Starting phenix.real_space_refine
on Wed Jul 30 09:16:46 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8gv9_34288/07_2025/8gv9_34288.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8gv9_34288/07_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_34288/07_2025/8gv9_34288.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8gv9_34288/07_2025/8gv9_34288.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8gv9_34288/07_2025/8gv9_34288.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8gv9_34288/07_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): 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/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: 7.57, per 1000 atoms: 0.62
  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: 2.96
  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: 1.39
  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: 3.59

  Time building geometry restraints manager: 3.50 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:             0.910
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.470
  Check model and map are aligned:         0.090
  Set scattering table:                    0.120
  Process input model:                     30.740
  Find NCS groups from input model:        0.490
  Set up NCS constraints:                  0.060
  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:3.050
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   35.960
-------------------------------------------------------------------------------
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  : 1.462 
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: 0.2983
  time to fit residues: 74.1165
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  : 1.599 
-------------------------------------------------------------------------------
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 = 0.172016 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3497 r_free = 0.3497 target = 0.132128 restraints weight = 12939.389|
|-----------------------------------------------------------------------------|
r_work (start): 0.3411 rms_B_bonded: 2.37
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: 0.7737
moved from start:          0.0744

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   9.645  16870  Z= 0.277
  Chirality :  0.040   0.150   1978
  Planarity :  0.005   0.060   2110
  Dihedral  :  4.107  30.275   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  : 16.24 %
    Favored  : 81.88 %
  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        0.05948 (  625)
  hydrogen bonds       : angle       4.08700 ( 1842)
  covalent geometry    : bond        0.00273 (12444)
  covalent geometry    : angle       0.53186 (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  : 1.265 
Fit side-chains
REVERT: A  697 LEU cc_start: 0.8619 (mm) cc_final: 0.8344 (mm)
REVERT: A 1156 LYS cc_start: 0.8267 (mtpt) cc_final: 0.7756 (mmtt)
REVERT: B  321 HIS cc_start: 0.6425 (OUTLIER) cc_final: 0.6214 (m-70)
REVERT: B  590 TYR cc_start: 0.7507 (OUTLIER) cc_final: 0.5951 (t80)
REVERT: B  701 ARG cc_start: 0.7957 (ttm170) cc_final: 0.7697 (ttm-80)
REVERT: B  925 ARG cc_start: 0.8048 (mtm180) cc_final: 0.7490 (ptp-170)
REVERT: B 1156 LYS cc_start: 0.8099 (mtpt) cc_final: 0.7572 (mptt)
  outliers start: 25
  outliers final: 15
  residues processed: 193
  average time/residue: 0.3044
  time to fit residues: 83.7174
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  : 1.791 
-------------------------------------------------------------------------------
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:    0.8980
   chunk 94 optimal weight:    2.9990
   chunk 125 optimal weight:    0.9980
   chunk 111 optimal weight:    3.9990
   chunk 32 optimal weight:    4.9990
   chunk 126 optimal weight:    0.6980
   chunk 91 optimal weight:    6.9990
   chunk 11 optimal weight:    6.9990
   overall best weight:    1.3182

-------------------------------------------------------------------------------
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 = 0.3899 r_free = 0.3899 target = 0.170401 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3483 r_free = 0.3483 target = 0.130930 restraints weight = 13122.156|
|-----------------------------------------------------------------------------|
r_work (start): 0.3382 rms_B_bonded: 2.37
r_work: 0.3208 rms_B_bonded: 3.06 restraints_weight: 0.5000
r_work: 0.3047 rms_B_bonded: 4.87 restraints_weight: 0.2500
r_work (final): 0.3047
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7893
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= 0.159
  Angle     :  0.548   6.257  16870  Z= 0.284
  Chirality :  0.042   0.158   1978
  Planarity :  0.005   0.055   2110
  Dihedral  :  4.051  20.828   1642
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 3.96
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  5.01 %
    Favored  : 94.85 %
  Rotamer:
    Outliers :  3.16 %
    Allowed  : 16.17 %
    Favored  : 80.68 %
  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:  0.17 (0.22), residues: 1516
  helix:  0.99 (0.18), residues: 876
  sheet:  0.79 (0.47), residues: 110
  loop : -1.50 (0.26), residues: 530

