Starting phenix.real_space_refine
on Sun Aug 24 08:53:15 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8r87_18997/08_2025/8r87_18997.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8r87_18997/08_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_18997/08_2025/8r87_18997.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8r87_18997/08_2025/8r87_18997.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8r87_18997/08_2025/8r87_18997.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8r87_18997/08_2025/8r87_18997.cif"
  }
  resolution = 3.0
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.001
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-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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:
    B, C
  Time building chain proxies: 5.45, per 1000 atoms: 0.30
  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 B 131 " - pdb=" SG  CYS B 166 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 131 " - pdb=" SG  CYS C 166 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 291 " - pdb=" SG  CYS B 301 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 291 " - pdb=" SG  CYS C 301 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 538 " - pdb=" SG  CYS B 590 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 538 " - pdb=" SG  CYS C 590 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 617 " - pdb=" SG  CYS B 649 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 617 " - pdb=" SG  CYS C 649 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 662 " - pdb=" SG  CYS B 671 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 662 " - pdb=" SG  CYS C 671 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 738 " - pdb=" SG  CYS B 760 " distance=2.02
    Simple disulfide: pdb=" SG  CYS C 738 " - pdb=" SG  CYS C 760 " distance=2.02
    Simple disulfide: pdb=" SG  CYS B 743 " - pdb=" SG  CYS B 749 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 743 " - pdb=" SG  CYS C 749 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B1032 " - pdb=" SG  CYS B1043 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C1032 " - pdb=" SG  CYS C1043 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B1082 " - pdb=" SG  CYS B1126 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C1082 " - pdb=" SG  CYS C1126 " 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: 1.50
  Conformation dependent library (CDL) restraints added in 550.6 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  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: 0.88
  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: 3.98

  Time building geometry restraints manager: 1.89 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: 0.05
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'C'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             5.500
  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:          0.310
  Check model and map are aligned:         0.050
  Set scattering table:                    0.040
  Process input model:                     17.740
  Find NCS groups from input model:        0.150
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:5.510
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   29.340
-------------------------------------------------------------------------------
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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.16 (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
 ARG   0.002   0.000   ARG A 983 
 TYR   0.011   0.001   TYR C1067 
 PHE   0.006   0.001   PHE B  55 
 TRP   0.006   0.001   TRP C 104 
 HIS   0.002   0.001   HIS C1088 

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

*********************** 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  : 0.588 
Fit side-chains
   revert: symmetry clash
REVERT: A   64 TRP cc_start: 0.8368 (t60) cc_final: 0.7255 (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: 0.7887 (t80)
  outliers start: 3
  outliers final: 2
  residues processed: 63
  average time/residue: 0.4615
  time to fit residues: 33.7481
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  : 0.756 
-------------------------------------------------------------------------------
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 216 optimal weight:    5.9990
   chunk 98 optimal weight:    2.9990
   chunk 194 optimal weight:    0.9980
   chunk 227 optimal weight:    1.9990
   chunk 107 optimal weight:   10.0000
   chunk 10 optimal weight:   10.0000
   chunk 66 optimal weight:    0.9990
   chunk 130 optimal weight:    4.9990
   chunk 124 optimal weight:    1.9990
   chunk 103 optimal weight:    9.9990
   chunk 200 optimal weight:    3.9990
   overall best weight:    1.7988

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

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

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3525 r_free = 0.3525 target = 0.071405 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.2928 r_free = 0.2928 target = 0.047203 restraints weight = 59952.480|
|-----------------------------------------------------------------------------|
r_work (start): 0.2864 rms_B_bonded: 3.17
r_work: 0.2730 rms_B_bonded: 3.42 restraints_weight: 0.5000
r_work (final): 0.2730
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8775
moved from start:          0.0985

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.052  18771  Z= 0.172
  Angle     :  0.497   5.599  25536  Z= 0.265
  Chirality :  0.043   0.134   2967
  Planarity :  0.003   0.030   3291
  Dihedral  :  4.122  36.961   2491
  Min Nonbonded Distance : 2.619

Molprobity Statistics.
  All-atom Clashscore : 2.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.35 %
    Favored  : 97.65 %
  Rotamer:
    Outliers :  0.53 %
    Allowed  :  3.61 %
    Favored  : 95.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.40 (0.17), residues: 2301
  helix:  3.40 (0.20), residues: 600
  sheet:  0.88 (0.22), residues: 507
  loop : -0.36 (0.17), residues: 1194

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG C 328 
 TYR   0.019   0.001   TYR C1067 
 PHE   0.022   0.001   PHE B 201 
 TRP   0.007   0.001   TRP A 886 
 HIS   0.002   0.001   HIS A1088 

