Starting phenix.real_space_refine
on Tue Mar  3 19:29:41 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8gv8_34287/03_2026/8gv8_34287.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8gv8_34287/03_2026/8gv8_34287.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.08
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8gv8_34287/03_2026/8gv8_34287.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8gv8_34287/03_2026/8gv8_34287.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8gv8_34287/03_2026/8gv8_34287.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8gv8_34287/03_2026/8gv8_34287.cif"
  }
  resolution = 3.08
  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=   0.002 sd=   0.179
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      54      5.16       5
     C    5422      2.51       5
     N    1334      2.21       5
     O    1351      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-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 8161
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 4057
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 514, 4057
          Classifications: {'peptide': 514}
          Link IDs: {'PTRANS': 28, 'TRANS': 485}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 4048
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 513, 4048
          Classifications: {'peptide': 513}
          Link IDs: {'PTRANS': 28, 'TRANS': 484}
          Chain breaks: 1
    Chain: "A"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 28
          Unusual residues: {'4KU': 1}
          Classifications: {'undetermined': 1}
    Chain: "B"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 28
          Unusual residues: {'4KU': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 1.89, per 1000 atoms: 0.23
  Number of scatterers: 8161
  At special positions: 0
  Unit cell: (86.9, 133.1, 79.2, 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      54     16.00
     O    1351      8.00
     N    1334      7.00
     C    5422      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: 0.63
  Conformation dependent library (CDL) restraints added in 305.2 milliseconds
  

  2038 Ramachandran restraints generated.
    1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1914

  Finding SS restraints...
    Secondary structure from input PDB file:
      50 helices and 4 sheets defined
      67.1% alpha, 1.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.19
  Creating SS restraints...
    Processing helix  chain 'A' and resid 682 through 693
    Processing helix  chain 'A' and resid 696 through 703
      removed outlier: 3.892A  pdb=" N   PHE A 700 " --> pdb=" O   TYR A 696 " (cutoff:3.500A)
      removed outlier: 3.683A  pdb=" N   ALA A 703 " --> pdb=" O   ASP A 699 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 705 through 734
      removed outlier: 3.983A  pdb=" N   LEU A 709 " --> pdb=" O   ASP A 705 " (cutoff:3.500A)
      removed outlier: 3.695A  pdb=" N   ALA A 710 " --> pdb=" O   PRO A 706 " (cutoff:3.500A)
      removed outlier: 4.005A  pdb=" N   PHE A 717 " --> pdb=" O   ILE A 713 " (cutoff:3.500A)
      removed outlier: 3.740A  pdb=" N   ALA A 718 " --> pdb=" O   PHE A 714 " (cutoff:3.500A)
      Proline residue:  A 722  - end of helix
    Processing helix  chain 'A' and resid 768 through 785
    Processing helix  chain 'A' and resid 788 through 810
      removed outlier: 3.678A  pdb=" N   VAL A 794 " --> pdb=" O   LEU A 790 " (cutoff:3.500A)
      removed outlier: 4.114A  pdb=" N   TRP A 795 " --> pdb=" O   VAL A 791 " (cutoff:3.500A)
      removed outlier: 3.784A  pdb=" N   ILE A 796 " --> pdb=" O   GLY A 792 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 811 through 819
      removed outlier: 4.050A  pdb=" N   PHE A 814 " --> pdb=" O   GLU A 811 " (cutoff:3.500A)
      removed outlier: 3.655A  pdb=" N   LEU A 815 " --> pdb=" O   GLY A 812 " (cutoff:3.500A)
      removed outlier: 3.545A  pdb=" N   VAL A 816 " --> pdb=" O   SER A 813 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 825 through 847
      removed outlier: 4.190A  pdb=" N   GLU A 838 " --> pdb=" O   ILE A 834 " (cutoff:3.500A)
      removed outlier: 4.112A  pdb=" N   THR A 839 " --> pdb=" O   PHE A 835 " (cutoff:3.500A)
      removed outlier: 3.947A  pdb=" N   PHE A 840 " --> pdb=" O   ILE A 836 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 899 through 923
      removed outlier: 3.518A  pdb=" N   LEU A 903 " --> pdb=" O   ASN A 899 " (cutoff:3.500A)
      removed outlier: 3.503A  pdb=" N   LEU A 905 " --> pdb=" O   ALA A 901 " (cutoff:3.500A)
      removed outlier: 3.964A  pdb=" N   ASN A 923 " --> pdb=" O   ARG A 919 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 928 through 938
    Processing helix  chain 'A' and resid 938 through 954
      removed outlier: 3.550A  pdb=" N   ILE A 942 " --> pdb=" O   PHE A 938 " (cutoff:3.500A)
      removed outlier: 3.640A  pdb=" N   ILE A 954 " --> pdb=" O   VAL A 950 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 990 through 997
      removed outlier: 3.816A  pdb=" N   MET A 994 " --> pdb=" O   PRO A 990 " (cutoff:3.500A)
      removed outlier: 3.702A  pdb=" N   VAL A 995 " --> pdb=" O   VAL A 991 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 997 through 1020
      removed outlier: 3.642A  pdb=" N   ALA A1001 " --> pdb=" O   SER A 997 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1038 through 1047
      removed outlier: 3.502A  pdb=" N   GLY A1043 " --> pdb=" O   ILE A1039 " (cutoff:3.500A)
      removed outlier: 4.016A  pdb=" N   GLY A1044 " --> pdb=" O   VAL A1040 " (cutoff:3.500A)
      removed outlier: 3.959A  pdb=" N   ILE A1045 " --> pdb=" O   ALA A1041 " (cutoff:3.500A)
      removed outlier: 3.553A  pdb=" N   ALA A1047 " --> pdb=" O   GLY A1043 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1057 through 1067
    Processing helix  chain 'A' and resid 1091 through 1102
    Processing helix  chain 'A' and resid 1109 through 1113
    Processing helix  chain 'A' and resid 1114 through 1129
      removed outlier: 4.061A  pdb=" N   LEU A1118 " --> pdb=" O   PRO A1114 " (cutoff:3.500A)
      removed outlier: 3.844A  pdb=" N   GLY A1120 " --> pdb=" O   ALA A1116 " (cutoff:3.500A)
      removed outlier: 3.661A  pdb=" N   ILE A1121 " --> pdb=" O   VAL A1117 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1133 through 1144
      removed outlier: 3.719A  pdb=" N   GLU A1137 " --> pdb=" O   ILE A1133 " (cutoff:3.500A)
      removed outlier: 3.600A  pdb=" N   LEU A1142 " --> pdb=" O   ARG A1138 " (cutoff:3.500A)
      removed outlier: 4.342A  pdb=" N   LEU A1143 " --> pdb=" O   LEU A1139 " (cutoff:3.500A)
      removed outlier: 3.737A  pdb=" N   MET A1144 " --> pdb=" O   HIS A1140 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1145 through 1149
      removed outlier: 3.926A  pdb=" N   HIS A1149 " --> pdb=" O   PRO A1146 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1152 through 1157
      removed outlier: 3.652A  pdb=" N   LYS A1157 " --> pdb=" O   THR A1153 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1159 through 1182
      removed outlier: 3.537A  pdb=" N   HIS A1164 " --> pdb=" O   THR A1160 " (cutoff:3.500A)
      removed outlier: 4.005A  pdb=" N   LEU A1165 " --> pdb=" O   LEU A1161 " (cutoff:3.500A)
      removed outlier: 3.910A  pdb=" N   PHE A1166 " --> pdb=" O   ARG A1162 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1188 through 1195
    Processing helix  chain 'A' and resid 1195 through 1208
      removed outlier: 4.289A  pdb=" N   LEU A1204 " --> pdb=" O   ARG A1200 " (cutoff:3.500A)
      removed outlier: 5.383A  pdb=" N   THR A1205 " --> pdb=" O   MET A1201 " (cutoff:3.500A)
      removed outlier: 3.759A  pdb=" N   ARG A1206 " --> pdb=" O   VAL A1202 " (cutoff:3.500A)
      removed outlier: 3.634A  pdb=" N   ILE A1207 " --> pdb=" O   VAL A1203 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1209 through 1217
    Processing helix  chain 'B' and resid 682 through 693
    Processing helix  chain 'B' and resid 696 through 703
      removed outlier: 3.884A  pdb=" N   PHE B 700 " --> pdb=" O   TYR B 696 " (cutoff:3.500A)
      removed outlier: 3.690A  pdb=" N   ALA B 703 " --> pdb=" O   ASP B 699 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 705 through 734
      removed outlier: 3.983A  pdb=" N   LEU B 709 " --> pdb=" O   ASP B 705 " (cutoff:3.500A)
      removed outlier: 3.692A  pdb=" N   ALA B 710 " --> pdb=" O   PRO B 706 " (cutoff:3.500A)
      removed outlier: 4.001A  pdb=" N   PHE B 717 " --> pdb=" O   ILE B 713 " (cutoff:3.500A)
      removed outlier: 3.732A  pdb=" N   ALA B 718 " --> pdb=" O   PHE B 714 " (cutoff:3.500A)
      Proline residue:  B 722  - end of helix
    Processing helix  chain 'B' and resid 739 through 758
      removed outlier: 3.849A  pdb=" N   LEU B 743 " --> pdb=" O   GLY B 739 " (cutoff:3.500A)
      removed outlier: 3.712A  pdb=" N   LEU B 749 " --> pdb=" O   MET B 745 " (cutoff:3.500A)
      removed outlier: 3.533A  pdb=" N   VAL B 753 " --> pdb=" O   LEU B 749 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 768 through 785
    Processing helix  chain 'B' and resid 788 through 810
      removed outlier: 3.677A  pdb=" N   VAL B 794 " --> pdb=" O   LEU B 790 " (cutoff:3.500A)
      removed outlier: 4.113A  pdb=" N   TRP B 795 " --> pdb=" O   VAL B 791 " (cutoff:3.500A)
      removed outlier: 3.786A  pdb=" N   ILE B 796 " --> pdb=" O   GLY B 792 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 812 through 819
      removed outlier: 3.739A  pdb=" N   VAL B 816 " --> pdb=" O   SER B 813 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 829 through 834
      removed outlier: 3.578A  pdb=" N   ILE B 834 " --> pdb=" O   LEU B 830 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 899 through 923
      removed outlier: 3.518A  pdb=" N   LEU B 903 " --> pdb=" O   ASN B 899 " (cutoff:3.500A)
      removed outlier: 3.702A  pdb=" N   PHE B 916 " --> pdb=" O   PHE B 912 " (cutoff:3.500A)
      removed outlier: 3.513A  pdb=" N   PHE B 917 " --> pdb=" O   PHE B 913 " (cutoff:3.500A)
      removed outlier: 3.937A  pdb=" N   LYS B 920 " --> pdb=" O   PHE B 916 " (cutoff:3.500A)
      removed outlier: 3.958A  pdb=" N   ASN B 923 " --> pdb=" O   ARG B 919 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 928 through 938
    Processing helix  chain 'B' and resid 938 through 954
      removed outlier: 3.550A  pdb=" N   ILE B 942 " --> pdb=" O   PHE B 938 " (cutoff:3.500A)
      removed outlier: 3.637A  pdb=" N   ILE B 954 " --> pdb=" O   VAL B 950 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 990 through 997
      removed outlier: 3.821A  pdb=" N   MET B 994 " --> pdb=" O   PRO B 990 " (cutoff:3.500A)
      removed outlier: 3.696A  pdb=" N   VAL B 995 " --> pdb=" O   VAL B 991 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 997 through 1020
      removed outlier: 3.637A  pdb=" N   ALA B1001 " --> pdb=" O   SER B 997 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1035 through 1047
      removed outlier: 3.679A  pdb=" N   ILE B1039 " --> pdb=" O   ASP B1035 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1057 through 1067
    Processing helix  chain 'B' and resid 1091 through 1102
    Processing helix  chain 'B' and resid 1103 through 1105
      No H-bonds generated for 'chain 'B' and resid 1103 through 1105'
    Processing helix  chain 'B' and resid 1109 through 1113
      removed outlier: 3.633A  pdb=" N   ILE B1113 " --> pdb=" O   LEU B1110 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1114 through 1129
      removed outlier: 4.023A  pdb=" N   LEU B1118 " --> pdb=" O   PRO B1114 " (cutoff:3.500A)
      removed outlier: 3.872A  pdb=" N   GLY B1120 " --> pdb=" O   ALA B1116 " (cutoff:3.500A)
      removed outlier: 3.682A  pdb=" N   ILE B1121 " --> pdb=" O   VAL B1117 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1133 through 1144
      removed outlier: 3.719A  pdb=" N   GLU B1137 " --> pdb=" O   ILE B1133 " (cutoff:3.500A)
      removed outlier: 3.598A  pdb=" N   LEU B1142 " --> pdb=" O   ARG B1138 " (cutoff:3.500A)
      removed outlier: 4.333A  pdb=" N   LEU B1143 " --> pdb=" O   LEU B1139 " (cutoff:3.500A)
      removed outlier: 3.739A  pdb=" N   MET B1144 " --> pdb=" O   HIS B1140 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1145 through 1149
      removed outlier: 3.935A  pdb=" N   HIS B1149 " --> pdb=" O   PRO B1146 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1152 through 1157
      removed outlier: 3.542A  pdb=" N   LYS B1156 " --> pdb=" O   VAL B1152 " (cutoff:3.500A)
      removed outlier: 3.678A  pdb=" N   LYS B1157 " --> pdb=" O   THR B1153 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 1152 through 1157'
    Processing helix  chain 'B' and resid 1159 through 1183
      removed outlier: 3.549A  pdb=" N   HIS B1164 " --> pdb=" O   THR B1160 " (cutoff:3.500A)
      removed outlier: 4.010A  pdb=" N   LEU B1165 " --> pdb=" O   LEU B1161 " (cutoff:3.500A)
      removed outlier: 3.888A  pdb=" N   PHE B1166 " --> pdb=" O   ARG B1162 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1188 through 1195
    Processing helix  chain 'B' and resid 1195 through 1208
      removed outlier: 4.287A  pdb=" N   LEU B1204 " --> pdb=" O   ARG B1200 " (cutoff:3.500A)
      removed outlier: 5.384A  pdb=" N   THR B1205 " --> pdb=" O   MET B1201 " (cutoff:3.500A)
      removed outlier: 3.759A  pdb=" N   ARG B1206 " --> pdb=" O   VAL B1202 " (cutoff:3.500A)
      removed outlier: 3.631A  pdb=" N   ILE B1207 " --> pdb=" O   VAL B1203 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1209 through 1217
    Processing sheet with id=AA1, first strand: chain 'A' and resid 765 through 766
    Processing sheet with id=AA2, first strand: chain 'A' and resid 1070 through 1071
      removed outlier: 6.827A  pdb=" N   VAL A1070 " --> pdb=" O   GLN A1084 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 765 through 766
    Processing sheet with id=AA4, first strand: chain 'B' and resid 1070 through 1071
      removed outlier: 6.842A  pdb=" N   VAL B1070 " --> pdb=" O   GLN B1084 " (cutoff:3.500A)

