Starting phenix.real_space_refine
on Thu Jul 31 22:26:30 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7oo8_13007/07_2025/7oo8_13007.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7oo8_13007/07_2025/7oo8_13007.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.7
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7oo8_13007/07_2025/7oo8_13007.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7oo8_13007/07_2025/7oo8_13007.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7oo8_13007/07_2025/7oo8_13007.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7oo8_13007/07_2025/7oo8_13007.cif"
  }
  resolution = 3.7
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.006
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      42      5.16       5
     C    8932      2.51       5
     N    2436      2.21       5
     O    2513      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 13923
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 1989
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 261, 1989
          Classifications: {'peptide': 261}
          Link IDs: {'PTRANS': 5, 'TRANS': 255}
  Restraints were copied for chains:
    C, B, E, D, G, F
  Time building chain proxies: 5.28, per 1000 atoms: 0.38
  Number of scatterers: 13923
  At special positions: 0
  Unit cell: (98.9055, 98.9055, 141.446, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      42     16.00
     O    2513      8.00
     N    2436      7.00
     C    8932      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: 3.25
  Conformation dependent library (CDL) restraints added in 1.8 seconds
  

  3626 Ramachandran restraints generated.
    1813 Oldfield, 0 Emsley, 1813 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3374

  Finding SS restraints...
    Secondary structure from input PDB file:
      42 helices and 9 sheets defined
      55.9% alpha, 19.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.16
  Creating SS restraints...
    Processing helix  chain 'A' and resid 22 through 59
      removed outlier: 3.508A  pdb=" N   ARG A  59 " --> pdb=" O   LEU A  55 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 62 through 90
    Processing helix  chain 'A' and resid 93 through 128
      removed outlier: 4.700A  pdb=" N   GLY A 113 " --> pdb=" O   LEU A 109 " (cutoff:3.500A)
      removed outlier: 5.093A  pdb=" N   SER A 114 " --> pdb=" O   ALA A 110 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 167 through 172
    Processing helix  chain 'A' and resid 197 through 212
    Processing helix  chain 'A' and resid 245 through 265
    Processing helix  chain 'B' and resid 22 through 59
      removed outlier: 3.508A  pdb=" N   ARG B  59 " --> pdb=" O   LEU B  55 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 62 through 90
    Processing helix  chain 'B' and resid 93 through 128
      removed outlier: 4.700A  pdb=" N   GLY B 113 " --> pdb=" O   LEU B 109 " (cutoff:3.500A)
      removed outlier: 5.093A  pdb=" N   SER B 114 " --> pdb=" O   ALA B 110 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 167 through 172
    Processing helix  chain 'B' and resid 197 through 212
    Processing helix  chain 'B' and resid 245 through 265
    Processing helix  chain 'C' and resid 22 through 59
      removed outlier: 3.508A  pdb=" N   ARG C  59 " --> pdb=" O   LEU C  55 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 62 through 90
    Processing helix  chain 'C' and resid 93 through 128
      removed outlier: 4.700A  pdb=" N   GLY C 113 " --> pdb=" O   LEU C 109 " (cutoff:3.500A)
      removed outlier: 5.093A  pdb=" N   SER C 114 " --> pdb=" O   ALA C 110 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 167 through 172
    Processing helix  chain 'C' and resid 197 through 212
    Processing helix  chain 'C' and resid 245 through 265
    Processing helix  chain 'D' and resid 22 through 59
      removed outlier: 3.509A  pdb=" N   ARG D  59 " --> pdb=" O   LEU D  55 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 62 through 90
    Processing helix  chain 'D' and resid 93 through 128
      removed outlier: 4.700A  pdb=" N   GLY D 113 " --> pdb=" O   LEU D 109 " (cutoff:3.500A)
      removed outlier: 5.093A  pdb=" N   SER D 114 " --> pdb=" O   ALA D 110 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 167 through 172
    Processing helix  chain 'D' and resid 197 through 212
