Starting phenix.real_space_refine
on Sat Dec 28 04:40:28 2024 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9bcv_44440/12_2024/9bcv_44440.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9bcv_44440/12_2024/9bcv_44440.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.2
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9bcv_44440/12_2024/9bcv_44440.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9bcv_44440/12_2024/9bcv_44440.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9bcv_44440/12_2024/9bcv_44440.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9bcv_44440/12_2024/9bcv_44440.cif"
  }
  resolution = 3.2
  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=   0.002 sd=   0.127
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: 6
    Type Number    sf(0)   Gaussians
     P       6      5.49       5
     Mg      2      5.21       5
     S      17      5.16       5
     C    4736      2.51       5
     N    1469      2.21       5
     O    1499      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib"
  Total number of atoms: 7729
  Number of models: 1
  Model: ""
    Number of chains: 12
    Chain: "A"
      Number of atoms: 1568
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 211, 1568
          Classifications: {'peptide': 211}
          Incomplete info: {'truncation_to_alanine': 23}
          Link IDs: {'PTRANS': 6, 'TRANS': 204}
          Unresolved non-hydrogen bonds: 76
          Unresolved non-hydrogen angles: 92
          Unresolved non-hydrogen dihedrals: 60
          Unresolved non-hydrogen chiralities: 3
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 6, 'ARG:plan': 1, 'ASP:plan': 5}
          Unresolved non-hydrogen planarities: 48
    Chain: "B"
      Number of atoms: 1580
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 211, 1580
          Classifications: {'peptide': 211}
          Incomplete info: {'truncation_to_alanine': 18}
          Link IDs: {'PTRANS': 6, 'TRANS': 204}
          Unresolved non-hydrogen bonds: 63
          Unresolved non-hydrogen angles: 74
          Unresolved non-hydrogen dihedrals: 52
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 5, 'ARG:plan': 1, 'ASP:plan': 2}
          Unresolved non-hydrogen planarities: 35
    Chain: "G"
      Number of atoms: 595
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 119, 595
          Classifications: {'peptide': 119}
          Incomplete info: {'truncation_to_alanine': 119}
          Link IDs: {'TRANS': 118}
          Unresolved non-hydrogen bonds: 238
          Unresolved non-hydrogen angles: 357
          Unresolved non-hydrogen dihedrals: 119
          Planarities with less than four sites: {'UNK:plan-1': 119}
          Unresolved non-hydrogen planarities: 119
    Chain: "H"
      Number of atoms: 560
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 112, 560
          Classifications: {'peptide': 112}
          Incomplete info: {'truncation_to_alanine': 112}
          Link IDs: {'TRANS': 111}
          Unresolved non-hydrogen bonds: 224
          Unresolved non-hydrogen angles: 336
          Unresolved non-hydrogen dihedrals: 112
          Planarities with less than four sites: {'UNK:plan-1': 112}
          Unresolved non-hydrogen planarities: 112
    Chain: "J"
      Number of atoms: 585
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 117, 585
          Classifications: {'peptide': 117}
          Incomplete info: {'truncation_to_alanine': 117}
          Link IDs: {'TRANS': 116}
          Unresolved non-hydrogen bonds: 234
          Unresolved non-hydrogen angles: 351
          Unresolved non-hydrogen dihedrals: 117
          Planarities with less than four sites: {'UNK:plan-1': 117}
          Unresolved non-hydrogen planarities: 117
    Chain: "I"
      Number of atoms: 560
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 112, 560
          Classifications: {'peptide': 112}
          Incomplete info: {'truncation_to_alanine': 112}
          Link IDs: {'TRANS': 111}
          Unresolved non-hydrogen bonds: 224
          Unresolved non-hydrogen angles: 336
          Unresolved non-hydrogen dihedrals: 112
          Planarities with less than four sites: {'UNK:plan-1': 112}
          Unresolved non-hydrogen planarities: 112
    Chain: "C"
      Number of atoms: 575
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 115, 575
          Classifications: {'peptide': 115}
          Incomplete info: {'truncation_to_alanine': 115}
          Link IDs: {'TRANS': 114}
          Unresolved non-hydrogen bonds: 230
          Unresolved non-hydrogen angles: 345
          Unresolved non-hydrogen dihedrals: 115
          Planarities with less than four sites: {'UNK:plan-1': 115}
          Unresolved non-hydrogen planarities: 115
    Chain: "D"
      Number of atoms: 530
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 106, 530
          Classifications: {'peptide': 106}
          Incomplete info: {'truncation_to_alanine': 106}
          Link IDs: {'TRANS': 105}
          Unresolved non-hydrogen bonds: 212
          Unresolved non-hydrogen angles: 318
          Unresolved non-hydrogen dihedrals: 106
          Planarities with less than four sites: {'UNK:plan-1': 106}
          Unresolved non-hydrogen planarities: 106
    Chain: "E"
      Number of atoms: 580
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 116, 580
          Classifications: {'peptide': 116}
          Incomplete info: {'truncation_to_alanine': 116}
          Link IDs: {'TRANS': 115}
          Unresolved non-hydrogen bonds: 232
          Unresolved non-hydrogen angles: 348
          Unresolved non-hydrogen dihedrals: 116
          Planarities with less than four sites: {'UNK:plan-1': 116}
          Unresolved non-hydrogen planarities: 116
    Chain: "F"
      Number of atoms: 530
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 106, 530
          Classifications: {'peptide': 106}
          Incomplete info: {'truncation_to_alanine': 106}
          Link IDs: {'TRANS': 105}
          Unresolved non-hydrogen bonds: 212
          Unresolved non-hydrogen angles: 318
          Unresolved non-hydrogen dihedrals: 106
          Planarities with less than four sites: {'UNK:plan-1': 106}
          Unresolved non-hydrogen planarities: 106
    Chain: "A"
      Number of atoms: 65
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 65
          Unusual residues: {' MG': 1, 'G2P': 2}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
    Chain: "B"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' MG': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 5.68, per 1000 atoms: 0.73
  Number of scatterers: 7729
  At special positions: 0
  Unit cell: (102.34, 128.52, 107.1, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S      17     16.00
     P       6     15.00
     Mg      2     11.99
     O    1499      8.00
     N    1469      7.00
     C    4736      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=1, symmetry=0
  Number of additional bonds: simple=1, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 2.34
  Conformation dependent library (CDL) restraints added in 459.0 milliseconds
  

