Starting phenix.real_space_refine
on Fri Dec  8 11:23:50 2023 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8odv_16819/12_2023/8odv_16819.pdb
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8odv_16819/12_2023/8odv_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8odv_16819/12_2023/8odv_16819.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8odv_16819/12_2023/8odv_16819.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8odv_16819/12_2023/8odv_16819.pdb"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8odv_16819/12_2023/8odv_16819.pdb"
  }
  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
    Residue "A GLU   94": "OE1" <-> "OE2"
    Residue "A GLU  151": "OE1" <-> "OE2"
    Residue "A GLU  212": "OE1" <-> "OE2"
    Residue "A ARG  289": "NH1" <-> "NH2"
    Residue "A GLU  300": "OE1" <-> "OE2"
    Residue "B GLU   94": "OE1" <-> "OE2"
    Residue "B GLU  151": "OE1" <-> "OE2"
    Residue "B GLU  212": "OE1" <-> "OE2"
    Residue "B ARG  289": "NH1" <-> "NH2"
    Residue "B GLU  300": "OE1" <-> "OE2"
    Residue "C GLU  309": "OE1" <-> "OE2"
    Residue "C GLU 1047": "OE1" <-> "OE2"
    Residue "C GLU 1089": "OE1" <-> "OE2"
    Residue "C GLU 1143": "OE1" <-> "OE2"
    Residue "D GLU  309": "OE1" <-> "OE2"
    Residue "D GLU 1047": "OE1" <-> "OE2"
    Residue "D GLU 1089": "OE1" <-> "OE2"
    Residue "D GLU 1143": "OE1" <-> "OE2"
  Time to flip residues: 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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: 4.91, per 1000 atoms: 0.60
  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  - 3.50
        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: 3.20
  Conformation dependent library (CDL) restraints added in 1.7 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: 0.80
  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: 2.01

  Time building geometry restraints manager: 3.49 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:
       99.48 -   106.39: 234
      106.39 -   113.30: 4643
      113.30 -   120.21: 3383
      120.21 -   127.12: 3014
      127.12 -   134.03: 110
  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 2.440
  nonbonded pdb=" O   PHE D1032 "
            pdb=" OG  SER D1035 "
     model   vdw
     2.193 2.440
  nonbonded pdb=" O   HIS A 265 "
            pdb=" ND2 ASN A 307 "
     model   vdw
     2.220 2.520
  nonbonded pdb=" O   HIS B 265 "
            pdb=" ND2 ASN B 307 "
     model   vdw
     2.221 2.520
  nonbonded pdb=" OE1 GLU B 251 "
            pdb=" OH  TYR B 302 "
     model   vdw
     2.232 2.440
  ... (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
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:             0.700
  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:          3.890
  Check model and map are aligned:         0.130
  Set scattering table:                    0.080
  Process input model:                     26.430
  Find NCS groups from input model:        0.450
  Set up NCS constraints:                  0.040
  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:2.680
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   34.420
-------------------------------------------------------------------------------
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 fitting.
    rotamer outliers: 0
    poor density    : 199
  time to evaluate  : 1.069 
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
  outliers start: 0
  outliers final: 0
  residues processed: 199
  average time/residue: 0.2605
  time to fit residues: 67.6971
Evaluate side-chains
  120 residues out of total 904 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 120
  time to evaluate  : 1.172 
Switching outliers to nearest non-outliers
  outliers start: 0
  outliers final: 0
  residues processed: 0
  time to fit residues: 1.3702
-------------------------------------------------------------------------------
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:    0.6980
   chunk 75 optimal weight:    8.9990
   chunk 42 optimal weight:    2.9990
   chunk 25 optimal weight:    2.9990
   chunk 51 optimal weight:    3.9990
   chunk 40 optimal weight:    6.9990
   chunk 78 optimal weight:   10.0000
   chunk 30 optimal weight:    0.8980
   chunk 47 optimal weight:    1.9990
   chunk 58 optimal weight:    2.9990
   chunk 90 optimal weight:    2.9990
   overall best weight:    1.9186

