Starting phenix.real_space_refine
on Tue Feb 13 23:17:17 2024 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gva_34289/02_2024/8gva_34289.pdb
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gva_34289/02_2024/8gva_34289.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.25
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gva_34289/02_2024/8gva_34289.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gva_34289/02_2024/8gva_34289.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gva_34289/02_2024/8gva_34289.pdb"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gva_34289/02_2024/8gva_34289.pdb"
  }
  resolution = 3.25
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.002 sd=   0.125
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      46      5.16       5
     C    5370      2.51       5
     N    1326      2.21       5
     O    1330      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped
    None
  Time to flip residues: 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib"
  Total number of atoms: 8072
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 4036
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 511, 4036
          Classifications: {'peptide': 511}
          Link IDs: {'PTRANS': 27, 'TRANS': 483}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 4036
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 511, 4036
          Classifications: {'peptide': 511}
          Link IDs: {'PTRANS': 27, 'TRANS': 483}
          Chain breaks: 1
  Time building chain proxies: 4.75, per 1000 atoms: 0.59
  Number of scatterers: 8072
  At special positions: 0
  Unit cell: (89.1, 122.1, 82.5, 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      46     16.00
     O    1330      8.00
     N    1326      7.00
     C    5370      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  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 3.02
  Conformation dependent library (CDL) restraints added in 1.5 seconds
  