  836 Ramachandran restraints generated.
    418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2580

  Finding SS restraints...
    Secondary structure from input PDB file:
      18 helices and 23 sheets defined
      45.0% alpha, 119.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.30
  Creating SS restraints...
    Processing helix  chain 'A' and resid 845 through 849
    Processing helix  chain 'A' and resid 854 through 863
    Processing helix  chain 'A' and resid 884 through 889
      removed outlier: 3.774A  pdb=" N   LEU A 888 " --> pdb=" O   GLY A 884 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 893 through 913
      removed outlier: 3.660A  pdb=" N   VAL A 897 " --> pdb=" O   THR A 893 " (cutoff:3.500A)
      removed outlier: 3.615A  pdb=" N   VAL A 898 " --> pdb=" O   PRO A 894 " (cutoff:3.500A)
      removed outlier: 3.661A  pdb=" N   ALA A 910 " --> pdb=" O   THR A 906 " (cutoff:3.500A)
      removed outlier: 3.886A  pdb=" N   VAL A 911 " --> pdb=" O   CYS A 907 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 939 through 957
      removed outlier: 4.530A  pdb=" N   CYS A 943 " --> pdb=" O   ARG A 939 " (cutoff:3.500A)
      removed outlier: 3.556A  pdb=" N   LEU A 950 " --> pdb=" O   ALA A 946 " (cutoff:3.500A)
      removed outlier: 3.614A  pdb=" N   ARG A 957 " --> pdb=" O   LEU A 953 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 996 through 1009
      removed outlier: 4.256A  pdb=" N   ASN A1000 " --> pdb=" O   GLY A 996 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1017 through 1028
      removed outlier: 3.538A  pdb=" N   LYS A1021 " --> pdb=" O   SER A1017 " (cutoff:3.500A)
      removed outlier: 3.616A  pdb=" N   ALA A1022 " --> pdb=" O   SER A1018 " (cutoff:3.500A)
      removed outlier: 3.962A  pdb=" N   VAL A1023 " --> pdb=" O   GLU A1019 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 842 through 846
      removed outlier: 4.225A  pdb=" N   TYR B 846 " --> pdb=" O   ALA B 843 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 850 through 860
    Processing helix  chain 'B' and resid 889 through 909
      removed outlier: 3.655A  pdb=" N   ALA B 906 " --> pdb=" O   THR B 902 " (cutoff:3.500A)
      removed outlier: 3.651A  pdb=" N   VAL B 907 " --> pdb=" O   CYS B 903 " (cutoff:3.500A)
      removed outlier: 3.685A  pdb=" N   ASP B 909 " --> pdb=" O   ASP B 905 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 935 through 952
      removed outlier: 4.601A  pdb=" N   CYS B 939 " --> pdb=" O   ARG B 935 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 993 through 1004
      removed outlier: 3.554A  pdb=" N   GLU B1002 " --> pdb=" O   ALA B 998 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1013 through 1024
      removed outlier: 3.756A  pdb=" N   ALA B1018 " --> pdb=" O   SER B1014 " (cutoff:3.500A)
      removed outlier: 4.030A  pdb=" N   VAL B1019 " --> pdb=" O   GLU B1015 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 28 through 32
      removed outlier: 3.771A  pdb=" N   UNK G  32 " --> pdb=" O   UNK G  29 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 62 through 65
    Processing helix  chain 'C' and resid 28 through 32
      removed outlier: 3.549A  pdb=" N   UNK C  32 " --> pdb=" O   UNK C  29 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 28 through 32
      removed outlier: 3.573A  pdb=" N   UNK E  32 " --> pdb=" O   UNK E  29 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 87 through 91
    Processing sheet with id=AA1, first strand: chain 'A' and resid 918 through 923
      removed outlier: 7.252A  pdb=" N   MET A 928 " --> pdb=" O   VAL A 920 " (cutoff:3.500A)
      removed outlier: 4.815A  pdb=" N   THR A 922 " --> pdb=" O   ALA A 926 " (cutoff:3.500A)
      removed outlier: 6.883A  pdb=" N   ALA A 926 " --> pdb=" O   THR A 922 " (cutoff:3.500A)
      removed outlier: 4.335A  pdb=" N   SER A 874 " --> pdb=" O   GLY A 978 " (cutoff:3.500A)
      removed outlier: 6.216A  pdb=" N   GLY A 978 " --> pdb=" O   SER A 874 " (cutoff:3.500A)
      removed outlier: 4.502A  pdb=" N   THR A 876 " --> pdb=" O   HIS A 976 " (cutoff:3.500A)
      removed outlier: 6.513A  pdb=" N   HIS A 976 " --> pdb=" O   THR A 876 " (cutoff:3.500A)
      removed outlier: 4.473A  pdb=" N   TYR A 878 " --> pdb=" O   GLY A 974 " (cutoff:3.500A)
      removed outlier: 6.634A  pdb=" N   GLY A 974 " --> pdb=" O   TYR A 878 " (cutoff:3.500A)
      removed outlier: 4.255A  pdb=" N   SER A 880 " --> pdb=" O   ARG A 972 " (cutoff:3.500A)
      removed outlier: 6.657A  pdb=" N   ARG A 972 " --> pdb=" O   SER A 880 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 918 through 923
      removed outlier: 7.252A  pdb=" N   MET A 928 " --> pdb=" O   VAL A 920 " (cutoff:3.500A)
      removed outlier: 4.815A  pdb=" N   THR A 922 " --> pdb=" O   ALA A 926 " (cutoff:3.500A)
      removed outlier: 6.883A  pdb=" N   ALA A 926 " --> pdb=" O   THR A 922 " (cutoff:3.500A)
      removed outlier: 4.335A  pdb=" N   SER A 874 " --> pdb=" O   GLY A 978 " (cutoff:3.500A)
      removed outlier: 6.216A  pdb=" N   GLY A 978 " --> pdb=" O   SER A 874 " (cutoff:3.500A)
      removed outlier: 4.502A  pdb=" N   THR A 876 " --> pdb=" O   HIS A 976 " (cutoff:3.500A)
      removed outlier: 6.513A  pdb=" N   HIS A 976 " --> pdb=" O   THR A 876 " (cutoff:3.500A)
      removed outlier: 4.473A  pdb=" N   TYR A 878 " --> pdb=" O   GLY A 974 " (cutoff:3.500A)
      removed outlier: 6.634A  pdb=" N   GLY A 974 " --> pdb=" O   TYR A 878 " (cutoff:3.500A)
      removed outlier: 4.255A  pdb=" N   SER A 880 " --> pdb=" O   ARG A 972 " (cutoff:3.500A)
      removed outlier: 6.657A  pdb=" N   ARG A 972 " --> pdb=" O   SER A 880 " (cutoff:3.500A)
      removed outlier: 6.869A  pdb=" N   ILE A 973 " --> pdb=" O   HIS A1015 " (cutoff:3.500A)
      removed outlier: 4.386A  pdb=" N   ILE A1014 " --> pdb=" O   LEU A1051 " (cutoff:3.500A)
      removed outlier: 7.710A  pdb=" N   THR A1048 " --> pdb=" O   ARG A1035 " (cutoff:3.500A)
      removed outlier: 6.678A  pdb=" N   GLU A1031 " --> pdb=" O   LEU A1052 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 914 through 919
      removed outlier: 7.166A  pdb=" N   MET B 924 " --> pdb=" O   VAL B 916 " (cutoff:3.500A)
      removed outlier: 4.766A  pdb=" N   THR B 918 " --> pdb=" O   ALA B 922 " (cutoff:3.500A)
      removed outlier: 6.695A  pdb=" N   ALA B 922 " --> pdb=" O   THR B 918 " (cutoff:3.500A)
      removed outlier: 5.725A  pdb=" N   ALA B 867 " --> pdb=" O   ALA B 978 " (cutoff:3.500A)
      removed outlier: 7.148A  pdb=" N   ALA B 978 " --> pdb=" O   ALA B 867 " (cutoff:3.500A)
      removed outlier: 5.179A  pdb=" N   ASP B 869 " --> pdb=" O   VAL B 976 " (cutoff:3.500A)
      removed outlier: 5.554A  pdb=" N   VAL B 976 " --> pdb=" O   ASP B 869 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 914 through 919
      removed outlier: 7.166A  pdb=" N   MET B 924 " --> pdb=" O   VAL B 916 " (cutoff:3.500A)
      removed outlier: 4.766A  pdb=" N   THR B 918 " --> pdb=" O   ALA B 922 " (cutoff:3.500A)
      removed outlier: 6.695A  pdb=" N   ALA B 922 " --> pdb=" O   THR B 918 " (cutoff:3.500A)
      removed outlier: 5.725A  pdb=" N   ALA B 867 " --> pdb=" O   ALA B 978 " (cutoff:3.500A)
      removed outlier: 7.148A  pdb=" N   ALA B 978 " --> pdb=" O   ALA B 867 " (cutoff:3.500A)
