98
r_work: 0.2802 rms_B_bonded: 4.03 restraints_weight: 0.5000
r_work (final): 0.2802
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8707
moved from start:          0.0929

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   9792  Z= 0.107
  Angle     :  0.480   6.055  13562  Z= 0.245
  Chirality :  0.035   0.148   1529
  Planarity :  0.003   0.035   1497
  Dihedral  : 17.796 103.053   2178
  Min Nonbonded Distance : 2.362

Molprobity Statistics.
  All-atom Clashscore : 2.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.09 %
    Favored  : 97.91 %
  Rotamer:
    Outliers :  0.81 %
    Allowed  : 14.29 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.44 (0.27), residues: 958
  helix:  2.11 (0.24), residues: 495
  sheet:  0.42 (0.48), residues: 103
  loop : -0.50 (0.31), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG C 746 
 TYR   0.006   0.001   TYR A1229 
 PHE   0.011   0.001   PHE A1148 
 TRP   0.016   0.001   TRP A1357 
 HIS   0.006   0.001   HIS C 730 

Details of bonding type rmsd
  covalent geometry    : bond        0.00235 ( 9784)
  covalent geometry    : angle       0.47794 (13558)
  hydrogen bonds       : bond        0.04400 (  423)
  hydrogen bonds       : angle       3.52654 ( 1208)
  metal coordination   : bond        0.01141 (    8)
  metal coordination   : angle       2.57073 (    4)

*********************** 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: 7
    poor density    : 53
  time to evaluate  : 0.365 
Fit side-chains
   revert: symmetry clash
REVERT: A 1355 MET cc_start: 0.7882 (ttm) cc_final: 0.7595 (ttp)
REVERT: C  737 GLU cc_start: 0.8520 (pm20) cc_final: 0.8312 (pm20)
  outliers start: 7
  outliers final: 3
  residues processed: 59
  average time/residue: 0.8087
  time to fit residues: 50.4898
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  : 0.425 
-------------------------------------------------------------------------------
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=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 66 optimal weight:    4.9990
   chunk 38 optimal weight:    3.9990
   chunk 84 optimal weight:    0.9980
   chunk 99 optimal weight:   10.0000
   chunk 6 optimal weight:    3.9990
   chunk 98 optimal weight:   10.0000
   chunk 25 optimal weight:    4.9990
   chunk 34 optimal weight:    1.9990
   chunk 52 optimal weight:    1.9990
   chunk 33 optimal weight:    1.9990
   chunk 93 optimal weight:    0.0020
   overall best weight:    1.3994

-------------------------------------------------------------------------------
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 = 0.3510 r_free = 0.3510 target = 0.069189 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.2949 r_free = 0.2949 target = 0.046895 restraints weight = 28464.676|
|-----------------------------------------------------------------------------|
r_work (start): 0.2926 rms_B_bonded: 3.00
r_work: 0.2746 rms_B_bonded: 4.03 restraints_weight: 0.5000
r_work (final): 0.2746
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8769
moved from start:          0.1180

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   9792  Z= 0.176
  Angle     :  0.530   6.301  13562  Z= 0.271
  Chirality :  0.038   0.167   1529
  Planarity :  0.004   0.036   1497
  Dihedral  : 17.810  96.158   2176
  Min Nonbonded Distance : 2.403

Molprobity Statistics.
  All-atom Clashscore : 3.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.30 %
    Favored  : 97.70 %
  Rotamer:
    Outliers :  1.38 %
    Allowed  : 14.17 %
    Favored  : 84.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.34 (0.28), residues: 958
  helix:  2.03 (0.24), residues: 494
  sheet:  0.34 (0.49), residues: 103
  loop : -0.54 (0.31), residues: 361

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG C 746 
 TYR   0.011   0.001   TYR A1332 
 PHE   0.011   0.001   PHE A1148 
 TRP   0.016   0.001   TRP A1357 
 HIS   0.005   0.001   HIS C 730 

