Starting phenix.real_space_refine
on Wed Jan 15 11:06:07 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8odv_16819/01_2025/8odv_16819.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8odv_16819/01_2025/8odv_16819.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.7
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8odv_16819/01_2025/8odv_16819.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8odv_16819/01_2025/8odv_16819.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8odv_16819/01_2025/8odv_16819.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8odv_16819/01_2025/8odv_16819.cif"
  }
  resolution = 4.7
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.021
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: 5
    Type Number    sf(0)   Gaussians
     Zn      1      6.06       5
     S      52      5.16       5
     C    5330      2.51       5
     N    1366      2.21       5
     O    1484      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 18 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib"
  Total number of atoms: 8233
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 2317
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 293, 2317
          Classifications: {'peptide': 293}
          Link IDs: {'PTRANS': 13, 'TRANS': 279}
          Chain breaks: 2
    Chain: "B"
      Number of atoms: 2317
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 293, 2317
          Classifications: {'peptide': 293}
          Link IDs: {'PTRANS': 13, 'TRANS': 279}
          Chain breaks: 2
    Chain: "C"
      Number of atoms: 1799
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 218, 1799
          Classifications: {'peptide': 218}
          Link IDs: {'PTRANS': 8, 'TRANS': 209}
          Chain breaks: 2
    Chain: "D"
      Number of atoms: 1799
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 218, 1799
          Classifications: {'peptide': 218}
          Link IDs: {'PTRANS': 8, 'TRANS': 209}
          Chain breaks: 2
    Chain: "A"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' ZN': 1}
          Classifications: {'undetermined': 1}

List of CYS excluded from plausible disulfide bonds:
  (reason: may participate in coordination)
  ATOM   1822  SG  CYS A 281      44.572  43.672  14.092  1.00167.44           S
  ATOM   1846  SG  CYS A 284      41.703  43.987  16.312  1.00153.79           S
  ATOM   4139  SG  CYS B 281      41.903  47.146  14.049  1.00167.06           S
  ATOM   4163  SG  CYS B 284      44.773  46.863  16.271  1.00154.18           S

  Time building chain proxies: 5.15, per 1000 atoms: 0.63
  Number of scatterers: 8233
  At special positions: 0
  Unit cell: (87.69, 93.24, 146.52, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     Zn      1     29.99
     S      52     16.00
     O    1484      8.00
     N    1366      7.00
     C    5330      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=0, symmetry=0
  Time building additional restraints: 2.22
  Conformation dependent library (CDL) restraints added in 1.0 seconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN A 401 "
        pdb="ZN    ZN A 401 " - pdb=" SG  CYS A 281 "
        pdb="ZN    ZN A 401 " - pdb=" SG  CYS B 281 "
        pdb="ZN    ZN A 401 " - pdb=" SG  CYS B 284 "
        pdb="ZN    ZN A 401 " - pdb=" SG  CYS A 284 "
      Number of angles added : 6


