Starting phenix.real_space_refine
on Wed Mar  4 04:17:29 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7u5m_26355/03_2026/7u5m_26355.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7u5m_26355/03_2026/7u5m_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_26355/03_2026/7u5m_26355.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7u5m_26355/03_2026/7u5m_26355.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7u5m_26355/03_2026/7u5m_26355.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7u5m_26355/03_2026/7u5m_26355.cif"
  }
  resolution = 2.28
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.108
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-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/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:
    B, C, D
  Time building chain proxies: 2.06, per 1000 atoms: 0.19
  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: 0.59
  Conformation dependent library (CDL) restraints added in 448.2 milliseconds
  

  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: 0.39
  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: 1.73

  Time building geometry restraints manager: 0.78 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: 0.03
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'C'
  selection = chain 'D'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as 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:             1.570
  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:          0.120
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     10.060
  Find NCS groups from input model:        0.090
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:9.580
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   21.510
-------------------------------------------------------------------------------
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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  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
 ARG   0.005   0.001   ARG D 232 
 TYR   0.014   0.002   TYR C 318 
 PHE   0.020   0.002   PHE D 231 
 TRP   0.004   0.001   TRP D 194 
 HIS   0.004   0.001   HIS B  51 

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

*********************** 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  : 0.298 
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: 0.6876
  time to fit residues: 163.6968
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  : 0.419 
-------------------------------------------------------------------------------
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 98 optimal weight:    1.9990
   chunk 107 optimal weight:    1.9990
   chunk 10 optimal weight:    3.9990
   chunk 66 optimal weight:    0.7980
   chunk 130 optimal weight:    1.9990
   chunk 124 optimal weight:    3.9990
   chunk 103 optimal weight:    4.9990
   chunk 77 optimal weight:    2.9990
   chunk 122 optimal weight:    1.9990
   chunk 91 optimal weight:    3.9990
   chunk 55 optimal weight:    3.9990
   overall best weight:    1.7588

-------------------------------------------------------------------------------
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 = 0.3876 r_free = 0.3876 target = 0.173761 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3676 r_free = 0.3676 target = 0.155819 restraints weight = 8858.338|
|-----------------------------------------------------------------------------|
r_work (start): 0.3670 rms_B_bonded: 0.75
r_work: 0.3585 rms_B_bonded: 1.31 restraints_weight: 0.5000
r_work: 0.3500 rms_B_bonded: 2.28 restraints_weight: 0.2500
r_work (final): 0.3500
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8270
moved from start:          0.1094

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.081  10444  Z= 0.228
  Angle     :  0.638   5.219  14176  Z= 0.355
  Chirality :  0.052   0.181   1612
  Planarity :  0.005   0.035   1804
  Dihedral  : 12.821  87.044   1640
  Min Nonbonded Distance : 2.414

Molprobity Statistics.
  All-atom Clashscore : 5.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.11 %
    Favored  : 96.89 %
  Rotamer:
    Outliers :  2.15 %
    Allowed  : 10.82 %
    Favored  : 87.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.31 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.49 (0.23), residues: 1320
  helix:  0.68 (0.24), residues: 408
  sheet: -1.29 (0.31), residues: 264
  loop : -0.42 (0.25), residues: 648

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG C 232 
 TYR   0.022   0.003   TYR D 318 
 PHE   0.013   0.002   PHE C 284 
 TRP   0.004   0.002   TRP B 194 
 HIS   0.005   0.002   HIS B  51 

Details of bonding type rmsd
  covalent geometry    : bond        0.00502 (10444)
  covalent geometry    : angle       0.63794 (14176)
  hydrogen bonds       : bond        0.05280 (  464)
  hydrogen bonds       : angle       6.09861 ( 1212)

*********************** 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
  211 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 188
  time to evaluate  : 0.372 
Fit side-chains
REVERT: A   37 ASP cc_start: 0.7084 (OUTLIER) cc_final: 0.6718 (p0)
REVERT: A   41 MET cc_start: 0.8636 (mtp) cc_final: 0.8306 (mtp)
REVERT: A   75 PHE cc_start: 0.8462 (m-80) cc_final: 0.8077 (m-80)
REVERT: A  131 MET cc_start: 0.8803 (mmm) cc_final: 0.8540 (mmm)
REVERT: A  170 GLU cc_start: 0.8891 (pt0) cc_final: 0.8562 (pt0)
REVERT: A  316 PHE cc_start: 0.8478 (OUTLIER) cc_final: 0.8244 (t80)
REVERT: B   37 ASP cc_start: 0.7099 (OUTLIER) cc_final: 0.6705 (p0)
REVERT: B   41 MET cc_start: 0.8639 (mtp) cc_final: 0.8314 (mtp)
REVERT: B   75 PHE cc_start: 0.8492 (m-80) cc_final: 0.8157 (m-80)
REVERT: B  131 MET cc_start: 0.8782 (mmm) cc_final: 0.8519 (mmm)
REVERT: B  170 GLU cc_start: 0.8873 (pt0) cc_final: 0.8549 (pt0)
REVERT: B  316 PHE cc_start: 0.8487 (OUTLIER) cc_final: 0.8254 (t80)
REVERT: C   37 ASP cc_start: 0.7098 (OUTLIER) cc_final: 0.6710 (p0)
REVERT: C   41 MET cc_start: 0.8633 (mtp) cc_final: 0.8304 (mtp)
REVERT: C   75 PHE cc_start: 0.8465 (m-80) cc_final: 0.8141 (m-80)
REVERT: C  103 MET cc_start: 0.8004 (mmm) cc_final: 0.7566 (mmm)
REVERT: C  131 MET cc_start: 0.8785 (mmm) cc_final: 0.8519 (mmm)
REVERT: C  170 GLU cc_start: 0.8873 (pt0) cc_final: 0.8546 (pt0)
REVERT: C  316 PHE cc_start: 0.8492 (OUTLIER) cc_final: 0.8261 (t80)
REVERT: D   37 ASP cc_start: 0.7122 (OUTLIER) cc_final: 0.6727 (p0)
REVERT: D   41 MET cc_start: 0.8635 (mtp) cc_final: 0.8307 (mtp)
REVERT: D   75 PHE cc_start: 0.8462 (m-80) cc_final: 0.8074 (m-80)
REVERT: D  103 MET cc_start: 0.8014 (mmm) cc_final: 0.7565 (mmm)
REVERT: D  131 MET cc_start: 0.8796 (mmm) cc_final: 0.8532 (mmm)
REVERT: D  170 GLU cc_start: 0.8871 (pt0) cc_final: 0.8549 (pt0)
REVERT: D  316 PHE cc_start: 0.8476 (OUTLIER) cc_final: 0.8244 (t80)
  outliers start: 23
  outliers final: 10
  residues processed: 196
  average time/residue: 0.6519
  time to fit residues: 136.1312
Evaluate side-chains
  203 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 185
  time to evaluate  : 0.385 
-------------------------------------------------------------------------------
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  104 GLU
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 96 optimal weight:    0.6980
   chunk 107 optimal weight:    5.9990
   chunk 112 optimal weight:    0.0370
   chunk 95 optimal weight:    0.5980
   chunk 109 optimal weight:    0.3980
   chunk 66 optimal weight:   10.0000
   chunk 71 optimal weight:    0.0980
   chunk 74 optimal weight:    0.8980
   chunk 86 optimal weight:    0.7980
   chunk 0 optimal weight:   10.0000
   chunk 93 optimal weight:    0.8980
   overall best weight:    0.3658