    410 hydrogen bonds defined for protein.
    1188 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: 1.06

  Time building geometry restraints manager: 0.85 seconds

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

  Histogram of bond lengths:
        1.00 -     1.17: 93
        1.17 -     1.33: 1783
        1.33 -     1.50: 3074
        1.50 -     1.67: 3329
        1.67 -     1.83: 86
  Bond restraints: 8365
  Sorted by residual:
  bond pdb=" C   ILE B 836 "
       pdb=" O   ILE B 836 "
    ideal  model  delta    sigma   weight residual
    1.241  1.015  0.226 1.03e-02 9.43e+03 4.80e+02
  bond pdb=" C   LEU B 843 "
       pdb=" O   LEU B 843 "
    ideal  model  delta    sigma   weight residual
    1.234  1.000  0.235 1.17e-02 7.31e+03 4.03e+02
  bond pdb=" C   ILE B 834 "
       pdb=" O   ILE B 834 "
    ideal  model  delta    sigma   weight residual
    1.238  1.024  0.214 1.18e-02 7.18e+03 3.30e+02
  bond pdb=" C   ILE A 836 "
       pdb=" O   ILE A 836 "
    ideal  model  delta    sigma   weight residual
    1.241  1.054  0.187 1.03e-02 9.43e+03 3.29e+02
  bond pdb=" C   TYR B 837 "
       pdb=" O   TYR B 837 "
    ideal  model  delta    sigma   weight residual
    1.236  1.035  0.201 1.22e-02 6.72e+03 2.72e+02
  ... (remaining 8360 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     8.16: 11227
        8.16 -    16.33: 120
       16.33 -    24.49: 10
       24.49 -    32.65: 2
       32.65 -    40.81: 1
  Bond angle restraints: 11360
  Sorted by residual:
  angle pdb=" C   ASP A1217 "
        pdb=" CA  ASP A1217 "
        pdb=" CB  ASP A1217 "
      ideal   model   delta    sigma   weight residual
     111.31   70.50   40.81 1.68e+00 3.54e-01 5.90e+02
  angle pdb=" O   ILE B 914 "
        pdb=" C   ILE B 914 "
        pdb=" N   ALA B 915 "
      ideal   model   delta    sigma   weight residual
     122.57  102.86   19.71 1.25e+00 6.40e-01 2.49e+02
  angle pdb=" C   PHE B 840 "
        pdb=" CA  PHE B 840 "
        pdb=" CB  PHE B 840 "
      ideal   model   delta    sigma   weight residual
     110.42   81.24   29.18 1.99e+00 2.53e-01 2.15e+02
  angle pdb=" C   GLN A 824 "
        pdb=" CA  GLN A 824 "
        pdb=" CB  GLN A 824 "
      ideal   model   delta    sigma   weight residual
     109.75   85.11   24.64 1.72e+00 3.38e-01 2.05e+02
  angle pdb=" N   LEU A1037 "
        pdb=" CA  LEU A1037 "
        pdb=" C   LEU A1037 "
      ideal   model   delta    sigma   weight residual
     114.31   97.28   17.03 1.29e+00 6.01e-01 1.74e+02
  ... (remaining 11355 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.71: 4405
       17.71 -    35.42: 403
       35.42 -    53.13: 94
       53.13 -    70.84: 21
       70.84 -    88.55: 8
  Dihedral angle restraints: 4931
    sinusoidal: 1972
      harmonic: 2959
  Sorted by residual:
  dihedral pdb=" C   ASP A1217 "
           pdb=" N   ASP A1217 "
           pdb=" CA  ASP A1217 "
           pdb=" CB  ASP A1217 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60  -76.87  -45.73     0      2.50e+00 1.60e-01 3.35e+02
  dihedral pdb=" C   PHE B 840 "
           pdb=" N   PHE B 840 "
           pdb=" CA  PHE B 840 "
           pdb=" CB  PHE B 840 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60  -88.67  -33.93     0      2.50e+00 1.60e-01 1.84e+02
  dihedral pdb=" C   GLN A 824 "
           pdb=" N   GLN A 824 "
           pdb=" CA  GLN A 824 "
           pdb=" CB  GLN A 824 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60  -92.85  -29.75     0      2.50e+00 1.60e-01 1.42e+02
  ... (remaining 4928 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.145: 1231
       0.145 -    0.290: 68
       0.290 -    0.434: 23
       0.434 -    0.579: 9
       0.579 -    0.724: 4
  Chirality restraints: 1335
  Sorted by residual:
  chirality pdb=" CB  VAL A 752 "
            pdb=" CA  VAL A 752 "
            pdb=" CG1 VAL A 752 "
            pdb=" CG2 VAL A 752 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -1.91   -0.72 2.00e-01 2.50e+01 1.31e+01
  chirality pdb=" CA  TYR A 841 "
            pdb=" N   TYR A 841 "
            pdb=" C   TYR A 841 "
            pdb=" CB  TYR A 841 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.81    0.70 2.00e-01 2.50e+01 1.22e+01
  chirality pdb=" CA  GLU A 838 "
            pdb=" N   GLU A 838 "
            pdb=" C   GLU A 838 "
            pdb=" CB  GLU A 838 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.88    0.63 2.00e-01 2.50e+01 1.01e+01
  ... (remaining 1332 not shown)