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 340 
 HIS   0.008   0.001   HIS B 586 
 PHE   0.021   0.002   PHE A1189 
 TYR   0.010   0.001   TYR A 789 
 ARG   0.003   0.000   ARG A 624 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06418 (  625)
  hydrogen bonds       : angle       4.01904 ( 1842)
  covalent geometry    : bond        0.00382 (12444)
  covalent geometry    : angle       0.54828 (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: 42
    poor density    : 180
  time to evaluate  : 1.436 
Fit side-chains
REVERT: A  697 LEU cc_start: 0.8720 (mm) cc_final: 0.8515 (mm)
REVERT: A  702 ASP cc_start: 0.7995 (m-30) cc_final: 0.7781 (m-30)
REVERT: A 1156 LYS cc_start: 0.8319 (mtpt) cc_final: 0.7766 (mptt)
REVERT: B  321 HIS cc_start: 0.6590 (OUTLIER) cc_final: 0.6237 (m-70)
REVERT: B  701 ARG cc_start: 0.7947 (ttm170) cc_final: 0.7629 (ttm-80)
REVERT: B  981 ASN cc_start: 0.8612 (p0) cc_final: 0.8274 (p0)
REVERT: B 1156 LYS cc_start: 0.8167 (mtpt) cc_final: 0.7556 (mptt)
  outliers start: 42
  outliers final: 30
  residues processed: 205
  average time/residue: 0.2552
  time to fit residues: 74.7661
Evaluate side-chains
  207 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 176
  time to evaluate  : 1.332 
-------------------------------------------------------------------------------
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 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:    2.9990
   chunk 131 optimal weight:    0.8980
   chunk 39 optimal weight:    4.9990
   chunk 119 optimal weight:    2.9990
   chunk 62 optimal weight:    3.9990
   chunk 83 optimal weight:    9.9990
   chunk 121 optimal weight:    0.7980
   chunk 33 optimal weight:    3.9990
   chunk 91 optimal weight:    2.9990
   chunk 94 optimal weight:    0.5980
   overall best weight:    1.6584

-------------------------------------------------------------------------------
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 = 0.3852 r_free = 0.3852 target = 0.166684 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3402 r_free = 0.3402 target = 0.125448 restraints weight = 13089.122|
|-----------------------------------------------------------------------------|
r_work (start): 0.3282 rms_B_bonded: 2.30
r_work: 0.3117 rms_B_bonded: 3.21 restraints_weight: 0.5000
r_work (final): 0.3117
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7795
moved from start:          0.1141

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.043  12444  Z= 0.184
  Angle     :  0.575   6.230  16870  Z= 0.299
  Chirality :  0.043   0.166   1978
  Planarity :  0.005   0.054   2110
  Dihedral  :  4.221  23.838   1642
  Min Nonbonded Distance : 2.542

Molprobity Statistics.
  All-atom Clashscore : 4.08
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  5.28 %
    Favored  : 94.59 %
  Rotamer:
    Outliers :  4.14 %
    Allowed  : 16.02 %
    Favored  : 79.85 %
  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:  0.02 (0.22), residues: 1516
  helix:  0.84 (0.18), residues: 876
  sheet:  0.83 (0.48), residues: 110
  loop : -1.53 (0.26), residues: 530

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B 340 
 HIS   0.008   0.001   HIS B 586 
 PHE   0.023   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        0.06890 (  625)
  hydrogen bonds       : angle       4.06181 ( 1842)
  covalent geometry    : bond        0.00451 (12444)
  covalent geometry    : angle       0.57507 (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
  235 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 55
    poor density    : 180
  time to evaluate  : 1.421 
Fit side-chains
REVERT: A  633 MET cc_start: 0.8125 (ttp) cc_final: 0.7833 (ttm)
REVERT: A  697 LEU cc_start: 0.8731 (mm) cc_final: 0.8524 (mm)
REVERT: A 1156 LYS cc_start: 0.8320 (mtpt) cc_final: 0.7793 (mptt)
REVERT: B  586 HIS cc_start: 0.7309 (OUTLIER) cc_final: 0.6911 (p90)
REVERT: B  743 LEU cc_start: 0.8016 (OUTLIER) cc_final: 0.7626 (mp)
REVERT: B  981 ASN cc_start: 0.8583 (p0) cc_final: 0.8280 (p0)
REVERT: B 1141 LEU cc_start: 0.8384 (OUTLIER) cc_final: 0.7829 (mp)
REVERT: B 1156 LYS cc_start: 0.8153 (mtpt) cc_final: 0.7602 (mptt)
  outliers start: 55
  outliers final: 43
  residues processed: 219
  average time/residue: 0.2381
  time to fit residues: 75.5961
Evaluate side-chains
  216 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 170
  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  368 LEU
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  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 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  374 LEU
Chi-restraints excluded: chain B residue  518 VAL
Chi-restraints excluded: chain B residue  532 MET
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  743 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 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 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=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 48 optimal weight:    3.9990
   chunk 45 optimal weight:    2.9990
   chunk 113 optimal weight:    4.9990
   chunk 39 optimal weight:    4.9990
   chunk 147 optimal weight:    2.9990
   chunk 86 optimal weight:    6.9990
   chunk 141 optimal weight:    3.9990
   chunk 121 optimal weight:    1.9990
   chunk 8 optimal weight:    6.9990
   chunk 2 optimal weight:    1.9990
   chunk 77 optimal weight:    3.9990
   overall best weight:    2.7990

