Starting phenix.real_space_refine
on Wed May 14 20:16:09 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8gv9_34288/05_2025/8gv9_34288.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8gv9_34288/05_2025/8gv9_34288.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.06
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8gv9_34288/05_2025/8gv9_34288.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8gv9_34288/05_2025/8gv9_34288.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8gv9_34288/05_2025/8gv9_34288.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8gv9_34288/05_2025/8gv9_34288.cif"
  }
  resolution = 3.06
  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=  -0.001 sd=   0.152
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: 5
    Type Number    sf(0)   Gaussians
     S      60      5.16       5
     Cl      2      4.86       5
     C    7964      2.51       5
     N    2046      2.21       5
     O    2098      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 49 residue(s): 0.05s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 12170
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 6084
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 766, 6084
          Classifications: {'peptide': 766}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 38, 'TRANS': 727}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 2
          Planarities with less than four sites: {'ASN:plan1': 1}
          Unresolved non-hydrogen planarities: 3
    Chain: "B"
      Number of atoms: 6084
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 766, 6084
          Classifications: {'peptide': 766}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 38, 'TRANS': 727}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 2
          Planarities with less than four sites: {'ASN:plan1': 1}
          Unresolved non-hydrogen planarities: 3
    Chain: "A"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' CL': 1}
          Classifications: {'undetermined': 1}
    Chain: "B"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' CL': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 7.63, per 1000 atoms: 0.63
  Number of scatterers: 12170
  At special positions: 0
  Unit cell: (91.3, 127.6, 123.2, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     Cl      2     17.00
     S      60     16.00
     O    2098      8.00
     N    2046      7.00
     C    7964      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: 2.70
  Conformation dependent library (CDL) restraints added in 1.5 seconds
  

  3032 Ramachandran restraints generated.
    1516 Oldfield, 0 Emsley, 1516 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2892

