Starting phenix.real_space_refine
on Mon Jul 28 23:12:33 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7u5m_26355/07_2025/7u5m_26355.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7u5m_26355/07_2025/7u5m_26355.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.28
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7u5m_26355/07_2025/7u5m_26355.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7u5m_26355/07_2025/7u5m_26355.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7u5m_26355/07_2025/7u5m_26355.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7u5m_26355/07_2025/7u5m_26355.cif"
  }
  resolution = 2.28
  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=   0.108
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
     P       8      5.49       5
     S      52      5.16       5
     C    6448      2.51       5
     N    1772      2.21       5
     O    2347      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 10627
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 2513
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 332, 2513
          Classifications: {'peptide': 332}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 12, 'TRANS': 319}
    Chain: "A"
      Number of atoms: 44
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 44
          Unusual residues: {'NAD': 1}
          Classifications: {'undetermined': 1}
    Chain: "A"
      Number of atoms: 101
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 101, 101
          Classifications: {'water': 101}
          Link IDs: {None: 100}
    Chain: "B"
      Number of atoms: 99
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 99, 99
          Classifications: {'water': 99}
          Link IDs: {None: 98}
    Chain: "C"
      Number of atoms: 99
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 99, 99
          Classifications: {'water': 99}
          Link IDs: {None: 98}
    Chain: "D"
      Number of atoms: 100
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 100, 100
          Classifications: {'water': 100}
          Link IDs: {None: 99}
  Restraints were copied for chains:
    C, B, D
  Time building chain proxies: 5.95, per 1000 atoms: 0.56
  Number of scatterers: 10627
  At special positions: 0
  Unit cell: (99.51, 93.09, 82.39, 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)
     S      52     16.00
     P       8     15.00
     O    2347      8.00
     N    1772      7.00
     C    6448      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.54
  Conformation dependent library (CDL) restraints added in 1.3 seconds
  