      removed outlier: 5.179A  pdb=" N   ASP B 869 " --> pdb=" O   VAL B 976 " (cutoff:3.500A)
      removed outlier: 5.554A  pdb=" N   VAL B 976 " --> pdb=" O   ASP B 869 " (cutoff:3.500A)
      removed outlier: 7.450A  pdb=" N   LEU B 967 " --> pdb=" O   LYS B1009 " (cutoff:3.500A)
      removed outlier: 8.591A  pdb=" N   HIS B1011 " --> pdb=" O   LEU B 967 " (cutoff:3.500A)
      removed outlier: 6.779A  pdb=" N   ILE B 969 " --> pdb=" O   HIS B1011 " (cutoff:3.500A)
      removed outlier: 4.466A  pdb=" N   ILE B1010 " --> pdb=" O   LEU B1047 " (cutoff:3.500A)
      removed outlier: 6.292A  pdb=" N   LYS B1041 " --> pdb=" O   GLU B1035 " (cutoff:3.500A)
      removed outlier: 6.844A  pdb=" N   GLU B1035 " --> pdb=" O   LYS B1041 " (cutoff:3.500A)
      removed outlier: 6.363A  pdb=" N   ARG B1043 " --> pdb=" O   ASP B1033 " (cutoff:3.500A)
      removed outlier: 7.118A  pdb=" N   ASP B1033 " --> pdb=" O   ARG B1043 " (cutoff:3.500A)
      removed outlier: 7.481A  pdb=" N   TYR B1045 " --> pdb=" O   ARG B1031 " (cutoff:3.500A)
      removed outlier: 5.689A  pdb=" N   ARG B1031 " --> pdb=" O   TYR B1045 " (cutoff:3.500A)
      removed outlier: 5.550A  pdb=" N   LEU B1047 " --> pdb=" O   GLU B1029 " (cutoff:3.500A)
      removed outlier: 7.059A  pdb=" N   GLU B1029 " --> pdb=" O   LEU B1047 " (cutoff:3.500A)
      removed outlier: 4.016A  pdb=" N   GLY B1049 " --> pdb=" O   GLU B1027 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'G' and resid 5 through 6
      removed outlier: 3.548A  pdb=" N   UNK G   5 " --> pdb=" O   UNK G  23 " (cutoff:3.500A)
      removed outlier: 3.691A  pdb=" N   UNK G  23 " --> pdb=" O   UNK G   5 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'G' and resid 57 through 60
      removed outlier: 4.189A  pdb=" N   UNK G  57 " --> pdb=" O   UNK G  52 " (cutoff:3.500A)
      removed outlier: 3.505A  pdb=" N   UNK G  59 " --> pdb=" O   UNK G  50 " (cutoff:3.500A)
      removed outlier: 6.745A  pdb=" N   UNK G  36 " --> pdb=" O   UNK G  48 " (cutoff:3.500A)
      removed outlier: 4.552A  pdb=" N   UNK G  50 " --> pdb=" O   UNK G  34 " (cutoff:3.500A)
      removed outlier: 6.626A  pdb=" N   UNK G  34 " --> pdb=" O   UNK G  50 " (cutoff:3.500A)
      removed outlier: 6.722A  pdb=" N   UNK G  96 " --> pdb=" O   UNK G 111 " (cutoff:3.500A)
      removed outlier: 4.668A  pdb=" N   UNK G 111 " --> pdb=" O   UNK G  96 " (cutoff:3.500A)
      removed outlier: 6.681A  pdb=" N   UNK G  98 " --> pdb=" O   UNK G 109 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'H' and resid 5 through 6
    Processing sheet with id=AA8, first strand: chain 'H' and resid 10 through 12
      removed outlier: 3.732A  pdb=" N   UNK H  92 " --> pdb=" O   UNK H 108 " (cutoff:3.500A)
      removed outlier: 6.559A  pdb=" N   UNK H  39 " --> pdb=" O   UNK H  55 " (cutoff:3.500A)
      removed outlier: 4.773A  pdb=" N   UNK H  55 " --> pdb=" O   UNK H  39 " (cutoff:3.500A)
      removed outlier: 6.808A  pdb=" N   UNK H  41 " --> pdb=" O   UNK H  53 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'J' and resid 3 through 5
    Processing sheet with id=AB1, first strand: chain 'J' and resid 58 through 60
      removed outlier: 6.782A  pdb=" N   UNK J  36 " --> pdb=" O   UNK J  48 " (cutoff:3.500A)
      removed outlier: 4.495A  pdb=" N   UNK J  50 " --> pdb=" O   UNK J  34 " (cutoff:3.500A)
      removed outlier: 6.661A  pdb=" N   UNK J  34 " --> pdb=" O   UNK J  50 " (cutoff:3.500A)
      removed outlier: 6.769A  pdb=" N   UNK J  96 " --> pdb=" O   UNK J 111 " (cutoff:3.500A)
      removed outlier: 4.694A  pdb=" N   UNK J 111 " --> pdb=" O   UNK J  96 " (cutoff:3.500A)
      removed outlier: 6.612A  pdb=" N   UNK J  98 " --> pdb=" O   UNK J 109 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'J' and resid 58 through 60
      removed outlier: 6.782A  pdb=" N   UNK J  36 " --> pdb=" O   UNK J  48 " (cutoff:3.500A)
      removed outlier: 4.495A  pdb=" N   UNK J  50 " --> pdb=" O   UNK J  34 " (cutoff:3.500A)
      removed outlier: 6.661A  pdb=" N   UNK J  34 " --> pdb=" O   UNK J  50 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'I' and resid 5 through 6
    Processing sheet with id=AB4, first strand: chain 'I' and resid 10 through 12
      removed outlier: 3.749A  pdb=" N   UNK I  92 " --> pdb=" O   UNK I 108 " (cutoff:3.500A)
      removed outlier: 5.938A  pdb=" N   UNK I  43 " --> pdb=" O   UNK I  52 " (cutoff:3.500A)
      removed outlier: 5.640A  pdb=" N   UNK I  52 " --> pdb=" O   UNK I  43 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'C' and resid 3 through 6
      removed outlier: 3.569A  pdb=" N   UNK C  23 " --> pdb=" O   UNK C   5 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'C' and resid 45 through 50
      removed outlier: 5.047A  pdb=" N   UNK C  47 " --> pdb=" O   UNK C  38 " (cutoff:3.500A)
      removed outlier: 5.849A  pdb=" N   UNK C  38 " --> pdb=" O   UNK C  47 " (cutoff:3.500A)
      removed outlier: 3.752A  pdb=" N   UNK C  49 " --> pdb=" O   UNK C  36 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'D' and resid 10 through 12
      removed outlier: 6.549A  pdb=" N   UNK D  11 " --> pdb=" O   UNK D 105 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB7
    Processing sheet with id=AB8, first strand: chain 'D' and resid 19 through 22
    Processing sheet with id=AB9, first strand: chain 'D' and resid 53 through 54
      removed outlier: 5.492A  pdb=" N   UNK D  46 " --> pdb=" O   UNK D  37 " (cutoff:3.500A)
      removed outlier: 5.960A  pdb=" N   UNK D  37 " --> pdb=" O   UNK D  46 " (cutoff:3.500A)
      removed outlier: 3.817A  pdb=" N   UNK D  97 " --> pdb=" O   UNK D  90 " (cutoff:3.500A)
    Processing sheet with id=AC1, first strand: chain 'E' and resid 3 through 7
    Processing sheet with id=AC2, first strand: chain 'E' and resid 11 through 12
      removed outlier: 3.788A  pdb=" N   UNK E  99 " --> pdb=" O   UNK E  33 " (cutoff:3.500A)
      removed outlier: 7.132A  pdb=" N   UNK E  34 " --> pdb=" O   UNK E  50 " (cutoff:3.500A)
      removed outlier: 4.856A  pdb=" N   UNK E  50 " --> pdb=" O   UNK E  34 " (cutoff:3.500A)
      removed outlier: 6.689A  pdb=" N   UNK E  36 " --> pdb=" O   UNK E  48 " (cutoff:3.500A)
    Processing sheet with id=AC3, first strand: chain 'F' and resid 10 through 12
      removed outlier: 3.535A  pdb=" N   UNK F 105 " --> pdb=" O   UNK F  11 " (cutoff:3.500A)
      removed outlier: 3.846A  pdb=" N   UNK F  86 " --> pdb=" O   UNK F 102 " (cutoff:3.500A)
      removed outlier: 4.502A  pdb=" N   UNK F  84 " --> pdb=" O   UNK F 104 " (cutoff:3.500A)
      removed outlier: 6.466A  pdb=" N   UNK F  37 " --> pdb=" O   UNK F  46 " (cutoff:3.500A)
      removed outlier: 5.803A  pdb=" N   UNK F  46 " --> pdb=" O   UNK F  37 " (cutoff:3.500A)
    Processing sheet with id=AC4, first strand: chain 'F' and resid 10 through 12
      removed outlier: 3.535A  pdb=" N   UNK F 105 " --> pdb=" O   UNK F  11 " (cutoff:3.500A)
      removed outlier: 3.846A  pdb=" N   UNK F  86 " --> pdb=" O   UNK F 102 " (cutoff:3.500A)
      removed outlier: 4.502A  pdb=" N   UNK F  84 " --> pdb=" O   UNK F 104 " (cutoff:3.500A)
      removed outlier: 3.954A  pdb=" N   UNK F  97 " --> pdb=" O   UNK F  90 " (cutoff:3.500A)
    Processing sheet with id=AC5, first strand: chain 'F' and resid 19 through 24