  Finding SS restraints...
    Secondary structure from input PDB file:
      67 helices and 7 sheets defined
      60.4% alpha, 8.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.28
  Creating SS restraints...
    Processing helix  chain 'A' and resid 370 through 381
    Processing helix  chain 'A' and resid 393 through 407
    Processing helix  chain 'A' and resid 412 through 414
      No H-bonds generated for 'chain 'A' and resid 412 through 414'
    Processing helix  chain 'A' and resid 415 through 424
    Processing helix  chain 'A' and resid 500 through 510
    Processing helix  chain 'A' and resid 568 through 580
    Processing helix  chain 'A' and resid 582 through 591
      removed outlier: 3.944A  pdb=" N   TYR A 590 " --> pdb=" O   HIS A 586 " (cutoff:3.500A)
      removed outlier: 4.125A  pdb=" N   LEU A 591 " --> pdb=" O   GLU A 587 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 594 through 607
      removed outlier: 3.916A  pdb=" N   LEU A 598 " --> pdb=" O   GLU A 594 " (cutoff:3.500A)
      removed outlier: 3.510A  pdb=" N   ASP A 607 " --> pdb=" O   ASN A 603 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 621 through 641
      removed outlier: 4.088A  pdb=" N   SER A 625 " --> pdb=" O   GLU A 621 " (cutoff:3.500A)
      removed outlier: 3.785A  pdb=" N   VAL A 626 " --> pdb=" O   LEU A 622 " (cutoff:3.500A)
      removed outlier: 4.795A  pdb=" N   ALA A 627 " --> pdb=" O   LEU A 623 " (cutoff:3.500A)
      removed outlier: 3.731A  pdb=" N   HIS A 628 " --> pdb=" O   ARG A 624 " (cutoff:3.500A)
      removed outlier: 3.573A  pdb=" N   ARG A 631 " --> pdb=" O   ALA A 627 " (cutoff:3.500A)
      removed outlier: 3.549A  pdb=" N   GLN A 632 " --> pdb=" O   HIS A 628 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 682 through 693
    Processing helix  chain 'A' and resid 694 through 696
      No H-bonds generated for 'chain 'A' and resid 694 through 696'
    Processing helix  chain 'A' and resid 697 through 702
      removed outlier: 3.674A  pdb=" N   ASP A 702 " --> pdb=" O   SER A 698 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 705 through 734
      removed outlier: 4.234A  pdb=" N   LEU A 709 " --> pdb=" O   ASP A 705 " (cutoff:3.500A)
      removed outlier: 3.935A  pdb=" N   ALA A 710 " --> pdb=" O   PRO A 706 " (cutoff:3.500A)
      removed outlier: 3.947A  pdb=" N   SER A 721 " --> pdb=" O   PHE A 717 " (cutoff:3.500A)
      Proline residue:  A 722  - end of helix
    Processing helix  chain 'A' and resid 739 through 758
    Processing helix  chain 'A' and resid 768 through 785
    Processing helix  chain 'A' and resid 788 through 810
      removed outlier: 3.654A  pdb=" N   GLY A 792 " --> pdb=" O   GLU A 788 " (cutoff:3.500A)
      removed outlier: 4.059A  pdb=" N   ARG A 793 " --> pdb=" O   TYR A 789 " (cutoff:3.500A)
      removed outlier: 4.191A  pdb=" N   VAL A 794 " --> pdb=" O   LEU A 790 " (cutoff:3.500A)
      removed outlier: 3.665A  pdb=" N   TRP A 795 " --> pdb=" O   VAL A 791 " (cutoff:3.500A)
      removed outlier: 3.717A  pdb=" N   PHE A 802 " --> pdb=" O   PHE A 798 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 811 through 819
      removed outlier: 4.296A  pdb=" N   PHE A 814 " --> pdb=" O   GLU A 811 " (cutoff:3.500A)
      removed outlier: 3.717A  pdb=" N   VAL A 816 " --> pdb=" O   SER A 813 " (cutoff:3.500A)
      removed outlier: 3.520A  pdb=" N   VAL A 819 " --> pdb=" O   VAL A 816 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 820 through 850
      removed outlier: 3.505A  pdb=" N   GLN A 824 " --> pdb=" O   SER A 820 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 899 through 923
      removed outlier: 3.960A  pdb=" N   LEU A 903 " --> pdb=" O   ASN A 899 " (cutoff:3.500A)
      removed outlier: 3.792A  pdb=" N   ASN A 923 " --> pdb=" O   ARG A 919 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 928 through 937
    Processing helix  chain 'A' and resid 938 through 954
      removed outlier: 3.554A  pdb=" N   ILE A 954 " --> pdb=" O   VAL A 950 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 990 through 996
      removed outlier: 3.722A  pdb=" N   MET A 994 " --> pdb=" O   PRO A 990 " (cutoff:3.500A)
      removed outlier: 3.753A  pdb=" N   VAL A 995 " --> pdb=" O   VAL A 991 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 999 through 1020
      removed outlier: 3.791A  pdb=" N   LEU A1003 " --> pdb=" O   LEU A 999 " (cutoff:3.500A)
      removed outlier: 3.573A  pdb=" N   VAL A1004 " --> pdb=" O   PRO A1000 " (cutoff:3.500A)
      removed outlier: 3.785A  pdb=" N   PHE A1005 " --> pdb=" O   ALA A1001 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1031 through 1046
      removed outlier: 4.203A  pdb=" N   LEU A1036 " --> pdb=" O   PHE A1032 " (cutoff:3.500A)
      removed outlier: 4.056A  pdb=" N   LEU A1037 " --> pdb=" O   HIS A1033 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1057 through 1067
    Processing helix  chain 'A' and resid 1091 through 1102
    Processing helix  chain 'A' and resid 1106 through 1111
    Processing helix  chain 'A' and resid 1114 through 1129
      removed outlier: 3.941A  pdb=" N   LEU A1118 " --> pdb=" O   PRO A1114 " (cutoff:3.500A)
      removed outlier: 3.509A  pdb=" N   SER A1129 " --> pdb=" O   MET A1125 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1133 through 1141
    Processing helix  chain 'A' and resid 1142 through 1144
      No H-bonds generated for 'chain 'A' and resid 1142 through 1144'
    Processing helix  chain 'A' and resid 1145 through 1149
      removed outlier: 3.570A  pdb=" N   HIS A1149 " --> pdb=" O   PRO A1146 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1152 through 1157
      removed outlier: 4.006A  pdb=" N   LYS A1157 " --> pdb=" O   THR A1153 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1159 through 1183
      removed outlier: 3.639A  pdb=" N   THR A1183 " --> pdb=" O   ALA A1179 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1185 through 1187
      No H-bonds generated for 'chain 'A' and resid 1185 through 1187'
    Processing helix  chain 'A' and resid 1188 through 1195
      removed outlier: 3.549A  pdb=" N   ILE A1192 " --> pdb=" O   ALA A1188 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1195 through 1208
      removed outlier: 3.675A  pdb=" N   LEU A1199 " --> pdb=" O   LEU A1195 " (cutoff:3.500A)
      removed outlier: 3.949A  pdb=" N   LEU A1204 " --> pdb=" O   ARG A1200 " (cutoff:3.500A)
      removed outlier: 4.783A  pdb=" N   THR A1205 " --> pdb=" O   MET A1201 " (cutoff:3.500A)
      removed outlier: 3.555A  pdb=" N   ARG A1206 " --> pdb=" O   VAL A1202 " (cutoff:3.500A)
      removed outlier: 3.546A  pdb=" N   ILE A1207 " --> pdb=" O   VAL A1203 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 370 through 381
      removed outlier: 3.842A  pdb=" N   ALA B 381 " --> pdb=" O   ARG B 377 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 393 through 408
    Processing helix  chain 'B' and resid 415 through 424
    Processing helix  chain 'B' and resid 500 through 510
      removed outlier: 3.636A  pdb=" N   GLU B 508 " --> pdb=" O   LEU B 504 " (cutoff:3.500A)
      removed outlier: 3.809A  pdb=" N   LYS B 509 " --> pdb=" O   LYS B 505 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 568 through 580
    Processing helix  chain 'B' and resid 582 through 591
      removed outlier: 3.793A  pdb=" N   LEU B 591 " --> pdb=" O   GLU B 587 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 596 through 607
      removed outlier: 3.536A  pdb=" N   THR B 600 " --> pdb=" O   GLU B 596 " (cutoff:3.500A)
      removed outlier: 3.782A  pdb=" N   ALA B 601 " --> pdb=" O   ASP B 597 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 625 through 641
      removed outlier: 3.920A  pdb=" N   GLN B 630 " --> pdb=" O   VAL B 626 " (cutoff:3.500A)
      removed outlier: 3.566A  pdb=" N   ARG B 631 " --> pdb=" O   ALA B 627 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 682 through 693
    Processing helix  chain 'B' and resid 695 through 700
      removed outlier: 4.059A  pdb=" N   ASP B 699 " --> pdb=" O   HIS B 695 " (cutoff:3.500A)
      removed outlier: 3.870A  pdb=" N   PHE B 700 " --> pdb=" O   TYR B 696 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 695 through 700'
    Processing helix  chain 'B' and resid 705 through 734
      removed outlier: 3.580A  pdb=" N   LEU B 709 " --> pdb=" O   ASP B 705 " (cutoff:3.500A)
      removed outlier: 3.677A  pdb=" N   VAL B 712 " --> pdb=" O   CYS B 708 " (cutoff:3.500A)
      removed outlier: 4.848A  pdb=" N   ILE B 713 " --> pdb=" O   LEU B 709 " (cutoff:3.500A)
      removed outlier: 4.841A  pdb=" N   PHE B 714 " --> pdb=" O   ALA B 710 " (cutoff:3.500A)
      Proline residue:  B 722  - end of helix
    Processing helix  chain 'B' and resid 739 through 758
      removed outlier: 3.674A  pdb=" N   VAL B 753 " --> pdb=" O   LEU B 749 " (cutoff:3.500A)
      removed outlier: 3.838A  pdb=" N   PHE B 754 " --> pdb=" O   GLN B 750 " (cutoff:3.500A)
      removed outlier: 3.750A  pdb=" N   CYS B 755 " --> pdb=" O   GLY B 751 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 768 through 784
    Processing helix  chain 'B' and resid 788 through 810
      removed outlier: 3.925A  pdb=" N   GLY B 792 " --> pdb=" O   GLU B 788 " (cutoff:3.500A)
      removed outlier: 4.033A  pdb=" N   ARG B 793 " --> pdb=" O   TYR B 789 " (cutoff:3.500A)
      removed outlier: 4.117A  pdb=" N   VAL B 794 " --> pdb=" O   LEU B 790 " (cutoff:3.500A)
      removed outlier: 3.936A  pdb=" N   TRP B 795 " --> pdb=" O   VAL B 791 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 812 through 819
    Processing helix  chain 'B' and resid 820 through 850
      removed outlier: 3.859A  pdb=" N   ILE B 826 " --> pdb=" O   PHE B 822 " (cutoff:3.500A)
      removed outlier: 3.750A  pdb=" N   GLN B 848 " --> pdb=" O   VAL B 844 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 899 through 923
      removed outlier: 3.504A  pdb=" N   LEU B 903 " --> pdb=" O   ASN B 899 " (cutoff:3.500A)
      removed outlier: 3.577A  pdb=" N   ALA B 915 " --> pdb=" O   THR B 911 " (cutoff:3.500A)
      removed outlier: 3.681A  pdb=" N   PHE B 917 " --> pdb=" O   PHE B 913 " (cutoff:3.500A)
      removed outlier: 3.519A  pdb=" N   LEU B 918 " --> pdb=" O   ILE B 914 " (cutoff:3.500A)
      removed outlier: 3.536A  pdb=" N   PHE B 921 " --> pdb=" O   PHE B 917 " (cutoff:3.500A)
      removed outlier: 3.632A  pdb=" N   ASN B 923 " --> pdb=" O   ARG B 919 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 928 through 937
    Processing helix  chain 'B' and resid 938 through 954
      removed outlier: 3.543A  pdb=" N   ILE B 942 " --> pdb=" O   PHE B 938 " (cutoff:3.500A)
      removed outlier: 3.555A  pdb=" N   ILE B 954 " --> pdb=" O   VAL B 950 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 997 through 1020
      removed outlier: 3.557A  pdb=" N   ALA B1001 " --> pdb=" O   SER B 997 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1033 through 1047
      removed outlier: 3.574A  pdb=" N   LEU B1037 " --> pdb=" O   HIS B1033 " (cutoff:3.500A)
      removed outlier: 3.527A  pdb=" N   ALA B1047 " --> pdb=" O   GLY B1043 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1048 through 1050
      No H-bonds generated for 'chain 'B' and resid 1048 through 1050'
    Processing helix  chain 'B' and resid 1057 through 1067
    Processing helix  chain 'B' and resid 1091 through 1102
    Processing helix  chain 'B' and resid 1109 through 1113
      removed outlier: 3.767A  pdb=" N   GLN B1112 " --> pdb=" O   LEU B1109 " (cutoff:3.500A)
      removed outlier: 3.775A  pdb=" N   ILE B1113 " --> pdb=" O   LEU B1110 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 1109 through 1113'
    Processing helix  chain 'B' and resid 1114 through 1129
      removed outlier: 3.913A  pdb=" N   LEU B1118 " --> pdb=" O   PRO B1114 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1135 through 1141
    Processing helix  chain 'B' and resid 1145 through 1149
      removed outlier: 3.654A  pdb=" N   HIS B1149 " --> pdb=" O   PRO B1146 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1152 through 1157
      removed outlier: 3.969A  pdb=" N   LYS B1157 " --> pdb=" O   THR B1153 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1159 through 1182
      removed outlier: 3.660A  pdb=" N   SER B1182 " --> pdb=" O   TRP B1178 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1188 through 1208
      Proline residue:  B1198  - end of helix
    Processing sheet with id=AA1, first strand: chain 'A' and resid 350 through 352
      removed outlier: 5.293A  pdb=" N   GLU A 342 " --> pdb=" O   GLU A 329 " (cutoff:3.500A)
      removed outlier: 6.157A  pdb=" N   GLU A 329 " --> pdb=" O   GLU A 342 " (cutoff:3.500A)
      removed outlier: 3.731A  pdb=" N   ALA A 344 " --> pdb=" O   LEU A 327 " (cutoff:3.500A)
      removed outlier: 4.854A  pdb=" N   CYS A 523 " --> pdb=" O   LEU A 330 " (cutoff:3.500A)
      removed outlier: 10.961A  pdb=" N   ALA A 514 " --> pdb=" O   VAL A 553 " (cutoff:3.500A)
      removed outlier: 9.919A  pdb=" N   PHE A 555 " --> pdb=" O   ALA A 514 " (cutoff:3.500A)
      removed outlier: 6.543A  pdb=" N   ALA A 516 " --> pdb=" O   PHE A 555 " (cutoff:3.500A)
      removed outlier: 8.390A  pdb=" N   PHE A 557 " --> pdb=" O   ALA A 516 " (cutoff:3.500A)
      removed outlier: 6.565A  pdb=" N   VAL A 518 " --> pdb=" O   PHE A 557 " (cutoff:3.500A)
      removed outlier: 8.043A  pdb=" N   LEU A 559 " --> pdb=" O   VAL A 518 " (cutoff:3.500A)
      removed outlier: 6.675A  pdb=" N   LEU A 520 " --> pdb=" O   LEU A 559 " (cutoff:3.500A)
      removed outlier: 8.125A  pdb=" N   GLY A 561 " --> pdb=" O   LEU A 520 " (cutoff:3.500A)
      removed outlier: 6.865A  pdb=" N   GLY A 522 " --> pdb=" O   GLY A 561 " (cutoff:3.500A)
      removed outlier: 7.940A  pdb=" N   PHE A 555 " --> pdb=" O   GLU A 539 " (cutoff:3.500A)
      removed outlier: 11.310A  pdb=" N   GLU A 539 " --> pdb=" O   PHE A 555 " (cutoff:3.500A)
      removed outlier: 12.346A  pdb=" N   PHE A 557 " --> pdb=" O   LEU A 537 " (cutoff:3.500A)
      removed outlier: 12.371A  pdb=" N   LEU A 537 " --> pdb=" O   PHE A 557 " (cutoff:3.500A)
      removed outlier: 11.774A  pdb=" N   LEU A 559 " --> pdb=" O   VAL A 535 " (cutoff:3.500A)
      removed outlier: 12.866A  pdb=" N   VAL A 535 " --> pdb=" O   LEU A 559 " (cutoff:3.500A)
      removed outlier: 11.497A  pdb=" N   GLY A 561 " --> pdb=" O   ALA A 533 " (cutoff:3.500A)
      removed outlier: 12.490A  pdb=" N   ALA A 533 " --> pdb=" O   GLY A 561 " (cutoff:3.500A)
      removed outlier: 4.357A  pdb=" N   VAL A 385 " --> pdb=" O   PHE A 534 " (cutoff:3.500A)
      removed outlier: 7.421A  pdb=" N   ARG A 536 " --> pdb=" O   VAL A 385 " (cutoff:3.500A)
      removed outlier: 5.145A  pdb=" N   LEU A 387 " --> pdb=" O   ARG A 536 " (cutoff:3.500A)
      removed outlier: 7.155A  pdb=" N   ARG A 538 " --> pdb=" O   LEU A 387 " (cutoff:3.500A)
      removed outlier: 7.227A  pdb=" N   LEU A 389 " --> pdb=" O   ARG A 538 " (cutoff:3.500A)
      removed outlier: 7.637A  pdb=" N   ALA A 540 " --> pdb=" O   LEU A 389 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 350 through 352
      removed outlier: 6.367A  pdb=" N   TRP A 340 " --> pdb=" O   SER A 428 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 368 through 369
      removed outlier: 3.603A  pdb=" N   VAL B 610 " --> pdb=" O   LEU A 612 " (cutoff:3.500A)
      removed outlier: 3.631A  pdb=" N   VAL A 610 " --> pdb=" O   LEU B 612 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 1069 through 1071
      removed outlier: 6.973A  pdb=" N   VAL A1070 " --> pdb=" O   GLN A1084 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 350 through 352
      removed outlier: 6.926A  pdb=" N   LEU B 327 " --> pdb=" O   THR B 343 " (cutoff:3.500A)
      removed outlier: 4.750A  pdb=" N   ARG B 345 " --> pdb=" O   VAL B 325 " (cutoff:3.500A)
      removed outlier: 6.911A  pdb=" N   VAL B 325 " --> pdb=" O   ARG B 345 " (cutoff:3.500A)
      removed outlier: 5.276A  pdb=" N   CYS B 523 " --> pdb=" O   LEU B 330 " (cutoff:3.500A)
      removed outlier: 5.976A  pdb=" N   ALA B 516 " --> pdb=" O   VAL B 553 " (cutoff:3.500A)
      removed outlier: 3.653A  pdb=" N   PHE B 555 " --> pdb=" O   ALA B 516 " (cutoff:3.500A)
      removed outlier: 3.730A  pdb=" N   GLY B 561 " --> pdb=" O   GLY B 522 " (cutoff:3.500A)
      removed outlier: 6.713A  pdb=" N   ARG B 554 " --> pdb=" O   LEU B 537 " (cutoff:3.500A)
      removed outlier: 3.538A  pdb=" N   LEU B 556 " --> pdb=" O   VAL B 535 " (cutoff:3.500A)
      removed outlier: 5.229A  pdb=" N   ARG B 538 " --> pdb=" O   ASP B 388 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 350 through 352
      removed outlier: 6.476A  pdb=" N   TRP B 340 " --> pdb=" O   SER B 428 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 1069 through 1071
      removed outlier: 7.105A  pdb=" N   VAL B1070 " --> pdb=" O   GLN B1084 " (cutoff:3.500A)