  2028 Ramachandran restraints generated.
    1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1904

  Finding SS restraints...
    Secondary structure from input PDB file:
      54 helices and 3 sheets defined
      70.6% alpha, 0.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.82
  Creating SS restraints...
    Processing helix  chain 'A' and resid 682 through 693
    Processing helix  chain 'A' and resid 694 through 696
      No H-bonds generated for 'chain 'A' and resid 694 through 696'
    Processing helix  chain 'A' and resid 697 through 702
    Processing helix  chain 'A' and resid 705 through 734
      removed outlier: 3.572A  pdb=" N   LEU A 709 " --> pdb=" O   ASP A 705 " (cutoff:3.500A)
      removed outlier: 3.992A  pdb=" N   ILE A 713 " --> pdb=" O   LEU A 709 " (cutoff:3.500A)
      removed outlier: 3.773A  pdb=" N   PHE A 714 " --> pdb=" O   ALA A 710 " (cutoff:3.500A)
      Proline residue:  A 722  - end of helix
      removed outlier: 4.636A  pdb=" N   PHE A 726 " --> pdb=" O   PRO A 722 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 739 through 758
      removed outlier: 3.789A  pdb=" N   LEU A 743 " --> pdb=" O   GLY A 739 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 768 through 784
    Processing helix  chain 'A' and resid 788 through 810
      removed outlier: 3.663A  pdb=" N   GLY A 792 " --> pdb=" O   GLU A 788 " (cutoff:3.500A)
      removed outlier: 3.811A  pdb=" N   ARG A 793 " --> pdb=" O   TYR A 789 " (cutoff:3.500A)
      removed outlier: 4.205A  pdb=" N   VAL A 794 " --> pdb=" O   LEU A 790 " (cutoff:3.500A)
      removed outlier: 3.784A  pdb=" N   TRP A 795 " --> pdb=" O   VAL A 791 " (cutoff:3.500A)
      removed outlier: 3.540A  pdb=" N   PHE A 802 " --> pdb=" O   PHE A 798 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 812 through 819
      removed outlier: 3.713A  pdb=" N   LEU A 815 " --> pdb=" O   GLY A 812 " (cutoff:3.500A)
      removed outlier: 3.988A  pdb=" N   VAL A 816 " --> pdb=" O   SER A 813 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 820 through 850
      removed outlier: 3.692A  pdb=" N   GLN A 824 " --> pdb=" O   SER A 820 " (cutoff:3.500A)
      removed outlier: 4.132A  pdb=" N   ILE A 826 " --> pdb=" O   PHE A 822 " (cutoff:3.500A)
      removed outlier: 4.176A  pdb=" N   THR A 839 " --> pdb=" O   PHE A 835 " (cutoff:3.500A)
      removed outlier: 4.033A  pdb=" N   PHE A 840 " --> pdb=" O   ILE A 836 " (cutoff:3.500A)
      removed outlier: 3.685A  pdb=" N   TYR A 841 " --> pdb=" O   TYR A 837 " (cutoff:3.500A)
      removed outlier: 4.645A  pdb=" N   LYS A 842 " --> pdb=" O   GLU A 838 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 900 through 924
      removed outlier: 3.869A  pdb=" N   LEU A 905 " --> pdb=" O   ALA A 901 " (cutoff:3.500A)
      removed outlier: 3.903A  pdb=" N   ASN A 923 " --> pdb=" O   ARG A 919 " (cutoff:3.500A)
      removed outlier: 3.584A  pdb=" N   SER A 924 " --> pdb=" O   LYS A 920 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 928 through 937
    Processing helix  chain 'A' and resid 938 through 954
      removed outlier: 3.773A  pdb=" N   ILE A 954 " --> pdb=" O   VAL A 950 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 990 through 994
      removed outlier: 4.023A  pdb=" N   MET A 994 " --> pdb=" O   VAL A 991 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 997 through 1020
      removed outlier: 3.697A  pdb=" N   ALA A1001 " --> pdb=" O   SER A 997 " (cutoff:3.500A)
      removed outlier: 3.606A  pdb=" N   LEU A1007 " --> pdb=" O   LEU A1003 " (cutoff:3.500A)
      removed outlier: 3.505A  pdb=" N   THR A1015 " --> pdb=" O   GLU A1011 " (cutoff:3.500A)
      removed outlier: 3.699A  pdb=" N   THR A1016 " --> pdb=" O   THR A1012 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1033 through 1047
    Processing helix  chain 'A' and resid 1048 through 1050
      No H-bonds generated for 'chain 'A' and resid 1048 through 1050'
    Processing helix  chain 'A' and resid 1057 through 1067
      removed outlier: 3.529A  pdb=" N   THR A1063 " --> pdb=" O   VAL A1059 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1090 through 1102
      removed outlier: 3.588A  pdb=" N   VAL A1096 " --> pdb=" O   THR A1092 " (cutoff:3.500A)
      removed outlier: 3.560A  pdb=" N   ALA A1097 " --> pdb=" O   GLY A1093 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1106 through 1111
    Processing helix  chain 'A' and resid 1114 through 1126
      removed outlier: 3.913A  pdb=" N   LEU A1118 " --> pdb=" O   PRO A1114 " (cutoff:3.500A)
      removed outlier: 3.618A  pdb=" N   PHE A1119 " --> pdb=" O   LEU A1115 " (cutoff:3.500A)
      removed outlier: 3.634A  pdb=" N   ILE A1121 " --> pdb=" O   VAL A1117 " (cutoff:3.500A)
      removed outlier: 3.610A  pdb=" N   GLY A1126 " --> pdb=" O   PHE A1122 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1133 through 1141
      removed outlier: 3.516A  pdb=" N   LEU A1139 " --> pdb=" O   PHE A1135 " (cutoff:3.500A)
      removed outlier: 3.575A  pdb=" N   HIS A1140 " --> pdb=" O   TYR A1136 " (cutoff:3.500A)
      removed outlier: 3.502A  pdb=" N   LEU A1141 " --> pdb=" O   GLU A1137 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1145 through 1149
      removed outlier: 3.666A  pdb=" N   HIS A1149 " --> pdb=" O   PRO A1146 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1152 through 1157
      removed outlier: 3.592A  pdb=" N   LYS A1157 " --> pdb=" O   THR A1153 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1159 through 1182
      removed outlier: 3.789A  pdb=" N   LEU A1165 " --> pdb=" O   LEU A1161 " (cutoff:3.500A)
      removed outlier: 3.986A  pdb=" N   PHE A1166 " --> pdb=" O   ARG A1162 " (cutoff:3.500A)
      removed outlier: 3.676A  pdb=" N   LEU A1174 " --> pdb=" O   GLN A1170 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1185 through 1187
      No H-bonds generated for 'chain 'A' and resid 1185 through 1187'
    Processing helix  chain 'A' and resid 1188 through 1195
      removed outlier: 3.609A  pdb=" N   ILE A1192 " --> pdb=" O   ALA A1188 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1195 through 1208
      removed outlier: 3.745A  pdb=" N   LEU A1199 " --> pdb=" O   LEU A1195 " (cutoff:3.500A)
      removed outlier: 4.136A  pdb=" N   LEU A1204 " --> pdb=" O   ARG A1200 " (cutoff:3.500A)
      removed outlier: 4.682A  pdb=" N   THR A1205 " --> pdb=" O   MET A1201 " (cutoff:3.500A)
      removed outlier: 3.830A  pdb=" N   ARG A1206 " --> pdb=" O   VAL A1202 " (cutoff:3.500A)
      removed outlier: 3.593A  pdb=" N   ILE A1207 " --> pdb=" O   VAL A1203 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 682 through 693
    Processing helix  chain 'B' and resid 695 through 702
      removed outlier: 3.776A  pdb=" N   ASP B 699 " --> pdb=" O   HIS B 695 " (cutoff:3.500A)
      removed outlier: 3.824A  pdb=" N   PHE B 700 " --> pdb=" O   TYR B 696 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 705 through 734
      removed outlier: 3.699A  pdb=" N   LEU B 709 " --> pdb=" O   ASP B 705 " (cutoff:3.500A)
      removed outlier: 4.224A  pdb=" N   ILE B 713 " --> pdb=" O   LEU B 709 " (cutoff:3.500A)
      removed outlier: 3.994A  pdb=" N   PHE B 714 " --> pdb=" O   ALA B 710 " (cutoff:3.500A)
      Proline residue:  B 722  - end of helix
      removed outlier: 4.669A  pdb=" N   PHE B 726 " --> pdb=" O   PRO B 722 " (cutoff:3.500A)
      removed outlier: 3.641A  pdb=" N   GLU B 732 " --> pdb=" O   GLY B 728 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 740 through 758
    Processing helix  chain 'B' and resid 768 through 784
    Processing helix  chain 'B' and resid 791 through 810
      removed outlier: 3.769A  pdb=" N   TRP B 795 " --> pdb=" O   VAL B 791 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 812 through 819
      removed outlier: 3.682A  pdb=" N   LEU B 815 " --> pdb=" O   GLY B 812 " (cutoff:3.500A)
      removed outlier: 4.038A  pdb=" N   VAL B 816 " --> pdb=" O   SER B 813 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 820 through 850
      removed outlier: 3.665A  pdb=" N   GLN B 824 " --> pdb=" O   SER B 820 " (cutoff:3.500A)
      removed outlier: 4.107A  pdb=" N   ILE B 826 " --> pdb=" O   PHE B 822 " (cutoff:3.500A)
      removed outlier: 4.162A  pdb=" N   THR B 839 " --> pdb=" O   PHE B 835 " (cutoff:3.500A)
      removed outlier: 3.993A  pdb=" N   PHE B 840 " --> pdb=" O   ILE B 836 " (cutoff:3.500A)
      removed outlier: 3.673A  pdb=" N   TYR B 841 " --> pdb=" O   TYR B 837 " (cutoff:3.500A)
      removed outlier: 4.625A  pdb=" N   LYS B 842 " --> pdb=" O   GLU B 838 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 901 through 923
      removed outlier: 3.654A  pdb=" N   LEU B 905 " --> pdb=" O   ALA B 901 " (cutoff:3.500A)
      removed outlier: 3.913A  pdb=" N   ASN B 923 " --> pdb=" O   ARG B 919 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 928 through 937
      removed outlier: 3.629A  pdb=" N   VAL B 934 " --> pdb=" O   ARG B 930 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 938 through 954
      removed outlier: 3.744A  pdb=" N   ILE B 954 " --> pdb=" O   VAL B 950 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 990 through 994
      removed outlier: 3.535A  pdb=" N   MET B 993 " --> pdb=" O   PRO B 990 " (cutoff:3.500A)
      removed outlier: 3.622A  pdb=" N   MET B 994 " --> pdb=" O   VAL B 991 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 990 through 994'
    Processing helix  chain 'B' and resid 997 through 1020
      removed outlier: 3.671A  pdb=" N   LEU B1007 " --> pdb=" O   LEU B1003 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1033 through 1047
      removed outlier: 3.671A  pdb=" N   LEU B1037 " --> pdb=" O   HIS B1033 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1048 through 1050
      No H-bonds generated for 'chain 'B' and resid 1048 through 1050'
    Processing helix  chain 'B' and resid 1057 through 1067
    Processing helix  chain 'B' and resid 1090 through 1102
      removed outlier: 3.554A  pdb=" N   VAL B1096 " --> pdb=" O   THR B1092 " (cutoff:3.500A)
      removed outlier: 3.587A  pdb=" N   LEU B1102 " --> pdb=" O   LEU B1098 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1106 through 1111
    Processing helix  chain 'B' and resid 1114 through 1126
      removed outlier: 3.860A  pdb=" N   LEU B1118 " --> pdb=" O   PRO B1114 " (cutoff:3.500A)
      removed outlier: 3.638A  pdb=" N   PHE B1119 " --> pdb=" O   LEU B1115 " (cutoff:3.500A)
      removed outlier: 3.715A  pdb=" N   ILE B1121 " --> pdb=" O   VAL B1117 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1127 through 1131
      removed outlier: 3.619A  pdb=" N   LEU B1130 " --> pdb=" O   VAL B1127 " (cutoff:3.500A)
      removed outlier: 3.972A  pdb=" N   ASN B1131 " --> pdb=" O   THR B1128 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 1127 through 1131'
    Processing helix  chain 'B' and resid 1133 through 1141
      removed outlier: 3.593A  pdb=" N   HIS B1140 " --> pdb=" O   TYR B1136 " (cutoff:3.500A)
      removed outlier: 3.627A  pdb=" N   LEU B1141 " --> pdb=" O   GLU B1137 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1145 through 1149
      removed outlier: 3.558A  pdb=" N   HIS B1149 " --> pdb=" O   PRO B1146 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1152 through 1157
      removed outlier: 3.626A  pdb=" N   LYS B1156 " --> pdb=" O   VAL B1152 " (cutoff:3.500A)
      removed outlier: 3.618A  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 1182
      removed outlier: 3.880A  pdb=" N   LEU B1165 " --> pdb=" O   LEU B1161 " (cutoff:3.500A)
      removed outlier: 3.955A  pdb=" N   PHE B1166 " --> pdb=" O   ARG B1162 " (cutoff:3.500A)
      removed outlier: 3.630A  pdb=" N   LEU B1174 " --> pdb=" O   GLN B1170 " (cutoff:3.500A)
      removed outlier: 3.629A  pdb=" N   MET B1181 " --> pdb=" O   LEU B1177 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1188 through 1195
    Processing helix  chain 'B' and resid 1195 through 1208
      removed outlier: 3.704A  pdb=" N   LEU B1199 " --> pdb=" O   LEU B1195 " (cutoff:3.500A)
      removed outlier: 4.150A  pdb=" N   LEU B1204 " --> pdb=" O   ARG B1200 " (cutoff:3.500A)
      removed outlier: 4.825A  pdb=" N   THR B1205 " --> pdb=" O   MET B1201 " (cutoff:3.500A)
      removed outlier: 3.943A  pdb=" N   ARG B1206 " --> pdb=" O   VAL B1202 " (cutoff:3.500A)
      removed outlier: 3.721A  pdb=" N   ILE B1207 " --> pdb=" O   VAL B1203 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1211 through 1215
      removed outlier: 3.703A  pdb=" N   LYS B1214 " --> pdb=" O   ARG B1211 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 765 through 766
      removed outlier: 3.514A  pdb=" N   ALA A1055 " --> pdb=" O   GLY A 766 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 1070 through 1071
      removed outlier: 4.367A  pdb=" N   VAL A1070 " --> pdb=" O   GLN A1084 " (cutoff:3.500A)
      removed outlier: 3.559A  pdb=" N   GLN A1084 " --> pdb=" O   VAL A1070 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA2
    Processing sheet with id=AA3, first strand: chain 'B' and resid 765 through 766
      removed outlier: 3.543A  pdb=" N   ALA B1055 " --> pdb=" O   GLY B 766 " (cutoff:3.500A)

