Starting phenix.real_space_refine
on Mon May 19 13:21:59 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8r87_18997/05_2025/8r87_18997.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8r87_18997/05_2025/8r87_18997.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.0
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8r87_18997/05_2025/8r87_18997.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8r87_18997/05_2025/8r87_18997.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8r87_18997/05_2025/8r87_18997.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8r87_18997/05_2025/8r87_18997.cif"
  }
  resolution = 3.0
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.001
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: 4
    Type Number    sf(0)   Gaussians
     S      78      5.16       5
     C   11712      2.51       5
     N    3042      2.21       5
     O    3540      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 18372
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 6124
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 789, 6124
          Classifications: {'peptide': 789}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 41, 'TRANS': 747}
          Chain breaks: 10
          Unresolved chain link angles: 2
          Unresolved non-hydrogen bonds: 6
          Unresolved non-hydrogen angles: 8
          Unresolved non-hydrogen dihedrals: 6
  Restraints were copied for chains:
    C, B
  Time building chain proxies: 13.80, per 1000 atoms: 0.75
  Number of scatterers: 18372
  At special positions: 0
  Unit cell: (128.52, 126.84, 151.2, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      78     16.00
     O    3540      8.00
     N    3042      7.00
     C   11712      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=27, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 131 " - pdb=" SG  CYS A 166 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 291 " - pdb=" SG  CYS A 301 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 538 " - pdb=" SG  CYS A 590 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 617 " - pdb=" SG  CYS A 649 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 662 " - pdb=" SG  CYS A 671 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 738 " - pdb=" SG  CYS A 760 " distance=2.02
    Simple disulfide: pdb=" SG  CYS A 743 " - pdb=" SG  CYS A 749 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A1032 " - pdb=" SG  CYS A1043 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A1082 " - pdb=" SG  CYS A1126 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 131 " - pdb=" SG  CYS C 166 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 131 " - pdb=" SG  CYS B 166 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 291 " - pdb=" SG  CYS C 301 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 291 " - pdb=" SG  CYS B 301 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 538 " - pdb=" SG  CYS C 590 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 538 " - pdb=" SG  CYS B 590 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 617 " - pdb=" SG  CYS C 649 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 617 " - pdb=" SG  CYS B 649 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 662 " - pdb=" SG  CYS C 671 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 662 " - pdb=" SG  CYS B 671 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 738 " - pdb=" SG  CYS C 760 " distance=2.02
    Simple disulfide: pdb=" SG  CYS B 738 " - pdb=" SG  CYS B 760 " distance=2.02
    Simple disulfide: pdb=" SG  CYS C 743 " - pdb=" SG  CYS C 749 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 743 " - pdb=" SG  CYS B 749 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C1032 " - pdb=" SG  CYS C1043 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B1032 " - pdb=" SG  CYS B1043 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C1082 " - pdb=" SG  CYS C1126 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B1082 " - pdb=" SG  CYS B1126 " distance=2.03

  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: 4.26
  Conformation dependent library (CDL) restraints added in 2.2 seconds
  

  4602 Ramachandran restraints generated.
    2301 Oldfield, 0 Emsley, 2301 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  4434

