Starting phenix.real_space_refine
on Thu Dec  7 18:26:57 2023 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u16_26279/12_2023/7u16_26279.pdb
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u16_26279/12_2023/7u16_26279.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.7
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u16_26279/12_2023/7u16_26279.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u16_26279/12_2023/7u16_26279.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u16_26279/12_2023/7u16_26279.pdb"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u16_26279/12_2023/7u16_26279.pdb"
  }
  resolution = 2.7
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.003
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      21      5.16       5
     C    2202      2.51       5
     N     531      2.21       5
     O     702      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped
    None
  Time to flip residues: 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib"
  Total number of atoms: 3456
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 1096
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 135, 1087
          Classifications: {'peptide': 135}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 132}
      Conformer: "B"
        Number of residues, atoms: 135, 1087
          Classifications: {'peptide': 135}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 132}
          bond proxies already assigned to first conformer: 1094
    Chain: "B"
      Number of atoms: 1096
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 135, 1087
          Classifications: {'peptide': 135}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 132}
      Conformer: "B"
        Number of residues, atoms: 135, 1087
          Classifications: {'peptide': 135}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 132}
          bond proxies already assigned to first conformer: 1094
    Chain: "C"
      Number of atoms: 1096
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 135, 1087
          Classifications: {'peptide': 135}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 132}
      Conformer: "B"
        Number of residues, atoms: 135, 1087
          Classifications: {'peptide': 135}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 132}
          bond proxies already assigned to first conformer: 1094
    Chain: "A"
      Number of atoms: 56
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 56
          Unusual residues: {'NAG': 4}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 8
          Unresolved non-hydrogen dihedrals: 12
          Unresolved non-hydrogen chiralities: 4
    Chain: "B"
      Number of atoms: 56
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 56
          Unusual residues: {'NAG': 4}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 8
          Unresolved non-hydrogen dihedrals: 12
          Unresolved non-hydrogen chiralities: 4
    Chain: "C"
      Number of atoms: 56
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 56
          Unusual residues: {'NAG': 4}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 8
          Unresolved non-hydrogen dihedrals: 12
          Unresolved non-hydrogen chiralities: 4
  Time building chain proxies: 3.82, per 1000 atoms: 1.11
  Number of scatterers: 3456
  At special positions: 0
  Unit cell: (105.252, 99.882, 32.22, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      21     16.00
     O     702      8.00
     N     531      7.00
     C    2202      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 214 " - pdb=" SG  CYS A 253 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 214 " - pdb=" SG  CYS B 253 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 214 " - pdb=" SG  CYS C 253 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Links applied
    NAG-ASN
      " NAG A 301 " - " ASN A 183 "
      " NAG A 302 " - " ASN A 151 "
      " NAG A 303 " - " ASN A 145 "
      " NAG A 304 " - " ASN A 164 "
      " NAG B 301 " - " ASN B 183 "
      " NAG B 302 " - " ASN B 151 "
      " NAG B 303 " - " ASN B 145 "
      " NAG B 304 " - " ASN B 164 "
      " NAG C 301 " - " ASN C 183 "
      " NAG C 302 " - " ASN C 151 "
      " NAG C 303 " - " ASN C 145 "
      " NAG C 304 " - " ASN C 164 "
  Time building additional restraints: 1.27
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  804 Ramachandran restraints generated.
    402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  786

