Starting phenix.real_space_refine
on Thu Sep 26 18:40:45 2024 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zy6_11551/09_2024/6zy6_11551.cif
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zy6_11551/09_2024/6zy6_11551.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.1
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zy6_11551/09_2024/6zy6_11551.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zy6_11551/09_2024/6zy6_11551.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zy6_11551/09_2024/6zy6_11551.cif"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zy6_11551/09_2024/6zy6_11551.cif"
  }
  resolution = 4.1
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.005 sd=   0.065
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
     P      56      5.49       5
     S      52      5.16       5
     C    8418      2.51       5
     N    2312      2.21       5
     O    2666      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 4 residue(s): 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib"
  Total number of atoms: 13504
  Number of models: 1
  Model: ""
    Number of chains: 8
    Chain: "A"
      Number of atoms: 6101
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 760, 6101
          Classifications: {'peptide': 760}
          Incomplete info: {'truncation_to_alanine': 15}
          Link IDs: {'PTRANS': 34, 'TRANS': 725}
          Chain breaks: 1
          Unresolved chain link angles: 2
          Unresolved non-hydrogen bonds: 51
          Unresolved non-hydrogen angles: 59
          Unresolved non-hydrogen dihedrals: 45
          Unresolved non-hydrogen chiralities: 3
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 13
    Chain: "B"
      Number of atoms: 6101
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 760, 6101
          Classifications: {'peptide': 760}
          Incomplete info: {'truncation_to_alanine': 15}
          Link IDs: {'PTRANS': 34, 'TRANS': 725}
          Chain breaks: 1
          Unresolved chain link angles: 2
          Unresolved non-hydrogen bonds: 51
          Unresolved non-hydrogen angles: 59
          Unresolved non-hydrogen dihedrals: 45
          Unresolved non-hydrogen chiralities: 3
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 13
    Chain: "D"
      Number of atoms: 337
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 17, 337
          Classifications: {'DNA': 17}
          Modifications used: {'5*END': 1}
          Link IDs: {'rna3p': 16}
    Chain: "E"
      Number of atoms: 272
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 13, 272
          Classifications: {'DNA': 13}
          Modifications used: {'5*END': 1}
          Link IDs: {'rna3p': 12}
    Chain: "F"
      Number of atoms: 337
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 17, 337
          Classifications: {'DNA': 17}
          Modifications used: {'5*END': 1}
          Link IDs: {'rna3p': 16}
    Chain: "C"
      Number of atoms: 272
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 13, 272
          Classifications: {'DNA': 13}
          Modifications used: {'5*END': 1}
          Link IDs: {'rna3p': 12}
    Chain: "D"
      Number of atoms: 42
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 42
          Unusual residues: {'EVP': 1}
          Classifications: {'undetermined': 1}
    Chain: "F"
      Number of atoms: 42
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 42
          Unusual residues: {'EVP': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 8.03, per 1000 atoms: 0.59
  Number of scatterers: 13504
  At special positions: 0
  Unit cell: (100.969, 119.053, 122.067, 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)
     S      52     16.00
     P      56     15.00
     O    2666      8.00
     N    2312      7.00
     C    8418      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: 3.31
  Conformation dependent library (CDL) restraints added in 1.6 seconds
  

