Starting phenix.real_space_refine
on Fri Aug 22 22:26:17 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8odv_16819/08_2025/8odv_16819.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8odv_16819/08_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 {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8odv_16819/08_2025/8odv_16819.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8odv_16819/08_2025/8odv_16819.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8odv_16819/08_2025/8odv_16819.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8odv_16819/08_2025/8odv_16819.map"
  }
  resolution = 4.7
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 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): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 2.14, per 1000 atoms: 0.26
  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: 0.71
  Conformation dependent library (CDL) restraints added in 336.6 milliseconds
  
  Enol-peptide restraints added in 953.7 nanoseconds
  
  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: 0.19
  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: 1.07

  Time building geometry restraints manager: 0.90 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:             1.090
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.110
  Check model and map are aligned:         0.020
  Set scattering table:                    0.040
  Process input model:                     9.400
  Find NCS groups from input model:        0.130
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.330
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   12.150
-------------------------------------------------------------------------------
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   0.208   8416  Z= 0.336
  Angle     :  1.149  27.853  11390  Z= 0.617
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  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
 ARG   0.006   0.001   ARG C1099 
 TYR   0.019   0.002   TYR A 302 
 PHE   0.024   0.002   PHE B 169 
 TRP   0.036   0.003   TRP A  29 
 HIS   0.007   0.003   HIS A 265 

Details of bonding type rmsd
  covalent geometry    : bond        0.00655 ( 8412)
  covalent geometry    : angle       1.10490 (11384)
  hydrogen bonds       : bond        0.14436 (  438)
  hydrogen bonds       : angle       7.16919 ( 1314)
  metal coordination   : bond        0.12844 (    4)
  metal coordination   : angle      13.74501 (    6)

*********************** 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  : 0.344 
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: 0.1034
  time to fit residues: 27.2206
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  : 0.340 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 49 optimal weight:    0.6980
   chunk 97 optimal weight:    5.9990
   chunk 53 optimal weight:    0.7980
   chunk 5 optimal weight:    3.9990
   chunk 33 optimal weight:    3.9990
   chunk 65 optimal weight:    6.9990
   chunk 62 optimal weight:    4.9990
   chunk 51 optimal weight:    6.9990
   chunk 38 optimal weight:    5.9990
   chunk 61 optimal weight:   20.0000
   chunk 45 optimal weight:    0.7980
   overall best weight:    2.0584

-------------------------------------------------------------------------------
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 265 HIS
A 271 GLN
A 297 GLN
** B 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 265 HIS
B 271 GLN
B 297 GLN
** D1052 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3762 r_free = 0.3762 target = 0.102505 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3068 r_free = 0.3068 target = 0.065900 restraints weight = 31772.248|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3114 r_free = 0.3114 target = 0.067894 restraints weight = 18931.800|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3141 r_free = 0.3141 target = 0.069159 restraints weight = 13768.504|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3154 r_free = 0.3154 target = 0.069741 restraints weight = 11371.924|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3168 r_free = 0.3168 target = 0.070337 restraints weight = 10294.059|
|-----------------------------------------------------------------------------|
r_work (final): 0.3110
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7950
moved from start:          0.2864

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   8416  Z= 0.182
  Angle     :  0.740   8.778  11390  Z= 0.374
  Chirality :  0.043   0.138   1286
  Planarity :  0.005   0.056   1426
  Dihedral  :  5.317  22.456   1086
  Min Nonbonded Distance : 2.511

Molprobity Statistics.
  All-atom Clashscore : 15.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.51 %
    Favored  : 96.49 %
  Rotamer:
    Outliers :  0.22 %
    Allowed  :  5.31 %
    Favored  : 94.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.74 (0.24), residues: 998
  helix: -0.64 (0.19), residues: 630
  sheet: -1.33 (0.53), residues: 86
  loop : -1.96 (0.35), residues: 282

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG B  55 
 TYR   0.016   0.002   TYR D1109 
 PHE   0.014   0.002   PHE A 244 
 TRP   0.016   0.001   TRP A  29 
 HIS   0.006   0.002   HIS D1060 

Details of bonding type rmsd
  covalent geometry    : bond        0.00392 ( 8412)
  covalent geometry    : angle       0.72919 (11384)
  hydrogen bonds       : bond        0.04733 (  438)
  hydrogen bonds       : angle       5.32395 ( 1314)
  metal coordination   : bond        0.00143 (    4)
  metal coordination   : angle       5.50485 (    6)