Details of bonding type rmsd
  covalent geometry    : bond        0.00413 ( 9784)
  covalent geometry    : angle       0.52659 (13558)
  hydrogen bonds       : bond        0.05697 (  423)
  hydrogen bonds       : angle       3.66869 ( 1208)
  metal coordination   : bond        0.01495 (    8)
  metal coordination   : angle       3.73404 (    4)

*********************** 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
  65 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 53
  time to evaluate  : 0.219 
Fit side-chains
   revert: symmetry clash
REVERT: A 1355 MET cc_start: 0.7943 (ttm) cc_final: 0.7620 (ttp)
REVERT: C  734 LYS cc_start: 0.8855 (mtpp) cc_final: 0.8592 (mtmt)
  outliers start: 12
  outliers final: 6
  residues processed: 61
  average time/residue: 0.7603
  time to fit residues: 49.0814
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  : 0.239 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  672 SER
Chi-restraints excluded: chain A residue  804 LEU
Chi-restraints excluded: chain A residue  875 CYS
Chi-restraints excluded: chain A residue  933 HIS
Chi-restraints excluded: chain A residue 1048 ILE
Chi-restraints excluded: chain A residue 1154 MET
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 50 optimal weight:    1.9990
   chunk 71 optimal weight:    2.9990
   chunk 94 optimal weight:    0.8980
   chunk 36 optimal weight:    2.9990
   chunk 56 optimal weight:    0.5980
   chunk 74 optimal weight:    2.9990
   chunk 24 optimal weight:    1.9990
   chunk 62 optimal weight:    0.5980
   chunk 26 optimal weight:    0.9990
   chunk 5 optimal weight:    0.0270
   chunk 42 optimal weight:    0.9990
   overall best weight:    0.6240

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

Flipped N/Q/H residues before XYZ refinement:
A 724 GLN
A1340 GLN
C 730 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3542 r_free = 0.3542 target = 0.070611 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.2993 r_free = 0.2993 target = 0.048447 restraints weight = 28390.529|
|-----------------------------------------------------------------------------|
r_work (start): 0.2967 rms_B_bonded: 3.00
r_work: 0.2792 rms_B_bonded: 4.04 restraints_weight: 0.5000
r_work (final): 0.2792
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8709
moved from start:          0.1198

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034   9792  Z= 0.106
  Angle     :  0.479   6.265  13562  Z= 0.244
  Chirality :  0.035   0.169   1529
  Planarity :  0.003   0.035   1497
  Dihedral  : 17.636  88.721   2176
  Min Nonbonded Distance : 2.352

Molprobity Statistics.
  All-atom Clashscore : 2.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.19 %
    Favored  : 97.81 %
  Rotamer:
    Outliers :  1.27 %
    Allowed  : 14.40 %
    Favored  : 84.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.42 (0.28), residues: 958
  helix:  2.10 (0.24), residues: 494
  sheet:  0.39 (0.49), residues: 103
  loop : -0.51 (0.32), residues: 361

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG C 741 
 TYR   0.007   0.001   TYR A 705 
 PHE   0.012   0.001   PHE A1148 
 TRP   0.018   0.001   TRP A1357 
 HIS   0.005   0.001   HIS C 730 

Details of bonding type rmsd
  covalent geometry    : bond        0.00236 ( 9784)
  covalent geometry    : angle       0.47669 (13558)
  hydrogen bonds       : bond        0.04179 (  423)
  hydrogen bonds       : angle       3.45401 ( 1208)
  metal coordination   : bond        0.01220 (    8)
  metal coordination   : angle       2.56321 (    4)

*********************** 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
  64 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 53
  time to evaluate  : 0.348 
Fit side-chains
   revert: symmetry clash
REVERT: A 1355 MET cc_start: 0.7930 (ttm) cc_final: 0.7598 (ttp)
REVERT: C  737 GLU cc_start: 0.8628 (OUTLIER) cc_final: 0.8412 (pm20)
  outliers start: 11
  outliers final: 3
  residues processed: 61
  average time/residue: 0.7208
  time to fit residues: 46.3970
Evaluate side-chains
  56 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 52
  time to evaluate  : 0.300 
-------------------------------------------------------------------------------
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 1154 MET
Chi-restraints excluded: chain C residue  737 GLU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 12 optimal weight:    0.5980
   chunk 77 optimal weight:    3.9990
   chunk 22 optimal weight:    0.6980
   chunk 4 optimal weight:    3.9990
   chunk 29 optimal weight:    2.9990
   chunk 32 optimal weight:    2.9990
   chunk 69 optimal weight:    0.0980
   chunk 84 optimal weight:    0.0040
   chunk 8 optimal weight:    0.8980
   chunk 83 optimal weight:    0.8980
   chunk 64 optimal weight:    0.9980
   overall best weight:    0.4592