  3024 Ramachandran restraints generated.
    1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2848

  Finding SS restraints...
    Secondary structure from input PDB file:
      62 helices and 16 sheets defined
      50.7% alpha, 6.7% beta
      30 base pairs and 40 stacking pairs defined.
    Time for finding SS restraints: 4.73
  Creating SS restraints...
    Processing helix  chain 'A' and resid 463 through 477
      removed outlier: 3.642A  pdb=" N   THR A 467 " --> pdb=" O   ASP A 463 " (cutoff:3.500A)
      removed outlier: 3.970A  pdb=" N   GLY A 474 " --> pdb=" O   VAL A 470 " (cutoff:3.500A)
      removed outlier: 5.370A  pdb=" N   VAL A 475 " --> pdb=" O   SER A 471 " (cutoff:3.500A)
      removed outlier: 4.120A  pdb=" N   VAL A 476 " --> pdb=" O   GLY A 472 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 497 through 502
      removed outlier: 3.691A  pdb=" N   MET A 502 " --> pdb=" O   HIS A 498 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 504 through 515
      removed outlier: 3.683A  pdb=" N   ILE A 511 " --> pdb=" O   ILE A 507 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 524 through 531
      removed outlier: 3.612A  pdb=" N   LEU A 531 " --> pdb=" O   SER A 527 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 544 through 559
      removed outlier: 3.960A  pdb=" N   HIS A 548 " --> pdb=" O   GLN A 544 " (cutoff:3.500A)
      removed outlier: 3.643A  pdb=" N   ILE A 549 " --> pdb=" O   ASP A 545 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 562 through 567
      removed outlier: 3.691A  pdb=" N   ARG A 566 " --> pdb=" O   SER A 563 " (cutoff:3.500A)
      removed outlier: 3.978A  pdb=" N   HIS A 567 " --> pdb=" O   LEU A 564 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 591 through 602
    Processing helix  chain 'A' and resid 620 through 630
      removed outlier: 3.585A  pdb=" N   GLU A 626 " --> pdb=" O   LYS A 622 " (cutoff:3.500A)
      removed outlier: 3.720A  pdb=" N   ASP A 630 " --> pdb=" O   GLU A 626 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 630 through 635
      removed outlier: 4.036A  pdb=" N   HIS A 634 " --> pdb=" O   ASP A 630 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 643 through 652
      removed outlier: 3.744A  pdb=" N   ALA A 647 " --> pdb=" O   PRO A 643 " (cutoff:3.500A)
      removed outlier: 3.534A  pdb=" N   ALA A 648 " --> pdb=" O   GLU A 644 " (cutoff:3.500A)
      removed outlier: 3.663A  pdb=" N   ALA A 652 " --> pdb=" O   ALA A 648 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 657 through 679
    Processing helix  chain 'A' and resid 694 through 702
    Processing helix  chain 'A' and resid 702 through 715
      removed outlier: 3.567A  pdb=" N   PHE A 706 " --> pdb=" O   GLU A 702 " (cutoff:3.500A)
      removed outlier: 3.674A  pdb=" N   ILE A 715 " --> pdb=" O   ASN A 711 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 723 through 736
      removed outlier: 3.639A  pdb=" N   ARG A 736 " --> pdb=" O   THR A 732 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 744 through 755
      removed outlier: 3.582A  pdb=" N   GLY A 749 " --> pdb=" O   ALA A 745 " (cutoff:3.500A)
      removed outlier: 3.553A  pdb=" N   SER A 750 " --> pdb=" O   GLN A 746 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 761 through 773
    Processing helix  chain 'A' and resid 813 through 818
    Processing helix  chain 'A' and resid 819 through 825
      removed outlier: 3.891A  pdb=" N   HIS A 824 " --> pdb=" O   LYS A 821 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 847 through 852
    Processing helix  chain 'A' and resid 869 through 882
      removed outlier: 3.906A  pdb=" N   VAL A 873 " --> pdb=" O   VAL A 869 " (cutoff:3.500A)
      removed outlier: 3.708A  pdb=" N   ASN A 874 " --> pdb=" O   ARG A 870 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 931 through 945
      removed outlier: 4.684A  pdb=" N   GLU A 941 " --> pdb=" O   GLU A 937 " (cutoff:3.500A)
      Proline residue:  A 942  - end of helix
      removed outlier: 3.642A  pdb=" N   ASN A 945 " --> pdb=" O   GLU A 941 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 973 through 984
      removed outlier: 3.678A  pdb=" N   ALA A 978 " --> pdb=" O   GLU A 974 " (cutoff:3.500A)
      removed outlier: 3.815A  pdb=" N   GLU A 979 " --> pdb=" O   GLU A 975 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 984 through 989
    Processing helix  chain 'A' and resid 1014 through 1038
      removed outlier: 3.811A  pdb=" N   ILE A1018 " --> pdb=" O   THR A1014 " (cutoff:3.500A)
      removed outlier: 3.950A  pdb=" N   TYR A1029 " --> pdb=" O   LEU A1025 " (cutoff:3.500A)
      removed outlier: 3.686A  pdb=" N   TYR A1030 " --> pdb=" O   ARG A1026 " (cutoff:3.500A)
      removed outlier: 4.540A  pdb=" N   GLY A1031 " --> pdb=" O   LEU A1027 " (cutoff:3.500A)
      removed outlier: 4.269A  pdb=" N   LEU A1032 " --> pdb=" O   LYS A1028 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1039 through 1061
      removed outlier: 3.606A  pdb=" N   GLU A1044 " --> pdb=" O   MET A1040 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1069 through 1080
    Processing helix  chain 'A' and resid 1085 through 1093
    Processing helix  chain 'A' and resid 1125 through 1129
    Processing helix  chain 'A' and resid 1132 through 1136
      removed outlier: 3.696A  pdb=" N   TYR A1135 " --> pdb=" O   PRO A1132 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1137 through 1161
      removed outlier: 3.708A  pdb=" N   ARG A1146 " --> pdb=" O   ASP A1142 " (cutoff:3.500A)
      removed outlier: 4.168A  pdb=" N   ASN A1149 " --> pdb=" O   CYS A1145 " (cutoff:3.500A)
      removed outlier: 3.664A  pdb=" N   LYS A1151 " --> pdb=" O   LEU A1147 " (cutoff:3.500A)
      removed outlier: 3.728A  pdb=" N   GLU A1152 " --> pdb=" O   ARG A1148 " (cutoff:3.500A)
      removed outlier: 3.616A  pdb=" N   GLU A1154 " --> pdb=" O   GLU A1150 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1165 through 1192
      removed outlier: 3.917A  pdb=" N   GLU A1169 " --> pdb=" O   ASP A1165 " (cutoff:3.500A)
      removed outlier: 4.052A  pdb=" N   THR A1173 " --> pdb=" O   GLU A1169 " (cutoff:3.500A)
      removed outlier: 3.619A  pdb=" N   PHE A1174 " --> pdb=" O   ASP A1170 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 463 through 477
      removed outlier: 3.639A  pdb=" N   THR B 467 " --> pdb=" O   ASP B 463 " (cutoff:3.500A)
      removed outlier: 3.969A  pdb=" N   GLY B 474 " --> pdb=" O   VAL B 470 " (cutoff:3.500A)
      removed outlier: 5.373A  pdb=" N   VAL B 475 " --> pdb=" O   SER B 471 " (cutoff:3.500A)
      removed outlier: 4.121A  pdb=" N   VAL B 476 " --> pdb=" O   GLY B 472 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 497 through 502
      removed outlier: 3.692A  pdb=" N   MET B 502 " --> pdb=" O   HIS B 498 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 504 through 515
      removed outlier: 3.684A  pdb=" N   ILE B 511 " --> pdb=" O   ILE B 507 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 524 through 531
      removed outlier: 3.612A  pdb=" N   LEU B 531 " --> pdb=" O   SER B 527 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 544 through 559
      removed outlier: 3.959A  pdb=" N   HIS B 548 " --> pdb=" O   GLN B 544 " (cutoff:3.500A)
      removed outlier: 3.641A  pdb=" N   ILE B 549 " --> pdb=" O   ASP B 545 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 562 through 567
      removed outlier: 3.691A  pdb=" N   ARG B 566 " --> pdb=" O   SER B 563 " (cutoff:3.500A)
      removed outlier: 3.978A  pdb=" N   HIS B 567 " --> pdb=" O   LEU B 564 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 591 through 602
    Processing helix  chain 'B' and resid 620 through 630
      removed outlier: 3.589A  pdb=" N   GLU B 626 " --> pdb=" O   LYS B 622 " (cutoff:3.500A)
      removed outlier: 3.720A  pdb=" N   ASP B 630 " --> pdb=" O   GLU B 626 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 630 through 635
      removed outlier: 4.036A  pdb=" N   HIS B 634 " --> pdb=" O   ASP B 630 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 643 through 652
      removed outlier: 3.746A  pdb=" N   ALA B 647 " --> pdb=" O   PRO B 643 " (cutoff:3.500A)
      removed outlier: 3.534A  pdb=" N   ALA B 648 " --> pdb=" O   GLU B 644 " (cutoff:3.500A)
      removed outlier: 3.662A  pdb=" N   ALA B 652 " --> pdb=" O   ALA B 648 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 657 through 679
    Processing helix  chain 'B' and resid 694 through 702
    Processing helix  chain 'B' and resid 702 through 715
      removed outlier: 3.566A  pdb=" N   PHE B 706 " --> pdb=" O   GLU B 702 " (cutoff:3.500A)
      removed outlier: 3.671A  pdb=" N   ILE B 715 " --> pdb=" O   ASN B 711 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 723 through 736
      removed outlier: 3.638A  pdb=" N   ARG B 736 " --> pdb=" O   THR B 732 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 744 through 755
      removed outlier: 3.582A  pdb=" N   GLY B 749 " --> pdb=" O   ALA B 745 " (cutoff:3.500A)
      removed outlier: 3.554A  pdb=" N   SER B 750 " --> pdb=" O   GLN B 746 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 761 through 773
    Processing helix  chain 'B' and resid 813 through 818
    Processing helix  chain 'B' and resid 819 through 825
      removed outlier: 3.890A  pdb=" N   HIS B 824 " --> pdb=" O   LYS B 821 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 847 through 852
    Processing helix  chain 'B' and resid 869 through 882
      removed outlier: 3.906A  pdb=" N   VAL B 873 " --> pdb=" O   VAL B 869 " (cutoff:3.500A)
      removed outlier: 3.708A  pdb=" N   ASN B 874 " --> pdb=" O   ARG B 870 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 931 through 945
      removed outlier: 4.685A  pdb=" N   GLU B 941 " --> pdb=" O   GLU B 937 " (cutoff:3.500A)
      Proline residue:  B 942  - end of helix
      removed outlier: 3.643A  pdb=" N   ASN B 945 " --> pdb=" O   GLU B 941 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 973 through 984
      removed outlier: 3.680A  pdb=" N   ALA B 978 " --> pdb=" O   GLU B 974 " (cutoff:3.500A)
      removed outlier: 3.817A  pdb=" N   GLU B 979 " --> pdb=" O   GLU B 975 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 984 through 989
    Processing helix  chain 'B' and resid 1014 through 1038
      removed outlier: 3.811A  pdb=" N   ILE B1018 " --> pdb=" O   THR B1014 " (cutoff:3.500A)
      removed outlier: 3.949A  pdb=" N   TYR B1029 " --> pdb=" O   LEU B1025 " (cutoff:3.500A)
      removed outlier: 3.686A  pdb=" N   TYR B1030 " --> pdb=" O   ARG B1026 " (cutoff:3.500A)
      removed outlier: 4.540A  pdb=" N   GLY B1031 " --> pdb=" O   LEU B1027 " (cutoff:3.500A)
      removed outlier: 4.268A  pdb=" N   LEU B1032 " --> pdb=" O   LYS B1028 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1039 through 1061
      removed outlier: 3.605A  pdb=" N   GLU B1044 " --> pdb=" O   MET B1040 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1069 through 1080
    Processing helix  chain 'B' and resid 1085 through 1093
    Processing helix  chain 'B' and resid 1125 through 1129
    Processing helix  chain 'B' and resid 1132 through 1136
      removed outlier: 3.695A  pdb=" N   TYR B1135 " --> pdb=" O   PRO B1132 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1137 through 1161
      removed outlier: 3.708A  pdb=" N   ARG B1146 " --> pdb=" O   ASP B1142 " (cutoff:3.500A)
      removed outlier: 4.169A  pdb=" N   ASN B1149 " --> pdb=" O   CYS B1145 " (cutoff:3.500A)
      removed outlier: 3.665A  pdb=" N   LYS B1151 " --> pdb=" O   LEU B1147 " (cutoff:3.500A)
      removed outlier: 3.727A  pdb=" N   GLU B1152 " --> pdb=" O   ARG B1148 " (cutoff:3.500A)
      removed outlier: 3.616A  pdb=" N   GLU B1154 " --> pdb=" O   GLU B1150 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1165 through 1192
      removed outlier: 3.917A  pdb=" N   GLU B1169 " --> pdb=" O   ASP B1165 " (cutoff:3.500A)
      removed outlier: 4.053A  pdb=" N   THR B1173 " --> pdb=" O   GLU B1169 " (cutoff:3.500A)
      removed outlier: 3.619A  pdb=" N   PHE B1174 " --> pdb=" O   ASP B1170 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 482 through 485
      removed outlier: 6.285A  pdb=" N   ILE A 536 " --> pdb=" O   GLU A 571 " (cutoff:3.500A)
      removed outlier: 7.326A  pdb=" N   PHE A 573 " --> pdb=" O   ILE A 536 " (cutoff:3.500A)
      removed outlier: 6.330A  pdb=" N   ILE A 538 " --> pdb=" O   PHE A 573 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 586 through 589
      removed outlier: 3.713A  pdb=" N   VAL A 580 " --> pdb=" O   MET A 587 " (cutoff:3.500A)
      removed outlier: 3.687A  pdb=" N   PHE A 589 " --> pdb=" O   VAL A 578 " (cutoff:3.500A)
      removed outlier: 3.865A  pdb=" N   VAL A 578 " --> pdb=" O   PHE A 589 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 742 through 743
    Processing sheet with id=AA4, first strand: chain 'A' and resid 830 through 831
      removed outlier: 3.794A  pdb=" N   ASP A 831 " --> pdb=" O   GLN A 834 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 854 through 856
    Processing sheet with id=AA6, first strand: chain 'A' and resid 899 through 900
      removed outlier: 3.827A  pdb=" N   GLU A 900 " --> pdb=" O   VAL A 908 " (cutoff:3.500A)
      removed outlier: 3.786A  pdb=" N   VAL A 908 " --> pdb=" O   GLU A 900 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 912 through 914
      removed outlier: 6.213A  pdb=" N   GLU A 912 " --> pdb=" O   SER A 924 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 1001 through 1003
      removed outlier: 3.970A  pdb=" N   LEU A1002 " --> pdb=" O   LYS A1010 " (cutoff:3.500A)
      removed outlier: 3.842A  pdb=" N   LYS A1010 " --> pdb=" O   LEU A1002 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA8
    Processing sheet with id=AA9, first strand: chain 'B' and resid 482 through 485
      removed outlier: 6.286A  pdb=" N   ILE B 536 " --> pdb=" O   GLU B 571 " (cutoff:3.500A)
      removed outlier: 7.328A  pdb=" N   PHE B 573 " --> pdb=" O   ILE B 536 " (cutoff:3.500A)
      removed outlier: 6.330A  pdb=" N   ILE B 538 " --> pdb=" O   PHE B 573 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'B' and resid 586 through 589
      removed outlier: 3.713A  pdb=" N   VAL B 580 " --> pdb=" O   MET B 587 " (cutoff:3.500A)
      removed outlier: 3.686A  pdb=" N   PHE B 589 " --> pdb=" O   VAL B 578 " (cutoff:3.500A)
      removed outlier: 3.866A  pdb=" N   VAL B 578 " --> pdb=" O   PHE B 589 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'B' and resid 742 through 743
    Processing sheet with id=AB3, first strand: chain 'B' and resid 830 through 831
      removed outlier: 3.793A  pdb=" N   ASP B 831 " --> pdb=" O   GLN B 834 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'B' and resid 854 through 856
    Processing sheet with id=AB5, first strand: chain 'B' and resid 899 through 900
      removed outlier: 3.825A  pdb=" N   GLU B 900 " --> pdb=" O   VAL B 908 " (cutoff:3.500A)
      removed outlier: 3.782A  pdb=" N   VAL B 908 " --> pdb=" O   GLU B 900 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'B' and resid 912 through 914
      removed outlier: 6.213A  pdb=" N   GLU B 912 " --> pdb=" O   SER B 924 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'B' and resid 1001 through 1003
      removed outlier: 3.967A  pdb=" N   LEU B1002 " --> pdb=" O   LYS B1010 " (cutoff:3.500A)
      removed outlier: 3.841A  pdb=" N   LYS B1010 " --> pdb=" O   LEU B1002 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB7

    494 hydrogen bonds defined for protein.
    1398 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      78 hydrogen bonds
      156 hydrogen bond angles
      0 basepair planarities
      30 basepair parallelities
      40 stacking parallelities
  Total time for adding SS restraints: 4.61