  1996 Ramachandran restraints generated.
    998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1952

  Finding SS restraints...
    Secondary structure from input PDB file:
      44 helices and 2 sheets defined
      65.9% alpha, 3.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.86
  Creating SS restraints...
    Processing helix  chain 'A' and resid 18 through 25
      removed outlier: 3.607A  pdb=" N   LEU A  22 " --> pdb=" O   LEU A  18 " (cutoff:3.500A)
      removed outlier: 3.647A  pdb=" N   GLN A  24 " --> pdb=" O   SER A  20 " (cutoff:3.500A)
      removed outlier: 4.449A  pdb=" N   ARG A  25 " --> pdb=" O   ILE A  21 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 39 through 52
      removed outlier: 3.534A  pdb=" N   THR A  43 " --> pdb=" O   GLY A  39 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 53 through 55
      No H-bonds generated for 'chain 'A' and resid 53 through 55'
    Processing helix  chain 'A' and resid 67 through 74
      removed outlier: 4.070A  pdb=" N   ASP A  71 " --> pdb=" O   HIS A  67 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 97 through 105
      removed outlier: 3.812A  pdb=" N   MET A 101 " --> pdb=" O   PRO A  97 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 121 through 129
    Processing helix  chain 'A' and resid 132 through 146
    Processing helix  chain 'A' and resid 159 through 164
    Processing helix  chain 'A' and resid 165 through 167
      No H-bonds generated for 'chain 'A' and resid 165 through 167'
    Processing helix  chain 'A' and resid 168 through 185
    Processing helix  chain 'A' and resid 206 through 229
      removed outlier: 4.102A  pdb=" N   VAL A 210 " --> pdb=" O   THR A 206 " (cutoff:3.500A)
      removed outlier: 3.593A  pdb=" N   LYS A 229 " --> pdb=" O   ASN A 225 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 243 through 259
    Processing helix  chain 'A' and resid 281 through 303
      removed outlier: 3.755A  pdb=" N   ALA A 286 " --> pdb=" O   GLU A 282 " (cutoff:3.500A)
      removed outlier: 3.869A  pdb=" N   ASP A 303 " --> pdb=" O   GLU A 299 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 320 through 330
      removed outlier: 4.137A  pdb=" N   MET A 330 " --> pdb=" O   LYS A 326 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 18 through 25
      removed outlier: 3.608A  pdb=" N   LEU B  22 " --> pdb=" O   LEU B  18 " (cutoff:3.500A)
      removed outlier: 3.647A  pdb=" N   GLN B  24 " --> pdb=" O   SER B  20 " (cutoff:3.500A)
      removed outlier: 4.449A  pdb=" N   ARG B  25 " --> pdb=" O   ILE B  21 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 39 through 52
      removed outlier: 3.533A  pdb=" N   THR B  43 " --> pdb=" O   GLY B  39 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 53 through 55
      No H-bonds generated for 'chain 'B' and resid 53 through 55'
    Processing helix  chain 'B' and resid 67 through 74
      removed outlier: 4.070A  pdb=" N   ASP B  71 " --> pdb=" O   HIS B  67 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 97 through 105
      removed outlier: 3.812A  pdb=" N   MET B 101 " --> pdb=" O   PRO B  97 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 121 through 129
    Processing helix  chain 'B' and resid 132 through 146
    Processing helix  chain 'B' and resid 159 through 164
    Processing helix  chain 'B' and resid 165 through 167
      No H-bonds generated for 'chain 'B' and resid 165 through 167'
    Processing helix  chain 'B' and resid 168 through 185
    Processing helix  chain 'B' and resid 206 through 229
      removed outlier: 4.101A  pdb=" N   VAL B 210 " --> pdb=" O   THR B 206 " (cutoff:3.500A)
      removed outlier: 3.592A  pdb=" N   LYS B 229 " --> pdb=" O   ASN B 225 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 243 through 259
    Processing helix  chain 'B' and resid 281 through 303
      removed outlier: 3.756A  pdb=" N   ALA B 286 " --> pdb=" O   GLU B 282 " (cutoff:3.500A)
      removed outlier: 3.869A  pdb=" N   ASP B 303 " --> pdb=" O   GLU B 299 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 320 through 330
      removed outlier: 4.138A  pdb=" N   MET B 330 " --> pdb=" O   LYS B 326 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 303 through 310
      removed outlier: 3.738A  pdb=" N   PHE C 310 " --> pdb=" O   LEU C 306 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 336 through 356
      removed outlier: 3.900A  pdb=" N   TRP C 354 " --> pdb=" O   GLY C 350 " (cutoff:3.500A)
      removed outlier: 4.286A  pdb=" N   TRP C 355 " --> pdb=" O   ALA C 351 " (cutoff:3.500A)
      removed outlier: 3.967A  pdb=" N   ARG C 356 " --> pdb=" O   VAL C 352 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 1002 through 1019
    Processing helix  chain 'C' and resid 1023 through 1034
      removed outlier: 3.630A  pdb=" N   ARG C1031 " --> pdb=" O   ASN C1027 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 1039 through 1065
      removed outlier: 3.551A  pdb=" N   LYS C1043 " --> pdb=" O   SER C1039 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 1070 through 1124
      removed outlier: 3.674A  pdb=" N   ASP C1086 " --> pdb=" O   ASP C1082 " (cutoff:3.500A)
      removed outlier: 3.925A  pdb=" N   GLU C1087 " --> pdb=" O   LYS C1083 " (cutoff:3.500A)
      removed outlier: 4.180A  pdb=" N   GLU C1089 " --> pdb=" O   MET C1085 " (cutoff:3.500A)
      removed outlier: 3.875A  pdb=" N   LYS C1090 " --> pdb=" O   ASP C1086 " (cutoff:3.500A)
      removed outlier: 3.917A  pdb=" N   LYS C1091 " --> pdb=" O   GLU C1087 " (cutoff:3.500A)
      removed outlier: 3.652A  pdb=" N   LYS C1092 " --> pdb=" O   LEU C1088 " (cutoff:3.500A)
      removed outlier: 3.591A  pdb=" N   ALA C1097 " --> pdb=" O   SER C1093 " (cutoff:3.500A)
      removed outlier: 3.925A  pdb=" N   ILE C1108 " --> pdb=" O   ARG C1104 " (cutoff:3.500A)
      removed outlier: 3.980A  pdb=" N   LEU C1113 " --> pdb=" O   TYR C1109 " (cutoff:3.500A)
      removed outlier: 4.007A  pdb=" N   MET C1117 " --> pdb=" O   LEU C1113 " (cutoff:3.500A)
      removed outlier: 4.016A  pdb=" N   LEU C1121 " --> pdb=" O   MET C1117 " (cutoff:3.500A)
      removed outlier: 5.288A  pdb=" N   CYS C1122 " --> pdb=" O   GLN C1118 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 1139 through 1148
      removed outlier: 4.616A  pdb=" N   LEU C1145 " --> pdb=" O   TRP C1141 " (cutoff:3.500A)
      removed outlier: 4.904A  pdb=" N   VAL C1146 " --> pdb=" O   VAL C1142 " (cutoff:3.500A)
      removed outlier: 3.656A  pdb=" N   SER C1147 " --> pdb=" O   GLU C1143 " (cutoff:3.500A)
      removed outlier: 3.577A  pdb=" N   PHE C1148 " --> pdb=" O   TRP C1144 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 1164 through 1181
      removed outlier: 3.932A  pdb=" N   VAL C1168 " --> pdb=" O   ALA C1164 " (cutoff:3.500A)
      removed outlier: 3.822A  pdb=" N   LEU C1169 " --> pdb=" O   CYS C1165 " (cutoff:3.500A)
      removed outlier: 3.562A  pdb=" N   LEU C1171 " --> pdb=" O   GLY C1167 " (cutoff:3.500A)
      removed outlier: 4.265A  pdb=" N   VAL C1172 " --> pdb=" O   VAL C1168 " (cutoff:3.500A)
      removed outlier: 3.579A  pdb=" N   ARG C1181 " --> pdb=" O   MET C1177 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 303 through 310
      removed outlier: 3.737A  pdb=" N   PHE D 310 " --> pdb=" O   LEU D 306 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 336 through 356
      removed outlier: 3.900A  pdb=" N   TRP D 354 " --> pdb=" O   GLY D 350 " (cutoff:3.500A)
      removed outlier: 4.287A  pdb=" N   TRP D 355 " --> pdb=" O   ALA D 351 " (cutoff:3.500A)
      removed outlier: 3.966A  pdb=" N   ARG D 356 " --> pdb=" O   VAL D 352 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 1002 through 1019
    Processing helix  chain 'D' and resid 1023 through 1034
      removed outlier: 3.631A  pdb=" N   ARG D1031 " --> pdb=" O   ASN D1027 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 1039 through 1065
      removed outlier: 3.551A  pdb=" N   LYS D1043 " --> pdb=" O   SER D1039 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 1070 through 1124
      removed outlier: 3.674A  pdb=" N   ASP D1086 " --> pdb=" O   ASP D1082 " (cutoff:3.500A)
      removed outlier: 3.925A  pdb=" N   GLU D1087 " --> pdb=" O   LYS D1083 " (cutoff:3.500A)
      removed outlier: 4.180A  pdb=" N   GLU D1089 " --> pdb=" O   MET D1085 " (cutoff:3.500A)
      removed outlier: 3.875A  pdb=" N   LYS D1090 " --> pdb=" O   ASP D1086 " (cutoff:3.500A)
      removed outlier: 3.917A  pdb=" N   LYS D1091 " --> pdb=" O   GLU D1087 " (cutoff:3.500A)
      removed outlier: 3.652A  pdb=" N   LYS D1092 " --> pdb=" O   LEU D1088 " (cutoff:3.500A)
      removed outlier: 3.591A  pdb=" N   ALA D1097 " --> pdb=" O   SER D1093 " (cutoff:3.500A)
      removed outlier: 3.924A  pdb=" N   ILE D1108 " --> pdb=" O   ARG D1104 " (cutoff:3.500A)
      removed outlier: 3.979A  pdb=" N   LEU D1113 " --> pdb=" O   TYR D1109 " (cutoff:3.500A)
      removed outlier: 4.007A  pdb=" N   MET D1117 " --> pdb=" O   LEU D1113 " (cutoff:3.500A)
      removed outlier: 4.016A  pdb=" N   LEU D1121 " --> pdb=" O   MET D1117 " (cutoff:3.500A)
      removed outlier: 5.288A  pdb=" N   CYS D1122 " --> pdb=" O   GLN D1118 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 1139 through 1148
      removed outlier: 4.616A  pdb=" N   LEU D1145 " --> pdb=" O   TRP D1141 " (cutoff:3.500A)
      removed outlier: 4.904A  pdb=" N   VAL D1146 " --> pdb=" O   VAL D1142 " (cutoff:3.500A)
      removed outlier: 3.656A  pdb=" N   SER D1147 " --> pdb=" O   GLU D1143 " (cutoff:3.500A)
      removed outlier: 3.577A  pdb=" N   PHE D1148 " --> pdb=" O   TRP D1144 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 1164 through 1181
      removed outlier: 3.931A  pdb=" N   VAL D1168 " --> pdb=" O   ALA D1164 " (cutoff:3.500A)
      removed outlier: 3.823A  pdb=" N   LEU D1169 " --> pdb=" O   CYS D1165 " (cutoff:3.500A)
      removed outlier: 3.561A  pdb=" N   LEU D1171 " --> pdb=" O   GLY D1167 " (cutoff:3.500A)
      removed outlier: 4.265A  pdb=" N   VAL D1172 " --> pdb=" O   VAL D1168 " (cutoff:3.500A)
      removed outlier: 3.579A  pdb=" N   ARG D1181 " --> pdb=" O   MET D1177 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 90 through 92
      removed outlier: 3.895A  pdb=" N   TYR A  91 " --> pdb=" O   VAL A  58 " (cutoff:3.500A)
      removed outlier: 6.783A  pdb=" N   TRP A  29 " --> pdb=" O   THR A 235 " (cutoff:3.500A)
      removed outlier: 8.128A  pdb=" N   VAL A 237 " --> pdb=" O   TRP A  29 " (cutoff:3.500A)
      removed outlier: 6.219A  pdb=" N   PHE A  31 " --> pdb=" O   VAL A 237 " (cutoff:3.500A)
      removed outlier: 8.022A  pdb=" N   VAL A 239 " --> pdb=" O   PHE A  31 " (cutoff:3.500A)
      removed outlier: 6.886A  pdb=" N   GLY A  33 " --> pdb=" O   VAL A 239 " (cutoff:3.500A)
      removed outlier: 11.078A  pdb=" N   CYS A 266 " --> pdb=" O   THR A 234 " (cutoff:3.500A)
      removed outlier: 7.342A  pdb=" N   PHE A 236 " --> pdb=" O   CYS A 266 " (cutoff:3.500A)
      removed outlier: 8.706A  pdb=" N   VAL A 268 " --> pdb=" O   PHE A 236 " (cutoff:3.500A)
      removed outlier: 6.630A  pdb=" N   CYS A 238 " --> pdb=" O   VAL A 268 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 90 through 92
      removed outlier: 3.895A  pdb=" N   TYR B  91 " --> pdb=" O   VAL B  58 " (cutoff:3.500A)
      removed outlier: 6.783A  pdb=" N   TRP B  29 " --> pdb=" O   THR B 235 " (cutoff:3.500A)
      removed outlier: 8.127A  pdb=" N   VAL B 237 " --> pdb=" O   TRP B  29 " (cutoff:3.500A)
      removed outlier: 6.219A  pdb=" N   PHE B  31 " --> pdb=" O   VAL B 237 " (cutoff:3.500A)
      removed outlier: 8.021A  pdb=" N   VAL B 239 " --> pdb=" O   PHE B  31 " (cutoff:3.500A)
      removed outlier: 6.884A  pdb=" N   GLY B  33 " --> pdb=" O   VAL B 239 " (cutoff:3.500A)
      removed outlier: 11.077A  pdb=" N   CYS B 266 " --> pdb=" O   THR B 234 " (cutoff:3.500A)
      removed outlier: 7.342A  pdb=" N   PHE B 236 " --> pdb=" O   CYS B 266 " (cutoff:3.500A)
      removed outlier: 8.706A  pdb=" N   VAL B 268 " --> pdb=" O   PHE B 236 " (cutoff:3.500A)
      removed outlier: 6.630A  pdb=" N   CYS B 238 " --> pdb=" O   VAL B 268 " (cutoff:3.500A)