    420 hydrogen bonds defined for protein.
    1230 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.05

  Time building geometry restraints manager: 3.30 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 2467
        1.34 -     1.46: 1949
        1.46 -     1.58: 3778
        1.58 -     1.70: 0
        1.70 -     1.82: 78
  Bond restraints: 8272
  Sorted by residual:
  bond pdb=" C   THR B 900 "
       pdb=" N   ALA B 901 "
    ideal  model  delta    sigma   weight residual
    1.332  1.305  0.028 1.40e-02 5.10e+03 3.86e+00
  bond pdb=" CA  ASP B1079 "
       pdb=" CB  ASP B1079 "
    ideal  model  delta    sigma   weight residual
    1.539  1.520  0.019 1.36e-02 5.41e+03 2.01e+00
  bond pdb=" C   ALA B1076 "
       pdb=" N   PRO B1077 "
    ideal  model  delta    sigma   weight residual
    1.333  1.353 -0.020 1.44e-02 4.82e+03 1.92e+00
  bond pdb=" CG1 ILE A1121 "
       pdb=" CD1 ILE A1121 "
    ideal  model  delta    sigma   weight residual
    1.513  1.461  0.052 3.90e-02 6.57e+02 1.79e+00
  bond pdb=" C   ALA A1076 "
       pdb=" N   PRO A1077 "
    ideal  model  delta    sigma   weight residual
    1.332  1.347 -0.016 1.33e-02 5.65e+03 1.39e+00
  ... (remaining 8267 not shown)

  Histogram of bond angle deviations from ideal:
       99.62 -   106.51: 267
      106.51 -   113.40: 4564
      113.40 -   120.28: 3089
      120.28 -   127.17: 3212
      127.17 -   134.06: 94
  Bond angle restraints: 11226
  Sorted by residual:
  angle pdb=" N   LYS B1028 "
        pdb=" CA  LYS B1028 "
        pdb=" C   LYS B1028 "
      ideal   model   delta    sigma   weight residual
     114.75  107.76    6.99 1.26e+00 6.30e-01 3.08e+01
  angle pdb=" N   ALA B 723 "
        pdb=" CA  ALA B 723 "
        pdb=" C   ALA B 723 "
      ideal   model   delta    sigma   weight residual
     113.43  106.61    6.82 1.26e+00 6.30e-01 2.93e+01
  angle pdb=" N   ALA A 723 "
        pdb=" CA  ALA A 723 "
        pdb=" C   ALA A 723 "
      ideal   model   delta    sigma   weight residual
     112.72  106.20    6.52 1.28e+00 6.10e-01 2.59e+01
  angle pdb=" C   ASN B 899 "
        pdb=" CA  ASN B 899 "
        pdb=" CB  ASN B 899 "
      ideal   model   delta    sigma   weight residual
     116.63  110.80    5.83 1.16e+00 7.43e-01 2.53e+01
  angle pdb=" N   VAL A1086 "
        pdb=" CA  VAL A1086 "
        pdb=" C   VAL A1086 "
      ideal   model   delta    sigma   weight residual
     113.47  108.47    5.00 1.01e+00 9.80e-01 2.45e+01
  ... (remaining 11221 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.95: 4414
       17.95 -    35.91: 393
       35.91 -    53.86: 70
       53.86 -    71.82: 11
       71.82 -    89.77: 6
  Dihedral angle restraints: 4894
    sinusoidal: 1950
      harmonic: 2944
  Sorted by residual:
  dihedral pdb=" CB  GLU A 838 "
           pdb=" CG  GLU A 838 "
           pdb=" CD  GLU A 838 "
           pdb=" OE1 GLU A 838 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   89.77  -89.77     1      3.00e+01 1.11e-03 1.06e+01
  dihedral pdb=" CA  TRP B 992 "
           pdb=" C   TRP B 992 "
           pdb=" N   MET B 993 "
           pdb=" CA  MET B 993 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.98   16.02     0      5.00e+00 4.00e-02 1.03e+01
  dihedral pdb=" CG  ARG A 692 "
           pdb=" CD  ARG A 692 "
           pdb=" NE  ARG A 692 "
           pdb=" CZ  ARG A 692 "
      ideal   model   delta sinusoidal    sigma   weight residual
     180.00  137.06   42.94     2      1.50e+01 4.44e-03 9.90e+00
  ... (remaining 4891 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.037: 861
       0.037 -    0.074: 380
       0.074 -    0.111: 61
       0.111 -    0.148: 26
       0.148 -    0.185: 2
  Chirality restraints: 1330
  Sorted by residual:
  chirality pdb=" CB  VAL A 970 "
            pdb=" CA  VAL A 970 "
            pdb=" CG1 VAL A 970 "
            pdb=" CG2 VAL A 970 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.44   -0.19 2.00e-01 2.50e+01 8.60e-01
  chirality pdb=" CA  TYR A 693 "
            pdb=" N   TYR A 693 "
            pdb=" C   TYR A 693 "
            pdb=" CB  TYR A 693 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.35    0.16 2.00e-01 2.50e+01 6.54e-01
  chirality pdb=" CA  SER B 721 "
            pdb=" N   SER B 721 "
            pdb=" C   SER B 721 "
            pdb=" CB  SER B 721 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.36    0.15 2.00e-01 2.50e+01 5.39e-01
  ... (remaining 1327 not shown)