*********************** 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
  166 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 164
  time to evaluate  : 0.334 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   35 LYS cc_start: 0.8836 (mmtt) cc_final: 0.8519 (mmmt)
REVERT: A   55 ARG cc_start: 0.7103 (mmt180) cc_final: 0.6768 (mmt180)
REVERT: A  101 MET cc_start: 0.8253 (tmm) cc_final: 0.7566 (mtt)
REVERT: A  136 MET cc_start: 0.9128 (ptm) cc_final: 0.8871 (ptm)
REVERT: A  223 GLU cc_start: 0.8990 (mt-10) cc_final: 0.8537 (mm-30)
REVERT: A  330 MET cc_start: 0.8850 (mtm) cc_final: 0.8324 (tpp)
REVERT: B   14 MET cc_start: 0.8084 (mmt) cc_final: 0.6893 (mtp)
REVERT: B   55 ARG cc_start: 0.7179 (mmt180) cc_final: 0.6948 (mmt180)
REVERT: B  101 MET cc_start: 0.8283 (tmm) cc_final: 0.7656 (mtt)
REVERT: B  223 GLU cc_start: 0.9043 (mt-10) cc_final: 0.8605 (mm-30)
REVERT: B  239 VAL cc_start: 0.9182 (m) cc_final: 0.8974 (p)
REVERT: B  294 TYR cc_start: 0.9324 (m-80) cc_final: 0.9091 (m-10)
REVERT: B  330 MET cc_start: 0.8982 (mtm) cc_final: 0.8278 (tpp)
REVERT: C  340 ARG cc_start: 0.8670 (mmt-90) cc_final: 0.8398 (mmm160)
REVERT: C 1028 LEU cc_start: 0.9492 (tp) cc_final: 0.9116 (tp)
REVERT: C 1032 PHE cc_start: 0.8277 (m-10) cc_final: 0.7747 (m-80)
REVERT: C 1061 ASP cc_start: 0.9411 (m-30) cc_final: 0.9129 (m-30)
REVERT: C 1085 MET cc_start: 0.8662 (tpp) cc_final: 0.8436 (tpp)
REVERT: C 1088 LEU cc_start: 0.9365 (mt) cc_final: 0.9121 (tp)
REVERT: C 1153 MET cc_start: 0.7273 (tpt) cc_final: 0.7043 (mmp)
REVERT: D  336 MET cc_start: 0.3725 (ptt) cc_final: 0.3514 (ptp)
REVERT: D 1028 LEU cc_start: 0.9547 (tp) cc_final: 0.9120 (tp)
REVERT: D 1032 PHE cc_start: 0.8117 (m-10) cc_final: 0.7532 (m-80)
REVERT: D 1153 MET cc_start: 0.7337 (tpt) cc_final: 0.6995 (tpt)
  outliers start: 2
  outliers final: 0
  residues processed: 164
  average time/residue: 0.0817
  time to fit residues: 19.0634
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  : 0.329 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 97 optimal weight:    0.5980
   chunk 55 optimal weight:    2.9990
   chunk 49 optimal weight:    0.6980
   chunk 35 optimal weight:    0.1980
   chunk 27 optimal weight:    2.9990
   chunk 44 optimal weight:    4.9990
   chunk 83 optimal weight:    7.9990
   chunk 39 optimal weight:    0.5980
   chunk 59 optimal weight:   30.0000
   chunk 86 optimal weight:    6.9990
   chunk 16 optimal weight:    2.9990
   overall best weight:    1.0182

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

Flipped N/Q/H residues before XYZ refinement:
A 162 HIS
B  75 GLN
B 162 HIS
D1052 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3772 r_free = 0.3772 target = 0.103509 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3103 r_free = 0.3103 target = 0.067500 restraints weight = 30565.181|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3148 r_free = 0.3148 target = 0.069623 restraints weight = 17891.765|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3175 r_free = 0.3175 target = 0.070873 restraints weight = 12855.226|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 47)----------------|
| r_work = 0.3193 r_free = 0.3193 target = 0.071718 restraints weight = 10582.333|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3204 r_free = 0.3204 target = 0.072196 restraints weight = 9365.932|
|-----------------------------------------------------------------------------|
r_work (final): 0.3149
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7904
moved from start:          0.3666

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   8416  Z= 0.135
  Angle     :  0.660   8.279  11390  Z= 0.329
  Chirality :  0.042   0.165   1286
  Planarity :  0.004   0.053   1426
  Dihedral  :  4.897  20.472   1086
  Min Nonbonded Distance : 2.476

Molprobity Statistics.
  All-atom Clashscore : 11.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.61 %
    Favored  : 97.39 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.87 %
    Favored  : 95.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.81 (0.26), residues: 998
  helix: -0.03 (0.20), residues: 626
  sheet: -0.54 (0.53), residues: 86
  loop : -1.40 (0.37), residues: 286

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG B 232 
 TYR   0.019   0.002   TYR C1033 
 PHE   0.010   0.001   PHE D1102 
 TRP   0.020   0.001   TRP C 339 
 HIS   0.003   0.001   HIS C1098 

Details of bonding type rmsd
  covalent geometry    : bond        0.00286 ( 8412)
  covalent geometry    : angle       0.65019 (11384)
  hydrogen bonds       : bond        0.04047 (  438)
  hydrogen bonds       : angle       4.67919 ( 1314)
  metal coordination   : bond        0.00302 (    4)
  metal coordination   : angle       5.02109 (    6)