  Planarity restraints: 1390
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE B 914 "    0.046 2.00e-02 2.50e+03   7.85e-02 6.16e+01
        pdb=" C   ILE B 914 "   -0.136 2.00e-02 2.50e+03
        pdb=" O   ILE B 914 "    0.043 2.00e-02 2.50e+03
        pdb=" N   ALA B 915 "    0.047 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLU B 838 "    0.034 2.00e-02 2.50e+03   7.12e-02 5.07e+01
        pdb=" C   GLU B 838 "   -0.123 2.00e-02 2.50e+03
        pdb=" O   GLU B 838 "    0.046 2.00e-02 2.50e+03
        pdb=" N   THR B 839 "    0.043 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLU A 825 "    0.032 2.00e-02 2.50e+03   6.42e-02 4.12e+01
        pdb=" C   GLU A 825 "   -0.111 2.00e-02 2.50e+03
        pdb=" O   GLU A 825 "    0.040 2.00e-02 2.50e+03
        pdb=" N   ILE A 826 "    0.039 2.00e-02 2.50e+03
  ... (remaining 1387 not shown)

  Histogram of nonbonded interaction distances:
        1.61 -     2.27: 9
        2.27 -     2.93: 3346
        2.93 -     3.59: 11005
        3.59 -     4.24: 16892
        4.24 -     4.90: 30620
  Nonbonded interactions: 61872
  Sorted by model distance:
  nonbonded pdb=" O   PHE B 840 "
            pdb=" CB  PHE B 840 "
     model   vdw
     1.614 2.752
  nonbonded pdb=" O   ASP A1217 "
            pdb=" CB  ASP A1217 "
     model   vdw
     1.635 2.752
  nonbonded pdb=" O   GLN A 824 "
            pdb=" CB  GLN A 824 "
     model   vdw
     2.077 2.752
  nonbonded pdb=" O   LEU A 730 "
            pdb=" OG1 THR A 734 "
     model   vdw
     2.191 3.040
  nonbonded pdb=" O   GLN B 824 "
            pdb=" CB  GLN B 824 "
     model   vdw
     2.238 2.752
  ... (remaining 61867 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 673 through 855 or resid 894 through 1501))
  selection = chain 'B'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.250
  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:             0.000
  Extract box with map and model:          0.110
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     8.230
  Find NCS groups from input model:        0.120
  Set up NCS constraints:                  0.010
  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:1.460
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   11.250
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7815
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      :  0.019   0.235   8366  Z= 1.379
  Angle     :  1.928  40.813  11360  Z= 1.269
  Chirality :  0.094   0.724   1335
  Planarity :  0.010   0.098   1390
  Dihedral  : 14.992  88.551   3017
  Min Nonbonded Distance : 1.614

Molprobity Statistics.
  All-atom Clashscore : 6.04
  Ramachandran Plot:
    Outliers :  0.69 %
    Allowed  :  5.59 %
    Favored  : 93.72 %
  Rotamer:
    Outliers :  3.97 %
    Allowed  :  3.63 %
    Favored  : 92.40 %
  Cbeta Deviations :  5.33 %
  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 are not related in a simple way.
  whole: -0.32 (0.28), residues: 1019
  helix:  0.62 (0.23), residues: 636
  sheet:  None (None), residues: 0
  loop : -1.63 (0.30), residues: 383

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B1200 
 TYR   0.028   0.002   TYR B 837 
 PHE   0.040   0.003   PHE B 912 
 TRP   0.007   0.001   TRP A 795 
 HIS   0.016   0.001   HIS A 850 

Details of bonding type rmsd
  covalent geometry    : bond        0.01851 ( 8365)
  covalent geometry    : angle       1.92791 (11360)
  hydrogen bonds       : bond        0.16091 (  410)
  hydrogen bonds       : angle       5.26131 ( 1188)
  Misc. bond           : bond        0.01977 (    1)

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

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

  2038 Ramachandran restraints generated.
    1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2038 Ramachandran restraints generated.
    1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  221 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 186
  time to evaluate  : 0.295 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  740 VAL cc_start: 0.9134 (OUTLIER) cc_final: 0.8842 (t)
REVERT: A  838 GLU cc_start: 0.7749 (OUTLIER) cc_final: 0.7233 (mt-10)
REVERT: A  842 LYS cc_start: 0.8231 (OUTLIER) cc_final: 0.7930 (mttp)
REVERT: A  935 ILE cc_start: 0.8158 (mt) cc_final: 0.7885 (mm)
REVERT: A  947 MET cc_start: 0.8339 (mmt) cc_final: 0.7884 (mmt)
REVERT: A  993 MET cc_start: 0.7368 (tpt) cc_final: 0.6611 (tpt)
REVERT: A 1080 LYS cc_start: 0.7653 (OUTLIER) cc_final: 0.7378 (mptt)
REVERT: A 1082 LYS cc_start: 0.8069 (mmmt) cc_final: 0.7358 (ptmm)
REVERT: B  817 ARG cc_start: 0.8243 (OUTLIER) cc_final: 0.8017 (ttp-170)
REVERT: B  916 PHE cc_start: 0.8381 (OUTLIER) cc_final: 0.7774 (t80)
REVERT: B  925 ARG cc_start: 0.7553 (mtm-85) cc_final: 0.7287 (mtm180)
REVERT: B  935 ILE cc_start: 0.8159 (mt) cc_final: 0.7884 (mm)
REVERT: B  993 MET cc_start: 0.7265 (tpt) cc_final: 0.6521 (tpt)
REVERT: B 1075 VAL cc_start: 0.5532 (OUTLIER) cc_final: 0.5227 (t)
REVERT: B 1080 LYS cc_start: 0.7693 (OUTLIER) cc_final: 0.7488 (mppt)
REVERT: B 1082 LYS cc_start: 0.7573 (mmtm) cc_final: 0.7236 (ptmm)
REVERT: B 1109 LEU cc_start: 0.7477 (mp) cc_final: 0.7065 (tp)
REVERT: B 1220 GLU cc_start: 0.7468 (OUTLIER) cc_final: 0.7101 (pt0)
  outliers start: 35
  outliers final: 16
  residues processed: 212
  average time/residue: 0.1045
  time to fit residues: 28.8175
Evaluate side-chains
  154 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 129
  time to evaluate  : 0.293 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  701 ARG
Chi-restraints excluded: chain A residue  740 VAL
Chi-restraints excluded: chain A residue  741 SER
Chi-restraints excluded: chain A residue  742 GLU
Chi-restraints excluded: chain A residue  744 ILE
Chi-restraints excluded: chain A residue  746 SER
Chi-restraints excluded: chain A residue  749 LEU
Chi-restraints excluded: chain A residue  752 VAL
Chi-restraints excluded: chain A residue  820 SER
Chi-restraints excluded: chain A residue  832 SER
Chi-restraints excluded: chain A residue  838 GLU
Chi-restraints excluded: chain A residue  842 LYS
Chi-restraints excluded: chain A residue 1045 ILE
Chi-restraints excluded: chain A residue 1048 LEU
Chi-restraints excluded: chain A residue 1080 LYS
Chi-restraints excluded: chain A residue 1083 ILE
Chi-restraints excluded: chain A residue 1220 GLU
Chi-restraints excluded: chain B residue  817 ARG
Chi-restraints excluded: chain B residue  820 SER
Chi-restraints excluded: chain B residue  832 SER
Chi-restraints excluded: chain B residue  842 LYS
Chi-restraints excluded: chain B residue  916 PHE
Chi-restraints excluded: chain B residue 1075 VAL
Chi-restraints excluded: chain B residue 1080 LYS
Chi-restraints excluded: chain B residue 1220 GLU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 49 optimal weight:    1.9990
   chunk 97 optimal weight:    0.7980
   chunk 53 optimal weight:    0.0010
   chunk 5 optimal weight:    0.7980
   chunk 33 optimal weight:    2.9990
   chunk 65 optimal weight:    0.9980
   chunk 62 optimal weight:    0.8980
   chunk 51 optimal weight:   10.0000
   chunk 100 optimal weight:    0.5980
   chunk 38 optimal weight:    0.9990
   chunk 61 optimal weight:    0.9980
   overall best weight:    0.6186