-------------------------------------------------------------------------------
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 = 0.3949 r_free = 0.3949 target = 0.180773 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3765 r_free = 0.3765 target = 0.163799 restraints weight = 8774.646|
|-----------------------------------------------------------------------------|
r_work (start): 0.3765 rms_B_bonded: 0.73
r_work: 0.3692 rms_B_bonded: 1.21 restraints_weight: 0.5000
r_work: 0.3607 rms_B_bonded: 2.17 restraints_weight: 0.2500
r_work (final): 0.3607
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8172
moved from start:          0.1459

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026  10444  Z= 0.101
  Angle     :  0.473   4.880  14176  Z= 0.263
  Chirality :  0.046   0.161   1612
  Planarity :  0.004   0.033   1804
  Dihedral  : 11.328  82.897   1636
  Min Nonbonded Distance : 2.555

Molprobity Statistics.
  All-atom Clashscore : 5.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.20 %
    Favored  : 97.80 %
  Rotamer:
    Outliers :  2.24 %
    Allowed  : 12.22 %
    Favored  : 85.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.31 (0.23), residues: 1320
  helix:  0.92 (0.25), residues: 416
  sheet: -1.32 (0.31), residues: 272
  loop : -0.32 (0.26), residues: 632

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 116 
 TYR   0.014   0.002   TYR B 318 
 PHE   0.010   0.001   PHE A 284 
 TRP   0.004   0.001   TRP D  85 
 HIS   0.003   0.001   HIS B  51 

Details of bonding type rmsd
  covalent geometry    : bond        0.00216 (10444)
  covalent geometry    : angle       0.47314 (14176)
  hydrogen bonds       : bond        0.03506 (  464)
  hydrogen bonds       : angle       5.62834 ( 1212)

*********************** 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
  214 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 190
  time to evaluate  : 0.416 
Fit side-chains
   revert: symmetry clash
REVERT: A   41 MET cc_start: 0.8547 (mtp) cc_final: 0.8260 (mtp)
REVERT: A   75 PHE cc_start: 0.8427 (m-80) cc_final: 0.7997 (m-80)
REVERT: A  131 MET cc_start: 0.8824 (mmm) cc_final: 0.8579 (mmm)
REVERT: A  170 GLU cc_start: 0.8894 (pt0) cc_final: 0.8505 (pt0)
REVERT: A  316 PHE cc_start: 0.8372 (OUTLIER) cc_final: 0.8085 (t80)
REVERT: B   41 MET cc_start: 0.8558 (mtp) cc_final: 0.8281 (mtp)
REVERT: B   75 PHE cc_start: 0.8436 (m-80) cc_final: 0.8007 (m-80)
REVERT: B  131 MET cc_start: 0.8817 (mmm) cc_final: 0.8576 (mmm)
REVERT: B  170 GLU cc_start: 0.8888 (pt0) cc_final: 0.8535 (pt0)
REVERT: B  316 PHE cc_start: 0.8367 (OUTLIER) cc_final: 0.8083 (t80)
REVERT: C   41 MET cc_start: 0.8555 (mtp) cc_final: 0.8277 (mtp)
REVERT: C   75 PHE cc_start: 0.8418 (m-80) cc_final: 0.7988 (m-80)
REVERT: C  103 MET cc_start: 0.7705 (mmm) cc_final: 0.7397 (mmm)
REVERT: C  131 MET cc_start: 0.8832 (mmm) cc_final: 0.8590 (mmm)
REVERT: C  170 GLU cc_start: 0.8873 (pt0) cc_final: 0.8479 (pt0)
REVERT: C  316 PHE cc_start: 0.8363 (OUTLIER) cc_final: 0.8079 (t80)
REVERT: D   41 MET cc_start: 0.8550 (mtp) cc_final: 0.8262 (mtp)
REVERT: D   75 PHE cc_start: 0.8425 (m-80) cc_final: 0.8041 (m-80)
REVERT: D  103 MET cc_start: 0.7681 (mmm) cc_final: 0.7351 (mmm)
REVERT: D  131 MET cc_start: 0.8816 (mmm) cc_final: 0.8573 (mmm)
REVERT: D  170 GLU cc_start: 0.8882 (pt0) cc_final: 0.8501 (pt0)
REVERT: D  316 PHE cc_start: 0.8361 (OUTLIER) cc_final: 0.8076 (t80)
  outliers start: 24
  outliers final: 7
  residues processed: 202
  average time/residue: 0.6273
  time to fit residues: 135.6253
Evaluate side-chains
  195 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 184
  time to evaluate  : 0.395 
-------------------------------------------------------------------------------
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  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=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 15 optimal weight:    0.9980
   chunk 90 optimal weight:    0.3980
   chunk 95 optimal weight:    1.9990
   chunk 11 optimal weight:    3.9990
   chunk 33 optimal weight:   10.0000
   chunk 129 optimal weight:    4.9990
   chunk 68 optimal weight:    3.9990
   chunk 2 optimal weight:    5.9990
   chunk 122 optimal weight:    0.5980
   chunk 82 optimal weight:    1.9990
   chunk 61 optimal weight:    0.8980
   overall best weight:    0.9782