-------------------------------------------------------------------------------
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 = 0.3561 r_free = 0.3561 target = 0.071421 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3023 r_free = 0.3023 target = 0.049448 restraints weight = 28192.119|
|-----------------------------------------------------------------------------|
r_work (start): 0.2997 rms_B_bonded: 2.98
r_work: 0.2824 rms_B_bonded: 4.02 restraints_weight: 0.5000
r_work (final): 0.2824
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8688
moved from start:          0.1347

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030   9792  Z= 0.095
  Angle     :  0.474   7.002  13562  Z= 0.240
  Chirality :  0.034   0.153   1529
  Planarity :  0.003   0.038   1497
  Dihedral  : 17.440  88.804   2174
  Min Nonbonded Distance : 2.354

Molprobity Statistics.
  All-atom Clashscore : 3.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.09 %
    Favored  : 97.91 %
  Rotamer:
    Outliers :  0.92 %
    Allowed  : 15.44 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.59 (0.28), residues: 958
  helix:  2.25 (0.24), residues: 494
  sheet:  0.49 (0.47), residues: 108
  loop : -0.47 (0.32), residues: 356

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG C 746 
 TYR   0.006   0.001   TYR A 705 
 PHE   0.011   0.001   PHE A1148 
 TRP   0.025   0.001   TRP A1357 
 HIS   0.007   0.001   HIS C 730 

Details of bonding type rmsd
  covalent geometry    : bond        0.00208 ( 9784)
  covalent geometry    : angle       0.47198 (13558)
  hydrogen bonds       : bond        0.03659 (  423)
  hydrogen bonds       : angle       3.30271 ( 1208)
  metal coordination   : bond        0.01113 (    8)
  metal coordination   : angle       2.27216 (    4)

*********************** 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  : 0.358 
Fit side-chains
   revert: symmetry clash
REVERT: A 1355 MET cc_start: 0.7917 (ttm) cc_final: 0.7581 (ttp)
REVERT: C  734 LYS cc_start: 0.8834 (mtpp) cc_final: 0.8549 (mtmt)
  outliers start: 8
  outliers final: 3
  residues processed: 58
  average time/residue: 0.7400
  time to fit residues: 45.3821
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  : 0.426 
-------------------------------------------------------------------------------
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=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 5 optimal weight:    8.9990
   chunk 59 optimal weight:    0.7980
   chunk 92 optimal weight:    4.9990
   chunk 79 optimal weight:    0.9980
   chunk 35 optimal weight:    1.9990
   chunk 57 optimal weight:    0.8980
   chunk 94 optimal weight:    0.8980
   chunk 17 optimal weight:    0.0170
   chunk 67 optimal weight:    3.9990
   chunk 49 optimal weight:    5.9990
   chunk 89 optimal weight:    2.9990
   overall best weight:    0.7218

-------------------------------------------------------------------------------
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 = 0.3555 r_free = 0.3555 target = 0.071038 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3002 r_free = 0.3002 target = 0.048864 restraints weight = 28237.225|
|-----------------------------------------------------------------------------|
r_work (start): 0.2981 rms_B_bonded: 2.96
r_work: 0.2812 rms_B_bonded: 3.98 restraints_weight: 0.5000
r_work (final): 0.2812
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8694
moved from start:          0.1365

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= 0.112
  Angle     :  0.488   7.267  13562  Z= 0.247
  Chirality :  0.035   0.142   1529
  Planarity :  0.003   0.034   1497
  Dihedral  : 17.390  88.216   2174
  Min Nonbonded Distance : 2.383