  2640 Ramachandran restraints generated.
    1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2400

  Finding SS restraints...
    Secondary structure from input PDB file:
      52 helices and 8 sheets defined
      39.2% alpha, 23.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.37
  Creating SS restraints...
    Processing helix  chain 'A' and resid 10 through 24
    Processing helix  chain 'A' and resid 37 through 47
    Processing helix  chain 'A' and resid 79 through 83
    Processing helix  chain 'A' and resid 84 through 89
    Processing helix  chain 'A' and resid 102 through 112
      removed outlier: 3.817A  pdb=" N   ALA A 108 " --> pdb=" O   GLU A 104 " (cutoff:3.500A)
      removed outlier: 4.665A  pdb=" N   HIS A 109 " --> pdb=" O   LYS A 105 " (cutoff:3.500A)
      removed outlier: 3.979A  pdb=" N   LEU A 110 " --> pdb=" O   ALA A 106 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 134 through 138
    Processing helix  chain 'A' and resid 149 through 166
      Proline residue:  A 157  - end of helix
    Processing helix  chain 'A' and resid 193 through 198
    Processing helix  chain 'A' and resid 210 through 219
      removed outlier: 3.923A  pdb=" N   GLY A 216 " --> pdb=" O   ALA A 212 " (cutoff:3.500A)
      removed outlier: 3.876A  pdb=" N   LYS A 217 " --> pdb=" O   LYS A 213 " (cutoff:3.500A)
      removed outlier: 3.566A  pdb=" N   VAL A 218 " --> pdb=" O   ALA A 214 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 220 through 223
    Processing helix  chain 'A' and resid 252 through 266
    Processing helix  chain 'A' and resid 280 through 285
    Processing helix  chain 'A' and resid 315 through 332
    Processing helix  chain 'B' and resid 10 through 24
    Processing helix  chain 'B' and resid 37 through 47
    Processing helix  chain 'B' and resid 79 through 83
    Processing helix  chain 'B' and resid 84 through 89
    Processing helix  chain 'B' and resid 102 through 112
      removed outlier: 3.816A  pdb=" N   ALA B 108 " --> pdb=" O   GLU B 104 " (cutoff:3.500A)
      removed outlier: 4.665A  pdb=" N   HIS B 109 " --> pdb=" O   LYS B 105 " (cutoff:3.500A)
      removed outlier: 3.979A  pdb=" N   LEU B 110 " --> pdb=" O   ALA B 106 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 134 through 138
    Processing helix  chain 'B' and resid 149 through 166
      Proline residue:  B 157  - end of helix
    Processing helix  chain 'B' and resid 193 through 198
    Processing helix  chain 'B' and resid 210 through 219
      removed outlier: 3.923A  pdb=" N   GLY B 216 " --> pdb=" O   ALA B 212 " (cutoff:3.500A)
      removed outlier: 3.876A  pdb=" N   LYS B 217 " --> pdb=" O   LYS B 213 " (cutoff:3.500A)
      removed outlier: 3.566A  pdb=" N   VAL B 218 " --> pdb=" O   ALA B 214 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 220 through 223
    Processing helix  chain 'B' and resid 252 through 266
    Processing helix  chain 'B' and resid 280 through 285
    Processing helix  chain 'B' and resid 315 through 332
    Processing helix  chain 'C' and resid 10 through 24
    Processing helix  chain 'C' and resid 37 through 47
    Processing helix  chain 'C' and resid 79 through 83
    Processing helix  chain 'C' and resid 84 through 89
    Processing helix  chain 'C' and resid 102 through 112
      removed outlier: 3.817A  pdb=" N   ALA C 108 " --> pdb=" O   GLU C 104 " (cutoff:3.500A)
      removed outlier: 4.665A  pdb=" N   HIS C 109 " --> pdb=" O   LYS C 105 " (cutoff:3.500A)
      removed outlier: 3.979A  pdb=" N   LEU C 110 " --> pdb=" O   ALA C 106 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 134 through 138
    Processing helix  chain 'C' and resid 149 through 166
      Proline residue:  C 157  - end of helix
    Processing helix  chain 'C' and resid 193 through 198
    Processing helix  chain 'C' and resid 210 through 219
      removed outlier: 3.923A  pdb=" N   GLY C 216 " --> pdb=" O   ALA C 212 " (cutoff:3.500A)
      removed outlier: 3.876A  pdb=" N   LYS C 217 " --> pdb=" O   LYS C 213 " (cutoff:3.500A)
      removed outlier: 3.566A  pdb=" N   VAL C 218 " --> pdb=" O   ALA C 214 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 220 through 223
    Processing helix  chain 'C' and resid 252 through 266
    Processing helix  chain 'C' and resid 280 through 285
    Processing helix  chain 'C' and resid 315 through 332
    Processing helix  chain 'D' and resid 10 through 24
    Processing helix  chain 'D' and resid 37 through 47
    Processing helix  chain 'D' and resid 79 through 83
    Processing helix  chain 'D' and resid 84 through 89
    Processing helix  chain 'D' and resid 102 through 112
      removed outlier: 3.817A  pdb=" N   ALA D 108 " --> pdb=" O   GLU D 104 " (cutoff:3.500A)
      removed outlier: 4.664A  pdb=" N   HIS D 109 " --> pdb=" O   LYS D 105 " (cutoff:3.500A)
      removed outlier: 3.978A  pdb=" N   LEU D 110 " --> pdb=" O   ALA D 106 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 134 through 138
    Processing helix  chain 'D' and resid 149 through 166
      Proline residue:  D 157  - end of helix
    Processing helix  chain 'D' and resid 193 through 198
    Processing helix  chain 'D' and resid 210 through 219
      removed outlier: 3.923A  pdb=" N   GLY D 216 " --> pdb=" O   ALA D 212 " (cutoff:3.500A)
      removed outlier: 3.876A  pdb=" N   LYS D 217 " --> pdb=" O   LYS D 213 " (cutoff:3.500A)
      removed outlier: 3.566A  pdb=" N   VAL D 218 " --> pdb=" O   ALA D 214 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 220 through 223
    Processing helix  chain 'D' and resid 252 through 266
    Processing helix  chain 'D' and resid 280 through 285
    Processing helix  chain 'D' and resid 315 through 332
    Processing sheet with id=AA1, first strand: chain 'A' and resid 58 through 61
      removed outlier: 10.194A  pdb=" N   ASP A  27 " --> pdb=" O   ALA A  71 " (cutoff:3.500A)
      removed outlier: 9.589A  pdb=" N   THR A  73 " --> pdb=" O   ASP A  27 " (cutoff:3.500A)
      removed outlier: 6.680A  pdb=" N   VAL A  29 " --> pdb=" O   THR A  73 " (cutoff:3.500A)
      removed outlier: 7.915A  pdb=" N   PHE A  75 " --> pdb=" O   VAL A  29 " (cutoff:3.500A)
      removed outlier: 6.406A  pdb=" N   ILE A  31 " --> pdb=" O   PHE A  75 " (cutoff:3.500A)
      removed outlier: 7.443A  pdb=" N   VAL A   6 " --> pdb=" O   VAL A  29 " (cutoff:3.500A)
      removed outlier: 4.291A  pdb=" N   ILE A  31 " --> pdb=" O   VAL A   6 " (cutoff:3.500A)
      removed outlier: 6.156A  pdb=" N   VAL A  93 " --> pdb=" O   ILE A 118 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 205 through 208
      removed outlier: 9.303A  pdb=" N   THR A 227 " --> pdb=" O   VAL A 169 " (cutoff:3.500A)
      removed outlier: 6.515A  pdb=" N   GLY A 171 " --> pdb=" O   THR A 227 " (cutoff:3.500A)
      removed outlier: 8.601A  pdb=" N   MET A 229 " --> pdb=" O   GLY A 171 " (cutoff:3.500A)
      removed outlier: 6.220A  pdb=" N   MET A 173 " --> pdb=" O   MET A 229 " (cutoff:3.500A)
      removed outlier: 7.809A  pdb=" N   PHE A 231 " --> pdb=" O   MET A 173 " (cutoff:3.500A)
      removed outlier: 6.395A  pdb=" N   THR A 175 " --> pdb=" O   PHE A 231 " (cutoff:3.500A)
      removed outlier: 3.646A  pdb=" N   GLU A 170 " --> pdb=" O   ARG A 246 " (cutoff:3.500A)
      removed outlier: 6.817A  pdb=" N   PHE A 305 " --> pdb=" O   LEU A 301 " (cutoff:3.500A)
      removed outlier: 6.401A  pdb=" N   ILE A 309 " --> pdb=" O   ALA A 297 " (cutoff:3.500A)
      removed outlier: 6.839A  pdb=" N   ALA A 297 " --> pdb=" O   ILE A 309 " (cutoff:3.500A)
      removed outlier: 10.841A  pdb=" N   TRP A 311 " --> pdb=" O   ALA A 295 " (cutoff:3.500A)
      removed outlier: 10.293A  pdb=" N   ALA A 295 " --> pdb=" O   TRP A 311 " (cutoff:3.500A)
      removed outlier: 11.812A  pdb=" N   ASP A 313 " --> pdb=" O   PHE A 293 " (cutoff:3.500A)
      removed outlier: 12.302A  pdb=" N   PHE A 293 " --> pdb=" O   ASP A 313 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 61
      removed outlier: 10.194A  pdb=" N   ASP B  27 " --> pdb=" O   ALA B  71 " (cutoff:3.500A)
      removed outlier: 9.589A  pdb=" N   THR B  73 " --> pdb=" O   ASP B  27 " (cutoff:3.500A)
      removed outlier: 6.680A  pdb=" N   VAL B  29 " --> pdb=" O   THR B  73 " (cutoff:3.500A)
      removed outlier: 7.915A  pdb=" N   PHE B  75 " --> pdb=" O   VAL B  29 " (cutoff:3.500A)
      removed outlier: 6.406A  pdb=" N   ILE B  31 " --> pdb=" O   PHE B  75 " (cutoff:3.500A)
      removed outlier: 7.443A  pdb=" N   VAL B   6 " --> pdb=" O   VAL B  29 " (cutoff:3.500A)
      removed outlier: 4.291A  pdb=" N   ILE B  31 " --> pdb=" O   VAL B   6 " (cutoff:3.500A)
      removed outlier: 6.156A  pdb=" N   VAL B  93 " --> pdb=" O   ILE B 118 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 205 through 208
      removed outlier: 9.303A  pdb=" N   THR B 227 " --> pdb=" O   VAL B 169 " (cutoff:3.500A)
      removed outlier: 6.515A  pdb=" N   GLY B 171 " --> pdb=" O   THR B 227 " (cutoff:3.500A)
      removed outlier: 8.601A  pdb=" N   MET B 229 " --> pdb=" O   GLY B 171 " (cutoff:3.500A)
      removed outlier: 6.220A  pdb=" N   MET B 173 " --> pdb=" O   MET B 229 " (cutoff:3.500A)
      removed outlier: 7.810A  pdb=" N   PHE B 231 " --> pdb=" O   MET B 173 " (cutoff:3.500A)
      removed outlier: 6.396A  pdb=" N   THR B 175 " --> pdb=" O   PHE B 231 " (cutoff:3.500A)
      removed outlier: 3.646A  pdb=" N   GLU B 170 " --> pdb=" O   ARG B 246 " (cutoff:3.500A)
      removed outlier: 6.817A  pdb=" N   PHE B 305 " --> pdb=" O   LEU B 301 " (cutoff:3.500A)
      removed outlier: 6.401A  pdb=" N   ILE B 309 " --> pdb=" O   ALA B 297 " (cutoff:3.500A)
      removed outlier: 6.840A  pdb=" N   ALA B 297 " --> pdb=" O   ILE B 309 " (cutoff:3.500A)
      removed outlier: 10.840A  pdb=" N   TRP B 311 " --> pdb=" O   ALA B 295 " (cutoff:3.500A)
      removed outlier: 10.292A  pdb=" N   ALA B 295 " --> pdb=" O   TRP B 311 " (cutoff:3.500A)
      removed outlier: 11.812A  pdb=" N   ASP B 313 " --> pdb=" O   PHE B 293 " (cutoff:3.500A)
      removed outlier: 12.302A  pdb=" N   PHE B 293 " --> pdb=" O   ASP B 313 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'C' and resid 58 through 61
      removed outlier: 10.195A  pdb=" N   ASP C  27 " --> pdb=" O   ALA C  71 " (cutoff:3.500A)
      removed outlier: 9.589A  pdb=" N   THR C  73 " --> pdb=" O   ASP C  27 " (cutoff:3.500A)
      removed outlier: 6.680A  pdb=" N   VAL C  29 " --> pdb=" O   THR C  73 " (cutoff:3.500A)
      removed outlier: 7.915A  pdb=" N   PHE C  75 " --> pdb=" O   VAL C  29 " (cutoff:3.500A)
      removed outlier: 6.406A  pdb=" N   ILE C  31 " --> pdb=" O   PHE C  75 " (cutoff:3.500A)
      removed outlier: 7.443A  pdb=" N   VAL C   6 " --> pdb=" O   VAL C  29 " (cutoff:3.500A)
      removed outlier: 4.291A  pdb=" N   ILE C  31 " --> pdb=" O   VAL C   6 " (cutoff:3.500A)
      removed outlier: 6.156A  pdb=" N   VAL C  93 " --> pdb=" O   ILE C 118 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'C' and resid 205 through 208
      removed outlier: 9.303A  pdb=" N   THR C 227 " --> pdb=" O   VAL C 169 " (cutoff:3.500A)
      removed outlier: 6.515A  pdb=" N   GLY C 171 " --> pdb=" O   THR C 227 " (cutoff:3.500A)
      removed outlier: 8.601A  pdb=" N   MET C 229 " --> pdb=" O   GLY C 171 " (cutoff:3.500A)
      removed outlier: 6.220A  pdb=" N   MET C 173 " --> pdb=" O   MET C 229 " (cutoff:3.500A)
      removed outlier: 7.809A  pdb=" N   PHE C 231 " --> pdb=" O   MET C 173 " (cutoff:3.500A)
      removed outlier: 6.395A  pdb=" N   THR C 175 " --> pdb=" O   PHE C 231 " (cutoff:3.500A)
      removed outlier: 3.646A  pdb=" N   GLU C 170 " --> pdb=" O   ARG C 246 " (cutoff:3.500A)
      removed outlier: 6.817A  pdb=" N   PHE C 305 " --> pdb=" O   LEU C 301 " (cutoff:3.500A)
      removed outlier: 6.400A  pdb=" N   ILE C 309 " --> pdb=" O   ALA C 297 " (cutoff:3.500A)
      removed outlier: 6.839A  pdb=" N   ALA C 297 " --> pdb=" O   ILE C 309 " (cutoff:3.500A)
      removed outlier: 10.841A  pdb=" N   TRP C 311 " --> pdb=" O   ALA C 295 " (cutoff:3.500A)
      removed outlier: 10.293A  pdb=" N   ALA C 295 " --> pdb=" O   TRP C 311 " (cutoff:3.500A)
      removed outlier: 11.812A  pdb=" N   ASP C 313 " --> pdb=" O   PHE C 293 " (cutoff:3.500A)
      removed outlier: 12.302A  pdb=" N   PHE C 293 " --> pdb=" O   ASP C 313 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'D' and resid 58 through 61
      removed outlier: 10.194A  pdb=" N   ASP D  27 " --> pdb=" O   ALA D  71 " (cutoff:3.500A)
      removed outlier: 9.588A  pdb=" N   THR D  73 " --> pdb=" O   ASP D  27 " (cutoff:3.500A)
      removed outlier: 6.679A  pdb=" N   VAL D  29 " --> pdb=" O   THR D  73 " (cutoff:3.500A)
      removed outlier: 7.914A  pdb=" N   PHE D  75 " --> pdb=" O   VAL D  29 " (cutoff:3.500A)
      removed outlier: 6.406A  pdb=" N   ILE D  31 " --> pdb=" O   PHE D  75 " (cutoff:3.500A)
      removed outlier: 7.443A  pdb=" N   VAL D   6 " --> pdb=" O   VAL D  29 " (cutoff:3.500A)
      removed outlier: 4.291A  pdb=" N   ILE D  31 " --> pdb=" O   VAL D   6 " (cutoff:3.500A)
      removed outlier: 6.156A  pdb=" N   VAL D  93 " --> pdb=" O   ILE D 118 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'D' and resid 205 through 208
      removed outlier: 9.303A  pdb=" N   THR D 227 " --> pdb=" O   VAL D 169 " (cutoff:3.500A)
      removed outlier: 6.515A  pdb=" N   GLY D 171 " --> pdb=" O   THR D 227 " (cutoff:3.500A)
      removed outlier: 8.601A  pdb=" N   MET D 229 " --> pdb=" O   GLY D 171 " (cutoff:3.500A)
      removed outlier: 6.220A  pdb=" N   MET D 173 " --> pdb=" O   MET D 229 " (cutoff:3.500A)
      removed outlier: 7.809A  pdb=" N   PHE D 231 " --> pdb=" O   MET D 173 " (cutoff:3.500A)
      removed outlier: 6.395A  pdb=" N   THR D 175 " --> pdb=" O   PHE D 231 " (cutoff:3.500A)
      removed outlier: 3.646A  pdb=" N   GLU D 170 " --> pdb=" O   ARG D 246 " (cutoff:3.500A)
      removed outlier: 6.817A  pdb=" N   PHE D 305 " --> pdb=" O   LEU D 301 " (cutoff:3.500A)
      removed outlier: 6.400A  pdb=" N   ILE D 309 " --> pdb=" O   ALA D 297 " (cutoff:3.500A)
      removed outlier: 6.839A  pdb=" N   ALA D 297 " --> pdb=" O   ILE D 309 " (cutoff:3.500A)
      removed outlier: 10.841A  pdb=" N   TRP D 311 " --> pdb=" O   ALA D 295 " (cutoff:3.500A)
      removed outlier: 10.293A  pdb=" N   ALA D 295 " --> pdb=" O   TRP D 311 " (cutoff:3.500A)
      removed outlier: 11.812A  pdb=" N   ASP D 313 " --> pdb=" O   PHE D 293 " (cutoff:3.500A)
      removed outlier: 12.302A  pdb=" N   PHE D 293 " --> pdb=" O   ASP D 313 " (cutoff:3.500A)

    464 hydrogen bonds defined for protein.
    1212 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: 3.25