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

Flipped N/Q/H residues before XYZ refinement:
A 824 GLN
B 824 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3549 r_free = 0.3549 target = 0.143016 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3105 r_free = 0.3105 target = 0.106671 restraints weight = 8723.341|
|-----------------------------------------------------------------------------|
r_work (start): 0.3099 rms_B_bonded: 1.80
r_work: 0.2971 rms_B_bonded: 2.39 restraints_weight: 0.5000
r_work: 0.2833 rms_B_bonded: 3.87 restraints_weight: 0.2500
r_work (final): 0.2833
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7781
moved from start:          0.1778

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.055   8366  Z= 0.133
  Angle     :  0.609   7.240  11360  Z= 0.313
  Chirality :  0.039   0.144   1335
  Planarity :  0.006   0.074   1390
  Dihedral  :  9.307  75.472   1172
  Min Nonbonded Distance : 2.534

Molprobity Statistics.
  All-atom Clashscore : 3.53
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  3.04 %
    Favored  : 96.86 %
  Rotamer:
    Outliers :  2.61 %
    Allowed  :  8.29 %
    Favored  : 89.10 %
  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 are not related in a simple way.
  whole:  0.01 (0.27), residues: 1019
  helix:  0.79 (0.22), residues: 660
  sheet:  None (None), residues: 0
  loop : -1.44 (0.30), residues: 359

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A1200 
 TYR   0.010   0.001   TYR B 789 
 PHE   0.011   0.001   PHE A1135 
 TRP   0.007   0.001   TRP B 795 
 HIS   0.003   0.001   HIS A 850 

Details of bonding type rmsd
  covalent geometry    : bond        0.00301 ( 8365)
  covalent geometry    : angle       0.60934 (11360)
  hydrogen bonds       : bond        0.04816 (  410)
  hydrogen bonds       : angle       3.84041 ( 1188)
  Misc. bond           : bond        0.00014 (    1)

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

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

  2038 Ramachandran restraints generated.
    1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2038 Ramachandran restraints generated.
    1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  151 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 128
  time to evaluate  : 0.318 
Fit side-chains
REVERT: A  745 MET cc_start: 0.8334 (mtp) cc_final: 0.8014 (mtt)
REVERT: A  842 LYS cc_start: 0.7877 (OUTLIER) cc_final: 0.7618 (mttt)
REVERT: A  935 ILE cc_start: 0.7943 (mt) cc_final: 0.7705 (mm)
REVERT: A 1035 ASP cc_start: 0.8338 (m-30) cc_final: 0.8094 (m-30)
REVERT: A 1045 ILE cc_start: 0.8324 (OUTLIER) cc_final: 0.7824 (tp)
REVERT: A 1080 LYS cc_start: 0.7325 (OUTLIER) cc_final: 0.6753 (mptt)
REVERT: B  745 MET cc_start: 0.7981 (mtp) cc_final: 0.7640 (mtt)
REVERT: B  925 ARG cc_start: 0.7873 (mtm-85) cc_final: 0.7228 (mtm180)
REVERT: B  935 ILE cc_start: 0.7940 (mt) cc_final: 0.7698 (mm)
REVERT: B 1220 GLU cc_start: 0.6942 (OUTLIER) cc_final: 0.6648 (pt0)
  outliers start: 23
  outliers final: 11
  residues processed: 138
  average time/residue: 0.0914
  time to fit residues: 17.1436
Evaluate side-chains
  132 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 117
  time to evaluate  : 0.292 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  808 VAL
Chi-restraints excluded: chain A residue  842 LYS
Chi-restraints excluded: chain A residue 1045 ILE
Chi-restraints excluded: chain A residue 1080 LYS
Chi-restraints excluded: chain A residue 1088 GLU
Chi-restraints excluded: chain A residue 1128 THR
Chi-restraints excluded: chain A residue 1180 VAL
Chi-restraints excluded: chain A residue 1205 THR
Chi-restraints excluded: chain A residue 1220 GLU
Chi-restraints excluded: chain B residue  970 VAL
Chi-restraints excluded: chain B residue 1088 GLU
Chi-restraints excluded: chain B residue 1128 THR
Chi-restraints excluded: chain B residue 1180 VAL
Chi-restraints excluded: chain B residue 1205 THR
Chi-restraints excluded: chain B residue 1220 GLU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 64 optimal weight:    1.9990
   chunk 13 optimal weight:    2.9990
   chunk 0 optimal weight:   10.0000
   chunk 26 optimal weight:    0.1980
   chunk 28 optimal weight:    6.9990
   chunk 46 optimal weight:    2.9990
   chunk 68 optimal weight:    1.9990
   chunk 22 optimal weight:    2.9990
   chunk 47 optimal weight:    0.9990
   chunk 42 optimal weight:    1.9990
   chunk 29 optimal weight:    1.9990
   overall best weight:    1.4388

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

Flipped N/Q/H residues before XYZ refinement:
A 735 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3454 r_free = 0.3454 target = 0.135135 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.2981 r_free = 0.2981 target = 0.097605 restraints weight = 8685.773|
|-----------------------------------------------------------------------------|
r_work (start): 0.2970 rms_B_bonded: 1.83
r_work: 0.2838 rms_B_bonded: 2.34 restraints_weight: 0.5000
r_work: 0.2701 rms_B_bonded: 3.73 restraints_weight: 0.2500
r_work (final): 0.2701
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7898
moved from start:          0.2540

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.052   8366  Z= 0.189
  Angle     :  0.632   8.689  11360  Z= 0.320
  Chirality :  0.042   0.160   1335
  Planarity :  0.007   0.092   1390
  Dihedral  :  7.659  72.212   1131
  Min Nonbonded Distance : 2.484

Molprobity Statistics.
  All-atom Clashscore : 3.77
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  3.63 %
    Favored  : 96.27 %
  Rotamer:
    Outliers :  2.50 %
    Allowed  :  9.53 %
    Favored  : 87.97 %
  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 are not related in a simple way.
  whole: -0.04 (0.26), residues: 1019
  helix:  0.73 (0.22), residues: 656
  sheet:  None (None), residues: 0
  loop : -1.38 (0.29), residues: 363

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 701 
 TYR   0.010   0.002   TYR A 789 
 PHE   0.023   0.002   PHE A1135 
 TRP   0.007   0.001   TRP A 795 
 HIS   0.004   0.001   HIS B1149 

Details of bonding type rmsd
  covalent geometry    : bond        0.00468 ( 8365)
  covalent geometry    : angle       0.63153 (11360)
  hydrogen bonds       : bond        0.06612 (  410)
  hydrogen bonds       : angle       3.80878 ( 1188)
  Misc. bond           : bond        0.00064 (    1)