  Planarity restraints: 1378
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP B 992 "   -0.018 2.00e-02 2.50e+03   1.69e-02 7.16e+00
        pdb=" CG  TRP B 992 "    0.046 2.00e-02 2.50e+03
        pdb=" CD1 TRP B 992 "   -0.018 2.00e-02 2.50e+03
        pdb=" CD2 TRP B 992 "   -0.001 2.00e-02 2.50e+03
        pdb=" NE1 TRP B 992 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE2 TRP B 992 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE3 TRP B 992 "   -0.006 2.00e-02 2.50e+03
        pdb=" CZ2 TRP B 992 "   -0.001 2.00e-02 2.50e+03
        pdb=" CZ3 TRP B 992 "   -0.001 2.00e-02 2.50e+03
        pdb=" CH2 TRP B 992 "   -0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TYR A 693 "    0.042 5.00e-02 4.00e+02   6.33e-02 6.40e+00
        pdb=" N   PRO A 694 "   -0.109 5.00e-02 4.00e+02
        pdb=" CA  PRO A 694 "    0.032 5.00e-02 4.00e+02
        pdb=" CD  PRO A 694 "    0.036 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA B1076 "    0.024 5.00e-02 4.00e+02   3.62e-02 2.10e+00
        pdb=" N   PRO B1077 "   -0.063 5.00e-02 4.00e+02
        pdb=" CA  PRO B1077 "    0.019 5.00e-02 4.00e+02
        pdb=" CD  PRO B1077 "    0.020 5.00e-02 4.00e+02
  ... (remaining 1375 not shown)

  Histogram of nonbonded interaction distances:
        2.26 -     2.79: 1859
        2.79 -     3.32: 7680
        3.32 -     3.84: 11999
        3.84 -     4.37: 13920
        4.37 -     4.90: 24890
  Nonbonded interactions: 60348
  Sorted by model distance:
  nonbonded pdb=" OG1 THR A1209 "
            pdb=" OE1 GLU A1212 "
     model   vdw
     2.259 2.440
  nonbonded pdb=" OG1 THR B1209 "
            pdb=" OE1 GLU B1212 "
     model   vdw
     2.313 2.440
  nonbonded pdb=" O   GLY B 758 "
            pdb=" NH2 ARG B1090 "
     model   vdw
     2.315 2.520
  nonbonded pdb=" O   ASN B 785 "
            pdb=" ND1 HIS B 786 "
     model   vdw
     2.331 2.520
  nonbonded pdb=" O   LEU B 730 "
            pdb=" OG1 THR B 734 "
     model   vdw
     2.332 2.440
  ... (remaining 60343 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Found NCS groups:
ncs_group {
  reference = chain 'A'
  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:             2.050
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          4.060
  Check model and map are aligned:         0.120
  Set scattering table:                    0.070
  Process input model:                     24.600
  Find NCS groups from input model:        0.390
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.460
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   33.790
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7806
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      :  0.004   0.052   8272  Z= 0.236
  Angle     :  0.680   9.572  11226  Z= 0.373
  Chirality :  0.042   0.185   1330
  Planarity :  0.005   0.063   1378
  Dihedral  : 14.126  89.770   2990
  Min Nonbonded Distance : 2.259

Molprobity Statistics.
  All-atom Clashscore : 5.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.62 %
    Favored  : 94.38 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.57 %
    Favored  : 99.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.61 (0.27), residues: 1014
  helix:  0.04 (0.21), residues: 634
  sheet:  None (None), residues: 0
  loop : -1.01 (0.33), residues: 380

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.046   0.002   TRP B 992 
 HIS   0.008   0.001   HIS B 695 
 PHE   0.016   0.001   PHE A1122 
 TYR   0.019   0.002   TYR A 693 
 ARG   0.005   0.000   ARG B1200 

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

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

  2028 Ramachandran restraints generated.
    1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2028 Ramachandran restraints generated.
    1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  158 residues out of total 878 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 158
  time to evaluate  : 0.933 
Fit side-chains
REVERT: A  785 ASN cc_start: 0.8292 (t0) cc_final: 0.7987 (t0)
REVERT: B  785 ASN cc_start: 0.8075 (t0) cc_final: 0.7834 (t0)
REVERT: B  807 MET cc_start: 0.7848 (tpt) cc_final: 0.6940 (tpp)
REVERT: B 1088 GLU cc_start: 0.7346 (pm20) cc_final: 0.7081 (pm20)
  outliers start: 0
  outliers final: 0
  residues processed: 158
  average time/residue: 0.1698
  time to fit residues: 38.1314
Evaluate side-chains
  126 residues out of total 878 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 126
  time to evaluate  : 0.911 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 86 optimal weight:    1.9990
   chunk 77 optimal weight:    0.8980
   chunk 42 optimal weight:    0.8980
   chunk 26 optimal weight:    8.9990
   chunk 52 optimal weight:    5.9990
   chunk 41 optimal weight:    0.4980
   chunk 79 optimal weight:    0.0040
   chunk 30 optimal weight:    3.9990
   chunk 48 optimal weight:    0.8980
   chunk 59 optimal weight:    1.9990
   chunk 92 optimal weight:    0.5980
   overall best weight:    0.5792

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

Flipped N/Q/H residues before XYZ refinement:
B1164 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7753
moved from start:          0.1210