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

Flipped N/Q/H residues before XYZ refinement:
** A 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 307 ASN
** B 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 297 GLN
B 307 ASN
C1052 GLN
C1068 GLN
D1052 GLN
D1068 GLN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7978
moved from start:          0.2914

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   8412  Z= 0.241
  Angle     :  0.734   9.021  11384  Z= 0.374
  Chirality :  0.043   0.139   1286
  Planarity :  0.005   0.056   1426
  Dihedral  :  5.359  21.925   1086
  Min Nonbonded Distance : 2.138

Molprobity Statistics.
  All-atom Clashscore : 18.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.71 %
    Favored  : 96.29 %
  Rotamer:
    Outliers :  0.22 %
    Allowed  :  5.86 %
    Favored  : 93.92 %
  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: -1.51 (0.25), residues: 998
  helix: -0.53 (0.19), residues: 626
  sheet: -1.23 (0.51), residues: 88
  loop : -1.66 (0.39), residues: 284

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.018   0.001   TRP A  29 
   HIS   0.005   0.002   HIS D1060 
   PHE   0.018   0.002   PHE C1102 
   TYR   0.017   0.002   TYR C1033 
   ARG   0.004   0.001   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
  174 residues out of total 904 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 2
    poor density    : 172
  time to evaluate  : 1.033 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 2
  outliers final: 0
  residues processed: 172
  average time/residue: 0.1848
  time to fit residues: 44.5038
Evaluate side-chains
  106 residues out of total 904 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 106
  time to evaluate  : 0.999 
Switching outliers to nearest non-outliers
  outliers start: 0
  outliers final: 0
  residues processed: 0
  time to fit residues: 1.3982
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 50 optimal weight:    7.9990
   chunk 28 optimal weight:    6.9990
   chunk 75 optimal weight:    1.9990
   chunk 61 optimal weight:   30.0000
   chunk 25 optimal weight:    0.0980
   chunk 90 optimal weight:    3.9990
   chunk 98 optimal weight:    6.9990
   chunk 81 optimal weight:    7.9990
   chunk 31 optimal weight:    0.9980
   chunk 72 optimal weight:   10.0000
   chunk 89 optimal weight:    0.7980
   overall best weight:    1.5784

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

Flipped N/Q/H residues before XYZ refinement:
A 162 HIS
A 265 HIS
** A 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 162 HIS
** B 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 307 ASN
C1052 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7986
moved from start:          0.3733

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   8412  Z= 0.207
  Angle     :  0.679   8.476  11384  Z= 0.342
  Chirality :  0.042   0.173   1286
  Planarity :  0.005   0.054   1426
  Dihedral  :  5.030  22.030   1086
  Min Nonbonded Distance : 2.128

Molprobity Statistics.
  All-atom Clashscore : 15.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.51 %
    Favored  : 96.49 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.76 %
    Favored  : 95.24 %
  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: -0.63 (0.27), residues: 998
  helix:  0.09 (0.20), residues: 628
  sheet: -0.84 (0.52), residues: 88
  loop : -1.15 (0.42), residues: 282

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.017   0.001   TRP C 339 
   HIS   0.003   0.001   HIS C1098 
   PHE   0.017   0.002   PHE D1032 
   TYR   0.032   0.002   TYR C1033 
   ARG   0.003   0.000   ARG A  25 

*********************** 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
  160 residues out of total 904 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 160
  time to evaluate  : 1.007 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 0
  outliers final: 0
  residues processed: 160
  average time/residue: 0.1925
  time to fit residues: 43.0912
Evaluate side-chains
  101 residues out of total 904 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 101
  time to evaluate  : 0.960 
Switching outliers to nearest non-outliers
  outliers start: 0
  outliers final: 0
  residues processed: 0
  time to fit residues: 1.2843
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 68 optimal weight:    0.0040
   chunk 47 optimal weight:    0.8980
   chunk 10 optimal weight:    0.0870
   chunk 43 optimal weight:    0.9980
   chunk 61 optimal weight:    0.0170
   chunk 91 optimal weight:    0.3980
   chunk 96 optimal weight:    4.9990
   chunk 86 optimal weight:    0.9990
   chunk 26 optimal weight:    3.9990
   chunk 80 optimal weight:   20.0000
   chunk 54 optimal weight:    0.0020
   overall best weight:    0.1016