  Finding SS restraints...
    Secondary structure from input PDB file:
      48 helices and 33 sheets defined
      28.8% alpha, 26.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 2.61
  Creating SS restraints...
    Processing helix  chain 'A' and resid 294 through 304
    Processing helix  chain 'A' and resid 616 through 620
    Processing helix  chain 'A' and resid 737 through 744
      removed outlier: 3.543A  pdb=" N   GLY A 744 " --> pdb=" O   MET A 740 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 746 through 755
      removed outlier: 3.754A  pdb=" N   GLN A 755 " --> pdb=" O   ASN A 751 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 758 through 783
    Processing helix  chain 'A' and resid 816 through 825
    Processing helix  chain 'A' and resid 866 through 885
    Processing helix  chain 'A' and resid 886 through 890
    Processing helix  chain 'A' and resid 897 through 909
    Processing helix  chain 'A' and resid 913 through 919
    Processing helix  chain 'A' and resid 919 through 941
    Processing helix  chain 'A' and resid 946 through 965
    Processing helix  chain 'A' and resid 966 through 968
      No H-bonds generated for 'chain 'A' and resid 966 through 968'
    Processing helix  chain 'A' and resid 976 through 984
    Processing helix  chain 'A' and resid 985 through 1033
      removed outlier: 4.046A  pdb=" N   VAL A 991 " --> pdb=" O   PRO A 987 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1140 through 1147
      removed outlier: 4.143A  pdb=" N   GLU A1144 " --> pdb=" O   PRO A1140 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 294 through 304
    Processing helix  chain 'B' and resid 616 through 620
    Processing helix  chain 'B' and resid 737 through 744
      removed outlier: 3.543A  pdb=" N   GLY B 744 " --> pdb=" O   MET B 740 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 746 through 755
      removed outlier: 3.755A  pdb=" N   GLN B 755 " --> pdb=" O   ASN B 751 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 758 through 783
    Processing helix  chain 'B' and resid 816 through 825
    Processing helix  chain 'B' and resid 866 through 885
    Processing helix  chain 'B' and resid 886 through 890
    Processing helix  chain 'B' and resid 897 through 909
    Processing helix  chain 'B' and resid 913 through 919
    Processing helix  chain 'B' and resid 919 through 941
    Processing helix  chain 'B' and resid 946 through 965
    Processing helix  chain 'B' and resid 966 through 968
      No H-bonds generated for 'chain 'B' and resid 966 through 968'
    Processing helix  chain 'B' and resid 976 through 984
    Processing helix  chain 'B' and resid 985 through 1033
      removed outlier: 4.046A  pdb=" N   VAL B 991 " --> pdb=" O   PRO B 987 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1140 through 1147
      removed outlier: 4.143A  pdb=" N   GLU B1144 " --> pdb=" O   PRO B1140 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 294 through 304
    Processing helix  chain 'C' and resid 616 through 620
    Processing helix  chain 'C' and resid 737 through 744
      removed outlier: 3.543A  pdb=" N   GLY C 744 " --> pdb=" O   MET C 740 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 746 through 755
      removed outlier: 3.755A  pdb=" N   GLN C 755 " --> pdb=" O   ASN C 751 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 758 through 783
    Processing helix  chain 'C' and resid 816 through 825
    Processing helix  chain 'C' and resid 866 through 885
    Processing helix  chain 'C' and resid 886 through 890
    Processing helix  chain 'C' and resid 897 through 909
    Processing helix  chain 'C' and resid 913 through 919
    Processing helix  chain 'C' and resid 919 through 941
    Processing helix  chain 'C' and resid 946 through 965
    Processing helix  chain 'C' and resid 966 through 968
      No H-bonds generated for 'chain 'C' and resid 966 through 968'
    Processing helix  chain 'C' and resid 976 through 984
    Processing helix  chain 'C' and resid 985 through 1033
      removed outlier: 4.046A  pdb=" N   VAL C 991 " --> pdb=" O   PRO C 987 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 1140 through 1147
      removed outlier: 4.143A  pdb=" N   GLU C1144 " --> pdb=" O   PRO C1140 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30
      removed outlier: 8.391A  pdb=" N   ASN A  61 " --> pdb=" O   TYR A 269 " (cutoff:3.500A)
      removed outlier: 6.367A  pdb=" N   TYR A 269 " --> pdb=" O   ASN A  61 " (cutoff:3.500A)
      removed outlier: 6.263A  pdb=" N   PHE A 201 " --> pdb=" O   ASP A 228 " (cutoff:3.500A)
      removed outlier: 3.991A  pdb=" N   ASP A 228 " --> pdb=" O   PHE A 201 " (cutoff:3.500A)
      removed outlier: 6.604A  pdb=" N   ILE A 203 " --> pdb=" O   LEU A 226 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43
      removed outlier: 5.517A  pdb=" N   ASP C 574 " --> pdb=" O   ILE C 587 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 47 through 55
      removed outlier: 3.916A  pdb=" N   ASP A 287 " --> pdb=" O   LYS A 278 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85
      removed outlier: 3.834A  pdb=" N   VAL A 126 " --> pdb=" O   SER A 172 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 319
      removed outlier: 6.596A  pdb=" N   VAL A 595 " --> pdb=" O   THR A 315 " (cutoff:3.500A)
      removed outlier: 4.702A  pdb=" N   ASN A 317 " --> pdb=" O   GLY A 593 " (cutoff:3.500A)
      removed outlier: 6.527A  pdb=" N   GLY A 593 " --> pdb=" O   ASN A 317 " (cutoff:3.500A)
      removed outlier: 4.251A  pdb=" N   GLY A 594 " --> pdb=" O   GLN A 613 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 325 through 328
      removed outlier: 5.517A  pdb=" N   ASP A 574 " --> pdb=" O   ILE A 587 " (cutoff:3.500A)
      removed outlier: 7.006A  pdb=" N   PHE A 565 " --> pdb=" O   PHE B  43 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 654 through 655
      removed outlier: 6.500A  pdb=" N   ILE A 670 " --> pdb=" O   ILE A 666 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 702 through 704
      removed outlier: 3.962A  pdb=" N   LYS B 790 " --> pdb=" O   ASN A 703 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'A' and resid 711 through 715
      removed outlier: 3.779A  pdb=" N   ALA A1078 " --> pdb=" O   PHE A1095 " (cutoff:3.500A)
      removed outlier: 4.655A  pdb=" N   PHE A1095 " --> pdb=" O   ALA A1078 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'A' and resid 718 through 728
      removed outlier: 5.966A  pdb=" N   TYR A1067 " --> pdb=" O   HIS A1048 " (cutoff:3.500A)
      removed outlier: 5.669A  pdb=" N   HIS A1048 " --> pdb=" O   TYR A1067 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'A' and resid 733 through 736
      removed outlier: 4.502A  pdb=" N   LYS A 733 " --> pdb=" O   LEU A 861 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'A' and resid 788 through 790
      removed outlier: 5.776A  pdb=" N   ILE A 788 " --> pdb=" O   ASN C 703 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB3
    Processing sheet with id=AB4, first strand: chain 'A' and resid 1120 through 1125
      removed outlier: 4.179A  pdb=" N   ALA A1087 " --> pdb=" O   SER A1123 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'B' and resid 28 through 30
      removed outlier: 8.390A  pdb=" N   ASN B  61 " --> pdb=" O   TYR B 269 " (cutoff:3.500A)
      removed outlier: 6.367A  pdb=" N   TYR B 269 " --> pdb=" O   ASN B  61 " (cutoff:3.500A)
      removed outlier: 6.263A  pdb=" N   PHE B 201 " --> pdb=" O   ASP B 228 " (cutoff:3.500A)
      removed outlier: 3.992A  pdb=" N   ASP B 228 " --> pdb=" O   PHE B 201 " (cutoff:3.500A)
      removed outlier: 6.604A  pdb=" N   ILE B 203 " --> pdb=" O   LEU B 226 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'B' and resid 47 through 55
      removed outlier: 3.916A  pdb=" N   ASP B 287 " --> pdb=" O   LYS B 278 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'B' and resid 84 through 85
      removed outlier: 3.834A  pdb=" N   VAL B 126 " --> pdb=" O   SER B 172 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'B' and resid 311 through 319
      removed outlier: 6.597A  pdb=" N   VAL B 595 " --> pdb=" O   THR B 315 " (cutoff:3.500A)
      removed outlier: 4.702A  pdb=" N   ASN B 317 " --> pdb=" O   GLY B 593 " (cutoff:3.500A)
      removed outlier: 6.528A  pdb=" N   GLY B 593 " --> pdb=" O   ASN B 317 " (cutoff:3.500A)
      removed outlier: 4.251A  pdb=" N   GLY B 594 " --> pdb=" O   GLN B 613 " (cutoff:3.500A)
    Processing sheet with id=AB9, first strand: chain 'B' and resid 325 through 328
      removed outlier: 5.517A  pdb=" N   ASP B 574 " --> pdb=" O   ILE B 587 " (cutoff:3.500A)
      removed outlier: 7.006A  pdb=" N   PHE B 565 " --> pdb=" O   PHE C  43 " (cutoff:3.500A)
    Processing sheet with id=AC1, first strand: chain 'B' and resid 654 through 655
      removed outlier: 6.500A  pdb=" N   ILE B 670 " --> pdb=" O   ILE B 666 " (cutoff:3.500A)
    Processing sheet with id=AC2, first strand: chain 'B' and resid 702 through 704
      removed outlier: 3.967A  pdb=" N   LYS C 790 " --> pdb=" O   ASN B 703 " (cutoff:3.500A)
    Processing sheet with id=AC3, first strand: chain 'B' and resid 711 through 715
      removed outlier: 3.779A  pdb=" N   ALA B1078 " --> pdb=" O   PHE B1095 " (cutoff:3.500A)
      removed outlier: 4.655A  pdb=" N   PHE B1095 " --> pdb=" O   ALA B1078 " (cutoff:3.500A)
    Processing sheet with id=AC4, first strand: chain 'B' and resid 718 through 728
      removed outlier: 5.966A  pdb=" N   TYR B1067 " --> pdb=" O   HIS B1048 " (cutoff:3.500A)
      removed outlier: 5.670A  pdb=" N   HIS B1048 " --> pdb=" O   TYR B1067 " (cutoff:3.500A)
    Processing sheet with id=AC5, first strand: chain 'B' and resid 733 through 736
      removed outlier: 4.502A  pdb=" N   LYS B 733 " --> pdb=" O   LEU B 861 " (cutoff:3.500A)
    Processing sheet with id=AC6, first strand: chain 'B' and resid 1120 through 1125
      removed outlier: 4.178A  pdb=" N   ALA B1087 " --> pdb=" O   SER B1123 " (cutoff:3.500A)
    Processing sheet with id=AC7, first strand: chain 'C' and resid 28 through 30
      removed outlier: 8.391A  pdb=" N   ASN C  61 " --> pdb=" O   TYR C 269 " (cutoff:3.500A)
      removed outlier: 6.367A  pdb=" N   TYR C 269 " --> pdb=" O   ASN C  61 " (cutoff:3.500A)
      removed outlier: 6.263A  pdb=" N   PHE C 201 " --> pdb=" O   ASP C 228 " (cutoff:3.500A)
      removed outlier: 3.992A  pdb=" N   ASP C 228 " --> pdb=" O   PHE C 201 " (cutoff:3.500A)
      removed outlier: 6.604A  pdb=" N   ILE C 203 " --> pdb=" O   LEU C 226 " (cutoff:3.500A)
    Processing sheet with id=AC8, first strand: chain 'C' and resid 47 through 55
      removed outlier: 3.915A  pdb=" N   ASP C 287 " --> pdb=" O   LYS C 278 " (cutoff:3.500A)
    Processing sheet with id=AC9, first strand: chain 'C' and resid 84 through 85
      removed outlier: 3.834A  pdb=" N   VAL C 126 " --> pdb=" O   SER C 172 " (cutoff:3.500A)
    Processing sheet with id=AD1, first strand: chain 'C' and resid 311 through 319
      removed outlier: 6.596A  pdb=" N   VAL C 595 " --> pdb=" O   THR C 315 " (cutoff:3.500A)
      removed outlier: 4.702A  pdb=" N   ASN C 317 " --> pdb=" O   GLY C 593 " (cutoff:3.500A)
      removed outlier: 6.526A  pdb=" N   GLY C 593 " --> pdb=" O   ASN C 317 " (cutoff:3.500A)
      removed outlier: 4.251A  pdb=" N   GLY C 594 " --> pdb=" O   GLN C 613 " (cutoff:3.500A)
    Processing sheet with id=AD2, first strand: chain 'C' and resid 654 through 655
      removed outlier: 6.500A  pdb=" N   ILE C 670 " --> pdb=" O   ILE C 666 " (cutoff:3.500A)
    Processing sheet with id=AD3, first strand: chain 'C' and resid 711 through 715
      removed outlier: 3.780A  pdb=" N   ALA C1078 " --> pdb=" O   PHE C1095 " (cutoff:3.500A)
      removed outlier: 4.656A  pdb=" N   PHE C1095 " --> pdb=" O   ALA C1078 " (cutoff:3.500A)
    Processing sheet with id=AD4, first strand: chain 'C' and resid 718 through 728
      removed outlier: 5.966A  pdb=" N   TYR C1067 " --> pdb=" O   HIS C1048 " (cutoff:3.500A)
      removed outlier: 5.669A  pdb=" N   HIS C1048 " --> pdb=" O   TYR C1067 " (cutoff:3.500A)
    Processing sheet with id=AD5, first strand: chain 'C' and resid 733 through 736
      removed outlier: 4.501A  pdb=" N   LYS C 733 " --> pdb=" O   LEU C 861 " (cutoff:3.500A)
    Processing sheet with id=AD6, first strand: chain 'C' and resid 1120 through 1125
      removed outlier: 4.179A  pdb=" N   ALA C1087 " --> pdb=" O   SER C1123 " (cutoff:3.500A)