    629 hydrogen bonds defined for protein.
    1842 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 3.39

  Time building geometry restraints manager: 3.19 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: 3861
        1.34 -     1.46: 1894
        1.46 -     1.57: 6586
        1.57 -     1.69: 1
        1.69 -     1.81: 102
  Bond restraints: 12444
  Sorted by residual:
  bond pdb=" CA  LEU B 591 "
       pdb=" C   LEU B 591 "
    ideal  model  delta    sigma   weight residual
    1.528  1.579 -0.051 1.04e-02 9.25e+03 2.36e+01
  bond pdb=" CA  ASN A 923 "
       pdb=" C   ASN A 923 "
    ideal  model  delta    sigma   weight residual
    1.522  1.561 -0.039 1.37e-02 5.33e+03 8.08e+00
  bond pdb=" C   GLN B 336 "
       pdb=" N   GLU B 337 "
    ideal  model  delta    sigma   weight residual
    1.330  1.367 -0.037 1.47e-02 4.63e+03 6.26e+00
  bond pdb=" CA  ARG B 930 "
       pdb=" C   ARG B 930 "
    ideal  model  delta    sigma   weight residual
    1.524  1.551 -0.026 1.28e-02 6.10e+03 4.25e+00
  bond pdb=" CA  LEU B 843 "
       pdb=" C   LEU B 843 "
    ideal  model  delta    sigma   weight residual
    1.523  1.550 -0.027 1.35e-02 5.49e+03 3.98e+00
  ... (remaining 12439 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.94: 16503
        1.94 -     3.89: 279
        3.89 -     5.83: 60
        5.83 -     7.78: 23
        7.78 -     9.72: 5
  Bond angle restraints: 16870
  Sorted by residual:
  angle pdb=" N   ILE B 931 "
        pdb=" CA  ILE B 931 "
        pdb=" C   ILE B 931 "
      ideal   model   delta    sigma   weight residual
     110.62  118.74   -8.12 1.02e+00 9.61e-01 6.34e+01
  angle pdb=" N   VAL B 844 "
        pdb=" CA  VAL B 844 "
        pdb=" C   VAL B 844 "
      ideal   model   delta    sigma   weight residual
     110.72  103.33    7.39 1.01e+00 9.80e-01 5.35e+01
  angle pdb=" N   LYS B 842 "
        pdb=" CA  LYS B 842 "
        pdb=" C   LYS B 842 "
      ideal   model   delta    sigma   weight residual
     111.07  118.61   -7.54 1.07e+00 8.73e-01 4.97e+01
  angle pdb=" N   PHE B1135 "
        pdb=" CA  PHE B1135 "
        pdb=" C   PHE B1135 "
      ideal   model   delta    sigma   weight residual
     114.62  106.69    7.93 1.14e+00 7.69e-01 4.83e+01
  angle pdb=" N   LEU B 806 "
        pdb=" CA  LEU B 806 "
        pdb=" C   LEU B 806 "
      ideal   model   delta    sigma   weight residual
     111.28  118.21   -6.93 1.09e+00 8.42e-01 4.05e+01
  ... (remaining 16865 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.97: 6499
       17.97 -    35.94: 755
       35.94 -    53.92: 173
       53.92 -    71.89: 21
       71.89 -    89.86: 18
  Dihedral angle restraints: 7466
    sinusoidal: 3024
      harmonic: 4442
  Sorted by residual:
  dihedral pdb=" CA  ARG B 624 "
           pdb=" C   ARG B 624 "
           pdb=" N   SER B 625 "
           pdb=" CA  SER B 625 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -159.29  -20.71     0      5.00e+00 4.00e-02 1.72e+01
  dihedral pdb=" CA  SER A 625 "
           pdb=" C   SER A 625 "
           pdb=" N   VAL A 626 "
           pdb=" CA  VAL A 626 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -160.19  -19.81     0      5.00e+00 4.00e-02 1.57e+01
  dihedral pdb=" CB  GLU A1212 "
           pdb=" CG  GLU A1212 "
           pdb=" CD  GLU A1212 "
           pdb=" OE1 GLU A1212 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   89.64  -89.64     1      3.00e+01 1.11e-03 1.06e+01
  ... (remaining 7463 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.061: 1691
       0.061 -    0.122: 256
       0.122 -    0.183: 21
       0.183 -    0.244: 6
       0.244 -    0.305: 4
  Chirality restraints: 1978
  Sorted by residual:
  chirality pdb=" CA  LYS B 842 "
            pdb=" N   LYS B 842 "
            pdb=" C   LYS B 842 "
            pdb=" CB  LYS B 842 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.21    0.31 2.00e-01 2.50e+01 2.33e+00
  chirality pdb=" CA  TYR B 590 "
            pdb=" N   TYR B 590 "
            pdb=" C   TYR B 590 "
            pdb=" CB  TYR B 590 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.23    0.28 2.00e-01 2.50e+01 1.97e+00
  chirality pdb=" CA  LEU B 591 "
            pdb=" N   LEU B 591 "
            pdb=" C   LEU B 591 "
            pdb=" CB  LEU B 591 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.78   -0.27 2.00e-01 2.50e+01 1.86e+00
  ... (remaining 1975 not shown)

  Planarity restraints: 2110
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU A 394 "    0.055 5.00e-02 4.00e+02   8.20e-02 1.08e+01
        pdb=" N   PRO A 395 "   -0.142 5.00e-02 4.00e+02
        pdb=" CA  PRO A 395 "    0.041 5.00e-02 4.00e+02
        pdb=" CD  PRO A 395 "    0.046 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU B 394 "   -0.054 5.00e-02 4.00e+02   8.13e-02 1.06e+01
        pdb=" N   PRO B 395 "    0.141 5.00e-02 4.00e+02
        pdb=" CA  PRO B 395 "   -0.042 5.00e-02 4.00e+02
        pdb=" CD  PRO B 395 "   -0.045 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE A 510 "    0.048 5.00e-02 4.00e+02   7.21e-02 8.31e+00
        pdb=" N   PRO A 511 "   -0.125 5.00e-02 4.00e+02
        pdb=" CA  PRO A 511 "    0.038 5.00e-02 4.00e+02
        pdb=" CD  PRO A 511 "    0.039 5.00e-02 4.00e+02
  ... (remaining 2107 not shown)

  Histogram of nonbonded interaction distances:
        2.03 -     2.60: 60
        2.60 -     3.18: 9792
        3.18 -     3.75: 17282
        3.75 -     4.33: 23625
        4.33 -     4.90: 41144
  Nonbonded interactions: 91903
  Sorted by model distance:
  nonbonded pdb=" O   ASN B 785 "
            pdb=" OD1 ASN B 785 "
     model   vdw
     2.028 3.040
  nonbonded pdb=" O   LEU A 730 "
            pdb=" OG1 THR A 734 "
     model   vdw
     2.085 3.040
  nonbonded pdb=" O   LEU B 591 "
            pdb=" CD1 LEU B 591 "
     model   vdw
     2.141 3.460
  nonbonded pdb=" O   ALA B1076 "
            pdb=" OD1 ASP B1079 "
     model   vdw
     2.161 3.040
  nonbonded pdb=" OE2 GLU A 350 "
            pdb=" OD1 ASP A 352 "
     model   vdw
     2.189 3.040
  ... (remaining 91898 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: 0.06
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}

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:             1.030
  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:          0.540
  Check model and map are aligned:         0.100
  Set scattering table:                    0.130
  Process input model:                     28.140
  Find NCS groups from input model:        0.400
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:2.630
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   33.030
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7894
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.072  12444  Z= 0.168
  Angle     :  0.686   9.725  16870  Z= 0.431
  Chirality :  0.046   0.305   1978
  Planarity :  0.005   0.082   2110
  Dihedral  : 16.238  89.859   4574
  Min Nonbonded Distance : 2.028

Molprobity Statistics.
  All-atom Clashscore : 6.06
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  :  5.01 %
    Favored  : 94.79 %
  Rotamer:
    Outliers :  0.23 %
    Allowed  : 15.04 %
    Favored  : 84.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.09 (0.22), residues: 1516
  helix:  0.72 (0.18), residues: 842
  sheet:  0.48 (0.44), residues: 114
  loop : -1.33 (0.26), residues: 560

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 340 
 HIS   0.006   0.001   HIS B 586 
 PHE   0.019   0.001   PHE A1189 
 TYR   0.007   0.001   TYR B1154 
 ARG   0.003   0.000   ARG A 624 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.18140 (  625)
  hydrogen bonds       : angle       5.26480 ( 1842)
  covalent geometry    : bond        0.00360 (12444)
  covalent geometry    : angle       0.68585 (16870)

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

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

  3032 Ramachandran restraints generated.
    1516 Oldfield, 0 Emsley, 1516 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3032 Ramachandran restraints generated.
    1516 Oldfield, 0 Emsley, 1516 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  178 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 175
  time to evaluate  : 1.344 
Fit side-chains
REVERT: B 1196 THR cc_start: 0.7948 (t) cc_final: 0.7719 (p)
  outliers start: 3
  outliers final: 2
  residues processed: 176
  average time/residue: 0.2597
  time to fit residues: 64.4320
Evaluate side-chains
  168 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 166
  time to evaluate  : 1.402 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 1109 LEU
Chi-restraints excluded: chain B residue  323 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 128 optimal weight:    5.9990
   chunk 115 optimal weight:    0.9980
   chunk 63 optimal weight:    0.3980
   chunk 39 optimal weight:    0.5980
   chunk 77 optimal weight:    0.8980
   chunk 61 optimal weight:    0.3980
   chunk 119 optimal weight:    2.9990
   chunk 46 optimal weight:    3.9990
   chunk 72 optimal weight:    2.9990
   chunk 88 optimal weight:    0.9980
   chunk 138 optimal weight:    9.9990
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
A 382 HIS
A 853 HIS
B 750 GLN
B 853 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3913 r_free = 0.3913 target = 0.172015 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3497 r_free = 0.3497 target = 0.132162 restraints weight = 12939.148|
|-----------------------------------------------------------------------------|
r_work (start): 0.3412 rms_B_bonded: 2.36
r_work: 0.3238 rms_B_bonded: 3.15 restraints_weight: 0.5000
r_work (final): 0.3238
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7739
moved from start:          0.0743