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

Flipped N/Q/H residues before XYZ refinement:
A 853 HIS
A1064 HIS
B 853 HIS
B 899 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3797 r_free = 0.3797 target = 0.162018 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3342 r_free = 0.3342 target = 0.120229 restraints weight = 13119.285|
|-----------------------------------------------------------------------------|
r_work (start): 0.3258 rms_B_bonded: 2.57
r_work: 0.3086 rms_B_bonded: 3.14 restraints_weight: 0.5000
r_work: 0.2923 rms_B_bonded: 4.99 restraints_weight: 0.2500
r_work (final): 0.2923
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7969
moved from start:          0.1448

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.055  12444  Z= 0.280
  Angle     :  0.686   7.078  16870  Z= 0.355
  Chirality :  0.048   0.181   1978
  Planarity :  0.006   0.055   2110
  Dihedral  :  4.603  29.159   1642
  Min Nonbonded Distance : 2.533

Molprobity Statistics.
  All-atom Clashscore : 4.40
  Ramachandran Plot:
    Outliers :  0.33 %
    Allowed  :  5.94 %
    Favored  : 93.73 %
  Rotamer:
    Outliers :  5.04 %
    Allowed  : 16.17 %
    Favored  : 78.80 %
  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: -0.43 (0.21), residues: 1516
  helix:  0.44 (0.18), residues: 876
  sheet:  0.68 (0.48), residues: 110
  loop : -1.67 (0.26), residues: 530

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP B 340 
 HIS   0.012   0.002   HIS A1064 
 PHE   0.026   0.003   PHE B 921 
 TYR   0.014   0.002   TYR A 789 
 ARG   0.007   0.001   ARG A 624 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.08399 (  625)
  hydrogen bonds       : angle       4.32124 ( 1842)
  covalent geometry    : bond        0.00709 (12444)
  covalent geometry    : angle       0.68602 (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
  251 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 67
    poor density    : 184
  time to evaluate  : 1.601 
Fit side-chains
REVERT: A 1156 LYS cc_start: 0.8332 (mtpt) cc_final: 0.7842 (mptt)
REVERT: B  586 HIS cc_start: 0.7699 (OUTLIER) cc_final: 0.7107 (p90)
REVERT: B  743 LEU cc_start: 0.8162 (OUTLIER) cc_final: 0.7808 (mp)
REVERT: B  981 ASN cc_start: 0.8634 (p0) cc_final: 0.8368 (p0)
REVERT: B 1141 LEU cc_start: 0.8568 (OUTLIER) cc_final: 0.8003 (mp)
REVERT: B 1156 LYS cc_start: 0.8263 (mtpt) cc_final: 0.7671 (mptt)
  outliers start: 67
  outliers final: 47
  residues processed: 236
  average time/residue: 0.2514
  time to fit residues: 86.6034
Evaluate side-chains
  231 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 181
  time to evaluate  : 1.313 
-------------------------------------------------------------------------------
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  518 VAL
Chi-restraints excluded: chain A residue  535 VAL
Chi-restraints excluded: chain A residue  547 LEU
Chi-restraints excluded: chain A residue  556 LEU
Chi-restraints excluded: chain A residue  623 LEU
Chi-restraints excluded: chain A residue  721 SER
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  785 ASN
Chi-restraints excluded: chain A residue  971 THR
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 1152 VAL
Chi-restraints excluded: chain A residue 1158 VAL
Chi-restraints excluded: chain A residue 1205 THR
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  374 LEU
Chi-restraints excluded: chain B residue  518 VAL
Chi-restraints excluded: chain B residue  524 VAL
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  721 SER
Chi-restraints excluded: chain B residue  740 VAL
Chi-restraints excluded: chain B residue  743 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 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:    0.1980
   chunk 78 optimal weight:    0.9980
   chunk 151 optimal weight:    2.9990
   chunk 38 optimal weight:    2.9990
   chunk 66 optimal weight:    0.9990
   chunk 131 optimal weight:    0.9980
   chunk 74 optimal weight:    0.5980
   chunk 105 optimal weight:    2.9990
   overall best weight:    0.7582