    925 hydrogen bonds defined for protein.
    2550 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 7.37

  Time building geometry restraints manager: 5.01 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 5958
        1.34 -     1.46: 4346
        1.46 -     1.58: 8338
        1.58 -     1.70: 0
        1.70 -     1.81: 102
  Bond restraints: 18744
  Sorted by residual:
  bond pdb=" N   PRO B 899 "
       pdb=" CA  PRO B 899 "
    ideal  model  delta    sigma   weight residual
    1.472  1.458  0.014 1.32e-02 5.74e+03 1.14e+00
  bond pdb=" N   PRO A 899 "
       pdb=" CA  PRO A 899 "
    ideal  model  delta    sigma   weight residual
    1.472  1.458  0.014 1.32e-02 5.74e+03 1.09e+00
  bond pdb=" N   PRO B 892 "
       pdb=" CA  PRO B 892 "
    ideal  model  delta    sigma   weight residual
    1.467  1.454  0.013 1.21e-02 6.83e+03 1.09e+00
  bond pdb=" N   PRO A 892 "
       pdb=" CA  PRO A 892 "
    ideal  model  delta    sigma   weight residual
    1.467  1.454  0.013 1.21e-02 6.83e+03 1.08e+00
  bond pdb=" N   PRO C 899 "
       pdb=" CA  PRO C 899 "
    ideal  model  delta    sigma   weight residual
    1.472  1.458  0.014 1.32e-02 5.74e+03 1.05e+00
  ... (remaining 18739 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.40: 24932
        1.40 -     2.79: 409
        2.79 -     4.19: 129
        4.19 -     5.58: 6
        5.58 -     6.98: 6
  Bond angle restraints: 25482
  Sorted by residual:
  angle pdb=" N   PRO B 892 "
        pdb=" CA  PRO B 892 "
        pdb=" CB  PRO B 892 "
      ideal   model   delta    sigma   weight residual
     103.31  110.29   -6.98 8.90e-01 1.26e+00 6.15e+01
  angle pdb=" N   PRO C 892 "
        pdb=" CA  PRO C 892 "
        pdb=" CB  PRO C 892 "
      ideal   model   delta    sigma   weight residual
     103.31  110.27   -6.96 8.90e-01 1.26e+00 6.11e+01
  angle pdb=" N   PRO A 892 "
        pdb=" CA  PRO A 892 "
        pdb=" CB  PRO A 892 "
      ideal   model   delta    sigma   weight residual
     103.31  110.26   -6.95 8.90e-01 1.26e+00 6.10e+01
  angle pdb=" N   PRO A 899 "
        pdb=" CA  PRO A 899 "
        pdb=" CB  PRO A 899 "
      ideal   model   delta    sigma   weight residual
     103.33  110.06   -6.73 1.10e+00 8.26e-01 3.74e+01
  angle pdb=" N   PRO C 899 "
        pdb=" CA  PRO C 899 "
        pdb=" CB  PRO C 899 "
      ideal   model   delta    sigma   weight residual
     103.33  110.05   -6.72 1.10e+00 8.26e-01 3.73e+01
  ... (remaining 25477 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.53: 10688
       17.53 -    35.06: 373
       35.06 -    52.59: 90
       52.59 -    70.11: 60
       70.11 -    87.64: 12
  Dihedral angle restraints: 11223
    sinusoidal: 4371
      harmonic: 6852
  Sorted by residual:
  dihedral pdb=" CB  CYS B1032 "
           pdb=" SG  CYS B1032 "
           pdb=" SG  CYS B1043 "
           pdb=" CB  CYS B1043 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  176.02  -83.02     1      1.00e+01 1.00e-02 8.43e+01
  dihedral pdb=" CB  CYS A1032 "
           pdb=" SG  CYS A1032 "
           pdb=" SG  CYS A1043 "
           pdb=" CB  CYS A1043 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  176.02  -83.02     1      1.00e+01 1.00e-02 8.43e+01
  dihedral pdb=" CB  CYS C1032 "
           pdb=" SG  CYS C1032 "
           pdb=" SG  CYS C1043 "
           pdb=" CB  CYS C1043 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  176.02  -83.02     1      1.00e+01 1.00e-02 8.43e+01
  ... (remaining 11220 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.044: 2355
       0.044 -    0.088: 365
       0.088 -    0.132: 229
       0.132 -    0.175: 12
       0.175 -    0.219: 6
  Chirality restraints: 2967
  Sorted by residual:
  chirality pdb=" CA  PRO B 899 "
            pdb=" N   PRO B 899 "
            pdb=" C   PRO B 899 "
            pdb=" CB  PRO B 899 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.50    0.22 2.00e-01 2.50e+01 1.20e+00
  chirality pdb=" CA  PRO C 899 "
            pdb=" N   PRO C 899 "
            pdb=" C   PRO C 899 "
            pdb=" CB  PRO C 899 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.50    0.22 2.00e-01 2.50e+01 1.20e+00
  chirality pdb=" CA  PRO A 899 "
            pdb=" N   PRO A 899 "
            pdb=" C   PRO A 899 "
            pdb=" CB  PRO A 899 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.50    0.22 2.00e-01 2.50e+01 1.19e+00
  ... (remaining 2964 not shown)

  Planarity restraints: 3291
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE B1052 "   -0.017 5.00e-02 4.00e+02   2.54e-02 1.03e+00
        pdb=" N   PRO B1053 "    0.044 5.00e-02 4.00e+02
        pdb=" CA  PRO B1053 "   -0.013 5.00e-02 4.00e+02
        pdb=" CD  PRO B1053 "   -0.014 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE A1052 "   -0.017 5.00e-02 4.00e+02   2.52e-02 1.02e+00
        pdb=" N   PRO A1053 "    0.044 5.00e-02 4.00e+02
        pdb=" CA  PRO A1053 "   -0.013 5.00e-02 4.00e+02
        pdb=" CD  PRO A1053 "   -0.014 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE C1052 "    0.017 5.00e-02 4.00e+02   2.51e-02 1.01e+00
        pdb=" N   PRO C1053 "   -0.043 5.00e-02 4.00e+02
        pdb=" CA  PRO C1053 "    0.013 5.00e-02 4.00e+02
        pdb=" CD  PRO C1053 "    0.014 5.00e-02 4.00e+02
  ... (remaining 3288 not shown)