    400 hydrogen bonds defined for protein.
    1026 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: 2.47

  Time building geometry restraints manager: 2.56 seconds

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

  Histogram of bond lengths:
        1.22 -     1.35: 2864
        1.35 -     1.47: 1689
        1.47 -     1.60: 3190
        1.60 -     1.73: 6
        1.73 -     1.85: 30
  Bond restraints: 7779
  Sorted by residual:
  bond pdb=" CA  GLY A 938 "
       pdb=" C   GLY A 938 "
    ideal  model  delta    sigma   weight residual
    1.530  1.512  0.019 1.04e-02 9.25e+03 3.19e+00
  bond pdb=" N   GLY A 938 "
       pdb=" CA  GLY A 938 "
    ideal  model  delta    sigma   weight residual
    1.464  1.448  0.016 1.12e-02 7.97e+03 2.13e+00
  bond pdb=" C   UNK C   7 "
       pdb=" N   UNK C   8 "
    ideal  model  delta    sigma   weight residual
    1.329  1.341 -0.012 1.40e-02 5.10e+03 7.26e-01
  bond pdb=" CA  UNK E 101 "
       pdb=" CB  UNK E 101 "
    ideal  model  delta    sigma   weight residual
    1.530  1.514  0.016 2.00e-02 2.50e+03 6.32e-01
  bond pdb=" CA  UNK H   1 "
       pdb=" CB  UNK H   1 "
    ideal  model  delta    sigma   weight residual
    1.530  1.514  0.016 2.00e-02 2.50e+03 6.19e-01
  ... (remaining 7774 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.31: 9574
        1.31 -     2.62: 1005
        2.62 -     3.93: 143
        3.93 -     5.24: 29
        5.24 -     6.55: 6
  Bond angle restraints: 10757
  Sorted by residual:
  angle pdb=" C   UNK I  56 "
        pdb=" N   UNK I  57 "
        pdb=" CA  UNK I  57 "
      ideal   model   delta    sigma   weight residual
     121.70  127.17   -5.47 1.80e+00 3.09e-01 9.25e+00
  angle pdb=" C   UNK J  25 "
        pdb=" N   UNK J  26 "
        pdb=" CA  UNK J  26 "
      ideal   model   delta    sigma   weight residual
     121.70  126.94   -5.24 1.80e+00 3.09e-01 8.48e+00
  angle pdb=" C   UNK I  62 "
        pdb=" CA  UNK I  62 "
        pdb=" CB  UNK I  62 "
      ideal   model   delta    sigma   weight residual
     110.08  115.57   -5.49 1.90e+00 2.77e-01 8.35e+00
  angle pdb=" C   UNK H  71 "
        pdb=" N   UNK H  72 "
        pdb=" CA  UNK H  72 "
      ideal   model   delta    sigma   weight residual
     121.70  126.83   -5.13 1.80e+00 3.09e-01 8.13e+00
  angle pdb=" C   UNK F  65 "
        pdb=" N   UNK F  66 "
        pdb=" CA  UNK F  66 "
      ideal   model   delta    sigma   weight residual
     121.70  126.79   -5.09 1.80e+00 3.09e-01 7.99e+00
  ... (remaining 10752 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    18.32: 4355
       18.32 -    36.63: 215
       36.63 -    54.95: 57
       54.95 -    73.27: 19
       73.27 -    91.59: 15
  Dihedral angle restraints: 4661
    sinusoidal: 752
      harmonic: 3909
  Sorted by residual:
  dihedral pdb=" CA  UNK G   7 "
           pdb=" C   UNK G   7 "
           pdb=" N   UNK G   8 "
           pdb=" CA  UNK G   8 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.89   19.11     0      5.00e+00 4.00e-02 1.46e+01
  dihedral pdb=" CA  UNK G   6 "
           pdb=" C   UNK G   6 "
           pdb=" N   UNK G   7 "
           pdb=" CA  UNK G   7 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -161.55  -18.45     0      5.00e+00 4.00e-02 1.36e+01
  dihedral pdb=" CA  UNK H   6 "
           pdb=" C   UNK H   6 "
           pdb=" N   UNK H   7 "
           pdb=" CA  UNK H   7 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -163.07  -16.93     0      5.00e+00 4.00e-02 1.15e+01
  ... (remaining 4658 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.033: 948
       0.033 -    0.067: 327
       0.067 -    0.100: 104
       0.100 -    0.133: 40
       0.133 -    0.167: 6
  Chirality restraints: 1425
  Sorted by residual:
  chirality pdb=" C3' G2P A1102 "
            pdb=" C2' G2P A1102 "
            pdb=" C4' G2P A1102 "
            pdb=" O3' G2P A1102 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.71   -2.54   -0.17 2.00e-01 2.50e+01 6.96e-01
  chirality pdb=" CA  VAL B 871 "
            pdb=" N   VAL B 871 "
            pdb=" C   VAL B 871 "
            pdb=" CB  VAL B 871 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.58   -0.14 2.00e-01 2.50e+01 5.08e-01
  chirality pdb=" CA  UNK J  26 "
            pdb=" N   UNK J  26 "
            pdb=" C   UNK J  26 "
            pdb=" CB  UNK J  26 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.52    2.38    0.14 2.00e-01 2.50e+01 4.77e-01
  ... (remaining 1422 not shown)

  Planarity restraints: 1457
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR A 893 "   -0.027 5.00e-02 4.00e+02   4.05e-02 2.63e+00
        pdb=" N   PRO A 894 "    0.070 5.00e-02 4.00e+02
        pdb=" CA  PRO A 894 "   -0.021 5.00e-02 4.00e+02
        pdb=" CD  PRO A 894 "   -0.023 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR B 889 "   -0.024 5.00e-02 4.00e+02   3.67e-02 2.15e+00
        pdb=" N   PRO B 890 "    0.063 5.00e-02 4.00e+02
        pdb=" CA  PRO B 890 "   -0.019 5.00e-02 4.00e+02
        pdb=" CD  PRO B 890 "   -0.021 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  UNK C 103 "   -0.006 2.00e-02 2.50e+03   1.23e-02 1.51e+00
        pdb=" C   UNK C 103 "    0.021 2.00e-02 2.50e+03
        pdb=" O   UNK C 103 "   -0.008 2.00e-02 2.50e+03
        pdb=" N   UNK C 104 "   -0.007 2.00e-02 2.50e+03
  ... (remaining 1454 not shown)

  Histogram of nonbonded interaction distances:
        1.99 -     2.58: 24
        2.58 -     3.16: 5744
        3.16 -     3.74: 10116
        3.74 -     4.32: 12201
        4.32 -     4.90: 23131
  Nonbonded interactions: 51216
  Sorted by model distance:
  nonbonded pdb=" O1G G2P A1101 "
            pdb="MG    MG A1103 "
     model   vdw
     1.994 2.170
  nonbonded pdb=" O2B G2P A1102 "
            pdb="MG    MG B1101 "
     model   vdw
     2.009 2.170
  nonbonded pdb=" OD2 ASP B 921 "
            pdb="MG    MG B1101 "
     model   vdw
     2.082 2.170
  nonbonded pdb=" O2B G2P A1101 "
            pdb="MG    MG A1103 "
     model   vdw
     2.133 2.170
  nonbonded pdb=" OH  TYR A 905 "
            pdb=" O   GLY A 924 "
     model   vdw
     2.181 3.040
  ... (remaining 51211 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'A' and (resid 846 through 858 or (resid 859 and (name N or name CA or na \ 
me C or name O or name CB )) or resid 860 through 988 or (resid 989 and (name N  \ 
or name CA or name C or name O or name CB )) or resid 990 through 1016 or (resid \ 
 1017 through 1018 and (name N or name CA or name C or name O or name CB )) or r \ 
esid 1019 through 1046 or (resid 1047 through 1048 and (name N or name CA or nam \ 
e C or name O or name CB )) or resid 1049 through 1055))
  selection = (chain 'B' and (resid 842 through 908 or (resid 909 and (name N or name CA or na \ 
me C or name O or name CB )) or resid 910 through 949 or (resid 950 through 951  \ 
and (name N or name CA or name C or name O or name CB )) or resid 952 through 95 \ 
3 or (resid 954 and (name N or name CA or name C or name O or name CB )) or resi \ 
d 955 through 992 or (resid 993 and (name N or name CA or name C or name O or na \ 
me CB )) or resid 994 through 1013 or (resid 1014 and (name N or name CA or name \ 
 C or name O or name CB )) or resid 1015 through 1020 or (resid 1021 through 102 \ 
2 and (name N or name CA or name C or name O or name CB )) or resid 1023 through \ 
 1043 or (resid 1044 and (name N or name CA or name C or name O or name CB )) or \ 
 resid 1045 through 1050 or (resid 1051 and (name N or name CA or name C or name \ 
 O or name CB ))))
}
ncs_group {
  reference = (chain 'C' and resid 10 through 115)
  selection = chain 'D'
  selection = (chain 'E' and resid 11 through 116)
  selection = chain 'F'
  selection = (chain 'G' and resid 14 through 119)
  selection = (chain 'H' and resid 7 through 112)
  selection = (chain 'I' and resid 7 through 112)
  selection = (chain 'J' and resid 12 through 117)
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.110
  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:          0.290
  Check model and map are aligned:         0.060
  Set scattering table:                    0.080
  Process input model:                     21.480
  Find NCS groups from input model:        0.410
  Set up NCS constraints:                  0.050
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.860
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   26.350
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7527
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   0.027   7779  Z= 0.217
  Angle     :  0.860   6.548  10757  Z= 0.408
  Chirality :  0.041   0.167   1425
  Planarity :  0.003   0.041   1457
  Dihedral  : 15.566  91.586   2081
  Min Nonbonded Distance : 1.994

Molprobity Statistics.
  All-atom Clashscore : 2.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.91 %
    Favored  : 98.09 %
  Rotamer:
    Outliers :  0.64 %
    Allowed  : 30.55 %
    Favored  : 68.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.32 (0.40), residues: 418
  helix:  0.59 (0.42), residues: 155
  sheet:  0.09 (0.46), residues: 95
  loop : -1.07 (0.48), residues: 168