  Finding SS restraints...
    Secondary structure from input PDB file:
      0 helices and 11 sheets defined
      0.0% alpha, 67.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.32
  Creating SS restraints...
    Processing sheet with id=AA1, first strand: chain 'A' and resid 122 through 126
    Processing sheet with id=AA2, first strand: chain 'A' and resid 129 through 137
      removed outlier: 6.371A  pdb=" N   LYS A 129 " --> pdb=" O   SER B 130 " (cutoff:3.500A)
      removed outlier: 8.229A  pdb=" N   TYR B 132 " --> pdb=" O   LYS A 129 " (cutoff:3.500A)
      removed outlier: 9.088A  pdb=" N   ALA A 131 " --> pdb=" O   TYR B 132 " (cutoff:3.500A)
      removed outlier: 6.498A  pdb=" N   SER B 134 " --> pdb=" O   ALA A 131 " (cutoff:3.500A)
      removed outlier: 9.018A  pdb=" N   VAL A 133 " --> pdb=" O   SER B 134 " (cutoff:3.500A)
      removed outlier: 9.432A  pdb=" N   ASP B 136 " --> pdb=" O   VAL A 133 " (cutoff:3.500A)
      removed outlier: 8.667A  pdb=" N   TYR A 135 " --> pdb=" O   ASP B 136 " (cutoff:3.500A)
      removed outlier: 6.392A  pdb=" N   LYS B 129 " --> pdb=" O   SER C 130 " (cutoff:3.500A)
      removed outlier: 8.254A  pdb=" N   TYR C 132 " --> pdb=" O   LYS B 129 " (cutoff:3.500A)
      removed outlier: 9.092A  pdb=" N   ALA B 131 " --> pdb=" O   TYR C 132 " (cutoff:3.500A)
      removed outlier: 6.505A  pdb=" N   SER C 134 " --> pdb=" O   ALA B 131 " (cutoff:3.500A)
      removed outlier: 8.999A  pdb=" N   VAL B 133 " --> pdb=" O   SER C 134 " (cutoff:3.500A)
      removed outlier: 9.419A  pdb=" N   ASP C 136 " --> pdb=" O   VAL B 133 " (cutoff:3.500A)
      removed outlier: 8.650A  pdb=" N   TYR B 135 " --> pdb=" O   ASP C 136 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA2
    Processing sheet with id=AA3, first strand: chain 'A' and resid 142 through 165
      removed outlier: 6.342A  pdb=" N   ILE A 142 " --> pdb=" O   TYR B 143 " (cutoff:3.500A)
      removed outlier: 7.798A  pdb=" N   ASN B 145 " --> pdb=" O   ILE A 142 " (cutoff:3.500A)
      removed outlier: 8.827A  pdb=" N   LEU A 144 " --> pdb=" O   ASN B 145 " (cutoff:3.500A)
      removed outlier: 8.022A  pdb=" N   THR B 147 " --> pdb=" O   LEU A 144 " (cutoff:3.500A)
      removed outlier: 9.195A  pdb=" N   ILE A 146 " --> pdb=" O   THR B 147 " (cutoff:3.500A)
      removed outlier: 10.073A  pdb=" N   THR B 149 " --> pdb=" O   ILE A 146 " (cutoff:3.500A)
      removed outlier: 9.033A  pdb=" N   ASN A 148 " --> pdb=" O   THR B 149 " (cutoff:3.500A)
      removed outlier: 10.294A  pdb=" N   ASN B 151 " --> pdb=" O   ASN A 148 " (cutoff:3.500A)
      removed outlier: 8.986A  pdb=" N   LEU A 150 " --> pdb=" O   ASN B 151 " (cutoff:3.500A)
      removed outlier: 10.178A  pdb=" N   THR B 153 " --> pdb=" O   LEU A 150 " (cutoff:3.500A)
      removed outlier: 9.199A  pdb=" N   ILE A 152 " --> pdb=" O   THR B 153 " (cutoff:3.500A)
      removed outlier: 9.734A  pdb=" N   ASN B 155 " --> pdb=" O   ILE A 152 " (cutoff:3.500A)
      removed outlier: 8.872A  pdb=" N   ASN A 154 " --> pdb=" O   ASN B 155 " (cutoff:3.500A)
      removed outlier: 10.389A  pdb=" N   TYR B 157 " --> pdb=" O   ASN A 154 " (cutoff:3.500A)
      removed outlier: 9.051A  pdb=" N   ASN A 156 " --> pdb=" O   TYR B 157 " (cutoff:3.500A)
      removed outlier: 10.322A  pdb=" N   SER B 159 " --> pdb=" O   ASN A 156 " (cutoff:3.500A)
      removed outlier: 9.519A  pdb=" N   TYR A 158 " --> pdb=" O   SER B 159 " (cutoff:3.500A)
      removed outlier: 10.246A  pdb=" N   GLU B 161 " --> pdb=" O   TYR A 158 " (cutoff:3.500A)
      removed outlier: 6.018A  pdb=" N   VAL A 160 " --> pdb=" O   GLU B 161 " (cutoff:3.500A)
      removed outlier: 8.788A  pdb=" N   GLU B 163 " --> pdb=" O   VAL A 160 " (cutoff:3.500A)
      removed outlier: 6.595A  pdb=" N   VAL A 162 " --> pdb=" O   GLU B 163 " (cutoff:3.500A)
      removed outlier: 7.846A  pdb=" N   ILE B 165 " --> pdb=" O   VAL A 162 " (cutoff:3.500A)
      removed outlier: 5.974A  pdb=" N   ASN A 164 " --> pdb=" O   ILE B 165 " (cutoff:3.500A)
      removed outlier: 6.379A  pdb=" N   ILE B 142 " --> pdb=" O   TYR C 143 " (cutoff:3.500A)
      removed outlier: 7.842A  pdb=" N   ASN C 145 " --> pdb=" O   ILE B 142 " (cutoff:3.500A)
      removed outlier: 8.843A  pdb=" N   LEU B 144 " --> pdb=" O   ASN C 145 " (cutoff:3.500A)
      removed outlier: 8.030A  pdb=" N   THR C 147 " --> pdb=" O   LEU B 144 " (cutoff:3.500A)
      removed outlier: 9.182A  pdb=" N   ILE B 146 " --> pdb=" O   THR C 147 " (cutoff:3.500A)
      removed outlier: 10.050A  pdb=" N   THR C 149 " --> pdb=" O   ILE B 146 " (cutoff:3.500A)
      removed outlier: 9.001A  pdb=" N   ASN B 148 " --> pdb=" O   THR C 149 " (cutoff:3.500A)
      removed outlier: 10.256A  pdb=" N   ASN C 151 " --> pdb=" O   ASN B 148 " (cutoff:3.500A)
      removed outlier: 8.938A  pdb=" N   LEU B 150 " --> pdb=" O   ASN C 151 " (cutoff:3.500A)
      removed outlier: 10.126A  pdb=" N   THR C 153 " --> pdb=" O   LEU B 150 " (cutoff:3.500A)
      removed outlier: 9.141A  pdb=" N   ILE B 152 " --> pdb=" O   THR C 153 " (cutoff:3.500A)
      removed outlier: 9.671A  pdb=" N   ASN C 155 " --> pdb=" O   ILE B 152 " (cutoff:3.500A)
      removed outlier: 8.802A  pdb=" N   ASN B 154 " --> pdb=" O   ASN C 155 " (cutoff:3.500A)