  Histogram of nonbonded interaction distances:
        2.27 -     2.80: 4554
        2.80 -     3.32: 16985
        3.32 -     3.85: 29873
        3.85 -     4.37: 35622
        4.37 -     4.90: 61709
  Nonbonded interactions: 148743
  Sorted by model distance:
  nonbonded pdb=" NZ  LYS A 790 "
            pdb=" OE2 GLU C 702 "
     model   vdw
     2.273 3.120
  nonbonded pdb=" OE2 GLU A 702 "
            pdb=" NZ  LYS B 790 "
     model   vdw
     2.277 3.120
  nonbonded pdb=" OE2 GLU B 702 "
            pdb=" NZ  LYS C 790 "
     model   vdw
     2.279 3.120
  nonbonded pdb=" OD2 ASP C 568 "
            pdb=" OG1 THR C 572 "
     model   vdw
     2.317 3.040
  nonbonded pdb=" OD2 ASP A 568 "
            pdb=" OG1 THR A 572 "
     model   vdw
     2.317 3.040
  ... (remaining 148738 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: 0.11
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'C'
  selection = chain 'B'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             3.280
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.670
  Check model and map are aligned:         0.110
  Set scattering table:                    0.150
  Process input model:                     44.820
  Find NCS groups from input model:        0.330
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:11.880
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   61.300
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8800
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  18771  Z= 0.140
  Angle     :  0.519   6.979  25536  Z= 0.308
  Chirality :  0.043   0.219   2967
  Planarity :  0.003   0.025   3291
  Dihedral  : 11.244  87.644   6708
  Min Nonbonded Distance : 2.273

Molprobity Statistics.
  All-atom Clashscore : 2.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.09 %
    Favored  : 97.91 %
  Rotamer:
    Outliers :  0.14 %
    Allowed  :  3.32 %
    Favored  : 96.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.16 (0.17), residues: 2301
  helix:  3.27 (0.20), residues: 600
  sheet:  0.58 (0.21), residues: 513
  loop : -0.47 (0.17), residues: 1188

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP C 104 
 HIS   0.002   0.001   HIS C1088 
 PHE   0.006   0.001   PHE B  55 
 TYR   0.011   0.001   TYR C1067 
 ARG   0.002   0.000   ARG A 983 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.09753 (  925)
  hydrogen bonds       : angle       6.31838 ( 2550)
  SS BOND              : bond        0.00308 (   27)
  SS BOND              : angle       0.84987 (   54)
  covalent geometry    : bond        0.00272 (18744)
  covalent geometry    : angle       0.51762 (25482)

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

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

  4602 Ramachandran restraints generated.
    2301 Oldfield, 0 Emsley, 2301 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4602 Ramachandran restraints generated.
    2301 Oldfield, 0 Emsley, 2301 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  65 residues out of total 2082 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 62
  time to evaluate  : 2.170 
Fit side-chains
   revert: symmetry clash
REVERT: A   64 TRP cc_start: 0.8368 (t60) cc_final: 0.7254 (t60)
REVERT: A  104 TRP cc_start: 0.7557 (m-90) cc_final: 0.7299 (m-90)
REVERT: B   64 TRP cc_start: 0.8315 (t60) cc_final: 0.7806 (t60)
REVERT: B  104 TRP cc_start: 0.7501 (m-90) cc_final: 0.7061 (m-90)
REVERT: C   64 TRP cc_start: 0.8345 (t60) cc_final: 0.7396 (t60)
REVERT: C  104 TRP cc_start: 0.7513 (m-90) cc_final: 0.6996 (m-90)
REVERT: C  201 PHE cc_start: 0.8112 (t80) cc_final: 0.7888 (t80)
  outliers start: 3
  outliers final: 2
  residues processed: 63
  average time/residue: 1.1380
  time to fit residues: 84.1762
Evaluate side-chains
  55 residues out of total 2082 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 53
  time to evaluate  : 2.116 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  140 PHE
Chi-restraints excluded: chain B residue  140 PHE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 234
   random chunks:
   chunk 197 optimal weight:    3.9990
   chunk 177 optimal weight:    2.9990
   chunk 98 optimal weight:    2.9990
   chunk 60 optimal weight:    7.9990
   chunk 119 optimal weight:    4.9990
   chunk 94 optimal weight:    4.9990
   chunk 183 optimal weight:    0.4980
   chunk 70 optimal weight:    4.9990
   chunk 111 optimal weight:    5.9990
   chunk 136 optimal weight:   10.0000
   chunk 212 optimal weight:    5.9990
   overall best weight:    3.0988

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

Flipped N/Q/H residues before XYZ refinement:
A 755 GLN
B 207 HIS
B 755 GLN
C 755 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3497 r_free = 0.3497 target = 0.070062 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2888 r_free = 0.2888 target = 0.045797 restraints weight = 59936.784|
|-----------------------------------------------------------------------------|
r_work (start): 0.2826 rms_B_bonded: 3.17
r_work: 0.2690 rms_B_bonded: 3.41 restraints_weight: 0.5000
r_work (final): 0.2690
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8816
moved from start:          0.1103

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.059  18771  Z= 0.272
  Angle     :  0.567   6.878  25536  Z= 0.299
  Chirality :  0.045   0.133   2967
  Planarity :  0.003   0.030   3291
  Dihedral  :  4.337  37.401   2491
  Min Nonbonded Distance : 2.606

Molprobity Statistics.
  All-atom Clashscore : 3.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.65 %
    Favored  : 97.35 %
  Rotamer:
    Outliers :  0.63 %
    Allowed  :  3.76 %
    Favored  : 95.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.25 (0.17), residues: 2301
  helix:  3.30 (0.21), residues: 582
  sheet:  0.84 (0.22), residues: 507
  loop : -0.42 (0.17), residues: 1212

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP A 886 
 HIS   0.003   0.001   HIS C1064 
 PHE   0.019   0.001   PHE B 201 
 TYR   0.019   0.002   TYR C1067 
 ARG   0.005   0.001   ARG A 328 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04834 (  925)
  hydrogen bonds       : angle       5.36719 ( 2550)
  SS BOND              : bond        0.00621 (   27)
  SS BOND              : angle       1.60624 (   54)
  covalent geometry    : bond        0.00630 (18744)
  covalent geometry    : angle       0.56240 (25482)

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

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

  4602 Ramachandran restraints generated.
    2301 Oldfield, 0 Emsley, 2301 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4602 Ramachandran restraints generated.
    2301 Oldfield, 0 Emsley, 2301 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  63 residues out of total 2082 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 50
  time to evaluate  : 2.250 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  104 TRP cc_start: 0.7348 (m-90) cc_final: 0.7114 (m-90)
REVERT: B   64 TRP cc_start: 0.8482 (t60) cc_final: 0.8002 (t60)
REVERT: B  104 TRP cc_start: 0.7415 (m-90) cc_final: 0.6915 (m-90)
REVERT: C  104 TRP cc_start: 0.7410 (m-90) cc_final: 0.6989 (m-90)
  outliers start: 13
  outliers final: 6
  residues processed: 54
  average time/residue: 1.1270
  time to fit residues: 71.9560
Evaluate side-chains
  53 residues out of total 2082 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 47
  time to evaluate  : 2.135 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  200 TYR
Chi-restraints excluded: chain A residue  565 PHE
Chi-restraints excluded: chain B residue  200 TYR
Chi-restraints excluded: chain B residue  565 PHE
Chi-restraints excluded: chain C residue  140 PHE
Chi-restraints excluded: chain C residue  200 TYR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 234
   random chunks:
   chunk 205 optimal weight:    4.9990
   chunk 16 optimal weight:    4.9990
   chunk 49 optimal weight:    6.9990
   chunk 231 optimal weight:    0.8980
   chunk 217 optimal weight:   10.0000
   chunk 66 optimal weight:    0.9980
   chunk 195 optimal weight:    1.9990
   chunk 50 optimal weight:    0.6980
   chunk 90 optimal weight:    8.9990
   chunk 172 optimal weight:   10.0000
   chunk 144 optimal weight:    2.9990
   overall best weight:    1.5184