  Time building geometry restraints manager: 3.00 seconds

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

  Histogram of bond lengths:
        1.17 -     1.30: 1708
        1.30 -     1.43: 2633
        1.43 -     1.56: 5971
        1.56 -     1.69: 36
        1.69 -     1.82: 96
  Bond restraints: 10444
  Sorted by residual:
  bond pdb=" O5D NAD B 401 "
       pdb=" PN  NAD B 401 "
    ideal  model  delta    sigma   weight residual
    1.637  1.773 -0.136 2.00e-02 2.50e+03 4.60e+01
  bond pdb=" O5D NAD A 401 "
       pdb=" PN  NAD A 401 "
    ideal  model  delta    sigma   weight residual
    1.637  1.773 -0.136 2.00e-02 2.50e+03 4.60e+01
  bond pdb=" O5D NAD C 401 "
       pdb=" PN  NAD C 401 "
    ideal  model  delta    sigma   weight residual
    1.637  1.773 -0.136 2.00e-02 2.50e+03 4.60e+01
  bond pdb=" O5D NAD D 401 "
       pdb=" PN  NAD D 401 "
    ideal  model  delta    sigma   weight residual
    1.637  1.773 -0.136 2.00e-02 2.50e+03 4.60e+01
  bond pdb=" O5B NAD C 401 "
       pdb=" PA  NAD C 401 "
    ideal  model  delta    sigma   weight residual
    1.638  1.766 -0.128 2.00e-02 2.50e+03 4.08e+01
  ... (remaining 10439 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.56: 14004
        3.56 -     7.12: 128
        7.12 -    10.68: 28
       10.68 -    14.24: 8
       14.24 -    17.80: 8
  Bond angle restraints: 14176
  Sorted by residual:
  angle pdb=" N   ASN A 203 "
        pdb=" CA  ASN A 203 "
        pdb=" C   ASN A 203 "
      ideal   model   delta    sigma   weight residual
     109.50  127.30  -17.80 1.58e+00 4.01e-01 1.27e+02
  angle pdb=" N   ASN C 203 "
        pdb=" CA  ASN C 203 "
        pdb=" C   ASN C 203 "
      ideal   model   delta    sigma   weight residual
     109.50  127.30  -17.80 1.58e+00 4.01e-01 1.27e+02
  angle pdb=" N   ASN D 203 "
        pdb=" CA  ASN D 203 "
        pdb=" C   ASN D 203 "
      ideal   model   delta    sigma   weight residual
     109.50  127.30  -17.80 1.58e+00 4.01e-01 1.27e+02
  angle pdb=" N   ASN B 203 "
        pdb=" CA  ASN B 203 "
        pdb=" C   ASN B 203 "
      ideal   model   delta    sigma   weight residual
     109.50  127.28  -17.78 1.58e+00 4.01e-01 1.27e+02
  angle pdb=" N   GLN B 202 "
        pdb=" CA  GLN B 202 "
        pdb=" C   GLN B 202 "
      ideal   model   delta    sigma   weight residual
     111.82  119.98   -8.16 1.16e+00 7.43e-01 4.94e+01
  ... (remaining 14171 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.44: 5848
       17.44 -    34.89: 308
       34.89 -    52.33: 100
       52.33 -    69.77: 28
       69.77 -    87.21: 24
  Dihedral angle restraints: 6308
    sinusoidal: 2548
      harmonic: 3760
  Sorted by residual:
  dihedral pdb=" CA  ASN A 237 "
           pdb=" C   ASN A 237 "
           pdb=" N   VAL A 238 "
           pdb=" CA  VAL A 238 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -160.85  -19.15     0      5.00e+00 4.00e-02 1.47e+01
  dihedral pdb=" CA  ASN D 237 "
           pdb=" C   ASN D 237 "
           pdb=" N   VAL D 238 "
           pdb=" CA  VAL D 238 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -160.85  -19.15     0      5.00e+00 4.00e-02 1.47e+01
  dihedral pdb=" CA  ASN C 237 "
           pdb=" C   ASN C 237 "
           pdb=" N   VAL C 238 "
           pdb=" CA  VAL C 238 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -160.85  -19.15     0      5.00e+00 4.00e-02 1.47e+01
  ... (remaining 6305 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.082: 1392
       0.082 -    0.164: 176
       0.164 -    0.246: 16
       0.246 -    0.328: 20
       0.328 -    0.410: 8
  Chirality restraints: 1612
  Sorted by residual:
  chirality pdb=" C2D NAD B 401 "
            pdb=" C1D NAD B 401 "
            pdb=" C3D NAD B 401 "
            pdb=" O2D NAD B 401 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.56   -2.97    0.41 2.00e-01 2.50e+01 4.21e+00
  chirality pdb=" C2D NAD D 401 "
            pdb=" C1D NAD D 401 "
            pdb=" C3D NAD D 401 "
            pdb=" O2D NAD D 401 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.56   -2.97    0.41 2.00e-01 2.50e+01 4.21e+00
  chirality pdb=" C2D NAD C 401 "
            pdb=" C1D NAD C 401 "
            pdb=" C3D NAD C 401 "
            pdb=" O2D NAD C 401 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.56   -2.97    0.41 2.00e-01 2.50e+01 4.21e+00
  ... (remaining 1609 not shown)

  Planarity restraints: 1804
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASP C 196 "    0.014 2.00e-02 2.50e+03   2.83e-02 7.98e+00
        pdb=" C   ASP C 196 "   -0.049 2.00e-02 2.50e+03
        pdb=" O   ASP C 196 "    0.018 2.00e-02 2.50e+03
        pdb=" N   GLY C 197 "    0.017 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASP B 196 "   -0.014 2.00e-02 2.50e+03   2.82e-02 7.97e+00
        pdb=" C   ASP B 196 "    0.049 2.00e-02 2.50e+03
        pdb=" O   ASP B 196 "   -0.018 2.00e-02 2.50e+03
        pdb=" N   GLY B 197 "   -0.017 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASP D 196 "   -0.014 2.00e-02 2.50e+03   2.82e-02 7.97e+00
        pdb=" C   ASP D 196 "    0.049 2.00e-02 2.50e+03
        pdb=" O   ASP D 196 "   -0.018 2.00e-02 2.50e+03
        pdb=" N   GLY D 197 "   -0.017 2.00e-02 2.50e+03
  ... (remaining 1801 not shown)

  Histogram of nonbonded interaction distances:
        2.30 -     2.82: 3183
        2.82 -     3.34: 10416
        3.34 -     3.86: 21685
        3.86 -     4.38: 24737
        4.38 -     4.90: 39436
  Nonbonded interactions: 99457
  Sorted by model distance:
  nonbonded pdb=" O   TRP D 194 "
            pdb=" O   HOH D 501 "
     model   vdw
     2.296 3.040
  nonbonded pdb=" O1N NAD D 401 "
            pdb=" O   HOH D 502 "
     model   vdw
     2.297 3.040
  nonbonded pdb=" O   TRP C 194 "
            pdb=" O   HOH C 501 "
     model   vdw
     2.301 3.040
  nonbonded pdb=" O   TRP A 194 "
            pdb=" O   HOH A 501 "
     model   vdw
     2.301 3.040
  nonbonded pdb=" O   ASP B 294 "
            pdb=" O   HOH B 501 "
     model   vdw
     2.310 3.040
  ... (remaining 99452 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: 0.07
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'C'
  selection = chain 'B'
  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 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:             1.470
  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:          0.410
  Check model and map are aligned:         0.080
  Set scattering table:                    0.090
  Process input model:                     26.270
  Find NCS groups from input model:        0.220
  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:12.730
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   41.310
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8081
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      :  0.008   0.136  10444  Z= 0.457
  Angle     :  0.961  17.802  14176  Z= 0.511
  Chirality :  0.068   0.410   1612
  Planarity :  0.005   0.039   1804
  Dihedral  : 14.032  87.213   3908
  Min Nonbonded Distance : 2.296

Molprobity Statistics.
  All-atom Clashscore : 4.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.64 %
    Favored  : 96.36 %
  Rotamer:
    Outliers :  1.87 %
    Allowed  :  5.60 %
    Favored  : 92.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.13 (0.23), residues: 1320
  helix:  0.98 (0.26), residues: 392
  sheet: -0.92 (0.31), residues: 264
  loop : -0.27 (0.25), residues: 664

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP D 194 
 HIS   0.004   0.001   HIS B  51 
 PHE   0.020   0.002   PHE D 231 
 TYR   0.014   0.002   TYR C 318 
 ARG   0.005   0.001   ARG D 232 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.16727 (  464)
  hydrogen bonds       : angle       7.18341 ( 1212)
  covalent geometry    : bond        0.00802 (10444)
  covalent geometry    : angle       0.96135 (14176)

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

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

  2640 Ramachandran restraints generated.
    1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2640 Ramachandran restraints generated.
    1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  228 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 208
  time to evaluate  : 1.199 
Fit side-chains
REVERT: A   41 MET cc_start: 0.8276 (mtp) cc_final: 0.7962 (mtp)
REVERT: A  103 MET cc_start: 0.7867 (mmm) cc_final: 0.7537 (mmm)
REVERT: A  131 MET cc_start: 0.8693 (mmm) cc_final: 0.8409 (mmm)
REVERT: A  170 GLU cc_start: 0.8668 (pt0) cc_final: 0.8182 (pt0)
REVERT: B   41 MET cc_start: 0.8277 (mtp) cc_final: 0.7964 (mtp)
REVERT: B  103 MET cc_start: 0.7877 (mmm) cc_final: 0.7559 (mmm)
REVERT: B  131 MET cc_start: 0.8687 (mmm) cc_final: 0.8400 (mmm)
REVERT: B  170 GLU cc_start: 0.8656 (pt0) cc_final: 0.8166 (pt0)
REVERT: C   41 MET cc_start: 0.8267 (mtp) cc_final: 0.7953 (mtp)
REVERT: C  103 MET cc_start: 0.7858 (mmm) cc_final: 0.7522 (mmm)
REVERT: C  131 MET cc_start: 0.8691 (mmm) cc_final: 0.8402 (mmm)
REVERT: C  170 GLU cc_start: 0.8656 (pt0) cc_final: 0.8176 (pt0)
REVERT: D   41 MET cc_start: 0.8275 (mtp) cc_final: 0.7961 (mtp)
REVERT: D  103 MET cc_start: 0.7872 (mmm) cc_final: 0.7528 (mmm)
REVERT: D  131 MET cc_start: 0.8693 (mmm) cc_final: 0.8410 (mmm)
REVERT: D  170 GLU cc_start: 0.8654 (pt0) cc_final: 0.8180 (pt0)
  outliers start: 20
  outliers final: 12
  residues processed: 224
  average time/residue: 1.4248
  time to fit residues: 340.4147
Evaluate side-chains
  204 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 192
  time to evaluate  : 1.440 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 VAL
Chi-restraints excluded: chain A residue  175 THR
Chi-restraints excluded: chain A residue  316 PHE
Chi-restraints excluded: chain B residue   58 VAL
Chi-restraints excluded: chain B residue  175 THR
Chi-restraints excluded: chain B residue  316 PHE
Chi-restraints excluded: chain C residue   58 VAL
Chi-restraints excluded: chain C residue  175 THR
Chi-restraints excluded: chain C residue  316 PHE
Chi-restraints excluded: chain D residue   58 VAL
Chi-restraints excluded: chain D residue  175 THR
Chi-restraints excluded: chain D residue  316 PHE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 111 optimal weight:    0.7980
   chunk 100 optimal weight:    0.8980
   chunk 55 optimal weight:    3.9990
   chunk 34 optimal weight:    0.6980
   chunk 67 optimal weight:    0.8980
   chunk 53 optimal weight:    3.9990
   chunk 103 optimal weight:    2.9990
   chunk 40 optimal weight:    6.9990
   chunk 62 optimal weight:    1.9990
   chunk 77 optimal weight:    2.9990
   chunk 119 optimal weight:    1.9990
   overall best weight:    1.0582