  Time building geometry restraints manager: 3.91 seconds

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

  Histogram of bond lengths:
        1.20 -     1.32: 2441
        1.32 -     1.45: 3612
        1.45 -     1.57: 7651
        1.57 -     1.69: 112
        1.69 -     1.81: 92
  Bond restraints: 13908
  Sorted by residual:
  bond pdb=" N   VAL A 939 "
       pdb=" CA  VAL A 939 "
    ideal  model  delta    sigma   weight residual
    1.458  1.490 -0.032 9.00e-03 1.23e+04 1.29e+01
  bond pdb=" N   VAL B 939 "
       pdb=" CA  VAL B 939 "
    ideal  model  delta    sigma   weight residual
    1.458  1.489 -0.032 9.00e-03 1.23e+04 1.24e+01
  bond pdb=" N   ILE A 438 "
       pdb=" CA  ILE A 438 "
    ideal  model  delta    sigma   weight residual
    1.457  1.488 -0.031 9.00e-03 1.23e+04 1.15e+01
  bond pdb=" N   ILE B 438 "
       pdb=" CA  ILE B 438 "
    ideal  model  delta    sigma   weight residual
    1.457  1.488 -0.030 9.00e-03 1.23e+04 1.14e+01
  bond pdb=" N   ILE B 864 "
       pdb=" CA  ILE B 864 "
    ideal  model  delta    sigma   weight residual
    1.456  1.485 -0.028 8.70e-03 1.32e+04 1.06e+01
  ... (remaining 13903 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.08: 13176
        1.08 -     2.17: 5044
        2.17 -     3.25: 744
        3.25 -     4.34: 60
        4.34 -     5.42: 6
  Bond angle restraints: 19030
  Sorted by residual:
  angle pdb=" N   ILE B1065 "
        pdb=" CA  ILE B1065 "
        pdb=" C   ILE B1065 "
      ideal   model   delta    sigma   weight residual
     111.91  108.89    3.02 8.90e-01 1.26e+00 1.15e+01
  angle pdb=" N   ILE A1065 "
        pdb=" CA  ILE A1065 "
        pdb=" C   ILE A1065 "
      ideal   model   delta    sigma   weight residual
     111.91  108.91    3.00 8.90e-01 1.26e+00 1.14e+01
  angle pdb=" C   GLY A 437 "
        pdb=" N   ILE A 438 "
        pdb=" CA  ILE A 438 "
      ideal   model   delta    sigma   weight residual
     123.33  120.41    2.92 8.70e-01 1.32e+00 1.13e+01
  angle pdb=" C   GLY B 437 "
        pdb=" N   ILE B 438 "
        pdb=" CA  ILE B 438 "
      ideal   model   delta    sigma   weight residual
     123.33  120.41    2.92 8.70e-01 1.32e+00 1.13e+01
  angle pdb=" CA  GLU B1066 "
        pdb=" C   GLU B1066 "
        pdb=" O   GLU B1066 "
      ideal   model   delta    sigma   weight residual
     122.64  118.66    3.98 1.25e+00 6.40e-01 1.02e+01
  ... (remaining 19025 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.97: 8145
       35.97 -    71.95: 231
       71.95 -   107.92: 2
      107.92 -   143.89: 4
      143.89 -   179.87: 2
  Dihedral angle restraints: 8384
    sinusoidal: 3964
      harmonic: 4420
  Sorted by residual:
  dihedral pdb=" C   ASN B 604 "
           pdb=" N   ASN B 604 "
           pdb=" CA  ASN B 604 "
           pdb=" CB  ASN B 604 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -133.46   10.86     0      2.50e+00 1.60e-01 1.89e+01
  dihedral pdb=" C   ASN A 604 "
           pdb=" N   ASN A 604 "
           pdb=" CA  ASN A 604 "
           pdb=" CB  ASN A 604 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -133.41   10.81     0      2.50e+00 1.60e-01 1.87e+01
  dihedral pdb=" C4'  DG D   9 "
           pdb=" C3'  DG D   9 "
           pdb=" O3'  DG D   9 "
           pdb=" P    DT D  10 "
      ideal   model   delta sinusoidal    sigma   weight residual
     220.00   40.13  179.87     1      3.50e+01 8.16e-04 1.57e+01
  ... (remaining 8381 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.075: 1440
       0.075 -    0.149: 523
       0.149 -    0.224: 121
       0.224 -    0.299: 6
       0.299 -    0.374: 4
  Chirality restraints: 2094
  Sorted by residual:
  chirality pdb=" CA  ASN B 604 "
            pdb=" N   ASN B 604 "
            pdb=" C   ASN B 604 "
            pdb=" CB  ASN B 604 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.14    0.37 2.00e-01 2.50e+01 3.49e+00
  chirality pdb=" CA  ASN A 604 "
            pdb=" N   ASN A 604 "
            pdb=" C   ASN A 604 "
            pdb=" CB  ASN A 604 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.14    0.37 2.00e-01 2.50e+01 3.45e+00
  chirality pdb=" C9  EVP F 101 "
            pdb=" C10 EVP F 101 "
            pdb=" C6  EVP F 101 "
            pdb=" C8  EVP F 101 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.49    2.81   -0.32 2.00e-01 2.50e+01 2.51e+00
  ... (remaining 2091 not shown)

  Planarity restraints: 2220
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PRO B 603 "    0.016 2.00e-02 2.50e+03   3.25e-02 1.05e+01
        pdb=" C   PRO B 603 "   -0.056 2.00e-02 2.50e+03
        pdb=" O   PRO B 603 "    0.021 2.00e-02 2.50e+03
        pdb=" N   ASN B 604 "    0.019 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PRO A 603 "   -0.016 2.00e-02 2.50e+03   3.22e-02 1.04e+01
        pdb=" C   PRO A 603 "    0.056 2.00e-02 2.50e+03
        pdb=" O   PRO A 603 "   -0.021 2.00e-02 2.50e+03
        pdb=" N   ASN A 604 "   -0.019 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLY A 617 "    0.014 2.00e-02 2.50e+03   2.88e-02 8.32e+00
        pdb=" C   GLY A 617 "   -0.050 2.00e-02 2.50e+03
        pdb=" O   GLY A 617 "    0.019 2.00e-02 2.50e+03
        pdb=" N   THR A 618 "    0.017 2.00e-02 2.50e+03
  ... (remaining 2217 not shown)

  Histogram of nonbonded interaction distances:
        2.30 -     2.82: 3891
        2.82 -     3.34: 12123
        3.34 -     3.86: 21350
        3.86 -     4.38: 24247
        4.38 -     4.90: 39727
  Nonbonded interactions: 101338
  Sorted by model distance:
  nonbonded pdb=" OG  SER A1045 "
            pdb=" OE2 GLU A1152 "
     model   vdw
     2.304 3.040
  nonbonded pdb=" OG  SER B1045 "
            pdb=" OE2 GLU B1152 "
     model   vdw
     2.304 3.040
  nonbonded pdb=" OG1 THR A 456 "
            pdb=" O   LYS A 480 "
     model   vdw
     2.326 3.040
  nonbonded pdb=" OG1 THR B 456 "
            pdb=" O   LYS B 480 "
     model   vdw
     2.327 3.040
  nonbonded pdb=" O   ASP A 524 "
            pdb=" OG  SER A 527 "
     model   vdw
     2.349 3.040
  ... (remaining 101333 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}
ncs_group {
  reference = chain 'C'
  selection = chain 'E'
}
ncs_group {
  reference = chain 'D'
  selection = chain 'F'
}

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 group one per residue
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:             0.680
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.020
  Extract box with map and model:          0.470
  Check model and map are aligned:         0.100
  Set scattering table:                    0.130
  Process input model:                     35.300
  Find NCS groups from input model:        0.340
  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:             0.000
  Load rotamer database and sin/cos tables:2.670
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   39.770
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7683
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      :  0.010   0.040  13908  Z= 0.661
  Angle     :  1.070   5.421  19030  Z= 0.811
  Chirality :  0.079   0.374   2094
  Planarity :  0.007   0.032   2220
  Dihedral  : 13.750 179.868   5536
  Min Nonbonded Distance : 2.304

Molprobity Statistics.
  All-atom Clashscore : 5.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.59 %
    Favored  : 98.41 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.11 %
    Favored  : 97.89 %
  Cbeta Deviations :  0.14 %
  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: -0.70 (0.21), residues: 1512
  helix:  1.33 (0.19), residues: 650
  sheet: -1.64 (0.44), residues: 154
  loop : -1.98 (0.22), residues: 708

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP A 664 
 HIS   0.006   0.001   HIS A 634 
 PHE   0.008   0.002   PHE A1003 
 TYR   0.010   0.002   TYR B 590 
 ARG   0.007   0.001   ARG B 929 

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

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

  3024 Ramachandran restraints generated.
    1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3024 Ramachandran restraints generated.
    1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  421 residues out of total 1358 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 421
  time to evaluate  : 1.518 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  486 LEU cc_start: 0.8294 (mt) cc_final: 0.7579 (mt)
REVERT: A  526 ASP cc_start: 0.9352 (m-30) cc_final: 0.8966 (t0)
REVERT: A  537 MET cc_start: 0.7995 (ttp) cc_final: 0.7622 (ttt)
REVERT: A  552 LEU cc_start: 0.8969 (mt) cc_final: 0.8613 (mt)
REVERT: A  573 PHE cc_start: 0.9095 (t80) cc_final: 0.8758 (t80)
REVERT: A  675 ARG cc_start: 0.9395 (mtt180) cc_final: 0.8940 (mtp85)
REVERT: A  754 MET cc_start: 0.9090 (mtt) cc_final: 0.8795 (mpp)
REVERT: A  795 HIS cc_start: 0.8240 (m90) cc_final: 0.7232 (m90)
REVERT: A  809 MET cc_start: 0.8202 (ttt) cc_final: 0.7991 (tpp)
REVERT: A  815 ARG cc_start: 0.8721 (mmm160) cc_final: 0.8470 (mmm160)
REVERT: A  862 CYS cc_start: 0.8359 (t) cc_final: 0.7650 (p)
REVERT: A  932 THR cc_start: 0.8262 (m) cc_final: 0.7653 (p)
REVERT: A  956 ASP cc_start: 0.8527 (t0) cc_final: 0.8302 (t0)
REVERT: A 1000 MET cc_start: 0.8338 (mtt) cc_final: 0.7810 (mmm)
REVERT: A 1067 ASN cc_start: 0.7890 (m110) cc_final: 0.7684 (m-40)
REVERT: A 1128 LEU cc_start: 0.9283 (mt) cc_final: 0.8964 (mt)
REVERT: A 1138 LYS cc_start: 0.8332 (tttp) cc_final: 0.8130 (tmmt)
REVERT: A 1171 LEU cc_start: 0.8917 (mt) cc_final: 0.8695 (mt)
REVERT: B  486 LEU cc_start: 0.8293 (mt) cc_final: 0.7567 (mt)
REVERT: B  526 ASP cc_start: 0.9336 (m-30) cc_final: 0.8956 (t0)
REVERT: B  537 MET cc_start: 0.8025 (ttp) cc_final: 0.7613 (ttt)
REVERT: B  552 LEU cc_start: 0.9017 (mt) cc_final: 0.8685 (mt)
REVERT: B  573 PHE cc_start: 0.9091 (t80) cc_final: 0.8730 (t80)
REVERT: B  675 ARG cc_start: 0.9395 (mtt180) cc_final: 0.8940 (mtp85)
REVERT: B  702 GLU cc_start: 0.8718 (tt0) cc_final: 0.8501 (mm-30)
REVERT: B  754 MET cc_start: 0.9092 (mtt) cc_final: 0.8786 (mpp)
REVERT: B  795 HIS cc_start: 0.8239 (m90) cc_final: 0.7240 (m90)
REVERT: B  809 MET cc_start: 0.8216 (ttt) cc_final: 0.8009 (tpp)
REVERT: B  815 ARG cc_start: 0.8736 (mmm160) cc_final: 0.8482 (mmm160)
REVERT: B  862 CYS cc_start: 0.8256 (t) cc_final: 0.7571 (p)
REVERT: B  932 THR cc_start: 0.8283 (m) cc_final: 0.7666 (p)
REVERT: B  956 ASP cc_start: 0.8517 (t0) cc_final: 0.8301 (t0)
REVERT: B 1000 MET cc_start: 0.8348 (mtt) cc_final: 0.7838 (mmm)
REVERT: B 1128 LEU cc_start: 0.9266 (mt) cc_final: 0.8957 (mt)
REVERT: B 1138 LYS cc_start: 0.8333 (tttp) cc_final: 0.8129 (tmmt)
REVERT: B 1171 LEU cc_start: 0.8912 (mt) cc_final: 0.8692 (mt)
  outliers start: 0
  outliers final: 0
  residues processed: 421
  average time/residue: 0.2997
  time to fit residues: 173.9648
Evaluate side-chains
  203 residues out of total 1358 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 203
  time to evaluate  : 1.455 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 131 optimal weight:    2.9990
   chunk 118 optimal weight:    1.9990
   chunk 65 optimal weight:    3.9990
   chunk 40 optimal weight:    1.9990
   chunk 79 optimal weight:    2.9990
   chunk 63 optimal weight:    4.9990
   chunk 122 optimal weight:    0.9980
   chunk 47 optimal weight:    0.9990
   chunk 74 optimal weight:    9.9990
   chunk 91 optimal weight:    0.9980
   chunk 141 optimal weight:    3.9990
   overall best weight:    1.3986