    438 hydrogen bonds defined for protein.
    1314 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: 2.11

  Time building geometry restraints manager: 2.50 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2601
        1.34 -     1.46: 1741
        1.46 -     1.58: 3982
        1.58 -     1.69: 0
        1.69 -     1.81: 88
  Bond restraints: 8412
  Sorted by residual:
  bond pdb=" CB  THR A 163 "
       pdb=" CG2 THR A 163 "
    ideal  model  delta    sigma   weight residual
    1.521  1.468  0.053 3.30e-02 9.18e+02 2.62e+00
  bond pdb=" CB  THR B 163 "
       pdb=" CG2 THR B 163 "
    ideal  model  delta    sigma   weight residual
    1.521  1.468  0.053 3.30e-02 9.18e+02 2.53e+00
  bond pdb=" CB  PHE A 228 "
       pdb=" CG  PHE A 228 "
    ideal  model  delta    sigma   weight residual
    1.502  1.468  0.034 2.30e-02 1.89e+03 2.18e+00
  bond pdb=" CB  VAL B 180 "
       pdb=" CG1 VAL B 180 "
    ideal  model  delta    sigma   weight residual
    1.521  1.473  0.048 3.30e-02 9.18e+02 2.09e+00
  bond pdb=" CB  VAL A 180 "
       pdb=" CG1 VAL A 180 "
    ideal  model  delta    sigma   weight residual
    1.521  1.473  0.048 3.30e-02 9.18e+02 2.09e+00
  ... (remaining 8407 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.98: 10628
        1.98 -     3.95: 622
        3.95 -     5.93: 94
        5.93 -     7.91: 28
        7.91 -     9.88: 12
  Bond angle restraints: 11384
  Sorted by residual:
  angle pdb=" N   PHE D1148 "
        pdb=" CA  PHE D1148 "
        pdb=" C   PHE D1148 "
      ideal   model   delta    sigma   weight residual
     109.81  118.96   -9.15 2.21e+00 2.05e-01 1.72e+01
  angle pdb=" N   PHE C1148 "
        pdb=" CA  PHE C1148 "
        pdb=" C   PHE C1148 "
      ideal   model   delta    sigma   weight residual
     109.81  118.91   -9.10 2.21e+00 2.05e-01 1.70e+01
  angle pdb=" C   ASP A 230 "
        pdb=" N   GLU A 231 "
        pdb=" CA  GLU A 231 "
      ideal   model   delta    sigma   weight residual
     121.54  129.37   -7.83 1.91e+00 2.74e-01 1.68e+01
  angle pdb=" C   ASP B 230 "
        pdb=" N   GLU B 231 "
        pdb=" CA  GLU B 231 "
      ideal   model   delta    sigma   weight residual
     121.54  129.31   -7.77 1.91e+00 2.74e-01 1.66e+01
  angle pdb=" C   GLU A  94 "
        pdb=" N   ILE A  95 "
        pdb=" CA  ILE A  95 "
      ideal   model   delta    sigma   weight residual
     122.48  118.28    4.20 1.13e+00 7.83e-01 1.38e+01
  ... (remaining 11379 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.26: 4497
       16.26 -    32.51: 416
       32.51 -    48.77: 109
       48.77 -    65.02: 22
       65.02 -    81.28: 6
  Dihedral angle restraints: 5050
    sinusoidal: 2064
      harmonic: 2986
  Sorted by residual:
  dihedral pdb=" CA  PRO B 159 "
           pdb=" C   PRO B 159 "
           pdb=" N   THR B 160 "
           pdb=" CA  THR B 160 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -153.05  -26.95     0      5.00e+00 4.00e-02 2.90e+01
  dihedral pdb=" CA  PRO A 159 "
           pdb=" C   PRO A 159 "
           pdb=" N   THR A 160 "
           pdb=" CA  THR A 160 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -153.06  -26.94     0      5.00e+00 4.00e-02 2.90e+01
  dihedral pdb=" CA  ILE D1020 "
           pdb=" C   ILE D1020 "
           pdb=" N   GLY D1021 "
           pdb=" CA  GLY D1021 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  155.69   24.31     0      5.00e+00 4.00e-02 2.36e+01
  ... (remaining 5047 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.043: 771
       0.043 -    0.085: 384
       0.085 -    0.128: 109
       0.128 -    0.171: 18
       0.171 -    0.213: 4
  Chirality restraints: 1286
  Sorted by residual:
  chirality pdb=" CB  ILE C1036 "
            pdb=" CA  ILE C1036 "
            pdb=" CG1 ILE C1036 "
            pdb=" CG2 ILE C1036 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.43    0.21 2.00e-01 2.50e+01 1.14e+00
  chirality pdb=" CB  ILE D1036 "
            pdb=" CA  ILE D1036 "
            pdb=" CG1 ILE D1036 "
            pdb=" CG2 ILE D1036 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.43    0.21 2.00e-01 2.50e+01 1.11e+00
  chirality pdb=" CA  TYR B 302 "
            pdb=" N   TYR B 302 "
            pdb=" C   TYR B 302 "
            pdb=" CB  TYR B 302 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.33    0.18 2.00e-01 2.50e+01 8.55e-01
  ... (remaining 1283 not shown)