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

Flipped N/Q/H residues before XYZ refinement:
A  22 ASN
A  55 ASN
A  68 ASN
A 237 ASN
A 289 HIS
A 328 HIS
B  22 ASN
B  55 ASN
B  68 ASN
B 237 ASN
B 289 HIS
B 328 HIS
C  22 ASN
C  55 ASN
C  68 ASN
C 237 ASN
C 289 HIS
C 328 HIS
D  22 ASN
D  55 ASN
D  68 ASN
D 237 ASN
D 289 HIS
D 328 HIS

Total number of N/Q/H flips: 24

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3915 r_free = 0.3915 target = 0.177979 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3715 r_free = 0.3715 target = 0.160271 restraints weight = 8740.815|
|-----------------------------------------------------------------------------|
r_work (start): 0.3705 rms_B_bonded: 0.74
r_work: 0.3629 rms_B_bonded: 1.24 restraints_weight: 0.5000
r_work: 0.3547 rms_B_bonded: 2.17 restraints_weight: 0.2500
r_work (final): 0.3547
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8231
moved from start:          0.1112

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.056  10444  Z= 0.163
  Angle     :  0.558   4.956  14176  Z= 0.311
  Chirality :  0.049   0.174   1612
  Planarity :  0.004   0.032   1804
  Dihedral  : 12.368  85.083   1640
  Min Nonbonded Distance : 2.468

Molprobity Statistics.
  All-atom Clashscore : 5.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.73 %
    Favored  : 97.27 %
  Rotamer:
    Outliers :  2.43 %
    Allowed  : 10.35 %
    Favored  : 87.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.35 (0.23), residues: 1320
  helix:  1.02 (0.25), residues: 392
  sheet: -1.36 (0.31), residues: 272
  loop : -0.39 (0.24), residues: 656

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP D  85 
 HIS   0.004   0.001   HIS A  51 
 PHE   0.013   0.002   PHE A 231 
 TYR   0.018   0.003   TYR D 318 
 ARG   0.003   0.001   ARG A 116 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04583 (  464)
  hydrogen bonds       : angle       5.99205 ( 1212)
  covalent geometry    : bond        0.00354 (10444)
  covalent geometry    : angle       0.55780 (14176)

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

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

  2640 Ramachandran restraints generated.
    1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2640 Ramachandran restraints generated.
    1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  220 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 194
  time to evaluate  : 1.154 
Fit side-chains
REVERT: A   37 ASP cc_start: 0.7224 (OUTLIER) cc_final: 0.6856 (p0)
REVERT: A   41 MET cc_start: 0.8622 (mtp) cc_final: 0.8300 (mtp)
REVERT: A   75 PHE cc_start: 0.8445 (m-80) cc_final: 0.8089 (m-80)
REVERT: A  131 MET cc_start: 0.8817 (mmm) cc_final: 0.8552 (mmm)
REVERT: A  170 GLU cc_start: 0.8882 (pt0) cc_final: 0.8511 (pt0)
REVERT: A  316 PHE cc_start: 0.8424 (OUTLIER) cc_final: 0.8195 (t80)
REVERT: B   37 ASP cc_start: 0.7231 (OUTLIER) cc_final: 0.6836 (p0)
REVERT: B   41 MET cc_start: 0.8623 (mtp) cc_final: 0.8302 (mtp)
REVERT: B   75 PHE cc_start: 0.8444 (m-80) cc_final: 0.8085 (m-80)
REVERT: B  103 MET cc_start: 0.7886 (mmm) cc_final: 0.7504 (mmm)
REVERT: B  131 MET cc_start: 0.8791 (mmm) cc_final: 0.8526 (mmm)
REVERT: B  170 GLU cc_start: 0.8861 (pt0) cc_final: 0.8487 (pt0)
REVERT: B  316 PHE cc_start: 0.8428 (OUTLIER) cc_final: 0.8198 (t80)
REVERT: C   37 ASP cc_start: 0.7239 (OUTLIER) cc_final: 0.6847 (p0)
REVERT: C   41 MET cc_start: 0.8622 (mtp) cc_final: 0.8300 (mtp)
REVERT: C   75 PHE cc_start: 0.8439 (m-80) cc_final: 0.8085 (m-80)
REVERT: C  103 MET cc_start: 0.7920 (mmm) cc_final: 0.7558 (mmm)
REVERT: C  131 MET cc_start: 0.8808 (mmm) cc_final: 0.8543 (mmm)
REVERT: C  170 GLU cc_start: 0.8857 (pt0) cc_final: 0.8483 (pt0)
REVERT: C  316 PHE cc_start: 0.8431 (OUTLIER) cc_final: 0.8203 (t80)
REVERT: D   37 ASP cc_start: 0.7253 (OUTLIER) cc_final: 0.6858 (p0)
REVERT: D   41 MET cc_start: 0.8624 (mtp) cc_final: 0.8300 (mtp)
REVERT: D   75 PHE cc_start: 0.8439 (m-80) cc_final: 0.8079 (m-80)
REVERT: D  103 MET cc_start: 0.7900 (mmm) cc_final: 0.7522 (mmm)
REVERT: D  131 MET cc_start: 0.8800 (mmm) cc_final: 0.8534 (mmm)
REVERT: D  170 GLU cc_start: 0.8859 (pt0) cc_final: 0.8492 (pt0)
REVERT: D  316 PHE cc_start: 0.8424 (OUTLIER) cc_final: 0.8195 (t80)
  outliers start: 26
  outliers final: 9
  residues processed: 206
  average time/residue: 1.6258
  time to fit residues: 358.1520
Evaluate side-chains
  202 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 185
  time to evaluate  : 1.547 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   37 ASP
Chi-restraints excluded: chain A residue   58 VAL
Chi-restraints excluded: chain A residue  316 PHE
Chi-restraints excluded: chain B residue   37 ASP
Chi-restraints excluded: chain B residue   58 VAL
Chi-restraints excluded: chain B residue  141 THR
Chi-restraints excluded: chain B residue  303 ASP
Chi-restraints excluded: chain B residue  316 PHE
Chi-restraints excluded: chain C residue   37 ASP
Chi-restraints excluded: chain C residue   58 VAL
Chi-restraints excluded: chain C residue  141 THR
Chi-restraints excluded: chain C residue  303 ASP
Chi-restraints excluded: chain C residue  316 PHE
Chi-restraints excluded: chain D residue   37 ASP
Chi-restraints excluded: chain D residue   58 VAL
Chi-restraints excluded: chain D residue  141 THR
Chi-restraints excluded: chain D residue  316 PHE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 70 optimal weight:    4.9990
   chunk 98 optimal weight:    4.9990
   chunk 12 optimal weight:    0.3980
   chunk 17 optimal weight:    0.9980
   chunk 33 optimal weight:   10.0000
   chunk 96 optimal weight:    1.9990
   chunk 62 optimal weight:    0.6980
   chunk 11 optimal weight:    4.9990
   chunk 23 optimal weight:    0.9990
   chunk 110 optimal weight:    3.9990
   chunk 112 optimal weight:    2.9990
   overall best weight:    1.0184

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

Flipped N/Q/H residues before XYZ refinement:
A  68 ASN
B  68 ASN
B 278 GLN
C  68 ASN
D  68 ASN
D 278 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3898 r_free = 0.3898 target = 0.176019 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3699 r_free = 0.3699 target = 0.158139 restraints weight = 8854.078|
|-----------------------------------------------------------------------------|
r_work (start): 0.3698 rms_B_bonded: 0.76
r_work: 0.3609 rms_B_bonded: 1.37 restraints_weight: 0.5000
r_work: 0.3521 rms_B_bonded: 2.41 restraints_weight: 0.2500
r_work (final): 0.3521
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8249
moved from start:          0.1219

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051  10444  Z= 0.156
  Angle     :  0.544   4.873  14176  Z= 0.302
  Chirality :  0.049   0.176   1612
  Planarity :  0.004   0.031   1804
  Dihedral  : 11.811  80.652   1636
  Min Nonbonded Distance : 2.455

Molprobity Statistics.
  All-atom Clashscore : 5.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.50 %
    Favored  : 97.50 %
  Rotamer:
    Outliers :  1.68 %
    Allowed  : 12.50 %
    Favored  : 85.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.49 (0.23), residues: 1320
  helix:  0.93 (0.26), residues: 396
  sheet: -1.48 (0.31), residues: 272
  loop : -0.48 (0.25), residues: 652

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP B  85 
 HIS   0.004   0.001   HIS D  51 
 PHE   0.012   0.002   PHE C 284 
 TYR   0.018   0.002   TYR C 318 
 ARG   0.002   0.001   ARG C 116 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04341 (  464)
  hydrogen bonds       : angle       5.88223 ( 1212)
  covalent geometry    : bond        0.00339 (10444)
  covalent geometry    : angle       0.54384 (14176)