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3520 r_free = 0.3520 target = 0.071057 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2924 r_free = 0.2924 target = 0.046976 restraints weight = 59532.790|
|-----------------------------------------------------------------------------|
r_work (start): 0.2861 rms_B_bonded: 3.15
r_work: 0.2727 rms_B_bonded: 3.42 restraints_weight: 0.5000
r_work (final): 0.2727
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8802
moved from start:          0.1320

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027  18771  Z= 0.145
  Angle     :  0.471   6.020  25536  Z= 0.248
  Chirality :  0.042   0.135   2967
  Planarity :  0.003   0.032   3291
  Dihedral  :  3.879  15.510   2487
  Min Nonbonded Distance : 2.626

Molprobity Statistics.
  All-atom Clashscore : 2.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.83 %
    Favored  : 98.17 %
  Rotamer:
    Outliers :  0.24 %
    Allowed  :  4.53 %
    Favored  : 95.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.44 (0.17), residues: 2301
  helix:  3.46 (0.20), residues: 582
  sheet:  0.99 (0.22), residues: 507
  loop : -0.33 (0.17), residues: 1212

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 886 
 HIS   0.002   0.000   HIS A1088 
 PHE   0.018   0.001   PHE B 201 
 TYR   0.018   0.001   TYR A1067 
 ARG   0.002   0.000   ARG C 328 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03979 (  925)
  hydrogen bonds       : angle       4.97686 ( 2550)
  SS BOND              : bond        0.00489 (   27)
  SS BOND              : angle       1.21747 (   54)
  covalent geometry    : bond        0.00328 (18744)
  covalent geometry    : angle       0.46836 (25482)

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

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

  4602 Ramachandran restraints generated.
    2301 Oldfield, 0 Emsley, 2301 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4602 Ramachandran restraints generated.
    2301 Oldfield, 0 Emsley, 2301 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  56 residues out of total 2082 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 51
  time to evaluate  : 2.021 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  104 TRP cc_start: 0.7252 (m-90) cc_final: 0.7029 (m-90)
REVERT: B   64 TRP cc_start: 0.8434 (t60) cc_final: 0.7927 (t60)
REVERT: B  104 TRP cc_start: 0.7311 (m-90) cc_final: 0.6783 (m-90)
REVERT: C  104 TRP cc_start: 0.7320 (m-90) cc_final: 0.7041 (m-90)
  outliers start: 5
  outliers final: 4
  residues processed: 52
  average time/residue: 1.1799
  time to fit residues: 72.3991
Evaluate side-chains
  55 residues out of total 2082 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 51
  time to evaluate  : 2.129 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  200 TYR
Chi-restraints excluded: chain B residue  200 TYR
Chi-restraints excluded: chain C residue  140 PHE
Chi-restraints excluded: chain C residue  200 TYR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 234
   random chunks:
   chunk 189 optimal weight:    0.9980
   chunk 83 optimal weight:    0.4980
   chunk 171 optimal weight:   10.0000
   chunk 8 optimal weight:   20.0000
   chunk 12 optimal weight:    6.9990
   chunk 6 optimal weight:   10.0000
   chunk 176 optimal weight:    3.9990
   chunk 216 optimal weight:    0.9990
   chunk 162 optimal weight:   10.0000
   chunk 52 optimal weight:    3.9990
   chunk 55 optimal weight:    1.9990
   overall best weight:    1.6986

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3520 r_free = 0.3520 target = 0.070642 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.2930 r_free = 0.2930 target = 0.046710 restraints weight = 60262.077|
|-----------------------------------------------------------------------------|
r_work (start): 0.2856 rms_B_bonded: 3.14
r_work: 0.2729 rms_B_bonded: 3.38 restraints_weight: 0.5000
r_work (final): 0.2729
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8840
moved from start:          0.1527

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029  18771  Z= 0.160
  Angle     :  0.471   5.607  25536  Z= 0.247
  Chirality :  0.042   0.133   2967
  Planarity :  0.003   0.033   3291
  Dihedral  :  3.811  15.467   2487
  Min Nonbonded Distance : 2.622

Molprobity Statistics.
  All-atom Clashscore : 2.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.35 %
    Favored  : 97.65 %
  Rotamer:
    Outliers :  0.72 %
    Allowed  :  4.53 %
    Favored  : 94.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.53 (0.18), residues: 2301
  helix:  3.52 (0.20), residues: 582
  sheet:  1.02 (0.22), residues: 525
  loop : -0.27 (0.18), residues: 1194

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 886 
 HIS   0.002   0.000   HIS C1064 
 PHE   0.014   0.001   PHE A 106 
 TYR   0.018   0.001   TYR B1067 
 ARG   0.001   0.000   ARG C 328 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04021 (  925)
  hydrogen bonds       : angle       4.91201 ( 2550)
  SS BOND              : bond        0.00465 (   27)
  SS BOND              : angle       1.21423 (   54)
  covalent geometry    : bond        0.00363 (18744)
  covalent geometry    : angle       0.46787 (25482)

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

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

  4602 Ramachandran restraints generated.
    2301 Oldfield, 0 Emsley, 2301 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4602 Ramachandran restraints generated.
    2301 Oldfield, 0 Emsley, 2301 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  72 residues out of total 2082 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 57
  time to evaluate  : 2.053 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  104 TRP cc_start: 0.7310 (m-90) cc_final: 0.7093 (m-90)
REVERT: B   64 TRP cc_start: 0.8399 (t60) cc_final: 0.7899 (t60)
REVERT: B  104 TRP cc_start: 0.7357 (m-90) cc_final: 0.7101 (m-90)
REVERT: C  104 TRP cc_start: 0.7407 (m-90) cc_final: 0.7163 (m-90)
  outliers start: 15
  outliers final: 7
  residues processed: 65
  average time/residue: 1.0221
  time to fit residues: 79.1895
Evaluate side-chains
  65 residues out of total 2082 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 58
  time to evaluate  : 1.991 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  135 PHE
Chi-restraints excluded: chain A residue  200 TYR
Chi-restraints excluded: chain B residue  135 PHE
Chi-restraints excluded: chain B residue  200 TYR
Chi-restraints excluded: chain C residue  135 PHE
Chi-restraints excluded: chain C residue  140 PHE
Chi-restraints excluded: chain C residue  200 TYR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 234
   random chunks:
   chunk 130 optimal weight:    3.9990
   chunk 171 optimal weight:    4.9990
   chunk 215 optimal weight:    1.9990
   chunk 4 optimal weight:   10.0000
   chunk 207 optimal weight:    0.8980
   chunk 105 optimal weight:    5.9990
   chunk 172 optimal weight:    0.0870
   chunk 232 optimal weight:    0.1980
   chunk 84 optimal weight:   10.0000
   chunk 164 optimal weight:   10.0000
   chunk 205 optimal weight:    8.9990
   overall best weight:    1.4362

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3528 r_free = 0.3528 target = 0.070956 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2942 r_free = 0.2942 target = 0.047096 restraints weight = 60635.622|
|-----------------------------------------------------------------------------|
r_work (start): 0.2868 rms_B_bonded: 3.14
r_work: 0.2740 rms_B_bonded: 3.38 restraints_weight: 0.5000
r_work (final): 0.2740
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8829
moved from start:          0.1674

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026  18771  Z= 0.137
  Angle     :  0.458   7.651  25536  Z= 0.238
  Chirality :  0.041   0.135   2967
  Planarity :  0.003   0.034   3291
  Dihedral  :  3.711  14.639   2487
  Min Nonbonded Distance : 2.627