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

Flipped N/Q/H residues before XYZ refinement:
A 500 GLN
A 795 HIS
A 824 HIS
** A 961 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 795 HIS
B 824 HIS
** B 961 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7904
moved from start:          0.3536

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.061  13908  Z= 0.225
  Angle     :  0.585   9.561  19030  Z= 0.297
  Chirality :  0.040   0.181   2094
  Planarity :  0.004   0.034   2220
  Dihedral  : 17.554 178.909   2420
  Min Nonbonded Distance : 2.498

Molprobity Statistics.
  All-atom Clashscore : 8.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.17 %
    Favored  : 96.83 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.51 %
    Favored  : 98.49 %
  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: -0.61 (0.22), residues: 1512
  helix:  1.34 (0.20), residues: 674
  sheet: -1.72 (0.44), residues: 160
  loop : -1.94 (0.22), residues: 678

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.002   TRP B1090 
 HIS   0.005   0.001   HIS A 634 
 PHE   0.012   0.001   PHE A 653 
 TYR   0.016   0.001   TYR B 686 
 ARG   0.006   0.001   ARG B1160 

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

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

  3024 Ramachandran restraints generated.
    1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3024 Ramachandran restraints generated.
    1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  239 residues out of total 1358 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 239
  time to evaluate  : 1.418 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  455 CYS cc_start: 0.8438 (m) cc_final: 0.7930 (m)
REVERT: A  526 ASP cc_start: 0.9372 (m-30) cc_final: 0.9134 (t0)
REVERT: A  537 MET cc_start: 0.8433 (ttp) cc_final: 0.7892 (ttt)
REVERT: A  539 MET cc_start: 0.7411 (ppp) cc_final: 0.7111 (ppp)
REVERT: A  701 LYS cc_start: 0.8806 (mmtp) cc_final: 0.8466 (tttt)
REVERT: A  712 GLU cc_start: 0.8435 (mt-10) cc_final: 0.7969 (mt-10)
REVERT: A  728 LYS cc_start: 0.9247 (mttt) cc_final: 0.8877 (mtpt)
REVERT: A  738 ASP cc_start: 0.7485 (m-30) cc_final: 0.7193 (m-30)
REVERT: A  754 MET cc_start: 0.9279 (mtt) cc_final: 0.9039 (mpp)
REVERT: A  815 ARG cc_start: 0.8708 (mmm160) cc_final: 0.8482 (mmm160)
REVERT: A  839 GLU cc_start: 0.8476 (mt-10) cc_final: 0.7818 (mm-30)
REVERT: A  856 ILE cc_start: 0.9100 (mt) cc_final: 0.8708 (tt)
REVERT: A  862 CYS cc_start: 0.8175 (t) cc_final: 0.7704 (p)
REVERT: A  959 GLU cc_start: 0.8040 (mp0) cc_final: 0.7793 (mp0)
REVERT: A 1000 MET cc_start: 0.8533 (mtt) cc_final: 0.7838 (mpp)
REVERT: A 1128 LEU cc_start: 0.9180 (mt) cc_final: 0.8954 (mt)
REVERT: A 1169 GLU cc_start: 0.9081 (tm-30) cc_final: 0.8827 (tm-30)
REVERT: A 1178 LEU cc_start: 0.9075 (tt) cc_final: 0.8711 (pp)
REVERT: B  455 CYS cc_start: 0.8412 (m) cc_final: 0.7924 (m)
REVERT: B  526 ASP cc_start: 0.9357 (m-30) cc_final: 0.9098 (t0)
REVERT: B  537 MET cc_start: 0.8457 (ttp) cc_final: 0.7867 (ttt)
REVERT: B  539 MET cc_start: 0.7373 (ppp) cc_final: 0.7062 (ppp)
REVERT: B  712 GLU cc_start: 0.8402 (mt-10) cc_final: 0.7938 (mt-10)
REVERT: B  728 LYS cc_start: 0.9244 (mttt) cc_final: 0.8874 (mtpt)
REVERT: B  738 ASP cc_start: 0.7492 (m-30) cc_final: 0.7187 (m-30)
REVERT: B  754 MET cc_start: 0.9279 (mtt) cc_final: 0.9036 (mpp)
REVERT: B  815 ARG cc_start: 0.8724 (mmm160) cc_final: 0.8496 (mmm160)
REVERT: B  839 GLU cc_start: 0.8432 (mt-10) cc_final: 0.7766 (mm-30)
REVERT: B  862 CYS cc_start: 0.8098 (t) cc_final: 0.7384 (p)
REVERT: B  912 GLU cc_start: 0.8415 (tt0) cc_final: 0.8204 (pt0)
REVERT: B  959 GLU cc_start: 0.8005 (mp0) cc_final: 0.7760 (mp0)
REVERT: B 1000 MET cc_start: 0.8551 (mtt) cc_final: 0.7869 (mpp)
REVERT: B 1036 TRP cc_start: 0.9021 (t-100) cc_final: 0.8705 (t-100)
REVERT: B 1128 LEU cc_start: 0.9174 (mt) cc_final: 0.8940 (mt)
REVERT: B 1169 GLU cc_start: 0.9080 (tm-30) cc_final: 0.8823 (tm-30)
REVERT: B 1178 LEU cc_start: 0.9083 (tt) cc_final: 0.8719 (pp)
  outliers start: 0
  outliers final: 0
  residues processed: 239
  average time/residue: 0.2477
  time to fit residues: 85.8029
Evaluate side-chains
  149 residues out of total 1358 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 149
  time to evaluate  : 1.585 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 78 optimal weight:    9.9990
   chunk 43 optimal weight:    1.9990
   chunk 117 optimal weight:    3.9990
   chunk 96 optimal weight:    2.9990
   chunk 39 optimal weight:    1.9990
   chunk 141 optimal weight:    4.9990
   chunk 153 optimal weight:    3.9990
   chunk 126 optimal weight:    0.9980
   chunk 140 optimal weight:    3.9990
   chunk 48 optimal weight:    4.9990
   chunk 113 optimal weight:    4.9990
   overall best weight:    2.3988

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

Flipped N/Q/H residues before XYZ refinement:
A 555 ASN
** A 961 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 509 ASN
B 555 ASN
** B 961 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8075
moved from start:          0.5365

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.089  13908  Z= 0.320
  Angle     :  0.675   8.965  19030  Z= 0.350
  Chirality :  0.043   0.165   2094
  Planarity :  0.005   0.060   2220
  Dihedral  : 17.860 176.416   2420
  Min Nonbonded Distance : 2.505

Molprobity Statistics.
  All-atom Clashscore : 9.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.37 %
    Favored  : 95.63 %
  Rotamer:
    Outliers :  0.15 %
    Allowed  :  1.96 %
    Favored  : 97.89 %
  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: -0.75 (0.21), residues: 1512
  helix:  1.25 (0.20), residues: 670
  sheet: -1.63 (0.44), residues: 150
  loop : -2.08 (0.22), residues: 692

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.038   0.003   TRP A1090 
 HIS   0.005   0.002   HIS B 605 
 PHE   0.011   0.002   PHE A 653 
 TYR   0.018   0.002   TYR A 907 
 ARG   0.005   0.001   ARG B 635 