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

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

  2640 Ramachandran restraints generated.
    1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2640 Ramachandran restraints generated.
    1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  208 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 190
  time to evaluate  : 1.319 
Fit side-chains
   revert: symmetry clash
REVERT: A   37 ASP cc_start: 0.7270 (OUTLIER) cc_final: 0.6922 (p0)
REVERT: A   41 MET cc_start: 0.8622 (mtp) cc_final: 0.8358 (mtp)
REVERT: A   75 PHE cc_start: 0.8493 (m-80) cc_final: 0.8041 (m-80)
REVERT: A  103 MET cc_start: 0.7851 (mmm) cc_final: 0.7468 (mmm)
REVERT: A  131 MET cc_start: 0.8811 (mmm) cc_final: 0.8555 (mmm)
REVERT: A  170 GLU cc_start: 0.8896 (pt0) cc_final: 0.8569 (pt0)
REVERT: A  316 PHE cc_start: 0.8489 (OUTLIER) cc_final: 0.8259 (t80)
REVERT: B   37 ASP cc_start: 0.7292 (OUTLIER) cc_final: 0.6923 (p0)
REVERT: B   75 PHE cc_start: 0.8490 (m-80) cc_final: 0.8041 (m-80)
REVERT: B  111 LYS cc_start: 0.7197 (mtpt) cc_final: 0.6974 (mtmt)
REVERT: B  131 MET cc_start: 0.8785 (mmm) cc_final: 0.8532 (mmm)
REVERT: B  170 GLU cc_start: 0.8899 (pt0) cc_final: 0.8575 (pt0)
REVERT: B  316 PHE cc_start: 0.8487 (OUTLIER) cc_final: 0.8257 (t80)
REVERT: C   37 ASP cc_start: 0.7292 (OUTLIER) cc_final: 0.6922 (p0)
REVERT: C   75 PHE cc_start: 0.8488 (m-80) cc_final: 0.8045 (m-80)
REVERT: C  131 MET cc_start: 0.8795 (mmm) cc_final: 0.8541 (mmm)
REVERT: C  170 GLU cc_start: 0.8896 (pt0) cc_final: 0.8576 (pt0)
REVERT: C  316 PHE cc_start: 0.8493 (OUTLIER) cc_final: 0.8263 (t80)
REVERT: D   37 ASP cc_start: 0.7298 (OUTLIER) cc_final: 0.6925 (p0)
REVERT: D   75 PHE cc_start: 0.8489 (m-80) cc_final: 0.8037 (m-80)
REVERT: D  131 MET cc_start: 0.8810 (mmm) cc_final: 0.8552 (mmm)
REVERT: D  170 GLU cc_start: 0.8902 (pt0) cc_final: 0.8585 (pt0)
REVERT: D  316 PHE cc_start: 0.8481 (OUTLIER) cc_final: 0.8249 (t80)
  outliers start: 18
  outliers final: 9
  residues processed: 198
  average time/residue: 1.6192
  time to fit residues: 342.2512
Evaluate side-chains
  202 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 185
  time to evaluate  : 1.247 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   37 ASP
Chi-restraints excluded: chain A residue   58 VAL
Chi-restraints excluded: chain A residue  316 PHE
Chi-restraints excluded: chain B residue   37 ASP
Chi-restraints excluded: chain B residue   58 VAL
Chi-restraints excluded: chain B residue  141 THR
Chi-restraints excluded: chain B residue  303 ASP
Chi-restraints excluded: chain B residue  316 PHE
Chi-restraints excluded: chain C residue   37 ASP
Chi-restraints excluded: chain C residue   58 VAL
Chi-restraints excluded: chain C residue  141 THR
Chi-restraints excluded: chain C residue  303 ASP
Chi-restraints excluded: chain C residue  316 PHE
Chi-restraints excluded: chain D residue   37 ASP
Chi-restraints excluded: chain D residue   58 VAL
Chi-restraints excluded: chain D residue  141 THR
Chi-restraints excluded: chain D residue  316 PHE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 58 optimal weight:    2.9990
   chunk 46 optimal weight:    3.9990
   chunk 12 optimal weight:    0.7980
   chunk 97 optimal weight:    1.9990
   chunk 29 optimal weight:    4.9990
   chunk 41 optimal weight:    5.9990
   chunk 106 optimal weight:    7.9990
   chunk 86 optimal weight:    0.0970
   chunk 36 optimal weight:    2.9990
   chunk 131 optimal weight:    4.9990
   chunk 49 optimal weight:    0.4980
   overall best weight:    1.2782

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

Flipped N/Q/H residues before XYZ refinement:
A  68 ASN
A 278 GLN
B  68 ASN
C  68 ASN
C 278 GLN
D  68 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3904 r_free = 0.3904 target = 0.177191 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3706 r_free = 0.3706 target = 0.159473 restraints weight = 8789.315|
|-----------------------------------------------------------------------------|
r_work (start): 0.3699 rms_B_bonded: 0.74
r_work: 0.3617 rms_B_bonded: 1.31 restraints_weight: 0.5000
r_work: 0.3533 rms_B_bonded: 2.29 restraints_weight: 0.2500
r_work (final): 0.3533
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8256
moved from start:          0.1259

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.067  10444  Z= 0.180
  Angle     :  0.576   5.275  14176  Z= 0.318
  Chirality :  0.050   0.173   1612
  Planarity :  0.004   0.033   1804
  Dihedral  : 11.809  82.181   1636
  Min Nonbonded Distance : 2.435

Molprobity Statistics.
  All-atom Clashscore : 5.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.18 %
    Favored  : 96.82 %
  Rotamer:
    Outliers :  2.15 %
    Allowed  : 12.13 %
    Favored  : 85.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.31 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.55 (0.23), residues: 1320
  helix:  0.71 (0.25), residues: 412
  sheet: -1.40 (0.31), residues: 264
  loop : -0.50 (0.25), residues: 644

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.002   TRP C  85 
 HIS   0.004   0.001   HIS D  51 
 PHE   0.011   0.002   PHE C 284 
 TYR   0.019   0.003   TYR D 318 
 ARG   0.002   0.001   ARG D  18 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04484 (  464)
  hydrogen bonds       : angle       5.89621 ( 1212)
  covalent geometry    : bond        0.00397 (10444)
  covalent geometry    : angle       0.57570 (14176)

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

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

  2640 Ramachandran restraints generated.
    1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2640 Ramachandran restraints generated.
    1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  208 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 185
  time to evaluate  : 2.552 
Fit side-chains
   revert: symmetry clash
REVERT: A   37 ASP cc_start: 0.7245 (OUTLIER) cc_final: 0.6881 (p0)
REVERT: A   75 PHE cc_start: 0.8545 (m-80) cc_final: 0.8096 (m-80)
REVERT: A  131 MET cc_start: 0.8813 (mmm) cc_final: 0.8569 (mmm)
REVERT: A  170 GLU cc_start: 0.8895 (pt0) cc_final: 0.8545 (pt0)
REVERT: A  316 PHE cc_start: 0.8492 (OUTLIER) cc_final: 0.8264 (t80)
REVERT: B   75 PHE cc_start: 0.8547 (m-80) cc_final: 0.8101 (m-80)
REVERT: B  103 MET cc_start: 0.7804 (OUTLIER) cc_final: 0.7422 (mmm)
REVERT: B  111 LYS cc_start: 0.7194 (mtpt) cc_final: 0.6980 (mtmt)
REVERT: B  131 MET cc_start: 0.8810 (mmm) cc_final: 0.8565 (mmm)
REVERT: B  170 GLU cc_start: 0.8878 (pt0) cc_final: 0.8528 (pt0)
REVERT: B  316 PHE cc_start: 0.8498 (OUTLIER) cc_final: 0.8270 (t80)
REVERT: C   75 PHE cc_start: 0.8537 (m-80) cc_final: 0.8092 (m-80)
REVERT: C  103 MET cc_start: 0.7811 (OUTLIER) cc_final: 0.7556 (mmm)
REVERT: C  111 LYS cc_start: 0.7198 (OUTLIER) cc_final: 0.6933 (mtpt)
REVERT: C  131 MET cc_start: 0.8811 (mmm) cc_final: 0.8565 (mmm)
REVERT: C  170 GLU cc_start: 0.8873 (pt0) cc_final: 0.8524 (pt0)
REVERT: C  316 PHE cc_start: 0.8498 (OUTLIER) cc_final: 0.8271 (t80)
REVERT: D   59 LYS cc_start: 0.8229 (pttm) cc_final: 0.7977 (pttm)
REVERT: D   75 PHE cc_start: 0.8544 (m-80) cc_final: 0.8099 (m-80)
REVERT: D  103 MET cc_start: 0.7805 (mmm) cc_final: 0.7506 (mmm)
REVERT: D  131 MET cc_start: 0.8817 (mmm) cc_final: 0.8568 (mmm)
REVERT: D  170 GLU cc_start: 0.8871 (pt0) cc_final: 0.8528 (pt0)
REVERT: D  316 PHE cc_start: 0.8488 (OUTLIER) cc_final: 0.8257 (t80)
  outliers start: 23
  outliers final: 12
  residues processed: 197
  average time/residue: 2.0287
  time to fit residues: 429.2743
Evaluate side-chains
  204 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 184
  time to evaluate  : 2.097 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   37 ASP
Chi-restraints excluded: chain A residue   58 VAL
Chi-restraints excluded: chain A residue  241 VAL
Chi-restraints excluded: chain A residue  316 PHE
Chi-restraints excluded: chain B residue   58 VAL
Chi-restraints excluded: chain B residue  103 MET
Chi-restraints excluded: chain B residue  141 THR
Chi-restraints excluded: chain B residue  241 VAL
Chi-restraints excluded: chain B residue  303 ASP
Chi-restraints excluded: chain B residue  316 PHE
Chi-restraints excluded: chain C residue   58 VAL
Chi-restraints excluded: chain C residue  103 MET
Chi-restraints excluded: chain C residue  111 LYS
Chi-restraints excluded: chain C residue  141 THR
Chi-restraints excluded: chain C residue  241 VAL
Chi-restraints excluded: chain C residue  316 PHE
Chi-restraints excluded: chain D residue   58 VAL
Chi-restraints excluded: chain D residue  141 THR
Chi-restraints excluded: chain D residue  241 VAL
Chi-restraints excluded: chain D residue  316 PHE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 62 optimal weight:    0.8980
   chunk 8 optimal weight:    5.9990
   chunk 6 optimal weight:    1.9990
   chunk 127 optimal weight:    0.9980
   chunk 82 optimal weight:    4.9990
   chunk 92 optimal weight:    1.9990
   chunk 106 optimal weight:    9.9990
   chunk 33 optimal weight:   10.0000
   chunk 118 optimal weight:    5.9990
   chunk 128 optimal weight:    3.9990
   chunk 104 optimal weight:    3.9990
   overall best weight:    1.9786