      removed outlier: 10.322A  pdb=" N   TYR C 157 " --> pdb=" O   ASN B 154 " (cutoff:3.500A)
      removed outlier: 8.976A  pdb=" N   ASN B 156 " --> pdb=" O   TYR C 157 " (cutoff:3.500A)
      removed outlier: 10.247A  pdb=" N   SER C 159 " --> pdb=" O   ASN B 156 " (cutoff:3.500A)
      removed outlier: 9.437A  pdb=" N   TYR B 158 " --> pdb=" O   SER C 159 " (cutoff:3.500A)
      removed outlier: 10.166A  pdb=" N   GLU C 161 " --> pdb=" O   TYR B 158 " (cutoff:3.500A)
      removed outlier: 5.955A  pdb=" N   VAL B 160 " --> pdb=" O   GLU C 161 " (cutoff:3.500A)
      removed outlier: 8.720A  pdb=" N   GLU C 163 " --> pdb=" O   VAL B 160 " (cutoff:3.500A)
      removed outlier: 6.541A  pdb=" N   VAL B 162 " --> pdb=" O   GLU C 163 " (cutoff:3.500A)
      removed outlier: 7.797A  pdb=" N   ILE C 165 " --> pdb=" O   VAL B 162 " (cutoff:3.500A)
      removed outlier: 5.912A  pdb=" N   ASN B 164 " --> pdb=" O   ILE C 165 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA3
    Processing sheet with id=AA4, first strand: chain 'A' and resid 168 through 177
    Processing sheet with id=AA5, first strand: chain 'A' and resid 180 through 181
      removed outlier: 6.572A  pdb=" N   ARG A 180 " --> pdb=" O   LEU B 181 " (cutoff:3.500A)
      removed outlier: 6.560A  pdb=" N   ARG B 180 " --> pdb=" O   LEU C 181 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA5
    Processing sheet with id=AA6, first strand: chain 'A' and resid 184 through 187
    Processing sheet with id=AA7, first strand: chain 'A' and resid 191 through 198
      removed outlier: 8.944A  pdb=" N   MET A 192 " --> pdb=" O   LYS B 193 " (cutoff:3.500A)
      removed outlier: 9.058A  pdb=" N   ILE B 195 " --> pdb=" O   MET A 192 " (cutoff:3.500A)
      removed outlier: 6.798A  pdb=" N   GLN A 194 " --> pdb=" O   ILE B 195 " (cutoff:3.500A)
      removed outlier: 7.984A  pdb=" N   TYR B 197 " --> pdb=" O   GLN A 194 " (cutoff:3.500A)
      removed outlier: 6.438A  pdb=" N   ASP A 196 " --> pdb=" O   TYR B 197 " (cutoff:3.500A)
      removed outlier: 8.933A  pdb=" N   MET B 192 " --> pdb=" O   LYS C 193 " (cutoff:3.500A)
      removed outlier: 9.066A  pdb=" N   ILE C 195 " --> pdb=" O   MET B 192 " (cutoff:3.500A)
      removed outlier: 6.830A  pdb=" N   GLN B 194 " --> pdb=" O   ILE C 195 " (cutoff:3.500A)
      removed outlier: 8.015A  pdb=" N   TYR C 197 " --> pdb=" O   GLN B 194 " (cutoff:3.500A)
      removed outlier: 6.470A  pdb=" N   ASP B 196 " --> pdb=" O   TYR C 197 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA7
    Processing sheet with id=AA8, first strand: chain 'A' and resid 201 through 204
    Processing sheet with id=AA9, first strand: chain 'A' and resid 209 through 228
      removed outlier: 6.946A  pdb=" N   MET A 210 " --> pdb=" O   TYR B 209 " (cutoff:3.500A)
      removed outlier: 6.954A  pdb=" N   TYR B 211 " --> pdb=" O   MET A 210 " (cutoff:3.500A)
      removed outlier: 6.974A  pdb=" N   ASP A 212 " --> pdb=" O   TYR B 211 " (cutoff:3.500A)
      removed outlier: 6.941A  pdb=" N   PHE B 213 " --> pdb=" O   ASP A 212 " (cutoff:3.500A)
      removed outlier: 6.744A  pdb=" N   VAL B 221 " --> pdb=" O   LYS A 220 " (cutoff:3.500A)
      removed outlier: 7.012A  pdb=" N   HIS A 222 " --> pdb=" O   VAL B 221 " (cutoff:3.500A)
      removed outlier: 6.873A  pdb=" N   ASN B 223 " --> pdb=" O   HIS A 222 " (cutoff:3.500A)
      removed outlier: 6.102A  pdb=" N   TYR B 209 " --> pdb=" O   MET C 210 " (cutoff:3.500A)
      removed outlier: 7.336A  pdb=" N   ASP C 212 " --> pdb=" O   TYR B 209 " (cutoff:3.500A)
      removed outlier: 6.357A  pdb=" N   TYR B 211 " --> pdb=" O   ASP C 212 " (cutoff:3.500A)
      removed outlier: 7.255A  pdb=" N   CYS C 214 " --> pdb=" O   TYR B 211 " (cutoff:3.500A)
      removed outlier: 8.371A  pdb=" N   PHE B 213 " --> pdb=" O   CYS C 214 " (cutoff:3.500A)
      removed outlier: 10.442A  pdb=" N   LEU C 216 " --> pdb=" O   PHE B 213 " (cutoff:3.500A)
      removed outlier: 8.876A  pdb=" N   THR B 215 " --> pdb=" O   LEU C 216 " (cutoff:3.500A)
      removed outlier: 9.799A  pdb=" N   SER C 218 " --> pdb=" O   THR B 215 " (cutoff:3.500A)
      removed outlier: 8.795A  pdb=" N   ILE B 217 " --> pdb=" O   SER C 218 " (cutoff:3.500A)
      removed outlier: 9.946A  pdb=" N   LYS C 220 " --> pdb=" O   ILE B 217 " (cutoff:3.500A)
      removed outlier: 6.071A  pdb=" N   ILE B 219 " --> pdb=" O   LYS C 220 " (cutoff:3.500A)
      removed outlier: 8.299A  pdb=" N   HIS C 222 " --> pdb=" O   ILE B 219 " (cutoff:3.500A)
      removed outlier: 5.887A  pdb=" N   VAL B 221 " --> pdb=" O   HIS C 222 " (cutoff:3.500A)
      removed outlier: 7.500A  pdb=" N   ILE C 224 " --> pdb=" O   VAL B 221 " (cutoff:3.500A)
      removed outlier: 7.857A  pdb=" N   ASN B 223 " --> pdb=" O   ILE C 224 " (cutoff:3.500A)
      removed outlier: 9.821A  pdb=" N   LEU C 226 " --> pdb=" O   ASN B 223 " (cutoff:3.500A)
      removed outlier: 8.747A  pdb=" N   VAL B 225 " --> pdb=" O   LEU C 226 " (cutoff:3.500A)
      removed outlier: 10.088A  pdb=" N   MET C 228 " --> pdb=" O   VAL B 225 " (cutoff:3.500A)
      removed outlier: 9.225A  pdb=" N   MET B 227 " --> pdb=" O   MET C 228 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'A' and resid 233 through 245
    Processing sheet with id=AB2, first strand: chain 'A' and resid 251 through 253