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.002   TRP A1050 
 HIS   0.006   0.002   HIS A 963 
 PHE   0.007   0.001   PHE B 868 
 TYR   0.010   0.001   TYR A 878 
 ARG   0.002   0.000   ARG B1000 

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

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

  836 Ramachandran restraints generated.
    418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  836 Ramachandran restraints generated.
    418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  34 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 32
  time to evaluate  : 0.535 
Fit side-chains
  outliers start: 2
  outliers final: 1
  residues processed: 34
  average time/residue: 0.2046
  time to fit residues: 9.7546
Evaluate side-chains
  33 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 32
  time to evaluate  : 0.541 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  952 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 108 optimal weight:   10.0000
   chunk 97 optimal weight:   10.0000
   chunk 53 optimal weight:   10.0000
   chunk 33 optimal weight:    1.9990
   chunk 65 optimal weight:    9.9990
   chunk 51 optimal weight:   10.0000
   chunk 100 optimal weight:    8.9990
   chunk 38 optimal weight:    2.9990
   chunk 61 optimal weight:    9.9990
   chunk 74 optimal weight:    6.9990
   chunk 116 optimal weight:    7.9990
   overall best weight:    5.7990

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7690
moved from start:          0.1638

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.011   0.063   7779  Z= 0.671
  Angle     :  1.252   9.131  10757  Z= 0.562
  Chirality :  0.060   0.228   1425
  Planarity :  0.004   0.049   1457
  Dihedral  : 10.838  79.866   1422
  Min Nonbonded Distance : 1.882

Molprobity Statistics.
  All-atom Clashscore : 2.45
  Ramachandran Plot:
    Outliers :  0.24 %
    Allowed  :  3.35 %
    Favored  : 96.41 %
  Rotamer:
    Outliers :  9.97 %
    Allowed  : 26.37 %
    Favored  : 63.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.88 (0.41), residues: 418
  helix: -0.18 (0.41), residues: 163
  sheet:  0.32 (0.55), residues: 77
  loop : -1.31 (0.47), residues: 178

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.003   TRP A1050 
 HIS   0.013   0.004   HIS A 963 
 PHE   0.014   0.003   PHE B 868 
 TYR   0.014   0.003   TYR A 878 
 ARG   0.007   0.001   ARG B 932 

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

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

  836 Ramachandran restraints generated.
    418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  836 Ramachandran restraints generated.
    418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  63 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 32
  time to evaluate  : 0.592 
Fit side-chains
REVERT: A  962 ARG cc_start: 0.8620 (OUTLIER) cc_final: 0.8241 (ptm160)
REVERT: A  995 PHE cc_start: 0.8503 (OUTLIER) cc_final: 0.8135 (m-80)
REVERT: B  936 LEU cc_start: 0.8367 (OUTLIER) cc_final: 0.7882 (mp)
  outliers start: 31
  outliers final: 21
  residues processed: 62
  average time/residue: 0.2196
  time to fit residues: 18.0991
Evaluate side-chains
  63 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 39
  time to evaluate  : 0.566 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  848 LEU
Chi-restraints excluded: chain A residue  877 ILE
Chi-restraints excluded: chain A residue  878 TYR
Chi-restraints excluded: chain A residue  895 MET
Chi-restraints excluded: chain A residue  907 CYS
Chi-restraints excluded: chain A residue  923 ILE
Chi-restraints excluded: chain A residue  953 LEU
Chi-restraints excluded: chain A residue  956 VAL
Chi-restraints excluded: chain A residue  962 ARG
Chi-restraints excluded: chain A residue  981 CYS
Chi-restraints excluded: chain A residue  995 PHE
Chi-restraints excluded: chain A residue  998 THR
Chi-restraints excluded: chain A residue 1010 GLU
Chi-restraints excluded: chain A residue 1020 THR
Chi-restraints excluded: chain A residue 1032 LEU
Chi-restraints excluded: chain B residue  870 SER
Chi-restraints excluded: chain B residue  879 VAL
Chi-restraints excluded: chain B residue  936 LEU
Chi-restraints excluded: chain B residue  939 CYS
Chi-restraints excluded: chain B residue  949 LEU
Chi-restraints excluded: chain B residue  952 VAL
Chi-restraints excluded: chain B residue  976 VAL
Chi-restraints excluded: chain B residue  994 THR
Chi-restraints excluded: chain B residue 1023 PHE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 64 optimal weight:   10.0000
   chunk 36 optimal weight:    0.9990
   chunk 96 optimal weight:    2.9990
   chunk 79 optimal weight:   10.0000
   chunk 32 optimal weight:    1.9990
   chunk 116 optimal weight:    2.9990
   chunk 125 optimal weight:    7.9990
   chunk 103 optimal weight:    5.9990
   chunk 115 optimal weight:    8.9990
   chunk 39 optimal weight:    1.9990
   chunk 93 optimal weight:    6.9990
   overall best weight:    2.1990

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7601
moved from start:          0.1329

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   7779  Z= 0.281
  Angle     :  0.781   6.358  10757  Z= 0.349
  Chirality :  0.041   0.168   1425
  Planarity :  0.003   0.044   1457
  Dihedral  :  9.623  83.444   1422
  Min Nonbonded Distance : 1.968

Molprobity Statistics.
  All-atom Clashscore : 2.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.63 %
    Favored  : 97.37 %
  Rotamer:
    Outliers :  4.50 %
    Allowed  : 31.51 %
    Favored  : 63.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.54 (0.41), residues: 418
  helix:  0.31 (0.42), residues: 161
  sheet:  0.13 (0.51), residues: 84
  loop : -1.16 (0.49), residues: 173

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP A1050 
 HIS   0.008   0.002   HIS A 963 
 PHE   0.010   0.002   PHE B 868 
 TYR   0.012   0.002   TYR A 878 
 ARG   0.003   0.000   ARG B 932 

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

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

  836 Ramachandran restraints generated.
    418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  836 Ramachandran restraints generated.
    418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  58 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 44
  time to evaluate  : 0.553 
Fit side-chains
REVERT: A  995 PHE cc_start: 0.8443 (OUTLIER) cc_final: 0.7932 (m-80)
REVERT: A 1054 GLU cc_start: 0.7607 (pt0) cc_final: 0.7382 (tt0)
REVERT: B 1002 GLU cc_start: 0.8287 (tm-30) cc_final: 0.7984 (tm-30)
  outliers start: 14
  outliers final: 11
  residues processed: 58
  average time/residue: 0.1713
  time to fit residues: 14.3010
Evaluate side-chains
  54 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 42
  time to evaluate  : 0.615 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  852 ILE
Chi-restraints excluded: chain A residue  875 VAL
Chi-restraints excluded: chain A residue  877 ILE
Chi-restraints excluded: chain A residue  953 LEU
Chi-restraints excluded: chain A residue  995 PHE
Chi-restraints excluded: chain B residue  852 SER
Chi-restraints excluded: chain B residue  870 SER
Chi-restraints excluded: chain B residue  876 SER
Chi-restraints excluded: chain B residue  879 VAL
Chi-restraints excluded: chain B residue  939 CYS
Chi-restraints excluded: chain B residue  952 VAL
Chi-restraints excluded: chain B residue 1023 PHE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 115 optimal weight:    9.9990
   chunk 87 optimal weight:    9.9990
   chunk 60 optimal weight:    7.9990
   chunk 12 optimal weight:    0.6980
   chunk 55 optimal weight:    6.9990
   chunk 78 optimal weight:    8.9990
   chunk 116 optimal weight:    6.9990
   chunk 123 optimal weight:    6.9990
   chunk 61 optimal weight:    9.9990
   chunk 110 optimal weight:    3.9990
   chunk 33 optimal weight:    5.9990
   overall best weight:    4.9388

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7677
moved from start:          0.1763

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.009   0.053   7779  Z= 0.573
  Angle     :  1.135   9.052  10757  Z= 0.508
  Chirality :  0.055   0.199   1425
  Planarity :  0.004   0.048   1457
  Dihedral  : 10.033  73.295   1422
  Min Nonbonded Distance : 1.927

Molprobity Statistics.
  All-atom Clashscore : 2.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.59 %
    Favored  : 96.41 %
  Rotamer:
    Outliers : 12.54 %
    Allowed  : 24.44 %
    Favored  : 63.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.89 (0.41), residues: 418
  helix: -0.11 (0.41), residues: 162
  sheet:  0.22 (0.57), residues: 77
  loop : -1.34 (0.46), residues: 179

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.003   TRP A1050 
 HIS   0.011   0.003   HIS A 963 
 PHE   0.012   0.003   PHE B 868 
 TYR   0.014   0.003   TYR A 878 
 ARG   0.005   0.001   ARG B1000 