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

Flipped N/Q/H residues before XYZ refinement:
A  68 ASN
B  68 ASN
C  68 ASN
D  68 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3868 r_free = 0.3868 target = 0.173149 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3670 r_free = 0.3670 target = 0.155323 restraints weight = 8808.016|
|-----------------------------------------------------------------------------|
r_work (start): 0.3666 rms_B_bonded: 0.74
r_work: 0.3579 rms_B_bonded: 1.32 restraints_weight: 0.5000
r_work: 0.3495 rms_B_bonded: 2.30 restraints_weight: 0.2500
r_work (final): 0.3495
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8278
moved from start:          0.1242

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.084  10444  Z= 0.248
  Angle     :  0.665   5.449  14176  Z= 0.367
  Chirality :  0.053   0.204   1612
  Planarity :  0.005   0.038   1804
  Dihedral  : 12.240  83.273   1636
  Min Nonbonded Distance : 2.394

Molprobity Statistics.
  All-atom Clashscore : 6.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.86 %
    Favored  : 96.14 %
  Rotamer:
    Outliers :  2.61 %
    Allowed  : 11.47 %
    Favored  : 85.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.31 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.67 (0.23), residues: 1320
  helix:  0.66 (0.25), residues: 408
  sheet: -1.53 (0.31), residues: 264
  loop : -0.56 (0.25), residues: 648

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.002   TRP C 311 
 HIS   0.006   0.002   HIS C  39 
 PHE   0.012   0.003   PHE B 284 
 TYR   0.023   0.004   TYR D 318 
 ARG   0.004   0.001   ARG B  18 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05091 (  464)
  hydrogen bonds       : angle       6.02366 ( 1212)
  covalent geometry    : bond        0.00549 (10444)
  covalent geometry    : angle       0.66540 (14176)

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

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

  2640 Ramachandran restraints generated.
    1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2640 Ramachandran restraints generated.
    1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  209 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 181
  time to evaluate  : 1.234 
Fit side-chains
REVERT: A   75 PHE cc_start: 0.8572 (m-80) cc_final: 0.8147 (m-80)
REVERT: A  111 LYS cc_start: 0.7239 (OUTLIER) cc_final: 0.6930 (mtpt)
REVERT: A  131 MET cc_start: 0.8814 (mmm) cc_final: 0.8574 (mmm)
REVERT: A  316 PHE cc_start: 0.8500 (OUTLIER) cc_final: 0.8262 (t80)
REVERT: B   75 PHE cc_start: 0.8573 (m-80) cc_final: 0.8153 (m-80)
REVERT: B  111 LYS cc_start: 0.7236 (OUTLIER) cc_final: 0.7018 (mtmt)
REVERT: B  131 MET cc_start: 0.8790 (mmm) cc_final: 0.8552 (mmm)
REVERT: B  316 PHE cc_start: 0.8496 (OUTLIER) cc_final: 0.8259 (t80)
REVERT: C   75 PHE cc_start: 0.8532 (m-80) cc_final: 0.8118 (m-80)
REVERT: C  131 MET cc_start: 0.8790 (mmm) cc_final: 0.8551 (mmm)
REVERT: C  316 PHE cc_start: 0.8503 (OUTLIER) cc_final: 0.8269 (t80)
REVERT: D   75 PHE cc_start: 0.8567 (m-80) cc_final: 0.8143 (m-80)
REVERT: D  103 MET cc_start: 0.7893 (mmm) cc_final: 0.7554 (mmm)
REVERT: D  111 LYS cc_start: 0.7223 (OUTLIER) cc_final: 0.6892 (mtpt)
REVERT: D  131 MET cc_start: 0.8794 (mmm) cc_final: 0.8550 (mmm)
REVERT: D  316 PHE cc_start: 0.8492 (OUTLIER) cc_final: 0.8253 (t80)
  outliers start: 28
  outliers final: 8
  residues processed: 194
  average time/residue: 1.4940
  time to fit residues: 309.5261
Evaluate side-chains
  189 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 174
  time to evaluate  : 1.174 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 VAL
Chi-restraints excluded: chain A residue  111 LYS
Chi-restraints excluded: chain A residue  316 PHE
Chi-restraints excluded: chain B residue   58 VAL
Chi-restraints excluded: chain B residue  111 LYS
Chi-restraints excluded: chain B residue  141 THR
Chi-restraints excluded: chain B residue  316 PHE
Chi-restraints excluded: chain C residue   58 VAL
Chi-restraints excluded: chain C residue  141 THR
Chi-restraints excluded: chain C residue  316 PHE
Chi-restraints excluded: chain D residue   58 VAL
Chi-restraints excluded: chain D residue  111 LYS
Chi-restraints excluded: chain D residue  141 THR
Chi-restraints excluded: chain D residue  241 VAL
Chi-restraints excluded: chain D residue  316 PHE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 81 optimal weight:    0.5980
   chunk 114 optimal weight:    0.5980
   chunk 20 optimal weight:    0.5980
   chunk 62 optimal weight:    3.9990
   chunk 40 optimal weight:   10.0000
   chunk 64 optimal weight:    0.8980
   chunk 91 optimal weight:    2.9990
   chunk 63 optimal weight:    0.9980
   chunk 69 optimal weight:    2.9990
   chunk 13 optimal weight:    0.8980
   chunk 45 optimal weight:    0.9980
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
A  68 ASN
B  68 ASN
C  68 ASN
D  68 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3912 r_free = 0.3912 target = 0.177299 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3724 r_free = 0.3724 target = 0.160052 restraints weight = 8765.270|
|-----------------------------------------------------------------------------|
r_work (start): 0.3724 rms_B_bonded: 0.73
r_work: 0.3647 rms_B_bonded: 1.23 restraints_weight: 0.5000
r_work: 0.3566 rms_B_bonded: 2.15 restraints_weight: 0.2500
r_work (final): 0.3566
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8215
moved from start:          0.1439

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  10444  Z= 0.131
  Angle     :  0.533   5.109  14176  Z= 0.294
  Chirality :  0.047   0.163   1612
  Planarity :  0.004   0.032   1804
  Dihedral  : 11.429  83.813   1636
  Min Nonbonded Distance : 2.489

Molprobity Statistics.
  All-atom Clashscore : 5.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.58 %
    Favored  : 97.42 %
  Rotamer:
    Outliers :  2.05 %
    Allowed  : 13.25 %
    Favored  : 84.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.53 (0.23), residues: 1320
  helix:  0.80 (0.25), residues: 416
  sheet: -1.52 (0.31), residues: 272
  loop : -0.47 (0.26), residues: 632

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A  85 
 HIS   0.004   0.001   HIS B  51 
 PHE   0.010   0.001   PHE A 231 
 TYR   0.015   0.002   TYR D 318 
 ARG   0.006   0.001   ARG B  78 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03958 (  464)
  hydrogen bonds       : angle       5.74608 ( 1212)
  covalent geometry    : bond        0.00286 (10444)
  covalent geometry    : angle       0.53310 (14176)

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

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

  2640 Ramachandran restraints generated.
    1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2640 Ramachandran restraints generated.
    1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  211 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 189
  time to evaluate  : 1.280 
Fit side-chains
   revert: symmetry clash
REVERT: A   75 PHE cc_start: 0.8551 (m-80) cc_final: 0.8112 (m-80)
REVERT: A  103 MET cc_start: 0.7664 (mmm) cc_final: 0.7378 (mmm)
REVERT: A  316 PHE cc_start: 0.8445 (OUTLIER) cc_final: 0.8211 (t80)
REVERT: B   75 PHE cc_start: 0.8552 (m-80) cc_final: 0.8115 (m-80)
REVERT: B  103 MET cc_start: 0.7685 (mmm) cc_final: 0.7414 (mmm)
REVERT: B  316 PHE cc_start: 0.8443 (OUTLIER) cc_final: 0.8211 (t80)
REVERT: C   75 PHE cc_start: 0.8551 (m-80) cc_final: 0.8116 (m-80)
REVERT: C  103 MET cc_start: 0.7713 (mmm) cc_final: 0.7448 (mmm)
REVERT: C  316 PHE cc_start: 0.8439 (OUTLIER) cc_final: 0.8206 (t80)
REVERT: D   75 PHE cc_start: 0.8541 (m-80) cc_final: 0.8105 (m-80)
REVERT: D  103 MET cc_start: 0.7805 (mmm) cc_final: 0.7424 (mmm)
REVERT: D  316 PHE cc_start: 0.8433 (OUTLIER) cc_final: 0.8203 (t80)
  outliers start: 22
  outliers final: 10
  residues processed: 204
  average time/residue: 1.5402
  time to fit residues: 335.6454
Evaluate side-chains
  206 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 192
  time to evaluate  : 2.786 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 VAL
Chi-restraints excluded: chain A residue  241 VAL
Chi-restraints excluded: chain A residue  316 PHE
Chi-restraints excluded: chain B residue   58 VAL
Chi-restraints excluded: chain B residue  141 THR
Chi-restraints excluded: chain B residue  316 PHE
Chi-restraints excluded: chain C residue   58 VAL
Chi-restraints excluded: chain C residue  141 THR
Chi-restraints excluded: chain C residue  316 PHE
Chi-restraints excluded: chain D residue   58 VAL
Chi-restraints excluded: chain D residue  141 THR
Chi-restraints excluded: chain D residue  175 THR
Chi-restraints excluded: chain D residue  241 VAL
Chi-restraints excluded: chain D residue  316 PHE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 76 optimal weight:    5.9990
   chunk 23 optimal weight:    1.9990
   chunk 52 optimal weight:    4.9990
   chunk 46 optimal weight:    1.9990
   chunk 128 optimal weight:    0.9980
   chunk 117 optimal weight:    0.8980
   chunk 21 optimal weight:    0.0970
   chunk 112 optimal weight:    1.9990
   chunk 55 optimal weight:    0.6980
   chunk 40 optimal weight:    6.9990
   chunk 87 optimal weight:    0.8980
   overall best weight:    0.7178