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

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

  2038 Ramachandran restraints generated.
    1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2038 Ramachandran restraints generated.
    1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  145 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 123
  time to evaluate  : 0.316 
Fit side-chains
REVERT: A  745 MET cc_start: 0.8398 (mtp) cc_final: 0.8103 (mtt)
REVERT: A  842 LYS cc_start: 0.8159 (OUTLIER) cc_final: 0.7820 (mttt)
REVERT: A  916 PHE cc_start: 0.7941 (OUTLIER) cc_final: 0.7553 (t80)
REVERT: A  935 ILE cc_start: 0.8086 (mt) cc_final: 0.7885 (mm)
REVERT: A 1045 ILE cc_start: 0.8206 (OUTLIER) cc_final: 0.7687 (tp)
REVERT: A 1073 LYS cc_start: 0.7888 (OUTLIER) cc_final: 0.7400 (ttmt)
REVERT: B  745 MET cc_start: 0.8114 (mtp) cc_final: 0.7811 (mtt)
REVERT: B  925 ARG cc_start: 0.8135 (mtm-85) cc_final: 0.7541 (mtm180)
REVERT: B  935 ILE cc_start: 0.8070 (mt) cc_final: 0.7868 (mm)
REVERT: B 1192 ILE cc_start: 0.7995 (mm) cc_final: 0.7767 (mt)
REVERT: B 1210 ASP cc_start: 0.7121 (m-30) cc_final: 0.6916 (t0)
REVERT: B 1220 GLU cc_start: 0.7202 (OUTLIER) cc_final: 0.6613 (pt0)
  outliers start: 22
  outliers final: 14
  residues processed: 131
  average time/residue: 0.0863
  time to fit residues: 15.5876
Evaluate side-chains
  130 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 111
  time to evaluate  : 0.225 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  808 VAL
Chi-restraints excluded: chain A residue  842 LYS
Chi-restraints excluded: chain A residue  916 PHE
Chi-restraints excluded: chain A residue 1045 ILE
Chi-restraints excluded: chain A residue 1073 LYS
Chi-restraints excluded: chain A residue 1088 GLU
Chi-restraints excluded: chain A residue 1128 THR
Chi-restraints excluded: chain A residue 1144 MET
Chi-restraints excluded: chain A residue 1180 VAL
Chi-restraints excluded: chain A residue 1205 THR
Chi-restraints excluded: chain A residue 1220 GLU
Chi-restraints excluded: chain B residue  808 VAL
Chi-restraints excluded: chain B residue  970 VAL
Chi-restraints excluded: chain B residue 1128 THR
Chi-restraints excluded: chain B residue 1144 MET
Chi-restraints excluded: chain B residue 1153 THR
Chi-restraints excluded: chain B residue 1180 VAL
Chi-restraints excluded: chain B residue 1205 THR
Chi-restraints excluded: chain B residue 1220 GLU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 38 optimal weight:    0.9980
   chunk 39 optimal weight:    0.7980
   chunk 92 optimal weight:    2.9990
   chunk 0 optimal weight:   10.0000
   chunk 58 optimal weight:    1.9990
   chunk 7 optimal weight:    2.9990
   chunk 25 optimal weight:    2.9990
   chunk 59 optimal weight:    0.1980
   chunk 3 optimal weight:    2.9990
   chunk 11 optimal weight:    0.5980
   chunk 17 optimal weight:    1.9990
   overall best weight:    0.9182

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

Flipped N/Q/H residues before XYZ refinement:
A 735 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3474 r_free = 0.3474 target = 0.136963 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3000 r_free = 0.3000 target = 0.099143 restraints weight = 8856.654|
|-----------------------------------------------------------------------------|
r_work (start): 0.2997 rms_B_bonded: 1.85
r_work: 0.2860 rms_B_bonded: 2.45 restraints_weight: 0.5000
r_work: 0.2720 rms_B_bonded: 3.89 restraints_weight: 0.2500
r_work (final): 0.2720
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7933
moved from start:          0.2703

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   8366  Z= 0.134
  Angle     :  0.542   7.755  11360  Z= 0.274
  Chirality :  0.039   0.134   1335
  Planarity :  0.006   0.076   1390
  Dihedral  :  7.051  69.676   1127
  Min Nonbonded Distance : 2.486

Molprobity Statistics.
  All-atom Clashscore : 3.71
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  2.45 %
    Favored  : 97.45 %
  Rotamer:
    Outliers :  2.16 %
    Allowed  :  9.31 %
    Favored  : 88.54 %
  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 are not related in a simple way.
  whole:  0.24 (0.27), residues: 1019
  helix:  0.93 (0.22), residues: 653
  sheet:  None (None), residues: 0
  loop : -1.22 (0.29), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 701 
 TYR   0.010   0.001   TYR A 789 
 PHE   0.011   0.001   PHE B 822 
 TRP   0.008   0.001   TRP B 795 
 HIS   0.002   0.001   HIS B1149 

Details of bonding type rmsd
  covalent geometry    : bond        0.00321 ( 8365)
  covalent geometry    : angle       0.54210 (11360)
  hydrogen bonds       : bond        0.05313 (  410)
  hydrogen bonds       : angle       3.63926 ( 1188)
  Misc. bond           : bond        0.00033 (    1)

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

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

  2038 Ramachandran restraints generated.
    1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2038 Ramachandran restraints generated.
    1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  146 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 127
  time to evaluate  : 0.305 
Fit side-chains
REVERT: A  745 MET cc_start: 0.8427 (mtp) cc_final: 0.8165 (mtt)
REVERT: A  842 LYS cc_start: 0.8203 (OUTLIER) cc_final: 0.7895 (mttt)
REVERT: A  916 PHE cc_start: 0.7959 (OUTLIER) cc_final: 0.7641 (t80)
REVERT: B  702 ASP cc_start: 0.7346 (t0) cc_final: 0.7098 (t0)
REVERT: B  745 MET cc_start: 0.8112 (mtp) cc_final: 0.7828 (mtt)
REVERT: B  925 ARG cc_start: 0.8219 (mtm-85) cc_final: 0.7649 (mtm180)
REVERT: B 1210 ASP cc_start: 0.7158 (m-30) cc_final: 0.6904 (t0)
REVERT: B 1220 GLU cc_start: 0.7075 (tt0) cc_final: 0.6392 (pt0)
  outliers start: 19
  outliers final: 15
  residues processed: 136
  average time/residue: 0.0860
  time to fit residues: 16.2778
Evaluate side-chains
  134 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 117
  time to evaluate  : 0.303 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  808 VAL
Chi-restraints excluded: chain A residue  842 LYS
Chi-restraints excluded: chain A residue  916 PHE
Chi-restraints excluded: chain A residue  970 VAL
Chi-restraints excluded: chain A residue 1048 LEU
Chi-restraints excluded: chain A residue 1075 VAL
Chi-restraints excluded: chain A residue 1088 GLU
Chi-restraints excluded: chain A residue 1128 THR
Chi-restraints excluded: chain A residue 1144 MET
Chi-restraints excluded: chain A residue 1180 VAL
Chi-restraints excluded: chain A residue 1220 GLU
Chi-restraints excluded: chain B residue  970 VAL
Chi-restraints excluded: chain B residue 1023 GLU
Chi-restraints excluded: chain B residue 1088 GLU
Chi-restraints excluded: chain B residue 1128 THR
Chi-restraints excluded: chain B residue 1153 THR
Chi-restraints excluded: chain B residue 1180 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 69 optimal weight:    4.9990
   chunk 31 optimal weight:    0.0870
   chunk 82 optimal weight:    5.9990
   chunk 83 optimal weight:    0.8980
   chunk 23 optimal weight:    0.5980
   chunk 65 optimal weight:    0.9990
   chunk 59 optimal weight:    0.9990
   chunk 2 optimal weight:    0.0970
   chunk 71 optimal weight:    0.4980
   chunk 13 optimal weight:    0.9990
   chunk 52 optimal weight:    3.9990
   overall best weight:    0.4356

-------------------------------------------------------------------------------
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 = 0.3509 r_free = 0.3509 target = 0.140170 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3045 r_free = 0.3045 target = 0.102675 restraints weight = 8715.441|
|-----------------------------------------------------------------------------|
r_work (start): 0.3067 rms_B_bonded: 1.82
r_work: 0.2933 rms_B_bonded: 2.41 restraints_weight: 0.5000
r_work: 0.2794 rms_B_bonded: 3.86 restraints_weight: 0.2500
r_work (final): 0.2794
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7898
moved from start:          0.2822

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035   8366  Z= 0.102
  Angle     :  0.498   8.786  11360  Z= 0.248
  Chirality :  0.038   0.127   1335
  Planarity :  0.006   0.067   1390
  Dihedral  :  6.343  65.500   1122
  Min Nonbonded Distance : 2.436

Molprobity Statistics.
  All-atom Clashscore : 3.53
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  2.85 %
    Favored  : 97.06 %
  Rotamer:
    Outliers :  1.59 %
    Allowed  : 10.56 %
    Favored  : 87.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.63 (0.27), residues: 1019
  helix:  1.24 (0.22), residues: 652
  sheet:  None (None), residues: 0
  loop : -1.06 (0.29), residues: 367

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 701 
 TYR   0.010   0.001   TYR A 789 
 PHE   0.008   0.001   PHE A 822 
 TRP   0.008   0.001   TRP B 795 
 HIS   0.001   0.000   HIS B 853 

Details of bonding type rmsd
  covalent geometry    : bond        0.00233 ( 8365)
  covalent geometry    : angle       0.49799 (11360)
  hydrogen bonds       : bond        0.04048 (  410)
  hydrogen bonds       : angle       3.39769 ( 1188)
  Misc. bond           : bond        0.00018 (    1)