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  12444  Z= 0.126
  Angle     :  0.532   9.647  16870  Z= 0.277
  Chirality :  0.040   0.150   1978
  Planarity :  0.005   0.060   2110
  Dihedral  :  4.107  30.285   1645
  Min Nonbonded Distance : 2.505

Molprobity Statistics.
  All-atom Clashscore : 4.12
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  :  4.62 %
    Favored  : 95.18 %
  Rotamer:
    Outliers :  1.88 %
    Allowed  : 16.17 %
    Favored  : 81.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.25 (0.22), residues: 1516
  helix:  1.07 (0.18), residues: 864
  sheet:  0.67 (0.47), residues: 110
  loop : -1.42 (0.25), residues: 542

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 346 
 HIS   0.008   0.001   HIS B 586 
 PHE   0.018   0.001   PHE A 822 
 TYR   0.006   0.001   TYR A 569 
 ARG   0.002   0.000   ARG A 624 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05949 (  625)
  hydrogen bonds       : angle       4.08729 ( 1842)
  covalent geometry    : bond        0.00273 (12444)
  covalent geometry    : angle       0.53185 (16870)

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

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

  3032 Ramachandran restraints generated.
    1516 Oldfield, 0 Emsley, 1516 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3032 Ramachandran restraints generated.
    1516 Oldfield, 0 Emsley, 1516 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  205 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 180
  time to evaluate  : 1.453 
Fit side-chains
REVERT: A  697 LEU cc_start: 0.8620 (mm) cc_final: 0.8346 (mm)
REVERT: A 1156 LYS cc_start: 0.8270 (mtpt) cc_final: 0.7758 (mmtt)
REVERT: B  321 HIS cc_start: 0.6428 (OUTLIER) cc_final: 0.6216 (m-70)
REVERT: B  590 TYR cc_start: 0.7510 (OUTLIER) cc_final: 0.5953 (t80)
REVERT: B  701 ARG cc_start: 0.7958 (ttm170) cc_final: 0.7699 (ttm-80)
REVERT: B  925 ARG cc_start: 0.8048 (mtm180) cc_final: 0.7491 (ptp-170)
REVERT: B 1156 LYS cc_start: 0.8101 (mtpt) cc_final: 0.7576 (mptt)
  outliers start: 25
  outliers final: 15
  residues processed: 193
  average time/residue: 0.2504
  time to fit residues: 68.8460
Evaluate side-chains
  183 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 166
  time to evaluate  : 1.270 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  518 VAL
Chi-restraints excluded: chain A residue  532 MET
Chi-restraints excluded: chain A residue  556 LEU
Chi-restraints excluded: chain A residue  591 LEU
Chi-restraints excluded: chain A residue  623 LEU
Chi-restraints excluded: chain A residue  745 MET
Chi-restraints excluded: chain A residue  762 LEU
Chi-restraints excluded: chain A residue  999 LEU
Chi-restraints excluded: chain A residue 1046 CYS
Chi-restraints excluded: chain A residue 1142 LEU
Chi-restraints excluded: chain A residue 1205 THR
Chi-restraints excluded: chain B residue  321 HIS
Chi-restraints excluded: chain B residue  590 TYR
Chi-restraints excluded: chain B residue  623 LEU
Chi-restraints excluded: chain B residue  964 VAL
Chi-restraints excluded: chain B residue 1108 ASP
Chi-restraints excluded: chain B residue 1205 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 42 optimal weight:    0.9980
   chunk 110 optimal weight:    2.9990
   chunk 151 optimal weight:    4.9990
   chunk 69 optimal weight:    0.9990
   chunk 94 optimal weight:    2.9990
   chunk 125 optimal weight:    0.9990
   chunk 111 optimal weight:    2.9990
   chunk 32 optimal weight:    4.9990
   chunk 126 optimal weight:    0.9990
   chunk 91 optimal weight:    4.9990
   chunk 11 optimal weight:    7.9990
   overall best weight:    1.3988

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

Flipped N/Q/H residues before XYZ refinement:
A 853 HIS
B 853 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3895 r_free = 0.3895 target = 0.170050 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3487 r_free = 0.3487 target = 0.131412 restraints weight = 13126.775|
|-----------------------------------------------------------------------------|
r_work (start): 0.3383 rms_B_bonded: 2.44
r_work: 0.3195 rms_B_bonded: 3.12 restraints_weight: 0.5000
r_work: 0.3032 rms_B_bonded: 4.97 restraints_weight: 0.2500
r_work (final): 0.3032
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7898
moved from start:          0.0933

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040  12444  Z= 0.165
  Angle     :  0.556   6.275  16870  Z= 0.288
  Chirality :  0.042   0.159   1978
  Planarity :  0.005   0.055   2110
  Dihedral  :  4.074  21.135   1642
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 3.96
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  4.95 %
    Favored  : 94.92 %
  Rotamer:
    Outliers :  3.23 %
    Allowed  : 16.47 %
    Favored  : 80.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.14 (0.22), residues: 1516
  helix:  0.96 (0.18), residues: 876
  sheet:  0.78 (0.47), residues: 110
  loop : -1.51 (0.26), residues: 530

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 340 
 HIS   0.008   0.001   HIS B 586 
 PHE   0.022   0.002   PHE A1189 
 TYR   0.010   0.001   TYR A 789 
 ARG   0.004   0.000   ARG A 624 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06553 (  625)
  hydrogen bonds       : angle       4.03925 ( 1842)
  covalent geometry    : bond        0.00402 (12444)
  covalent geometry    : angle       0.55590 (16870)

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

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

  3032 Ramachandran restraints generated.
    1516 Oldfield, 0 Emsley, 1516 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3032 Ramachandran restraints generated.
    1516 Oldfield, 0 Emsley, 1516 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  222 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 179
  time to evaluate  : 1.510 
Fit side-chains
REVERT: A  697 LEU cc_start: 0.8718 (mm) cc_final: 0.8513 (mm)
REVERT: A 1156 LYS cc_start: 0.8322 (mtpt) cc_final: 0.7763 (mptt)
REVERT: B  321 HIS cc_start: 0.6599 (OUTLIER) cc_final: 0.6221 (m-70)
REVERT: B  701 ARG cc_start: 0.7947 (ttm170) cc_final: 0.7627 (ttm-80)
REVERT: B  981 ASN cc_start: 0.8725 (p0) cc_final: 0.8373 (p0)
REVERT: B 1156 LYS cc_start: 0.8170 (mtpt) cc_final: 0.7550 (mptt)
  outliers start: 43
  outliers final: 31
  residues processed: 205
  average time/residue: 0.2529
  time to fit residues: 74.2963
Evaluate side-chains
  208 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 176
  time to evaluate  : 1.545 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  325 VAL
Chi-restraints excluded: chain A residue  368 LEU
Chi-restraints excluded: chain A residue  518 VAL
Chi-restraints excluded: chain A residue  535 VAL
Chi-restraints excluded: chain A residue  556 LEU
Chi-restraints excluded: chain A residue  623 LEU
Chi-restraints excluded: chain A residue  701 ARG
Chi-restraints excluded: chain A residue  740 VAL
Chi-restraints excluded: chain A residue  743 LEU
Chi-restraints excluded: chain A residue  745 MET
Chi-restraints excluded: chain A residue  999 LEU
Chi-restraints excluded: chain A residue 1046 CYS
Chi-restraints excluded: chain A residue 1058 THR
Chi-restraints excluded: chain A residue 1105 VAL
Chi-restraints excluded: chain A residue 1109 LEU
Chi-restraints excluded: chain A residue 1142 LEU
Chi-restraints excluded: chain A residue 1205 THR
Chi-restraints excluded: chain B residue  321 HIS
Chi-restraints excluded: chain B residue  323 VAL
Chi-restraints excluded: chain B residue  518 VAL
Chi-restraints excluded: chain B residue  532 MET
Chi-restraints excluded: chain B residue  623 LEU
Chi-restraints excluded: chain B residue  697 LEU
Chi-restraints excluded: chain B residue  918 LEU
Chi-restraints excluded: chain B residue  964 VAL
Chi-restraints excluded: chain B residue 1070 VAL
Chi-restraints excluded: chain B residue 1108 ASP
Chi-restraints excluded: chain B residue 1109 LEU
Chi-restraints excluded: chain B residue 1137 GLU
Chi-restraints excluded: chain B residue 1196 THR
Chi-restraints excluded: chain B residue 1205 THR
Chi-restraints excluded: chain B residue 1215 CYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 71 optimal weight:    2.9990
   chunk 13 optimal weight:    0.8980
   chunk 131 optimal weight:    1.9990
   chunk 39 optimal weight:    4.9990
   chunk 119 optimal weight:    2.9990
   chunk 62 optimal weight:    0.8980
   chunk 83 optimal weight:    0.0980
   chunk 121 optimal weight:    0.6980
   chunk 33 optimal weight:    2.9990
   chunk 91 optimal weight:    0.3980
   chunk 94 optimal weight:    2.9990
   overall best weight:    0.5980

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

Flipped N/Q/H residues before XYZ refinement:
A 853 HIS
B 853 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3930 r_free = 0.3930 target = 0.173546 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3526 r_free = 0.3526 target = 0.134532 restraints weight = 12962.469|
|-----------------------------------------------------------------------------|
r_work (start): 0.3427 rms_B_bonded: 2.30
r_work: 0.3260 rms_B_bonded: 2.98 restraints_weight: 0.5000
r_work: 0.3099 rms_B_bonded: 4.79 restraints_weight: 0.2500
r_work (final): 0.3099
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7804
moved from start:          0.1103

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033  12444  Z= 0.109
  Angle     :  0.482   6.153  16870  Z= 0.251
  Chirality :  0.039   0.141   1978
  Planarity :  0.004   0.053   2110
  Dihedral  :  3.885  19.029   1642
  Min Nonbonded Distance : 2.558

Molprobity Statistics.
  All-atom Clashscore : 4.00
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  4.42 %
    Favored  : 95.45 %
  Rotamer:
    Outliers :  3.01 %
    Allowed  : 17.07 %
    Favored  : 79.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.48 (0.22), residues: 1516
  helix:  1.29 (0.18), residues: 876
  sheet:  0.90 (0.48), residues: 110
  loop : -1.48 (0.26), residues: 530

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 346 
 HIS   0.008   0.001   HIS A 586 
 PHE   0.018   0.001   PHE A1189 
 TYR   0.007   0.001   TYR A 569 
 ARG   0.002   0.000   ARG A 624 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05019 (  625)
  hydrogen bonds       : angle       3.81664 ( 1842)
  covalent geometry    : bond        0.00239 (12444)
  covalent geometry    : angle       0.48195 (16870)