*********************** 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
  167 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 167
  time to evaluate  : 0.284 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   14 MET cc_start: 0.8452 (mmt) cc_final: 0.7464 (mtp)
REVERT: A  101 MET cc_start: 0.8321 (tmm) cc_final: 0.7742 (mtt)
REVERT: A  136 MET cc_start: 0.9083 (ptm) cc_final: 0.8409 (ppp)
REVERT: A  223 GLU cc_start: 0.8994 (mt-10) cc_final: 0.8541 (mm-30)
REVERT: A  253 MET cc_start: 0.9131 (ttm) cc_final: 0.8742 (ttm)
REVERT: A  256 GLU cc_start: 0.9460 (tp30) cc_final: 0.9021 (tm-30)
REVERT: A  330 MET cc_start: 0.8980 (mtm) cc_final: 0.8426 (tpp)
REVERT: B   14 MET cc_start: 0.8284 (mmt) cc_final: 0.7017 (mtp)
REVERT: B   55 ARG cc_start: 0.7089 (mmt180) cc_final: 0.6866 (mmt180)
REVERT: B  101 MET cc_start: 0.8778 (tmm) cc_final: 0.7850 (mtt)
REVERT: B  223 GLU cc_start: 0.8995 (mt-10) cc_final: 0.8502 (mm-30)
REVERT: B  253 MET cc_start: 0.9257 (ttm) cc_final: 0.8981 (ttm)
REVERT: B  256 GLU cc_start: 0.9456 (tp30) cc_final: 0.9026 (tm-30)
REVERT: B  294 TYR cc_start: 0.9277 (m-80) cc_final: 0.8745 (m-80)
REVERT: B  301 LEU cc_start: 0.8726 (tp) cc_final: 0.8466 (tp)
REVERT: B  330 MET cc_start: 0.8918 (mtm) cc_final: 0.8352 (tpp)
REVERT: C  340 ARG cc_start: 0.8699 (mmt-90) cc_final: 0.8419 (mmp-170)
REVERT: C 1028 LEU cc_start: 0.9432 (tp) cc_final: 0.9215 (tp)
REVERT: C 1032 PHE cc_start: 0.8303 (m-10) cc_final: 0.7947 (m-80)
REVERT: C 1033 TYR cc_start: 0.8717 (m-80) cc_final: 0.8340 (m-80)
REVERT: C 1061 ASP cc_start: 0.9369 (m-30) cc_final: 0.9116 (m-30)
REVERT: C 1153 MET cc_start: 0.7144 (tpt) cc_final: 0.6935 (mmp)
REVERT: D  336 MET cc_start: 0.4273 (ptt) cc_final: 0.4072 (ptp)
REVERT: D 1028 LEU cc_start: 0.9523 (tp) cc_final: 0.9195 (tp)
REVERT: D 1032 PHE cc_start: 0.8201 (m-10) cc_final: 0.7630 (m-80)
REVERT: D 1073 LYS cc_start: 0.9521 (mmtm) cc_final: 0.9291 (mmmt)
REVERT: D 1088 LEU cc_start: 0.9323 (mt) cc_final: 0.8981 (tp)
REVERT: D 1153 MET cc_start: 0.6803 (tpt) cc_final: 0.6390 (tpt)
  outliers start: 0
  outliers final: 0
  residues processed: 167
  average time/residue: 0.0703
  time to fit residues: 17.1593
Evaluate side-chains
  115 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 115
  time to evaluate  : 0.262 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 60 optimal weight:    9.9990
   chunk 1 optimal weight:    0.4980
   chunk 51 optimal weight:    2.9990
   chunk 11 optimal weight:    3.9990
   chunk 71 optimal weight:   10.0000
   chunk 30 optimal weight:    4.9990
   chunk 28 optimal weight:    1.9990
   chunk 93 optimal weight:    5.9990
   chunk 49 optimal weight:    3.9990
   chunk 94 optimal weight:    7.9990
   chunk 59 optimal weight:   30.0000
   overall best weight:    2.6988

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

Flipped N/Q/H residues before XYZ refinement:
A 162 HIS
B 162 HIS
C1068 GLN
D1068 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3712 r_free = 0.3712 target = 0.099808 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3019 r_free = 0.3019 target = 0.063658 restraints weight = 32684.255|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3064 r_free = 0.3064 target = 0.065612 restraints weight = 19430.503|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3091 r_free = 0.3091 target = 0.066808 restraints weight = 14180.778|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 22)----------------|
| r_work = 0.3107 r_free = 0.3107 target = 0.067511 restraints weight = 11741.488|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3119 r_free = 0.3119 target = 0.067978 restraints weight = 10509.457|
|-----------------------------------------------------------------------------|
r_work (final): 0.3057
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8016
moved from start:          0.4225

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.039   8416  Z= 0.210
  Angle     :  0.747   8.203  11390  Z= 0.380
  Chirality :  0.043   0.141   1286
  Planarity :  0.005   0.051   1426
  Dihedral  :  5.059  21.626   1086
  Min Nonbonded Distance : 2.449

Molprobity Statistics.
  All-atom Clashscore : 15.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.41 %
    Favored  : 95.59 %
  Rotamer:
    Outliers :  0.11 %
    Allowed  :  4.31 %
    Favored  : 95.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.66 (0.26), residues: 998
  helix:  0.12 (0.20), residues: 624
  sheet: -0.11 (0.60), residues: 70
  loop : -1.49 (0.36), residues: 304

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG B  55 
 TYR   0.018   0.002   TYR C1033 
 PHE   0.015   0.002   PHE A 236 
 TRP   0.022   0.001   TRP C 339 
 HIS   0.007   0.002   HIS C1060 

Details of bonding type rmsd
  covalent geometry    : bond        0.00450 ( 8412)
  covalent geometry    : angle       0.74162 (11384)
  hydrogen bonds       : bond        0.04290 (  438)
  hydrogen bonds       : angle       4.97409 ( 1314)
  metal coordination   : bond        0.00226 (    4)
  metal coordination   : angle       4.06583 (    6)

*********************** 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
  143 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 142
  time to evaluate  : 0.338 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   14 MET cc_start: 0.8657 (mmt) cc_final: 0.7741 (mtp)
REVERT: A  101 MET cc_start: 0.8376 (tmm) cc_final: 0.7679 (mtt)
REVERT: A  136 MET cc_start: 0.9091 (ptm) cc_final: 0.8788 (ptm)
REVERT: A  223 GLU cc_start: 0.9019 (mt-10) cc_final: 0.8536 (mm-30)
REVERT: A  256 GLU cc_start: 0.9510 (tp30) cc_final: 0.9299 (tm-30)
REVERT: A  330 MET cc_start: 0.9017 (mtm) cc_final: 0.8287 (tpp)
REVERT: B   14 MET cc_start: 0.8537 (mmt) cc_final: 0.7353 (mtp)
REVERT: B  101 MET cc_start: 0.8520 (tmm) cc_final: 0.7859 (mtt)
REVERT: B  123 GLN cc_start: 0.7995 (mp10) cc_final: 0.7585 (tm-30)
REVERT: B  223 GLU cc_start: 0.9016 (mt-10) cc_final: 0.8529 (mm-30)
REVERT: B  294 TYR cc_start: 0.9435 (m-80) cc_final: 0.9009 (m-80)
REVERT: B  330 MET cc_start: 0.9040 (mtm) cc_final: 0.8247 (tpp)
REVERT: C 1033 TYR cc_start: 0.8772 (m-80) cc_final: 0.8317 (m-80)
REVERT: D  308 LEU cc_start: 0.7348 (tt) cc_final: 0.6855 (pp)
REVERT: D 1153 MET cc_start: 0.7021 (tpt) cc_final: 0.6730 (tpt)
  outliers start: 1
  outliers final: 0
  residues processed: 142
  average time/residue: 0.0716
  time to fit residues: 14.7902
Evaluate side-chains
  106 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 106
  time to evaluate  : 0.325 
-------------------------------------------------------------------------------
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:   20.0000
   chunk 37 optimal weight:    5.9990
   chunk 75 optimal weight:    0.7980
   chunk 16 optimal weight:    3.9990
   chunk 63 optimal weight:    9.9990
   chunk 10 optimal weight:    1.9990
   chunk 73 optimal weight:   10.0000
   chunk 54 optimal weight:    0.9990
   chunk 44 optimal weight:    0.0980
   chunk 3 optimal weight:    3.9990
   chunk 1 optimal weight:    5.9990
   overall best weight:    1.5786