    78 hydrogen bonds defined for protein.
    234 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: 0.74

  Time building geometry restraints manager: 1.39 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 1053
        1.34 -     1.46: 791
        1.46 -     1.58: 1636
        1.58 -     1.69: 0
        1.69 -     1.81: 36
  Bond restraints: 3516
  Sorted by residual:
  bond pdb=" C1  NAG A 304 "
       pdb=" O5  NAG A 304 "
    ideal  model  delta    sigma   weight residual
    1.406  1.478 -0.072 2.00e-02 2.50e+03 1.31e+01
  bond pdb=" C1  NAG C 304 "
       pdb=" O5  NAG C 304 "
    ideal  model  delta    sigma   weight residual
    1.406  1.478 -0.072 2.00e-02 2.50e+03 1.30e+01
  bond pdb=" C1  NAG B 304 "
       pdb=" O5  NAG B 304 "
    ideal  model  delta    sigma   weight residual
    1.406  1.478 -0.072 2.00e-02 2.50e+03 1.30e+01
  bond pdb=" C1  NAG B 301 "
       pdb=" O5  NAG B 301 "
    ideal  model  delta    sigma   weight residual
    1.406  1.438 -0.032 2.00e-02 2.50e+03 2.60e+00
  bond pdb=" C1  NAG A 301 "
       pdb=" O5  NAG A 301 "
    ideal  model  delta    sigma   weight residual
    1.406  1.438 -0.032 2.00e-02 2.50e+03 2.49e+00
  ... (remaining 3511 not shown)

  Histogram of bond angle deviations from ideal:
      100.54 -   106.79: 75
      106.79 -   113.04: 1984
      113.04 -   119.29: 878
      119.29 -   125.54: 1839
      125.54 -   131.80: 12
  Bond angle restraints: 4788
  Sorted by residual:
  angle pdb=" CA  ARG C 247 "
        pdb=" CB  ARG C 247 "
        pdb=" CG  ARG C 247 "
      ideal   model   delta    sigma   weight residual
     114.10  118.77   -4.67 2.00e+00 2.50e-01 5.45e+00
  angle pdb=" CA  ARG B 247 "
        pdb=" CB  ARG B 247 "
        pdb=" CG  ARG B 247 "
      ideal   model   delta    sigma   weight residual
     114.10  118.75   -4.65 2.00e+00 2.50e-01 5.40e+00
  angle pdb=" CA  ARG A 247 "
        pdb=" CB  ARG A 247 "
        pdb=" CG  ARG A 247 "
      ideal   model   delta    sigma   weight residual
     114.10  118.74   -4.64 2.00e+00 2.50e-01 5.39e+00
  angle pdb=" N   TYR A 236 "
        pdb=" CA  TYR A 236 "
        pdb=" C   TYR A 236 "
      ideal   model   delta    sigma   weight residual
     109.07  112.27   -3.20 1.52e+00 4.33e-01 4.45e+00
  angle pdb=" N   TYR C 236 "
        pdb=" CA  TYR C 236 "
        pdb=" C   TYR C 236 "
      ideal   model   delta    sigma   weight residual
     109.07  112.27   -3.20 1.52e+00 4.33e-01 4.43e+00
  ... (remaining 4783 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    24.47: 2115
       24.47 -    48.94: 117
       48.94 -    73.41: 27
       73.41 -    97.88: 3
       97.88 -   122.35: 9
  Dihedral angle restraints: 2271
    sinusoidal: 1038
      harmonic: 1233
  Sorted by residual:
  dihedral pdb=" CB  CYS C 214 "
           pdb=" SG  CYS C 214 "
           pdb=" SG  CYS C 253 "
           pdb=" CB  CYS C 253 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  134.10  -41.10     1      1.00e+01 1.00e-02 2.37e+01
  dihedral pdb=" CB  CYS B 214 "
           pdb=" SG  CYS B 214 "
           pdb=" SG  CYS B 253 "
           pdb=" CB  CYS B 253 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  134.08  -41.08     1      1.00e+01 1.00e-02 2.36e+01
  dihedral pdb=" CB  CYS A 214 "
           pdb=" SG  CYS A 214 "
           pdb=" SG  CYS A 253 "
           pdb=" CB  CYS A 253 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  134.06  -41.06     1      1.00e+01 1.00e-02 2.36e+01
  ... (remaining 2268 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.038: 361
       0.038 -    0.075: 125
       0.075 -    0.113: 86
       0.113 -    0.151: 28
       0.151 -    0.188: 6
  Chirality restraints: 606
  Sorted by residual:
  chirality pdb=" C1  NAG A 301 "
            pdb=" ND2 ASN A 183 "
            pdb=" C2  NAG A 301 "
            pdb=" O5  NAG A 301 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.21   -0.19 2.00e-01 2.50e+01 8.87e-01
  chirality pdb=" C1  NAG C 301 "
            pdb=" ND2 ASN C 183 "
            pdb=" C2  NAG C 301 "
            pdb=" O5  NAG C 301 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.22   -0.18 2.00e-01 2.50e+01 8.40e-01
  chirality pdb=" CA  TYR C 236 "
            pdb=" N   TYR C 236 "
            pdb=" C   TYR C 236 "
            pdb=" CB  TYR C 236 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.33    0.18 2.00e-01 2.50e+01 8.27e-01
  ... (remaining 603 not shown)