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

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

  3024 Ramachandran restraints generated.
    1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3024 Ramachandran restraints generated.
    1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  178 residues out of total 1358 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 2
    poor density    : 176
  time to evaluate  : 1.552 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  537 MET cc_start: 0.8392 (ttp) cc_final: 0.7869 (ttt)
REVERT: A  712 GLU cc_start: 0.8550 (mt-10) cc_final: 0.8138 (mt-10)
REVERT: A  726 GLN cc_start: 0.8885 (mp10) cc_final: 0.8682 (mp10)
REVERT: A  728 LYS cc_start: 0.9290 (mttt) cc_final: 0.9019 (mtpt)
REVERT: A  766 MET cc_start: 0.9283 (mmp) cc_final: 0.9060 (mmp)
REVERT: A  767 THR cc_start: 0.9320 (m) cc_final: 0.9029 (m)
REVERT: A  768 ILE cc_start: 0.9495 (mm) cc_final: 0.9292 (mt)
REVERT: A  847 MET cc_start: 0.9138 (mmp) cc_final: 0.8905 (mmm)
REVERT: A  856 ILE cc_start: 0.9142 (mt) cc_final: 0.8894 (tt)
REVERT: A  862 CYS cc_start: 0.8488 (t) cc_final: 0.8217 (p)
REVERT: A  924 SER cc_start: 0.7315 (m) cc_final: 0.6529 (t)
REVERT: A  956 ASP cc_start: 0.8505 (t0) cc_final: 0.8288 (t0)
REVERT: A  977 LEU cc_start: 0.9096 (mt) cc_final: 0.8892 (mt)
REVERT: A 1000 MET cc_start: 0.8605 (mtt) cc_final: 0.8253 (mpp)
REVERT: A 1131 MET cc_start: 0.9171 (ttt) cc_final: 0.8861 (tpp)
REVERT: B  537 MET cc_start: 0.8272 (ttp) cc_final: 0.7584 (ttt)
REVERT: B  539 MET cc_start: 0.7534 (ppp) cc_final: 0.7184 (ppp)
REVERT: B  712 GLU cc_start: 0.8566 (mt-10) cc_final: 0.8153 (mt-10)
REVERT: B  728 LYS cc_start: 0.9286 (mttt) cc_final: 0.9016 (mtpt)
REVERT: B  766 MET cc_start: 0.9299 (mmp) cc_final: 0.9094 (mmp)
REVERT: B  767 THR cc_start: 0.9301 (m) cc_final: 0.9007 (m)
REVERT: B  768 ILE cc_start: 0.9505 (mm) cc_final: 0.9300 (mt)
REVERT: B  847 MET cc_start: 0.9015 (mmm) cc_final: 0.8736 (mmm)
REVERT: B  862 CYS cc_start: 0.8545 (t) cc_final: 0.8299 (p)
REVERT: B  912 GLU cc_start: 0.8607 (tt0) cc_final: 0.8002 (tp30)
REVERT: B  956 ASP cc_start: 0.8492 (t0) cc_final: 0.8286 (t0)
REVERT: B  977 LEU cc_start: 0.9100 (mt) cc_final: 0.8897 (mt)
REVERT: B 1000 MET cc_start: 0.8645 (mtt) cc_final: 0.8287 (mpp)
REVERT: B 1131 MET cc_start: 0.9175 (ttt) cc_final: 0.8867 (tpp)
  outliers start: 2
  outliers final: 0
  residues processed: 178
  average time/residue: 0.2690
  time to fit residues: 68.9070
Evaluate side-chains
  123 residues out of total 1358 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 123
  time to evaluate  : 1.593 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 140 optimal weight:    2.9990
   chunk 106 optimal weight:    2.9990
   chunk 73 optimal weight:    4.9990
   chunk 15 optimal weight:    0.9990
   chunk 67 optimal weight:    0.9980
   chunk 95 optimal weight:    6.9990
   chunk 142 optimal weight:    4.9990
   chunk 150 optimal weight:    5.9990
   chunk 74 optimal weight:    4.9990
   chunk 134 optimal weight:    1.9990
   chunk 40 optimal weight:    5.9990
   overall best weight:    1.9988

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

Flipped N/Q/H residues before XYZ refinement:
** A 555 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 559 HIS
** A 961 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A1067 ASN
B 509 ASN
B 559 HIS
** B 961 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B1067 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8090
moved from start:          0.6077

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041  13908  Z= 0.252
  Angle     :  0.585   6.535  19030  Z= 0.309
  Chirality :  0.040   0.141   2094
  Planarity :  0.004   0.042   2220
  Dihedral  : 18.028 175.251   2420
  Min Nonbonded Distance : 2.503

Molprobity Statistics.
  All-atom Clashscore : 9.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.03 %
    Favored  : 95.97 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.88 %
    Favored  : 98.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.39 (0.22), residues: 1512
  helix:  1.61 (0.20), residues: 670
  sheet: -1.52 (0.45), residues: 136
  loop : -1.94 (0.22), residues: 706

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.002   TRP A1090 
 HIS   0.003   0.001   HIS B 605 
 PHE   0.013   0.001   PHE A 573 
 TYR   0.012   0.001   TYR B1135 
 ARG   0.004   0.001   ARG B 487 

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

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

  3024 Ramachandran restraints generated.
    1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3024 Ramachandran restraints generated.
    1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  155 residues out of total 1358 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 155
  time to evaluate  : 1.577 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  537 MET cc_start: 0.8063 (ttp) cc_final: 0.7557 (ttt)
REVERT: A  663 GLU cc_start: 0.9022 (pp20) cc_final: 0.8772 (pp20)
REVERT: A  675 ARG cc_start: 0.9177 (mtt180) cc_final: 0.8907 (mtp-110)
REVERT: A  712 GLU cc_start: 0.8576 (mt-10) cc_final: 0.8080 (mp0)
REVERT: A  726 GLN cc_start: 0.8854 (mp10) cc_final: 0.8495 (mp10)
REVERT: A  728 LYS cc_start: 0.9104 (mttt) cc_final: 0.8887 (mtpt)
REVERT: A  754 MET cc_start: 0.8231 (mpp) cc_final: 0.7950 (mpp)
REVERT: A  767 THR cc_start: 0.9238 (m) cc_final: 0.9024 (p)
REVERT: A  768 ILE cc_start: 0.9491 (mm) cc_final: 0.9257 (mt)
REVERT: A  847 MET cc_start: 0.9197 (mmp) cc_final: 0.8700 (mmm)
REVERT: A  862 CYS cc_start: 0.8836 (t) cc_final: 0.8353 (p)
REVERT: A  956 ASP cc_start: 0.8621 (t0) cc_final: 0.8411 (t0)
REVERT: A 1000 MET cc_start: 0.8668 (mtt) cc_final: 0.8376 (mpp)
REVERT: A 1030 TYR cc_start: 0.6032 (m-10) cc_final: 0.5670 (m-80)
REVERT: A 1054 PHE cc_start: 0.9292 (t80) cc_final: 0.9070 (t80)
REVERT: A 1131 MET cc_start: 0.9247 (ttt) cc_final: 0.8915 (tpp)
REVERT: A 1178 LEU cc_start: 0.9197 (tt) cc_final: 0.8864 (pp)
REVERT: B  537 MET cc_start: 0.8117 (ttp) cc_final: 0.7557 (ttt)
REVERT: B  675 ARG cc_start: 0.9190 (mtt180) cc_final: 0.8839 (mtp-110)
REVERT: B  712 GLU cc_start: 0.8615 (mt-10) cc_final: 0.8090 (mp0)
REVERT: B  728 LYS cc_start: 0.9059 (mttt) cc_final: 0.8854 (mtpt)
REVERT: B  754 MET cc_start: 0.8223 (mpp) cc_final: 0.7940 (mpp)
REVERT: B  768 ILE cc_start: 0.9501 (mm) cc_final: 0.9269 (mt)
REVERT: B  847 MET cc_start: 0.9155 (mmm) cc_final: 0.8679 (mmm)
REVERT: B  862 CYS cc_start: 0.8719 (t) cc_final: 0.8350 (p)
REVERT: B  912 GLU cc_start: 0.8607 (tt0) cc_final: 0.8264 (tp30)
REVERT: B  956 ASP cc_start: 0.8617 (t0) cc_final: 0.8414 (t0)
REVERT: B 1000 MET cc_start: 0.8673 (mtt) cc_final: 0.8382 (mpp)
REVERT: B 1030 TYR cc_start: 0.6016 (m-10) cc_final: 0.5665 (m-80)
REVERT: B 1131 MET cc_start: 0.9209 (ttt) cc_final: 0.8920 (tpp)
REVERT: B 1178 LEU cc_start: 0.9199 (tt) cc_final: 0.8872 (pp)
  outliers start: 0
  outliers final: 0
  residues processed: 155
  average time/residue: 0.2474
  time to fit residues: 57.1821
Evaluate side-chains
  114 residues out of total 1358 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 114
  time to evaluate  : 1.643 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 125 optimal weight:    6.9990
   chunk 85 optimal weight:    3.9990
   chunk 2 optimal weight:    9.9990
   chunk 112 optimal weight:    3.9990
   chunk 62 optimal weight:    0.9980
   chunk 128 optimal weight:    0.9990
   chunk 104 optimal weight:    4.9990
   chunk 0 optimal weight:    9.9990
   chunk 76 optimal weight:    9.9990
   chunk 135 optimal weight:    3.9990
   chunk 38 optimal weight:    4.9990
   overall best weight:    2.7988

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

Flipped N/Q/H residues before XYZ refinement:
A 795 HIS
** A 961 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A1067 ASN
B 795 HIS
** B 961 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B1067 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8157
moved from start:          0.6990

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.092  13908  Z= 0.343
  Angle     :  0.677   9.554  19030  Z= 0.353
  Chirality :  0.042   0.164   2094
  Planarity :  0.005   0.042   2220
  Dihedral  : 18.273 172.346   2420
  Min Nonbonded Distance : 2.465

Molprobity Statistics.
  All-atom Clashscore : 11.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.89 %
    Favored  : 94.11 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.48 %
    Favored  : 97.52 %
  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: -0.45 (0.22), residues: 1512
  helix:  1.44 (0.20), residues: 670
  sheet: -1.37 (0.44), residues: 150
  loop : -1.86 (0.23), residues: 692

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.030   0.003   TRP A1090 
 HIS   0.005   0.002   HIS A 559 
 PHE   0.016   0.002   PHE B1054 
 TYR   0.017   0.002   TYR B 907 
 ARG   0.004   0.001   ARG B 870 