  Planarity restraints: 1426
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LYS C1092 "   -0.015 2.00e-02 2.50e+03   3.05e-02 9.28e+00
        pdb=" C   LYS C1092 "    0.053 2.00e-02 2.50e+03
        pdb=" O   LYS C1092 "   -0.020 2.00e-02 2.50e+03
        pdb=" N   SER C1093 "   -0.018 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LYS D1092 "    0.015 2.00e-02 2.50e+03   3.02e-02 9.13e+00
        pdb=" C   LYS D1092 "   -0.052 2.00e-02 2.50e+03
        pdb=" O   LYS D1092 "    0.020 2.00e-02 2.50e+03
        pdb=" N   SER D1093 "    0.018 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LYS B 293 "    0.014 2.00e-02 2.50e+03   2.73e-02 7.46e+00
        pdb=" C   LYS B 293 "   -0.047 2.00e-02 2.50e+03
        pdb=" O   LYS B 293 "    0.018 2.00e-02 2.50e+03
        pdb=" N   TYR B 294 "    0.016 2.00e-02 2.50e+03
  ... (remaining 1423 not shown)

  Histogram of nonbonded interaction distances:
        2.19 -     2.73: 1178
        2.73 -     3.28: 8988
        3.28 -     3.82: 13647
        3.82 -     4.36: 15866
        4.36 -     4.90: 24146
  Nonbonded interactions: 63825
  Sorted by model distance:
  nonbonded pdb=" O   PHE C1032 "
            pdb=" OG  SER C1035 "
     model   vdw
     2.192 3.040
  nonbonded pdb=" O   PHE D1032 "
            pdb=" OG  SER D1035 "
     model   vdw
     2.193 3.040
  nonbonded pdb=" O   HIS A 265 "
            pdb=" ND2 ASN A 307 "
     model   vdw
     2.220 3.120
  nonbonded pdb=" O   HIS B 265 "
            pdb=" ND2 ASN B 307 "
     model   vdw
     2.221 3.120
  nonbonded pdb=" OE1 GLU B 251 "
            pdb=" OH  TYR B 302 "
     model   vdw
     2.232 3.040
  ... (remaining 63820 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 14 through 339)
  selection = chain 'B'
}
ncs_group {
  reference = chain 'C'
  selection = chain 'D'
}

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 group one per residue
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:             1.260
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.260
  Check model and map are aligned:         0.060
  Set scattering table:                    0.070
  Process input model:                     22.700
  Find NCS groups from input model:        0.270
  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:             0.010
  Load rotamer database and sin/cos tables:2.710
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   27.380
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7988
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      :  0.007   0.053   8412  Z= 0.420
  Angle     :  1.105   9.883  11384  Z= 0.614
  Chirality :  0.052   0.213   1286
  Planarity :  0.008   0.055   1426
  Dihedral  : 14.056  81.277   3098
  Min Nonbonded Distance : 2.192

Molprobity Statistics.
  All-atom Clashscore : 25.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.61 %
    Favored  : 95.39 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  : 10.51 %
    Favored  : 89.49 %
  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: -4.04 (0.21), residues: 998
  helix: -2.54 (0.15), residues: 628
  sheet: -2.19 (0.54), residues: 78
  loop : -2.58 (0.33), residues: 292

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.036   0.003   TRP A  29 
 HIS   0.007   0.003   HIS A 265 
 PHE   0.024   0.002   PHE B 169 
 TYR   0.019   0.002   TYR A 302 
 ARG   0.006   0.001   ARG C1099 

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

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

  1996 Ramachandran restraints generated.
    998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1996 Ramachandran restraints generated.
    998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  199 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 199
  time to evaluate  : 1.057 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   14 MET cc_start: 0.8201 (mmt) cc_final: 0.7461 (mtp)
REVERT: A   55 ARG cc_start: 0.7240 (mmt180) cc_final: 0.5304 (mmm160)
REVERT: A  136 MET cc_start: 0.9038 (ptm) cc_final: 0.8824 (ptm)
REVERT: A  223 GLU cc_start: 0.9358 (mt-10) cc_final: 0.8602 (mm-30)
REVERT: A  311 MET cc_start: 0.8447 (tpp) cc_final: 0.7978 (mmm)
REVERT: A  330 MET cc_start: 0.8806 (mtm) cc_final: 0.8473 (mmm)
REVERT: A  331 LEU cc_start: 0.9495 (mt) cc_final: 0.9207 (mm)
REVERT: B   14 MET cc_start: 0.7817 (mmt) cc_final: 0.6771 (mtp)
REVERT: B  127 TYR cc_start: 0.8579 (t80) cc_final: 0.8309 (t80)
REVERT: B  223 GLU cc_start: 0.9398 (mt-10) cc_final: 0.8678 (mm-30)
REVERT: B  294 TYR cc_start: 0.9439 (m-80) cc_final: 0.8869 (m-10)
REVERT: B  304 GLU cc_start: 0.8834 (mm-30) cc_final: 0.8595 (mp0)
REVERT: B  311 MET cc_start: 0.8544 (tpp) cc_final: 0.8140 (mmp)
REVERT: B  330 MET cc_start: 0.8792 (mtm) cc_final: 0.8221 (mmm)
REVERT: C  340 ARG cc_start: 0.8614 (mmt-90) cc_final: 0.8200 (tpt170)
REVERT: C 1033 TYR cc_start: 0.8982 (m-80) cc_final: 0.8757 (m-80)
REVERT: C 1073 LYS cc_start: 0.9466 (mmpt) cc_final: 0.9262 (mmmt)
REVERT: C 1088 LEU cc_start: 0.9401 (mt) cc_final: 0.9181 (mt)
REVERT: C 1153 MET cc_start: 0.7657 (tpt) cc_final: 0.7368 (mmp)
REVERT: D  336 MET cc_start: 0.3465 (ptt) cc_final: 0.3085 (ptp)
REVERT: D 1088 LEU cc_start: 0.9349 (mt) cc_final: 0.9136 (mt)
REVERT: D 1153 MET cc_start: 0.7514 (tpt) cc_final: 0.7164 (tpt)
  outliers start: 0
  outliers final: 0
  residues processed: 199
  average time/residue: 0.2523
  time to fit residues: 65.3379
Evaluate side-chains
  125 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 125
  time to evaluate  : 1.134 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 84 optimal weight:    9.9990
   chunk 75 optimal weight:    0.9980
   chunk 42 optimal weight:    2.9990
   chunk 25 optimal weight:    1.9990
   chunk 51 optimal weight:    3.9990
   chunk 40 optimal weight:    6.9990
   chunk 78 optimal weight:    0.0040
   chunk 30 optimal weight:    0.6980
   chunk 47 optimal weight:    0.6980
   chunk 58 optimal weight:    8.9990
   chunk 90 optimal weight:    0.9980
   overall best weight:    0.6792