  Planarity restraints: 591
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR B 236 "   -0.005 2.00e-02 2.50e+03   2.80e-02 1.57e+01
        pdb=" CG  TYR B 236 "    0.056 2.00e-02 2.50e+03
        pdb=" CD1 TYR B 236 "   -0.046 2.00e-02 2.50e+03
        pdb=" CD2 TYR B 236 "   -0.023 2.00e-02 2.50e+03
        pdb=" CE1 TYR B 236 "    0.020 2.00e-02 2.50e+03
        pdb=" CE2 TYR B 236 "   -0.002 2.00e-02 2.50e+03
        pdb=" CZ  TYR B 236 "   -0.003 2.00e-02 2.50e+03
        pdb=" OH  TYR B 236 "    0.003 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR C 236 "   -0.005 2.00e-02 2.50e+03   2.79e-02 1.56e+01
        pdb=" CG  TYR C 236 "    0.056 2.00e-02 2.50e+03
        pdb=" CD1 TYR C 236 "   -0.046 2.00e-02 2.50e+03
        pdb=" CD2 TYR C 236 "   -0.024 2.00e-02 2.50e+03
        pdb=" CE1 TYR C 236 "    0.020 2.00e-02 2.50e+03
        pdb=" CE2 TYR C 236 "   -0.002 2.00e-02 2.50e+03
        pdb=" CZ  TYR C 236 "   -0.003 2.00e-02 2.50e+03
        pdb=" OH  TYR C 236 "    0.003 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR A 236 "   -0.005 2.00e-02 2.50e+03   2.79e-02 1.56e+01
        pdb=" CG  TYR A 236 "    0.056 2.00e-02 2.50e+03
        pdb=" CD1 TYR A 236 "   -0.046 2.00e-02 2.50e+03
        pdb=" CD2 TYR A 236 "   -0.023 2.00e-02 2.50e+03
        pdb=" CE1 TYR A 236 "    0.020 2.00e-02 2.50e+03
        pdb=" CE2 TYR A 236 "   -0.002 2.00e-02 2.50e+03
        pdb=" CZ  TYR A 236 "   -0.003 2.00e-02 2.50e+03
        pdb=" OH  TYR A 236 "    0.003 2.00e-02 2.50e+03
  ... (remaining 588 not shown)

  Histogram of nonbonded interaction distances:
        2.31 -     2.83: 883
        2.83 -     3.35: 2777
        3.35 -     3.86: 5897
        3.86 -     4.38: 6080
        4.38 -     4.90: 11940
  Nonbonded interactions: 27577
  Sorted by model distance:
  nonbonded pdb=" NZ  LYS A 129 "
            pdb=" OD2 ASP A 136 "
     model   vdw
     2.310 2.520
  nonbonded pdb=" NZ  LYS B 129 "
            pdb=" OD2 ASP B 136 "
     model   vdw
     2.311 2.520
  nonbonded pdb=" NZ  LYS C 129 "
            pdb=" OD2 ASP C 136 "
     model   vdw
     2.311 2.520
  nonbonded pdb=" OD1 ASN C 145 "
            pdb=" N2  NAG C 303 "
     model   vdw
     2.361 2.520
  nonbonded pdb=" OD1 ASN B 145 "
            pdb=" N2  NAG B 303 "
     model   vdw
     2.362 2.520
  ... (remaining 27572 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Found NCS groups:
ncs_group {
  reference = (chain 'A' and (resid 120 through 210 or resid 212 through 254 or resid 301 thro \ 
ugh 304))
  selection = (chain 'B' and (resid 120 through 210 or resid 212 through 254 or resid 301 thro \ 
ugh 304))
  selection = (chain 'C' and (resid 120 through 210 or resid 212 through 254 or resid 301 thro \ 
ugh 304))
}

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=0.50 max=1.00 mean=0.99
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.970
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          9.190
  Check model and map are aligned:         0.050
  Set scattering table:                    0.030
  Process input model:                     15.920
  Find NCS groups from input model:        0.200
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:12.460
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   39.850
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6573
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.072   3516  Z= 0.265
  Angle     :  0.622   4.668   4788  Z= 0.319
  Chirality :  0.056   0.188    606
  Planarity :  0.004   0.028    579
  Dihedral  : 16.836 122.352   1476
  Min Nonbonded Distance : 2.310

Molprobity Statistics.
  All-atom Clashscore : 8.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.77 %
    Favored  : 93.23 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.57 %
    Favored  : 98.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.67 (0.39), residues: 402
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.03 (0.30), residues: 402

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   HIS   0.007   0.002   HIS C 239 
   PHE   0.023   0.003   PHE B 237 
   TYR   0.056   0.003   TYR B 236 
   ARG   0.003   0.001   ARG B 247 

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

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

  804 Ramachandran restraints generated.
    402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  804 Ramachandran restraints generated.
    402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  60 residues out of total 375 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 60
  time to evaluate  : 0.380 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 60
  average time/residue: 1.0843
  time to fit residues: 67.2277
Evaluate side-chains
  47 residues out of total 375 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 47
  time to evaluate  : 0.367 
Switching outliers to nearest non-outliers
  outliers start: 0
  outliers final: 0
  residues processed: 0
  time to fit residues: 0.5137
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 32 optimal weight:    1.9990
   chunk 29 optimal weight:    3.9990
   chunk 16 optimal weight:    0.8980
   chunk 10 optimal weight:    7.9990
   chunk 19 optimal weight:    0.9990
   chunk 15 optimal weight:    5.9990
   chunk 30 optimal weight:    0.9990
   chunk 11 optimal weight:    4.9990
   chunk 18 optimal weight:    3.9990
   chunk 22 optimal weight:    9.9990
   chunk 35 optimal weight:    0.9980
   overall best weight:    1.1786

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6719
moved from start:          0.2079

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   3516  Z= 0.196
  Angle     :  0.580   7.120   4788  Z= 0.293
  Chirality :  0.056   0.321    606
  Planarity :  0.002   0.024    579
  Dihedral  : 14.626 109.661    711
  Min Nonbonded Distance : 2.328

Molprobity Statistics.
  All-atom Clashscore : 7.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.51 %
    Favored  : 94.49 %
  Rotamer:
    Outliers :  2.36 %
    Allowed  : 11.81 %
    Favored  : 85.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.52 (0.39), residues: 402
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.92 (0.30), residues: 402

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   HIS   0.005   0.001   HIS B 239 
   PHE   0.009   0.002   PHE A 237 
   TYR   0.013   0.001   TYR B 236 
   ARG   0.006   0.001   ARG B 247 