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

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

  3032 Ramachandran restraints generated.
    1516 Oldfield, 0 Emsley, 1516 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3032 Ramachandran restraints generated.
    1516 Oldfield, 0 Emsley, 1516 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  219 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 179
  time to evaluate  : 1.450 
Fit side-chains
REVERT: A  702 ASP cc_start: 0.7998 (m-30) cc_final: 0.7782 (m-30)
REVERT: A 1085 GLU cc_start: 0.8045 (pt0) cc_final: 0.7772 (pt0)
REVERT: A 1156 LYS cc_start: 0.8224 (mtpt) cc_final: 0.7631 (mptt)
REVERT: A 1172 LEU cc_start: 0.8421 (tp) cc_final: 0.8189 (tp)
REVERT: B  586 HIS cc_start: 0.7258 (OUTLIER) cc_final: 0.6922 (p90)
REVERT: B  590 TYR cc_start: 0.7494 (OUTLIER) cc_final: 0.6038 (t80)
REVERT: B  701 ARG cc_start: 0.7934 (ttm170) cc_final: 0.7628 (ttm-80)
REVERT: B  918 LEU cc_start: 0.8134 (OUTLIER) cc_final: 0.7891 (mt)
REVERT: B  981 ASN cc_start: 0.8542 (p0) cc_final: 0.8197 (p0)
REVERT: B 1156 LYS cc_start: 0.8082 (mtpt) cc_final: 0.7503 (mptt)
  outliers start: 40
  outliers final: 24
  residues processed: 203
  average time/residue: 0.2489
  time to fit residues: 72.4297
Evaluate side-chains
  192 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 165
  time to evaluate  : 1.292 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  325 VAL
Chi-restraints excluded: chain A residue  532 MET
Chi-restraints excluded: chain A residue  535 VAL
Chi-restraints excluded: chain A residue  556 LEU
Chi-restraints excluded: chain A residue  586 HIS
Chi-restraints excluded: chain A residue  591 LEU
Chi-restraints excluded: chain A residue  623 LEU
Chi-restraints excluded: chain A residue  721 SER
Chi-restraints excluded: chain A residue  762 LEU
Chi-restraints excluded: chain A residue  918 LEU
Chi-restraints excluded: chain A residue  999 LEU
Chi-restraints excluded: chain A residue 1046 CYS
Chi-restraints excluded: chain A residue 1094 LEU
Chi-restraints excluded: chain A residue 1109 LEU
Chi-restraints excluded: chain A residue 1142 LEU
Chi-restraints excluded: chain B residue  325 VAL
Chi-restraints excluded: chain B residue  518 VAL
Chi-restraints excluded: chain B residue  586 HIS
Chi-restraints excluded: chain B residue  590 TYR
Chi-restraints excluded: chain B residue  591 LEU
Chi-restraints excluded: chain B residue  697 LEU
Chi-restraints excluded: chain B residue  918 LEU
Chi-restraints excluded: chain B residue  964 VAL
Chi-restraints excluded: chain B residue  970 VAL
Chi-restraints excluded: chain B residue 1108 ASP
Chi-restraints excluded: chain B residue 1109 LEU
Chi-restraints excluded: chain B residue 1196 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 48 optimal weight:    4.9990
   chunk 45 optimal weight:    3.9990
   chunk 113 optimal weight:    3.9990
   chunk 39 optimal weight:    4.9990
   chunk 147 optimal weight:    3.9990
   chunk 86 optimal weight:    5.9990
   chunk 141 optimal weight:    5.9990
   chunk 121 optimal weight:    1.9990
   chunk 8 optimal weight:    1.9990
   chunk 2 optimal weight:    0.7980
   chunk 77 optimal weight:    2.9990
   overall best weight:    2.3588

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

Flipped N/Q/H residues before XYZ refinement:
A 853 HIS
B 853 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3834 r_free = 0.3834 target = 0.165193 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3386 r_free = 0.3386 target = 0.123598 restraints weight = 13059.068|
|-----------------------------------------------------------------------------|
r_work (start): 0.3288 rms_B_bonded: 2.43
r_work: 0.3115 rms_B_bonded: 3.17 restraints_weight: 0.5000
r_work (final): 0.3115
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7832
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      :  0.006   0.048  12444  Z= 0.241
  Angle     :  0.626   6.557  16870  Z= 0.322
  Chirality :  0.045   0.168   1978
  Planarity :  0.005   0.053   2110
  Dihedral  :  4.248  24.455   1642
  Min Nonbonded Distance : 2.547

Molprobity Statistics.
  All-atom Clashscore : 4.00
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  5.67 %
    Favored  : 94.20 %
  Rotamer:
    Outliers :  4.44 %
    Allowed  : 15.86 %
    Favored  : 79.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.05 (0.21), residues: 1516
  helix:  0.77 (0.18), residues: 876
  sheet:  0.81 (0.47), residues: 110
  loop : -1.56 (0.25), residues: 530

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP B 340 
 HIS   0.010   0.002   HIS A1064 
 PHE   0.022   0.002   PHE A1189 
 TYR   0.014   0.002   TYR A 789 
 ARG   0.005   0.000   ARG A 624 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.07526 (  625)
  hydrogen bonds       : angle       4.09431 ( 1842)
  covalent geometry    : bond        0.00605 (12444)
  covalent geometry    : angle       0.62582 (16870)

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

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

  3032 Ramachandran restraints generated.
    1516 Oldfield, 0 Emsley, 1516 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3032 Ramachandran restraints generated.
    1516 Oldfield, 0 Emsley, 1516 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  236 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 59
    poor density    : 177
  time to evaluate  : 1.295 
Fit side-chains
REVERT: A 1156 LYS cc_start: 0.8365 (mtpt) cc_final: 0.7812 (mptt)
REVERT: B  558 LEU cc_start: 0.8199 (OUTLIER) cc_final: 0.7780 (tp)
REVERT: B  586 HIS cc_start: 0.7367 (OUTLIER) cc_final: 0.6951 (p90)
REVERT: B  981 ASN cc_start: 0.8584 (p0) cc_final: 0.8309 (p0)
REVERT: B 1141 LEU cc_start: 0.8369 (OUTLIER) cc_final: 0.7813 (mp)
REVERT: B 1156 LYS cc_start: 0.8215 (mtpt) cc_final: 0.7635 (mptt)
  outliers start: 59
  outliers final: 45
  residues processed: 222
  average time/residue: 0.2348
  time to fit residues: 74.9114
Evaluate side-chains
  221 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 173
  time to evaluate  : 1.288 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  321 HIS
Chi-restraints excluded: chain A residue  325 VAL
Chi-restraints excluded: chain A residue  374 LEU
Chi-restraints excluded: chain A residue  535 VAL
Chi-restraints excluded: chain A residue  556 LEU
Chi-restraints excluded: chain A residue  586 HIS
Chi-restraints excluded: chain A residue  623 LEU
Chi-restraints excluded: chain A residue  721 SER
Chi-restraints excluded: chain A residue  729 LEU
Chi-restraints excluded: chain A residue  740 VAL
Chi-restraints excluded: chain A residue  743 LEU
Chi-restraints excluded: chain A residue  999 LEU
Chi-restraints excluded: chain A residue 1046 CYS
Chi-restraints excluded: chain A residue 1058 THR
Chi-restraints excluded: chain A residue 1094 LEU
Chi-restraints excluded: chain A residue 1105 VAL
Chi-restraints excluded: chain A residue 1109 LEU
Chi-restraints excluded: chain A residue 1142 LEU
Chi-restraints excluded: chain A residue 1158 VAL
Chi-restraints excluded: chain A residue 1205 THR
Chi-restraints excluded: chain B residue  323 VAL
Chi-restraints excluded: chain B residue  325 VAL
Chi-restraints excluded: chain B residue  332 LEU
Chi-restraints excluded: chain B residue  374 LEU
Chi-restraints excluded: chain B residue  387 LEU
Chi-restraints excluded: chain B residue  518 VAL
Chi-restraints excluded: chain B residue  558 LEU
Chi-restraints excluded: chain B residue  586 HIS
Chi-restraints excluded: chain B residue  591 LEU
Chi-restraints excluded: chain B residue  610 VAL
Chi-restraints excluded: chain B residue  623 LEU
Chi-restraints excluded: chain B residue  697 LEU
Chi-restraints excluded: chain B residue  709 LEU
Chi-restraints excluded: chain B residue  721 SER
Chi-restraints excluded: chain B residue  918 LEU
Chi-restraints excluded: chain B residue  964 VAL
Chi-restraints excluded: chain B residue  970 VAL
Chi-restraints excluded: chain B residue 1058 THR
Chi-restraints excluded: chain B residue 1070 VAL
Chi-restraints excluded: chain B residue 1105 VAL
Chi-restraints excluded: chain B residue 1109 LEU
Chi-restraints excluded: chain B residue 1137 GLU
Chi-restraints excluded: chain B residue 1141 LEU
Chi-restraints excluded: chain B residue 1152 VAL
Chi-restraints excluded: chain B residue 1194 ILE
Chi-restraints excluded: chain B residue 1196 THR
Chi-restraints excluded: chain B residue 1205 THR
Chi-restraints excluded: chain B residue 1215 CYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 81 optimal weight:    2.9990
   chunk 10 optimal weight:    7.9990
   chunk 34 optimal weight:    2.9990
   chunk 51 optimal weight:    0.0170
   chunk 78 optimal weight:    0.9990
   chunk 151 optimal weight:    3.9990
   chunk 38 optimal weight:    0.7980
   chunk 66 optimal weight:    0.8980
   chunk 131 optimal weight:    0.5980
   chunk 74 optimal weight:    1.9990
   chunk 105 optimal weight:    4.9990
   overall best weight:    0.6620

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

Flipped N/Q/H residues before XYZ refinement:
A 853 HIS
** B 586 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 853 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3892 r_free = 0.3892 target = 0.170553 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3454 r_free = 0.3454 target = 0.129710 restraints weight = 13101.118|
|-----------------------------------------------------------------------------|
r_work (start): 0.3330 rms_B_bonded: 2.30
r_work: 0.3169 rms_B_bonded: 3.21 restraints_weight: 0.5000
r_work (final): 0.3169
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7735
moved from start:          0.1244

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  12444  Z= 0.118
  Angle     :  0.495   6.098  16870  Z= 0.258
  Chirality :  0.040   0.143   1978
  Planarity :  0.004   0.052   2110
  Dihedral  :  3.991  20.869   1642
  Min Nonbonded Distance : 2.559