-------------------------------------------------------------------------------
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 785 ASN
B 853 HIS
B 899 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3875 r_free = 0.3875 target = 0.168887 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3438 r_free = 0.3438 target = 0.128251 restraints weight = 13124.205|
|-----------------------------------------------------------------------------|
r_work (start): 0.3317 rms_B_bonded: 2.29
r_work: 0.3153 rms_B_bonded: 3.21 restraints_weight: 0.5000
r_work (final): 0.3153
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7754
moved from start:          0.1396

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  12444  Z= 0.124
  Angle     :  0.509   6.392  16870  Z= 0.266
  Chirality :  0.040   0.146   1978
  Planarity :  0.005   0.054   2110
  Dihedral  :  4.164  24.411   1642
  Min Nonbonded Distance : 2.560

Molprobity Statistics.
  All-atom Clashscore : 4.36
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  4.75 %
    Favored  : 95.12 %
  Rotamer:
    Outliers :  3.01 %
    Allowed  : 18.57 %
    Favored  : 78.42 %
  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:  0.15 (0.22), residues: 1516
  helix:  0.98 (0.18), residues: 876
  sheet:  0.84 (0.48), residues: 110
  loop : -1.55 (0.26), residues: 530

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 340 
 HIS   0.012   0.001   HIS A 586 
 PHE   0.020   0.001   PHE B 921 
 TYR   0.007   0.001   TYR B1154 
 ARG   0.002   0.000   ARG A 793 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05524 (  625)
  hydrogen bonds       : angle       3.93608 ( 1842)
  covalent geometry    : bond        0.00280 (12444)
  covalent geometry    : angle       0.50909 (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
  218 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 178
  time to evaluate  : 1.352 
Fit side-chains
REVERT: A  633 MET cc_start: 0.7984 (ttp) cc_final: 0.7770 (ttm)
REVERT: A 1156 LYS cc_start: 0.8294 (mtpt) cc_final: 0.7806 (mptt)
REVERT: A 1172 LEU cc_start: 0.8195 (tp) cc_final: 0.7955 (tp)
REVERT: B  586 HIS cc_start: 0.7392 (OUTLIER) cc_final: 0.6977 (p90)
REVERT: B  590 TYR cc_start: 0.7615 (OUTLIER) cc_final: 0.6152 (t80)
REVERT: B  981 ASN cc_start: 0.8464 (p0) cc_final: 0.8214 (p0)
REVERT: B 1156 LYS cc_start: 0.8120 (mtpt) cc_final: 0.7586 (mptt)
  outliers start: 40
  outliers final: 32
  residues processed: 207
  average time/residue: 0.2487
  time to fit residues: 74.5943
Evaluate side-chains
  207 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 173
  time to evaluate  : 1.356 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  321 HIS
Chi-restraints excluded: chain A residue  323 VAL
Chi-restraints excluded: chain A residue  325 VAL
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  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 1094 LEU
Chi-restraints excluded: chain A residue 1109 LEU
Chi-restraints excluded: chain A residue 1142 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  697 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  971 THR
Chi-restraints excluded: chain B residue 1058 THR
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 1142 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:    1.9990
   chunk 148 optimal weight:    2.9990
   chunk 118 optimal weight:    3.9990
   chunk 129 optimal weight:    7.9990
   chunk 73 optimal weight:    2.9990
   chunk 145 optimal weight:    0.0040
   chunk 51 optimal weight:    2.9990
   chunk 122 optimal weight:    3.9990
   chunk 131 optimal weight:    2.9990
   chunk 6 optimal weight:    1.9990
   chunk 150 optimal weight:    1.9990
   overall best weight:    1.8000