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

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

  3024 Ramachandran restraints generated.
    1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3024 Ramachandran restraints generated.
    1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 1358 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 128
  time to evaluate  : 1.701 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  457 LEU cc_start: 0.9392 (tp) cc_final: 0.9073 (tp)
REVERT: A  675 ARG cc_start: 0.9132 (mtt180) cc_final: 0.8838 (mtp-110)
REVERT: A  712 GLU cc_start: 0.8469 (mt-10) cc_final: 0.8030 (mt-10)
REVERT: A  726 GLN cc_start: 0.8898 (mp10) cc_final: 0.8533 (mp10)
REVERT: A  728 LYS cc_start: 0.9129 (mttt) cc_final: 0.8890 (mtpt)
REVERT: A  754 MET cc_start: 0.8252 (mpp) cc_final: 0.7861 (mpp)
REVERT: A  767 THR cc_start: 0.9316 (m) cc_final: 0.9088 (m)
REVERT: A  847 MET cc_start: 0.9338 (mmp) cc_final: 0.8601 (mmm)
REVERT: A  862 CYS cc_start: 0.8866 (t) cc_final: 0.8502 (p)
REVERT: A  956 ASP cc_start: 0.8651 (t0) cc_final: 0.8428 (t0)
REVERT: A 1030 TYR cc_start: 0.6279 (m-10) cc_final: 0.5884 (m-80)
REVERT: A 1054 PHE cc_start: 0.9370 (t80) cc_final: 0.9115 (t80)
REVERT: A 1131 MET cc_start: 0.9216 (ttt) cc_final: 0.8933 (tpp)
REVERT: B  457 LEU cc_start: 0.9411 (tp) cc_final: 0.8982 (tp)
REVERT: B  675 ARG cc_start: 0.9129 (mtt180) cc_final: 0.8853 (mtp-110)
REVERT: B  712 GLU cc_start: 0.8476 (mt-10) cc_final: 0.8034 (mt-10)
REVERT: B  726 GLN cc_start: 0.8998 (mp10) cc_final: 0.8663 (mp10)
REVERT: B  728 LYS cc_start: 0.9118 (mttt) cc_final: 0.8883 (mtpt)
REVERT: B  754 MET cc_start: 0.8306 (mpp) cc_final: 0.7945 (mpp)
REVERT: B  847 MET cc_start: 0.9273 (mmm) cc_final: 0.8541 (mmm)
REVERT: B  862 CYS cc_start: 0.8785 (t) cc_final: 0.8465 (p)
REVERT: B  956 ASP cc_start: 0.8645 (t0) cc_final: 0.8439 (t0)
REVERT: B 1030 TYR cc_start: 0.6262 (m-10) cc_final: 0.5887 (m-80)
REVERT: B 1054 PHE cc_start: 0.9329 (t80) cc_final: 0.9066 (t80)
REVERT: B 1131 MET cc_start: 0.9212 (ttt) cc_final: 0.8973 (tpp)
  outliers start: 0
  outliers final: 0
  residues processed: 128
  average time/residue: 0.2356
  time to fit residues: 45.5765
Evaluate side-chains
  101 residues out of total 1358 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 101
  time to evaluate  : 1.421 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 50 optimal weight:    0.6980
   chunk 135 optimal weight:    3.9990
   chunk 29 optimal weight:    0.9980
   chunk 88 optimal weight:    0.9980
   chunk 37 optimal weight:    0.2980
   chunk 150 optimal weight:    2.9990
   chunk 125 optimal weight:    5.9990
   chunk 69 optimal weight:    4.9990
   chunk 12 optimal weight:    1.9990
   chunk 49 optimal weight:    2.9990
   chunk 79 optimal weight:    3.9990
   overall best weight:    0.9982

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

Flipped N/Q/H residues before XYZ refinement:
** A 555 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 961 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A1067 ASN
** B 555 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 961 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B1067 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8092
moved from start:          0.6954

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  13908  Z= 0.165
  Angle     :  0.535   6.129  19030  Z= 0.282
  Chirality :  0.038   0.134   2094
  Planarity :  0.004   0.042   2220
  Dihedral  : 18.142 175.329   2420
  Min Nonbonded Distance : 2.487

Molprobity Statistics.
  All-atom Clashscore : 7.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.64 %
    Favored  : 96.36 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.13 %
    Favored  : 98.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -0.03 (0.22), residues: 1512
  helix:  1.71 (0.20), residues: 684
  sheet: -1.34 (0.47), residues: 136
  loop : -1.59 (0.23), residues: 692

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.002   TRP B1090 
 HIS   0.003   0.001   HIS A 548 
 PHE   0.013   0.001   PHE B1054 
 TYR   0.008   0.001   TYR B 907 
 ARG   0.003   0.000   ARG B 487 

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

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

  3024 Ramachandran restraints generated.
    1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3024 Ramachandran restraints generated.
    1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  155 residues out of total 1358 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 155
  time to evaluate  : 1.412 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  489 LYS cc_start: 0.8061 (mmpt) cc_final: 0.7860 (mmmm)
REVERT: A  663 GLU cc_start: 0.8998 (pp20) cc_final: 0.8607 (pp20)
REVERT: A  675 ARG cc_start: 0.9149 (mtt180) cc_final: 0.8831 (mtp-110)
REVERT: A  712 GLU cc_start: 0.8451 (mt-10) cc_final: 0.8000 (mt-10)
REVERT: A  726 GLN cc_start: 0.8847 (mp10) cc_final: 0.8346 (pm20)
REVERT: A  728 LYS cc_start: 0.8940 (mttt) cc_final: 0.8720 (mtpt)
REVERT: A  754 MET cc_start: 0.8361 (mpp) cc_final: 0.8011 (mpp)
REVERT: A  767 THR cc_start: 0.9294 (m) cc_final: 0.8994 (m)
REVERT: A  847 MET cc_start: 0.9307 (mmp) cc_final: 0.8610 (mmm)
REVERT: A  862 CYS cc_start: 0.8636 (t) cc_final: 0.8359 (p)
REVERT: A  867 PHE cc_start: 0.7237 (m-10) cc_final: 0.6556 (m-10)
REVERT: A  956 ASP cc_start: 0.8683 (t0) cc_final: 0.8430 (t0)
REVERT: A 1030 TYR cc_start: 0.6130 (m-10) cc_final: 0.5753 (m-80)
REVERT: A 1054 PHE cc_start: 0.9397 (t80) cc_final: 0.9192 (t80)
REVERT: A 1131 MET cc_start: 0.9210 (ttt) cc_final: 0.8927 (tpp)
REVERT: A 1178 LEU cc_start: 0.9230 (tt) cc_final: 0.8907 (pp)
REVERT: B  510 ILE cc_start: 0.9270 (mm) cc_final: 0.9058 (mm)
REVERT: B  663 GLU cc_start: 0.9002 (pp20) cc_final: 0.8611 (pp20)
REVERT: B  675 ARG cc_start: 0.9139 (mtt180) cc_final: 0.8850 (mtp-110)
REVERT: B  712 GLU cc_start: 0.8452 (mt-10) cc_final: 0.8004 (mt-10)
REVERT: B  728 LYS cc_start: 0.8944 (mttt) cc_final: 0.8717 (mtpt)
REVERT: B  754 MET cc_start: 0.8353 (mpp) cc_final: 0.8005 (mpp)
REVERT: B  847 MET cc_start: 0.9249 (mmm) cc_final: 0.8700 (mmm)
REVERT: B  862 CYS cc_start: 0.8597 (t) cc_final: 0.8338 (p)
REVERT: B  867 PHE cc_start: 0.7321 (m-10) cc_final: 0.6513 (m-10)
REVERT: B  922 GLU cc_start: 0.7815 (tt0) cc_final: 0.7517 (tm-30)
REVERT: B  956 ASP cc_start: 0.8674 (t0) cc_final: 0.8439 (t0)
REVERT: B 1030 TYR cc_start: 0.6117 (m-10) cc_final: 0.5756 (m-80)
REVERT: B 1054 PHE cc_start: 0.9342 (t80) cc_final: 0.9096 (t80)
REVERT: B 1131 MET cc_start: 0.9204 (ttt) cc_final: 0.8926 (tpp)
REVERT: B 1178 LEU cc_start: 0.9230 (tt) cc_final: 0.8912 (pp)
  outliers start: 0
  outliers final: 0
  residues processed: 155
  average time/residue: 0.2535
  time to fit residues: 58.0369
Evaluate side-chains
  110 residues out of total 1358 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 110
  time to evaluate  : 1.622 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 145 optimal weight:    4.9990
   chunk 17 optimal weight:    9.9990
   chunk 85 optimal weight:    3.9990
   chunk 110 optimal weight:    0.8980
   chunk 127 optimal weight:    3.9990
   chunk 84 optimal weight:    0.9980
   chunk 150 optimal weight:    9.9990
   chunk 94 optimal weight:    7.9990
   chunk 91 optimal weight:    2.9990
   chunk 69 optimal weight:    0.8980
   chunk 93 optimal weight:    4.9990
   overall best weight:    1.9584

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

Flipped N/Q/H residues before XYZ refinement:
** A 961 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A1051 GLN
A1067 ASN
** B 961 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B1067 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8138
moved from start:          0.7372

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.065  13908  Z= 0.250
  Angle     :  0.599   8.367  19030  Z= 0.312
  Chirality :  0.040   0.162   2094
  Planarity :  0.004   0.039   2220
  Dihedral  : 18.272 175.258   2420
  Min Nonbonded Distance : 2.485

Molprobity Statistics.
  All-atom Clashscore : 9.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.56 %
    Favored  : 94.44 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.98 %
    Favored  : 99.02 %
  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: -0.06 (0.23), residues: 1512
  helix:  1.60 (0.20), residues: 684
  sheet: -1.16 (0.46), residues: 146
  loop : -1.54 (0.24), residues: 682

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.002   TRP B1090 
 HIS   0.004   0.001   HIS B 634 
 PHE   0.013   0.001   PHE B 867 
 TYR   0.014   0.002   TYR B 907 
 ARG   0.004   0.000   ARG B1148 