-------------------------------------------------------------------------------
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
B 278 GLN
C  68 ASN
C 278 GLN
D  68 ASN
D 278 GLN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3911 r_free = 0.3911 target = 0.176941 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3718 r_free = 0.3718 target = 0.159389 restraints weight = 8829.395|
|-----------------------------------------------------------------------------|
r_work (start): 0.3759 rms_B_bonded: 0.73
r_work: 0.3674 rms_B_bonded: 1.26 restraints_weight: 0.5000
r_work: 0.3589 rms_B_bonded: 2.23 restraints_weight: 0.2500
r_work (final): 0.3589
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8228
moved from start:          0.1349

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050  10444  Z= 0.152
  Angle     :  0.540   4.869  14176  Z= 0.299
  Chirality :  0.048   0.170   1612
  Planarity :  0.004   0.032   1804
  Dihedral  : 11.281  79.661   1636
  Min Nonbonded Distance : 2.444

Molprobity Statistics.
  All-atom Clashscore : 5.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.73 %
    Favored  : 97.27 %
  Rotamer:
    Outliers :  2.33 %
    Allowed  : 12.22 %
    Favored  : 85.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.49 (0.23), residues: 1320
  helix:  0.83 (0.25), residues: 412
  sheet: -1.54 (0.31), residues: 272
  loop : -0.42 (0.25), residues: 636

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.001   ARG C 232 
 TYR   0.017   0.002   TYR C 318 
 PHE   0.012   0.002   PHE B 284 
 TRP   0.005   0.001   TRP D  85 
 HIS   0.004   0.001   HIS A  51 

Details of bonding type rmsd
  covalent geometry    : bond        0.00333 (10444)
  covalent geometry    : angle       0.54035 (14176)
  hydrogen bonds       : bond        0.04169 (  464)
  hydrogen bonds       : angle       5.78344 ( 1212)

*********************** 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
  212 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 187
  time to evaluate  : 0.323 
Fit side-chains
REVERT: A   37 ASP cc_start: 0.7221 (OUTLIER) cc_final: 0.6850 (p0)
REVERT: A   75 PHE cc_start: 0.8509 (m-80) cc_final: 0.8063 (m-80)
REVERT: A  131 MET cc_start: 0.8868 (mmm) cc_final: 0.8615 (mmm)
REVERT: A  170 GLU cc_start: 0.8887 (pt0) cc_final: 0.8558 (pt0)
REVERT: A  316 PHE cc_start: 0.8494 (OUTLIER) cc_final: 0.8269 (t80)
REVERT: B   37 ASP cc_start: 0.7230 (OUTLIER) cc_final: 0.6836 (p0)
REVERT: B   75 PHE cc_start: 0.8522 (m-80) cc_final: 0.8081 (m-80)
REVERT: B  131 MET cc_start: 0.8844 (mmm) cc_final: 0.8589 (mmm)
REVERT: B  170 GLU cc_start: 0.8887 (pt0) cc_final: 0.8558 (pt0)
REVERT: B  316 PHE cc_start: 0.8497 (OUTLIER) cc_final: 0.8275 (t80)
REVERT: C   37 ASP cc_start: 0.7237 (OUTLIER) cc_final: 0.6846 (p0)
REVERT: C   75 PHE cc_start: 0.8511 (m-80) cc_final: 0.8071 (m-80)
REVERT: C  103 MET cc_start: 0.7694 (mmm) cc_final: 0.7404 (mmm)
REVERT: C  131 MET cc_start: 0.8860 (mmm) cc_final: 0.8606 (mmm)
REVERT: C  170 GLU cc_start: 0.8879 (pt0) cc_final: 0.8553 (pt0)
REVERT: C  316 PHE cc_start: 0.8497 (OUTLIER) cc_final: 0.8275 (t80)
REVERT: D   37 ASP cc_start: 0.7249 (OUTLIER) cc_final: 0.6854 (p0)
REVERT: D   59 LYS cc_start: 0.8199 (pttm) cc_final: 0.7815 (pttm)
REVERT: D   75 PHE cc_start: 0.8506 (m-80) cc_final: 0.8061 (m-80)
REVERT: D  131 MET cc_start: 0.8869 (mmm) cc_final: 0.8613 (mmm)
REVERT: D  170 GLU cc_start: 0.8888 (pt0) cc_final: 0.8570 (pt0)
REVERT: D  316 PHE cc_start: 0.8490 (OUTLIER) cc_final: 0.8268 (t80)
  outliers start: 25
  outliers final: 11
  residues processed: 199
  average time/residue: 0.6287
  time to fit residues: 133.7925
Evaluate side-chains
  205 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 186
  time to evaluate  : 0.406 
-------------------------------------------------------------------------------
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  175 THR
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  175 THR
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  175 THR
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  175 THR
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 84 optimal weight:    0.9980
   chunk 93 optimal weight:    0.9990
   chunk 30 optimal weight:    1.9990
   chunk 89 optimal weight:    2.9990
   chunk 54 optimal weight:    0.0370
   chunk 73 optimal weight:   10.0000
   chunk 37 optimal weight:    1.9990
   chunk 101 optimal weight:    4.9990
   chunk 48 optimal weight:    0.5980
   chunk 47 optimal weight:    0.9990
   chunk 65 optimal weight:    2.9990
   overall best weight:    0.7262

-------------------------------------------------------------------------------
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 = 0.3943 r_free = 0.3943 target = 0.180077 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3757 r_free = 0.3757 target = 0.162942 restraints weight = 8763.923|
|-----------------------------------------------------------------------------|
r_work (start): 0.3554 rms_B_bonded: 0.73
r_work: 0.3484 rms_B_bonded: 1.10 restraints_weight: 0.5000
r_work: 0.3398 rms_B_bonded: 1.91 restraints_weight: 0.2500
r_work (final): 0.3398
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8165
moved from start:          0.1426

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  10444  Z= 0.129
  Angle     :  0.513   4.989  14176  Z= 0.283
  Chirality :  0.047   0.165   1612
  Planarity :  0.004   0.032   1804
  Dihedral  : 10.966  81.084   1636
  Min Nonbonded Distance : 2.488