Details of bonding type rmsd
  covalent geometry    : bond        0.00395 (18744)
  covalent geometry    : angle       0.49383 (25482)
  SS BOND              : bond        0.00540 (   27)
  SS BOND              : angle       1.27843 (   54)
  hydrogen bonds       : bond        0.04233 (  925)
  hydrogen bonds       : angle       5.15822 ( 2550)

*********************** 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
  61 residues out of total 2082 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 50
  time to evaluate  : 0.646 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  104 TRP cc_start: 0.7340 (m-90) cc_final: 0.7092 (m-90)
REVERT: B   64 TRP cc_start: 0.8454 (t60) cc_final: 0.8001 (t60)
REVERT: B  104 TRP cc_start: 0.7341 (m-90) cc_final: 0.6879 (m-90)
REVERT: C  104 TRP cc_start: 0.7319 (m-90) cc_final: 0.6879 (m-90)
  outliers start: 11
  outliers final: 4
  residues processed: 54
  average time/residue: 0.4480
  time to fit residues: 28.3813
Evaluate side-chains
  50 residues out of total 2082 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 46
  time to evaluate  : 0.534 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  200 TYR
Chi-restraints excluded: chain B residue  200 TYR
Chi-restraints excluded: chain B residue  565 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 60 optimal weight:    6.9990
   chunk 104 optimal weight:    7.9990
   chunk 212 optimal weight:    1.9990
   chunk 54 optimal weight:    0.5980
   chunk 203 optimal weight:    2.9990
   chunk 220 optimal weight:    4.9990
   chunk 48 optimal weight:    0.7980
   chunk 189 optimal weight:    7.9990
   chunk 118 optimal weight:    0.9980
   chunk 224 optimal weight:    3.9990
   chunk 2 optimal weight:    3.9990
   overall best weight:    1.4784

-------------------------------------------------------------------------------
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 = 0.071435 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2933 r_free = 0.2933 target = 0.047255 restraints weight = 60316.296|
|-----------------------------------------------------------------------------|
r_work (start): 0.2868 rms_B_bonded: 3.18
r_work: 0.2733 rms_B_bonded: 3.45 restraints_weight: 0.5000
r_work (final): 0.2733
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8794
moved from start:          0.1239

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= 0.144
  Angle     :  0.467   6.202  25536  Z= 0.246
  Chirality :  0.042   0.135   2967
  Planarity :  0.003   0.032   3291
  Dihedral  :  3.828  15.258   2487
  Min Nonbonded Distance : 2.625

Molprobity Statistics.
  All-atom Clashscore : 2.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.65 %
    Favored  : 98.35 %
  Rotamer:
    Outliers :  0.39 %
    Allowed  :  4.38 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.51 (0.17), residues: 2301
  helix:  3.50 (0.20), residues: 582
  sheet:  1.06 (0.22), residues: 507
  loop : -0.28 (0.17), residues: 1212

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C 328 
 TYR   0.018   0.001   TYR A1067 
 PHE   0.017   0.001   PHE B 201 
 TRP   0.007   0.001   TRP B 886 
 HIS   0.002   0.000   HIS B1088 

Details of bonding type rmsd
  covalent geometry    : bond        0.00326 (18744)
  covalent geometry    : angle       0.46431 (25482)
  SS BOND              : bond        0.00484 (   27)
  SS BOND              : angle       1.18705 (   54)
  hydrogen bonds       : bond        0.03946 (  925)
  hydrogen bonds       : angle       4.94527 ( 2550)

*********************** 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
  64 residues out of total 2082 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 56
  time to evaluate  : 0.542 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  104 TRP cc_start: 0.7283 (m-90) cc_final: 0.7020 (m-90)
REVERT: A  200 TYR cc_start: 0.9033 (m-80) cc_final: 0.8740 (OUTLIER)
REVERT: B   64 TRP cc_start: 0.8459 (t60) cc_final: 0.7986 (t60)
REVERT: B  104 TRP cc_start: 0.7301 (m-90) cc_final: 0.6770 (m-90)
REVERT: C   64 TRP cc_start: 0.8312 (t60) cc_final: 0.7885 (t60)
REVERT: C  104 TRP cc_start: 0.7328 (m-90) cc_final: 0.6852 (m-90)
  outliers start: 8
  outliers final: 6
  residues processed: 59
  average time/residue: 0.4905
  time to fit residues: 33.7445
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  : 0.690 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 234
   random chunks:
   chunk 110 optimal weight:    0.9990
   chunk 70 optimal weight:    2.9990
   chunk 26 optimal weight:    6.9990
   chunk 195 optimal weight:    1.9990
   chunk 208 optimal weight:    3.9990
   chunk 115 optimal weight:    5.9990
   chunk 186 optimal weight:    7.9990
   chunk 210 optimal weight:    0.5980
   chunk 193 optimal weight:    0.9990
   chunk 43 optimal weight:    0.6980
   chunk 151 optimal weight:    0.6980
   overall best weight:    0.7984