Molprobity Statistics.
  All-atom Clashscore : 2.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.19 %
    Favored  : 97.81 %
  Rotamer:
    Outliers :  0.69 %
    Allowed  : 15.44 %
    Favored  : 83.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.62 (0.28), residues: 958
  helix:  2.25 (0.24), residues: 495
  sheet:  0.51 (0.47), residues: 108
  loop : -0.42 (0.32), residues: 355

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG C 741 
 TYR   0.007   0.001   TYR A 705 
 PHE   0.011   0.001   PHE A1148 
 TRP   0.013   0.001   TRP A1357 
 HIS   0.005   0.001   HIS C 730 

Details of bonding type rmsd
  covalent geometry    : bond        0.00258 ( 9784)
  covalent geometry    : angle       0.48637 (13558)
  hydrogen bonds       : bond        0.04200 (  423)
  hydrogen bonds       : angle       3.33382 ( 1208)
  metal coordination   : bond        0.01240 (    8)
  metal coordination   : angle       2.68002 (    4)

*********************** 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
  59 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 53
  time to evaluate  : 0.420 
Fit side-chains
   revert: symmetry clash
REVERT: A 1355 MET cc_start: 0.7880 (ttm) cc_final: 0.7540 (ttp)
REVERT: C  734 LYS cc_start: 0.8837 (mtpp) cc_final: 0.8559 (mtmt)
  outliers start: 6
  outliers final: 3
  residues processed: 58
  average time/residue: 0.8211
  time to fit residues: 50.2743
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  : 0.341 
-------------------------------------------------------------------------------
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 23 optimal weight:    0.0980
   chunk 62 optimal weight:    2.9990
   chunk 51 optimal weight:    1.9990
   chunk 36 optimal weight:    5.9990
   chunk 94 optimal weight:    1.9990
   chunk 39 optimal weight:    5.9990
   chunk 0 optimal weight:    6.9990
   chunk 49 optimal weight:    4.9990
   chunk 17 optimal weight:    0.6980
   chunk 56 optimal weight:    0.9980
   chunk 28 optimal weight:    4.9990
   overall best weight:    1.1584

-------------------------------------------------------------------------------
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 = 0.3526 r_free = 0.3526 target = 0.069869 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2969 r_free = 0.2969 target = 0.047617 restraints weight = 28175.868|
|-----------------------------------------------------------------------------|
r_work (start): 0.2945 rms_B_bonded: 2.99
r_work: 0.2769 rms_B_bonded: 4.01 restraints_weight: 0.5000
r_work (final): 0.2769
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8734
moved from start:          0.1429

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   9792  Z= 0.151
  Angle     :  0.522   8.576  13562  Z= 0.264
  Chirality :  0.036   0.154   1529
  Planarity :  0.004   0.034   1497
  Dihedral  : 17.389  87.877   2174
  Min Nonbonded Distance : 2.395

Molprobity Statistics.
  All-atom Clashscore : 3.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.51 %
    Favored  : 97.49 %
  Rotamer:
    Outliers :  1.04 %
    Allowed  : 15.67 %
    Favored  : 83.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.52 (0.28), residues: 958
  helix:  2.17 (0.24), residues: 494
  sheet:  0.45 (0.47), residues: 108
  loop : -0.46 (0.32), residues: 356

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG C 741 
 TYR   0.009   0.001   TYR A1332 
 PHE   0.015   0.001   PHE A 906 
 TRP   0.024   0.001   TRP A1357 
 HIS   0.005   0.001   HIS C 730 

Details of bonding type rmsd
  covalent geometry    : bond        0.00356 ( 9784)
  covalent geometry    : angle       0.51940 (13558)
  hydrogen bonds       : bond        0.04965 (  423)
  hydrogen bonds       : angle       3.43754 ( 1208)
  metal coordination   : bond        0.01366 (    8)
  metal coordination   : angle       3.28037 (    4)