Molprobity Statistics.
  All-atom Clashscore : 5.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.27 %
    Favored  : 97.73 %
  Rotamer:
    Outliers :  1.77 %
    Allowed  : 12.78 %
    Favored  : 85.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.47 (0.23), residues: 1320
  helix:  0.86 (0.25), residues: 416
  sheet: -1.53 (0.31), residues: 272
  loop : -0.42 (0.25), residues: 632

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 116 
 TYR   0.015   0.002   TYR D 318 
 PHE   0.011   0.001   PHE B 284 
 TRP   0.005   0.001   TRP C  85 
 HIS   0.003   0.001   HIS D  51 

Details of bonding type rmsd
  covalent geometry    : bond        0.00280 (10444)
  covalent geometry    : angle       0.51276 (14176)
  hydrogen bonds       : bond        0.03832 (  464)
  hydrogen bonds       : angle       5.67623 ( 1212)

*********************** 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
  203 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 184
  time to evaluate  : 0.384 
Fit side-chains
   revert: symmetry clash
REVERT: A   75 PHE cc_start: 0.8528 (m-80) cc_final: 0.8090 (m-80)
REVERT: A  103 MET cc_start: 0.7627 (mmm) cc_final: 0.7353 (mmm)
REVERT: A  131 MET cc_start: 0.8864 (mmm) cc_final: 0.8625 (mmm)
REVERT: A  170 GLU cc_start: 0.8852 (pt0) cc_final: 0.8434 (pt0)
REVERT: A  316 PHE cc_start: 0.8465 (OUTLIER) cc_final: 0.8235 (t80)
REVERT: B   75 PHE cc_start: 0.8530 (m-80) cc_final: 0.8087 (m-80)
REVERT: B  131 MET cc_start: 0.8851 (mmm) cc_final: 0.8608 (mmm)
REVERT: B  170 GLU cc_start: 0.8855 (pt0) cc_final: 0.8436 (pt0)
REVERT: B  316 PHE cc_start: 0.8466 (OUTLIER) cc_final: 0.8238 (t80)
REVERT: C   75 PHE cc_start: 0.8530 (m-80) cc_final: 0.8090 (m-80)
REVERT: C  103 MET cc_start: 0.7715 (mmm) cc_final: 0.7255 (mmm)
REVERT: C  131 MET cc_start: 0.8866 (mmm) cc_final: 0.8624 (mmm)
REVERT: C  170 GLU cc_start: 0.8847 (pt0) cc_final: 0.8514 (pt0)
REVERT: C  316 PHE cc_start: 0.8468 (OUTLIER) cc_final: 0.8243 (t80)
REVERT: D   61 GLU cc_start: 0.7223 (mt-10) cc_final: 0.6942 (mt-10)
REVERT: D   75 PHE cc_start: 0.8521 (m-80) cc_final: 0.8075 (m-80)
REVERT: D  103 MET cc_start: 0.7713 (mmm) cc_final: 0.7453 (mmm)
REVERT: D  131 MET cc_start: 0.8865 (mmm) cc_final: 0.8623 (mmm)
REVERT: D  170 GLU cc_start: 0.8844 (pt0) cc_final: 0.8435 (pt0)
REVERT: D  316 PHE cc_start: 0.8463 (OUTLIER) cc_final: 0.8235 (t80)
  outliers start: 19
  outliers final: 11
  residues processed: 196
  average time/residue: 0.6205
  time to fit residues: 129.9710
Evaluate side-chains
  199 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 184
  time to evaluate  : 0.383 
-------------------------------------------------------------------------------
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  141 THR
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  141 THR
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  141 THR
Chi-restraints excluded: chain D residue  175 THR
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 6 optimal weight:    1.9990
   chunk 128 optimal weight:    0.7980
   chunk 108 optimal weight:    1.9990
   chunk 119 optimal weight:    1.9990
   chunk 9 optimal weight:    8.9990
   chunk 69 optimal weight:    2.9990
   chunk 72 optimal weight:    1.9990
   chunk 117 optimal weight:    0.9990
   chunk 51 optimal weight:    0.0980
   chunk 58 optimal weight:    2.9990
   chunk 92 optimal weight:    0.5980
   overall best weight:    0.8984

-------------------------------------------------------------------------------
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 = 0.3915 r_free = 0.3915 target = 0.177410 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3724 r_free = 0.3724 target = 0.159949 restraints weight = 8833.630|
|-----------------------------------------------------------------------------|
r_work (start): 0.3515 rms_B_bonded: 0.74
r_work: 0.3444 rms_B_bonded: 1.12 restraints_weight: 0.5000
r_work: 0.3355 rms_B_bonded: 1.94 restraints_weight: 0.2500
r_work (final): 0.3355
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8185
moved from start:          0.1420

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045  10444  Z= 0.146
  Angle     :  0.542   5.418  14176  Z= 0.298
  Chirality :  0.048   0.167   1612
  Planarity :  0.004   0.033   1804
  Dihedral  : 10.991  82.448   1636
  Min Nonbonded Distance : 2.473

Molprobity Statistics.
  All-atom Clashscore : 5.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.35 %
    Favored  : 97.65 %
  Rotamer:
    Outliers :  2.61 %
    Allowed  : 12.03 %
    Favored  : 85.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.51 (0.23), residues: 1320
  helix:  0.89 (0.25), residues: 412
  sheet: -1.58 (0.31), residues: 272
  loop : -0.47 (0.25), residues: 636

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.001   ARG A 232 
 TYR   0.016   0.002   TYR C 318 
 PHE   0.011   0.002   PHE B 284 
 TRP   0.005   0.001   TRP C  85 
 HIS   0.004   0.001   HIS D  39 

Details of bonding type rmsd
  covalent geometry    : bond        0.00318 (10444)
  covalent geometry    : angle       0.54239 (14176)
  hydrogen bonds       : bond        0.04035 (  464)
  hydrogen bonds       : angle       5.74396 ( 1212)