-------------------------------------------------------------------------------
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 = 0.3548 r_free = 0.3548 target = 0.072269 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2962 r_free = 0.2962 target = 0.048204 restraints weight = 60290.531|
|-----------------------------------------------------------------------------|
r_work (start): 0.2894 rms_B_bonded: 3.17
r_work: 0.2761 rms_B_bonded: 3.44 restraints_weight: 0.5000
r_work (final): 0.2761
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8754
moved from start:          0.1533

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026  18771  Z= 0.099
  Angle     :  0.437   7.580  25536  Z= 0.229
  Chirality :  0.041   0.135   2967
  Planarity :  0.003   0.034   3291
  Dihedral  :  3.604  14.116   2487
  Min Nonbonded Distance : 2.632

Molprobity Statistics.
  All-atom Clashscore : 2.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.96 %
    Favored  : 98.04 %
  Rotamer:
    Outliers :  0.48 %
    Allowed  :  4.14 %
    Favored  : 95.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.70 (0.18), residues: 2301
  helix:  3.67 (0.20), residues: 582
  sheet:  1.14 (0.22), residues: 528
  loop : -0.19 (0.18), residues: 1191

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C 328 
 TYR   0.017   0.001   TYR A1067 
 PHE   0.015   0.001   PHE C 106 
 TRP   0.005   0.001   TRP B 886 
 HIS   0.002   0.000   HIS A1088 

Details of bonding type rmsd
  covalent geometry    : bond        0.00217 (18744)
  covalent geometry    : angle       0.43515 (25482)
  SS BOND              : bond        0.00395 (   27)
  SS BOND              : angle       0.93277 (   54)
  hydrogen bonds       : bond        0.03431 (  925)
  hydrogen bonds       : angle       4.68318 ( 2550)

*********************** 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
  73 residues out of total 2082 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 63
  time to evaluate  : 0.743 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   64 TRP cc_start: 0.8192 (t60) cc_final: 0.7808 (t60)
REVERT: A  104 TRP cc_start: 0.7154 (m-90) cc_final: 0.6890 (m-90)
REVERT: A  200 TYR cc_start: 0.9101 (m-80) cc_final: 0.8737 (OUTLIER)
REVERT: A  740 MET cc_start: 0.8316 (OUTLIER) cc_final: 0.8106 (ttt)
REVERT: B   64 TRP cc_start: 0.8395 (t60) cc_final: 0.7888 (t60)
REVERT: B  104 TRP cc_start: 0.7243 (m-90) cc_final: 0.6707 (m-90)
REVERT: C   64 TRP cc_start: 0.8267 (t60) cc_final: 0.7790 (t60)
REVERT: C  104 TRP cc_start: 0.7209 (m-90) cc_final: 0.6737 (m-90)
REVERT: C  740 MET cc_start: 0.8430 (OUTLIER) cc_final: 0.8209 (ttt)
  outliers start: 10
  outliers final: 5
  residues processed: 66
  average time/residue: 0.4070
  time to fit residues: 31.8233
Evaluate side-chains
  62 residues out of total 2082 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 56
  time to evaluate  : 0.601 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  740 MET
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
Chi-restraints excluded: chain C residue  740 MET
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 234
   random chunks:
   chunk 178 optimal weight:    0.2980
   chunk 207 optimal weight:    4.9990
   chunk 57 optimal weight:    4.9990
   chunk 125 optimal weight:    3.9990
   chunk 60 optimal weight:    6.9990
   chunk 140 optimal weight:    2.9990
   chunk 218 optimal weight:    0.2980
   chunk 155 optimal weight:    0.8980
   chunk 121 optimal weight:    0.9990
   chunk 69 optimal weight:    4.9990
   chunk 114 optimal weight:    6.9990
   overall best weight:    1.0984

-------------------------------------------------------------------------------
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 = 0.3546 r_free = 0.3546 target = 0.071730 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.2964 r_free = 0.2964 target = 0.047764 restraints weight = 60232.257|
|-----------------------------------------------------------------------------|
r_work (start): 0.2888 rms_B_bonded: 3.15
r_work: 0.2761 rms_B_bonded: 3.40 restraints_weight: 0.5000
r_work (final): 0.2761
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8807
moved from start:          0.1650