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

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

  2038 Ramachandran restraints generated.
    1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2038 Ramachandran restraints generated.
    1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  146 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 132
  time to evaluate  : 0.322 
Fit side-chains
REVERT: A  702 ASP cc_start: 0.7261 (t0) cc_final: 0.6985 (t0)
REVERT: A  745 MET cc_start: 0.8371 (mtp) cc_final: 0.8108 (mtt)
REVERT: A  842 LYS cc_start: 0.8085 (OUTLIER) cc_final: 0.7826 (mttt)
REVERT: A  916 PHE cc_start: 0.7934 (OUTLIER) cc_final: 0.7675 (t80)
REVERT: A 1073 LYS cc_start: 0.7890 (OUTLIER) cc_final: 0.7199 (ttmm)
REVERT: B  702 ASP cc_start: 0.7408 (t0) cc_final: 0.7107 (t0)
REVERT: B  745 MET cc_start: 0.8101 (mtp) cc_final: 0.7887 (mtt)
REVERT: B  925 ARG cc_start: 0.8199 (mtm-85) cc_final: 0.7588 (mtm180)
REVERT: B 1210 ASP cc_start: 0.7217 (m-30) cc_final: 0.6927 (t0)
REVERT: B 1220 GLU cc_start: 0.7187 (tt0) cc_final: 0.6357 (pt0)
  outliers start: 14
  outliers final: 7
  residues processed: 140
  average time/residue: 0.0789
  time to fit residues: 15.4836
Evaluate side-chains
  136 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 126
  time to evaluate  : 0.286 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  808 VAL
Chi-restraints excluded: chain A residue  842 LYS
Chi-restraints excluded: chain A residue  916 PHE
Chi-restraints excluded: chain A residue 1048 LEU
Chi-restraints excluded: chain A residue 1073 LYS
Chi-restraints excluded: chain A residue 1075 VAL
Chi-restraints excluded: chain A residue 1088 GLU
Chi-restraints excluded: chain A residue 1220 GLU
Chi-restraints excluded: chain B residue  749 LEU
Chi-restraints excluded: chain B residue 1128 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 31 optimal weight:    2.9990
   chunk 35 optimal weight:    1.9990
   chunk 13 optimal weight:    4.9990
   chunk 20 optimal weight:    0.6980
   chunk 24 optimal weight:    0.9980
   chunk 100 optimal weight:    0.7980
   chunk 1 optimal weight:    0.9980
   chunk 72 optimal weight:    1.9990
   chunk 77 optimal weight:    3.9990
   chunk 33 optimal weight:    4.9990
   chunk 32 optimal weight:    2.9990
   overall best weight:    1.0982

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

Flipped N/Q/H residues before XYZ refinement:
A 735 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3467 r_free = 0.3467 target = 0.136807 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.2986 r_free = 0.2986 target = 0.098399 restraints weight = 8667.148|
|-----------------------------------------------------------------------------|
r_work (start): 0.2981 rms_B_bonded: 1.87
r_work: 0.2843 rms_B_bonded: 2.45 restraints_weight: 0.5000
r_work: 0.2703 rms_B_bonded: 3.88 restraints_weight: 0.2500
r_work (final): 0.2703
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7887
moved from start:          0.2930

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   8366  Z= 0.145
  Angle     :  0.538   8.585  11360  Z= 0.270
  Chirality :  0.040   0.139   1335
  Planarity :  0.006   0.068   1390
  Dihedral  :  6.334  63.651   1122
  Min Nonbonded Distance : 2.408

Molprobity Statistics.
  All-atom Clashscore : 3.59
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  2.75 %
    Favored  : 97.15 %
  Rotamer:
    Outliers :  2.38 %
    Allowed  : 10.67 %
    Favored  : 86.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.58 (0.27), residues: 1019
  helix:  1.20 (0.22), residues: 652
  sheet:  None (None), residues: 0
  loop : -1.07 (0.29), residues: 367

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 701 
 TYR   0.012   0.001   TYR A 789 
 PHE   0.011   0.001   PHE B 822 
 TRP   0.007   0.001   TRP A 795 
 HIS   0.002   0.001   HIS A1149 

Details of bonding type rmsd
  covalent geometry    : bond        0.00357 ( 8365)
  covalent geometry    : angle       0.53813 (11360)
  hydrogen bonds       : bond        0.05299 (  410)
  hydrogen bonds       : angle       3.47986 ( 1188)
  Misc. bond           : bond        0.00024 (    1)

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

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

  2038 Ramachandran restraints generated.
    1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2038 Ramachandran restraints generated.
    1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  145 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 124
  time to evaluate  : 0.287 
Fit side-chains
REVERT: A  702 ASP cc_start: 0.7389 (t0) cc_final: 0.7073 (t0)
REVERT: A  745 MET cc_start: 0.8399 (mtp) cc_final: 0.8129 (mtt)
REVERT: A  842 LYS cc_start: 0.8180 (OUTLIER) cc_final: 0.7869 (mttt)
REVERT: A  916 PHE cc_start: 0.7958 (OUTLIER) cc_final: 0.7682 (t80)
REVERT: A 1073 LYS cc_start: 0.7873 (OUTLIER) cc_final: 0.7162 (ttmm)
REVERT: A 1210 ASP cc_start: 0.7237 (m-30) cc_final: 0.7012 (t0)
REVERT: B  702 ASP cc_start: 0.7446 (t0) cc_final: 0.7085 (t0)
REVERT: B  745 MET cc_start: 0.8101 (mtp) cc_final: 0.7825 (mtt)
REVERT: B  925 ARG cc_start: 0.8190 (mtm-85) cc_final: 0.7559 (mtm180)
REVERT: B 1210 ASP cc_start: 0.7182 (m-30) cc_final: 0.6876 (t0)
REVERT: B 1220 GLU cc_start: 0.7176 (tt0) cc_final: 0.6326 (pt0)
  outliers start: 21
  outliers final: 16
  residues processed: 135
  average time/residue: 0.0797
  time to fit residues: 15.2475
Evaluate side-chains
  141 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 122
  time to evaluate  : 0.311 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  808 VAL
Chi-restraints excluded: chain A residue  842 LYS
Chi-restraints excluded: chain A residue  916 PHE
Chi-restraints excluded: chain A residue 1023 GLU
Chi-restraints excluded: chain A residue 1048 LEU
Chi-restraints excluded: chain A residue 1073 LYS
Chi-restraints excluded: chain A residue 1075 VAL
Chi-restraints excluded: chain A residue 1088 GLU
Chi-restraints excluded: chain A residue 1128 THR
Chi-restraints excluded: chain A residue 1144 MET
Chi-restraints excluded: chain A residue 1180 VAL
Chi-restraints excluded: chain A residue 1220 GLU
Chi-restraints excluded: chain B residue  749 LEU
Chi-restraints excluded: chain B residue  808 VAL
Chi-restraints excluded: chain B residue  970 VAL
Chi-restraints excluded: chain B residue 1088 GLU
Chi-restraints excluded: chain B residue 1128 THR
Chi-restraints excluded: chain B residue 1153 THR
Chi-restraints excluded: chain B residue 1180 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 60 optimal weight:    2.9990
   chunk 31 optimal weight:    2.9990
   chunk 19 optimal weight:    0.5980
   chunk 37 optimal weight:    0.9980
   chunk 79 optimal weight:    0.9980
   chunk 7 optimal weight:    2.9990
   chunk 45 optimal weight:    3.9990
   chunk 5 optimal weight:    1.9990
   chunk 70 optimal weight:    1.9990
   chunk 34 optimal weight:    0.0060
   chunk 22 optimal weight:    2.9990
   overall best weight:    0.9198

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

Flipped N/Q/H residues before XYZ refinement:
A 735 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3467 r_free = 0.3467 target = 0.136755 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.2983 r_free = 0.2983 target = 0.098216 restraints weight = 8739.364|
|-----------------------------------------------------------------------------|
r_work (start): 0.2984 rms_B_bonded: 1.89
r_work: 0.2847 rms_B_bonded: 2.43 restraints_weight: 0.5000
r_work: 0.2705 rms_B_bonded: 3.89 restraints_weight: 0.2500
r_work (final): 0.2705
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7875
moved from start:          0.3038

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   8366  Z= 0.132
  Angle     :  0.538   8.363  11360  Z= 0.265
  Chirality :  0.039   0.141   1335
  Planarity :  0.006   0.068   1390
  Dihedral  :  6.215  61.392   1122
  Min Nonbonded Distance : 2.448

Molprobity Statistics.
  All-atom Clashscore : 3.65
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  2.45 %
    Favored  : 97.45 %
  Rotamer:
    Outliers :  2.04 %
    Allowed  : 10.78 %
    Favored  : 87.17 %
  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 are not related in a simple way.
  whole:  0.63 (0.27), residues: 1019
  helix:  1.24 (0.21), residues: 652
  sheet:  None (None), residues: 0
  loop : -1.05 (0.29), residues: 367

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A 701 
 TYR   0.011   0.001   TYR A 789 
 PHE   0.010   0.001   PHE B1135 
 TRP   0.007   0.001   TRP A 795 
 HIS   0.002   0.001   HIS A1149 

Details of bonding type rmsd
  covalent geometry    : bond        0.00320 ( 8365)
  covalent geometry    : angle       0.53805 (11360)
  hydrogen bonds       : bond        0.05134 (  410)
  hydrogen bonds       : angle       3.47118 ( 1188)
  Misc. bond           : bond        0.00022 (    1)