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

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

  836 Ramachandran restraints generated.
    418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  836 Ramachandran restraints generated.
    418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  79 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 40
  time to evaluate  : 0.603 
Fit side-chains
REVERT: A  962 ARG cc_start: 0.8652 (OUTLIER) cc_final: 0.8149 (ptm160)
REVERT: A  995 PHE cc_start: 0.8503 (OUTLIER) cc_final: 0.8105 (m-80)
REVERT: B  936 LEU cc_start: 0.8386 (OUTLIER) cc_final: 0.7912 (mp)
  outliers start: 39
  outliers final: 31
  residues processed: 77
  average time/residue: 0.1811
  time to fit residues: 19.3727
Evaluate side-chains
  73 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 39
  time to evaluate  : 0.585 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  848 LEU
Chi-restraints excluded: chain A residue  852 ILE
Chi-restraints excluded: chain A residue  875 VAL
Chi-restraints excluded: chain A residue  877 ILE
Chi-restraints excluded: chain A residue  878 TYR
Chi-restraints excluded: chain A residue  879 PHE
Chi-restraints excluded: chain A residue  880 SER
Chi-restraints excluded: chain A residue  883 VAL
Chi-restraints excluded: chain A residue  892 SER
Chi-restraints excluded: chain A residue  895 MET
Chi-restraints excluded: chain A residue  897 VAL
Chi-restraints excluded: chain A residue  907 CYS
Chi-restraints excluded: chain A residue  923 ILE
Chi-restraints excluded: chain A residue  953 LEU
Chi-restraints excluded: chain A residue  956 VAL
Chi-restraints excluded: chain A residue  961 ILE
Chi-restraints excluded: chain A residue  962 ARG
Chi-restraints excluded: chain A residue  995 PHE
Chi-restraints excluded: chain A residue  998 THR
Chi-restraints excluded: chain A residue 1010 GLU
Chi-restraints excluded: chain A residue 1020 THR
Chi-restraints excluded: chain A residue 1032 LEU
Chi-restraints excluded: chain B residue  852 SER
Chi-restraints excluded: chain B residue  870 SER
Chi-restraints excluded: chain B residue  876 SER
Chi-restraints excluded: chain B residue  879 VAL
Chi-restraints excluded: chain B residue  936 LEU
Chi-restraints excluded: chain B residue  939 CYS
Chi-restraints excluded: chain B residue  949 LEU
Chi-restraints excluded: chain B residue  952 VAL
Chi-restraints excluded: chain B residue  976 VAL
Chi-restraints excluded: chain B residue  994 THR
Chi-restraints excluded: chain B residue 1016 THR
Chi-restraints excluded: chain B residue 1023 PHE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 103 optimal weight:    6.9990
   chunk 70 optimal weight:    8.9990
   chunk 1 optimal weight:    0.9980
   chunk 92 optimal weight:    7.9990
   chunk 51 optimal weight:    7.9990
   chunk 105 optimal weight:    6.9990
   chunk 85 optimal weight:    8.9990
   chunk 0 optimal weight:    0.6980
   chunk 63 optimal weight:    5.9990
   chunk 111 optimal weight:    4.9990
   chunk 31 optimal weight:    0.5980
   overall best weight:    2.6584

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7622
moved from start:          0.1557

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.037   7779  Z= 0.329
  Angle     :  0.833   6.681  10757  Z= 0.372
  Chirality :  0.043   0.171   1425
  Planarity :  0.003   0.046   1457
  Dihedral  :  8.899  72.197   1422
  Min Nonbonded Distance : 1.963

Molprobity Statistics.
  All-atom Clashscore : 2.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.63 %
    Favored  : 97.37 %
  Rotamer:
    Outliers :  9.32 %
    Allowed  : 27.97 %
    Favored  : 62.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.68 (0.41), residues: 418
  helix:  0.15 (0.42), residues: 162
  sheet:  0.16 (0.57), residues: 77
  loop : -1.22 (0.47), residues: 179

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP A1050 
 HIS   0.009   0.002   HIS A 963 
 PHE   0.009   0.002   PHE B 868 
 TYR   0.012   0.002   TYR A 878 
 ARG   0.002   0.000   ARG B1000 

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

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

  836 Ramachandran restraints generated.
    418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  836 Ramachandran restraints generated.
    418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  67 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 38
  time to evaluate  : 0.524 
Fit side-chains
REVERT: A  995 PHE cc_start: 0.8469 (OUTLIER) cc_final: 0.7934 (m-80)
REVERT: B 1002 GLU cc_start: 0.8256 (tm-30) cc_final: 0.8049 (tm-30)
  outliers start: 29
  outliers final: 24
  residues processed: 64
  average time/residue: 0.1558
  time to fit residues: 14.6570
Evaluate side-chains
  62 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 37
  time to evaluate  : 0.430 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  852 ILE
Chi-restraints excluded: chain A residue  875 VAL
Chi-restraints excluded: chain A residue  877 ILE
Chi-restraints excluded: chain A residue  892 SER
Chi-restraints excluded: chain A residue  897 VAL
Chi-restraints excluded: chain A residue  953 LEU
Chi-restraints excluded: chain A residue  956 VAL
Chi-restraints excluded: chain A residue  961 ILE
Chi-restraints excluded: chain A residue  995 PHE
Chi-restraints excluded: chain A residue  998 THR
Chi-restraints excluded: chain A residue 1020 THR
Chi-restraints excluded: chain A residue 1032 LEU
Chi-restraints excluded: chain A residue 1034 LEU
Chi-restraints excluded: chain B residue  852 SER
Chi-restraints excluded: chain B residue  870 SER
Chi-restraints excluded: chain B residue  876 SER
Chi-restraints excluded: chain B residue  879 VAL
Chi-restraints excluded: chain B residue  939 CYS
Chi-restraints excluded: chain B residue  949 LEU
Chi-restraints excluded: chain B residue  952 VAL
Chi-restraints excluded: chain B residue  994 THR
Chi-restraints excluded: chain B residue 1016 THR
Chi-restraints excluded: chain B residue 1021 GLU
Chi-restraints excluded: chain B residue 1022 GLU
Chi-restraints excluded: chain B residue 1023 PHE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 41 optimal weight:    1.9990
   chunk 111 optimal weight:    6.9990
   chunk 24 optimal weight:    1.9990
   chunk 72 optimal weight:   20.0000
   chunk 30 optimal weight:    0.6980
   chunk 123 optimal weight:    6.9990
   chunk 102 optimal weight:    6.9990
   chunk 57 optimal weight:    8.9990
   chunk 10 optimal weight:    0.6980
   chunk 40 optimal weight:    3.9990
   chunk 65 optimal weight:    9.9990
   overall best weight:    1.8786

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7588
moved from start:          0.1485

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   7779  Z= 0.243
  Angle     :  0.711   6.130  10757  Z= 0.319
  Chirality :  0.039   0.165   1425
  Planarity :  0.003   0.045   1457
  Dihedral  :  8.373  71.177   1422
  Min Nonbonded Distance : 1.986

Molprobity Statistics.
  All-atom Clashscore : 2.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.63 %
    Favored  : 97.37 %
  Rotamer:
    Outliers :  8.04 %
    Allowed  : 29.58 %
    Favored  : 62.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.49 (0.41), residues: 418
  helix:  0.39 (0.42), residues: 161
  sheet:  0.04 (0.52), residues: 84
  loop : -1.13 (0.49), residues: 173

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP A1050 
 HIS   0.007   0.002   HIS A 963 
 PHE   0.008   0.001   PHE B 868 
 TYR   0.011   0.002   TYR A 878 
 ARG   0.002   0.000   ARG B1000 