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

Flipped N/Q/H residues before XYZ refinement:
A 162 HIS
A 297 GLN
B 162 HIS
B 297 GLN
C1052 GLN
D1052 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3815 r_free = 0.3815 target = 0.105685 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3137 r_free = 0.3137 target = 0.069160 restraints weight = 30754.841|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3181 r_free = 0.3181 target = 0.071234 restraints weight = 17862.141|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3209 r_free = 0.3209 target = 0.072514 restraints weight = 12885.837|
|-----------------------------------------------------------------------------|
r_work (final): 0.3155
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7887
moved from start:          0.2942

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.053   8412  Z= 0.184
  Angle     :  0.693   8.846  11384  Z= 0.348
  Chirality :  0.043   0.141   1286
  Planarity :  0.005   0.054   1426
  Dihedral  :  5.134  20.854   1086
  Min Nonbonded Distance : 2.508

Molprobity Statistics.
  All-atom Clashscore : 12.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.21 %
    Favored  : 96.79 %
  Rotamer:
    Outliers :  0.22 %
    Allowed  :  4.42 %
    Favored  : 95.35 %
  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: -1.79 (0.24), residues: 998
  helix: -0.77 (0.19), residues: 630
  sheet: -1.04 (0.50), residues: 86
  loop : -1.84 (0.36), residues: 282

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP A  29 
 HIS   0.007   0.002   HIS D1060 
 PHE   0.013   0.001   PHE D1131 
 TYR   0.016   0.001   TYR D1109 
 ARG   0.003   0.000   ARG B  55 

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

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

  1996 Ramachandran restraints generated.
    998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1996 Ramachandran restraints generated.
    998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  184 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 182
  time to evaluate  : 0.960 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   14 MET cc_start: 0.8172 (mmt) cc_final: 0.7455 (mtp)
REVERT: A   35 LYS cc_start: 0.8926 (mmtt) cc_final: 0.8548 (mmmt)
REVERT: A  101 MET cc_start: 0.8255 (tmm) cc_final: 0.7560 (mtt)
REVERT: A  223 GLU cc_start: 0.9034 (mt-10) cc_final: 0.8684 (mm-30)
REVERT: A  253 MET cc_start: 0.9282 (ttm) cc_final: 0.8980 (ttm)
REVERT: A  311 MET cc_start: 0.8360 (tpp) cc_final: 0.7803 (mmm)
REVERT: A  330 MET cc_start: 0.8771 (mtm) cc_final: 0.8422 (mmm)
REVERT: A  331 LEU cc_start: 0.9283 (mt) cc_final: 0.9045 (mm)
REVERT: B   14 MET cc_start: 0.7922 (mmt) cc_final: 0.6868 (mtp)
REVERT: B  101 MET cc_start: 0.8205 (tmm) cc_final: 0.7530 (mtt)
REVERT: B  223 GLU cc_start: 0.9057 (mt-10) cc_final: 0.8671 (mm-30)
REVERT: B  253 MET cc_start: 0.9213 (ttm) cc_final: 0.8965 (ttm)
REVERT: B  299 GLU cc_start: 0.8807 (mt-10) cc_final: 0.8499 (mt-10)
REVERT: B  311 MET cc_start: 0.8526 (tpp) cc_final: 0.7855 (mmt)
REVERT: B  330 MET cc_start: 0.8930 (mtm) cc_final: 0.8208 (tpp)
REVERT: C  340 ARG cc_start: 0.8681 (mmt-90) cc_final: 0.8391 (mmm160)
REVERT: C 1028 LEU cc_start: 0.9407 (tp) cc_final: 0.9037 (tp)
REVERT: C 1032 PHE cc_start: 0.8220 (m-10) cc_final: 0.7659 (m-80)
REVERT: C 1061 ASP cc_start: 0.9372 (m-30) cc_final: 0.9089 (m-30)
REVERT: C 1085 MET cc_start: 0.8541 (tpp) cc_final: 0.8330 (tpp)
REVERT: C 1153 MET cc_start: 0.7014 (tpt) cc_final: 0.6749 (mmp)
REVERT: D  336 MET cc_start: 0.3842 (ptt) cc_final: 0.3619 (ptp)
REVERT: D 1028 LEU cc_start: 0.9548 (tp) cc_final: 0.9140 (tp)
REVERT: D 1032 PHE cc_start: 0.7991 (m-10) cc_final: 0.7431 (m-80)
REVERT: D 1153 MET cc_start: 0.7100 (tpt) cc_final: 0.6767 (mmp)
  outliers start: 2
  outliers final: 0
  residues processed: 182
  average time/residue: 0.1789
  time to fit residues: 45.3479
Evaluate side-chains
  116 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 116
  time to evaluate  : 0.947 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 38 optimal weight:    0.8980
   chunk 93 optimal weight:    0.9990
   chunk 82 optimal weight:   40.0000
   chunk 84 optimal weight:   10.0000
   chunk 80 optimal weight:   20.0000
   chunk 72 optimal weight:    7.9990
   chunk 90 optimal weight:    0.8980
   chunk 31 optimal weight:    0.0870
   chunk 91 optimal weight:    0.9990
   chunk 41 optimal weight:    3.9990
   chunk 75 optimal weight:    0.8980
   overall best weight:    0.7560

-------------------------------------------------------------------------------
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 = 0.3802 r_free = 0.3802 target = 0.105391 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3148 r_free = 0.3148 target = 0.069512 restraints weight = 31019.665|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3196 r_free = 0.3196 target = 0.071705 restraints weight = 17909.135|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3227 r_free = 0.3227 target = 0.073071 restraints weight = 12761.291|
|-----------------------------------------------------------------------------|
r_work (final): 0.3162
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7894
moved from start:          0.3710

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   8412  Z= 0.159
  Angle     :  0.638   8.141  11384  Z= 0.318
  Chirality :  0.041   0.164   1286
  Planarity :  0.004   0.052   1426
  Dihedral  :  4.754  19.840   1086
  Min Nonbonded Distance : 2.555

Molprobity Statistics.
  All-atom Clashscore : 9.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.51 %
    Favored  : 97.49 %
  Rotamer:
    Outliers :  0.11 %
    Allowed  :  3.32 %
    Favored  : 96.57 %
  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: -0.86 (0.25), residues: 998
  helix: -0.06 (0.20), residues: 630
  sheet: -0.51 (0.51), residues: 86
  loop : -1.48 (0.36), residues: 282

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP C 339 
 HIS   0.004   0.001   HIS D1060 
 PHE   0.012   0.001   PHE D1102 
 TYR   0.017   0.001   TYR C1033 
 ARG   0.005   0.000   ARG A  55 