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

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

  804 Ramachandran restraints generated.
    402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  804 Ramachandran restraints generated.
    402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  58 residues out of total 375 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 9
    poor density    : 49
  time to evaluate  : 0.373 
Fit side-chains
  outliers start: 9
  outliers final: 3
  residues processed: 50
  average time/residue: 1.2401
  time to fit residues: 63.9407
Evaluate side-chains
  48 residues out of total 375 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 3
    poor density    : 45
  time to evaluate  : 0.346 
Switching outliers to nearest non-outliers
  outliers start: 3
  outliers final: 0
  residues processed: 3
  average time/residue: 0.0332
  time to fit residues: 0.6652
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 19 optimal weight:    3.9990
   chunk 10 optimal weight:    0.9980
   chunk 29 optimal weight:    7.9990
   chunk 24 optimal weight:    5.9990
   chunk 9 optimal weight:    5.9990
   chunk 35 optimal weight:    5.9990
   chunk 38 optimal weight:    2.9990
   chunk 31 optimal weight:    5.9990
   chunk 12 optimal weight:    0.9990
   chunk 28 optimal weight:    6.9990
   chunk 26 optimal weight:    1.9990
   overall best weight:    2.1988

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6837
moved from start:          0.3032

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.028   3516  Z= 0.311
  Angle     :  0.638   7.438   4788  Z= 0.323
  Chirality :  0.062   0.572    606
  Planarity :  0.003   0.027    579
  Dihedral  : 14.229 110.418    711
  Min Nonbonded Distance : 2.218

Molprobity Statistics.
  All-atom Clashscore : 7.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.77 %
    Favored  : 92.23 %
  Rotamer:
    Outliers :  2.62 %
    Allowed  : 11.55 %
    Favored  : 85.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.60 (0.38), residues: 402
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.97 (0.29), residues: 402

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   HIS   0.006   0.002   HIS C 239 
   PHE   0.009   0.002   PHE A 171 
   TYR   0.011   0.002   TYR A 143 
   ARG   0.007   0.001   ARG B 247 

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

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

  804 Ramachandran restraints generated.
    402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  804 Ramachandran restraints generated.
    402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  56 residues out of total 375 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 10
    poor density    : 46
  time to evaluate  : 0.394 
Fit side-chains
  outliers start: 10
  outliers final: 6
  residues processed: 49
  average time/residue: 1.2530
  time to fit residues: 63.2929
Evaluate side-chains
  47 residues out of total 375 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 6
    poor density    : 41
  time to evaluate  : 0.344 
Switching outliers to nearest non-outliers
  outliers start: 6
  outliers final: 2
  residues processed: 4
  average time/residue: 0.0320
  time to fit residues: 0.7293
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 18 optimal weight:    4.9990
   chunk 3 optimal weight:    3.9990
   chunk 16 optimal weight:    3.9990
   chunk 23 optimal weight:    1.9990
   chunk 35 optimal weight:    4.9990
   chunk 37 optimal weight:    0.9990
   chunk 33 optimal weight:    0.0970
   chunk 10 optimal weight:    2.9990
   chunk 31 optimal weight:    3.9990
   chunk 21 optimal weight:    5.9990
   chunk 0 optimal weight:    5.9990
   overall best weight:    2.0186

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6850
moved from start:          0.3429

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.024   3516  Z= 0.275
  Angle     :  0.613   8.529   4788  Z= 0.306
  Chirality :  0.059   0.442    606
  Planarity :  0.003   0.030    579
  Dihedral  : 13.333 104.277    711
  Min Nonbonded Distance : 2.221

Molprobity Statistics.
  All-atom Clashscore : 7.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.77 %
    Favored  : 93.23 %
  Rotamer:
    Outliers :  3.15 %
    Allowed  : 12.34 %
    Favored  : 84.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.53 (0.38), residues: 402
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.92 (0.29), residues: 402

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   HIS   0.005   0.001   HIS C 239 
   PHE   0.011   0.002   PHE B 237 
   TYR   0.011   0.001   TYR A 143 
   ARG   0.009   0.001   ARG C 247 

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

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

  804 Ramachandran restraints generated.
    402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  804 Ramachandran restraints generated.
    402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  50 residues out of total 375 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 12
    poor density    : 38
  time to evaluate  : 0.387 
Fit side-chains
  outliers start: 12
  outliers final: 5
  residues processed: 44
  average time/residue: 1.4993
  time to fit residues: 67.7545
Evaluate side-chains
  41 residues out of total 375 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 5
    poor density    : 36
  time to evaluate  : 0.377 
Switching outliers to nearest non-outliers
  outliers start: 5
  outliers final: 4
  residues processed: 1
  average time/residue: 0.0341
  time to fit residues: 0.5930
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 28 optimal weight:    4.9990
   chunk 15 optimal weight:    5.9990
   chunk 32 optimal weight:    1.9990
   chunk 26 optimal weight:    3.9990
   chunk 0 optimal weight:    6.9990
   chunk 19 optimal weight:    2.9990
   chunk 33 optimal weight:    1.9990
   chunk 9 optimal weight:    0.3980
   chunk 12 optimal weight:    0.0670
   chunk 7 optimal weight:    0.9990
   chunk 22 optimal weight:    6.9990
   overall best weight:    1.0924

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6823
moved from start:          0.3499

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   3516  Z= 0.167
  Angle     :  0.574   8.960   4788  Z= 0.282
  Chirality :  0.057   0.365    606
  Planarity :  0.002   0.035    579
  Dihedral  : 12.537 100.684    711
  Min Nonbonded Distance : 2.295

Molprobity Statistics.
  All-atom Clashscore : 6.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.52 %
    Favored  : 92.48 %
  Rotamer:
    Outliers :  2.62 %
    Allowed  : 14.17 %
    Favored  : 83.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.46 (0.39), residues: 402
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.86 (0.30), residues: 402

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   HIS   0.004   0.001   HIS C 239 
   PHE   0.012   0.001   PHE B 237 
   TYR   0.010   0.001   TYR C 236 
   ARG   0.008   0.001   ARG C 247 