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

Flipped N/Q/H residues before XYZ refinement:
A  75 GLN
C1052 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3738 r_free = 0.3738 target = 0.101707 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3140 r_free = 0.3140 target = 0.069159 restraints weight = 31327.288|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3147 r_free = 0.3147 target = 0.070125 restraints weight = 19061.279|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3168 r_free = 0.3168 target = 0.070966 restraints weight = 13496.107|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3169 r_free = 0.3169 target = 0.070905 restraints weight = 12268.164|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3171 r_free = 0.3171 target = 0.070984 restraints weight = 11771.941|
|-----------------------------------------------------------------------------|
r_work (final): 0.3098
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7951
moved from start:          0.4645

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   8416  Z= 0.143
  Angle     :  0.663   8.146  11390  Z= 0.332
  Chirality :  0.042   0.140   1286
  Planarity :  0.004   0.047   1426
  Dihedral  :  4.807  20.795   1086
  Min Nonbonded Distance : 2.434

Molprobity Statistics.
  All-atom Clashscore : 11.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.51 %
    Favored  : 97.49 %
  Rotamer:
    Outliers :  0.11 %
    Allowed  :  4.54 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.28 (0.26), residues: 998
  helix:  0.39 (0.20), residues: 622
  sheet:  0.14 (0.59), residues: 70
  loop : -1.30 (0.37), residues: 306

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 288 
 TYR   0.013   0.001   TYR B 127 
 PHE   0.013   0.001   PHE B  31 
 TRP   0.016   0.001   TRP D 339 
 HIS   0.004   0.001   HIS C1060 

Details of bonding type rmsd
  covalent geometry    : bond        0.00309 ( 8412)
  covalent geometry    : angle       0.65614 (11384)
  hydrogen bonds       : bond        0.03811 (  438)
  hydrogen bonds       : angle       4.54236 ( 1314)
  metal coordination   : bond        0.00337 (    4)
  metal coordination   : angle       4.14396 (    6)

*********************** 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
  148 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 147
  time to evaluate  : 0.316 
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: 0.8660 (mmt) cc_final: 0.7736 (mtp)
REVERT: A  101 MET cc_start: 0.8558 (tmm) cc_final: 0.8009 (mtt)
REVERT: A  136 MET cc_start: 0.9072 (ptm) cc_final: 0.8854 (ptm)
REVERT: A  223 GLU cc_start: 0.9065 (mt-10) cc_final: 0.8585 (mm-30)
REVERT: A  330 MET cc_start: 0.9099 (mtm) cc_final: 0.8388 (tpp)
REVERT: B   14 MET cc_start: 0.8648 (mmt) cc_final: 0.7463 (mtp)
REVERT: B   55 ARG cc_start: 0.7164 (mmt180) cc_final: 0.6890 (mmt180)
REVERT: B  101 MET cc_start: 0.8530 (tmm) cc_final: 0.7806 (mtt)
REVERT: B  223 GLU cc_start: 0.9017 (mt-10) cc_final: 0.8505 (mm-30)
REVERT: B  294 TYR cc_start: 0.9378 (m-80) cc_final: 0.9011 (m-80)
REVERT: B  330 MET cc_start: 0.9103 (mtm) cc_final: 0.8405 (tpp)
REVERT: C 1033 TYR cc_start: 0.8795 (m-80) cc_final: 0.8440 (m-80)
REVERT: D  308 LEU cc_start: 0.7338 (tt) cc_final: 0.6898 (pp)
REVERT: D 1153 MET cc_start: 0.6886 (tpt) cc_final: 0.6583 (tpt)
  outliers start: 1
  outliers final: 1
  residues processed: 147
  average time/residue: 0.0672
  time to fit residues: 14.3799
Evaluate side-chains
  114 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 113
  time to evaluate  : 0.325 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 73 optimal weight:    3.9990
   chunk 29 optimal weight:    7.9990
   chunk 33 optimal weight:    2.9990
   chunk 7 optimal weight:    0.0050
   chunk 77 optimal weight:   20.0000
   chunk 62 optimal weight:    8.9990
   chunk 55 optimal weight:    2.9990
   chunk 93 optimal weight:    1.9990
   chunk 12 optimal weight:    3.9990
   chunk 64 optimal weight:    8.9990
   chunk 56 optimal weight:    0.2980
   overall best weight:    1.6600

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

Flipped N/Q/H residues before XYZ refinement:
C1052 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3737 r_free = 0.3737 target = 0.101437 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3058 r_free = 0.3058 target = 0.065536 restraints weight = 30938.923|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3106 r_free = 0.3106 target = 0.067627 restraints weight = 17895.695|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3137 r_free = 0.3137 target = 0.068927 restraints weight = 12743.529|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.3156 r_free = 0.3156 target = 0.069758 restraints weight = 10331.568|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 20)----------------|
| r_work = 0.3167 r_free = 0.3167 target = 0.070233 restraints weight = 9070.804|
|-----------------------------------------------------------------------------|
r_work (final): 0.3100
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7945
moved from start:          0.4947

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   8416  Z= 0.148
  Angle     :  0.682   8.034  11390  Z= 0.340
  Chirality :  0.042   0.137   1286
  Planarity :  0.004   0.045   1426
  Dihedral  :  4.895  19.896   1086
  Min Nonbonded Distance : 2.387