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

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

  3024 Ramachandran restraints generated.
    1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3024 Ramachandran restraints generated.
    1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  139 residues out of total 1358 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 139
  time to evaluate  : 1.562 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  457 LEU cc_start: 0.9283 (tp) cc_final: 0.9000 (tp)
REVERT: A  537 MET cc_start: 0.7815 (ttt) cc_final: 0.7379 (tpp)
REVERT: A  675 ARG cc_start: 0.9181 (mtt180) cc_final: 0.8889 (mtp-110)
REVERT: A  712 GLU cc_start: 0.8458 (mt-10) cc_final: 0.8014 (mt-10)
REVERT: A  726 GLN cc_start: 0.8844 (mp10) cc_final: 0.8486 (mp10)
REVERT: A  728 LYS cc_start: 0.8993 (mttt) cc_final: 0.8739 (mtpt)
REVERT: A  754 MET cc_start: 0.8315 (mpp) cc_final: 0.7814 (mpp)
REVERT: A  767 THR cc_start: 0.9315 (m) cc_final: 0.9083 (m)
REVERT: A  847 MET cc_start: 0.9365 (mmp) cc_final: 0.9110 (mmm)
REVERT: A  862 CYS cc_start: 0.8685 (t) cc_final: 0.8356 (p)
REVERT: A  867 PHE cc_start: 0.7378 (m-10) cc_final: 0.6760 (m-10)
REVERT: A  956 ASP cc_start: 0.8702 (t0) cc_final: 0.8450 (t0)
REVERT: A 1030 TYR cc_start: 0.6217 (m-10) cc_final: 0.5829 (m-80)
REVERT: A 1054 PHE cc_start: 0.9443 (t80) cc_final: 0.9232 (t80)
REVERT: A 1131 MET cc_start: 0.9197 (ttt) cc_final: 0.8931 (tpp)
REVERT: A 1178 LEU cc_start: 0.9335 (tt) cc_final: 0.8993 (pp)
REVERT: B  457 LEU cc_start: 0.9271 (tp) cc_final: 0.8821 (tp)
REVERT: B  510 ILE cc_start: 0.9289 (mm) cc_final: 0.9081 (mm)
REVERT: B  675 ARG cc_start: 0.9252 (mtt180) cc_final: 0.8913 (mtp-110)
REVERT: B  712 GLU cc_start: 0.8456 (mt-10) cc_final: 0.8014 (mt-10)
REVERT: B  728 LYS cc_start: 0.8984 (mttt) cc_final: 0.8726 (mtpt)
REVERT: B  754 MET cc_start: 0.8337 (mpp) cc_final: 0.7845 (mpp)
REVERT: B  847 MET cc_start: 0.9263 (mmm) cc_final: 0.8613 (mmm)
REVERT: B  862 CYS cc_start: 0.8681 (t) cc_final: 0.8361 (p)
REVERT: B  867 PHE cc_start: 0.7568 (m-10) cc_final: 0.7112 (m-10)
REVERT: B  922 GLU cc_start: 0.7826 (tt0) cc_final: 0.7507 (tm-30)
REVERT: B  956 ASP cc_start: 0.8690 (t0) cc_final: 0.8457 (t0)
REVERT: B 1030 TYR cc_start: 0.6223 (m-10) cc_final: 0.5840 (m-80)
REVERT: B 1054 PHE cc_start: 0.9423 (t80) cc_final: 0.9194 (t80)
REVERT: B 1131 MET cc_start: 0.9194 (ttt) cc_final: 0.8930 (tpp)
REVERT: B 1178 LEU cc_start: 0.9334 (tt) cc_final: 0.9000 (pp)
  outliers start: 0
  outliers final: 0
  residues processed: 139
  average time/residue: 0.2455
  time to fit residues: 50.9149
Evaluate side-chains
  106 residues out of total 1358 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 106
  time to evaluate  : 1.485 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 60 optimal weight:    5.9990
   chunk 89 optimal weight:    4.9990
   chunk 45 optimal weight:    0.3980
   chunk 29 optimal weight:    0.9990
   chunk 95 optimal weight:    0.9980
   chunk 102 optimal weight:    0.3980
   chunk 74 optimal weight:   20.0000
   chunk 14 optimal weight:    2.9990
   chunk 118 optimal weight:    0.3980
   chunk 136 optimal weight:    5.9990
   chunk 144 optimal weight:    0.9990
   overall best weight:    0.6382

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

Flipped N/Q/H residues before XYZ refinement:
A 555 ASN
A 782 ASN
** A 961 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A1067 ASN
B 555 ASN
B 782 ASN
** B 961 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B1067 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8075
moved from start:          0.7336

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.037  13908  Z= 0.138
  Angle     :  0.521   7.053  19030  Z= 0.272
  Chirality :  0.038   0.135   2094
  Planarity :  0.004   0.041   2220
  Dihedral  : 18.282 179.191   2420
  Min Nonbonded Distance : 2.511

Molprobity Statistics.
  All-atom Clashscore : 6.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.24 %
    Favored  : 96.76 %
  Rotamer:
    Outliers :  0.30 %
    Allowed  :  0.75 %
    Favored  : 98.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.18 (0.23), residues: 1512
  helix:  1.80 (0.20), residues: 682
  sheet: -1.11 (0.49), residues: 136
  loop : -1.40 (0.24), residues: 694

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP B1090 
 HIS   0.004   0.001   HIS B 548 
 PHE   0.011   0.001   PHE B1054 
 TYR   0.006   0.001   TYR B1029 
 ARG   0.003   0.000   ARG B 487 

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

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

  3024 Ramachandran restraints generated.
    1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3024 Ramachandran restraints generated.
    1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  173 residues out of total 1358 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 4
    poor density    : 169
  time to evaluate  : 1.437 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  461 GLU cc_start: 0.8217 (pt0) cc_final: 0.7644 (pt0)
REVERT: A  537 MET cc_start: 0.8283 (ttt) cc_final: 0.7733 (tpp)
REVERT: A  545 ASP cc_start: 0.8719 (m-30) cc_final: 0.8448 (m-30)
REVERT: A  555 ASN cc_start: 0.9286 (OUTLIER) cc_final: 0.9058 (t0)
REVERT: A  570 LEU cc_start: 0.8161 (mt) cc_final: 0.7625 (mt)
REVERT: A  663 GLU cc_start: 0.9021 (pp20) cc_final: 0.8659 (pp20)
REVERT: A  675 ARG cc_start: 0.9248 (mtt180) cc_final: 0.8911 (mtp-110)
REVERT: A  712 GLU cc_start: 0.8442 (mt-10) cc_final: 0.7977 (mt-10)
REVERT: A  726 GLN cc_start: 0.8809 (mp10) cc_final: 0.8347 (pm20)
REVERT: A  728 LYS cc_start: 0.8928 (mttt) cc_final: 0.8705 (mtpt)
REVERT: A  754 MET cc_start: 0.8348 (mpp) cc_final: 0.7861 (mpp)
REVERT: A  761 GLU cc_start: 0.9148 (mt-10) cc_final: 0.8925 (pm20)
REVERT: A  767 THR cc_start: 0.9268 (m) cc_final: 0.8953 (m)
REVERT: A  847 MET cc_start: 0.9243 (mmp) cc_final: 0.8765 (mmm)
REVERT: A  862 CYS cc_start: 0.8513 (t) cc_final: 0.8250 (p)
REVERT: A  867 PHE cc_start: 0.7314 (m-10) cc_final: 0.6716 (m-10)
REVERT: A  954 ILE cc_start: 0.9247 (mm) cc_final: 0.8967 (mm)
REVERT: A  956 ASP cc_start: 0.8759 (t0) cc_final: 0.8505 (t0)
REVERT: A 1030 TYR cc_start: 0.6151 (m-10) cc_final: 0.5821 (m-80)
REVERT: A 1054 PHE cc_start: 0.9405 (t80) cc_final: 0.9198 (t80)
REVERT: A 1131 MET cc_start: 0.9116 (ttt) cc_final: 0.8902 (tpp)
REVERT: A 1178 LEU cc_start: 0.9227 (tt) cc_final: 0.8906 (pp)
REVERT: B  555 ASN cc_start: 0.9298 (OUTLIER) cc_final: 0.9069 (t0)
REVERT: B  663 GLU cc_start: 0.9022 (pp20) cc_final: 0.8662 (pp20)
REVERT: B  675 ARG cc_start: 0.9246 (mtt180) cc_final: 0.8898 (mtp-110)
REVERT: B  712 GLU cc_start: 0.8427 (mt-10) cc_final: 0.7910 (mp0)
REVERT: B  728 LYS cc_start: 0.8925 (mttt) cc_final: 0.8710 (mtpt)
REVERT: B  847 MET cc_start: 0.9214 (mmm) cc_final: 0.8688 (mmm)
REVERT: B  862 CYS cc_start: 0.8759 (t) cc_final: 0.8188 (p)
REVERT: B  867 PHE cc_start: 0.7502 (m-10) cc_final: 0.6960 (m-10)
REVERT: B  922 GLU cc_start: 0.7764 (tt0) cc_final: 0.7495 (tp30)
REVERT: B  954 ILE cc_start: 0.9241 (mm) cc_final: 0.8961 (mm)
REVERT: B  956 ASP cc_start: 0.8704 (t0) cc_final: 0.8434 (t0)
REVERT: B 1030 TYR cc_start: 0.6052 (m-10) cc_final: 0.5624 (m-80)
REVERT: B 1131 MET cc_start: 0.9115 (ttt) cc_final: 0.8898 (tpp)
REVERT: B 1178 LEU cc_start: 0.9226 (tt) cc_final: 0.8911 (pp)
  outliers start: 4
  outliers final: 0
  residues processed: 173
  average time/residue: 0.2256
  time to fit residues: 59.7114
Evaluate side-chains
  122 residues out of total 1358 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 2
    poor density    : 120
  time to evaluate  : 1.485 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 131 optimal weight:    3.9990
   chunk 140 optimal weight:    1.9990
   chunk 144 optimal weight:    2.9990
   chunk 84 optimal weight:    0.6980
   chunk 61 optimal weight:    0.8980
   chunk 110 optimal weight:    0.0870
   chunk 42 optimal weight:    4.9990
   chunk 126 optimal weight:    1.9990
   chunk 132 optimal weight:    0.0370
   chunk 139 optimal weight:    0.9990
   chunk 92 optimal weight:    1.9990
   overall best weight:    0.5438

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

Flipped N/Q/H residues before XYZ refinement:
** A 961 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A1067 ASN
** B 961 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B1067 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8066
moved from start:          0.7380

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.037  13908  Z= 0.140
  Angle     :  0.528   7.037  19030  Z= 0.272
  Chirality :  0.038   0.134   2094
  Planarity :  0.003   0.039   2220
  Dihedral  : 18.262 178.918   2420
  Min Nonbonded Distance : 2.510

Molprobity Statistics.
  All-atom Clashscore : 7.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.17 %
    Favored  : 95.83 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.15 %
    Favored  : 99.85 %
  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:  0.23 (0.23), residues: 1512
  helix:  1.83 (0.21), residues: 682
  sheet: -1.06 (0.48), residues: 136
  loop : -1.36 (0.24), residues: 694

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP B1090 
 HIS   0.003   0.001   HIS B 548 
 PHE   0.006   0.001   PHE A 706 
 TYR   0.006   0.001   TYR B 907 
 ARG   0.003   0.000   ARG B 487 