*********************** 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
  61 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 52
  time to evaluate  : 0.303 
Fit side-chains
   revert: symmetry clash
REVERT: A 1355 MET cc_start: 0.7880 (ttm) cc_final: 0.7536 (ttp)
REVERT: C  734 LYS cc_start: 0.8858 (mtpp) cc_final: 0.8566 (mtmt)
  outliers start: 9
  outliers final: 4
  residues processed: 58
  average time/residue: 0.8133
  time to fit residues: 49.8799
Evaluate side-chains
  56 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 52
  time to evaluate  : 0.265 
-------------------------------------------------------------------------------
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
Chi-restraints excluded: chain A residue 1154 MET
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 81 optimal weight:    0.6980
   chunk 5 optimal weight:    0.4980
   chunk 59 optimal weight:    0.6980
   chunk 77 optimal weight:    2.9990
   chunk 60 optimal weight:    0.7980
   chunk 19 optimal weight:    1.9990
   chunk 20 optimal weight:    1.9990
   chunk 69 optimal weight:    3.9990
   chunk 35 optimal weight:    1.9990
   chunk 92 optimal weight:    3.9990
   chunk 11 optimal weight:    0.9990
   overall best weight:    0.7382

-------------------------------------------------------------------------------
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 = 0.3549 r_free = 0.3549 target = 0.070778 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.2992 r_free = 0.2992 target = 0.048517 restraints weight = 28132.674|
|-----------------------------------------------------------------------------|
r_work (start): 0.2973 rms_B_bonded: 2.97
r_work: 0.2807 rms_B_bonded: 3.96 restraints_weight: 0.5000
r_work (final): 0.2807
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8701
moved from start:          0.1443

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   9792  Z= 0.116
  Angle     :  0.509   8.764  13562  Z= 0.257
  Chirality :  0.035   0.138   1529
  Planarity :  0.003   0.034   1497
  Dihedral  : 17.363  88.195   2174
  Min Nonbonded Distance : 2.367

Molprobity Statistics.
  All-atom Clashscore : 2.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.09 %
    Favored  : 97.91 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.57 (0.28), residues: 958
  helix:  2.22 (0.24), residues: 494
  sheet:  0.48 (0.47), residues: 108
  loop : -0.46 (0.32), residues: 356

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG C 741 
 TYR   0.007   0.001   TYR A 705 
 PHE   0.013   0.001   PHE A 906 
 TRP   0.016   0.001   TRP A1357 
 HIS   0.006   0.001   HIS C 730 

Details of bonding type rmsd
  covalent geometry    : bond        0.00267 ( 9784)
  covalent geometry    : angle       0.50738 (13558)
  hydrogen bonds       : bond        0.04272 (  423)
  hydrogen bonds       : angle       3.37942 ( 1208)
  metal coordination   : bond        0.01226 (    8)
  metal coordination   : angle       2.67519 (    4)

*********************** 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
  60 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 53
  time to evaluate  : 0.302 
Fit side-chains
   revert: symmetry clash
REVERT: A  722 MET cc_start: 0.9412 (mtt) cc_final: 0.9091 (mtt)
REVERT: A 1355 MET cc_start: 0.7883 (ttm) cc_final: 0.7550 (ttp)
REVERT: C  734 LYS cc_start: 0.8836 (mtpp) cc_final: 0.8574 (mtmt)
  outliers start: 7
  outliers final: 3
  residues processed: 58
  average time/residue: 0.8964
  time to fit residues: 54.7769
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  : 0.344 
-------------------------------------------------------------------------------
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 97 optimal weight:    7.9990
   chunk 35 optimal weight:    1.9990
   chunk 92 optimal weight:    2.9990
   chunk 16 optimal weight:    3.9990
   chunk 18 optimal weight:    3.9990
   chunk 93 optimal weight:    0.4980
   chunk 52 optimal weight:    3.9990
   chunk 99 optimal weight:    8.9990
   chunk 8 optimal weight:    0.0030
   chunk 46 optimal weight:    0.6980
   chunk 56 optimal weight:    0.8980
   overall best weight:    0.8192

-------------------------------------------------------------------------------
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 = 0.3544 r_free = 0.3544 target = 0.070564 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.2985 r_free = 0.2985 target = 0.048302 restraints weight = 28146.571|
|-----------------------------------------------------------------------------|
r_work (start): 0.2968 rms_B_bonded: 2.96
r_work: 0.2798 rms_B_bonded: 3.99 restraints_weight: 0.5000
r_work (final): 0.2798
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8713
moved from start:          0.1513