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

Flipped N/Q/H residues before XYZ refinement:
A 162 HIS
A 265 HIS
** A 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 307 ASN
C1052 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7877
moved from start:          0.4424

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035   8412  Z= 0.153
  Angle     :  0.655   8.100  11384  Z= 0.321
  Chirality :  0.041   0.157   1286
  Planarity :  0.004   0.055   1426
  Dihedral  :  4.699  19.105   1086
  Min Nonbonded Distance : 2.145

Molprobity Statistics.
  All-atom Clashscore : 11.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.91 %
    Favored  : 97.09 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.99 %
    Favored  : 97.01 %
  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: -0.35 (0.27), residues: 998
  helix:  0.27 (0.20), residues: 626
  sheet: -0.39 (0.53), residues: 86
  loop : -1.05 (0.40), residues: 286

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.020   0.001   TRP D 339 
   HIS   0.004   0.001   HIS D1098 
   PHE   0.011   0.001   PHE D1102 
   TYR   0.011   0.001   TYR B 127 
   ARG   0.003   0.000   ARG C1099 

*********************** 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
  177 residues out of total 904 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 177
  time to evaluate  : 1.056 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 0
  outliers final: 0
  residues processed: 177
  average time/residue: 0.2019
  time to fit residues: 49.6148
Evaluate side-chains
  114 residues out of total 904 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 114
  time to evaluate  : 1.002 
Switching outliers to nearest non-outliers
  outliers start: 0
  outliers final: 0
  residues processed: 0
  time to fit residues: 1.3310
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 1 optimal weight:    5.9990
   chunk 71 optimal weight:    4.9990
   chunk 39 optimal weight:    0.9990
   chunk 82 optimal weight:   40.0000
   chunk 66 optimal weight:    1.9990
   chunk 0 optimal weight:    6.9990
   chunk 49 optimal weight:    1.9990
   chunk 86 optimal weight:    1.9990
   chunk 24 optimal weight:    1.9990
   chunk 32 optimal weight:    3.9990
   chunk 87 optimal weight:    3.9990
   overall best weight:    1.7990

-------------------------------------------------------------------------------
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**
A 265 HIS
** A 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 162 HIS
** B 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8002
moved from start:          0.4686

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= 0.217
  Angle     :  0.677   8.132  11384  Z= 0.339
  Chirality :  0.040   0.137   1286
  Planarity :  0.004   0.052   1426
  Dihedral  :  4.627  19.888   1086
  Min Nonbonded Distance : 2.121

Molprobity Statistics.
  All-atom Clashscore : 15.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.51 %
    Favored  : 96.49 %
  Rotamer:
    Outliers :  0.11 %
    Allowed  :  2.99 %
    Favored  : 96.90 %
  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:  0.01 (0.27), residues: 998
  helix:  0.57 (0.21), residues: 622
  sheet:  0.41 (0.61), residues: 72
  loop : -1.12 (0.39), residues: 304

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.008   0.001   TRP D1030 
   HIS   0.004   0.002   HIS D1060 
   PHE   0.012   0.002   PHE B 274 
   TYR   0.016   0.002   TYR C1033 
   ARG   0.004   0.000   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
  151 residues out of total 904 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 150
  time to evaluate  : 0.932 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 1
  outliers final: 0
  residues processed: 151
  average time/residue: 0.2129
  time to fit residues: 45.3002
Evaluate side-chains
  100 residues out of total 904 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 100
  time to evaluate  : 1.044 
Switching outliers to nearest non-outliers
  outliers start: 0
  outliers final: 0
  residues processed: 0
  time to fit residues: 1.3689
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 19 optimal weight:    0.0670
   chunk 56 optimal weight:    0.5980
   chunk 23 optimal weight:   20.0000
   chunk 96 optimal weight:   20.0000
   chunk 80 optimal weight:    7.9990
   chunk 44 optimal weight:    4.9990
   chunk 8 optimal weight:   10.0000
   chunk 32 optimal weight:    0.7980
   chunk 50 optimal weight:    0.1980
   chunk 93 optimal weight:    6.9990
   chunk 10 optimal weight:    2.9990
   overall best weight:    0.9320