    Processing helix  chain 'D' and resid 245 through 265
    Processing helix  chain 'E' and resid 22 through 59
      removed outlier: 3.509A  pdb=" N   ARG E  59 " --> pdb=" O   LEU E  55 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 62 through 90
    Processing helix  chain 'E' and resid 93 through 128
      removed outlier: 4.701A  pdb=" N   GLY E 113 " --> pdb=" O   LEU E 109 " (cutoff:3.500A)
      removed outlier: 5.093A  pdb=" N   SER E 114 " --> pdb=" O   ALA E 110 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 167 through 172
    Processing helix  chain 'E' and resid 197 through 212
    Processing helix  chain 'E' and resid 245 through 265
    Processing helix  chain 'F' and resid 22 through 59
      removed outlier: 3.509A  pdb=" N   ARG F  59 " --> pdb=" O   LEU F  55 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 62 through 90
    Processing helix  chain 'F' and resid 93 through 128
      removed outlier: 4.699A  pdb=" N   GLY F 113 " --> pdb=" O   LEU F 109 " (cutoff:3.500A)
      removed outlier: 5.093A  pdb=" N   SER F 114 " --> pdb=" O   ALA F 110 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 167 through 172
    Processing helix  chain 'F' and resid 197 through 212
    Processing helix  chain 'F' and resid 245 through 265
    Processing helix  chain 'G' and resid 22 through 59
      removed outlier: 3.509A  pdb=" N   ARG G  59 " --> pdb=" O   LEU G  55 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 62 through 90
    Processing helix  chain 'G' and resid 93 through 128
      removed outlier: 4.699A  pdb=" N   GLY G 113 " --> pdb=" O   LEU G 109 " (cutoff:3.500A)
      removed outlier: 5.093A  pdb=" N   SER G 114 " --> pdb=" O   ALA G 110 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 167 through 172
    Processing helix  chain 'G' and resid 197 through 212
    Processing helix  chain 'G' and resid 245 through 265
    Processing sheet with id=AA1, first strand: chain 'A' and resid 135 through 138
      removed outlier: 3.679A  pdb=" N   VAL A 141 " --> pdb=" O   LEU A 138 " (cutoff:3.500A)
      removed outlier: 6.823A  pdb=" N   THR A 154 " --> pdb=" O   LEU A 146 " (cutoff:3.500A)
      removed outlier: 5.371A  pdb=" N   VAL A 148 " --> pdb=" O   SER A 152 " (cutoff:3.500A)
      removed outlier: 7.016A  pdb=" N   SER A 152 " --> pdb=" O   VAL A 148 " (cutoff:3.500A)
      removed outlier: 3.679A  pdb=" N   VAL G 141 " --> pdb=" O   LEU G 138 " (cutoff:3.500A)
      removed outlier: 6.823A  pdb=" N   THR G 154 " --> pdb=" O   LEU G 146 " (cutoff:3.500A)
      removed outlier: 5.371A  pdb=" N   VAL G 148 " --> pdb=" O   SER G 152 " (cutoff:3.500A)
      removed outlier: 7.017A  pdb=" N   SER G 152 " --> pdb=" O   VAL G 148 " (cutoff:3.500A)
      removed outlier: 3.679A  pdb=" N   VAL F 141 " --> pdb=" O   LEU F 138 " (cutoff:3.500A)
      removed outlier: 6.823A  pdb=" N   THR F 154 " --> pdb=" O   LEU F 146 " (cutoff:3.500A)
      removed outlier: 5.371A  pdb=" N   VAL F 148 " --> pdb=" O   SER F 152 " (cutoff:3.500A)
      removed outlier: 7.017A  pdb=" N   SER F 152 " --> pdb=" O   VAL F 148 " (cutoff:3.500A)
      removed outlier: 3.679A  pdb=" N   VAL E 141 " --> pdb=" O   LEU E 138 " (cutoff:3.500A)
      removed outlier: 6.823A  pdb=" N   THR E 154 " --> pdb=" O   LEU E 146 " (cutoff:3.500A)
      removed outlier: 5.371A  pdb=" N   VAL E 148 " --> pdb=" O   SER E 152 " (cutoff:3.500A)
      removed outlier: 7.016A  pdb=" N   SER E 152 " --> pdb=" O   VAL E 148 " (cutoff:3.500A)
      removed outlier: 3.680A  pdb=" N   VAL D 141 " --> pdb=" O   LEU D 138 " (cutoff:3.500A)
      removed outlier: 6.824A  pdb=" N   THR D 154 " --> pdb=" O   LEU D 146 " (cutoff:3.500A)
      removed outlier: 5.371A  pdb=" N   VAL D 148 " --> pdb=" O   SER D 152 " (cutoff:3.500A)
      removed outlier: 7.016A  pdb=" N   SER D 152 " --> pdb=" O   VAL D 148 " (cutoff:3.500A)
      removed outlier: 3.679A  pdb=" N   VAL C 141 " --> pdb=" O   LEU C 138 " (cutoff:3.500A)
      removed outlier: 6.823A  pdb=" N   THR C 154 " --> pdb=" O   LEU C 146 " (cutoff:3.500A)
      removed outlier: 5.371A  pdb=" N   VAL C 148 " --> pdb=" O   SER C 152 " (cutoff:3.500A)
      removed outlier: 7.016A  pdb=" N   SER C 152 " --> pdb=" O   VAL C 148 " (cutoff:3.500A)
      removed outlier: 3.680A  pdb=" N   VAL B 141 " --> pdb=" O   LEU B 138 " (cutoff:3.500A)