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

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

  1996 Ramachandran restraints generated.
    998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1996 Ramachandran restraints generated.
    998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  184 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 183
  time to evaluate  : 1.014 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   14 MET cc_start: 0.8415 (mmt) cc_final: 0.7495 (mtp)
REVERT: A   55 ARG cc_start: 0.6738 (mmt180) cc_final: 0.6507 (mmt180)
REVERT: A  101 MET cc_start: 0.8166 (tmm) cc_final: 0.7361 (mtt)
REVERT: A  221 ILE cc_start: 0.9310 (tt) cc_final: 0.8943 (tt)
REVERT: A  223 GLU cc_start: 0.8979 (mt-10) cc_final: 0.8543 (mm-30)
REVERT: A  256 GLU cc_start: 0.9461 (tp30) cc_final: 0.8961 (tm-30)
REVERT: A  294 TYR cc_start: 0.9377 (m-10) cc_final: 0.9039 (m-80)
REVERT: A  311 MET cc_start: 0.8447 (tpp) cc_final: 0.7856 (mmm)
REVERT: A  330 MET cc_start: 0.8868 (mtm) cc_final: 0.8493 (mmm)
REVERT: B   14 MET cc_start: 0.8150 (mmt) cc_final: 0.6882 (mtp)
REVERT: B  101 MET cc_start: 0.8834 (tmm) cc_final: 0.7940 (mtt)
REVERT: B  164 LEU cc_start: 0.7249 (mt) cc_final: 0.6842 (mt)
REVERT: B  221 ILE cc_start: 0.9295 (tt) cc_final: 0.8933 (tt)
REVERT: B  223 GLU cc_start: 0.8971 (mt-10) cc_final: 0.8530 (mm-30)
REVERT: B  253 MET cc_start: 0.9333 (ttm) cc_final: 0.9100 (ttm)
REVERT: B  256 GLU cc_start: 0.9455 (tp30) cc_final: 0.8906 (tm-30)
REVERT: B  294 TYR cc_start: 0.9332 (m-10) cc_final: 0.9103 (m-80)
REVERT: B  295 LEU cc_start: 0.9584 (tt) cc_final: 0.9343 (tt)
REVERT: B  300 GLU cc_start: 0.8312 (OUTLIER) cc_final: 0.8094 (pt0)
REVERT: B  311 MET cc_start: 0.8474 (tpp) cc_final: 0.7778 (mmm)
REVERT: B  330 MET cc_start: 0.8915 (mtm) cc_final: 0.8639 (tpp)
REVERT: B  331 LEU cc_start: 0.9204 (mt) cc_final: 0.8948 (mm)
REVERT: C  340 ARG cc_start: 0.8693 (mmt-90) cc_final: 0.8397 (mmm160)
REVERT: C 1028 LEU cc_start: 0.9447 (tp) cc_final: 0.9243 (tp)
REVERT: C 1032 PHE cc_start: 0.8234 (m-10) cc_final: 0.7854 (m-80)
REVERT: C 1033 TYR cc_start: 0.8665 (m-80) cc_final: 0.8290 (m-80)
REVERT: C 1061 ASP cc_start: 0.9353 (m-30) cc_final: 0.9080 (m-30)
REVERT: C 1153 MET cc_start: 0.7130 (tpt) cc_final: 0.6916 (mmp)
REVERT: D  336 MET cc_start: 0.4089 (ptt) cc_final: 0.3885 (ptp)
REVERT: D 1028 LEU cc_start: 0.9528 (tp) cc_final: 0.9211 (tp)
REVERT: D 1032 PHE cc_start: 0.8230 (m-10) cc_final: 0.7672 (m-80)
REVERT: D 1084 LEU cc_start: 0.9443 (mm) cc_final: 0.9121 (mm)
REVERT: D 1153 MET cc_start: 0.6945 (tpt) cc_final: 0.6575 (tpt)
  outliers start: 1
  outliers final: 0
  residues processed: 183
  average time/residue: 0.1745
  time to fit residues: 45.1971
Evaluate side-chains
  125 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 124
  time to evaluate  : 0.844 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 58 optimal weight:   10.0000
   chunk 56 optimal weight:    0.9980
   chunk 27 optimal weight:    0.6980
   chunk 46 optimal weight:    0.6980
   chunk 44 optimal weight:    8.9990
   chunk 90 optimal weight:    1.9990
   chunk 33 optimal weight:    1.9990
   chunk 88 optimal weight:    0.7980
   chunk 92 optimal weight:    5.9990
   chunk 12 optimal weight:    3.9990
   chunk 59 optimal weight:   10.0000
   overall best weight:    1.0382

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

Flipped N/Q/H residues before XYZ refinement:
** A 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 225 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3787 r_free = 0.3787 target = 0.104311 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3198 r_free = 0.3198 target = 0.072116 restraints weight = 31081.929|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3191 r_free = 0.3191 target = 0.071846 restraints weight = 19377.656|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3202 r_free = 0.3202 target = 0.072291 restraints weight = 15282.202|
|-----------------------------------------------------------------------------|
r_work (final): 0.3148
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7897
moved from start:          0.4169

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   8412  Z= 0.171
  Angle     :  0.651   7.756  11384  Z= 0.325
  Chirality :  0.041   0.160   1286
  Planarity :  0.004   0.057   1426
  Dihedral  :  4.608  20.743   1086
  Min Nonbonded Distance : 2.489

Molprobity Statistics.
  All-atom Clashscore : 10.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.81 %
    Favored  : 97.19 %
  Rotamer:
    Outliers :  0.11 %
    Allowed  :  3.10 %
    Favored  : 96.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.41 (0.26), residues: 998
  helix:  0.24 (0.20), residues: 630
  sheet: -0.34 (0.53), residues: 86
  loop : -1.18 (0.37), residues: 282

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP D 339 
 HIS   0.010   0.001   HIS C1060 
 PHE   0.015   0.001   PHE B 274 
 TYR   0.014   0.001   TYR C1033 
 ARG   0.003   0.000   ARG B  55 