-------------------------------------------------------------------------------
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**
A 297 GLN
** B 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 307 ASN
C1052 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7958
moved from start:          0.5031

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   8412  Z= 0.165
  Angle     :  0.665   9.893  11384  Z= 0.329
  Chirality :  0.041   0.135   1286
  Planarity :  0.004   0.052   1426
  Dihedral  :  4.612  20.744   1086
  Min Nonbonded Distance : 2.137

Molprobity Statistics.
  All-atom Clashscore : 13.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.11 %
    Favored  : 96.89 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.43 %
    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:  0.17 (0.27), residues: 998
  helix:  0.68 (0.21), residues: 622
  sheet:  0.44 (0.61), residues: 72
  loop : -1.00 (0.40), residues: 304

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.052   0.001   TRP C1030 
   HIS   0.003   0.001   HIS D1060 
   PHE   0.017   0.001   PHE D1045 
   TYR   0.013   0.001   TYR B 127 
   ARG   0.002   0.000   ARG A  25 

*********************** 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
  157 residues out of total 904 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 157
  time to evaluate  : 1.018 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 0
  outliers final: 0
  residues processed: 157
  average time/residue: 0.1821
  time to fit residues: 40.6476
Evaluate side-chains
  104 residues out of total 904 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 104
  time to evaluate  : 1.045 
Switching outliers to nearest non-outliers
  outliers start: 0
  outliers final: 0
  residues processed: 0
  time to fit residues: 1.3209
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 55 optimal weight:    8.9990
   chunk 70 optimal weight:    3.9990
   chunk 54 optimal weight:    0.9990
   chunk 81 optimal weight:    7.9990
   chunk 96 optimal weight:    9.9990
   chunk 60 optimal weight:    5.9990
   chunk 58 optimal weight:    6.9990
   chunk 44 optimal weight:    0.6980
   chunk 59 optimal weight:    7.9990
   chunk 38 optimal weight:    5.9990
   chunk 57 optimal weight:    0.8980
   overall best weight:    2.5186

-------------------------------------------------------------------------------
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**
** A 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 265 HIS
B 307 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8059
moved from start:          0.5262

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   8412  Z= 0.278
  Angle     :  0.768  11.751  11384  Z= 0.389
  Chirality :  0.042   0.160   1286
  Planarity :  0.005   0.046   1426
  Dihedral  :  4.896  21.714   1086
  Min Nonbonded Distance : 2.117

Molprobity Statistics.
  All-atom Clashscore : 18.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.91 %
    Favored  : 96.09 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.10 %
    Favored  : 97.90 %
  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: -0.06 (0.28), residues: 998
  helix:  0.43 (0.21), residues: 624
  sheet:  0.05 (0.61), residues: 72
  loop : -0.83 (0.41), residues: 302

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.038   0.001   TRP C1030 
   HIS   0.005   0.002   HIS C1060 
   PHE   0.019   0.002   PHE A  31 
   TYR   0.014   0.002   TYR A 248 
   ARG   0.004   0.001   ARG B  55 