Molprobity Statistics.
  All-atom Clashscore : 12.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.81 %
    Favored  : 96.19 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.99 %
    Favored  : 98.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.06 (0.26), residues: 998
  helix:  0.55 (0.20), residues: 618
  sheet: -0.02 (0.56), residues: 70
  loop : -1.08 (0.37), residues: 310

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B  55 
 TYR   0.013   0.001   TYR A 302 
 PHE   0.013   0.002   PHE A  31 
 TRP   0.021   0.001   TRP D 339 
 HIS   0.002   0.001   HIS D1098 

Details of bonding type rmsd
  covalent geometry    : bond        0.00324 ( 8412)
  covalent geometry    : angle       0.67716 (11384)
  hydrogen bonds       : bond        0.03789 (  438)
  hydrogen bonds       : angle       4.57881 ( 1314)
  metal coordination   : bond        0.00242 (    4)
  metal coordination   : angle       3.67889 (    6)

*********************** 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
  149 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 149
  time to evaluate  : 0.341 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   14 MET cc_start: 0.8744 (mmt) cc_final: 0.7664 (mtp)
REVERT: A  101 MET cc_start: 0.8698 (tmm) cc_final: 0.7871 (mtt)
REVERT: A  123 GLN cc_start: 0.8125 (mp10) cc_final: 0.7848 (mp10)
REVERT: A  136 MET cc_start: 0.9096 (ptm) cc_final: 0.8413 (ppp)
REVERT: A  223 GLU cc_start: 0.9017 (mt-10) cc_final: 0.8542 (mm-30)
REVERT: A  330 MET cc_start: 0.9052 (mtm) cc_final: 0.8371 (tpp)
REVERT: B   14 MET cc_start: 0.8672 (mmt) cc_final: 0.7468 (mtp)
REVERT: B  101 MET cc_start: 0.8601 (tmm) cc_final: 0.7805 (mtt)
REVERT: B  223 GLU cc_start: 0.9018 (mt-10) cc_final: 0.8545 (mm-30)
REVERT: B  236 PHE cc_start: 0.8273 (t80) cc_final: 0.7847 (t80)
REVERT: B  294 TYR cc_start: 0.9391 (m-80) cc_final: 0.9045 (m-80)
REVERT: B  330 MET cc_start: 0.9037 (mtm) cc_final: 0.8340 (tpp)
REVERT: C 1032 PHE cc_start: 0.8256 (m-10) cc_final: 0.8000 (m-80)
REVERT: C 1033 TYR cc_start: 0.8863 (m-80) cc_final: 0.8567 (m-80)
REVERT: C 1073 LYS cc_start: 0.9681 (mmtm) cc_final: 0.9474 (mmmt)
REVERT: C 1083 LYS cc_start: 0.9695 (tttp) cc_final: 0.9490 (ptmm)
REVERT: D  308 LEU cc_start: 0.7212 (tt) cc_final: 0.6807 (pp)
REVERT: D 1153 MET cc_start: 0.7015 (tpt) cc_final: 0.6716 (tpt)
  outliers start: 0
  outliers final: 0
  residues processed: 149
  average time/residue: 0.0712
  time to fit residues: 15.0990
Evaluate side-chains
  113 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 113
  time to evaluate  : 0.285 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 89 optimal weight:    0.0020
   chunk 87 optimal weight:    6.9990
   chunk 59 optimal weight:    0.0970
   chunk 98 optimal weight:   30.0000
   chunk 18 optimal weight:    5.9990
   chunk 86 optimal weight:    2.9990
   chunk 95 optimal weight:   20.0000
   chunk 96 optimal weight:   10.0000
   chunk 66 optimal weight:    9.9990
   chunk 4 optimal weight:    4.9990
   chunk 67 optimal weight:    1.9990
   overall best weight:    2.0192

-------------------------------------------------------------------------------
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 = 0.3721 r_free = 0.3721 target = 0.100501 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 65)----------------|
| r_work = 0.3035 r_free = 0.3035 target = 0.064624 restraints weight = 31236.492|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3087 r_free = 0.3087 target = 0.066822 restraints weight = 17739.555|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3119 r_free = 0.3119 target = 0.068189 restraints weight = 12444.258|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3139 r_free = 0.3139 target = 0.069009 restraints weight = 9978.305|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3152 r_free = 0.3152 target = 0.069548 restraints weight = 8741.883|
|-----------------------------------------------------------------------------|
r_work (final): 0.3081
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7952
moved from start:          0.5214

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   8416  Z= 0.167
  Angle     :  0.705  10.806  11390  Z= 0.353
  Chirality :  0.042   0.135   1286
  Planarity :  0.004   0.042   1426
  Dihedral  :  4.908  21.637   1086
  Min Nonbonded Distance : 2.411

Molprobity Statistics.
  All-atom Clashscore : 13.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.71 %
    Favored  : 96.29 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.02 (0.27), residues: 998
  helix:  0.59 (0.20), residues: 616
  sheet: -0.20 (0.57), residues: 70
  loop : -0.93 (0.38), residues: 312

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B  55 
 TYR   0.011   0.001   TYR B 248 
 PHE   0.013   0.002   PHE B  31 
 TRP   0.012   0.001   TRP D1030 
 HIS   0.003   0.001   HIS A  67 

Details of bonding type rmsd
  covalent geometry    : bond        0.00364 ( 8412)
  covalent geometry    : angle       0.70184 (11384)
  hydrogen bonds       : bond        0.03892 (  438)
  hydrogen bonds       : angle       4.52990 ( 1314)
  metal coordination   : bond        0.00124 (    4)
  metal coordination   : angle       3.17937 (    6)