-------------------------------------------------------------------------------
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 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 = 0.3841 r_free = 0.3841 target = 0.165691 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3390 r_free = 0.3390 target = 0.124519 restraints weight = 13184.672|
|-----------------------------------------------------------------------------|
r_work (start): 0.3253 rms_B_bonded: 2.31
r_work: 0.3089 rms_B_bonded: 3.21 restraints_weight: 0.5000
r_work (final): 0.3089
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7813
moved from start:          0.1459

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= 0.195
  Angle     :  0.578   6.189  16870  Z= 0.299
  Chirality :  0.043   0.159   1978
  Planarity :  0.005   0.055   2110
  Dihedral  :  4.274  27.443   1642
  Min Nonbonded Distance : 2.519

Molprobity Statistics.
  All-atom Clashscore : 4.52
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  5.41 %
    Favored  : 94.46 %
  Rotamer:
    Outliers :  3.98 %
    Allowed  : 18.35 %
    Favored  : 77.67 %
  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:  0.01 (0.22), residues: 1516
  helix:  0.82 (0.18), residues: 876
  sheet:  0.86 (0.48), residues: 110
  loop : -1.55 (0.26), residues: 530

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B 340 
 HIS   0.011   0.002   HIS A 586 
 PHE   0.023   0.002   PHE B1189 
 TYR   0.010   0.001   TYR B 789 
 ARG   0.004   0.000   ARG A 624 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06866 (  625)
  hydrogen bonds       : angle       4.03882 ( 1842)
  covalent geometry    : bond        0.00482 (12444)
  covalent geometry    : angle       0.57754 (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
  236 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 53
    poor density    : 183
  time to evaluate  : 1.412 
Fit side-chains
REVERT: A  834 ILE cc_start: 0.5434 (pt) cc_final: 0.5177 (pt)
REVERT: A 1156 LYS cc_start: 0.8282 (mtpt) cc_final: 0.7797 (mptt)
REVERT: A 1194 ILE cc_start: 0.7874 (OUTLIER) cc_final: 0.7054 (tp)
REVERT: B  586 HIS cc_start: 0.7411 (OUTLIER) cc_final: 0.7018 (p90)
REVERT: B  981 ASN cc_start: 0.8505 (p0) cc_final: 0.8260 (p0)
REVERT: B 1141 LEU cc_start: 0.8359 (OUTLIER) cc_final: 0.7866 (mp)
REVERT: B 1156 LYS cc_start: 0.8192 (mtpt) cc_final: 0.7634 (mptt)
  outliers start: 53
  outliers final: 46
  residues processed: 222
  average time/residue: 0.3126
  time to fit residues: 103.2258
Evaluate side-chains
  229 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 180
  time to evaluate  : 2.217 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  321 HIS
Chi-restraints excluded: chain A residue  323 VAL
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  591 LEU
Chi-restraints excluded: chain A residue  623 LEU
Chi-restraints excluded: chain A residue  697 LEU
Chi-restraints excluded: chain A residue  721 SER
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 1194 ILE
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  387 LEU
Chi-restraints excluded: chain B residue  518 VAL
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  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  971 THR
Chi-restraints excluded: chain B residue 1058 THR
Chi-restraints excluded: chain B residue 1070 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 1142 LEU
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=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 122 optimal weight:    0.9990
   chunk 80 optimal weight:    0.8980
   chunk 109 optimal weight:    2.9990
   chunk 9 optimal weight:    9.9990
   chunk 118 optimal weight:    2.9990
   chunk 85 optimal weight:   10.0000
   chunk 77 optimal weight:    0.0770
   chunk 98 optimal weight:    0.0970
   chunk 139 optimal weight:    3.9990
   chunk 73 optimal weight:    0.7980
   chunk 70 optimal weight:    0.0670
   overall best weight:    0.3874

-------------------------------------------------------------------------------
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 586 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
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 = 0.3902 r_free = 0.3902 target = 0.171874 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3464 r_free = 0.3464 target = 0.130731 restraints weight = 13155.261|
|-----------------------------------------------------------------------------|
r_work (start): 0.3325 rms_B_bonded: 2.34
r_work: 0.3166 rms_B_bonded: 3.24 restraints_weight: 0.5000
r_work (final): 0.3166
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7718
moved from start:          0.1507