*********************** 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
  213 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 185
  time to evaluate  : 0.368 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   75 PHE cc_start: 0.8540 (m-80) cc_final: 0.8094 (m-80)
REVERT: A  103 MET cc_start: 0.7802 (OUTLIER) cc_final: 0.7492 (mmm)
REVERT: A  131 MET cc_start: 0.8873 (mmm) cc_final: 0.8629 (mmm)
REVERT: A  170 GLU cc_start: 0.8865 (pt0) cc_final: 0.8535 (pt0)
REVERT: A  316 PHE cc_start: 0.8473 (OUTLIER) cc_final: 0.8245 (t80)
REVERT: B   75 PHE cc_start: 0.8540 (m-80) cc_final: 0.8090 (m-80)
REVERT: B  131 MET cc_start: 0.8851 (mmm) cc_final: 0.8606 (mmm)
REVERT: B  170 GLU cc_start: 0.8860 (pt0) cc_final: 0.8518 (pt0)
REVERT: B  316 PHE cc_start: 0.8479 (OUTLIER) cc_final: 0.8253 (t80)
REVERT: C   75 PHE cc_start: 0.8541 (m-80) cc_final: 0.8100 (m-80)
REVERT: C  103 MET cc_start: 0.7839 (mmm) cc_final: 0.7454 (mmm)
REVERT: C  131 MET cc_start: 0.8874 (mmm) cc_final: 0.8629 (mmm)
REVERT: C  170 GLU cc_start: 0.8861 (pt0) cc_final: 0.8527 (pt0)
REVERT: C  316 PHE cc_start: 0.8479 (OUTLIER) cc_final: 0.8255 (t80)
REVERT: D   75 PHE cc_start: 0.8532 (m-80) cc_final: 0.8080 (m-80)
REVERT: D  103 MET cc_start: 0.7862 (mmm) cc_final: 0.7433 (mmm)
REVERT: D  131 MET cc_start: 0.8873 (mmm) cc_final: 0.8626 (mmm)
REVERT: D  170 GLU cc_start: 0.8860 (pt0) cc_final: 0.8529 (pt0)
REVERT: D  316 PHE cc_start: 0.8473 (OUTLIER) cc_final: 0.8248 (t80)
  outliers start: 28
  outliers final: 16
  residues processed: 206
  average time/residue: 0.6119
  time to fit residues: 135.0334
Evaluate side-chains
  205 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 184
  time to evaluate  : 0.402 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 VAL
Chi-restraints excluded: chain A residue  103 MET
Chi-restraints excluded: chain A residue  175 THR
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   59 LYS
Chi-restraints excluded: chain B residue  141 THR
Chi-restraints excluded: chain B residue  175 THR
Chi-restraints excluded: chain B residue  241 VAL
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  175 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  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 116 optimal weight:    2.9990
   chunk 130 optimal weight:    0.9980
   chunk 126 optimal weight:    0.8980
   chunk 7 optimal weight:    6.9990
   chunk 66 optimal weight:   10.0000
   chunk 63 optimal weight:    4.9990
   chunk 38 optimal weight:    0.0570
   chunk 26 optimal weight:    0.0970
   chunk 17 optimal weight:    8.9990
   chunk 42 optimal weight:    7.9990
   chunk 96 optimal weight:    4.9990
   overall best weight:    1.0098

-------------------------------------------------------------------------------
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 = 0.3930 r_free = 0.3930 target = 0.178743 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3738 r_free = 0.3738 target = 0.161392 restraints weight = 8727.437|
|-----------------------------------------------------------------------------|
r_work (start): 0.3542 rms_B_bonded: 0.73
r_work: 0.3471 rms_B_bonded: 1.10 restraints_weight: 0.5000
r_work: 0.3384 rms_B_bonded: 1.91 restraints_weight: 0.2500
r_work (final): 0.3384
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8183
moved from start:          0.1415

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048  10444  Z= 0.156
  Angle     :  0.561   5.853  14176  Z= 0.307
  Chirality :  0.048   0.168   1612
  Planarity :  0.004   0.033   1804
  Dihedral  : 10.988  79.658   1636
  Min Nonbonded Distance : 2.449

Molprobity Statistics.
  All-atom Clashscore : 5.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.50 %
    Favored  : 97.50 %
  Rotamer:
    Outliers :  2.43 %
    Allowed  : 12.69 %
    Favored  : 84.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.31 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.55 (0.23), residues: 1320
  helix:  0.87 (0.25), residues: 412
  sheet: -1.60 (0.31), residues: 272
  loop : -0.50 (0.25), residues: 636

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG C  78 
 TYR   0.017   0.002   TYR D 318 
 PHE   0.012   0.002   PHE B 284 
 TRP   0.005   0.001   TRP C  85 
 HIS   0.004   0.001   HIS A  51 

Details of bonding type rmsd
  covalent geometry    : bond        0.00341 (10444)
  covalent geometry    : angle       0.56119 (14176)
  hydrogen bonds       : bond        0.04174 (  464)
  hydrogen bonds       : angle       5.76991 ( 1212)