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

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

  836 Ramachandran restraints generated.
    418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  836 Ramachandran restraints generated.
    418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  68 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 43
  time to evaluate  : 0.628 
Fit side-chains
REVERT: A  995 PHE cc_start: 0.8536 (OUTLIER) cc_final: 0.8023 (m-80)
REVERT: A 1054 GLU cc_start: 0.7605 (pt0) cc_final: 0.7393 (tt0)
REVERT: B 1002 GLU cc_start: 0.8235 (tm-30) cc_final: 0.7953 (tm-30)
  outliers start: 25
  outliers final: 20
  residues processed: 66
  average time/residue: 0.1594
  time to fit residues: 15.3797
Evaluate side-chains
  63 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 42
  time to evaluate  : 0.532 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  852 ILE
Chi-restraints excluded: chain A residue  875 VAL
Chi-restraints excluded: chain A residue  877 ILE
Chi-restraints excluded: chain A residue  880 SER
Chi-restraints excluded: chain A residue  892 SER
Chi-restraints excluded: chain A residue  956 VAL
Chi-restraints excluded: chain A residue  961 ILE
Chi-restraints excluded: chain A residue  995 PHE
Chi-restraints excluded: chain A residue  998 THR
Chi-restraints excluded: chain A residue 1020 THR
Chi-restraints excluded: chain B residue  852 SER
Chi-restraints excluded: chain B residue  870 SER
Chi-restraints excluded: chain B residue  876 SER
Chi-restraints excluded: chain B residue  879 VAL
Chi-restraints excluded: chain B residue  939 CYS
Chi-restraints excluded: chain B residue  949 LEU
Chi-restraints excluded: chain B residue  952 VAL
Chi-restraints excluded: chain B residue  976 VAL
Chi-restraints excluded: chain B residue 1016 THR
Chi-restraints excluded: chain B residue 1021 GLU
Chi-restraints excluded: chain B residue 1023 PHE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 119 optimal weight:    9.9990
   chunk 13 optimal weight:    0.8980
   chunk 70 optimal weight:    9.9990
   chunk 90 optimal weight:    9.9990
   chunk 104 optimal weight:    9.9990
   chunk 69 optimal weight:    7.9990
   chunk 123 optimal weight:    6.9990
   chunk 77 optimal weight:    9.9990
   chunk 75 optimal weight:   10.0000
   chunk 56 optimal weight:    7.9990
   chunk 76 optimal weight:    9.9990
   overall best weight:    6.7788

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7710
moved from start:          0.2024

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.012   0.069   7779  Z= 0.773
  Angle     :  1.345  11.951  10757  Z= 0.605
  Chirality :  0.064   0.249   1425
  Planarity :  0.005   0.050   1457
  Dihedral  : 10.069  73.412   1422
  Min Nonbonded Distance : 1.895

Molprobity Statistics.
  All-atom Clashscore : 2.95
  Ramachandran Plot:
    Outliers :  0.48 %
    Allowed  :  3.59 %
    Favored  : 95.93 %
  Rotamer:
    Outliers : 11.90 %
    Allowed  : 25.72 %
    Favored  : 62.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -1.21 (0.40), residues: 418
  helix: -0.38 (0.40), residues: 162
  sheet:  0.24 (0.63), residues: 68
  loop : -1.54 (0.44), residues: 188

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.003   TRP B1046 
 HIS   0.014   0.004   HIS A 963 
 PHE   0.019   0.003   PHE B 868 
 TYR   0.019   0.003   TYR B 923 
 ARG   0.006   0.001   ARG B1000 

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

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

  836 Ramachandran restraints generated.
    418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  836 Ramachandran restraints generated.
    418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  78 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 41
  time to evaluate  : 0.537 
Fit side-chains
REVERT: A  962 ARG cc_start: 0.8686 (OUTLIER) cc_final: 0.8195 (ptm160)
REVERT: A  995 PHE cc_start: 0.8515 (OUTLIER) cc_final: 0.8168 (m-80)
REVERT: B  915 LYS cc_start: 0.8952 (ttpp) cc_final: 0.8748 (ttpp)
REVERT: B  936 LEU cc_start: 0.8455 (OUTLIER) cc_final: 0.8000 (mp)
REVERT: B  991 PHE cc_start: 0.8863 (OUTLIER) cc_final: 0.8586 (m-80)
  outliers start: 37
  outliers final: 29
  residues processed: 75
  average time/residue: 0.1909
  time to fit residues: 19.7506
Evaluate side-chains
  74 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 41
  time to evaluate  : 0.636 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  848 LEU
Chi-restraints excluded: chain A residue  852 ILE
Chi-restraints excluded: chain A residue  875 VAL
Chi-restraints excluded: chain A residue  877 ILE
Chi-restraints excluded: chain A residue  878 TYR
Chi-restraints excluded: chain A residue  879 PHE
Chi-restraints excluded: chain A residue  880 SER
Chi-restraints excluded: chain A residue  892 SER
Chi-restraints excluded: chain A residue  895 MET
Chi-restraints excluded: chain A residue  907 CYS
Chi-restraints excluded: chain A residue  923 ILE
Chi-restraints excluded: chain A residue  953 LEU
Chi-restraints excluded: chain A residue  956 VAL
Chi-restraints excluded: chain A residue  962 ARG
Chi-restraints excluded: chain A residue  995 PHE
Chi-restraints excluded: chain A residue  998 THR
Chi-restraints excluded: chain A residue 1010 GLU
Chi-restraints excluded: chain A residue 1020 THR
Chi-restraints excluded: chain A residue 1032 LEU
Chi-restraints excluded: chain B residue  845 LEU
Chi-restraints excluded: chain B residue  870 SER
Chi-restraints excluded: chain B residue  872 THR
Chi-restraints excluded: chain B residue  876 SER
Chi-restraints excluded: chain B residue  936 LEU
Chi-restraints excluded: chain B residue  939 CYS
Chi-restraints excluded: chain B residue  949 LEU
Chi-restraints excluded: chain B residue  952 VAL
Chi-restraints excluded: chain B residue  976 VAL
Chi-restraints excluded: chain B residue  991 PHE
Chi-restraints excluded: chain B residue  994 THR
Chi-restraints excluded: chain B residue 1016 THR
Chi-restraints excluded: chain B residue 1022 GLU
Chi-restraints excluded: chain B residue 1023 PHE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 49 optimal weight:    7.9990
   chunk 73 optimal weight:    8.9990
   chunk 37 optimal weight:    0.6980
   chunk 24 optimal weight:    0.9990
   chunk 23 optimal weight:    3.9990
   chunk 78 optimal weight:    5.9990
   chunk 84 optimal weight:    4.9990
   chunk 60 optimal weight:    4.9990
   chunk 11 optimal weight:    0.8980
   chunk 96 optimal weight:    0.6980
   chunk 112 optimal weight:    0.6980
   overall best weight:    0.7982

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7526
moved from start:          0.1634

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.023   7779  Z= 0.146
  Angle     :  0.591   5.882  10757  Z= 0.268
  Chirality :  0.034   0.156   1425
  Planarity :  0.003   0.045   1457
  Dihedral  :  8.009  70.256   1422
  Min Nonbonded Distance : 2.029

Molprobity Statistics.
  All-atom Clashscore : 2.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.44 %
    Favored  : 98.56 %
  Rotamer:
    Outliers :  7.07 %
    Allowed  : 30.87 %
    Favored  : 62.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.49 (0.41), residues: 418
  helix:  0.62 (0.43), residues: 158
  sheet: -0.14 (0.50), residues: 90
  loop : -1.27 (0.48), residues: 170

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.003   TRP A1050 
 HIS   0.005   0.001   HIS A 963 
 PHE   0.009   0.001   PHE B 868 
 TYR   0.010   0.001   TYR A 878 
 ARG   0.002   0.000   ARG B1000 

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

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

  836 Ramachandran restraints generated.
    418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  836 Ramachandran restraints generated.
    418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  66 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 44
  time to evaluate  : 0.579 
Fit side-chains
REVERT: A  995 PHE cc_start: 0.8457 (OUTLIER) cc_final: 0.7943 (m-80)
REVERT: A 1054 GLU cc_start: 0.7693 (pt0) cc_final: 0.7466 (tt0)
  outliers start: 22
  outliers final: 16
  residues processed: 65
  average time/residue: 0.1731
  time to fit residues: 16.4683
Evaluate side-chains
  60 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 43
  time to evaluate  : 0.735 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  875 VAL
Chi-restraints excluded: chain A residue  877 ILE
Chi-restraints excluded: chain A residue  880 SER
Chi-restraints excluded: chain A residue  883 VAL
Chi-restraints excluded: chain A residue  892 SER
Chi-restraints excluded: chain A residue  923 ILE
Chi-restraints excluded: chain A residue  956 VAL
Chi-restraints excluded: chain A residue  995 PHE
Chi-restraints excluded: chain A residue  998 THR
Chi-restraints excluded: chain A residue 1020 THR
Chi-restraints excluded: chain A residue 1032 LEU
Chi-restraints excluded: chain B residue  870 SER
Chi-restraints excluded: chain B residue  876 SER
Chi-restraints excluded: chain B residue  879 VAL
Chi-restraints excluded: chain B residue  976 VAL
Chi-restraints excluded: chain B residue 1016 THR
Chi-restraints excluded: chain B residue 1023 PHE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 118 optimal weight:    9.9990
   chunk 107 optimal weight:   10.0000
   chunk 114 optimal weight:    8.9990
   chunk 69 optimal weight:    7.9990
   chunk 50 optimal weight:   10.0000
   chunk 90 optimal weight:   10.0000
   chunk 35 optimal weight:    0.0980
   chunk 103 optimal weight:    7.9990
   chunk 108 optimal weight:   10.0000
   chunk 75 optimal weight:    9.9990
   chunk 121 optimal weight:    8.9990
   overall best weight:    6.8188