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= 0.107
  Angle     :  0.484   6.980  16870  Z= 0.254
  Chirality :  0.039   0.141   1978
  Planarity :  0.004   0.053   2110
  Dihedral  :  3.991  23.666   1642
  Min Nonbonded Distance : 2.468

Molprobity Statistics.
  All-atom Clashscore : 4.52
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  4.35 %
    Favored  : 95.51 %
  Rotamer:
    Outliers :  2.86 %
    Allowed  : 19.47 %
    Favored  : 77.67 %
  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:  0.50 (0.22), residues: 1516
  helix:  1.30 (0.18), residues: 874
  sheet:  0.91 (0.48), residues: 110
  loop : -1.46 (0.26), residues: 532

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 346 
 HIS   0.011   0.001   HIS A 586 
 PHE   0.018   0.001   PHE A1189 
 TYR   0.007   0.001   TYR A 569 
 ARG   0.004   0.000   ARG A 701 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04789 (  625)
  hydrogen bonds       : angle       3.78110 ( 1842)
  covalent geometry    : bond        0.00223 (12444)
  covalent geometry    : angle       0.48378 (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
  216 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 178
  time to evaluate  : 2.049 
Fit side-chains
REVERT: A 1156 LYS cc_start: 0.8273 (mtpt) cc_final: 0.7762 (mptt)
REVERT: A 1172 LEU cc_start: 0.8206 (tp) cc_final: 0.7953 (tp)
REVERT: B  586 HIS cc_start: 0.7244 (OUTLIER) cc_final: 0.6893 (p90)
REVERT: B  701 ARG cc_start: 0.8011 (ttm170) cc_final: 0.7776 (ttm-80)
REVERT: B  981 ASN cc_start: 0.8415 (p0) cc_final: 0.8112 (p0)
REVERT: B 1141 LEU cc_start: 0.8275 (OUTLIER) cc_final: 0.7821 (mp)
REVERT: B 1156 LYS cc_start: 0.8103 (mtpt) cc_final: 0.7570 (mptt)
  outliers start: 38
  outliers final: 27
  residues processed: 200
  average time/residue: 0.3865
  time to fit residues: 110.9259
Evaluate side-chains
  201 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 172
  time to evaluate  : 1.515 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  321 HIS
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  591 LEU
Chi-restraints excluded: chain A residue  623 LEU
Chi-restraints excluded: chain A residue  697 LEU
Chi-restraints excluded: chain A residue  999 LEU
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 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  591 LEU
Chi-restraints excluded: chain B residue  697 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 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 1152 VAL
Chi-restraints excluded: chain B residue 1196 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 88 optimal weight:    5.9990
   chunk 124 optimal weight:    1.9990
   chunk 100 optimal weight:    3.9990
   chunk 8 optimal weight:    0.9990
   chunk 74 optimal weight:    0.9990
   chunk 60 optimal weight:    1.9990
   chunk 133 optimal weight:    4.9990
   chunk 15 optimal weight:    0.0060
   chunk 109 optimal weight:    3.9990
   chunk 67 optimal weight:    3.9990
   chunk 42 optimal weight:    0.8980
   overall best weight:    0.9802

-------------------------------------------------------------------------------
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 586 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
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 = 0.3869 r_free = 0.3869 target = 0.168811 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3412 r_free = 0.3412 target = 0.126554 restraints weight = 13097.182|
|-----------------------------------------------------------------------------|
r_work (start): 0.3287 rms_B_bonded: 2.41
r_work: 0.3124 rms_B_bonded: 3.32 restraints_weight: 0.5000
r_work (final): 0.3124
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7744
moved from start:          0.1518

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  12444  Z= 0.132
  Angle     :  0.513   6.423  16870  Z= 0.265
  Chirality :  0.040   0.144   1978
  Planarity :  0.005   0.053   2110
  Dihedral  :  3.986  24.847   1642
  Min Nonbonded Distance : 2.536

Molprobity Statistics.
  All-atom Clashscore : 4.36
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  5.15 %
    Favored  : 94.72 %
  Rotamer:
    Outliers :  3.08 %
    Allowed  : 19.02 %
    Favored  : 77.89 %
  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:  0.51 (0.22), residues: 1516
  helix:  1.29 (0.18), residues: 874
  sheet:  0.95 (0.48), residues: 110
  loop : -1.43 (0.26), residues: 532