*********************** 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
  210 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 184
  time to evaluate  : 0.583 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   75 PHE cc_start: 0.8551 (m-80) cc_final: 0.8102 (m-80)
REVERT: A  103 MET cc_start: 0.7796 (OUTLIER) cc_final: 0.7494 (mmm)
REVERT: A  131 MET cc_start: 0.8863 (mmm) cc_final: 0.8622 (mmm)
REVERT: A  170 GLU cc_start: 0.8862 (pt0) cc_final: 0.8527 (pt0)
REVERT: A  316 PHE cc_start: 0.8497 (OUTLIER) cc_final: 0.8270 (t80)
REVERT: B   75 PHE cc_start: 0.8551 (m-80) cc_final: 0.8094 (m-80)
REVERT: B  131 MET cc_start: 0.8848 (mmm) cc_final: 0.8606 (mmm)
REVERT: B  170 GLU cc_start: 0.8863 (pt0) cc_final: 0.8506 (pt0)
REVERT: B  316 PHE cc_start: 0.8504 (OUTLIER) cc_final: 0.8278 (t80)
REVERT: C   75 PHE cc_start: 0.8553 (m-80) cc_final: 0.8112 (m-80)
REVERT: C  103 MET cc_start: 0.7926 (mmm) cc_final: 0.7478 (mmm)
REVERT: C  131 MET cc_start: 0.8869 (mmm) cc_final: 0.8624 (mmm)
REVERT: C  170 GLU cc_start: 0.8860 (pt0) cc_final: 0.8509 (pt0)
REVERT: C  316 PHE cc_start: 0.8501 (OUTLIER) cc_final: 0.8276 (t80)
REVERT: D   75 PHE cc_start: 0.8544 (m-80) cc_final: 0.8081 (m-80)
REVERT: D  103 MET cc_start: 0.7923 (mmm) cc_final: 0.7447 (mmm)
REVERT: D  131 MET cc_start: 0.8866 (mmm) cc_final: 0.8622 (mmm)
REVERT: D  170 GLU cc_start: 0.8860 (pt0) cc_final: 0.8518 (pt0)
REVERT: D  316 PHE cc_start: 0.8496 (OUTLIER) cc_final: 0.8272 (t80)
  outliers start: 26
  outliers final: 16
  residues processed: 203
  average time/residue: 0.6409
  time to fit residues: 139.0271
Evaluate side-chains
  204 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 183
  time to evaluate  : 0.348 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 VAL
Chi-restraints excluded: chain A residue  103 MET
Chi-restraints excluded: chain A residue  175 THR
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   59 LYS
Chi-restraints excluded: chain B residue  141 THR
Chi-restraints excluded: chain B residue  175 THR
Chi-restraints excluded: chain B residue  241 VAL
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  175 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  175 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 14 optimal weight:    2.9990
   chunk 23 optimal weight:    2.9990
   chunk 4 optimal weight:    2.9990
   chunk 82 optimal weight:    4.9990
   chunk 125 optimal weight:    0.9990
   chunk 72 optimal weight:    1.9990
   chunk 84 optimal weight:    0.7980
   chunk 86 optimal weight:    0.7980
   chunk 22 optimal weight:    0.9980
   chunk 42 optimal weight:    7.9990
   chunk 102 optimal weight:    0.9980
   overall best weight:    0.9182

-------------------------------------------------------------------------------
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 = 0.177186 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3721 r_free = 0.3721 target = 0.159775 restraints weight = 8747.115|
|-----------------------------------------------------------------------------|
r_work (start): 0.3539 rms_B_bonded: 0.73
r_work: 0.3470 rms_B_bonded: 1.10 restraints_weight: 0.5000
r_work: 0.3381 rms_B_bonded: 1.94 restraints_weight: 0.2500
r_work (final): 0.3381
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8182
moved from start:          0.1463

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045  10444  Z= 0.148
  Angle     :  0.558   6.579  14176  Z= 0.305
  Chirality :  0.048   0.166   1612
  Planarity :  0.004   0.036   1804
  Dihedral  : 10.941  80.863   1636
  Min Nonbonded Distance : 2.448

Molprobity Statistics.
  All-atom Clashscore : 5.64
  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 : 0.31 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.54 (0.23), residues: 1320
  helix:  0.87 (0.25), residues: 412
  sheet: -1.60 (0.31), residues: 272
  loop : -0.49 (0.25), residues: 636

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG B  78 
 TYR   0.016   0.002   TYR C 318 
 PHE   0.011   0.002   PHE B 284 
 TRP   0.005   0.001   TRP A  85 
 HIS   0.004   0.001   HIS A  51 

Details of bonding type rmsd
  covalent geometry    : bond        0.00324 (10444)
  covalent geometry    : angle       0.55768 (14176)
  hydrogen bonds       : bond        0.04084 (  464)
  hydrogen bonds       : angle       5.77001 ( 1212)

*********************** 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
  205 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 183
  time to evaluate  : 0.316 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   75 PHE cc_start: 0.8551 (m-80) cc_final: 0.8110 (m-80)
REVERT: A  103 MET cc_start: 0.7842 (OUTLIER) cc_final: 0.7528 (mmm)
REVERT: A  131 MET cc_start: 0.8862 (mmm) cc_final: 0.8627 (mmm)
REVERT: A  170 GLU cc_start: 0.8859 (pt0) cc_final: 0.8521 (pt0)
REVERT: A  316 PHE cc_start: 0.8468 (OUTLIER) cc_final: 0.8241 (t80)
REVERT: B   75 PHE cc_start: 0.8550 (m-80) cc_final: 0.8104 (m-80)
REVERT: B  131 MET cc_start: 0.8851 (mmm) cc_final: 0.8613 (mmm)
REVERT: B  170 GLU cc_start: 0.8863 (pt0) cc_final: 0.8504 (pt0)
REVERT: B  316 PHE cc_start: 0.8474 (OUTLIER) cc_final: 0.8246 (t80)
REVERT: C   75 PHE cc_start: 0.8549 (m-80) cc_final: 0.8104 (m-80)
REVERT: C  103 MET cc_start: 0.7910 (mmm) cc_final: 0.7491 (mmm)
REVERT: C  131 MET cc_start: 0.8867 (mmm) cc_final: 0.8627 (mmm)
REVERT: C  170 GLU cc_start: 0.8858 (pt0) cc_final: 0.8579 (pt0)
REVERT: C  316 PHE cc_start: 0.8475 (OUTLIER) cc_final: 0.8249 (t80)
REVERT: D   75 PHE cc_start: 0.8542 (m-80) cc_final: 0.8085 (m-80)
REVERT: D  103 MET cc_start: 0.7926 (mmm) cc_final: 0.7410 (mmm)
REVERT: D  131 MET cc_start: 0.8863 (mmm) cc_final: 0.8624 (mmm)
REVERT: D  170 GLU cc_start: 0.8862 (pt0) cc_final: 0.8518 (pt0)
REVERT: D  316 PHE cc_start: 0.8467 (OUTLIER) cc_final: 0.8240 (t80)
  outliers start: 22
  outliers final: 16
  residues processed: 199
  average time/residue: 0.6310
  time to fit residues: 134.1224
Evaluate side-chains
  203 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 182
  time to evaluate  : 0.378 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 VAL
Chi-restraints excluded: chain A residue  103 MET
Chi-restraints excluded: chain A residue  175 THR
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   59 LYS
Chi-restraints excluded: chain B residue  141 THR
Chi-restraints excluded: chain B residue  175 THR
Chi-restraints excluded: chain B residue  241 VAL
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  175 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  175 THR
Chi-restraints excluded: chain D residue  241 VAL
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 81 optimal weight:    0.9980
   chunk 83 optimal weight:    8.9990
   chunk 48 optimal weight:    0.8980
   chunk 92 optimal weight:    0.3980
   chunk 29 optimal weight:    3.9990
   chunk 114 optimal weight:    0.8980
   chunk 6 optimal weight:    0.6980
   chunk 41 optimal weight:    5.9990
   chunk 99 optimal weight:   10.0000
   chunk 113 optimal weight:    0.9990
   chunk 117 optimal weight:    0.9980
   overall best weight:    0.7780