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= 0.123
  Angle     :  0.522  10.353  13562  Z= 0.262
  Chirality :  0.035   0.143   1529
  Planarity :  0.003   0.033   1497
  Dihedral  : 17.338  87.499   2174
  Min Nonbonded Distance : 2.377

Molprobity Statistics.
  All-atom Clashscore : 2.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.30 %
    Favored  : 97.70 %
  Rotamer:
    Outliers :  0.46 %
    Allowed  : 16.24 %
    Favored  : 83.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.59 (0.28), residues: 958
  helix:  2.24 (0.24), residues: 494
  sheet:  0.45 (0.48), residues: 108
  loop : -0.45 (0.32), residues: 356

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG C 741 
 TYR   0.008   0.001   TYR A1332 
 PHE   0.013   0.001   PHE A 906 
 TRP   0.016   0.001   TRP A1357 
 HIS   0.006   0.001   HIS C 730 

Details of bonding type rmsd
  covalent geometry    : bond        0.00286 ( 9784)
  covalent geometry    : angle       0.51969 (13558)
  hydrogen bonds       : bond        0.04430 (  423)
  hydrogen bonds       : angle       3.38337 ( 1208)
  metal coordination   : bond        0.01291 (    8)
  metal coordination   : angle       2.88891 (    4)

********************** 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
  56 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 52
  time to evaluate  : 0.368 
Fit side-chains
   revert: symmetry clash
REVERT: A 1355 MET cc_start: 0.7859 (ttm) cc_final: 0.7551 (ttp)
  outliers start: 4
  outliers final: 3
  residues processed: 55
  average time/residue: 0.9164
  time to fit residues: 53.1127
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  : 0.331 
-------------------------------------------------------------------------------
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 20 optimal weight:    1.9990
   chunk 14 optimal weight:    0.0770
   chunk 18 optimal weight:    2.9990
   chunk 29 optimal weight:    0.5980
   chunk 68 optimal weight:    0.9980
   chunk 26 optimal weight:    0.7980
   chunk 22 optimal weight:    0.6980
   chunk 62 optimal weight:    0.9980
   chunk 37 optimal weight:    3.9990
   chunk 81 optimal weight:    0.0020
   chunk 1 optimal weight:    1.9990
   overall best weight:    0.4346

-------------------------------------------------------------------------------
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 = 0.3571 r_free = 0.3571 target = 0.071786 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3024 r_free = 0.3024 target = 0.049705 restraints weight = 28007.312|
|-----------------------------------------------------------------------------|
r_work (start): 0.3005 rms_B_bonded: 2.95
r_work: 0.2842 rms_B_bonded: 3.97 restraints_weight: 0.5000
r_work (final): 0.2842
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8664
moved from start:          0.1579

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.040   9792  Z= 0.098
  Angle     :  0.506  10.063  13562  Z= 0.254
  Chirality :  0.034   0.134   1529
  Planarity :  0.003   0.032   1497
  Dihedral  : 17.278  87.748   2174
  Min Nonbonded Distance : 2.351

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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.68 (0.28), residues: 958
  helix:  2.31 (0.24), residues: 495
  sheet:  0.53 (0.48), residues: 108
  loop : -0.41 (0.32), residues: 355

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG C 741 
 TYR   0.006   0.001   TYR A 705 
 PHE   0.013   0.001   PHE A 906 
 TRP   0.019   0.001   TRP A1357 
 HIS   0.006   0.001   HIS C 730 

Details of bonding type rmsd
  covalent geometry    : bond        0.00222 ( 9784)
  covalent geometry    : angle       0.50501 (13558)
  hydrogen bonds       : bond        0.03561 (  423)
  hydrogen bonds       : angle       3.26396 ( 1208)
  metal coordination   : bond        0.01069 (    8)
  metal coordination   : angle       2.24622 (    4)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2634.81 seconds
wall clock time: 45 minutes 47.25 seconds (2747.25 seconds total)