Molprobity Statistics.
  All-atom Clashscore : 2.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.17 %
    Favored  : 97.83 %
  Rotamer:
    Outliers :  0.72 %
    Allowed  :  4.91 %
    Favored  : 94.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.57 (0.18), residues: 2301
  helix:  3.60 (0.20), residues: 582
  sheet:  1.05 (0.22), residues: 528
  loop : -0.27 (0.18), residues: 1191

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 886 
 HIS   0.001   0.000   HIS A1088 
 PHE   0.014   0.001   PHE B 106 
 TYR   0.017   0.001   TYR A1067 
 ARG   0.002   0.000   ARG C 328 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03774 (  925)
  hydrogen bonds       : angle       4.79214 ( 2550)
  SS BOND              : bond        0.00435 (   27)
  SS BOND              : angle       1.08868 (   54)
  covalent geometry    : bond        0.00311 (18744)
  covalent geometry    : angle       0.45621 (25482)

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

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

  4602 Ramachandran restraints generated.
    2301 Oldfield, 0 Emsley, 2301 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4602 Ramachandran restraints generated.
    2301 Oldfield, 0 Emsley, 2301 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  80 residues out of total 2082 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 65
  time to evaluate  : 2.053 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  104 TRP cc_start: 0.7259 (m-90) cc_final: 0.7056 (m-90)
REVERT: B   64 TRP cc_start: 0.8409 (t60) cc_final: 0.7865 (t60)
REVERT: B  104 TRP cc_start: 0.7331 (m-90) cc_final: 0.7103 (m-90)
REVERT: C  104 TRP cc_start: 0.7375 (m-90) cc_final: 0.7136 (m-90)
REVERT: C  197 ILE cc_start: 0.9038 (mt) cc_final: 0.8835 (pp)
  outliers start: 15
  outliers final: 8
  residues processed: 74
  average time/residue: 0.9838
  time to fit residues: 86.7154
Evaluate side-chains
  68 residues out of total 2082 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 60
  time to evaluate  : 2.095 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  200 TYR
Chi-restraints excluded: chain A residue  565 PHE
Chi-restraints excluded: chain A residue  617 CYS
Chi-restraints excluded: chain B residue  135 PHE
Chi-restraints excluded: chain B residue  200 TYR
Chi-restraints excluded: chain C residue  135 PHE
Chi-restraints excluded: chain C residue  140 PHE
Chi-restraints excluded: chain C residue  200 TYR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 234
   random chunks:
   chunk 158 optimal weight:    5.9990
   chunk 83 optimal weight:    0.9980
   chunk 130 optimal weight:    5.9990
   chunk 47 optimal weight:    3.9990
   chunk 186 optimal weight:    7.9990
   chunk 116 optimal weight:    2.9990
   chunk 224 optimal weight:    0.9980
   chunk 85 optimal weight:    5.9990
   chunk 55 optimal weight:    0.6980
   chunk 120 optimal weight:   10.0000
   chunk 78 optimal weight:   10.0000
   overall best weight:    1.9384

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

Flipped N/Q/H residues before XYZ refinement:
A 207 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3514 r_free = 0.3514 target = 0.070336 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2923 r_free = 0.2923 target = 0.046440 restraints weight = 60809.304|
|-----------------------------------------------------------------------------|
r_work (start): 0.2849 rms_B_bonded: 3.13
r_work: 0.2721 rms_B_bonded: 3.37 restraints_weight: 0.5000
r_work (final): 0.2721
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8850
moved from start:          0.1807

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039  18771  Z= 0.174
  Angle     :  0.480   6.595  25536  Z= 0.249
  Chirality :  0.042   0.134   2967
  Planarity :  0.003   0.034   3291
  Dihedral  :  3.773  15.596   2487
  Min Nonbonded Distance : 2.623

Molprobity Statistics.
  All-atom Clashscore : 3.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.43 %
    Favored  : 97.57 %
  Rotamer:
    Outliers :  0.72 %
    Allowed  :  5.49 %
    Favored  : 93.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.56 (0.18), residues: 2301
  helix:  3.55 (0.20), residues: 582
  sheet:  1.06 (0.22), residues: 525
  loop : -0.27 (0.18), residues: 1194

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 886 
 HIS   0.002   0.001   HIS C1064 
 PHE   0.015   0.001   PHE A 106 
 TYR   0.017   0.001   TYR C1067 
 ARG   0.002   0.000   ARG C1107 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04068 (  925)
  hydrogen bonds       : angle       4.86080 ( 2550)
  SS BOND              : bond        0.00472 (   27)
  SS BOND              : angle       1.24560 (   54)
  covalent geometry    : bond        0.00399 (18744)
  covalent geometry    : angle       0.47711 (25482)

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

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

  4602 Ramachandran restraints generated.
    2301 Oldfield, 0 Emsley, 2301 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4602 Ramachandran restraints generated.
    2301 Oldfield, 0 Emsley, 2301 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  78 residues out of total 2082 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 63
  time to evaluate  : 2.003 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  104 TRP cc_start: 0.7228 (m-90) cc_final: 0.7013 (m-90)
REVERT: B   64 TRP cc_start: 0.8388 (t60) cc_final: 0.7808 (t60)
REVERT: C  104 TRP cc_start: 0.7389 (m-90) cc_final: 0.7158 (m-90)
REVERT: C  197 ILE cc_start: 0.9032 (mt) cc_final: 0.8831 (pp)
  outliers start: 15
  outliers final: 10
  residues processed: 70
  average time/residue: 0.9930
  time to fit residues: 82.9771
Evaluate side-chains
  68 residues out of total 2082 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 58
  time to evaluate  : 2.107 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  200 TYR
Chi-restraints excluded: chain A residue  233 ILE
Chi-restraints excluded: chain A residue  565 PHE
Chi-restraints excluded: chain A residue  617 CYS
Chi-restraints excluded: chain B residue  135 PHE
Chi-restraints excluded: chain B residue  200 TYR
Chi-restraints excluded: chain B residue  233 ILE
Chi-restraints excluded: chain C residue  135 PHE
Chi-restraints excluded: chain C residue  140 PHE
Chi-restraints excluded: chain C residue  200 TYR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 234
   random chunks:
   chunk 214 optimal weight:    7.9990
   chunk 16 optimal weight:    7.9990
   chunk 178 optimal weight:    0.0370
   chunk 28 optimal weight:    9.9990
   chunk 64 optimal weight:    4.9990
   chunk 187 optimal weight:    0.9980
   chunk 66 optimal weight:    0.8980
   chunk 103 optimal weight:    1.9990
   chunk 223 optimal weight:    0.3980
   chunk 225 optimal weight:    0.9990
   chunk 13 optimal weight:   20.0000
   overall best weight:    0.6660

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3544 r_free = 0.3544 target = 0.071663 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2968 r_free = 0.2968 target = 0.047946 restraints weight = 60130.424|
|-----------------------------------------------------------------------------|
r_work (start): 0.2897 rms_B_bonded: 3.14
r_work: 0.2771 rms_B_bonded: 3.39 restraints_weight: 0.5000
r_work (final): 0.2771
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8804
moved from start:          0.1975

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029  18771  Z= 0.092
  Angle     :  0.431   6.836  25536  Z= 0.226
  Chirality :  0.041   0.136   2967
  Planarity :  0.003   0.035   3291
  Dihedral  :  3.531  14.798   2487
  Min Nonbonded Distance : 2.636

Molprobity Statistics.
  All-atom Clashscore : 3.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.04 %
    Favored  : 97.96 %
  Rotamer:
    Outliers :  0.63 %
    Allowed  :  5.59 %
    Favored  : 93.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.71 (0.18), residues: 2301
  helix:  3.73 (0.20), residues: 582
  sheet:  1.14 (0.22), residues: 546
  loop : -0.22 (0.18), residues: 1173