-------------------------------------------------------------------------------
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 = 0.3920 r_free = 0.3920 target = 0.177977 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3729 r_free = 0.3729 target = 0.160580 restraints weight = 8816.108|
|-----------------------------------------------------------------------------|
r_work (start): 0.3694 rms_B_bonded: 0.74
r_work: 0.3617 rms_B_bonded: 1.23 restraints_weight: 0.5000
r_work: 0.3533 rms_B_bonded: 2.17 restraints_weight: 0.2500
r_work (final): 0.3533
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8214
moved from start:          0.1501

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= 0.136
  Angle     :  0.549   6.578  14176  Z= 0.299
  Chirality :  0.047   0.163   1612
  Planarity :  0.004   0.032   1804
  Dihedral  : 10.788  81.590   1636
  Min Nonbonded Distance : 2.475

Molprobity Statistics.
  All-atom Clashscore : 5.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.35 %
    Favored  : 97.65 %
  Rotamer:
    Outliers :  2.05 %
    Allowed  : 13.90 %
    Favored  : 84.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.51 (0.23), residues: 1320
  helix:  0.88 (0.25), residues: 416
  sheet: -1.59 (0.31), residues: 272
  loop : -0.45 (0.25), residues: 632

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG D  78 
 TYR   0.015   0.002   TYR D 318 
 PHE   0.011   0.002   PHE B 284 
 TRP   0.005   0.001   TRP A  85 
 HIS   0.004   0.001   HIS A  51 

Details of bonding type rmsd
  covalent geometry    : bond        0.00297 (10444)
  covalent geometry    : angle       0.54868 (14176)
  hydrogen bonds       : bond        0.03942 (  464)
  hydrogen bonds       : angle       5.71495 ( 1212)

*********************** 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
  201 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 179
  time to evaluate  : 0.403 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   75 PHE cc_start: 0.8547 (m-80) cc_final: 0.8104 (m-80)
REVERT: A  103 MET cc_start: 0.7850 (OUTLIER) cc_final: 0.7557 (mmm)
REVERT: A  131 MET cc_start: 0.8864 (mmm) cc_final: 0.8626 (mmm)
REVERT: A  170 GLU cc_start: 0.8883 (pt0) cc_final: 0.8546 (pt0)
REVERT: A  316 PHE cc_start: 0.8475 (OUTLIER) cc_final: 0.8246 (t80)
REVERT: B   75 PHE cc_start: 0.8556 (m-80) cc_final: 0.8115 (m-80)
REVERT: B  131 MET cc_start: 0.8837 (mmm) cc_final: 0.8593 (mmm)
REVERT: B  170 GLU cc_start: 0.8863 (pt0) cc_final: 0.8490 (pt0)
REVERT: B  316 PHE cc_start: 0.8478 (OUTLIER) cc_final: 0.8250 (t80)
REVERT: C   75 PHE cc_start: 0.8549 (m-80) cc_final: 0.8115 (m-80)
REVERT: C  103 MET cc_start: 0.7960 (mmm) cc_final: 0.7500 (mmm)
REVERT: C  131 MET cc_start: 0.8869 (mmm) cc_final: 0.8630 (mmm)
REVERT: C  170 GLU cc_start: 0.8861 (pt0) cc_final: 0.8494 (pt0)
REVERT: C  316 PHE cc_start: 0.8477 (OUTLIER) cc_final: 0.8251 (t80)
REVERT: D   75 PHE cc_start: 0.8540 (m-80) cc_final: 0.8094 (m-80)
REVERT: D  103 MET cc_start: 0.7914 (mmm) cc_final: 0.7407 (mmm)
REVERT: D  131 MET cc_start: 0.8872 (mmm) cc_final: 0.8632 (mmm)
REVERT: D  170 GLU cc_start: 0.8860 (pt0) cc_final: 0.8500 (pt0)
REVERT: D  316 PHE cc_start: 0.8473 (OUTLIER) cc_final: 0.8247 (t80)
  outliers start: 22
  outliers final: 16
  residues processed: 195
  average time/residue: 0.6264
  time to fit residues: 130.6204
Evaluate side-chains
  200 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 179
  time to evaluate  : 0.388 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 VAL
Chi-restraints excluded: chain A residue  103 MET
Chi-restraints excluded: chain A residue  175 THR
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   59 LYS
Chi-restraints excluded: chain B residue  141 THR
Chi-restraints excluded: chain B residue  175 THR
Chi-restraints excluded: chain B residue  241 VAL
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  175 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  175 THR
Chi-restraints excluded: chain D residue  241 VAL
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 72 optimal weight:    1.9990
   chunk 66 optimal weight:   10.0000
   chunk 96 optimal weight:    0.4980
   chunk 100 optimal weight:    2.9990
   chunk 47 optimal weight:    1.9990
   chunk 86 optimal weight:    0.8980
   chunk 80 optimal weight:    2.9990
   chunk 24 optimal weight:    7.9990
   chunk 0 optimal weight:   10.0000
   chunk 18 optimal weight:    0.0770
   chunk 42 optimal weight:    0.0670
   overall best weight:    0.7078

-------------------------------------------------------------------------------
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 = 0.3943 r_free = 0.3943 target = 0.180164 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3755 r_free = 0.3755 target = 0.162997 restraints weight = 8699.214|
|-----------------------------------------------------------------------------|
r_work (start): 0.3735 rms_B_bonded: 0.73
r_work: 0.3656 rms_B_bonded: 1.22 restraints_weight: 0.5000
r_work: 0.3573 rms_B_bonded: 2.15 restraints_weight: 0.2500
r_work (final): 0.3573
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8205
moved from start:          0.1561

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  10444  Z= 0.131
  Angle     :  0.555   7.784  14176  Z= 0.300
  Chirality :  0.047   0.163   1612
  Planarity :  0.004   0.032   1804
  Dihedral  : 10.674  82.124   1636
  Min Nonbonded Distance : 2.478