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 346 
 HIS   0.011   0.001   HIS A 586 
 PHE   0.019   0.001   PHE A1189 
 TYR   0.008   0.001   TYR B1154 
 ARG   0.006   0.000   ARG A 701 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05529 (  625)
  hydrogen bonds       : angle       3.80408 ( 1842)
  covalent geometry    : bond        0.00311 (12444)
  covalent geometry    : angle       0.51310 (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
  218 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 177
  time to evaluate  : 2.501 
Fit side-chains
REVERT: A 1156 LYS cc_start: 0.8278 (mtpt) cc_final: 0.7744 (mptt)
REVERT: B  586 HIS cc_start: 0.7281 (OUTLIER) cc_final: 0.6925 (p90)
REVERT: B  590 TYR cc_start: 0.7479 (OUTLIER) cc_final: 0.6203 (t80)
REVERT: B  701 ARG cc_start: 0.8007 (ttm170) cc_final: 0.7769 (ttm-80)
REVERT: B  981 ASN cc_start: 0.8443 (p0) cc_final: 0.8135 (p0)
REVERT: B 1156 LYS cc_start: 0.8116 (mtpt) cc_final: 0.7556 (mptt)
  outliers start: 41
  outliers final: 38
  residues processed: 203
  average time/residue: 0.2589
  time to fit residues: 76.6254
Evaluate side-chains
  213 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 173
  time to evaluate  : 1.388 
-------------------------------------------------------------------------------
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  591 LEU
Chi-restraints excluded: chain A residue  623 LEU
Chi-restraints excluded: chain A residue  697 LEU
Chi-restraints excluded: chain A residue  721 SER
Chi-restraints excluded: chain A residue  740 VAL
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  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  709 LEU
Chi-restraints excluded: chain B residue  721 SER
Chi-restraints excluded: chain B residue  785 ASN
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 1094 LEU
Chi-restraints excluded: chain B residue 1109 LEU
Chi-restraints excluded: chain B residue 1137 GLU
Chi-restraints excluded: chain B residue 1142 LEU
Chi-restraints excluded: chain B residue 1152 VAL
Chi-restraints excluded: chain B residue 1196 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 57 optimal weight:    2.9990
   chunk 28 optimal weight:    0.0670
   chunk 3 optimal weight:    3.9990
   chunk 107 optimal weight:    3.9990
   chunk 119 optimal weight:    0.9980
   chunk 53 optimal weight:    0.0870
   chunk 139 optimal weight:    2.9990
   chunk 49 optimal weight:    1.9990
   chunk 121 optimal weight:    0.5980
   chunk 13 optimal weight:    3.9990
   chunk 129 optimal weight:    5.9990
   overall best weight:    0.7498

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

Flipped N/Q/H residues before XYZ refinement:
A 391 GLN
A 628 HIS
A 853 HIS
** B 586 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 628 HIS
B 785 ASN
B 853 HIS

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3889 r_free = 0.3889 target = 0.170553 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3447 r_free = 0.3447 target = 0.129258 restraints weight = 13057.591|
|-----------------------------------------------------------------------------|
r_work (start): 0.3310 rms_B_bonded: 2.33
r_work: 0.3148 rms_B_bonded: 3.24 restraints_weight: 0.5000
r_work (final): 0.3148
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7739
moved from start:          0.1566

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= 0.119
  Angle     :  0.503   6.548  16870  Z= 0.261
  Chirality :  0.040   0.147   1978
  Planarity :  0.004   0.053   2110
  Dihedral  :  3.947  24.396   1642
  Min Nonbonded Distance : 2.506

Molprobity Statistics.
  All-atom Clashscore : 4.56
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  4.62 %
    Favored  : 95.25 %
  Rotamer:
    Outliers :  3.16 %
    Allowed  : 19.25 %
    Favored  : 77.59 %
  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:  0.59 (0.22), residues: 1516
  helix:  1.36 (0.18), residues: 874
  sheet:  0.97 (0.48), residues: 110
  loop : -1.41 (0.26), residues: 532