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7710
moved from start:          0.2044

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.012   0.069   7779  Z= 0.781
  Angle     :  1.345  11.514  10757  Z= 0.606
  Chirality :  0.064   0.251   1425
  Planarity :  0.005   0.051   1457
  Dihedral  :  9.962  73.191   1421
  Min Nonbonded Distance : 1.893

Molprobity Statistics.
  All-atom Clashscore : 2.53
  Ramachandran Plot:
    Outliers :  0.48 %
    Allowed  :  4.07 %
    Favored  : 95.45 %
  Rotamer:
    Outliers : 10.61 %
    Allowed  : 28.30 %
    Favored  : 61.09 %
  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: -1.27 (0.40), residues: 418
  helix: -0.39 (0.40), residues: 162
  sheet:  0.19 (0.64), residues: 68
  loop : -1.61 (0.43), residues: 188

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.003   TRP B1046 
 HIS   0.014   0.004   HIS A 963 
 PHE   0.021   0.003   PHE B 868 
 TYR   0.020   0.003   TYR A 878 
 ARG   0.006   0.001   ARG B1000 

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

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

  836 Ramachandran restraints generated.
    418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  836 Ramachandran restraints generated.
    418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  74 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 41
  time to evaluate  : 0.560 
Fit side-chains
REVERT: A  962 ARG cc_start: 0.8675 (OUTLIER) cc_final: 0.8316 (ptm160)
REVERT: A  995 PHE cc_start: 0.8507 (OUTLIER) cc_final: 0.8151 (m-80)
REVERT: B  874 TYR cc_start: 0.9047 (OUTLIER) cc_final: 0.8794 (t80)
REVERT: B  935 ARG cc_start: 0.8859 (OUTLIER) cc_final: 0.8500 (mtt90)
REVERT: B  991 PHE cc_start: 0.8813 (OUTLIER) cc_final: 0.8580 (m-80)
  outliers start: 33
  outliers final: 25
  residues processed: 72
  average time/residue: 0.2052
  time to fit residues: 19.9768
Evaluate side-chains
  70 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 40
  time to evaluate  : 0.547 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  848 LEU
Chi-restraints excluded: chain A residue  852 ILE
Chi-restraints excluded: chain A residue  875 VAL
Chi-restraints excluded: chain A residue  877 ILE
Chi-restraints excluded: chain A residue  879 PHE
Chi-restraints excluded: chain A residue  880 SER
Chi-restraints excluded: chain A residue  883 VAL
Chi-restraints excluded: chain A residue  892 SER
Chi-restraints excluded: chain A residue  895 MET
Chi-restraints excluded: chain A residue  907 CYS
Chi-restraints excluded: chain A residue  933 LEU
Chi-restraints excluded: chain A residue  956 VAL
Chi-restraints excluded: chain A residue  962 ARG
Chi-restraints excluded: chain A residue  995 PHE
Chi-restraints excluded: chain A residue  998 THR
Chi-restraints excluded: chain A residue 1010 GLU
Chi-restraints excluded: chain A residue 1020 THR
Chi-restraints excluded: chain A residue 1032 LEU
Chi-restraints excluded: chain B residue  845 LEU
Chi-restraints excluded: chain B residue  852 SER
Chi-restraints excluded: chain B residue  870 SER
Chi-restraints excluded: chain B residue  874 TYR
Chi-restraints excluded: chain B residue  876 SER
Chi-restraints excluded: chain B residue  879 VAL
Chi-restraints excluded: chain B residue  935 ARG
Chi-restraints excluded: chain B residue  939 CYS
Chi-restraints excluded: chain B residue  976 VAL
Chi-restraints excluded: chain B residue  991 PHE
Chi-restraints excluded: chain B residue 1016 THR
Chi-restraints excluded: chain B residue 1023 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 74 optimal weight:    0.7980
   chunk 57 optimal weight:    3.9990
   chunk 84 optimal weight:    4.9990
   chunk 127 optimal weight:    4.9990
   chunk 117 optimal weight:    0.7980
   chunk 101 optimal weight:    0.9990
   chunk 10 optimal weight:    0.7980
   chunk 78 optimal weight:    5.9990
   chunk 62 optimal weight:    0.7980
   chunk 80 optimal weight:    7.9990
   chunk 108 optimal weight:    7.9990
   overall best weight:    0.8382

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7542
moved from start:          0.1656

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.024   7779  Z= 0.156
  Angle     :  0.614   5.767  10757  Z= 0.278
  Chirality :  0.034   0.156   1425
  Planarity :  0.003   0.047   1457
  Dihedral  :  8.031  70.384   1421
  Min Nonbonded Distance : 2.022

Molprobity Statistics.
  All-atom Clashscore : 2.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.44 %
    Favored  : 98.56 %
  Rotamer:
    Outliers :  5.47 %
    Allowed  : 32.80 %
    Favored  : 61.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.53 (0.41), residues: 418
  helix:  0.58 (0.42), residues: 157
  sheet: -0.15 (0.51), residues: 90
  loop : -1.30 (0.48), residues: 171

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.003   TRP A1050 
 HIS   0.004   0.001   HIS A 963 
 PHE   0.006   0.001   PHE B 868 
 TYR   0.011   0.001   TYR B 874 
 ARG   0.002   0.000   ARG B1000 

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

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

  836 Ramachandran restraints generated.
    418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  836 Ramachandran restraints generated.
    418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  60 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 43
  time to evaluate  : 0.531 
Fit side-chains
REVERT: A  995 PHE cc_start: 0.8484 (OUTLIER) cc_final: 0.7955 (m-80)
  outliers start: 17
  outliers final: 15
  residues processed: 60
  average time/residue: 0.1720
  time to fit residues: 14.7576
Evaluate side-chains
  60 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 44
  time to evaluate  : 0.586 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  875 VAL
Chi-restraints excluded: chain A residue  877 ILE
Chi-restraints excluded: chain A residue  880 SER
Chi-restraints excluded: chain A residue  883 VAL
Chi-restraints excluded: chain A residue  892 SER
Chi-restraints excluded: chain A residue  956 VAL
Chi-restraints excluded: chain A residue  995 PHE
Chi-restraints excluded: chain A residue  998 THR
Chi-restraints excluded: chain A residue 1020 THR
Chi-restraints excluded: chain A residue 1032 LEU
Chi-restraints excluded: chain B residue  870 SER
Chi-restraints excluded: chain B residue  876 SER
Chi-restraints excluded: chain B residue  879 VAL
Chi-restraints excluded: chain B residue  976 VAL
Chi-restraints excluded: chain B residue 1016 THR
Chi-restraints excluded: chain B residue 1023 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 31 optimal weight:    0.6980
   chunk 93 optimal weight:    8.9990
   chunk 14 optimal weight:    0.5980
   chunk 28 optimal weight:    0.7980
   chunk 101 optimal weight:   10.0000
   chunk 42 optimal weight:    9.9990
   chunk 104 optimal weight:   10.0000
   chunk 12 optimal weight:    0.7980
   chunk 18 optimal weight:    5.9990
   chunk 89 optimal weight:    9.9990
   chunk 5 optimal weight:    0.7980
   overall best weight:    0.7380

-------------------------------------------------------------------------------
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 = 0.4057 r_free = 0.4057 target = 0.185677 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.4000 r_free = 0.4000 target = 0.179822 restraints weight = 9367.360|
|-----------------------------------------------------------------------------|
r_work (start): 0.3996 rms_B_bonded: 0.47
r_work: 0.3931 rms_B_bonded: 0.89 restraints_weight: 0.5000
r_work: 0.3825 rms_B_bonded: 2.48 restraints_weight: 0.2500
r_work (final): 0.3825
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7523
moved from start:          0.1700

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   7779  Z= 0.138
  Angle     :  0.538   5.373  10757  Z= 0.246
  Chirality :  0.032   0.152   1425
  Planarity :  0.003   0.046   1457
  Dihedral  :  7.318  68.291   1421
  Min Nonbonded Distance : 2.014

Molprobity Statistics.
  All-atom Clashscore : 1.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.67 %
    Favored  : 98.33 %
  Rotamer:
    Outliers :  4.82 %
    Allowed  : 33.76 %
    Favored  : 61.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.02 (0.42), residues: 418
  helix:  1.03 (0.43), residues: 158
  sheet:  0.05 (0.52), residues: 87
  loop : -0.97 (0.50), residues: 173

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP A1050 
 HIS   0.004   0.001   HIS A 963 
 PHE   0.006   0.001   PHE B 875 
 TYR   0.010   0.001   TYR A 878 
 ARG   0.001   0.000   ARG A 960 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1105.61 seconds
wall clock time: 21 minutes 4.18 seconds (1264.18 seconds total)