*********************** 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
  145 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 145
  time to evaluate  : 0.287 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   14 MET cc_start: 0.8843 (mmt) cc_final: 0.7729 (mtp)
REVERT: A  101 MET cc_start: 0.8674 (tmm) cc_final: 0.7865 (mtt)
REVERT: A  136 MET cc_start: 0.9055 (ptm) cc_final: 0.8749 (ptm)
REVERT: A  223 GLU cc_start: 0.9022 (mt-10) cc_final: 0.8474 (mm-30)
REVERT: A  330 MET cc_start: 0.9056 (mtm) cc_final: 0.8366 (tpp)
REVERT: B   14 MET cc_start: 0.8845 (mmt) cc_final: 0.7647 (mtp)
REVERT: B  101 MET cc_start: 0.8631 (tmm) cc_final: 0.7825 (mtt)
REVERT: B  123 GLN cc_start: 0.8043 (mp10) cc_final: 0.7772 (mp10)
REVERT: B  223 GLU cc_start: 0.9042 (mt-10) cc_final: 0.8509 (mm-30)
REVERT: B  294 TYR cc_start: 0.9400 (m-80) cc_final: 0.9050 (m-80)
REVERT: B  330 MET cc_start: 0.9035 (mtm) cc_final: 0.8334 (tpp)
REVERT: C 1032 PHE cc_start: 0.8242 (m-10) cc_final: 0.7887 (m-80)
REVERT: C 1073 LYS cc_start: 0.9687 (mmtm) cc_final: 0.9432 (mmmt)
REVERT: D  308 LEU cc_start: 0.7228 (tt) cc_final: 0.6781 (pp)
REVERT: D 1073 LYS cc_start: 0.9711 (mmtm) cc_final: 0.9456 (mmmt)
REVERT: D 1153 MET cc_start: 0.7120 (tpt) cc_final: 0.6823 (tpt)
  outliers start: 0
  outliers final: 0
  residues processed: 145
  average time/residue: 0.0666
  time to fit residues: 14.1264
Evaluate side-chains
  106 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 106
  time to evaluate  : 0.233 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 61 optimal weight:   30.0000
   chunk 94 optimal weight:    0.8980
   chunk 56 optimal weight:    1.9990
   chunk 48 optimal weight:    0.9990
   chunk 3 optimal weight:    0.9990
   chunk 66 optimal weight:   10.0000
   chunk 77 optimal weight:   30.0000
   chunk 17 optimal weight:    1.9990
   chunk 31 optimal weight:    2.9990
   chunk 21 optimal weight:    0.0050
   chunk 23 optimal weight:    7.9990
   overall best weight:    0.9800

-------------------------------------------------------------------------------
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 = 0.3741 r_free = 0.3741 target = 0.101773 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3121 r_free = 0.3121 target = 0.068725 restraints weight = 31110.391|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3192 r_free = 0.3192 target = 0.071305 restraints weight = 20295.154|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3196 r_free = 0.3196 target = 0.071469 restraints weight = 13118.735|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3209 r_free = 0.3209 target = 0.072065 restraints weight = 11608.131|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3210 r_free = 0.3210 target = 0.072060 restraints weight = 10456.553|
|-----------------------------------------------------------------------------|
r_work (final): 0.3108
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7946
moved from start:          0.5405

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   8416  Z= 0.127
  Angle     :  0.694   9.424  11390  Z= 0.342
  Chirality :  0.042   0.147   1286
  Planarity :  0.004   0.040   1426
  Dihedral  :  4.735  21.096   1086
  Min Nonbonded Distance : 2.356

Molprobity Statistics.
  All-atom Clashscore : 11.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.11 %
    Favored  : 96.89 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.55 %
    Favored  : 98.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.12 (0.27), residues: 998
  helix:  0.64 (0.20), residues: 618
  sheet: -0.09 (0.56), residues: 70
  loop : -0.84 (0.38), residues: 310

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C1079 
 TYR   0.015   0.001   TYR D1033 
 PHE   0.014   0.001   PHE B 274 
 TRP   0.014   0.001   TRP D 339 
 HIS   0.002   0.001   HIS C1098 

Details of bonding type rmsd
  covalent geometry    : bond        0.00273 ( 8412)
  covalent geometry    : angle       0.68968 (11384)
  hydrogen bonds       : bond        0.03650 (  438)
  hydrogen bonds       : angle       4.28090 ( 1314)
  metal coordination   : bond        0.00240 (    4)
  metal coordination   : angle       3.31136 (    6)

*********************** 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
  148 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 148
  time to evaluate  : 0.342 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   14 MET cc_start: 0.8834 (mmt) cc_final: 0.7724 (mtp)
REVERT: A  101 MET cc_start: 0.8722 (tmm) cc_final: 0.7934 (mtt)
REVERT: A  136 MET cc_start: 0.9033 (ptm) cc_final: 0.8720 (ptm)
REVERT: A  223 GLU cc_start: 0.9028 (mt-10) cc_final: 0.8495 (mm-30)
REVERT: B   14 MET cc_start: 0.8758 (mmt) cc_final: 0.7586 (mtp)
REVERT: B  101 MET cc_start: 0.8576 (tmm) cc_final: 0.7771 (mtt)
REVERT: B  123 GLN cc_start: 0.7994 (mp10) cc_final: 0.7652 (tm-30)
REVERT: B  223 GLU cc_start: 0.9055 (mt-10) cc_final: 0.8504 (mm-30)
REVERT: B  236 PHE cc_start: 0.8271 (t80) cc_final: 0.7800 (t80)
REVERT: B  294 TYR cc_start: 0.9392 (m-80) cc_final: 0.9003 (m-80)
REVERT: C 1032 PHE cc_start: 0.8379 (m-10) cc_final: 0.8026 (m-80)
REVERT: C 1073 LYS cc_start: 0.9695 (mmtm) cc_final: 0.9478 (mmmt)
REVERT: D  308 LEU cc_start: 0.7232 (tt) cc_final: 0.6842 (pp)
REVERT: D 1073 LYS cc_start: 0.9685 (mmtm) cc_final: 0.9359 (mmmt)
REVERT: D 1177 MET cc_start: 0.8782 (tmm) cc_final: 0.8567 (mmm)
  outliers start: 0
  outliers final: 0
  residues processed: 148
  average time/residue: 0.0715
  time to fit residues: 15.3303
Evaluate side-chains
  110 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 110
  time to evaluate  : 0.241 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 62 optimal weight:   10.0000
   chunk 83 optimal weight:    5.9990
   chunk 3 optimal weight:    3.9990
   chunk 37 optimal weight:    1.9990
   chunk 56 optimal weight:    0.8980
   chunk 79 optimal weight:   30.0000
   chunk 70 optimal weight:    0.9990
   chunk 89 optimal weight:    0.7980
   chunk 90 optimal weight:    0.7980
   chunk 51 optimal weight:    5.9990
   chunk 13 optimal weight:    2.9990
   overall best weight:    1.0984