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.056   8272  Z= 0.194
  Angle     :  0.595   7.643  11226  Z= 0.299
  Chirality :  0.041   0.231   1330
  Planarity :  0.005   0.066   1378
  Dihedral  :  3.860  17.120   1096
  Min Nonbonded Distance : 2.190

Molprobity Statistics.
  All-atom Clashscore : 5.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.82 %
    Favored  : 94.18 %
  Rotamer:
    Outliers :  0.68 %
    Allowed  :  8.54 %
    Favored  : 90.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.15 (0.27), residues: 1014
  helix:  0.71 (0.21), residues: 640
  sheet:  None (None), residues: 0
  loop : -0.87 (0.32), residues: 374

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.001   TRP B 992 
 HIS   0.003   0.001   HIS B 695 
 PHE   0.016   0.001   PHE A 802 
 TYR   0.008   0.001   TYR A1154 
 ARG   0.004   0.000   ARG B 701 

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

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

  2028 Ramachandran restraints generated.
    1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2028 Ramachandran restraints generated.
    1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  142 residues out of total 878 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 6
    poor density    : 136
  time to evaluate  : 0.917 
Fit side-chains
REVERT: B  931 ILE cc_start: 0.7787 (mm) cc_final: 0.7581 (mt)
  outliers start: 6
  outliers final: 4
  residues processed: 140
  average time/residue: 0.1578
  time to fit residues: 32.2681
Evaluate side-chains
  128 residues out of total 878 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 4
    poor density    : 124
  time to evaluate  : 0.881 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  983 LEU
Chi-restraints excluded: chain A residue 1103 SER
Chi-restraints excluded: chain A residue 1109 LEU
Chi-restraints excluded: chain B residue  765 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 51 optimal weight:    7.9990
   chunk 28 optimal weight:    6.9990
   chunk 77 optimal weight:    5.9990
   chunk 63 optimal weight:    4.9990
   chunk 25 optimal weight:    0.8980
   chunk 92 optimal weight:    0.9980
   chunk 100 optimal weight:    0.9980
   chunk 82 optimal weight:    7.9990
   chunk 31 optimal weight:    7.9990
   chunk 74 optimal weight:    0.9990
   chunk 91 optimal weight:    0.5980
   overall best weight:    0.8982

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7789
moved from start:          0.1534

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047   8272  Z= 0.227
  Angle     :  0.570   8.934  11226  Z= 0.286
  Chirality :  0.042   0.226   1330
  Planarity :  0.005   0.066   1378
  Dihedral  :  3.807  17.328   1096
  Min Nonbonded Distance : 2.203

Molprobity Statistics.
  All-atom Clashscore : 5.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.03 %
    Favored  : 94.97 %
  Rotamer:
    Outliers :  1.37 %
    Allowed  :  9.45 %
    Favored  : 89.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.26 (0.27), residues: 1014
  helix:  0.77 (0.21), residues: 668
  sheet:  None (None), residues: 0
  loop : -0.91 (0.34), residues: 346

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B 992 
 HIS   0.004   0.001   HIS B1164 
 PHE   0.020   0.002   PHE B1189 
 TYR   0.007   0.001   TYR A1154 
 ARG   0.004   0.000   ARG B 690 

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

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

  2028 Ramachandran restraints generated.
    1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2028 Ramachandran restraints generated.
    1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  151 residues out of total 878 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 12
    poor density    : 139
  time to evaluate  : 0.825 
Fit side-chains
   revert: symmetry clash
REVERT: B  931 ILE cc_start: 0.7798 (mm) cc_final: 0.7506 (mt)
  outliers start: 12
  outliers final: 9
  residues processed: 144
  average time/residue: 0.1677
  time to fit residues: 34.8422
Evaluate side-chains
  137 residues out of total 878 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 9
    poor density    : 128
  time to evaluate  : 0.986 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  899 ASN
Chi-restraints excluded: chain A residue  995 VAL
Chi-restraints excluded: chain A residue 1103 SER
Chi-restraints excluded: chain A residue 1109 LEU
Chi-restraints excluded: chain A residue 1182 SER
Chi-restraints excluded: chain B residue  765 ILE
Chi-restraints excluded: chain B residue  983 LEU
Chi-restraints excluded: chain B residue 1182 SER
Chi-restraints excluded: chain B residue 1199 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 69 optimal weight:    0.9980
   chunk 48 optimal weight:    0.9990
   chunk 10 optimal weight:    2.9990
   chunk 44 optimal weight:    0.9990
   chunk 62 optimal weight:    0.9990
   chunk 93 optimal weight:    0.8980
   chunk 98 optimal weight:    3.9990
   chunk 88 optimal weight:    5.9990
   chunk 26 optimal weight:    5.9990
   chunk 82 optimal weight:    5.9990
   chunk 55 optimal weight:    0.9990
   overall best weight:    0.9786

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7804
moved from start:          0.1747

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046   8272  Z= 0.234
  Angle     :  0.575  14.175  11226  Z= 0.285
  Chirality :  0.042   0.253   1330
  Planarity :  0.004   0.065   1378
  Dihedral  :  3.804  16.853   1096
  Min Nonbonded Distance : 2.207

Molprobity Statistics.
  All-atom Clashscore : 5.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.13 %
    Favored  : 94.87 %
  Rotamer:
    Outliers :  1.94 %
    Allowed  : 10.59 %
    Favored  : 87.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.47 (0.27), residues: 1014
  helix:  1.09 (0.21), residues: 638
  sheet:  None (None), residues: 0
  loop : -1.01 (0.32), residues: 376

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 992 
 HIS   0.003   0.001   HIS B1164 
 PHE   0.020   0.002   PHE B1189 
 TYR   0.007   0.001   TYR A1154 
 ARG   0.007   0.000   ARG A 690 

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

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

  2028 Ramachandran restraints generated.
    1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2028 Ramachandran restraints generated.
    1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  154 residues out of total 878 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 17
    poor density    : 137
  time to evaluate  : 0.921 
Fit side-chains
REVERT: A  993 MET cc_start: 0.8152 (tpt) cc_final: 0.7933 (tpp)
REVERT: B  931 ILE cc_start: 0.7784 (mm) cc_final: 0.7492 (mt)
  outliers start: 17
  outliers final: 12
  residues processed: 145
  average time/residue: 0.1631
  time to fit residues: 34.1951
Evaluate side-chains
  143 residues out of total 878 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 12
    poor density    : 131
  time to evaluate  : 0.924 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  899 ASN
Chi-restraints excluded: chain A residue  908 MET
Chi-restraints excluded: chain A residue 1103 SER
Chi-restraints excluded: chain A residue 1109 LEU
Chi-restraints excluded: chain A residue 1180 VAL
Chi-restraints excluded: chain A residue 1182 SER
Chi-restraints excluded: chain B residue  743 LEU
Chi-restraints excluded: chain B residue  765 ILE
Chi-restraints excluded: chain B residue  908 MET
Chi-restraints excluded: chain B residue 1017 LEU
Chi-restraints excluded: chain B residue 1182 SER
Chi-restraints excluded: chain B residue 1199 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 1 optimal weight:    0.9980
   chunk 73 optimal weight:    5.9990
   chunk 40 optimal weight:    0.9990
   chunk 84 optimal weight:    0.0170
   chunk 68 optimal weight:    0.5980
   chunk 0 optimal weight:    5.9990
   chunk 50 optimal weight:    2.9990
   chunk 88 optimal weight:    0.0770
   chunk 24 optimal weight:    0.0870
   chunk 33 optimal weight:    0.3980
   chunk 19 optimal weight:    0.6980
   overall best weight:    0.2354