Molprobity Statistics.
  All-atom Clashscore : 4.08
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  4.49 %
    Favored  : 95.38 %
  Rotamer:
    Outliers :  3.16 %
    Allowed  : 18.12 %
    Favored  : 78.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.38 (0.22), residues: 1516
  helix:  1.19 (0.18), residues: 874
  sheet:  0.89 (0.48), residues: 110
  loop : -1.48 (0.26), residues: 532

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 340 
 HIS   0.008   0.001   HIS A 586 
 PHE   0.018   0.001   PHE A1189 
 TYR   0.007   0.001   TYR A 569 
 ARG   0.002   0.000   ARG A 624 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05336 (  625)
  hydrogen bonds       : angle       3.83605 ( 1842)
  covalent geometry    : bond        0.00260 (12444)
  covalent geometry    : angle       0.49542 (16870)

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

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

  3032 Ramachandran restraints generated.
    1516 Oldfield, 0 Emsley, 1516 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3032 Ramachandran restraints generated.
    1516 Oldfield, 0 Emsley, 1516 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  213 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 171
  time to evaluate  : 1.405 
Fit side-chains
REVERT: A 1085 GLU cc_start: 0.8095 (pt0) cc_final: 0.7835 (pt0)
REVERT: A 1156 LYS cc_start: 0.8217 (mtpt) cc_final: 0.7656 (mptt)
REVERT: A 1172 LEU cc_start: 0.8206 (tp) cc_final: 0.7971 (tp)
REVERT: B  586 HIS cc_start: 0.7302 (OUTLIER) cc_final: 0.6936 (p90)
REVERT: B  590 TYR cc_start: 0.7561 (OUTLIER) cc_final: 0.6116 (t80)
REVERT: B  701 ARG cc_start: 0.8032 (ttm170) cc_final: 0.7800 (ttm-80)
REVERT: B  981 ASN cc_start: 0.8515 (p0) cc_final: 0.8150 (p0)
REVERT: B 1141 LEU cc_start: 0.8323 (OUTLIER) cc_final: 0.7805 (mp)
REVERT: B 1156 LYS cc_start: 0.8116 (mtpt) cc_final: 0.7570 (mptt)
  outliers start: 42
  outliers final: 38
  residues processed: 199
  average time/residue: 0.2490
  time to fit residues: 71.0318
Evaluate side-chains
  209 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 168
  time to evaluate  : 1.271 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  321 HIS
Chi-restraints excluded: chain A residue  325 VAL
Chi-restraints excluded: chain A residue  374 LEU
Chi-restraints excluded: chain A residue  532 MET
Chi-restraints excluded: chain A residue  535 VAL
Chi-restraints excluded: chain A residue  556 LEU
Chi-restraints excluded: chain A residue  586 HIS
Chi-restraints excluded: chain A residue  591 LEU
Chi-restraints excluded: chain A residue  623 LEU
Chi-restraints excluded: chain A residue  721 SER
Chi-restraints excluded: chain A residue  743 LEU
Chi-restraints excluded: chain A residue  999 LEU
Chi-restraints excluded: chain A residue 1046 CYS
Chi-restraints excluded: chain A residue 1058 THR
Chi-restraints excluded: chain A residue 1094 LEU
Chi-restraints excluded: chain A residue 1109 LEU
Chi-restraints excluded: chain A residue 1142 LEU
Chi-restraints excluded: chain A residue 1158 VAL
Chi-restraints excluded: chain B residue  323 VAL
Chi-restraints excluded: chain B residue  325 VAL
Chi-restraints excluded: chain B residue  332 LEU
Chi-restraints excluded: chain B residue  518 VAL
Chi-restraints excluded: chain B residue  586 HIS
Chi-restraints excluded: chain B residue  590 TYR
Chi-restraints excluded: chain B residue  591 LEU
Chi-restraints excluded: chain B residue  608 CYS
Chi-restraints excluded: chain B residue  610 VAL
Chi-restraints excluded: chain B residue  697 LEU
Chi-restraints excluded: chain B residue  709 LEU
Chi-restraints excluded: chain B residue  918 LEU
Chi-restraints excluded: chain B residue  964 VAL
Chi-restraints excluded: chain B residue  970 VAL
Chi-restraints excluded: chain B residue 1058 THR
Chi-restraints excluded: chain B residue 1070 VAL
Chi-restraints excluded: chain B residue 1094 LEU
Chi-restraints excluded: chain B residue 1108 ASP
Chi-restraints excluded: chain B residue 1109 LEU
Chi-restraints excluded: chain B residue 1137 GLU
Chi-restraints excluded: chain B residue 1141 LEU
Chi-restraints excluded: chain B residue 1196 THR
Chi-restraints excluded: chain B residue 1215 CYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 32 optimal weight:    5.9990
   chunk 148 optimal weight:    1.9990
   chunk 118 optimal weight:    0.6980
   chunk 129 optimal weight:    4.9990
   chunk 73 optimal weight:    3.9990
   chunk 145 optimal weight:    0.0010
   chunk 51 optimal weight:    2.9990
   chunk 122 optimal weight:    1.9990
   chunk 131 optimal weight:    0.9980
   chunk 6 optimal weight:    9.9990
   chunk 150 optimal weight:    0.9990
   overall best weight:    0.9390

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

Flipped N/Q/H residues before XYZ refinement:
A 853 HIS
B 391 GLN
B 785 ASN
B 853 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3884 r_free = 0.3884 target = 0.169755 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3444 r_free = 0.3444 target = 0.128883 restraints weight = 13120.471|
|-----------------------------------------------------------------------------|
r_work (start): 0.3342 rms_B_bonded: 2.30
r_work: 0.3183 rms_B_bonded: 3.19 restraints_weight: 0.5000
r_work (final): 0.3183
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7748
moved from start:          0.1296

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  12444  Z= 0.130
  Angle     :  0.508   6.128  16870  Z= 0.262
  Chirality :  0.041   0.255   1978
  Planarity :  0.004   0.052   2110
  Dihedral  :  3.934  21.103   1642
  Min Nonbonded Distance : 2.557

Molprobity Statistics.
  All-atom Clashscore : 4.00
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  5.01 %
    Favored  : 94.85 %
  Rotamer:
    Outliers :  3.91 %
    Allowed  : 17.74 %
    Favored  : 78.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.42 (0.22), residues: 1516
  helix:  1.21 (0.18), residues: 874
  sheet:  0.90 (0.48), residues: 110
  loop : -1.44 (0.25), residues: 532

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 346 
 HIS   0.007   0.001   HIS A 586 
 PHE   0.019   0.001   PHE A1189 
 TYR   0.007   0.001   TYR B1154 
 ARG   0.004   0.000   ARG A 701 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05550 (  625)
  hydrogen bonds       : angle       3.80883 ( 1842)
  covalent geometry    : bond        0.00302 (12444)
  covalent geometry    : angle       0.50784 (16870)

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

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

  3032 Ramachandran restraints generated.
    1516 Oldfield, 0 Emsley, 1516 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3032 Ramachandran restraints generated.
    1516 Oldfield, 0 Emsley, 1516 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  225 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 52
    poor density    : 173
  time to evaluate  : 1.458 
Fit side-chains
REVERT: A 1085 GLU cc_start: 0.8118 (pt0) cc_final: 0.7875 (pt0)
REVERT: A 1156 LYS cc_start: 0.8213 (mtpt) cc_final: 0.7660 (mptt)
REVERT: B  558 LEU cc_start: 0.8137 (OUTLIER) cc_final: 0.7882 (tp)
REVERT: B  586 HIS cc_start: 0.7311 (OUTLIER) cc_final: 0.6947 (p90)
REVERT: B  701 ARG cc_start: 0.8021 (ttm170) cc_final: 0.7791 (ttm-80)
REVERT: B  981 ASN cc_start: 0.8505 (p0) cc_final: 0.8173 (p0)
REVERT: B 1141 LEU cc_start: 0.8313 (OUTLIER) cc_final: 0.7809 (mp)
REVERT: B 1156 LYS cc_start: 0.8144 (mtpt) cc_final: 0.7588 (mptt)
  outliers start: 52
  outliers final: 42
  residues processed: 211
  average time/residue: 0.2516
  time to fit residues: 76.4604
Evaluate side-chains
  214 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 169
  time to evaluate  : 1.289 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  321 HIS
Chi-restraints excluded: chain A residue  325 VAL
Chi-restraints excluded: chain A residue  374 LEU
Chi-restraints excluded: chain A residue  532 MET
Chi-restraints excluded: chain A residue  535 VAL
Chi-restraints excluded: chain A residue  556 LEU
Chi-restraints excluded: chain A residue  586 HIS
Chi-restraints excluded: chain A residue  623 LEU
Chi-restraints excluded: chain A residue  721 SER
Chi-restraints excluded: chain A residue  729 LEU
Chi-restraints excluded: chain A residue  740 VAL
Chi-restraints excluded: chain A residue  743 LEU
Chi-restraints excluded: chain A residue  745 MET
Chi-restraints excluded: chain A residue  999 LEU
Chi-restraints excluded: chain A residue 1046 CYS
Chi-restraints excluded: chain A residue 1058 THR
Chi-restraints excluded: chain A residue 1094 LEU
Chi-restraints excluded: chain A residue 1109 LEU
Chi-restraints excluded: chain A residue 1142 LEU
Chi-restraints excluded: chain A residue 1158 VAL
Chi-restraints excluded: chain B residue  323 VAL
Chi-restraints excluded: chain B residue  325 VAL
Chi-restraints excluded: chain B residue  332 LEU
Chi-restraints excluded: chain B residue  518 VAL
Chi-restraints excluded: chain B residue  558 LEU
Chi-restraints excluded: chain B residue  586 HIS
Chi-restraints excluded: chain B residue  591 LEU
Chi-restraints excluded: chain B residue  610 VAL
Chi-restraints excluded: chain B residue  623 LEU
Chi-restraints excluded: chain B residue  697 LEU
Chi-restraints excluded: chain B residue  709 LEU
Chi-restraints excluded: chain B residue  721 SER
Chi-restraints excluded: chain B residue  785 ASN
Chi-restraints excluded: chain B residue  918 LEU
Chi-restraints excluded: chain B residue  964 VAL
Chi-restraints excluded: chain B residue  970 VAL
Chi-restraints excluded: chain B residue 1058 THR
Chi-restraints excluded: chain B residue 1070 VAL
Chi-restraints excluded: chain B residue 1094 LEU
Chi-restraints excluded: chain B residue 1105 VAL
Chi-restraints excluded: chain B residue 1109 LEU
Chi-restraints excluded: chain B residue 1137 GLU
Chi-restraints excluded: chain B residue 1141 LEU
Chi-restraints excluded: chain B residue 1196 THR
Chi-restraints excluded: chain B residue 1215 CYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 122 optimal weight:    1.9990
   chunk 80 optimal weight:    2.9990
   chunk 109 optimal weight:    3.9990
   chunk 9 optimal weight:    7.9990
   chunk 118 optimal weight:    3.9990
   chunk 85 optimal weight:   10.0000
   chunk 77 optimal weight:    0.0050
   chunk 98 optimal weight:    0.7980
   chunk 139 optimal weight:    5.9990
   chunk 73 optimal weight:    1.9990
   chunk 70 optimal weight:    0.7980
   overall best weight:    1.1198