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

Flipped N/Q/H residues before XYZ refinement:
A  68 ASN
B  68 ASN
C  68 ASN
D  68 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3916 r_free = 0.3916 target = 0.177676 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3727 r_free = 0.3727 target = 0.160265 restraints weight = 8938.597|
|-----------------------------------------------------------------------------|
r_work (start): 0.3552 rms_B_bonded: 0.74
r_work: 0.3481 rms_B_bonded: 1.12 restraints_weight: 0.5000
r_work: 0.3397 rms_B_bonded: 1.91 restraints_weight: 0.2500
r_work (final): 0.3397
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8172
moved from start:          0.1493

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  10444  Z= 0.131
  Angle     :  0.531   5.666  14176  Z= 0.293
  Chirality :  0.047   0.164   1612
  Planarity :  0.004   0.031   1804
  Dihedral  : 10.947  79.644   1636
  Min Nonbonded Distance : 2.466

Molprobity Statistics.
  All-atom Clashscore : 5.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.35 %
    Favored  : 97.65 %
  Rotamer:
    Outliers :  1.40 %
    Allowed  : 14.18 %
    Favored  : 84.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.51 (0.23), residues: 1320
  helix:  1.10 (0.26), residues: 396
  sheet: -1.57 (0.31), residues: 272
  loop : -0.60 (0.25), residues: 652

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A  85 
 HIS   0.004   0.001   HIS C  51 
 PHE   0.011   0.001   PHE A 231 
 TYR   0.015   0.002   TYR C 318 
 ARG   0.005   0.001   ARG C  78 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03902 (  464)
  hydrogen bonds       : angle       5.71839 ( 1212)
  covalent geometry    : bond        0.00286 (10444)
  covalent geometry    : angle       0.53104 (14176)

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

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

  2640 Ramachandran restraints generated.
    1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2640 Ramachandran restraints generated.
    1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  202 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 187
  time to evaluate  : 1.224 
Fit side-chains
   revert: symmetry clash
REVERT: A   75 PHE cc_start: 0.8552 (m-80) cc_final: 0.8112 (m-80)
REVERT: A  103 MET cc_start: 0.7762 (mmm) cc_final: 0.7494 (mmm)
REVERT: A  316 PHE cc_start: 0.8475 (OUTLIER) cc_final: 0.8246 (t80)
REVERT: B   75 PHE cc_start: 0.8540 (m-80) cc_final: 0.8104 (m-80)
REVERT: B  103 MET cc_start: 0.7779 (mmm) cc_final: 0.7506 (mmm)
REVERT: B  316 PHE cc_start: 0.8478 (OUTLIER) cc_final: 0.8250 (t80)
REVERT: C   75 PHE cc_start: 0.8546 (m-80) cc_final: 0.8112 (m-80)
REVERT: C  103 MET cc_start: 0.7778 (mmm) cc_final: 0.7375 (mmm)
REVERT: C  316 PHE cc_start: 0.8461 (OUTLIER) cc_final: 0.8231 (t80)
REVERT: D   75 PHE cc_start: 0.8543 (m-80) cc_final: 0.8106 (m-80)
REVERT: D  103 MET cc_start: 0.7888 (mmm) cc_final: 0.7456 (mmm)
REVERT: D  316 PHE cc_start: 0.8457 (OUTLIER) cc_final: 0.8230 (t80)
  outliers start: 15
  outliers final: 9
  residues processed: 198
  average time/residue: 1.8364
  time to fit residues: 388.6489
Evaluate side-chains
  199 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 186
  time to evaluate  : 1.093 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 VAL
Chi-restraints excluded: chain A residue  241 VAL
Chi-restraints excluded: chain A residue  316 PHE
Chi-restraints excluded: chain B residue   58 VAL
Chi-restraints excluded: chain B residue  141 THR
Chi-restraints excluded: chain B residue  316 PHE
Chi-restraints excluded: chain C residue   58 VAL
Chi-restraints excluded: chain C residue  141 THR
Chi-restraints excluded: chain C residue  316 PHE
Chi-restraints excluded: chain D residue   58 VAL
Chi-restraints excluded: chain D residue  141 THR
Chi-restraints excluded: chain D residue  241 VAL
Chi-restraints excluded: chain D residue  316 PHE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 45 optimal weight:    4.9990
   chunk 66 optimal weight:   10.0000
   chunk 130 optimal weight:    4.9990
   chunk 32 optimal weight:    3.9990
   chunk 49 optimal weight:    0.4980
   chunk 33 optimal weight:   10.0000
   chunk 88 optimal weight:    4.9990
   chunk 82 optimal weight:    3.9990
   chunk 72 optimal weight:    1.9990
   chunk 40 optimal weight:    7.9990
   chunk 83 optimal weight:    0.5980
   overall best weight:    2.2186

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

Flipped N/Q/H residues before XYZ refinement:
A  68 ASN
B  68 ASN
C  68 ASN
D  68 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3860 r_free = 0.3860 target = 0.172464 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3661 r_free = 0.3661 target = 0.154565 restraints weight = 8824.002|
|-----------------------------------------------------------------------------|
r_work (start): 0.3657 rms_B_bonded: 0.74
r_work: 0.3569 rms_B_bonded: 1.35 restraints_weight: 0.5000
r_work: 0.3481 rms_B_bonded: 2.38 restraints_weight: 0.2500
r_work (final): 0.3481
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8287
moved from start:          0.1394

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.084  10444  Z= 0.273
  Angle     :  0.705   6.392  14176  Z= 0.388
  Chirality :  0.055   0.216   1612
  Planarity :  0.005   0.035   1804
  Dihedral  : 11.971  84.294   1636
  Min Nonbonded Distance : 2.362

Molprobity Statistics.
  All-atom Clashscore : 6.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.09 %
    Favored  : 95.91 %
  Rotamer:
    Outliers :  1.68 %
    Allowed  : 13.90 %
    Favored  : 84.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.31 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.72 (0.23), residues: 1320
  helix:  0.66 (0.25), residues: 404
  sheet: -1.59 (0.31), residues: 264
  loop : -0.61 (0.24), residues: 652

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.002   TRP D 311 
 HIS   0.006   0.002   HIS A  39 
 PHE   0.012   0.003   PHE C 284 
 TYR   0.025   0.004   TYR B 318 
 ARG   0.006   0.001   ARG D  78 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05329 (  464)
  hydrogen bonds       : angle       6.05855 ( 1212)
  covalent geometry    : bond        0.00603 (10444)
  covalent geometry    : angle       0.70546 (14176)

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

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

  2640 Ramachandran restraints generated.
    1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2640 Ramachandran restraints generated.
    1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  196 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 178
  time to evaluate  : 1.694 
Fit side-chains
REVERT: A   75 PHE cc_start: 0.8566 (m-80) cc_final: 0.8128 (m-80)
REVERT: A  316 PHE cc_start: 0.8511 (OUTLIER) cc_final: 0.8277 (t80)
REVERT: B   75 PHE cc_start: 0.8588 (m-80) cc_final: 0.8156 (m-80)
REVERT: B  316 PHE cc_start: 0.8512 (OUTLIER) cc_final: 0.8282 (t80)
REVERT: C   75 PHE cc_start: 0.8557 (m-80) cc_final: 0.8128 (m-80)
REVERT: C  103 MET cc_start: 0.8007 (OUTLIER) cc_final: 0.7590 (mmm)
REVERT: C  316 PHE cc_start: 0.8516 (OUTLIER) cc_final: 0.8285 (t80)
REVERT: D   75 PHE cc_start: 0.8592 (m-80) cc_final: 0.8151 (m-80)
REVERT: D  103 MET cc_start: 0.8041 (mmm) cc_final: 0.7633 (mmm)
REVERT: D  316 PHE cc_start: 0.8518 (OUTLIER) cc_final: 0.8275 (t80)
  outliers start: 18
  outliers final: 8
  residues processed: 187
  average time/residue: 1.7143
  time to fit residues: 344.0165
Evaluate side-chains
  187 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 174
  time to evaluate  : 1.150 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 VAL
Chi-restraints excluded: chain A residue  316 PHE
Chi-restraints excluded: chain B residue   58 VAL
Chi-restraints excluded: chain B residue  141 THR
Chi-restraints excluded: chain B residue  316 PHE
Chi-restraints excluded: chain C residue   58 VAL
Chi-restraints excluded: chain C residue  103 MET
Chi-restraints excluded: chain C residue  141 THR
Chi-restraints excluded: chain C residue  316 PHE
Chi-restraints excluded: chain D residue   16 VAL
Chi-restraints excluded: chain D residue   58 VAL
Chi-restraints excluded: chain D residue  141 THR
Chi-restraints excluded: chain D residue  316 PHE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 103 optimal weight:    0.9990
   chunk 94 optimal weight:    0.0980
   chunk 5 optimal weight:    4.9990
   chunk 44 optimal weight:    3.9990
   chunk 24 optimal weight:    3.9990
   chunk 96 optimal weight:    1.9990
   chunk 45 optimal weight:    0.0050
   chunk 79 optimal weight:    0.9990
   chunk 63 optimal weight:    0.9980
   chunk 102 optimal weight:    2.9990
   chunk 91 optimal weight:    1.9990
   overall best weight:    0.6198

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

Flipped N/Q/H residues before XYZ refinement:
A  68 ASN
B  68 ASN
C  68 ASN
D  68 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3938 r_free = 0.3938 target = 0.179808 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3752 r_free = 0.3752 target = 0.162739 restraints weight = 8834.696|
|-----------------------------------------------------------------------------|
r_work (start): 0.3588 rms_B_bonded: 0.73
r_work: 0.3517 rms_B_bonded: 1.13 restraints_weight: 0.5000
r_work: 0.3430 rms_B_bonded: 1.99 restraints_weight: 0.2500
r_work (final): 0.3430
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8182
moved from start:          0.1529

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  10444  Z= 0.125
  Angle     :  0.532   6.101  14176  Z= 0.294
  Chirality :  0.047   0.161   1612
  Planarity :  0.004   0.031   1804
  Dihedral  : 11.009  83.005   1636
  Min Nonbonded Distance : 2.478