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP B 104 
 HIS   0.002   0.000   HIS A1088 
 PHE   0.015   0.001   PHE B 106 
 TYR   0.016   0.001   TYR B1067 
 ARG   0.002   0.000   ARG B1107 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03329 (  925)
  hydrogen bonds       : angle       4.58678 ( 2550)
  SS BOND              : bond        0.00366 (   27)
  SS BOND              : angle       0.86236 (   54)
  covalent geometry    : bond        0.00198 (18744)
  covalent geometry    : angle       0.42930 (25482)

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

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

  4602 Ramachandran restraints generated.
    2301 Oldfield, 0 Emsley, 2301 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4602 Ramachandran restraints generated.
    2301 Oldfield, 0 Emsley, 2301 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  79 residues out of total 2082 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 66
  time to evaluate  : 2.087 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   64 TRP cc_start: 0.8252 (t60) cc_final: 0.7764 (t60)
REVERT: A  104 TRP cc_start: 0.7166 (m-90) cc_final: 0.6954 (m-90)
REVERT: B   64 TRP cc_start: 0.8348 (t60) cc_final: 0.7779 (t60)
REVERT: C  104 TRP cc_start: 0.7294 (m-90) cc_final: 0.7050 (m-90)
  outliers start: 13
  outliers final: 7
  residues processed: 73
  average time/residue: 0.9422
  time to fit residues: 82.5237
Evaluate side-chains
  65 residues out of total 2082 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 58
  time to evaluate  : 2.090 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  200 TYR
Chi-restraints excluded: chain A residue  233 ILE
Chi-restraints excluded: chain A residue  617 CYS
Chi-restraints excluded: chain B residue  200 TYR
Chi-restraints excluded: chain B residue  233 ILE
Chi-restraints excluded: chain C residue  140 PHE
Chi-restraints excluded: chain C residue  200 TYR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 234
   random chunks:
   chunk 129 optimal weight:    3.9990
   chunk 167 optimal weight:    2.9990
   chunk 205 optimal weight:    5.9990
   chunk 36 optimal weight:    0.8980
   chunk 171 optimal weight:    6.9990
   chunk 151 optimal weight:    1.9990
   chunk 127 optimal weight:    8.9990
   chunk 22 optimal weight:    3.9990
   chunk 231 optimal weight:    0.4980
   chunk 219 optimal weight:    5.9990
   chunk 10 optimal weight:    9.9990
   overall best weight:    2.0786

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3514 r_free = 0.3514 target = 0.070295 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2921 r_free = 0.2921 target = 0.046362 restraints weight = 60373.355|
|-----------------------------------------------------------------------------|
r_work (start): 0.2845 rms_B_bonded: 3.12
r_work: 0.2719 rms_B_bonded: 3.35 restraints_weight: 0.5000
r_work (final): 0.2719
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8851
moved from start:          0.1982

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042  18771  Z= 0.186
  Angle     :  0.491   6.759  25536  Z= 0.254
  Chirality :  0.042   0.134   2967
  Planarity :  0.003   0.035   3291
  Dihedral  :  3.703  15.786   2487
  Min Nonbonded Distance : 2.517

Molprobity Statistics.
  All-atom Clashscore : 3.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.39 %
    Favored  : 97.61 %
  Rotamer:
    Outliers :  0.72 %
    Allowed  :  5.78 %
    Favored  : 93.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.66 (0.18), residues: 2301
  helix:  3.60 (0.20), residues: 600
  sheet:  1.09 (0.22), residues: 525
  loop : -0.24 (0.18), residues: 1176

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 104 
 HIS   0.002   0.001   HIS C1048 
 PHE   0.014   0.001   PHE C 106 
 TYR   0.018   0.001   TYR A 904 
 ARG   0.002   0.000   ARG C1019 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04068 (  925)
  hydrogen bonds       : angle       4.82465 ( 2550)
  SS BOND              : bond        0.00470 (   27)
  SS BOND              : angle       1.25956 (   54)
  covalent geometry    : bond        0.00426 (18744)
  covalent geometry    : angle       0.48854 (25482)

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

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

  4602 Ramachandran restraints generated.
    2301 Oldfield, 0 Emsley, 2301 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4602 Ramachandran restraints generated.
    2301 Oldfield, 0 Emsley, 2301 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  75 residues out of total 2082 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 60
  time to evaluate  : 2.266 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  104 TRP cc_start: 0.7198 (m-90) cc_final: 0.6987 (m-90)
REVERT: B   64 TRP cc_start: 0.8401 (t60) cc_final: 0.7779 (t60)
REVERT: C  104 TRP cc_start: 0.7350 (m-90) cc_final: 0.7126 (m-90)
  outliers start: 15
  outliers final: 12
  residues processed: 68
  average time/residue: 0.9453
  time to fit residues: 78.2762
Evaluate side-chains
  68 residues out of total 2082 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 56
  time to evaluate  : 2.046 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  135 PHE
Chi-restraints excluded: chain A residue  140 PHE
Chi-restraints excluded: chain A residue  200 TYR
Chi-restraints excluded: chain A residue  208 THR
Chi-restraints excluded: chain A residue  233 ILE
Chi-restraints excluded: chain A residue  565 PHE
Chi-restraints excluded: chain A residue  617 CYS
Chi-restraints excluded: chain B residue  135 PHE
Chi-restraints excluded: chain B residue  200 TYR
Chi-restraints excluded: chain B residue  233 ILE
Chi-restraints excluded: chain C residue  140 PHE
Chi-restraints excluded: chain C residue  200 TYR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 234
   random chunks:
   chunk 29 optimal weight:    1.9990
   chunk 42 optimal weight:   10.0000
   chunk 211 optimal weight:    0.9980
   chunk 24 optimal weight:    0.8980
   chunk 180 optimal weight:    7.9990
   chunk 63 optimal weight:    6.9990
   chunk 224 optimal weight:    4.9990
   chunk 53 optimal weight:    0.9990
   chunk 70 optimal weight:    3.9990
   chunk 182 optimal weight:    1.9990
   chunk 162 optimal weight:    9.9990
   overall best weight:    1.3786

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

Flipped N/Q/H residues before XYZ refinement:
C 207 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3526 r_free = 0.3526 target = 0.070842 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.2942 r_free = 0.2942 target = 0.047039 restraints weight = 60670.068|
|-----------------------------------------------------------------------------|
r_work (start): 0.2866 rms_B_bonded: 3.14
r_work: 0.2739 rms_B_bonded: 3.38 restraints_weight: 0.5000
r_work (final): 0.2739
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8834
moved from start:          0.2064

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  18771  Z= 0.134
  Angle     :  0.461   6.189  25536  Z= 0.240
  Chirality :  0.041   0.137   2967
  Planarity :  0.003   0.035   3291
  Dihedral  :  3.602  14.863   2487
  Min Nonbonded Distance : 2.517

Molprobity Statistics.
  All-atom Clashscore : 3.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.04 %
    Favored  : 97.96 %
  Rotamer:
    Outliers :  0.82 %
    Allowed  :  5.78 %
    Favored  : 93.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.67 (0.18), residues: 2301
  helix:  3.62 (0.20), residues: 600
  sheet:  1.10 (0.22), residues: 543
  loop : -0.26 (0.18), residues: 1158

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 104 
 HIS   0.001   0.000   HIS A1088 
 PHE   0.016   0.001   PHE C 565 
 TYR   0.016   0.001   TYR A1067 
 ARG   0.001   0.000   ARG C1019 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03704 (  925)
  hydrogen bonds       : angle       4.70840 ( 2550)
  SS BOND              : bond        0.00422 (   27)
  SS BOND              : angle       1.07562 (   54)
  covalent geometry    : bond        0.00305 (18744)
  covalent geometry    : angle       0.45884 (25482)