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

Flipped N/Q/H residues before XYZ refinement:
A1164 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7728
moved from start:          0.1980

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   8272  Z= 0.139
  Angle     :  0.542  14.028  11226  Z= 0.262
  Chirality :  0.040   0.249   1330
  Planarity :  0.004   0.065   1378
  Dihedral  :  3.632  18.453   1096
  Min Nonbonded Distance : 2.204

Molprobity Statistics.
  All-atom Clashscore : 5.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.83 %
    Favored  : 95.17 %
  Rotamer:
    Outliers :  1.71 %
    Allowed  : 12.76 %
    Favored  : 85.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.80 (0.27), residues: 1014
  helix:  1.33 (0.21), residues: 640
  sheet:  None (None), residues: 0
  loop : -0.85 (0.32), residues: 374

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B1178 
 HIS   0.002   0.001   HIS B 786 
 PHE   0.017   0.001   PHE A 802 
 TYR   0.016   0.001   TYR A 837 
 ARG   0.007   0.000   ARG A 690 

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

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

  2028 Ramachandran restraints generated.
    1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2028 Ramachandran restraints generated.
    1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  154 residues out of total 878 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 15
    poor density    : 139
  time to evaluate  : 0.851 
Fit side-chains
   revert: symmetry clash
REVERT: A  745 MET cc_start: 0.6764 (mmt) cc_final: 0.6541 (mmm)
REVERT: A  785 ASN cc_start: 0.8037 (t0) cc_final: 0.7795 (t0)
REVERT: A  922 LYS cc_start: 0.8148 (ttmt) cc_final: 0.7857 (ttpp)
REVERT: A  981 ASN cc_start: 0.8542 (t0) cc_final: 0.8275 (t0)
REVERT: B  785 ASN cc_start: 0.8106 (t0) cc_final: 0.7806 (t0)
REVERT: B  931 ILE cc_start: 0.7711 (mm) cc_final: 0.7436 (mt)
REVERT: B  993 MET cc_start: 0.7947 (tpp) cc_final: 0.7649 (tpp)
  outliers start: 15
  outliers final: 7
  residues processed: 149
  average time/residue: 0.2073
  time to fit residues: 44.0991
Evaluate side-chains
  139 residues out of total 878 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 7
    poor density    : 132
  time to evaluate  : 0.869 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  743 LEU
Chi-restraints excluded: chain A residue  899 ASN
Chi-restraints excluded: chain A residue 1103 SER
Chi-restraints excluded: chain A residue 1109 LEU
Chi-restraints excluded: chain B residue  765 ILE
Chi-restraints excluded: chain B residue  908 MET
Chi-restraints excluded: chain B residue 1103 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 57 optimal weight:    5.9990
   chunk 24 optimal weight:    3.9990
   chunk 98 optimal weight:    3.9990
   chunk 81 optimal weight:    1.9990
   chunk 45 optimal weight:    2.9990
   chunk 8 optimal weight:    0.9990
   chunk 32 optimal weight:    0.8980
   chunk 51 optimal weight:    6.9990
   chunk 95 optimal weight:    0.5980
   chunk 11 optimal weight:    0.1980
   chunk 56 optimal weight:    3.9990
   overall best weight:    0.9384

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7798
moved from start:          0.1977

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   8272  Z= 0.228
  Angle     :  0.572  15.000  11226  Z= 0.280
  Chirality :  0.042   0.265   1330
  Planarity :  0.004   0.063   1378
  Dihedral  :  3.701  17.525   1096
  Min Nonbonded Distance : 2.217

Molprobity Statistics.
  All-atom Clashscore : 5.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.83 %
    Favored  : 95.17 %
  Rotamer:
    Outliers :  1.71 %
    Allowed  : 14.46 %
    Favored  : 83.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.76 (0.27), residues: 1014
  helix:  1.33 (0.21), residues: 640
  sheet:  None (None), residues: 0
  loop : -0.92 (0.32), residues: 374

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP B1178 
 HIS   0.003   0.001   HIS B 786 
 PHE   0.020   0.001   PHE B1189 
 TYR   0.015   0.001   TYR A 837 
 ARG   0.006   0.000   ARG A 690 

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

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

  2028 Ramachandran restraints generated.
    1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2028 Ramachandran restraints generated.
    1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  146 residues out of total 878 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 15
    poor density    : 131
  time to evaluate  : 0.944 
Fit side-chains
REVERT: A  745 MET cc_start: 0.6771 (mmt) cc_final: 0.6515 (mmm)
REVERT: A  922 LYS cc_start: 0.8256 (ttmt) cc_final: 0.7995 (ttpp)
REVERT: B  931 ILE cc_start: 0.7758 (mm) cc_final: 0.7478 (mt)
  outliers start: 15
  outliers final: 15
  residues processed: 143
  average time/residue: 0.1677
  time to fit residues: 34.8726
Evaluate side-chains
  142 residues out of total 878 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 15
    poor density    : 127
  time to evaluate  : 0.953 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  743 LEU
Chi-restraints excluded: chain A residue  803 LEU
Chi-restraints excluded: chain A residue  899 ASN
Chi-restraints excluded: chain A residue  908 MET
Chi-restraints excluded: chain A residue  944 ILE
Chi-restraints excluded: chain A residue 1103 SER
Chi-restraints excluded: chain A residue 1109 LEU
Chi-restraints excluded: chain A residue 1161 LEU
Chi-restraints excluded: chain B residue  743 LEU
Chi-restraints excluded: chain B residue  765 ILE
Chi-restraints excluded: chain B residue  908 MET
Chi-restraints excluded: chain B residue  944 ILE
Chi-restraints excluded: chain B residue 1103 SER
Chi-restraints excluded: chain B residue 1158 VAL
Chi-restraints excluded: chain B residue 1199 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 72 optimal weight:    0.9980
   chunk 55 optimal weight:    1.9990
   chunk 83 optimal weight:    1.9990
   chunk 98 optimal weight:    0.0980
   chunk 61 optimal weight:    2.9990
   chunk 59 optimal weight:    0.0370
   chunk 45 optimal weight:    2.9990
   chunk 60 optimal weight:    0.8980
   chunk 39 optimal weight:    2.9990
   chunk 58 optimal weight:    0.9990
   chunk 29 optimal weight:    0.8980
   overall best weight:    0.5858