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

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

  804 Ramachandran restraints generated.
    402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  804 Ramachandran restraints generated.
    402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  51 residues out of total 375 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 10
    poor density    : 41
  time to evaluate  : 0.406 
Fit side-chains
   revert: symmetry clash
  outliers start: 10
  outliers final: 6
  residues processed: 48
  average time/residue: 1.3714
  time to fit residues: 67.6558
Evaluate side-chains
  44 residues out of total 375 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 6
    poor density    : 38
  time to evaluate  : 0.354 
Switching outliers to nearest non-outliers
  outliers start: 6
  outliers final: 4
  residues processed: 2
  average time/residue: 0.0340
  time to fit residues: 0.6439
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 9 optimal weight:    3.9990
   chunk 37 optimal weight:    2.9990
   chunk 31 optimal weight:    3.9990
   chunk 17 optimal weight:    1.9990
   chunk 3 optimal weight:    2.9990
   chunk 12 optimal weight:    2.9990
   chunk 19 optimal weight:    1.9990
   chunk 36 optimal weight:    1.9990
   chunk 4 optimal weight:    4.9990
   chunk 21 optimal weight:    6.9990
   chunk 27 optimal weight:    8.9990
   overall best weight:    2.3990

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6881
moved from start:          0.3841

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.051   3516  Z= 0.327
  Angle     :  0.686  10.066   4788  Z= 0.335
  Chirality :  0.062   0.513    606
  Planarity :  0.003   0.030    579
  Dihedral  : 12.130  94.033    711
  Min Nonbonded Distance : 2.217

Molprobity Statistics.
  All-atom Clashscore : 8.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.03 %
    Favored  : 89.97 %
  Rotamer:
    Outliers :  2.89 %
    Allowed  : 14.96 %
    Favored  : 82.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.55 (0.38), residues: 402
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.94 (0.29), residues: 402

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   HIS   0.006   0.001   HIS C 239 
   PHE   0.009   0.002   PHE B 171 
   TYR   0.015   0.002   TYR C 143 
   ARG   0.008   0.001   ARG C 247 

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

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

  804 Ramachandran restraints generated.
    402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  804 Ramachandran restraints generated.
    402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  49 residues out of total 375 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 11
    poor density    : 38
  time to evaluate  : 0.449 
Fit side-chains
  outliers start: 11
  outliers final: 6
  residues processed: 46
  average time/residue: 1.4108
  time to fit residues: 66.7185
Evaluate side-chains
  43 residues out of total 375 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 6
    poor density    : 37
  time to evaluate  : 0.391 
Switching outliers to nearest non-outliers
  outliers start: 6
  outliers final: 4
  residues processed: 2
  average time/residue: 0.0337
  time to fit residues: 0.6560
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 21 optimal weight:    9.9990
   chunk 31 optimal weight:    6.9990
   chunk 37 optimal weight:    0.6980
   chunk 23 optimal weight:    2.9990
   chunk 22 optimal weight:    6.9990
   chunk 17 optimal weight:    6.9990
   chunk 15 optimal weight:    3.9990
   chunk 11 optimal weight:    2.9990
   chunk 7 optimal weight:    3.9990
   chunk 25 optimal weight:    3.9990
   chunk 18 optimal weight:    1.9990
   overall best weight:    2.5388

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6888
moved from start:          0.4045

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.052   3516  Z= 0.342
  Angle     :  0.704  10.980   4788  Z= 0.340
  Chirality :  0.060   0.485    606
  Planarity :  0.003   0.029    579
  Dihedral  : 10.797  80.761    711
  Min Nonbonded Distance : 2.225

Molprobity Statistics.
  All-atom Clashscore : 8.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.77 %
    Favored  : 91.23 %
  Rotamer:
    Outliers :  1.57 %
    Allowed  : 17.06 %
    Favored  : 81.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.61 (0.38), residues: 402
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.98 (0.29), residues: 402

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   HIS   0.005   0.001   HIS C 239 
   PHE   0.015   0.003   PHE A 237 
   TYR   0.012   0.002   TYR C 143 
   ARG   0.008   0.001   ARG B 247 

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

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

  804 Ramachandran restraints generated.
    402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  804 Ramachandran restraints generated.
    402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  47 residues out of total 375 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 6
    poor density    : 41
  time to evaluate  : 0.382 
Fit side-chains
  outliers start: 6
  outliers final: 6
  residues processed: 45
  average time/residue: 1.5653
  time to fit residues: 72.3276
Evaluate side-chains
  46 residues out of total 375 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 6
    poor density    : 40
  time to evaluate  : 0.353 
Switching outliers to nearest non-outliers
  outliers start: 6
  outliers final: 4
  residues processed: 2
  average time/residue: 0.0345
  time to fit residues: 0.6222
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 3 optimal weight:    2.9990
   chunk 29 optimal weight:    2.9990
   chunk 34 optimal weight:    0.9990
   chunk 36 optimal weight:    0.0370
   chunk 32 optimal weight:    3.9990
   chunk 35 optimal weight:    0.9980
   chunk 21 optimal weight:    0.6980
   chunk 15 optimal weight:    1.9990
   chunk 27 optimal weight:    3.9990
   chunk 10 optimal weight:    0.8980
   chunk 31 optimal weight:    5.9990
   overall best weight:    0.7260

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6823
moved from start:          0.3990

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030   3516  Z= 0.140
  Angle     :  0.605  10.440   4788  Z= 0.290
  Chirality :  0.054   0.303    606
  Planarity :  0.003   0.037    579
  Dihedral  :  8.959  70.403    711
  Min Nonbonded Distance : 2.314

Molprobity Statistics.
  All-atom Clashscore : 6.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.51 %
    Favored  : 94.49 %
  Rotamer:
    Outliers :  1.57 %
    Allowed  : 17.85 %
    Favored  : 80.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.53 (0.39), residues: 402
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.92 (0.30), residues: 402

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   HIS   0.004   0.001   HIS C 239 
   PHE   0.019   0.002   PHE A 237 
   TYR   0.010   0.001   TYR A 143 
   ARG   0.008   0.001   ARG C 247 

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

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

  804 Ramachandran restraints generated.
    402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  804 Ramachandran restraints generated.
    402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  47 residues out of total 375 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 6
    poor density    : 41
  time to evaluate  : 0.362 
Fit side-chains
   revert: symmetry clash
  outliers start: 6
  outliers final: 5
  residues processed: 45
  average time/residue: 1.4963
  time to fit residues: 69.2106
Evaluate side-chains
  44 residues out of total 375 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 5
    poor density    : 39
  time to evaluate  : 0.393 
Switching outliers to nearest non-outliers
  outliers start: 5
  outliers final: 4
  residues processed: 1
  average time/residue: 0.0298
  time to fit residues: 0.5481
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 33 optimal weight:    0.5980
   chunk 34 optimal weight:    4.9990
   chunk 23 optimal weight:    6.9990
   chunk 37 optimal weight:    0.9990
   chunk 22 optimal weight:    4.9990
   chunk 17 optimal weight:    5.9990
   chunk 25 optimal weight:    4.9990
   chunk 38 optimal weight:    4.9990
   chunk 35 optimal weight:    4.9990
   chunk 30 optimal weight:    0.8980
   chunk 3 optimal weight:    3.9990
   overall best weight:    2.2986