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

Flipped N/Q/H residues before XYZ refinement:
A 162 HIS
B 162 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3749 r_free = 0.3749 target = 0.102159 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3081 r_free = 0.3081 target = 0.066789 restraints weight = 31673.234|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3129 r_free = 0.3129 target = 0.068850 restraints weight = 18890.450|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3159 r_free = 0.3159 target = 0.070144 restraints weight = 13653.581|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3177 r_free = 0.3177 target = 0.070910 restraints weight = 11160.209|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.3191 r_free = 0.3191 target = 0.071504 restraints weight = 9903.929|
|-----------------------------------------------------------------------------|
r_work (final): 0.3122
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7936
moved from start:          0.5606

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   8416  Z= 0.126
  Angle     :  0.685   8.441  11390  Z= 0.338
  Chirality :  0.042   0.138   1286
  Planarity :  0.004   0.042   1426
  Dihedral  :  4.623  20.028   1086
  Min Nonbonded Distance : 2.366

Molprobity Statistics.
  All-atom Clashscore : 11.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.11 %
    Favored  : 96.89 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.11 %
    Favored  : 98.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.20 (0.27), residues: 998
  helix:  0.63 (0.20), residues: 630
  sheet: -0.07 (0.56), residues: 70
  loop : -0.66 (0.40), residues: 298

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  55 
 TYR   0.011   0.001   TYR B 127 
 PHE   0.014   0.001   PHE B 169 
 TRP   0.013   0.001   TRP D 339 
 HIS   0.002   0.001   HIS C1098 

Details of bonding type rmsd
  covalent geometry    : bond        0.00274 ( 8412)
  covalent geometry    : angle       0.68123 (11384)
  hydrogen bonds       : bond        0.03615 (  438)
  hydrogen bonds       : angle       4.21011 ( 1314)
  metal coordination   : bond        0.00270 (    4)
  metal coordination   : angle       3.35536 (    6)

*********************** 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
  147 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 147
  time to evaluate  : 0.269 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   14 MET cc_start: 0.8843 (mmt) cc_final: 0.7851 (mtp)
REVERT: A  101 MET cc_start: 0.8711 (tmm) cc_final: 0.7928 (mtt)
REVERT: A  136 MET cc_start: 0.9050 (ptm) cc_final: 0.8739 (ptm)
REVERT: A  223 GLU cc_start: 0.9001 (mt-10) cc_final: 0.8470 (mm-30)
REVERT: B   14 MET cc_start: 0.8749 (mmt) cc_final: 0.7673 (mtp)
REVERT: B  101 MET cc_start: 0.8619 (tmm) cc_final: 0.7817 (mtp)
REVERT: B  123 GLN cc_start: 0.7974 (mp10) cc_final: 0.7717 (tm-30)
REVERT: B  223 GLU cc_start: 0.9062 (mt-10) cc_final: 0.8508 (mm-30)
REVERT: B  236 PHE cc_start: 0.8023 (t80) cc_final: 0.7709 (t80)
REVERT: B  294 TYR cc_start: 0.9394 (m-80) cc_final: 0.8991 (m-80)
REVERT: C 1032 PHE cc_start: 0.8354 (m-10) cc_final: 0.7988 (m-80)
REVERT: C 1073 LYS cc_start: 0.9712 (mmtm) cc_final: 0.9478 (mmmt)
REVERT: D  308 LEU cc_start: 0.7189 (tt) cc_final: 0.6780 (pp)
REVERT: D 1073 LYS cc_start: 0.9689 (mmtm) cc_final: 0.9371 (mmmt)
  outliers start: 0
  outliers final: 0
  residues processed: 147
  average time/residue: 0.0693
  time to fit residues: 14.6846
Evaluate side-chains
  108 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 108
  time to evaluate  : 0.254 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 64 optimal weight:    0.8980
   chunk 9 optimal weight:    9.9990
   chunk 14 optimal weight:    0.8980
   chunk 56 optimal weight:    0.9990
   chunk 21 optimal weight:    0.7980
   chunk 59 optimal weight:   20.0000
   chunk 84 optimal weight:    0.9990
   chunk 86 optimal weight:    0.7980
   chunk 30 optimal weight:    3.9990
   chunk 87 optimal weight:    0.9990
   chunk 38 optimal weight:    9.9990
   overall best weight:    0.8782

-------------------------------------------------------------------------------
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 = 0.3752 r_free = 0.3752 target = 0.102423 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3112 r_free = 0.3112 target = 0.068700 restraints weight = 31434.435|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3183 r_free = 0.3183 target = 0.071042 restraints weight = 20302.873|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3200 r_free = 0.3200 target = 0.071780 restraints weight = 13123.698|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3212 r_free = 0.3212 target = 0.072337 restraints weight = 10897.831|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3215 r_free = 0.3215 target = 0.072396 restraints weight = 9699.898|
|-----------------------------------------------------------------------------|
r_work (final): 0.3135
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7907
moved from start:          0.5777