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

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

  1996 Ramachandran restraints generated.
    998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1996 Ramachandran restraints generated.
    998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  161 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 160
  time to evaluate  : 0.935 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   14 MET cc_start: 0.8460 (mmt) cc_final: 0.7555 (mtp)
REVERT: A  101 MET cc_start: 0.8479 (tmm) cc_final: 0.7697 (mtt)
REVERT: A  136 MET cc_start: 0.8715 (ptt) cc_final: 0.7843 (ppp)
REVERT: A  217 LEU cc_start: 0.9417 (mt) cc_final: 0.9209 (mt)
REVERT: A  223 GLU cc_start: 0.9008 (mt-10) cc_final: 0.8580 (mm-30)
REVERT: A  256 GLU cc_start: 0.9451 (tp30) cc_final: 0.8987 (tm-30)
REVERT: A  330 MET cc_start: 0.9009 (mtm) cc_final: 0.8283 (mmm)
REVERT: B   14 MET cc_start: 0.8333 (mmt) cc_final: 0.7093 (mtp)
REVERT: B   55 ARG cc_start: 0.7145 (mmt180) cc_final: 0.6687 (mmt180)
REVERT: B  101 MET cc_start: 0.8384 (tmm) cc_final: 0.7751 (mtt)
REVERT: B  223 GLU cc_start: 0.9035 (mt-10) cc_final: 0.8539 (mm-30)
REVERT: B  256 GLU cc_start: 0.9430 (tp30) cc_final: 0.8984 (tm-30)
REVERT: B  294 TYR cc_start: 0.9349 (m-10) cc_final: 0.9080 (m-80)
REVERT: B  301 LEU cc_start: 0.8825 (tp) cc_final: 0.8578 (tp)
REVERT: B  302 TYR cc_start: 0.8754 (m-10) cc_final: 0.8079 (m-10)
REVERT: B  311 MET cc_start: 0.8514 (tpp) cc_final: 0.7787 (mmm)
REVERT: B  330 MET cc_start: 0.8954 (mtm) cc_final: 0.8495 (mmm)
REVERT: B  331 LEU cc_start: 0.9200 (mt) cc_final: 0.8937 (mm)
REVERT: C  340 ARG cc_start: 0.8656 (mmt-90) cc_final: 0.8291 (mmm160)
REVERT: C 1032 PHE cc_start: 0.8158 (m-10) cc_final: 0.7837 (m-80)
REVERT: C 1033 TYR cc_start: 0.8593 (m-80) cc_final: 0.8144 (m-80)
REVERT: C 1061 ASP cc_start: 0.9344 (m-30) cc_final: 0.9082 (m-30)
REVERT: C 1153 MET cc_start: 0.6949 (tpt) cc_final: 0.6738 (mmp)
REVERT: D 1028 LEU cc_start: 0.9514 (tp) cc_final: 0.9237 (tp)
REVERT: D 1032 PHE cc_start: 0.8062 (m-10) cc_final: 0.7687 (m-80)
REVERT: D 1153 MET cc_start: 0.6714 (tpt) cc_final: 0.6377 (tpt)
  outliers start: 1
  outliers final: 0
  residues processed: 160
  average time/residue: 0.1868
  time to fit residues: 41.8462
Evaluate side-chains
  118 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 118
  time to evaluate  : 1.008 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 99 optimal weight:    6.9990
   chunk 2 optimal weight:    1.9990
   chunk 64 optimal weight:    9.9990
   chunk 42 optimal weight:    1.9990
   chunk 31 optimal weight:    0.9980
   chunk 97 optimal weight:    8.9990
   chunk 81 optimal weight:    6.9990
   chunk 67 optimal weight:    2.9990
   chunk 73 optimal weight:    7.9990
   chunk 79 optimal weight:    9.9990
   chunk 25 optimal weight:    4.9990
   overall best weight:    2.5988

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

Flipped N/Q/H residues before XYZ refinement:
A  75 GLN
A 162 HIS
** A 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 265 HIS
A 271 GLN
B  75 GLN
B 225 ASN
B 265 HIS
C1068 GLN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3723 r_free = 0.3723 target = 0.100847 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3073 r_free = 0.3073 target = 0.065900 restraints weight = 30922.208|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3117 r_free = 0.3117 target = 0.067889 restraints weight = 18371.522|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3144 r_free = 0.3144 target = 0.069099 restraints weight = 13320.472|
|-----------------------------------------------------------------------------|
r_work (final): 0.3055
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8003
moved from start:          0.4545

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   8412  Z= 0.275
  Angle     :  0.698   7.705  11384  Z= 0.353
  Chirality :  0.041   0.134   1286
  Planarity :  0.005   0.049   1426
  Dihedral  :  4.771  20.196   1086
  Min Nonbonded Distance : 2.530

Molprobity Statistics.
  All-atom Clashscore : 13.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.31 %
    Favored  : 96.69 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.20 %
    Favored  : 95.80 %
  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 (0.26), residues: 998
  helix:  0.41 (0.20), residues: 624
  sheet:  0.27 (0.60), residues: 70
  loop : -1.34 (0.36), residues: 304

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP D1161 
 HIS   0.004   0.002   HIS B 162 
 PHE   0.023   0.002   PHE B  31 
 TYR   0.015   0.002   TYR A 248 
 ARG   0.006   0.001   ARG B  55 

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

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

  1996 Ramachandran restraints generated.
    998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1996 Ramachandran restraints generated.
    998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  143 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 143
  time to evaluate  : 1.028 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   14 MET cc_start: 0.8722 (mmt) cc_final: 0.7691 (mtp)
REVERT: A  223 GLU cc_start: 0.9073 (mt-10) cc_final: 0.8634 (mm-30)
REVERT: A  330 MET cc_start: 0.9060 (mtm) cc_final: 0.8340 (tpp)
REVERT: B   14 MET cc_start: 0.8664 (mmt) cc_final: 0.7311 (mtp)
REVERT: B   35 LYS cc_start: 0.8892 (mmtt) cc_final: 0.8667 (mmmt)
REVERT: B  101 MET cc_start: 0.8539 (tmm) cc_final: 0.7681 (mtt)
REVERT: B  123 GLN cc_start: 0.8153 (mp10) cc_final: 0.7772 (tm-30)
REVERT: B  223 GLU cc_start: 0.9039 (mt-10) cc_final: 0.8549 (mm-30)
REVERT: B  294 TYR cc_start: 0.9465 (m-10) cc_final: 0.9155 (m-80)
REVERT: B  302 TYR cc_start: 0.9318 (m-10) cc_final: 0.8425 (m-10)
REVERT: B  330 MET cc_start: 0.8999 (mtm) cc_final: 0.8381 (tpp)
REVERT: C 1033 TYR cc_start: 0.8804 (m-80) cc_final: 0.8426 (m-80)
REVERT: D  308 LEU cc_start: 0.7338 (tt) cc_final: 0.6917 (pp)
REVERT: D 1085 MET cc_start: 0.8688 (tpp) cc_final: 0.8229 (tpp)
REVERT: D 1153 MET cc_start: 0.6886 (tpt) cc_final: 0.6582 (tpt)
  outliers start: 0
  outliers final: 0
  residues processed: 143
  average time/residue: 0.1742
  time to fit residues: 35.9770
Evaluate side-chains
  111 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 111
  time to evaluate  : 0.974 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 49 optimal weight:    2.9990
   chunk 24 optimal weight:    4.9990
   chunk 58 optimal weight:    6.9990
   chunk 53 optimal weight:    2.9990
   chunk 6 optimal weight:    2.9990
   chunk 80 optimal weight:    9.9990
   chunk 39 optimal weight:    8.9990
   chunk 44 optimal weight:    6.9990
   chunk 90 optimal weight:    0.9980
   chunk 63 optimal weight:    6.9990
   chunk 71 optimal weight:    3.9990
   overall best weight:    2.7988

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

Flipped N/Q/H residues before XYZ refinement:
** A 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3715 r_free = 0.3715 target = 0.100053 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3111 r_free = 0.3111 target = 0.067369 restraints weight = 30994.902|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3130 r_free = 0.3130 target = 0.069001 restraints weight = 19663.645|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3139 r_free = 0.3139 target = 0.069239 restraints weight = 14173.276|
|-----------------------------------------------------------------------------|
r_work (final): 0.3056
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8021
moved from start:          0.4845

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   8412  Z= 0.283
  Angle     :  0.715   7.928  11384  Z= 0.359
  Chirality :  0.042   0.145   1286
  Planarity :  0.004   0.041   1426
  Dihedral  :  4.885  20.210   1086
  Min Nonbonded Distance : 2.401