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023  18771  Z= 0.115
  Angle     :  0.443   7.000  25536  Z= 0.230
  Chirality :  0.041   0.135   2967
  Planarity :  0.003   0.059   3291
  Dihedral  :  3.578  13.975   2487
  Min Nonbonded Distance : 2.630

Molprobity Statistics.
  All-atom Clashscore : 2.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.87 %
    Favored  : 98.13 %
  Rotamer:
    Outliers :  0.63 %
    Allowed  :  4.43 %
    Favored  : 94.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.75 (0.18), residues: 2301
  helix:  3.72 (0.20), residues: 582
  sheet:  1.21 (0.22), residues: 543
  loop : -0.20 (0.18), residues: 1176

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C 905 
 TYR   0.017   0.001   TYR C1067 
 PHE   0.015   0.001   PHE A 201 
 TRP   0.007   0.001   TRP B 886 
 HIS   0.002   0.000   HIS B1088 

Details of bonding type rmsd
  covalent geometry    : bond        0.00257 (18744)
  covalent geometry    : angle       0.44117 (25482)
  SS BOND              : bond        0.00398 (   27)
  SS BOND              : angle       0.99928 (   54)
  hydrogen bonds       : bond        0.03574 (  925)
  hydrogen bonds       : angle       4.65942 ( 2550)

*********************** 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
  74 residues out of total 2082 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 61
  time to evaluate  : 0.493 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   64 TRP cc_start: 0.8288 (t60) cc_final: 0.7887 (t60)
REVERT: A  104 TRP cc_start: 0.7223 (m-90) cc_final: 0.6953 (m-90)
REVERT: A  197 ILE cc_start: 0.8985 (mt) cc_final: 0.8772 (pp)
REVERT: A  200 TYR cc_start: 0.8971 (m-80) cc_final: 0.8662 (m-80)
REVERT: A  740 MET cc_start: 0.8380 (OUTLIER) cc_final: 0.8121 (ttt)
REVERT: B   64 TRP cc_start: 0.8401 (t60) cc_final: 0.7851 (t60)
REVERT: B  104 TRP cc_start: 0.7311 (m-90) cc_final: 0.6739 (m-90)
REVERT: B  740 MET cc_start: 0.8335 (OUTLIER) cc_final: 0.8069 (ttt)
REVERT: C   64 TRP cc_start: 0.8301 (t60) cc_final: 0.7849 (t60)
REVERT: C  104 TRP cc_start: 0.7325 (m-90) cc_final: 0.6847 (m-90)
REVERT: C  740 MET cc_start: 0.8479 (OUTLIER) cc_final: 0.8222 (ttt)
  outliers start: 13
  outliers final: 7
  residues processed: 68
  average time/residue: 0.3842
  time to fit residues: 31.3101
Evaluate side-chains
  69 residues out of total 2082 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 59
  time to evaluate  : 0.705 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  617 CYS
Chi-restraints excluded: chain A residue  740 MET
Chi-restraints excluded: chain B residue  200 TYR
Chi-restraints excluded: chain B residue  233 ILE
Chi-restraints excluded: chain B residue  617 CYS
Chi-restraints excluded: chain B residue  740 MET
Chi-restraints excluded: chain C residue  140 PHE
Chi-restraints excluded: chain C residue  200 TYR
Chi-restraints excluded: chain C residue  233 ILE
Chi-restraints excluded: chain C residue  740 MET
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 234
   random chunks:
   chunk 29 optimal weight:    9.9990
   chunk 225 optimal weight:    3.9990
   chunk 193 optimal weight:    4.9990
   chunk 60 optimal weight:    7.9990
   chunk 189 optimal weight:    6.9990
   chunk 33 optimal weight:    3.9990
   chunk 63 optimal weight:    8.9990
   chunk 95 optimal weight:   10.0000
   chunk 166 optimal weight:    9.9990
   chunk 162 optimal weight:   10.0000
   chunk 48 optimal weight:    0.9990
   overall best weight:    4.1990

-------------------------------------------------------------------------------
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 = 0.3485 r_free = 0.3485 target = 0.069010 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2879 r_free = 0.2879 target = 0.045028 restraints weight = 60729.297|
|-----------------------------------------------------------------------------|
r_work (start): 0.2801 rms_B_bonded: 3.11
r_work: 0.2673 rms_B_bonded: 3.34 restraints_weight: 0.5000
r_work (final): 0.2673
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8891
moved from start:          0.1806