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   8416  Z= 0.120
  Angle     :  0.700   8.153  11390  Z= 0.343
  Chirality :  0.042   0.138   1286
  Planarity :  0.004   0.045   1426
  Dihedral  :  4.551  19.710   1086
  Min Nonbonded Distance : 2.380

Molprobity Statistics.
  All-atom Clashscore : 10.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.21 %
    Favored  : 96.79 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.11 %
    Favored  : 99.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.22 (0.27), residues: 998
  helix:  0.61 (0.20), residues: 630
  sheet: -0.23 (0.54), residues: 78
  loop : -0.53 (0.40), residues: 290

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  55 
 TYR   0.011   0.001   TYR B 127 
 PHE   0.011   0.001   PHE B  31 
 TRP   0.015   0.001   TRP D 339 
 HIS   0.002   0.001   HIS D1098 

Details of bonding type rmsd
  covalent geometry    : bond        0.00259 ( 8412)
  covalent geometry    : angle       0.69609 (11384)
  hydrogen bonds       : bond        0.03563 (  438)
  hydrogen bonds       : angle       4.19303 ( 1314)
  metal coordination   : bond        0.00294 (    4)
  metal coordination   : angle       3.43116 (    6)

********************** 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
  150 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 150
  time to evaluate  : 0.316 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   14 MET cc_start: 0.8890 (mmt) cc_final: 0.7836 (mtp)
REVERT: A  101 MET cc_start: 0.8742 (tmm) cc_final: 0.7977 (mtt)
REVERT: A  123 GLN cc_start: 0.8018 (mp10) cc_final: 0.7790 (mp10)
REVERT: A  136 MET cc_start: 0.9041 (ptm) cc_final: 0.8742 (ptm)
REVERT: A  223 GLU cc_start: 0.9016 (mt-10) cc_final: 0.8479 (mm-30)
REVERT: A  330 MET cc_start: 0.9004 (mtm) cc_final: 0.8365 (tpp)
REVERT: B   14 MET cc_start: 0.8809 (mmt) cc_final: 0.7635 (mtp)
REVERT: B  101 MET cc_start: 0.8618 (tmm) cc_final: 0.7841 (mtp)
REVERT: B  123 GLN cc_start: 0.8014 (mp10) cc_final: 0.7786 (tm-30)
REVERT: B  223 GLU cc_start: 0.9074 (mt-10) cc_final: 0.8507 (mm-30)
REVERT: B  227 GLN cc_start: 0.8560 (tp-100) cc_final: 0.8155 (tp-100)
REVERT: B  294 TYR cc_start: 0.9356 (m-80) cc_final: 0.8974 (m-80)
REVERT: C 1028 LEU cc_start: 0.9468 (tp) cc_final: 0.9225 (tp)
REVERT: C 1032 PHE cc_start: 0.8433 (m-10) cc_final: 0.7849 (m-10)
REVERT: C 1073 LYS cc_start: 0.9721 (mmtm) cc_final: 0.9501 (mmmt)
REVERT: D  308 LEU cc_start: 0.7260 (tt) cc_final: 0.6866 (pp)
REVERT: D 1073 LYS cc_start: 0.9699 (mmtm) cc_final: 0.9366 (mmtm)
  outliers start: 0
  outliers final: 0
  residues processed: 150
  average time/residue: 0.0674
  time to fit residues: 14.7985
Evaluate side-chains
  114 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 114
  time to evaluate  : 0.256 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 82 optimal weight:   30.0000
   chunk 39 optimal weight:    1.9990
   chunk 19 optimal weight:    0.9980
   chunk 44 optimal weight:    2.9990
   chunk 22 optimal weight:    4.9990
   chunk 5 optimal weight:    0.8980
   chunk 0 optimal weight:    7.9990
   chunk 87 optimal weight:    0.9990
   chunk 61 optimal weight:   40.0000
   chunk 47 optimal weight:    5.9990
   chunk 66 optimal weight:    9.9990
   overall best weight:    1.5786

-------------------------------------------------------------------------------
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 = 0.3733 r_free = 0.3733 target = 0.101339 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3054 r_free = 0.3054 target = 0.065481 restraints weight = 32610.848|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3102 r_free = 0.3102 target = 0.067513 restraints weight = 19325.473|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3133 r_free = 0.3133 target = 0.068777 restraints weight = 13979.405|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 42)----------------|
| r_work = 0.3152 r_free = 0.3152 target = 0.069639 restraints weight = 11452.123|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3163 r_free = 0.3163 target = 0.070095 restraints weight = 10104.761|
|-----------------------------------------------------------------------------|
r_work (final): 0.3098
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7960
moved from start:          0.5895

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   8416  Z= 0.147
  Angle     :  0.725  13.052  11390  Z= 0.354
  Chirality :  0.042   0.191   1286
  Planarity :  0.004   0.042   1426
  Dihedral  :  4.610  20.083   1086
  Min Nonbonded Distance : 2.369

Molprobity Statistics.
  All-atom Clashscore : 12.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.31 %
    Favored  : 96.69 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.22 %
    Favored  : 99.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.23 (0.27), residues: 998
  helix:  0.62 (0.20), residues: 630
  sheet: -0.60 (0.54), residues: 80
  loop : -0.39 (0.41), residues: 288

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG D1031 
 TYR   0.015   0.001   TYR C1109 
 PHE   0.025   0.002   PHE A 274 
 TRP   0.014   0.001   TRP D 339 
 HIS   0.002   0.001   HIS B 162 

Details of bonding type rmsd
  covalent geometry    : bond        0.00320 ( 8412)
  covalent geometry    : angle       0.72169 (11384)
  hydrogen bonds       : bond        0.03758 (  438)
  hydrogen bonds       : angle       4.32208 ( 1314)
  metal coordination   : bond        0.00215 (    4)
  metal coordination   : angle       3.01492 (    6)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1325.02 seconds
wall clock time: 23 minutes 36.98 seconds (1416.98 seconds total)