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7769
moved from start:          0.2093

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   8272  Z= 0.172
  Angle     :  0.545  15.039  11226  Z= 0.267
  Chirality :  0.041   0.278   1330
  Planarity :  0.004   0.063   1378
  Dihedral  :  3.638  17.803   1096
  Min Nonbonded Distance : 2.219

Molprobity Statistics.
  All-atom Clashscore : 5.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.93 %
    Favored  : 95.07 %
  Rotamer:
    Outliers :  1.94 %
    Allowed  : 14.81 %
    Favored  : 83.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.90 (0.27), residues: 1014
  helix:  1.43 (0.21), residues: 640
  sheet:  None (None), residues: 0
  loop : -0.85 (0.32), residues: 374

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B1178 
 HIS   0.003   0.001   HIS B 786 
 PHE   0.019   0.001   PHE A 802 
 TYR   0.013   0.001   TYR A 837 
 ARG   0.007   0.000   ARG A 690 

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

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

  2028 Ramachandran restraints generated.
    1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2028 Ramachandran restraints generated.
    1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  150 residues out of total 878 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 17
    poor density    : 133
  time to evaluate  : 1.019 
Fit side-chains
REVERT: A  745 MET cc_start: 0.6736 (mmt) cc_final: 0.6479 (mmm)
REVERT: A  922 LYS cc_start: 0.8188 (ttmt) cc_final: 0.7906 (ttpp)
REVERT: A  993 MET cc_start: 0.8260 (tpt) cc_final: 0.7478 (tpp)
REVERT: B  785 ASN cc_start: 0.8255 (t0) cc_final: 0.8045 (t0)
REVERT: B  931 ILE cc_start: 0.7710 (mm) cc_final: 0.7438 (mt)
  outliers start: 17
  outliers final: 14
  residues processed: 147
  average time/residue: 0.1599
  time to fit residues: 34.3444
Evaluate side-chains
  140 residues out of total 878 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 14
    poor density    : 126
  time to evaluate  : 0.861 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  743 LEU
Chi-restraints excluded: chain A residue  899 ASN
Chi-restraints excluded: chain A residue  908 MET
Chi-restraints excluded: chain A residue  944 ILE
Chi-restraints excluded: chain A residue 1103 SER
Chi-restraints excluded: chain A residue 1109 LEU
Chi-restraints excluded: chain A residue 1161 LEU
Chi-restraints excluded: chain B residue  721 SER
Chi-restraints excluded: chain B residue  765 ILE
Chi-restraints excluded: chain B residue  908 MET
Chi-restraints excluded: chain B residue  944 ILE
Chi-restraints excluded: chain B residue 1103 SER
Chi-restraints excluded: chain B residue 1158 VAL
Chi-restraints excluded: chain B residue 1199 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 19 optimal weight:    1.9990
   chunk 62 optimal weight:    0.7980
   chunk 66 optimal weight:    1.9990
   chunk 48 optimal weight:    0.5980
   chunk 9 optimal weight:    2.9990
   chunk 77 optimal weight:    7.9990
   chunk 89 optimal weight:    0.7980
   chunk 94 optimal weight:    0.0170
   chunk 85 optimal weight:    1.9990
   chunk 91 optimal weight:    1.9990
   chunk 55 optimal weight:    2.9990
   overall best weight:    0.8420

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7795
moved from start:          0.2137

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   8272  Z= 0.210
  Angle     :  0.565  15.657  11226  Z= 0.277
  Chirality :  0.041   0.288   1330
  Planarity :  0.004   0.063   1378
  Dihedral  :  3.686  17.457   1096
  Min Nonbonded Distance : 2.234

Molprobity Statistics.
  All-atom Clashscore : 5.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.13 %
    Favored  : 94.87 %
  Rotamer:
    Outliers :  1.94 %
    Allowed  : 15.03 %
    Favored  : 83.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.85 (0.27), residues: 1014
  helix:  1.38 (0.21), residues: 642
  sheet:  None (None), residues: 0
  loop : -0.85 (0.33), residues: 372

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B1178 
 HIS   0.003   0.001   HIS A 786 
 PHE   0.020   0.001   PHE B1189 
 TYR   0.013   0.001   TYR A 837 
 ARG   0.007   0.000   ARG A 690 

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

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

  2028 Ramachandran restraints generated.
    1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2028 Ramachandran restraints generated.
    1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  150 residues out of total 878 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 17
    poor density    : 133
  time to evaluate  : 0.859 
Fit side-chains
REVERT: A  745 MET cc_start: 0.6774 (mmt) cc_final: 0.6515 (mmm)
REVERT: A  922 LYS cc_start: 0.8235 (ttmt) cc_final: 0.7944 (ttpp)
REVERT: A  993 MET cc_start: 0.8205 (tpt) cc_final: 0.7955 (tpt)
REVERT: B  931 ILE cc_start: 0.7735 (mm) cc_final: 0.7460 (mt)
  outliers start: 17
  outliers final: 15
  residues processed: 146
  average time/residue: 0.1606
  time to fit residues: 34.0378
Evaluate side-chains
  144 residues out of total 878 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 15
    poor density    : 129
  time to evaluate  : 0.972 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  743 LEU
Chi-restraints excluded: chain A residue  899 ASN
Chi-restraints excluded: chain A residue  908 MET
Chi-restraints excluded: chain A residue  944 ILE
Chi-restraints excluded: chain A residue 1103 SER
Chi-restraints excluded: chain A residue 1109 LEU
Chi-restraints excluded: chain A residue 1161 LEU
Chi-restraints excluded: chain B residue  721 SER
Chi-restraints excluded: chain B residue  743 LEU
Chi-restraints excluded: chain B residue  765 ILE
Chi-restraints excluded: chain B residue  908 MET
Chi-restraints excluded: chain B residue  944 ILE
Chi-restraints excluded: chain B residue 1103 SER
Chi-restraints excluded: chain B residue 1158 VAL
Chi-restraints excluded: chain B residue 1199 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 39 optimal weight:    0.1980
   chunk 71 optimal weight:    0.2980
   chunk 28 optimal weight:    0.0270
   chunk 82 optimal weight:    4.9990
   chunk 86 optimal weight:    0.0370
   chunk 91 optimal weight:    0.5980
   chunk 60 optimal weight:    3.9990
   chunk 96 optimal weight:    0.0970
   chunk 59 optimal weight:    0.3980
   chunk 45 optimal weight:    2.9990
   chunk 67 optimal weight:    1.9990
   overall best weight:    0.1314

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7702
moved from start:          0.2348