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.049  18771  Z= 0.354
  Angle     :  0.609   8.755  25536  Z= 0.313
  Chirality :  0.045   0.134   2967
  Planarity :  0.004   0.048   3291
  Dihedral  :  4.208  17.622   2487
  Min Nonbonded Distance : 2.579

Molprobity Statistics.
  All-atom Clashscore : 3.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.91 %
    Favored  : 97.09 %
  Rotamer:
    Outliers :  0.82 %
    Allowed  :  4.77 %
    Favored  : 94.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.38 (0.18), residues: 2301
  helix:  3.31 (0.20), residues: 600
  sheet:  0.98 (0.22), residues: 525
  loop : -0.40 (0.18), residues: 1176

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C1019 
 TYR   0.020   0.002   TYR A1067 
 PHE   0.016   0.002   PHE A  92 
 TRP   0.020   0.002   TRP A 886 
 HIS   0.004   0.001   HIS C1048 

Details of bonding type rmsd
  covalent geometry    : bond        0.00816 (18744)
  covalent geometry    : angle       0.60413 (25482)
  SS BOND              : bond        0.00667 (   27)
  SS BOND              : angle       1.82054 (   54)
  hydrogen bonds       : bond        0.05123 (  925)
  hydrogen bonds       : angle       5.29870 ( 2550)

*********************** 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
  81 residues out of total 2082 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 64
  time to evaluate  : 0.630 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  104 TRP cc_start: 0.7312 (m-90) cc_final: 0.7111 (m-90)
REVERT: A  200 TYR cc_start: 0.9089 (m-80) cc_final: 0.8774 (m-80)
REVERT: B   64 TRP cc_start: 0.8443 (t60) cc_final: 0.7843 (t60)
REVERT: B  104 TRP cc_start: 0.7410 (m-90) cc_final: 0.7176 (m-90)
REVERT: C  104 TRP cc_start: 0.7478 (m-90) cc_final: 0.7261 (m-90)
REVERT: C  197 ILE cc_start: 0.9032 (mt) cc_final: 0.8831 (pp)
  outliers start: 17
  outliers final: 9
  residues processed: 73
  average time/residue: 0.4124
  time to fit residues: 35.4648
Evaluate side-chains
  68 residues out of total 2082 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 59
  time to evaluate  : 0.445 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  135 PHE
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
Chi-restraints excluded: chain C residue  233 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 234
   random chunks:
   chunk 16 optimal weight:    6.9990
   chunk 98 optimal weight:    0.8980
   chunk 28 optimal weight:    0.6980
   chunk 27 optimal weight:    5.9990
   chunk 146 optimal weight:    0.7980
   chunk 149 optimal weight:    2.9990
   chunk 203 optimal weight:    0.9980
   chunk 79 optimal weight:    5.9990
   chunk 93 optimal weight:    9.9990
   chunk 92 optimal weight:    5.9990
   chunk 161 optimal weight:    3.9990
   overall best weight:    1.2782

-------------------------------------------------------------------------------
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 = 0.3523 r_free = 0.3523 target = 0.070765 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2936 r_free = 0.2936 target = 0.046891 restraints weight = 60809.403|
|-----------------------------------------------------------------------------|
r_work (start): 0.2872 rms_B_bonded: 3.14
r_work: 0.2747 rms_B_bonded: 3.38 restraints_weight: 0.5000
r_work (final): 0.2747
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8840
moved from start:          0.1851

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030  18771  Z= 0.132
  Angle     :  0.467   5.920  25536  Z= 0.244
  Chirality :  0.041   0.136   2967
  Planarity :  0.003   0.042   3291
  Dihedral  :  3.788  15.980   2487
  Min Nonbonded Distance : 2.630

Molprobity Statistics.
  All-atom Clashscore : 3.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.22 %
    Favored  : 97.78 %
  Rotamer:
    Outliers :  0.87 %
    Allowed  :  5.15 %
    Favored  : 93.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.50 (0.18), residues: 2301
  helix:  3.53 (0.20), residues: 582
  sheet:  0.96 (0.22), residues: 528
  loop : -0.29 (0.18), residues: 1191

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C 328 
 TYR   0.016   0.001   TYR A1067 
 PHE   0.014   0.001   PHE B 106 
 TRP   0.007   0.001   TRP A 886 
 HIS   0.002   0.000   HIS A1088 

Details of bonding type rmsd
  covalent geometry    : bond        0.00297 (18744)
  covalent geometry    : angle       0.46436 (25482)
  SS BOND              : bond        0.00465 (   27)
  SS BOND              : angle       1.16490 (   54)
  hydrogen bonds       : bond        0.03813 (  925)
  hydrogen bonds       : angle       4.83937 ( 2550)