*********************** REFINEMENT MACRO_CYCLE 7 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
  140 residues out of total 904 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 140
  time to evaluate  : 1.005 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 0
  outliers final: 0
  residues processed: 140
  average time/residue: 0.1887
  time to fit residues: 37.5453
Evaluate side-chains
  97 residues out of total 904 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 97
  time to evaluate  : 1.120 
Switching outliers to nearest non-outliers
  outliers start: 0
  outliers final: 0
  residues processed: 0
  time to fit residues: 1.3644
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 29 optimal weight:    7.9990
   chunk 18 optimal weight:    4.9990
   chunk 61 optimal weight:   30.0000
   chunk 65 optimal weight:    0.4980
   chunk 47 optimal weight:    0.1980
   chunk 8 optimal weight:    1.9990
   chunk 75 optimal weight:    5.9990
   chunk 87 optimal weight:    0.8980
   chunk 92 optimal weight:    0.9980
   chunk 84 optimal weight:    0.0870
   chunk 89 optimal weight:    0.9990
   overall best weight:    0.5358

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

Flipped N/Q/H residues before XYZ refinement:
A 225 ASN
B 225 ASN
C1052 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7965
moved from start:          0.5460

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   8412  Z= 0.160
  Angle     :  0.705   9.560  11384  Z= 0.343
  Chirality :  0.042   0.146   1286
  Planarity :  0.004   0.044   1426
  Dihedral  :  4.684  20.453   1086
  Min Nonbonded Distance : 2.157

Molprobity Statistics.
  All-atom Clashscore : 14.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.81 %
    Favored  : 97.19 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.22 %
    Favored  : 98.78 %
  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:  0.16 (0.28), residues: 998
  helix:  0.58 (0.21), residues: 626
  sheet:  0.31 (0.62), residues: 72
  loop : -0.76 (0.41), residues: 300

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.035   0.001   TRP C1030 
   HIS   0.003   0.001   HIS D1098 
   PHE   0.015   0.001   PHE D1045 
   TYR   0.013   0.001   TYR D1033 
   ARG   0.002   0.000   ARG D1079 

*********************** REFINEMENT MACRO_CYCLE 8 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
  153 residues out of total 904 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 153
  time to evaluate  : 1.022 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 0
  outliers final: 0
  residues processed: 153
  average time/residue: 0.1756
  time to fit residues: 38.2881
Evaluate side-chains
  99 residues out of total 904 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 99
  time to evaluate  : 0.908 
Switching outliers to nearest non-outliers
  outliers start: 0
  outliers final: 0
  residues processed: 0
  time to fit residues: 1.2803
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 92 optimal weight:    0.9990
   chunk 54 optimal weight:    0.4980
   chunk 39 optimal weight:    0.0270
   chunk 70 optimal weight:    0.7980
   chunk 27 optimal weight:    4.9990
   chunk 81 optimal weight:    5.9990
   chunk 84 optimal weight:   10.0000
   chunk 89 optimal weight:    4.9990
   chunk 58 optimal weight:    5.9990
   chunk 94 optimal weight:    6.9990
   chunk 57 optimal weight:    5.9990
   overall best weight:    1.4642

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

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8011
moved from start:          0.5644

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   8412  Z= 0.199
  Angle     :  0.725   9.833  11384  Z= 0.356
  Chirality :  0.041   0.171   1286
  Planarity :  0.004   0.047   1426
  Dihedral  :  4.742  19.850   1086
  Min Nonbonded Distance : 2.138

Molprobity Statistics.
  All-atom Clashscore : 17.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.41 %
    Favored  : 96.59 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.77 %
    Favored  : 99.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  0.21 (0.28), residues: 998
  helix:  0.55 (0.21), residues: 628
  sheet:  0.23 (0.60), residues: 72
  loop : -0.53 (0.41), residues: 298

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.029   0.001   TRP C1030 
   HIS   0.004   0.001   HIS C1060 
   PHE   0.016   0.002   PHE A  31 
   TYR   0.016   0.001   TYR A 302 
   ARG   0.004   0.000   ARG B  55 