Molprobity Statistics.
  All-atom Clashscore : 5.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.73 %
    Favored  : 97.27 %
  Rotamer:
    Outliers :  1.12 %
    Allowed  : 14.65 %
    Favored  : 84.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.54 (0.23), residues: 1320
  helix:  0.84 (0.25), residues: 416
  sheet: -1.56 (0.31), residues: 272
  loop : -0.49 (0.25), residues: 632

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP C  85 
 HIS   0.003   0.001   HIS A  51 
 PHE   0.011   0.001   PHE A 231 
 TYR   0.015   0.002   TYR D 318 
 ARG   0.006   0.001   ARG D  78 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03862 (  464)
  hydrogen bonds       : angle       5.71508 ( 1212)
  covalent geometry    : bond        0.00272 (10444)
  covalent geometry    : angle       0.53236 (14176)

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

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

  2640 Ramachandran restraints generated.
    1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2640 Ramachandran restraints generated.
    1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  190 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 178
  time to evaluate  : 2.024 
Fit side-chains
   revert: symmetry clash
REVERT: A   75 PHE cc_start: 0.8521 (m-80) cc_final: 0.8084 (m-80)
REVERT: A  103 MET cc_start: 0.7867 (mmm) cc_final: 0.7513 (mmm)
REVERT: A  316 PHE cc_start: 0.8418 (OUTLIER) cc_final: 0.8188 (t80)
REVERT: B   75 PHE cc_start: 0.8539 (m-80) cc_final: 0.8097 (m-80)
REVERT: B  103 MET cc_start: 0.7823 (mmm) cc_final: 0.7473 (mmm)
REVERT: B  316 PHE cc_start: 0.8431 (OUTLIER) cc_final: 0.8199 (t80)
REVERT: C   75 PHE cc_start: 0.8544 (m-80) cc_final: 0.8104 (m-80)
REVERT: C  103 MET cc_start: 0.7870 (OUTLIER) cc_final: 0.7387 (mmm)
REVERT: C  316 PHE cc_start: 0.8427 (OUTLIER) cc_final: 0.8196 (t80)
REVERT: D   75 PHE cc_start: 0.8536 (m-80) cc_final: 0.8089 (m-80)
REVERT: D  103 MET cc_start: 0.7942 (mmm) cc_final: 0.7418 (mmm)
REVERT: D  104 GLU cc_start: 0.7379 (pm20) cc_final: 0.6965 (pp20)
REVERT: D  316 PHE cc_start: 0.8410 (OUTLIER) cc_final: 0.8181 (t80)
  outliers start: 12
  outliers final: 6
  residues processed: 186
  average time/residue: 1.6565
  time to fit residues: 330.4267
Evaluate side-chains
  189 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 178
  time to evaluate  : 1.282 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 VAL
Chi-restraints excluded: chain A residue  316 PHE
Chi-restraints excluded: chain B residue  141 THR
Chi-restraints excluded: chain B residue  316 PHE
Chi-restraints excluded: chain C residue   58 VAL
Chi-restraints excluded: chain C residue  103 MET
Chi-restraints excluded: chain C residue  141 THR
Chi-restraints excluded: chain C residue  316 PHE
Chi-restraints excluded: chain D residue   58 VAL
Chi-restraints excluded: chain D residue  141 THR
Chi-restraints excluded: chain D residue  316 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 92 optimal weight:    2.9990
   chunk 104 optimal weight:    5.9990
   chunk 58 optimal weight:    1.9990
   chunk 89 optimal weight:    5.9990
   chunk 103 optimal weight:    1.9990
   chunk 16 optimal weight:    4.9990
   chunk 117 optimal weight:    1.9990
   chunk 91 optimal weight:    0.5980
   chunk 95 optimal weight:    1.9990
   chunk 131 optimal weight:    0.8980
   chunk 83 optimal weight:    1.9990
   overall best weight:    1.4986

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

Flipped N/Q/H residues before XYZ refinement:
A  68 ASN
B  68 ASN
C  68 ASN
D  68 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3889 r_free = 0.3889 target = 0.176292 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3694 r_free = 0.3694 target = 0.158659 restraints weight = 8810.309|
|-----------------------------------------------------------------------------|
r_work (start): 0.3701 rms_B_bonded: 0.74
r_work: 0.3618 rms_B_bonded: 1.28 restraints_weight: 0.5000
r_work: 0.3532 rms_B_bonded: 2.27 restraints_weight: 0.2500
r_work (final): 0.3532
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8253
moved from start:          0.1408

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.061  10444  Z= 0.204
  Angle     :  0.628   6.833  14176  Z= 0.346
  Chirality :  0.051   0.177   1612
  Planarity :  0.004   0.032   1804
  Dihedral  : 11.448  83.779   1635
  Min Nonbonded Distance : 2.407

Molprobity Statistics.
  All-atom Clashscore : 6.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.48 %
    Favored  : 96.52 %
  Rotamer:
    Outliers :  1.12 %
    Allowed  : 14.55 %
    Favored  : 84.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.31 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.61 (0.23), residues: 1320
  helix:  0.76 (0.25), residues: 408
  sheet: -1.52 (0.31), residues: 264
  loop : -0.56 (0.25), residues: 648

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.002   TRP D 311 
 HIS   0.005   0.001   HIS C  51 
 PHE   0.011   0.002   PHE A 284 
 TYR   0.020   0.003   TYR A 318 
 ARG   0.006   0.001   ARG D  78 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04713 (  464)
  hydrogen bonds       : angle       5.91013 ( 1212)
  covalent geometry    : bond        0.00446 (10444)
  covalent geometry    : angle       0.62839 (14176)

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

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

  2640 Ramachandran restraints generated.
    1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2640 Ramachandran restraints generated.
    1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  190 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 178
  time to evaluate  : 4.525 
Fit side-chains
   revert: symmetry clash
REVERT: A   75 PHE cc_start: 0.8595 (m-80) cc_final: 0.8134 (m-80)
REVERT: A  103 MET cc_start: 0.7995 (mmm) cc_final: 0.7498 (mmm)
REVERT: A  316 PHE cc_start: 0.8511 (OUTLIER) cc_final: 0.8278 (t80)
REVERT: B   75 PHE cc_start: 0.8590 (m-80) cc_final: 0.8130 (m-80)
REVERT: B  103 MET cc_start: 0.7965 (mmm) cc_final: 0.7600 (mmm)
REVERT: B  316 PHE cc_start: 0.8528 (OUTLIER) cc_final: 0.8298 (t80)
REVERT: C   75 PHE cc_start: 0.8586 (m-80) cc_final: 0.8135 (m-80)
REVERT: C  103 MET cc_start: 0.7957 (OUTLIER) cc_final: 0.7511 (mmm)
REVERT: C  316 PHE cc_start: 0.8513 (OUTLIER) cc_final: 0.8289 (t80)
REVERT: D   75 PHE cc_start: 0.8591 (m-80) cc_final: 0.8128 (m-80)
REVERT: D  103 MET cc_start: 0.8010 (mmm) cc_final: 0.7563 (mmm)
REVERT: D  316 PHE cc_start: 0.8508 (OUTLIER) cc_final: 0.8274 (t80)
  outliers start: 12
  outliers final: 6
  residues processed: 185
  average time/residue: 2.8508
  time to fit residues: 564.9771
Evaluate side-chains
  189 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 178
  time to evaluate  : 1.053 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 VAL
Chi-restraints excluded: chain A residue  316 PHE
Chi-restraints excluded: chain B residue  141 THR
Chi-restraints excluded: chain B residue  316 PHE
Chi-restraints excluded: chain C residue   58 VAL
Chi-restraints excluded: chain C residue  103 MET
Chi-restraints excluded: chain C residue  141 THR
Chi-restraints excluded: chain C residue  316 PHE
Chi-restraints excluded: chain D residue   58 VAL
Chi-restraints excluded: chain D residue  141 THR
Chi-restraints excluded: chain D residue  316 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 124 optimal weight:    1.9990
   chunk 107 optimal weight:    0.4980
   chunk 59 optimal weight:    0.2980
   chunk 91 optimal weight:    1.9990
   chunk 81 optimal weight:    0.5980
   chunk 45 optimal weight:    0.0070
   chunk 93 optimal weight:    0.8980
   chunk 49 optimal weight:    0.5980
   chunk 126 optimal weight:    0.9980
   chunk 85 optimal weight:    0.7980
   chunk 14 optimal weight:    3.9990
   overall best weight:    0.3998

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

Flipped N/Q/H residues before XYZ refinement:
A  68 ASN
B  68 ASN
C  68 ASN
C 237 ASN
D  68 ASN
D 237 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3941 r_free = 0.3941 target = 0.180112 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3758 r_free = 0.3758 target = 0.163149 restraints weight = 8801.307|
|-----------------------------------------------------------------------------|
r_work (start): 0.3795 rms_B_bonded: 0.73
r_work: 0.3711 rms_B_bonded: 1.25 restraints_weight: 0.5000
r_work: 0.3627 rms_B_bonded: 2.22 restraints_weight: 0.2500
r_work (final): 0.3627
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8174
moved from start:          0.1649

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.038  10444  Z= 0.109
  Angle     :  0.519   6.084  14176  Z= 0.284
  Chirality :  0.046   0.158   1612
  Planarity :  0.004   0.031   1804
  Dihedral  : 10.577  83.243   1635
  Min Nonbonded Distance : 2.513

Molprobity Statistics.
  All-atom Clashscore : 5.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.50 %
    Favored  : 97.50 %
  Rotamer:
    Outliers :  1.12 %
    Allowed  : 14.74 %
    Favored  : 84.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.44 (0.24), residues: 1320
  helix:  0.97 (0.26), residues: 416
  sheet: -1.50 (0.31), residues: 272
  loop : -0.47 (0.26), residues: 632

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A  85 
 HIS   0.003   0.001   HIS C  51 
 PHE   0.011   0.001   PHE D 231 
 TYR   0.013   0.002   TYR C 318 
 ARG   0.006   0.001   ARG D  78 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03515 (  464)
  hydrogen bonds       : angle       5.59481 ( 1212)
  covalent geometry    : bond        0.00237 (10444)
  covalent geometry    : angle       0.51921 (14176)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 10078.73 seconds
wall clock time: 186 minutes 59.91 seconds (11219.91 seconds total)