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6879
moved from start:          0.4136

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.066   3516  Z= 0.323
  Angle     :  0.688  10.180   4788  Z= 0.336
  Chirality :  0.059   0.474    606
  Planarity :  0.003   0.031    579
  Dihedral  :  8.262  51.461    711
  Min Nonbonded Distance : 2.237

Molprobity Statistics.
  All-atom Clashscore : 8.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.27 %
    Favored  : 90.73 %
  Rotamer:
    Outliers :  1.31 %
    Allowed  : 18.64 %
    Favored  : 80.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.59 (0.38), residues: 402
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.97 (0.29), residues: 402

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   HIS   0.006   0.002   HIS C 239 
   PHE   0.014   0.002   PHE A 237 
   TYR   0.012   0.002   TYR C 143 
   ARG   0.009   0.001   ARG C 247 

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

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

  804 Ramachandran restraints generated.
    402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  804 Ramachandran restraints generated.
    402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  45 residues out of total 375 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 5
    poor density    : 40
  time to evaluate  : 0.376 
Fit side-chains
  outliers start: 5
  outliers final: 5
  residues processed: 44
  average time/residue: 1.4209
  time to fit residues: 64.2743
Evaluate side-chains
  45 residues out of total 375 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 5
    poor density    : 40
  time to evaluate  : 0.298 
Switching outliers to nearest non-outliers
  outliers start: 5
  outliers final: 4
  residues processed: 1
  average time/residue: 0.0342
  time to fit residues: 0.5643
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 23 optimal weight:    2.9990
   chunk 18 optimal weight:    3.9990
   chunk 24 optimal weight:    0.9990
   chunk 32 optimal weight:    1.9990
   chunk 9 optimal weight:    3.9990
   chunk 28 optimal weight:    0.0470
   chunk 4 optimal weight:    4.9990
   chunk 8 optimal weight:    0.0470
   chunk 30 optimal weight:    0.5980
   chunk 12 optimal weight:    2.9990
   chunk 31 optimal weight:    2.9990
   overall best weight:    0.7380

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6831
moved from start:          0.4105

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.046   3516  Z= 0.155
  Angle     :  0.611   9.010   4788  Z= 0.300
  Chirality :  0.054   0.310    606
  Planarity :  0.003   0.035    579
  Dihedral  :  7.395  43.828    711
  Min Nonbonded Distance : 2.321

Molprobity Statistics.
  All-atom Clashscore : 7.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.26 %
    Favored  : 94.74 %
  Rotamer:
    Outliers :  1.31 %
    Allowed  : 18.64 %
    Favored  : 80.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.58 (0.38), residues: 402
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.96 (0.29), residues: 402

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   HIS   0.004   0.001   HIS C 239 
   PHE   0.018   0.002   PHE A 237 
   TYR   0.009   0.001   TYR C 143 
   ARG   0.009   0.001   ARG C 247 

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

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

  804 Ramachandran restraints generated.
    402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  804 Ramachandran restraints generated.
    402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  43 residues out of total 375 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 5
    poor density    : 38
  time to evaluate  : 0.389 
Fit side-chains
   revert: symmetry clash
  outliers start: 5
  outliers final: 4
  residues processed: 42
  average time/residue: 1.5251
  time to fit residues: 65.8161
Evaluate side-chains
  42 residues out of total 375 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 4
    poor density    : 38
  time to evaluate  : 0.367 
Switching outliers to nearest non-outliers
  outliers start: 4
  outliers final: 4
  residues processed: 0
  time to fit residues: 0.4713
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 3 optimal weight:    0.9980
   chunk 5 optimal weight:    3.9990
   chunk 27 optimal weight:    5.9990
   chunk 1 optimal weight:    6.9990
   chunk 22 optimal weight:    1.9990
   chunk 35 optimal weight:    6.9990
   chunk 20 optimal weight:    0.8980
   chunk 26 optimal weight:    0.3980
   chunk 24 optimal weight:    0.7980
   chunk 23 optimal weight:    0.6980
   chunk 15 optimal weight:    0.9990
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
C 249 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4385 r_free = 0.4385 target = 0.133318 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.4129 r_free = 0.4129 target = 0.112854 restraints weight = 10726.481|
|-----------------------------------------------------------------------------|
r_work (start): 0.4134 rms_B_bonded: 4.21
r_work: 0.3952 rms_B_bonded: 4.09 restraints_weight: 0.5000
r_work (final): 0.3952
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3994
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3994 r_free = 0.3994    target_work(ls_wunit_k1) = 0.101         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3994 r_free = 0.3994    target_work(ls_wunit_k1) = 0.101         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3994
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7675
moved from start:          0.4047

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.048   3516  Z= 0.155
  Angle     :  0.583   6.841   4788  Z= 0.294
  Chirality :  0.054   0.327    606
  Planarity :  0.003   0.035    579
  Dihedral  :  6.608  34.497    711
  Min Nonbonded Distance : 2.312

Molprobity Statistics.
  All-atom Clashscore : 6.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.52 %
    Favored  : 93.48 %
  Rotamer:
    Outliers :  1.05 %
    Allowed  : 18.90 %
    Favored  : 80.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.51 (0.39), residues: 402
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.90 (0.30), residues: 402

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   HIS   0.004   0.001   HIS C 239 
   PHE   0.018   0.002   PHE A 237 
   TYR   0.010   0.001   TYR C 143 
   ARG   0.009   0.001   ARG C 247 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1872.23 seconds
wall clock time: 34 minutes 53.91 seconds (2093.91 seconds total)