Molprobity Statistics.
  All-atom Clashscore : 5.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.65 %
    Favored  : 97.35 %
  Rotamer:
    Outliers :  1.96 %
    Allowed  : 14.09 %
    Favored  : 83.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.47 (0.23), residues: 1320
  helix:  0.90 (0.25), residues: 416
  sheet: -1.57 (0.30), residues: 272
  loop : -0.43 (0.26), residues: 632

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG D  78 
 TYR   0.015   0.002   TYR D 318 
 PHE   0.011   0.001   PHE C 231 
 TRP   0.005   0.001   TRP A  85 
 HIS   0.003   0.001   HIS D  51 

Details of bonding type rmsd
  covalent geometry    : bond        0.00287 (10444)
  covalent geometry    : angle       0.55537 (14176)
  hydrogen bonds       : bond        0.03869 (  464)
  hydrogen bonds       : angle       5.67456 ( 1212)

********************** 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
  200 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 179
  time to evaluate  : 0.267 
Fit side-chains
   revert: symmetry clash
REVERT: A   75 PHE cc_start: 0.8549 (m-80) cc_final: 0.8099 (m-80)
REVERT: A  103 MET cc_start: 0.7831 (OUTLIER) cc_final: 0.7511 (mmm)
REVERT: A  131 MET cc_start: 0.8865 (mmm) cc_final: 0.8626 (mmm)
REVERT: A  170 GLU cc_start: 0.8883 (pt0) cc_final: 0.8544 (pt0)
REVERT: A  316 PHE cc_start: 0.8478 (OUTLIER) cc_final: 0.8248 (t80)
REVERT: B   59 LYS cc_start: 0.8198 (OUTLIER) cc_final: 0.7892 (pttm)
REVERT: B   75 PHE cc_start: 0.8559 (m-80) cc_final: 0.8112 (m-80)
REVERT: B  103 MET cc_start: 0.7793 (mmm) cc_final: 0.7349 (mmm)
REVERT: B  131 MET cc_start: 0.8851 (mmm) cc_final: 0.8611 (mmm)
REVERT: B  170 GLU cc_start: 0.8831 (pt0) cc_final: 0.8436 (pt0)
REVERT: B  316 PHE cc_start: 0.8482 (OUTLIER) cc_final: 0.8252 (t80)
REVERT: C   75 PHE cc_start: 0.8555 (m-80) cc_final: 0.8113 (m-80)
REVERT: C  103 MET cc_start: 0.7950 (mmm) cc_final: 0.7540 (mmm)
REVERT: C  131 MET cc_start: 0.8872 (mmm) cc_final: 0.8632 (mmm)
REVERT: C  316 PHE cc_start: 0.8480 (OUTLIER) cc_final: 0.8253 (t80)
REVERT: D   75 PHE cc_start: 0.8553 (m-80) cc_final: 0.8105 (m-80)
REVERT: D  103 MET cc_start: 0.7915 (mmm) cc_final: 0.7402 (mmm)
REVERT: D  131 MET cc_start: 0.8877 (mmm) cc_final: 0.8635 (mmm)
REVERT: D  170 GLU cc_start: 0.8818 (pt0) cc_final: 0.8429 (pt0)
REVERT: D  316 PHE cc_start: 0.8473 (OUTLIER) cc_final: 0.8246 (t80)
  outliers start: 21
  outliers final: 14
  residues processed: 194
  average time/residue: 0.6299
  time to fit residues: 130.7200
Evaluate side-chains
  198 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 178
  time to evaluate  : 0.395 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 VAL
Chi-restraints excluded: chain A residue  103 MET
Chi-restraints excluded: chain A residue  175 THR
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   59 LYS
Chi-restraints excluded: chain B residue  141 THR
Chi-restraints excluded: chain B residue  175 THR
Chi-restraints excluded: chain B residue  241 VAL
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  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  175 THR
Chi-restraints excluded: chain D residue  241 VAL
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 48 optimal weight:    0.5980
   chunk 8 optimal weight:    1.9990
   chunk 28 optimal weight:    3.9990
   chunk 68 optimal weight:    4.9990
   chunk 55 optimal weight:    2.9990
   chunk 71 optimal weight:    0.0000
   chunk 122 optimal weight:    0.7980
   chunk 42 optimal weight:    2.9990
   chunk 13 optimal weight:    1.9990
   chunk 1 optimal weight:    0.9990
   chunk 111 optimal weight:    0.9980
   overall best weight:    0.6786

-------------------------------------------------------------------------------
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 = 0.3946 r_free = 0.3946 target = 0.180381 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3758 r_free = 0.3758 target = 0.163141 restraints weight = 8810.420|
|-----------------------------------------------------------------------------|
r_work (start): 0.3520 rms_B_bonded: 0.74
r_work: 0.3447 rms_B_bonded: 1.14 restraints_weight: 0.5000
r_work: 0.3358 rms_B_bonded: 1.99 restraints_weight: 0.2500
r_work (final): 0.3358
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8180
moved from start:          0.1539

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= 0.129
  Angle     :  0.556   8.633  14176  Z= 0.299
  Chirality :  0.047   0.162   1612
  Planarity :  0.004   0.032   1804
  Dihedral  : 10.607  82.558   1636
  Min Nonbonded Distance : 2.483

Molprobity Statistics.
  All-atom Clashscore : 5.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.27 %
    Favored  : 97.73 %
  Rotamer:
    Outliers :  1.87 %
    Allowed  : 14.09 %
    Favored  : 84.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.46 (0.23), residues: 1320
  helix:  0.91 (0.25), residues: 416
  sheet: -1.57 (0.30), residues: 272
  loop : -0.41 (0.26), residues: 632

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B  78 
 TYR   0.015   0.002   TYR C 318 
 PHE   0.011   0.001   PHE A 231 
 TRP   0.005   0.001   TRP A  85 
 HIS   0.003   0.001   HIS A  51 

Details of bonding type rmsd
  covalent geometry    : bond        0.00280 (10444)
  covalent geometry    : angle       0.55628 (14176)
  hydrogen bonds       : bond        0.03839 (  464)
  hydrogen bonds       : angle       5.64244 ( 1212)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4079.13 seconds
wall clock time: 70 minutes 22.56 seconds (4222.56 seconds total)