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

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

  2038 Ramachandran restraints generated.
    1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2038 Ramachandran restraints generated.
    1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  143 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 125
  time to evaluate  : 0.209 
Fit side-chains
REVERT: A  745 MET cc_start: 0.8363 (mtp) cc_final: 0.8097 (mtt)
REVERT: A  842 LYS cc_start: 0.8098 (OUTLIER) cc_final: 0.7796 (mttt)
REVERT: A  916 PHE cc_start: 0.7901 (OUTLIER) cc_final: 0.7617 (t80)
REVERT: A 1210 ASP cc_start: 0.7212 (m-30) cc_final: 0.6986 (t0)
REVERT: B  745 MET cc_start: 0.8070 (mtp) cc_final: 0.7796 (mtt)
REVERT: B  925 ARG cc_start: 0.8186 (mtm-85) cc_final: 0.7569 (mtm180)
REVERT: B 1210 ASP cc_start: 0.7123 (m-30) cc_final: 0.6757 (t0)
REVERT: B 1220 GLU cc_start: 0.7268 (tt0) cc_final: 0.6330 (pt0)
  outliers start: 18
  outliers final: 15
  residues processed: 136
  average time/residue: 0.0841
  time to fit residues: 15.8463
Evaluate side-chains
  128 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 111
  time to evaluate  : 0.282 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  808 VAL
Chi-restraints excluded: chain A residue  842 LYS
Chi-restraints excluded: chain A residue  916 PHE
Chi-restraints excluded: chain A residue 1023 GLU
Chi-restraints excluded: chain A residue 1048 LEU
Chi-restraints excluded: chain A residue 1075 VAL
Chi-restraints excluded: chain A residue 1088 GLU
Chi-restraints excluded: chain A residue 1128 THR
Chi-restraints excluded: chain A residue 1220 GLU
Chi-restraints excluded: chain B residue  749 LEU
Chi-restraints excluded: chain B residue  808 VAL
Chi-restraints excluded: chain B residue  970 VAL
Chi-restraints excluded: chain B residue 1023 GLU
Chi-restraints excluded: chain B residue 1088 GLU
Chi-restraints excluded: chain B residue 1128 THR
Chi-restraints excluded: chain B residue 1153 THR
Chi-restraints excluded: chain B residue 1180 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 97 optimal weight:    1.9990
   chunk 93 optimal weight:    1.9990
   chunk 78 optimal weight:    0.4980
   chunk 10 optimal weight:    1.9990
   chunk 32 optimal weight:    4.9990
   chunk 34 optimal weight:    0.8980
   chunk 50 optimal weight:    2.9990
   chunk 21 optimal weight:    0.5980
   chunk 55 optimal weight:    1.9990
   chunk 68 optimal weight:    0.8980
   chunk 100 optimal weight:    3.9990
   overall best weight:    0.9782

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

Flipped N/Q/H residues before XYZ refinement:
A 735 GLN
A 824 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3460 r_free = 0.3460 target = 0.136059 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.2976 r_free = 0.2976 target = 0.097598 restraints weight = 8664.417|
|-----------------------------------------------------------------------------|
r_work (start): 0.2975 rms_B_bonded: 1.88
r_work: 0.2842 rms_B_bonded: 2.37 restraints_weight: 0.5000
r_work: 0.2701 rms_B_bonded: 3.78 restraints_weight: 0.2500
r_work (final): 0.2701
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7839
moved from start:          0.3109

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   8366  Z= 0.138
  Angle     :  0.542   8.305  11360  Z= 0.268
  Chirality :  0.039   0.143   1335
  Planarity :  0.006   0.068   1390
  Dihedral  :  6.129  59.164   1122
  Min Nonbonded Distance : 2.478

Molprobity Statistics.
  All-atom Clashscore : 3.47
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  2.65 %
    Favored  : 97.25 %
  Rotamer:
    Outliers :  2.04 %
    Allowed  : 11.24 %
    Favored  : 86.72 %
  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 are not related in a simple way.
  whole:  0.67 (0.27), residues: 1019
  helix:  1.25 (0.21), residues: 652
  sheet:  None (None), residues: 0
  loop : -1.01 (0.29), residues: 367

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B 701 
 TYR   0.011   0.001   TYR A 789 
 PHE   0.010   0.001   PHE B1135 
 TRP   0.007   0.001   TRP A 795 
 HIS   0.002   0.001   HIS A1149 

Details of bonding type rmsd
  covalent geometry    : bond        0.00334 ( 8365)
  covalent geometry    : angle       0.54173 (11360)
  hydrogen bonds       : bond        0.05322 (  410)
  hydrogen bonds       : angle       3.49274 ( 1188)
  Misc. bond           : bond        0.00019 (    1)

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

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

  2038 Ramachandran restraints generated.
    1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2038 Ramachandran restraints generated.
    1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 117
  time to evaluate  : 0.301 
Fit side-chains
REVERT: A  745 MET cc_start: 0.8294 (mtp) cc_final: 0.8018 (mtt)
REVERT: A  916 PHE cc_start: 0.7876 (OUTLIER) cc_final: 0.7575 (t80)
REVERT: A 1075 VAL cc_start: 0.4560 (OUTLIER) cc_final: 0.4110 (t)
REVERT: A 1210 ASP cc_start: 0.7165 (m-30) cc_final: 0.6958 (t0)
REVERT: B  745 MET cc_start: 0.8015 (mtp) cc_final: 0.7736 (mtt)
REVERT: B  925 ARG cc_start: 0.8173 (mtm-85) cc_final: 0.7550 (mtm180)
REVERT: B 1210 ASP cc_start: 0.7057 (m-30) cc_final: 0.6711 (t0)
REVERT: B 1220 GLU cc_start: 0.7230 (tt0) cc_final: 0.6306 (pt0)
  outliers start: 18
  outliers final: 16
  residues processed: 127
  average time/residue: 0.0775
  time to fit residues: 14.1348
Evaluate side-chains
  129 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 111
  time to evaluate  : 0.319 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  808 VAL
Chi-restraints excluded: chain A residue  916 PHE
Chi-restraints excluded: chain A residue  970 VAL
Chi-restraints excluded: chain A residue 1023 GLU
Chi-restraints excluded: chain A residue 1048 LEU
Chi-restraints excluded: chain A residue 1075 VAL
Chi-restraints excluded: chain A residue 1088 GLU
Chi-restraints excluded: chain A residue 1128 THR
Chi-restraints excluded: chain A residue 1180 VAL
Chi-restraints excluded: chain A residue 1220 GLU
Chi-restraints excluded: chain B residue  749 LEU
Chi-restraints excluded: chain B residue  808 VAL
Chi-restraints excluded: chain B residue  970 VAL
Chi-restraints excluded: chain B residue 1023 GLU
Chi-restraints excluded: chain B residue 1088 GLU
Chi-restraints excluded: chain B residue 1128 THR
Chi-restraints excluded: chain B residue 1153 THR
Chi-restraints excluded: chain B residue 1180 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 34 optimal weight:    1.9990
   chunk 38 optimal weight:    2.9990
   chunk 53 optimal weight:    0.0050
   chunk 26 optimal weight:    0.8980
   chunk 43 optimal weight:    0.9990
   chunk 13 optimal weight:    3.9990
   chunk 52 optimal weight:    2.9990
   chunk 63 optimal weight:    0.7980
   chunk 40 optimal weight:    0.4980
   chunk 71 optimal weight:    0.6980
   chunk 86 optimal weight:    0.9990
   overall best weight:    0.5794

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

Flipped N/Q/H residues before XYZ refinement:
A 735 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3487 r_free = 0.3487 target = 0.138507 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3008 r_free = 0.3008 target = 0.100061 restraints weight = 8631.329|
|-----------------------------------------------------------------------------|
r_work (start): 0.3004 rms_B_bonded: 1.88
r_work: 0.2867 rms_B_bonded: 2.44 restraints_weight: 0.5000
r_work: 0.2725 rms_B_bonded: 3.91 restraints_weight: 0.2500
r_work (final): 0.2725
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7863
moved from start:          0.3150

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   8366  Z= 0.110
  Angle     :  0.508   7.873  11360  Z= 0.250
  Chirality :  0.038   0.136   1335
  Planarity :  0.005   0.067   1390
  Dihedral  :  5.708  56.990   1118
  Min Nonbonded Distance : 2.504

Molprobity Statistics.
  All-atom Clashscore : 3.59
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  2.55 %
    Favored  : 97.35 %
  Rotamer:
    Outliers :  1.82 %
    Allowed  : 11.46 %
    Favored  : 86.72 %
  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 are not related in a simple way.
  whole:  0.90 (0.27), residues: 1019
  helix:  1.43 (0.21), residues: 652
  sheet:  None (None), residues: 0
  loop : -0.92 (0.30), residues: 367

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A 701 
 TYR   0.010   0.001   TYR B 789 
 PHE   0.008   0.001   PHE A 822 
 TRP   0.010   0.001   TRP B 795 
 HIS   0.001   0.000   HIS B1149 

Details of bonding type rmsd
  covalent geometry    : bond        0.00257 ( 8365)
  covalent geometry    : angle       0.50756 (11360)
  hydrogen bonds       : bond        0.04371 (  410)
  hydrogen bonds       : angle       3.37544 ( 1188)
  Misc. bond           : bond        0.00016 (    1)