*********************** 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
  77 residues out of total 2082 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 59
  time to evaluate  : 0.536 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  104 TRP cc_start: 0.7247 (m-90) cc_final: 0.7046 (m-90)
REVERT: A  200 TYR cc_start: 0.9046 (m-80) cc_final: 0.8815 (OUTLIER)
REVERT: B   64 TRP cc_start: 0.8405 (t60) cc_final: 0.7771 (t60)
REVERT: B  104 TRP cc_start: 0.7334 (m-90) cc_final: 0.7123 (m-90)
REVERT: C  104 TRP cc_start: 0.7390 (m-90) cc_final: 0.7139 (m-90)
  outliers start: 18
  outliers final: 10
  residues processed: 72
  average time/residue: 0.4004
  time to fit residues: 34.1201
Evaluate side-chains
  67 residues out of total 2082 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 58
  time to evaluate  : 0.724 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  135 PHE
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
Chi-restraints excluded: chain C residue  233 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 234
   random chunks:
   chunk 23 optimal weight:    6.9990
   chunk 149 optimal weight:    1.9990
   chunk 69 optimal weight:    0.8980
   chunk 191 optimal weight:    7.9990
   chunk 28 optimal weight:    9.9990
   chunk 122 optimal weight:    4.9990
   chunk 46 optimal weight:    0.7980
   chunk 217 optimal weight:    9.9990
   chunk 144 optimal weight:    5.9990
   chunk 199 optimal weight:    4.9990
   chunk 4 optimal weight:    8.9990
   overall best weight:    2.7386

-------------------------------------------------------------------------------
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 = 0.3499 r_free = 0.3499 target = 0.069665 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.2900 r_free = 0.2900 target = 0.045734 restraints weight = 60509.665|
|-----------------------------------------------------------------------------|
r_work (start): 0.2830 rms_B_bonded: 3.13
r_work: 0.2698 rms_B_bonded: 3.39 restraints_weight: 0.5000
r_work (final): 0.2698
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8873
moved from start:          0.1926

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.054  18771  Z= 0.233
  Angle     :  0.523   7.080  25536  Z= 0.271
  Chirality :  0.043   0.132   2967
  Planarity :  0.003   0.040   3291
  Dihedral  :  3.924  16.016   2487
  Min Nonbonded Distance : 2.619

Molprobity Statistics.
  All-atom Clashscore : 3.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.52 %
    Favored  : 97.48 %
  Rotamer:
    Outliers :  0.67 %
    Allowed  :  5.59 %
    Favored  : 93.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.45 (0.18), residues: 2301
  helix:  3.40 (0.20), residues: 600
  sheet:  0.95 (0.22), residues: 525
  loop : -0.34 (0.18), residues: 1176

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C1019 
 TYR   0.018   0.001   TYR A1067 
 PHE   0.013   0.001   PHE B 898 
 TRP   0.010   0.001   TRP A 886 
 HIS   0.002   0.001   HIS C1048 

Details of bonding type rmsd
  covalent geometry    : bond        0.00538 (18744)
  covalent geometry    : angle       0.51896 (25482)
  SS BOND              : bond        0.00549 (   27)
  SS BOND              : angle       1.45345 (   54)
  hydrogen bonds       : bond        0.04400 (  925)
  hydrogen bonds       : angle       5.01172 ( 2550)

*********************** 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
  71 residues out of total 2082 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 57
  time to evaluate  : 0.488 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  104 TRP cc_start: 0.7247 (m-90) cc_final: 0.7020 (m-90)
REVERT: A  200 TYR cc_start: 0.9098 (m-80) cc_final: 0.8865 (OUTLIER)
REVERT: B   64 TRP cc_start: 0.8418 (t60) cc_final: 0.7838 (t60)
REVERT: B  104 TRP cc_start: 0.7377 (m-90) cc_final: 0.7166 (m-90)
REVERT: C  104 TRP cc_start: 0.7397 (m-90) cc_final: 0.7165 (m-90)
  outliers start: 14
  outliers final: 14
  residues processed: 64
  average time/residue: 0.3953
  time to fit residues: 30.0738
Evaluate side-chains
  69 residues out of total 2082 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 56
  time to evaluate  : 0.667 
-------------------------------------------------------------------------------
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  565 PHE
Chi-restraints excluded: chain A residue  617 CYS
Chi-restraints excluded: chain B residue  135 PHE
Chi-restraints excluded: chain B residue  140 PHE
Chi-restraints excluded: chain B residue  197 ILE
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
Chi-restraints excluded: chain C residue  233 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 234
   random chunks:
   chunk 32 optimal weight:    8.9990
   chunk 210 optimal weight:    0.7980
   chunk 65 optimal weight:    1.9990
   chunk 31 optimal weight:    0.9980
   chunk 208 optimal weight:    0.8980
   chunk 116 optimal weight:    1.9990
   chunk 66 optimal weight:    1.9990
   chunk 110 optimal weight:    0.9980
   chunk 211 optimal weight:    0.7980
   chunk 91 optimal weight:    8.9990
   chunk 158 optimal weight:    3.9990
   overall best weight:    0.8980