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

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

  3024 Ramachandran restraints generated.
    1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3024 Ramachandran restraints generated.
    1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  158 residues out of total 1358 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 158
  time to evaluate  : 1.367 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  461 GLU cc_start: 0.8220 (pt0) cc_final: 0.7341 (pt0)
REVERT: A  537 MET cc_start: 0.8294 (ttt) cc_final: 0.7720 (tpp)
REVERT: A  675 ARG cc_start: 0.9253 (mtt180) cc_final: 0.8912 (mtp-110)
REVERT: A  712 GLU cc_start: 0.8582 (mt-10) cc_final: 0.7930 (mp0)
REVERT: A  726 GLN cc_start: 0.8829 (mp10) cc_final: 0.8514 (pm20)
REVERT: A  728 LYS cc_start: 0.8925 (mttt) cc_final: 0.8682 (mtpt)
REVERT: A  761 GLU cc_start: 0.9098 (mt-10) cc_final: 0.8886 (pm20)
REVERT: A  767 THR cc_start: 0.9239 (m) cc_final: 0.8975 (m)
REVERT: A  847 MET cc_start: 0.9269 (mmp) cc_final: 0.8821 (mmm)
REVERT: A  862 CYS cc_start: 0.8713 (t) cc_final: 0.8257 (p)
REVERT: A  867 PHE cc_start: 0.7555 (m-10) cc_final: 0.6883 (m-10)
REVERT: A  956 ASP cc_start: 0.8657 (t0) cc_final: 0.8410 (t0)
REVERT: A  972 MET cc_start: 0.6960 (tpp) cc_final: 0.6203 (tpp)
REVERT: A 1094 GLN cc_start: 0.8637 (tm-30) cc_final: 0.7540 (mt0)
REVERT: A 1128 LEU cc_start: 0.9151 (mt) cc_final: 0.8939 (mt)
REVERT: A 1131 MET cc_start: 0.9109 (ttt) cc_final: 0.8871 (tpp)
REVERT: A 1178 LEU cc_start: 0.9211 (tt) cc_final: 0.8895 (pp)
REVERT: B  461 GLU cc_start: 0.7409 (pt0) cc_final: 0.6920 (pt0)
REVERT: B  504 ASN cc_start: 0.8307 (t0) cc_final: 0.7891 (t0)
REVERT: B  542 GLN cc_start: 0.7710 (mm110) cc_final: 0.7402 (mm110)
REVERT: B  675 ARG cc_start: 0.9247 (mtt180) cc_final: 0.8899 (mtp-110)
REVERT: B  712 GLU cc_start: 0.8535 (mt-10) cc_final: 0.7843 (mp0)
REVERT: B  728 LYS cc_start: 0.8911 (mttt) cc_final: 0.8698 (mtpt)
REVERT: B  754 MET cc_start: 0.8000 (mpp) cc_final: 0.7526 (mpp)
REVERT: B  768 ILE cc_start: 0.9527 (mm) cc_final: 0.9326 (mt)
REVERT: B  847 MET cc_start: 0.9221 (mmm) cc_final: 0.8790 (mmm)
REVERT: B  862 CYS cc_start: 0.8667 (t) cc_final: 0.8137 (p)
REVERT: B  867 PHE cc_start: 0.7539 (m-10) cc_final: 0.7031 (m-10)
REVERT: B  922 GLU cc_start: 0.8035 (tt0) cc_final: 0.7743 (tp30)
REVERT: B  956 ASP cc_start: 0.8633 (t0) cc_final: 0.8407 (t0)
REVERT: B  972 MET cc_start: 0.6914 (tpp) cc_final: 0.5992 (tpp)
REVERT: B 1030 TYR cc_start: 0.6137 (m-10) cc_final: 0.5826 (m-80)
REVERT: B 1128 LEU cc_start: 0.9180 (mt) cc_final: 0.8956 (mt)
REVERT: B 1131 MET cc_start: 0.9092 (ttt) cc_final: 0.8865 (tpp)
REVERT: B 1178 LEU cc_start: 0.9210 (tt) cc_final: 0.8899 (pp)
  outliers start: 0
  outliers final: 0
  residues processed: 158
  average time/residue: 0.2151
  time to fit residues: 51.7410
Evaluate side-chains
  124 residues out of total 1358 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 124
  time to evaluate  : 1.409 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 148 optimal weight:    7.9990
   chunk 90 optimal weight:    2.9990
   chunk 70 optimal weight:    0.7980
   chunk 102 optimal weight:    0.9990
   chunk 155 optimal weight:    4.9990
   chunk 143 optimal weight:    3.9990
   chunk 123 optimal weight:    0.6980
   chunk 12 optimal weight:    6.9990
   chunk 95 optimal weight:    1.9990
   chunk 75 optimal weight:    0.9990
   chunk 98 optimal weight:    4.9990
   overall best weight:    1.0986

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

Flipped N/Q/H residues before XYZ refinement:
** A 961 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A1067 ASN
B 961 HIS
B1067 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8090
moved from start:          0.7573

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  13908  Z= 0.170
  Angle     :  0.541   6.979  19030  Z= 0.281
  Chirality :  0.038   0.133   2094
  Planarity :  0.004   0.038   2220
  Dihedral  : 18.297 178.993   2420
  Min Nonbonded Distance : 2.495

Molprobity Statistics.
  All-atom Clashscore : 8.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.23 %
    Favored  : 95.77 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.23 %
    Favored  : 99.77 %
  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:  0.23 (0.23), residues: 1512
  helix:  1.87 (0.21), residues: 680
  sheet: -1.07 (0.48), residues: 136
  loop : -1.39 (0.24), residues: 696

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP B1090 
 HIS   0.008   0.001   HIS B 961 
 PHE   0.007   0.001   PHE B 867 
 TYR   0.028   0.001   TYR A1030 
 ARG   0.005   0.000   ARG B 958 

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

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

  3024 Ramachandran restraints generated.
    1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3024 Ramachandran restraints generated.
    1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  153 residues out of total 1358 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 153
  time to evaluate  : 1.872 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  461 GLU cc_start: 0.7999 (pt0) cc_final: 0.7335 (pt0)
REVERT: A  537 MET cc_start: 0.8300 (ttt) cc_final: 0.7705 (tpp)
REVERT: A  675 ARG cc_start: 0.9261 (mtt180) cc_final: 0.8918 (mtp-110)
REVERT: A  712 GLU cc_start: 0.8492 (mt-10) cc_final: 0.8086 (mt-10)
REVERT: A  726 GLN cc_start: 0.8823 (mp10) cc_final: 0.8348 (pm20)
REVERT: A  728 LYS cc_start: 0.8946 (mttt) cc_final: 0.8733 (mtpt)
REVERT: A  754 MET cc_start: 0.7999 (mpp) cc_final: 0.7521 (mpp)
REVERT: A  761 GLU cc_start: 0.9139 (mt-10) cc_final: 0.8912 (pm20)
REVERT: A  767 THR cc_start: 0.9271 (m) cc_final: 0.8964 (m)
REVERT: A  862 CYS cc_start: 0.8699 (t) cc_final: 0.8266 (p)
REVERT: A  867 PHE cc_start: 0.7610 (m-10) cc_final: 0.6902 (m-10)
REVERT: A  956 ASP cc_start: 0.8675 (t0) cc_final: 0.8421 (t0)
REVERT: A 1030 TYR cc_start: 0.5678 (m-80) cc_final: 0.5087 (m-80)
REVERT: A 1094 GLN cc_start: 0.8547 (tm-30) cc_final: 0.7385 (mt0)
REVERT: A 1128 LEU cc_start: 0.9227 (mt) cc_final: 0.8986 (mt)
REVERT: A 1131 MET cc_start: 0.9102 (ttt) cc_final: 0.8874 (tpp)
REVERT: A 1178 LEU cc_start: 0.9211 (tt) cc_final: 0.8889 (pp)
REVERT: B  675 ARG cc_start: 0.9252 (mtt180) cc_final: 0.8902 (mtp-110)
REVERT: B  712 GLU cc_start: 0.8506 (mt-10) cc_final: 0.7917 (mp0)
REVERT: B  728 LYS cc_start: 0.8942 (mttt) cc_final: 0.8729 (mtpt)
REVERT: B  741 GLU cc_start: 0.8747 (mp0) cc_final: 0.8535 (mp0)
REVERT: B  754 MET cc_start: 0.8048 (mpp) cc_final: 0.7570 (mpp)
REVERT: B  847 MET cc_start: 0.9266 (mmm) cc_final: 0.8475 (mmm)
REVERT: B  862 CYS cc_start: 0.8362 (t) cc_final: 0.8083 (p)
REVERT: B  867 PHE cc_start: 0.7538 (m-10) cc_final: 0.6971 (m-10)
REVERT: B  922 GLU cc_start: 0.7933 (tt0) cc_final: 0.7659 (tp30)
REVERT: B  956 ASP cc_start: 0.8599 (t0) cc_final: 0.8322 (t0)
REVERT: B 1030 TYR cc_start: 0.6102 (m-10) cc_final: 0.5784 (m-80)
REVERT: B 1128 LEU cc_start: 0.9218 (mt) cc_final: 0.8975 (mt)
REVERT: B 1178 LEU cc_start: 0.9211 (tt) cc_final: 0.8893 (pp)
  outliers start: 0
  outliers final: 0
  residues processed: 153
  average time/residue: 0.2340
  time to fit residues: 54.3507
Evaluate side-chains
  117 residues out of total 1358 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 117
  time to evaluate  : 1.676 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 131 optimal weight:    0.1980
   chunk 37 optimal weight:    4.9990
   chunk 114 optimal weight:    0.9980
   chunk 18 optimal weight:    0.9980
   chunk 34 optimal weight:    0.8980
   chunk 123 optimal weight:    0.9990
   chunk 51 optimal weight:    6.9990
   chunk 127 optimal weight:    0.0970
   chunk 15 optimal weight:    4.9990
   chunk 22 optimal weight:    0.3980
   chunk 108 optimal weight:    1.9990
   overall best weight:    0.5178

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

Flipped N/Q/H residues before XYZ refinement:
** A 961 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A1067 ASN
B1067 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3408 r_free = 0.3408 target = 0.073325 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3120 r_free = 0.3120 target = 0.060135 restraints weight = 56834.463|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3171 r_free = 0.3171 target = 0.062360 restraints weight = 31080.442|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3207 r_free = 0.3207 target = 0.063918 restraints weight = 20117.518|
|-----------------------------------------------------------------------------|
r_work (final): 0.3203
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8092
moved from start:          0.7587

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.038  13908  Z= 0.137
  Angle     :  0.531   7.234  19030  Z= 0.271
  Chirality :  0.038   0.134   2094
  Planarity :  0.003   0.040   2220
  Dihedral  : 18.231 178.570   2420
  Min Nonbonded Distance : 2.514

Molprobity Statistics.
  All-atom Clashscore : 6.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.97 %
    Favored  : 96.03 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.08 %
    Favored  : 99.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.31 (0.23), residues: 1512
  helix:  1.88 (0.21), residues: 682
  sheet: -1.02 (0.49), residues: 136
  loop : -1.29 (0.24), residues: 694

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP B1090 
 HIS   0.004   0.001   HIS B 548 
 PHE   0.006   0.001   PHE A 895 
 TYR   0.029   0.001   TYR A1030 
 ARG   0.002   0.000   ARG B 487 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2458.26 seconds
wall clock time: 45 minutes 10.73 seconds (2710.73 seconds total)