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

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

  2038 Ramachandran restraints generated.
    1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2038 Ramachandran restraints generated.
    1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  142 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 126
  time to evaluate  : 0.312 
Fit side-chains
REVERT: A  745 MET cc_start: 0.8268 (mtp) cc_final: 0.7989 (mtt)
REVERT: A  916 PHE cc_start: 0.7906 (OUTLIER) cc_final: 0.7666 (t80)
REVERT: A 1011 GLU cc_start: 0.7144 (mt-10) cc_final: 0.6764 (tt0)
REVERT: A 1075 VAL cc_start: 0.4626 (OUTLIER) cc_final: 0.4156 (t)
REVERT: A 1210 ASP cc_start: 0.7193 (m-30) cc_final: 0.6977 (t0)
REVERT: B  702 ASP cc_start: 0.7397 (t0) cc_final: 0.7179 (t0)
REVERT: B  745 MET cc_start: 0.8063 (mtp) cc_final: 0.7801 (mtt)
REVERT: B  925 ARG cc_start: 0.8213 (mtm-85) cc_final: 0.7620 (mtm180)
  outliers start: 16
  outliers final: 14
  residues processed: 133
  average time/residue: 0.0809
  time to fit residues: 15.2652
Evaluate side-chains
  139 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 123
  time to evaluate  : 0.315 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  808 VAL
Chi-restraints excluded: chain A residue  845 LYS
Chi-restraints excluded: chain A residue  916 PHE
Chi-restraints excluded: chain A residue 1023 GLU
Chi-restraints excluded: chain A residue 1048 LEU
Chi-restraints excluded: chain A residue 1075 VAL
Chi-restraints excluded: chain A residue 1088 GLU
Chi-restraints excluded: chain A residue 1205 THR
Chi-restraints excluded: chain A residue 1220 GLU
Chi-restraints excluded: chain B residue  749 LEU
Chi-restraints excluded: chain B residue  808 VAL
Chi-restraints excluded: chain B residue  970 VAL
Chi-restraints excluded: chain B residue 1088 GLU
Chi-restraints excluded: chain B residue 1128 THR
Chi-restraints excluded: chain B residue 1153 THR
Chi-restraints excluded: chain B residue 1180 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 52 optimal weight:    2.9990
   chunk 101 optimal weight:    0.7980
   chunk 15 optimal weight:    1.9990
   chunk 93 optimal weight:    1.9990
   chunk 83 optimal weight:    0.9990
   chunk 71 optimal weight:    2.9990
   chunk 11 optimal weight:    3.9990
   chunk 3 optimal weight:    0.2980
   chunk 80 optimal weight:    0.8980
   chunk 55 optimal weight:    1.9990
   chunk 4 optimal weight:    0.9980
   overall best weight:    0.7982

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

Flipped N/Q/H residues before XYZ refinement:
A 735 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3476 r_free = 0.3476 target = 0.137348 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.2989 r_free = 0.2989 target = 0.098519 restraints weight = 8682.228|
|-----------------------------------------------------------------------------|
r_work (start): 0.2985 rms_B_bonded: 1.92
r_work: 0.2839 rms_B_bonded: 2.59 restraints_weight: 0.5000
r_work: 0.2694 rms_B_bonded: 4.11 restraints_weight: 0.2500
r_work (final): 0.2694
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7966
moved from start:          0.3207

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   8366  Z= 0.123
  Angle     :  0.522   8.024  11360  Z= 0.257
  Chirality :  0.039   0.146   1335
  Planarity :  0.006   0.068   1390
  Dihedral  :  5.694  55.579   1118
  Min Nonbonded Distance : 2.512

Molprobity Statistics.
  All-atom Clashscore : 3.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.75 %
    Favored  : 97.25 %
  Rotamer:
    Outliers :  1.82 %
    Allowed  : 11.58 %
    Favored  : 86.61 %
  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 are not related in a simple way.
  whole:  0.88 (0.27), residues: 1019
  helix:  1.43 (0.21), residues: 653
  sheet:  None (None), residues: 0
  loop : -0.94 (0.30), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG B 701 
 TYR   0.011   0.001   TYR A 789 
 PHE   0.008   0.001   PHE A 822 
 TRP   0.010   0.001   TRP B 795 
 HIS   0.002   0.000   HIS A1149 

Details of bonding type rmsd
  covalent geometry    : bond        0.00295 ( 8365)
  covalent geometry    : angle       0.52180 (11360)
  hydrogen bonds       : bond        0.04833 (  410)
  hydrogen bonds       : angle       3.40368 ( 1188)
  Misc. bond           : bond        0.00015 (    1)

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

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

  2038 Ramachandran restraints generated.
    1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2038 Ramachandran restraints generated.
    1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  139 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 123
  time to evaluate  : 0.329 
Fit side-chains
REVERT: A  702 ASP cc_start: 0.7415 (t0) cc_final: 0.7213 (t0)
REVERT: A  745 MET cc_start: 0.8325 (mtp) cc_final: 0.8062 (mtt)
REVERT: A  916 PHE cc_start: 0.8005 (OUTLIER) cc_final: 0.7765 (t80)
REVERT: A 1011 GLU cc_start: 0.7254 (mt-10) cc_final: 0.6870 (tt0)
REVERT: A 1075 VAL cc_start: 0.4641 (OUTLIER) cc_final: 0.4160 (t)
REVERT: A 1210 ASP cc_start: 0.7273 (m-30) cc_final: 0.7038 (t0)
REVERT: B  702 ASP cc_start: 0.7479 (t0) cc_final: 0.7271 (t0)
REVERT: B  745 MET cc_start: 0.8145 (mtp) cc_final: 0.7910 (mtt)
REVERT: B  925 ARG cc_start: 0.8318 (mtm-85) cc_final: 0.7759 (mtm180)
REVERT: B 1210 ASP cc_start: 0.7144 (m-30) cc_final: 0.6770 (t0)
  outliers start: 16
  outliers final: 13
  residues processed: 132
  average time/residue: 0.0784
  time to fit residues: 14.6735
Evaluate side-chains
  138 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 123
  time to evaluate  : 0.314 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  808 VAL
Chi-restraints excluded: chain A residue  845 LYS
Chi-restraints excluded: chain A residue  916 PHE
Chi-restraints excluded: chain A residue 1048 LEU
Chi-restraints excluded: chain A residue 1075 VAL
Chi-restraints excluded: chain A residue 1088 GLU
Chi-restraints excluded: chain A residue 1205 THR
Chi-restraints excluded: chain A residue 1220 GLU
Chi-restraints excluded: chain B residue  749 LEU
Chi-restraints excluded: chain B residue  808 VAL
Chi-restraints excluded: chain B residue  970 VAL
Chi-restraints excluded: chain B residue 1088 GLU
Chi-restraints excluded: chain B residue 1128 THR
Chi-restraints excluded: chain B residue 1153 THR
Chi-restraints excluded: chain B residue 1180 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 86 optimal weight:    0.7980
   chunk 33 optimal weight:    1.9990
   chunk 37 optimal weight:    0.0870
   chunk 85 optimal weight:    1.9990
   chunk 61 optimal weight:    3.9990
   chunk 13 optimal weight:    0.8980
   chunk 56 optimal weight:    2.9990
   chunk 29 optimal weight:    0.7980
   chunk 40 optimal weight:    0.2980
   chunk 57 optimal weight:    0.7980
   chunk 9 optimal weight:    1.9990
   overall best weight:    0.5558

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

Flipped N/Q/H residues before XYZ refinement:
A 735 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3495 r_free = 0.3495 target = 0.139045 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3016 r_free = 0.3016 target = 0.100519 restraints weight = 8682.393|
|-----------------------------------------------------------------------------|
r_work (start): 0.3010 rms_B_bonded: 1.89
r_work: 0.2869 rms_B_bonded: 2.51 restraints_weight: 0.5000
r_work: 0.2726 rms_B_bonded: 3.99 restraints_weight: 0.2500
r_work (final): 0.2726
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7878
moved from start:          0.3241

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031   8366  Z= 0.107
  Angle     :  0.500   7.854  11360  Z= 0.246
  Chirality :  0.038   0.137   1335
  Planarity :  0.005   0.067   1390
  Dihedral  :  5.573  55.403   1118
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 3.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.55 %
    Favored  : 97.45 %
  Rotamer:
    Outliers :  1.82 %
    Allowed  : 11.35 %
    Favored  : 86.83 %
  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 are not related in a simple way.
  whole:  1.06 (0.27), residues: 1019
  helix:  1.57 (0.21), residues: 653
  sheet:  None (None), residues: 0
  loop : -0.87 (0.30), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG A 701 
 TYR   0.010   0.001   TYR A 789 
 PHE   0.007   0.001   PHE A 822 
 TRP   0.010   0.001   TRP B 795 
 HIS   0.001   0.000   HIS B1149 

Details of bonding type rmsd
  covalent geometry    : bond        0.00249 ( 8365)
  covalent geometry    : angle       0.50045 (11360)
  hydrogen bonds       : bond        0.04218 (  410)
  hydrogen bonds       : angle       3.31900 ( 1188)
  Misc. bond           : bond        0.00010 (    1)
Origin is already at (0, 0, 0), no shifts will be applied

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Job complete
usr+sys time: 2095.83 seconds
wall clock time: 36 minutes 19.81 seconds (2179.81 seconds total)