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

Flipped N/Q/H residues before XYZ refinement:
A 853 HIS
B 785 ASN
B 853 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3877 r_free = 0.3877 target = 0.169109 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3433 r_free = 0.3433 target = 0.128017 restraints weight = 13169.938|
|-----------------------------------------------------------------------------|
r_work (start): 0.3333 rms_B_bonded: 2.32
r_work: 0.3172 rms_B_bonded: 3.21 restraints_weight: 0.5000
r_work (final): 0.3172
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7757
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      :  0.003   0.036  12444  Z= 0.141
  Angle     :  0.517   6.130  16870  Z= 0.267
  Chirality :  0.041   0.233   1978
  Planarity :  0.005   0.052   2110
  Dihedral  :  3.975  21.719   1642
  Min Nonbonded Distance : 2.545

Molprobity Statistics.
  All-atom Clashscore : 4.16
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  4.95 %
    Favored  : 94.92 %
  Rotamer:
    Outliers :  4.06 %
    Allowed  : 17.67 %
    Favored  : 78.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.39 (0.22), residues: 1516
  helix:  1.18 (0.18), residues: 874
  sheet:  0.90 (0.48), residues: 110
  loop : -1.44 (0.25), residues: 532

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 340 
 HIS   0.007   0.001   HIS A 586 
 PHE   0.029   0.002   PHE B 921 
 TYR   0.008   0.001   TYR B 789 
 ARG   0.003   0.000   ARG A 701 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05744 (  625)
  hydrogen bonds       : angle       3.81844 ( 1842)
  covalent geometry    : bond        0.00334 (12444)
  covalent geometry    : angle       0.51749 (16870)

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

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

  3032 Ramachandran restraints generated.
    1516 Oldfield, 0 Emsley, 1516 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3032 Ramachandran restraints generated.
    1516 Oldfield, 0 Emsley, 1516 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  226 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 54
    poor density    : 172
  time to evaluate  : 1.375 
Fit side-chains
REVERT: A 1156 LYS cc_start: 0.8206 (mtpt) cc_final: 0.7658 (mptt)
REVERT: B  558 LEU cc_start: 0.8149 (OUTLIER) cc_final: 0.7883 (tp)
REVERT: B  586 HIS cc_start: 0.7329 (OUTLIER) cc_final: 0.6976 (p90)
REVERT: B  590 TYR cc_start: 0.7514 (OUTLIER) cc_final: 0.6133 (t80)
REVERT: B  701 ARG cc_start: 0.8031 (ttm170) cc_final: 0.7795 (ttm-80)
REVERT: B  981 ASN cc_start: 0.8500 (p0) cc_final: 0.8167 (p0)
REVERT: B 1156 LYS cc_start: 0.8138 (mtpt) cc_final: 0.7570 (mptt)
  outliers start: 54
  outliers final: 48
  residues processed: 211
  average time/residue: 0.2305
  time to fit residues: 70.9130
Evaluate side-chains
  220 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 51
    poor density    : 169
  time to evaluate  : 1.420 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  321 HIS
Chi-restraints excluded: chain A residue  325 VAL
Chi-restraints excluded: chain A residue  374 LEU
Chi-restraints excluded: chain A residue  532 MET
Chi-restraints excluded: chain A residue  535 VAL
Chi-restraints excluded: chain A residue  556 LEU
Chi-restraints excluded: chain A residue  586 HIS
Chi-restraints excluded: chain A residue  591 LEU
Chi-restraints excluded: chain A residue  623 LEU
Chi-restraints excluded: chain A residue  721 SER
Chi-restraints excluded: chain A residue  729 LEU
Chi-restraints excluded: chain A residue  740 VAL
Chi-restraints excluded: chain A residue  743 LEU
Chi-restraints excluded: chain A residue  745 MET
Chi-restraints excluded: chain A residue  999 LEU
Chi-restraints excluded: chain A residue 1046 CYS
Chi-restraints excluded: chain A residue 1058 THR
Chi-restraints excluded: chain A residue 1094 LEU
Chi-restraints excluded: chain A residue 1109 LEU
Chi-restraints excluded: chain A residue 1142 LEU
Chi-restraints excluded: chain A residue 1152 VAL
Chi-restraints excluded: chain A residue 1158 VAL
Chi-restraints excluded: chain A residue 1215 CYS
Chi-restraints excluded: chain B residue  323 VAL
Chi-restraints excluded: chain B residue  325 VAL
Chi-restraints excluded: chain B residue  332 LEU
Chi-restraints excluded: chain B residue  518 VAL
Chi-restraints excluded: chain B residue  531 THR
Chi-restraints excluded: chain B residue  558 LEU
Chi-restraints excluded: chain B residue  586 HIS
Chi-restraints excluded: chain B residue  590 TYR
Chi-restraints excluded: chain B residue  591 LEU
Chi-restraints excluded: chain B residue  610 VAL
Chi-restraints excluded: chain B residue  623 LEU
Chi-restraints excluded: chain B residue  697 LEU
Chi-restraints excluded: chain B residue  709 LEU
Chi-restraints excluded: chain B residue  721 SER
Chi-restraints excluded: chain B residue  740 VAL
Chi-restraints excluded: chain B residue  785 ASN
Chi-restraints excluded: chain B residue  918 LEU
Chi-restraints excluded: chain B residue  964 VAL
Chi-restraints excluded: chain B residue  970 VAL
Chi-restraints excluded: chain B residue 1058 THR
Chi-restraints excluded: chain B residue 1070 VAL
Chi-restraints excluded: chain B residue 1094 LEU
Chi-restraints excluded: chain B residue 1105 VAL
Chi-restraints excluded: chain B residue 1109 LEU
Chi-restraints excluded: chain B residue 1137 GLU
Chi-restraints excluded: chain B residue 1152 VAL
Chi-restraints excluded: chain B residue 1196 THR
Chi-restraints excluded: chain B residue 1215 CYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 88 optimal weight:    4.9990
   chunk 124 optimal weight:    0.0050
   chunk 100 optimal weight:    0.8980
   chunk 8 optimal weight:    2.9990
   chunk 74 optimal weight:    0.6980
   chunk 60 optimal weight:    1.9990
   chunk 133 optimal weight:    5.9990
   chunk 15 optimal weight:    0.8980
   chunk 109 optimal weight:    2.9990
   chunk 67 optimal weight:    3.9990
   chunk 42 optimal weight:    0.8980
   overall best weight:    0.6794

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

Flipped N/Q/H residues before XYZ refinement:
A 391 GLN
A 853 HIS
B 391 GLN
** B 586 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 785 ASN
B 853 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3896 r_free = 0.3896 target = 0.170983 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3459 r_free = 0.3459 target = 0.130143 restraints weight = 13075.300|
|-----------------------------------------------------------------------------|
r_work (start): 0.3369 rms_B_bonded: 2.30
r_work: 0.3208 rms_B_bonded: 3.22 restraints_weight: 0.5000
r_work (final): 0.3208
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7729
moved from start:          0.1402

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  12444  Z= 0.114
  Angle     :  0.491   6.087  16870  Z= 0.254
  Chirality :  0.040   0.208   1978
  Planarity :  0.004   0.051   2110
  Dihedral  :  3.882  20.580   1642
  Min Nonbonded Distance : 2.552

Molprobity Statistics.
  All-atom Clashscore : 3.88
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  4.75 %
    Favored  : 95.12 %
  Rotamer:
    Outliers :  3.91 %
    Allowed  : 18.35 %
    Favored  : 77.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.56 (0.22), residues: 1516
  helix:  1.35 (0.18), residues: 876
  sheet:  0.94 (0.48), residues: 110
  loop : -1.44 (0.26), residues: 530

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 346 
 HIS   0.007   0.001   HIS A 586 
 PHE   0.027   0.001   PHE B 921 
 TYR   0.007   0.001   TYR A 569 
 ARG   0.004   0.000   ARG A 701 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05136 (  625)
  hydrogen bonds       : angle       3.74730 ( 1842)
  covalent geometry    : bond        0.00254 (12444)
  covalent geometry    : angle       0.49107 (16870)