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 346 
 HIS   0.011   0.001   HIS A 586 
 PHE   0.019   0.001   PHE A1189 
 TYR   0.007   0.001   TYR A 569 
 ARG   0.006   0.000   ARG A 701 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05202 (  625)
  hydrogen bonds       : angle       3.76556 ( 1842)
  covalent geometry    : bond        0.00271 (12444)
  covalent geometry    : angle       0.50274 (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
  212 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 170
  time to evaluate  : 2.766 
Fit side-chains
REVERT: A  382 HIS cc_start: 0.6926 (p-80) cc_final: 0.6719 (p-80)
REVERT: A 1156 LYS cc_start: 0.8219 (mtpt) cc_final: 0.7680 (mptt)
REVERT: A 1172 LEU cc_start: 0.8293 (tp) cc_final: 0.8066 (tp)
REVERT: B  586 HIS cc_start: 0.7213 (OUTLIER) cc_final: 0.6827 (p90)
REVERT: B  590 TYR cc_start: 0.7487 (OUTLIER) cc_final: 0.6224 (t80)
REVERT: B  701 ARG cc_start: 0.8005 (ttm170) cc_final: 0.7772 (ttm-80)
REVERT: B  981 ASN cc_start: 0.8421 (p0) cc_final: 0.8158 (p0)
REVERT: B 1156 LYS cc_start: 0.8105 (mtpt) cc_final: 0.7564 (mptt)
  outliers start: 42
  outliers final: 38
  residues processed: 198
  average time/residue: 0.4428
  time to fit residues: 131.7348
Evaluate side-chains
  210 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 170
  time to evaluate  : 1.364 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  321 HIS
Chi-restraints excluded: chain A residue  323 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  591 LEU
Chi-restraints excluded: chain A residue  623 LEU
Chi-restraints excluded: chain A residue  697 LEU
Chi-restraints excluded: chain A residue  721 SER
Chi-restraints excluded: chain A residue  740 VAL
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 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  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  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 1094 LEU
Chi-restraints excluded: chain B residue 1109 LEU
Chi-restraints excluded: chain B residue 1137 GLU
Chi-restraints excluded: chain B residue 1142 LEU
Chi-restraints excluded: chain B residue 1152 VAL
Chi-restraints excluded: chain B residue 1196 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 144 optimal weight:    2.9990
   chunk 108 optimal weight:    2.9990
   chunk 119 optimal weight:    2.9990
   chunk 34 optimal weight:    3.9990
   chunk 101 optimal weight:    5.9990
   chunk 132 optimal weight:    0.9990
   chunk 141 optimal weight:    1.9990
   chunk 106 optimal weight:    1.9990
   chunk 43 optimal weight:    3.9990
   chunk 85 optimal weight:    9.9990
   chunk 109 optimal weight:    2.9990
   overall best weight:    2.1990

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

Flipped N/Q/H residues before XYZ refinement:
A 853 HIS
B 628 HIS
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 = 0.3816 r_free = 0.3816 target = 0.163784 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3367 r_free = 0.3367 target = 0.122250 restraints weight = 13215.091|
|-----------------------------------------------------------------------------|
r_work (start): 0.3273 rms_B_bonded: 2.42
r_work: 0.3101 rms_B_bonded: 3.16 restraints_weight: 0.5000
r_work (final): 0.3101
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7827
moved from start:          0.1595

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.047  12444  Z= 0.229
  Angle     :  0.623   6.542  16870  Z= 0.321
  Chirality :  0.045   0.174   1978
  Planarity :  0.005   0.054   2110
  Dihedral  :  4.281  29.293   1642
  Min Nonbonded Distance : 2.498

Molprobity Statistics.
  All-atom Clashscore : 4.64
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  5.87 %
    Favored  : 94.00 %
  Rotamer:
    Outliers :  3.83 %
    Allowed  : 18.57 %
    Favored  : 77.59 %
  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:  0.08 (0.22), residues: 1516
  helix:  0.85 (0.18), residues: 878
  sheet:  0.92 (0.47), residues: 110
  loop : -1.48 (0.26), residues: 528

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP A 340 
 HIS   0.011   0.002   HIS A 586 
 PHE   0.025   0.002   PHE B1189 
 TYR   0.011   0.002   TYR A 789 
 ARG   0.006   0.000   ARG A 701 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.07365 (  625)
  hydrogen bonds       : angle       4.04282 ( 1842)
  covalent geometry    : bond        0.00575 (12444)
  covalent geometry    : angle       0.62262 (16870)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 6503.22 seconds
wall clock time: 117 minutes 35.86 seconds (7055.86 seconds total)