-------------------------------------------------------------------------------
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 = 0.3533 r_free = 0.3533 target = 0.071227 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2952 r_free = 0.2952 target = 0.047433 restraints weight = 60333.190|
|-----------------------------------------------------------------------------|
r_work (start): 0.2881 rms_B_bonded: 3.14
r_work: 0.2755 rms_B_bonded: 3.39 restraints_weight: 0.5000
r_work (final): 0.2755
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8817
moved from start:          0.2040

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031  18771  Z= 0.106
  Angle     :  0.451   5.570  25536  Z= 0.235
  Chirality :  0.041   0.136   2967
  Planarity :  0.003   0.040   3291
  Dihedral  :  3.616  15.769   2487
  Min Nonbonded Distance : 2.629

Molprobity Statistics.
  All-atom Clashscore : 3.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.13 %
    Favored  : 97.87 %
  Rotamer:
    Outliers :  0.58 %
    Allowed  :  5.68 %
    Favored  : 93.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.64 (0.18), residues: 2301
  helix:  3.63 (0.20), residues: 600
  sheet:  1.03 (0.22), residues: 543
  loop : -0.27 (0.18), residues: 1158

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C 765 
 TYR   0.016   0.001   TYR B1067 
 PHE   0.014   0.001   PHE B 106 
 TRP   0.005   0.001   TRP A 886 
 HIS   0.002   0.000   HIS A1088 

Details of bonding type rmsd
  covalent geometry    : bond        0.00237 (18744)
  covalent geometry    : angle       0.44941 (25482)
  SS BOND              : bond        0.00389 (   27)
  SS BOND              : angle       0.94685 (   54)
  hydrogen bonds       : bond        0.03495 (  925)
  hydrogen bonds       : angle       4.69317 ( 2550)

*********************** 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
  72 residues out of total 2082 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 60
  time to evaluate  : 0.531 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   64 TRP cc_start: 0.8231 (t60) cc_final: 0.7749 (t60)
REVERT: A  104 TRP cc_start: 0.7209 (m-90) cc_final: 0.7002 (m-90)
REVERT: A  200 TYR cc_start: 0.9073 (m-80) cc_final: 0.8862 (OUTLIER)
REVERT: B   64 TRP cc_start: 0.8389 (t60) cc_final: 0.7746 (t60)
REVERT: B  104 TRP cc_start: 0.7297 (m-90) cc_final: 0.7086 (m-90)
REVERT: C  104 TRP cc_start: 0.7310 (m-90) cc_final: 0.7058 (m-90)
  outliers start: 12
  outliers final: 9
  residues processed: 68
  average time/residue: 0.3899
  time to fit residues: 31.7087
Evaluate side-chains
  67 residues out of total 2082 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 59
  time to evaluate  : 0.537 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  197 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  233 ILE
Chi-restraints excluded: chain C residue  140 PHE
Chi-restraints excluded: chain C residue  200 TYR
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 183 optimal weight:    3.9990
   chunk 186 optimal weight:    7.9990
   chunk 82 optimal weight:    7.9990
   chunk 107 optimal weight:    6.9990
   chunk 35 optimal weight:    8.9990
   chunk 40 optimal weight:    3.9990
   chunk 109 optimal weight:    0.7980
   chunk 193 optimal weight:    0.8980
   chunk 39 optimal weight:    3.9990
   chunk 91 optimal weight:    4.9990
   chunk 108 optimal weight:    0.9980
   overall best weight:    2.1384

-------------------------------------------------------------------------------
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 = 0.3510 r_free = 0.3510 target = 0.070145 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2918 r_free = 0.2918 target = 0.046295 restraints weight = 60480.795|
|-----------------------------------------------------------------------------|
r_work (start): 0.2844 rms_B_bonded: 3.12
r_work: 0.2716 rms_B_bonded: 3.37 restraints_weight: 0.5000
r_work (final): 0.2716
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8855
moved from start:          0.2035