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

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

  3032 Ramachandran restraints generated.
    1516 Oldfield, 0 Emsley, 1516 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3032 Ramachandran restraints generated.
    1516 Oldfield, 0 Emsley, 1516 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  222 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 52
    poor density    : 170
  time to evaluate  : 1.475 
Fit side-chains
REVERT: A  745 MET cc_start: 0.7928 (OUTLIER) cc_final: 0.7671 (mtt)
REVERT: A 1085 GLU cc_start: 0.8149 (pt0) cc_final: 0.7924 (pt0)
REVERT: A 1156 LYS cc_start: 0.8185 (mtpt) cc_final: 0.7630 (mptt)
REVERT: A 1172 LEU cc_start: 0.8299 (tp) cc_final: 0.8083 (tp)
REVERT: B  558 LEU cc_start: 0.8153 (OUTLIER) cc_final: 0.7938 (tp)
REVERT: B  586 HIS cc_start: 0.7177 (OUTLIER) cc_final: 0.6871 (p90)
REVERT: B  590 TYR cc_start: 0.7493 (OUTLIER) cc_final: 0.6181 (t80)
REVERT: B  701 ARG cc_start: 0.8026 (ttm170) cc_final: 0.7797 (ttm-80)
REVERT: B  918 LEU cc_start: 0.8164 (OUTLIER) cc_final: 0.7916 (mt)
REVERT: B  981 ASN cc_start: 0.8485 (p0) cc_final: 0.8173 (p0)
REVERT: B 1156 LYS cc_start: 0.8124 (mtpt) cc_final: 0.7574 (mptt)
  outliers start: 52
  outliers final: 44
  residues processed: 206
  average time/residue: 0.2294
  time to fit residues: 68.7439
Evaluate side-chains
  218 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 169
  time to evaluate  : 1.289 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  321 HIS
Chi-restraints excluded: chain A residue  325 VAL
Chi-restraints excluded: chain A residue  374 LEU
Chi-restraints excluded: chain A residue  532 MET
Chi-restraints excluded: chain A residue  535 VAL
Chi-restraints excluded: chain A residue  586 HIS
Chi-restraints excluded: chain A residue  591 LEU
Chi-restraints excluded: chain A residue  623 LEU
Chi-restraints excluded: chain A residue  721 SER
Chi-restraints excluded: chain A residue  729 LEU
Chi-restraints excluded: chain A residue  740 VAL
Chi-restraints excluded: chain A residue  743 LEU
Chi-restraints excluded: chain A residue  745 MET
Chi-restraints excluded: chain A residue  999 LEU
Chi-restraints excluded: chain A residue 1046 CYS
Chi-restraints excluded: chain A residue 1058 THR
Chi-restraints excluded: chain A residue 1094 LEU
Chi-restraints excluded: chain A residue 1109 LEU
Chi-restraints excluded: chain A residue 1142 LEU
Chi-restraints excluded: chain A residue 1158 VAL
Chi-restraints excluded: chain A residue 1215 CYS
Chi-restraints excluded: chain B residue  323 VAL
Chi-restraints excluded: chain B residue  325 VAL
Chi-restraints excluded: chain B residue  332 LEU
Chi-restraints excluded: chain B residue  518 VAL
Chi-restraints excluded: chain B residue  531 THR
Chi-restraints excluded: chain B residue  558 LEU
Chi-restraints excluded: chain B residue  586 HIS
Chi-restraints excluded: chain B residue  590 TYR
Chi-restraints excluded: chain B residue  591 LEU
Chi-restraints excluded: chain B residue  610 VAL
Chi-restraints excluded: chain B residue  623 LEU
Chi-restraints excluded: chain B residue  697 LEU
Chi-restraints excluded: chain B residue  709 LEU
Chi-restraints excluded: chain B residue  721 SER
Chi-restraints excluded: chain B residue  740 VAL
Chi-restraints excluded: chain B residue  785 ASN
Chi-restraints excluded: chain B residue  918 LEU
Chi-restraints excluded: chain B residue  964 VAL
Chi-restraints excluded: chain B residue  970 VAL
Chi-restraints excluded: chain B residue 1058 THR
Chi-restraints excluded: chain B residue 1070 VAL
Chi-restraints excluded: chain B residue 1094 LEU
Chi-restraints excluded: chain B residue 1105 VAL
Chi-restraints excluded: chain B residue 1109 LEU
Chi-restraints excluded: chain B residue 1137 GLU
Chi-restraints excluded: chain B residue 1152 VAL
Chi-restraints excluded: chain B residue 1196 THR
Chi-restraints excluded: chain B residue 1215 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 57 optimal weight:    3.9990
   chunk 28 optimal weight:    0.9990
   chunk 3 optimal weight:    0.3980
   chunk 107 optimal weight:    3.9990
   chunk 119 optimal weight:    2.9990
   chunk 53 optimal weight:    4.9990
   chunk 139 optimal weight:    4.9990
   chunk 49 optimal weight:    2.9990
   chunk 121 optimal weight:    0.6980
   chunk 13 optimal weight:    2.9990
   chunk 129 optimal weight:    5.9990
   overall best weight:    1.6186

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

Flipped N/Q/H residues before XYZ refinement:
A 853 HIS
B 785 ASN
B 853 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3863 r_free = 0.3863 target = 0.167737 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3414 r_free = 0.3414 target = 0.126490 restraints weight = 13064.163|
|-----------------------------------------------------------------------------|
r_work (start): 0.3291 rms_B_bonded: 2.30
r_work: 0.3129 rms_B_bonded: 3.20 restraints_weight: 0.5000
r_work (final): 0.3129
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7788
moved from start:          0.1413

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041  12444  Z= 0.179
  Angle     :  0.561   6.224  16870  Z= 0.289
  Chirality :  0.043   0.216   1978
  Planarity :  0.005   0.052   2110
  Dihedral  :  4.061  23.639   1642
  Min Nonbonded Distance : 2.519

Molprobity Statistics.
  All-atom Clashscore : 3.96
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  5.28 %
    Favored  : 94.59 %
  Rotamer:
    Outliers :  3.83 %
    Allowed  : 18.35 %
    Favored  : 77.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.29 (0.22), residues: 1516
  helix:  1.07 (0.18), residues: 876
  sheet:  0.93 (0.48), residues: 110
  loop : -1.44 (0.25), residues: 530

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 340 
 HIS   0.012   0.001   HIS B 786 
 PHE   0.026   0.002   PHE B 921 
 TYR   0.010   0.001   TYR A 789 
 ARG   0.006   0.000   ARG A 701 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06414 (  625)
  hydrogen bonds       : angle       3.89692 ( 1842)
  covalent geometry    : bond        0.00439 (12444)
  covalent geometry    : angle       0.56054 (16870)

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

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

  3032 Ramachandran restraints generated.
    1516 Oldfield, 0 Emsley, 1516 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3032 Ramachandran restraints generated.
    1516 Oldfield, 0 Emsley, 1516 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  224 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 51
    poor density    : 173
  time to evaluate  : 1.324 
Fit side-chains
REVERT: A 1156 LYS cc_start: 0.8239 (mtpt) cc_final: 0.7672 (mptt)
REVERT: B  558 LEU cc_start: 0.8152 (OUTLIER) cc_final: 0.7821 (tp)
REVERT: B  586 HIS cc_start: 0.7363 (OUTLIER) cc_final: 0.6982 (p90)
REVERT: B  701 ARG cc_start: 0.8044 (ttm170) cc_final: 0.7810 (ttm-80)
REVERT: B  981 ASN cc_start: 0.8517 (p0) cc_final: 0.8200 (p0)
REVERT: B 1156 LYS cc_start: 0.8155 (mtpt) cc_final: 0.7580 (mptt)
  outliers start: 51
  outliers final: 44
  residues processed: 210
  average time/residue: 0.2263
  time to fit residues: 69.2933
Evaluate side-chains
  215 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 169
  time to evaluate  : 1.350 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  321 HIS
Chi-restraints excluded: chain A residue  325 VAL
Chi-restraints excluded: chain A residue  374 LEU
Chi-restraints excluded: chain A residue  532 MET
Chi-restraints excluded: chain A residue  535 VAL
Chi-restraints excluded: chain A residue  556 LEU
Chi-restraints excluded: chain A residue  586 HIS
Chi-restraints excluded: chain A residue  623 LEU
Chi-restraints excluded: chain A residue  721 SER
Chi-restraints excluded: chain A residue  729 LEU
Chi-restraints excluded: chain A residue  740 VAL
Chi-restraints excluded: chain A residue  743 LEU
Chi-restraints excluded: chain A residue  745 MET
Chi-restraints excluded: chain A residue  999 LEU
Chi-restraints excluded: chain A residue 1046 CYS
Chi-restraints excluded: chain A residue 1058 THR
Chi-restraints excluded: chain A residue 1094 LEU
Chi-restraints excluded: chain A residue 1109 LEU
Chi-restraints excluded: chain A residue 1142 LEU
Chi-restraints excluded: chain A residue 1158 VAL
Chi-restraints excluded: chain A residue 1215 CYS
Chi-restraints excluded: chain B residue  323 VAL
Chi-restraints excluded: chain B residue  325 VAL
Chi-restraints excluded: chain B residue  332 LEU
Chi-restraints excluded: chain B residue  518 VAL
Chi-restraints excluded: chain B residue  531 THR
Chi-restraints excluded: chain B residue  558 LEU
Chi-restraints excluded: chain B residue  586 HIS
Chi-restraints excluded: chain B residue  610 VAL
Chi-restraints excluded: chain B residue  623 LEU
Chi-restraints excluded: chain B residue  697 LEU
Chi-restraints excluded: chain B residue  709 LEU
Chi-restraints excluded: chain B residue  721 SER
Chi-restraints excluded: chain B residue  740 VAL
Chi-restraints excluded: chain B residue  918 LEU
Chi-restraints excluded: chain B residue  964 VAL
Chi-restraints excluded: chain B residue  970 VAL
Chi-restraints excluded: chain B residue 1058 THR
Chi-restraints excluded: chain B residue 1070 VAL
Chi-restraints excluded: chain B residue 1094 LEU
Chi-restraints excluded: chain B residue 1105 VAL
Chi-restraints excluded: chain B residue 1109 LEU
Chi-restraints excluded: chain B residue 1137 GLU
Chi-restraints excluded: chain B residue 1152 VAL
Chi-restraints excluded: chain B residue 1196 THR
Chi-restraints excluded: chain B residue 1215 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 144 optimal weight:    0.9980
   chunk 108 optimal weight:    4.9990
   chunk 119 optimal weight:    1.9990
   chunk 34 optimal weight:    3.9990
   chunk 101 optimal weight:    3.9990
   chunk 132 optimal weight:    0.5980
   chunk 141 optimal weight:    2.9990
   chunk 106 optimal weight:    2.9990
   chunk 43 optimal weight:    3.9990
   chunk 85 optimal weight:    9.9990
   chunk 109 optimal weight:    2.9990
   overall best weight:    1.9186

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

Flipped N/Q/H residues before XYZ refinement:
A 628 HIS
A 853 HIS
B 391 GLN
B 853 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3844 r_free = 0.3844 target = 0.165860 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3393 r_free = 0.3393 target = 0.124504 restraints weight = 13134.981|
|-----------------------------------------------------------------------------|
r_work (start): 0.3269 rms_B_bonded: 2.30
r_work: 0.3106 rms_B_bonded: 3.19 restraints_weight: 0.5000
r_work (final): 0.3106
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7816
moved from start:          0.1492

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.044  12444  Z= 0.204
  Angle     :  0.598   6.372  16870  Z= 0.308
  Chirality :  0.044   0.219   1978
  Planarity :  0.005   0.052   2110
  Dihedral  :  4.293  27.648   1642
  Min Nonbonded Distance : 2.524

Molprobity Statistics.
  All-atom Clashscore : 4.16
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  5.61 %
    Favored  : 94.26 %
  Rotamer:
    Outliers :  3.61 %
    Allowed  : 18.27 %
    Favored  : 78.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.05 (0.22), residues: 1516
  helix:  0.84 (0.18), residues: 876
  sheet:  0.90 (0.48), residues: 110
  loop : -1.50 (0.26), residues: 530

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP B 340 
 HIS   0.008   0.001   HIS A1064 
 PHE   0.026   0.002   PHE B 921 
 TYR   0.011   0.002   TYR B 789 
 ARG   0.006   0.000   ARG A 701 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.07103 (  625)
  hydrogen bonds       : angle       4.04287 ( 1842)
  covalent geometry    : bond        0.00508 (12444)
  covalent geometry    : angle       0.59807 (16870)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5835.77 seconds
wall clock time: 101 minutes 41.80 seconds (6101.80 seconds total)