*********************** REFINEMENT MACRO_CYCLE 9 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
  141 residues out of total 904 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 141
  time to evaluate  : 1.064 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 0
  outliers final: 0
  residues processed: 141
  average time/residue: 0.1808
  time to fit residues: 36.8032
Evaluate side-chains
  100 residues out of total 904 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 100
  time to evaluate  : 1.010 
Switching outliers to nearest non-outliers
  outliers start: 0
  outliers final: 0
  residues processed: 0
  time to fit residues: 1.3246
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 45 optimal weight:    1.9990
   chunk 66 optimal weight:    7.9990
   chunk 99 optimal weight:    8.9990
   chunk 91 optimal weight:    0.9980
   chunk 79 optimal weight:   20.0000
   chunk 8 optimal weight:    0.7980
   chunk 61 optimal weight:   30.0000
   chunk 48 optimal weight:    0.9980
   chunk 63 optimal weight:    4.9990
   chunk 84 optimal weight:    7.9990
   chunk 24 optimal weight:    5.9990
   overall best weight:    1.9584

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

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8044
moved from start:          0.5799

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046   8412  Z= 0.234
  Angle     :  0.751   9.434  11384  Z= 0.374
  Chirality :  0.042   0.143   1286
  Planarity :  0.004   0.043   1426
  Dihedral  :  4.810  20.607   1086
  Min Nonbonded Distance : 2.126

Molprobity Statistics.
  All-atom Clashscore : 18.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.41 %
    Favored  : 96.59 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.00 %
    Favored  : 99.00 %
  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:  0.09 (0.28), residues: 998
  helix:  0.44 (0.21), residues: 630
  sheet: -0.04 (0.60), residues: 76
  loop : -0.49 (0.42), residues: 292

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.026   0.001   TRP C1030 
   HIS   0.003   0.001   HIS D1098 
   PHE   0.017   0.002   PHE B  31 
   TYR   0.014   0.001   TYR C1033 
   ARG   0.006   0.001   ARG B  55 

********************** REFINEMENT MACRO_CYCLE 10 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
  140 residues out of total 904 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 140
  time to evaluate  : 0.954 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 0
  outliers final: 0
  residues processed: 140
  average time/residue: 0.1808
  time to fit residues: 36.3962
Evaluate side-chains
  96 residues out of total 904 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 96
  time to evaluate  : 0.946 
Switching outliers to nearest non-outliers
  outliers start: 0
  outliers final: 0
  residues processed: 0
  time to fit residues: 1.3386
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 73 optimal weight:    3.9990
   chunk 11 optimal weight:    0.8980
   chunk 22 optimal weight:    3.9990
   chunk 79 optimal weight:    0.3980
   chunk 33 optimal weight:    3.9990
   chunk 81 optimal weight:    5.9990
   chunk 10 optimal weight:    1.9990
   chunk 14 optimal weight:    2.9990
   chunk 69 optimal weight:    1.9990
   chunk 4 optimal weight:    2.9990
   chunk 57 optimal weight:    0.0270
   overall best weight:    1.0642

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

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3753 r_free = 0.3753 target = 0.101993 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3124 r_free = 0.3124 target = 0.068355 restraints weight = 32530.725|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3132 r_free = 0.3132 target = 0.069142 restraints weight = 20473.209|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3160 r_free = 0.3160 target = 0.070222 restraints weight = 15367.808|
|-----------------------------------------------------------------------------|
r_work (final): 0.3106
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7959
moved from start:          0.5984

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   8412  Z= 0.186
  Angle     :  0.732   9.169  11384  Z= 0.362
  Chirality :  0.042   0.163   1286
  Planarity :  0.004   0.044   1426
  Dihedral  :  4.719  20.164   1086
  Min Nonbonded Distance : 2.152

Molprobity Statistics.
  All-atom Clashscore : 16.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.71 %
    Favored  : 96.29 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.44 %
    Favored  : 99.56 %
  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:  0.11 (0.27), residues: 998
  helix:  0.51 (0.20), residues: 634
  sheet: -0.04 (0.59), residues: 72
  loop : -0.62 (0.42), residues: 292

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.028   0.001   TRP C1030 
   HIS   0.003   0.001   HIS C1098 
   PHE   0.013   0.001   PHE A  31 
   TYR   0.008   0.001   TYR A 248 
   ARG   0.003   0.000   ARG B  55 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1798.58 seconds
wall clock time: 33 minutes 27.04 seconds (2007.04 seconds total)