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045  18771  Z= 0.191
  Angle     :  0.493   6.357  25536  Z= 0.255
  Chirality :  0.042   0.134   2967
  Planarity :  0.003   0.041   3291
  Dihedral  :  3.751  15.787   2487
  Min Nonbonded Distance : 2.624

Molprobity Statistics.
  All-atom Clashscore : 3.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.43 %
    Favored  : 97.57 %
  Rotamer:
    Outliers :  0.72 %
    Allowed  :  5.44 %
    Favored  : 93.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.59 (0.18), residues: 2301
  helix:  3.54 (0.20), residues: 600
  sheet:  1.00 (0.22), residues: 525
  loop : -0.25 (0.18), residues: 1176

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B1107 
 TYR   0.017   0.001   TYR C1067 
 PHE   0.014   0.001   PHE A 106 
 TRP   0.008   0.001   TRP A 886 
 HIS   0.002   0.001   HIS C1064 

Details of bonding type rmsd
  covalent geometry    : bond        0.00437 (18744)
  covalent geometry    : angle       0.48966 (25482)
  SS BOND              : bond        0.00491 (   27)
  SS BOND              : angle       1.30406 (   54)
  hydrogen bonds       : bond        0.04086 (  925)
  hydrogen bonds       : angle       4.85895 ( 2550)

********************** 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
  75 residues out of total 2082 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 60
  time to evaluate  : 0.754 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  104 TRP cc_start: 0.7291 (m-90) cc_final: 0.7070 (m-90)
REVERT: A  200 TYR cc_start: 0.9100 (m-80) cc_final: 0.8890 (OUTLIER)
REVERT: B   64 TRP cc_start: 0.8400 (t60) cc_final: 0.7821 (t60)
REVERT: B  104 TRP cc_start: 0.7370 (m-90) cc_final: 0.7155 (m-90)
REVERT: C  104 TRP cc_start: 0.7382 (m-90) cc_final: 0.7139 (m-90)
  outliers start: 15
  outliers final: 14
  residues processed: 69
  average time/residue: 0.4069
  time to fit residues: 33.4043
Evaluate side-chains
  70 residues out of total 2082 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 57
  time to evaluate  : 0.712 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  140 PHE
Chi-restraints excluded: chain A residue  197 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  140 PHE
Chi-restraints excluded: chain B residue  197 ILE
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
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 98 optimal weight:    4.9990
   chunk 61 optimal weight:    0.9990
   chunk 178 optimal weight:    0.0060
   chunk 116 optimal weight:    1.9990
   chunk 165 optimal weight:    0.5980
   chunk 183 optimal weight:   10.0000
   chunk 200 optimal weight:    3.9990
   chunk 91 optimal weight:   10.0000
   chunk 147 optimal weight:    0.7980
   chunk 201 optimal weight:    0.6980
   chunk 189 optimal weight:    4.9990
   overall best weight:    0.6198

-------------------------------------------------------------------------------
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 = 0.3543 r_free = 0.3543 target = 0.071660 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2967 r_free = 0.2967 target = 0.047919 restraints weight = 60654.760|
|-----------------------------------------------------------------------------|
r_work (start): 0.2897 rms_B_bonded: 3.16
r_work: 0.2770 rms_B_bonded: 3.40 restraints_weight: 0.5000
r_work (final): 0.2770
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8807
moved from start:          0.2170

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030  18771  Z= 0.091
  Angle     :  0.439   5.598  25536  Z= 0.229
  Chirality :  0.041   0.134   2967
  Planarity :  0.003   0.040   3291
  Dihedral  :  3.516  15.609   2487
  Min Nonbonded Distance : 2.614

Molprobity Statistics.
  All-atom Clashscore : 3.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.17 %
    Favored  : 97.83 %
  Rotamer:
    Outliers :  0.53 %
    Allowed  :  5.68 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.71 (0.18), residues: 2301
  helix:  3.66 (0.20), residues: 603
  sheet:  1.07 (0.22), residues: 543
  loop : -0.22 (0.18), residues: 1155

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B1107 
 TYR   0.016   0.001   TYR A 904 
 PHE   0.015   0.001   PHE B 106 
 TRP   0.005   0.001   TRP C 104 
 HIS   0.002   0.000   HIS A1088 

Details of bonding type rmsd
  covalent geometry    : bond        0.00198 (18744)
  covalent geometry    : angle       0.43808 (25482)
  SS BOND              : bond        0.00370 (   27)
  SS BOND              : angle       0.85041 (   54)
  hydrogen bonds       : bond        0.03313 (  925)
  hydrogen bonds       : angle       4.59915 ( 2550)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3874.28 seconds
wall clock time: 67 minutes 20.12 seconds (4040.12 seconds total)