Molprobity Statistics.
  All-atom Clashscore : 13.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.01 %
    Favored  : 95.99 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.32 %
    Favored  : 96.68 %
  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: -0.19 (0.27), residues: 998
  helix:  0.43 (0.20), residues: 624
  sheet:  0.02 (0.62), residues: 70
  loop : -1.16 (0.38), residues: 304

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP C 339 
 HIS   0.004   0.001   HIS B 162 
 PHE   0.024   0.002   PHE A 228 
 TYR   0.014   0.002   TYR A 248 
 ARG   0.005   0.001   ARG B  55 

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

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

  1996 Ramachandran restraints generated.
    998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1996 Ramachandran restraints generated.
    998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  145 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 145
  time to evaluate  : 0.939 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   14 MET cc_start: 0.8841 (mmt) cc_final: 0.7709 (mtp)
REVERT: A  123 GLN cc_start: 0.8302 (mp10) cc_final: 0.7951 (mp10)
REVERT: A  223 GLU cc_start: 0.9068 (mt-10) cc_final: 0.8649 (mm-30)
REVERT: A  294 TYR cc_start: 0.9452 (m-10) cc_final: 0.9236 (m-80)
REVERT: A  330 MET cc_start: 0.9121 (mtm) cc_final: 0.8264 (tpp)
REVERT: B   14 MET cc_start: 0.8802 (mmt) cc_final: 0.7603 (mtp)
REVERT: B   55 ARG cc_start: 0.7415 (mmt180) cc_final: 0.7072 (mmt180)
REVERT: B  101 MET cc_start: 0.8562 (tmm) cc_final: 0.7695 (mtt)
REVERT: B  123 GLN cc_start: 0.8123 (mp10) cc_final: 0.7759 (tm-30)
REVERT: B  223 GLU cc_start: 0.9075 (mt-10) cc_final: 0.8515 (mm-30)
REVERT: B  302 TYR cc_start: 0.9370 (m-10) cc_final: 0.8388 (m-10)
REVERT: B  330 MET cc_start: 0.9086 (mtm) cc_final: 0.8328 (tpp)
REVERT: C 1033 TYR cc_start: 0.8820 (m-80) cc_final: 0.8527 (m-80)
REVERT: D  308 LEU cc_start: 0.7350 (tt) cc_final: 0.6926 (pp)
REVERT: D 1073 LYS cc_start: 0.9600 (mmtm) cc_final: 0.9332 (mmmt)
REVERT: D 1085 MET cc_start: 0.8698 (tpp) cc_final: 0.8231 (tpp)
REVERT: D 1153 MET cc_start: 0.6880 (tpt) cc_final: 0.6583 (tpt)
  outliers start: 0
  outliers final: 0
  residues processed: 145
  average time/residue: 0.1817
  time to fit residues: 37.5914
Evaluate side-chains
  109 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 109
  time to evaluate  : 0.961 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Traceback (most recent call last):
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in <module>
    run_program(real_space_refine.Program)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program
    task.run()
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run
    log         = self.logger)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__
    log                   = log)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__
    self.caller(self.refine_xyz)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller
    func()
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz
    self.minimization_no_ncs()
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs
    log                         = self.log)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__
    gradients_method            = gradients_method)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__
    rms_angles_limit = rms_angles_limit)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine
    rms_angles_limit = rms_angles_limit)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__
    weight     = weight)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine
    states_collector                = self.states_accumulator)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__
    exception_handling_params=lbfgs_exception_handling_params)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run
    line_search)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus
    f, g = target_evaluator.compute_functional_and_gradients()
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients
    compute_gradients=True)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites
    flags=flags, sites_cart=sites_cart, site_labels=site_labels)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies
    check_bonded_distance_cutoff(sites_frac=sites_frac)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff
    raise RuntimeError(msg)
RuntimeError: Bond distance > max_reasonable_bond_distance: 56.3064 > 50:
  distance: 32 - 52:  24.042
  distance: 36 - 61:  22.969
  distance: 43 - 69:  13.789
  distance: 48 - 52:  21.899
  distance: 49 - 74:  10.248
  distance: 52 - 53:  10.097
  distance: 53 - 54:  20.317
  distance: 53 - 56:  11.081
  distance: 54 - 55:   6.498
  distance: 54 - 61:  21.204
  distance: 56 - 57:  22.106
  distance: 57 - 58:  16.559
  distance: 58 - 59:  25.687
  distance: 58 - 60:  12.552
  distance: 61 - 62:   7.443
  distance: 62 - 63:  34.790
  distance: 62 - 65:  21.099
  distance: 63 - 64:  19.755
  distance: 63 - 69:  21.920
  distance: 65 - 66:   8.878
  distance: 66 - 67:  33.693
  distance: 66 - 68:  43.867
  distance: 69 - 70:  18.724
  distance: 70 - 71:  21.261
  distance: 70 - 73:  11.863
  distance: 71 - 72:  18.976
  distance: 71 - 74:  31.392
  distance: 74 - 75:   7.053
  distance: 75 - 76:  11.307
  distance: 75 - 78:  15.923
  distance: 76 - 77:  24.447
  distance: 76 - 82:  24.669
  distance: 78 - 79:   9.881
  distance: 79 - 80:  13.563
  distance: 79 - 81:  20.402
  distance: 82 - 83:  12.495
  distance: 83 - 84:  12.866
  distance: 83 - 86:  15.537
  distance: 84 - 85:  31.835
  distance: 84 - 94:  24.279
  distance: 86 - 87:   5.384
  distance: 87 - 89:   6.274
  distance: 88 - 90:   8.160
  distance: 89 - 91:   6.759
  distance: 90 - 92:  10.311
  distance: 91 - 92:   9.959
  distance: 92 - 93:  12.461
  distance: 94 - 95:  22.649
  distance: 95 - 96:  15.731
  distance: 96 - 97:  22.055
  distance: 96 - 98:  21.743
  distance: 98 - 99:  10.238
  distance: 99 - 100:  13.970
  distance: 99 - 102:  10.556
  distance: 100 - 101:  14.123
  distance: 100 - 106:   7.991
  distance: 102 - 103:   8.945
  distance: 102 - 104:   4.732
  distance: 103 - 105:   6.647
  distance: 106 - 107:   3.737
  distance: 107 - 108:  12.950
  distance: 107 - 110:   8.118
  distance: 108 - 109:  13.175
  distance: 108 - 114:  26.891
  distance: 110 - 111:   8.606
  distance: 111 - 112:  11.843
  distance: 111 - 113:   7.175
  distance: 114 - 115:  12.754
  distance: 115 - 116:   5.429
  distance: 115 - 118:   5.665
  distance: 116 - 117:  21.767
  distance: 116 - 121:  18.067
  distance: 118 - 119:  10.816
  distance: 118 - 120:  21.022
  distance: 121 - 122:  13.920
  distance: 122 - 123:  21.253
  distance: 122 - 125:  18.283
  distance: 123 - 124:  16.703
  distance: 123 - 131:  18.144
  distance: 125 - 126:   9.055
  distance: 126 - 127:  17.068
  distance: 126 - 128:  13.972
  distance: 127 - 129:   9.493
  distance: 128 - 130:  10.986
  distance: 129 - 130:  16.276