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

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

  4602 Ramachandran restraints generated.
    2301 Oldfield, 0 Emsley, 2301 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4602 Ramachandran restraints generated.
    2301 Oldfield, 0 Emsley, 2301 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  77 residues out of total 2082 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 60
  time to evaluate  : 2.166 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  104 TRP cc_start: 0.7178 (m-90) cc_final: 0.6972 (m-90)
REVERT: B   64 TRP cc_start: 0.8410 (t60) cc_final: 0.7820 (t60)
REVERT: C  104 TRP cc_start: 0.7330 (m-90) cc_final: 0.7094 (m-90)
  outliers start: 17
  outliers final: 15
  residues processed: 71
  average time/residue: 0.8845
  time to fit residues: 76.4777
Evaluate side-chains
  74 residues out of total 2082 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 59
  time to evaluate  : 2.065 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  135 PHE
Chi-restraints excluded: chain A residue  140 PHE
Chi-restraints excluded: chain A residue  200 TYR
Chi-restraints excluded: chain A residue  233 ILE
Chi-restraints excluded: chain A residue  565 PHE
Chi-restraints excluded: chain A residue  617 CYS
Chi-restraints excluded: chain B residue  135 PHE
Chi-restraints excluded: chain B residue  200 TYR
Chi-restraints excluded: chain B residue  208 THR
Chi-restraints excluded: chain B residue  233 ILE
Chi-restraints excluded: chain C residue  135 PHE
Chi-restraints excluded: chain C residue  140 PHE
Chi-restraints excluded: chain C residue  200 TYR
Chi-restraints excluded: chain C residue  208 THR
Chi-restraints excluded: chain C residue  233 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 234
   random chunks:
   chunk 166 optimal weight:    9.9990
   chunk 120 optimal weight:    2.9990
   chunk 98 optimal weight:    4.9990
   chunk 12 optimal weight:    1.9990
   chunk 156 optimal weight:   10.0000
   chunk 160 optimal weight:    0.6980
   chunk 111 optimal weight:    0.9980
   chunk 32 optimal weight:    0.9980
   chunk 188 optimal weight:    0.8980
   chunk 18 optimal weight:    7.9990
   chunk 6 optimal weight:   10.0000
   overall best weight:    1.1182

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3532 r_free = 0.3532 target = 0.071154 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2949 r_free = 0.2949 target = 0.047341 restraints weight = 60445.618|
|-----------------------------------------------------------------------------|
r_work (start): 0.2874 rms_B_bonded: 3.14
r_work: 0.2746 rms_B_bonded: 3.39 restraints_weight: 0.5000
r_work (final): 0.2746
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8823
moved from start:          0.2153

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  18771  Z= 0.117
  Angle     :  0.448   6.128  25536  Z= 0.233
  Chirality :  0.041   0.136   2967
  Planarity :  0.003   0.035   3291
  Dihedral  :  3.512  14.703   2487
  Min Nonbonded Distance : 2.528

Molprobity Statistics.
  All-atom Clashscore : 3.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.17 %
    Favored  : 97.83 %
  Rotamer:
    Outliers :  0.82 %
    Allowed  :  5.78 %
    Favored  : 93.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.76 (0.18), residues: 2301
  helix:  3.70 (0.20), residues: 600
  sheet:  1.13 (0.22), residues: 546
  loop : -0.20 (0.18), residues: 1155

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B 104 
 HIS   0.002   0.000   HIS A1088 
 PHE   0.014   0.001   PHE C 106 
 TYR   0.016   0.001   TYR C1067 
 ARG   0.001   0.000   ARG C1019 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03510 (  925)
  hydrogen bonds       : angle       4.63183 ( 2550)
  SS BOND              : bond        0.00385 (   27)
  SS BOND              : angle       0.98236 (   54)
  covalent geometry    : bond        0.00264 (18744)
  covalent geometry    : angle       0.44593 (25482)

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

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

  4602 Ramachandran restraints generated.
    2301 Oldfield, 0 Emsley, 2301 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4602 Ramachandran restraints generated.
    2301 Oldfield, 0 Emsley, 2301 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  80 residues out of total 2082 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 63
  time to evaluate  : 2.153 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   64 TRP cc_start: 0.8202 (t60) cc_final: 0.7760 (t60)
REVERT: B   64 TRP cc_start: 0.8384 (t60) cc_final: 0.7793 (t60)
REVERT: C  104 TRP cc_start: 0.7259 (m-90) cc_final: 0.6991 (m-90)
  outliers start: 17
  outliers final: 14
  residues processed: 75
  average time/residue: 0.8490
  time to fit residues: 78.2449
Evaluate side-chains
  75 residues out of total 2082 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 61
  time to evaluate  : 2.140 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  140 PHE
Chi-restraints excluded: chain A residue  200 TYR
Chi-restraints excluded: chain A residue  208 THR
Chi-restraints excluded: chain A residue  233 ILE
Chi-restraints excluded: chain A residue  617 CYS
Chi-restraints excluded: chain B residue  135 PHE
Chi-restraints excluded: chain B residue  200 TYR
Chi-restraints excluded: chain B residue  208 THR
Chi-restraints excluded: chain B residue  233 ILE
Chi-restraints excluded: chain C residue  135 PHE
Chi-restraints excluded: chain C residue  140 PHE
Chi-restraints excluded: chain C residue  200 TYR
Chi-restraints excluded: chain C residue  208 THR
Chi-restraints excluded: chain C residue  760 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 234
   random chunks:
   chunk 79 optimal weight:    1.9990
   chunk 207 optimal weight:    1.9990
   chunk 84 optimal weight:    9.9990
   chunk 141 optimal weight:    0.9980
   chunk 226 optimal weight:    3.9990
   chunk 102 optimal weight:    8.9990
   chunk 222 optimal weight:    3.9990
   chunk 47 optimal weight:    0.9990
   chunk 67 optimal weight:    2.9990
   chunk 81 optimal weight:    8.9990
   chunk 133 optimal weight:    0.9990
   overall best weight:    1.3988

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3524 r_free = 0.3524 target = 0.070809 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2937 r_free = 0.2937 target = 0.046985 restraints weight = 60345.954|
|-----------------------------------------------------------------------------|
r_work (start): 0.2869 rms_B_bonded: 3.13
r_work: 0.2742 rms_B_bonded: 3.37 restraints_weight: 0.5000
r_work (final): 0.2742
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8833
moved from start:          0.2169

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045  18771  Z= 0.136
  Angle     :  0.457   5.964  25536  Z= 0.238
  Chirality :  0.041   0.136   2967
  Planarity :  0.003   0.035   3291
  Dihedral  :  3.549  14.810   2487
  Min Nonbonded Distance : 2.533

Molprobity Statistics.
  All-atom Clashscore : 3.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.00 %
    Favored  : 98.00 %
  Rotamer:
    Outliers :  0.92 %
    Allowed  :  5.68 %
    Favored  : 93.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.76 (0.18), residues: 2301
  helix:  3.62 (0.20), residues: 603
  sheet:  1.16 (0.22), residues: 543
  loop : -0.18 (0.18), residues: 1155

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.001   TRP A 104 
 HIS   0.001   0.000   HIS C1064 
 PHE   0.014   0.001   PHE B 106 
 TYR   0.017   0.001   TYR C 904 
 ARG   0.002   0.000   ARG B1107 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03684 (  925)
  hydrogen bonds       : angle       4.67205 ( 2550)
  SS BOND              : bond        0.00416 (   27)
  SS BOND              : angle       1.07898 (   54)
  covalent geometry    : bond        0.00310 (18744)
  covalent geometry    : angle       0.45519 (25482)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 8579.37 seconds
wall clock time: 150 minutes 1.04 seconds (9001.04 seconds total)