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028   8272  Z= 0.141
  Angle     :  0.533  15.922  11226  Z= 0.261
  Chirality :  0.040   0.303   1330
  Planarity :  0.004   0.063   1378
  Dihedral  :  3.512  19.191   1096
  Min Nonbonded Distance : 2.263

Molprobity Statistics.
  All-atom Clashscore : 5.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.83 %
    Favored  : 95.17 %
  Rotamer:
    Outliers :  0.80 %
    Allowed  : 16.29 %
    Favored  : 82.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.15 (0.28), residues: 1014
  helix:  1.59 (0.21), residues: 642
  sheet:  None (None), residues: 0
  loop : -0.67 (0.33), residues: 372

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B1178 
 HIS   0.004   0.001   HIS B 786 
 PHE   0.020   0.001   PHE A 802 
 TYR   0.011   0.001   TYR B1154 
 ARG   0.006   0.000   ARG A 690 

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

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

  2028 Ramachandran restraints generated.
    1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2028 Ramachandran restraints generated.
    1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  151 residues out of total 878 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 7
    poor density    : 144
  time to evaluate  : 0.918 
Fit side-chains
   revert: symmetry clash
REVERT: A  732 GLU cc_start: 0.6201 (mm-30) cc_final: 0.5878 (mm-30)
REVERT: A  922 LYS cc_start: 0.8118 (ttmt) cc_final: 0.7867 (ttpp)
REVERT: B  931 ILE cc_start: 0.7634 (mm) cc_final: 0.7291 (mt)
  outliers start: 7
  outliers final: 6
  residues processed: 150
  average time/residue: 0.1588
  time to fit residues: 34.8545
Evaluate side-chains
  142 residues out of total 878 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 6
    poor density    : 136
  time to evaluate  : 0.965 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  944 ILE
Chi-restraints excluded: chain A residue 1109 LEU
Chi-restraints excluded: chain B residue  721 SER
Chi-restraints excluded: chain B residue  765 ILE
Chi-restraints excluded: chain B residue 1103 SER
Chi-restraints excluded: chain B residue 1158 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 101 optimal weight:    0.0050
   chunk 93 optimal weight:    0.2980
   chunk 80 optimal weight:    3.9990
   chunk 8 optimal weight:    0.9990
   chunk 62 optimal weight:    0.0030
   chunk 49 optimal weight:    0.8980
   chunk 64 optimal weight:    0.6980
   chunk 86 optimal weight:    1.9990
   chunk 24 optimal weight:    2.9990
   chunk 74 optimal weight:    1.9990
   chunk 11 optimal weight:    0.6980
   overall best weight:    0.3404

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7723
moved from start:          0.2351

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   8272  Z= 0.150
  Angle     :  0.565  16.371  11226  Z= 0.268
  Chirality :  0.040   0.304   1330
  Planarity :  0.004   0.063   1378
  Dihedral  :  3.480  18.333   1096
  Min Nonbonded Distance : 2.211

Molprobity Statistics.
  All-atom Clashscore : 6.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.83 %
    Favored  : 95.17 %
  Rotamer:
    Outliers :  1.14 %
    Allowed  : 16.17 %
    Favored  : 82.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.16 (0.28), residues: 1014
  helix:  1.59 (0.21), residues: 642
  sheet:  None (None), residues: 0
  loop : -0.66 (0.33), residues: 372

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.000   TRP A 795 
 HIS   0.004   0.001   HIS B 786 
 PHE   0.019   0.001   PHE A 802 
 TYR   0.012   0.001   TYR A 837 
 ARG   0.007   0.000   ARG A 690 

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

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

  2028 Ramachandran restraints generated.
    1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2028 Ramachandran restraints generated.
    1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  145 residues out of total 878 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 10
    poor density    : 135
  time to evaluate  : 0.984 
Fit side-chains
REVERT: A  690 ARG cc_start: 0.8352 (mtp85) cc_final: 0.8134 (mtp-110)
REVERT: A  922 LYS cc_start: 0.8154 (ttmt) cc_final: 0.7920 (ttpp)
REVERT: B  931 ILE cc_start: 0.7650 (mm) cc_final: 0.7311 (mt)
  outliers start: 10
  outliers final: 8
  residues processed: 142
  average time/residue: 0.1661
  time to fit residues: 33.9554
Evaluate side-chains
  140 residues out of total 878 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 8
    poor density    : 132
  time to evaluate  : 0.806 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  743 LEU
Chi-restraints excluded: chain A residue  899 ASN
Chi-restraints excluded: chain A residue  944 ILE
Chi-restraints excluded: chain A residue 1109 LEU
Chi-restraints excluded: chain B residue  721 SER
Chi-restraints excluded: chain B residue  765 ILE
Chi-restraints excluded: chain B residue 1103 SER
Chi-restraints excluded: chain B residue 1158 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 22 optimal weight:    2.9990
   chunk 81 optimal weight:    0.9990
   chunk 33 optimal weight:    1.9990
   chunk 83 optimal weight:    1.9990
   chunk 10 optimal weight:    1.9990
   chunk 14 optimal weight:    0.8980
   chunk 71 optimal weight:    0.8980
   chunk 4 optimal weight:    0.6980
   chunk 58 optimal weight:    0.8980
   chunk 92 optimal weight:    0.6980
   chunk 54 optimal weight:    0.9980
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
B 785 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3880 r_free = 0.3880 target = 0.168309 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 72)----------------|
| r_work = 0.3292 r_free = 0.3292 target = 0.115830 restraints weight = 8946.275|
|-----------------------------------------------------------------------------|
r_work (start): 0.3213 rms_B_bonded: 2.15
r_work: 0.3049 rms_B_bonded: 3.12 restraints_weight: 0.5000
r_work: 0.2903 rms_B_bonded: 4.82 restraints_weight: 0.2500
r_work (final): 0.2903
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7916
moved from start:          0.2308

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   8272  Z= 0.207
  Angle     :  0.587  16.074  11226  Z= 0.283
  Chirality :  0.042   0.307   1330
  Planarity :  0.004   0.063   1378
  Dihedral  :  3.624  18.030   1096
  Min Nonbonded Distance : 2.199

Molprobity Statistics.
  All-atom Clashscore : 6.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.93 %
    Favored  : 95.07 %
  Rotamer:
    Outliers :  1.48 %
    Allowed  : 16.17 %
    Favored  : 82.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.99 (0.28), residues: 1014
  helix:  1.40 (0.21), residues: 656
  sheet:  None (None), residues: 0
  loop : -0.71 (0.34), residues: 358

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP A1178 
 HIS   0.003   0.001   HIS B 786 
 PHE   0.020   0.001   PHE A 802 
 TYR   0.013   0.001   TYR A 837 
 ARG   0.007   0.000   ARG A 690 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1943.97 seconds
wall clock time: 35 minutes 48.98 seconds (2148.98 seconds total)