      removed outlier: 6.822A  pdb=" N   THR B 154 " --> pdb=" O   LEU B 146 " (cutoff:3.500A)
      removed outlier: 5.370A  pdb=" N   VAL B 148 " --> pdb=" O   SER B 152 " (cutoff:3.500A)
      removed outlier: 7.017A  pdb=" N   SER B 152 " --> pdb=" O   VAL B 148 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 183 through 192
      removed outlier: 6.808A  pdb=" N   ASN A 234 " --> pdb=" O   ASN A 226 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 272 through 278
      removed outlier: 8.288A  pdb=" N   MET B 273 " --> pdb=" O   GLN A 272 " (cutoff:3.500A)
      removed outlier: 6.169A  pdb=" N   ASP A 274 " --> pdb=" O   MET B 273 " (cutoff:3.500A)
      removed outlier: 7.190A  pdb=" N   VAL B 275 " --> pdb=" O   ASP A 274 " (cutoff:3.500A)
      removed outlier: 6.012A  pdb=" N   ASN A 276 " --> pdb=" O   VAL B 275 " (cutoff:3.500A)
      removed outlier: 8.367A  pdb=" N   MET C 273 " --> pdb=" O   GLN B 272 " (cutoff:3.500A)
      removed outlier: 6.166A  pdb=" N   ASP B 274 " --> pdb=" O   MET C 273 " (cutoff:3.500A)
      removed outlier: 7.024A  pdb=" N   VAL C 275 " --> pdb=" O   ASP B 274 " (cutoff:3.500A)
      removed outlier: 5.829A  pdb=" N   ASN B 276 " --> pdb=" O   VAL C 275 " (cutoff:3.500A)
      removed outlier: 7.214A  pdb=" N   PHE C 277 " --> pdb=" O   ASN B 276 " (cutoff:3.500A)
      removed outlier: 8.369A  pdb=" N   MET D 273 " --> pdb=" O   GLN C 272 " (cutoff:3.500A)
      removed outlier: 6.231A  pdb=" N   ASP C 274 " --> pdb=" O   MET D 273 " (cutoff:3.500A)
      removed outlier: 7.192A  pdb=" N   VAL D 275 " --> pdb=" O   ASP C 274 " (cutoff:3.500A)
      removed outlier: 6.011A  pdb=" N   ASN C 276 " --> pdb=" O   VAL D 275 " (cutoff:3.500A)
      removed outlier: 7.481A  pdb=" N   PHE D 277 " --> pdb=" O   ASN C 276 " (cutoff:3.500A)
      removed outlier: 7.493A  pdb=" N   LYS C 278 " --> pdb=" O   PHE D 277 " (cutoff:3.500A)
      removed outlier: 8.297A  pdb=" N   MET E 273 " --> pdb=" O   GLN D 272 " (cutoff:3.500A)
      removed outlier: 6.183A  pdb=" N   ASP D 274 " --> pdb=" O   MET E 273 " (cutoff:3.500A)
      removed outlier: 7.210A  pdb=" N   VAL E 275 " --> pdb=" O   ASP D 274 " (cutoff:3.500A)
      removed outlier: 6.032A  pdb=" N   ASN D 276 " --> pdb=" O   VAL E 275 " (cutoff:3.500A)
      removed outlier: 7.564A  pdb=" N   PHE E 277 " --> pdb=" O   ASN D 276 " (cutoff:3.500A)
      removed outlier: 7.582A  pdb=" N   LYS D 278 " --> pdb=" O   PHE E 277 " (cutoff:3.500A)
      removed outlier: 8.306A  pdb=" N   MET F 273 " --> pdb=" O   GLN E 272 " (cutoff:3.500A)
      removed outlier: 6.182A  pdb=" N   ASP E 274 " --> pdb=" O   MET F 273 " (cutoff:3.500A)
      removed outlier: 7.180A  pdb=" N   VAL F 275 " --> pdb=" O   ASP E 274 " (cutoff:3.500A)
      removed outlier: 6.004A  pdb=" N   ASN E 276 " --> pdb=" O   VAL F 275 " (cutoff:3.500A)
      removed outlier: 7.513A  pdb=" N   PHE F 277 " --> pdb=" O   ASN E 276 " (cutoff:3.500A)
      removed outlier: 7.536A  pdb=" N   LYS E 278 " --> pdb=" O   PHE F 277 " (cutoff:3.500A)
      removed outlier: 8.278A  pdb=" N   MET G 273 " --> pdb=" O   GLN F 272 " (cutoff:3.500A)
      removed outlier: 6.148A  pdb=" N   ASP F 274 " --> pdb=" O   MET G 273 " (cutoff:3.500A)
      removed outlier: 7.150A  pdb=" N   VAL G 275 " --> pdb=" O   ASP F 274 " (cutoff:3.500A)
      removed outlier: 5.971A  pdb=" N   ASN F 276 " --> pdb=" O   VAL G 275 " (cutoff:3.500A)
      removed outlier: 7.494A  pdb=" N   PHE G 277 " --> pdb=" O   ASN F 276 " (cutoff:3.500A)
      removed outlier: 7.518A  pdb=" N   LYS F 278 " --> pdb=" O   PHE G 277 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 183 through 192
      removed outlier: 6.809A  pdb=" N   ASN B 234 " --> pdb=" O   ASN B 226 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'C' and resid 183 through 192
      removed outlier: 6.809A  pdb=" N   ASN C 234 " --> pdb=" O   ASN C 226 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'D' and resid 183 through 192
      removed outlier: 6.808A  pdb=" N   ASN D 234 " --> pdb=" O   ASN D 226 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'E' and resid 183 through 192
      removed outlier: 6.808A  pdb=" N   ASN E 234 " --> pdb=" O   ASN E 226 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'F' and resid 183 through 192
      removed outlier: 6.809A  pdb=" N   ASN F 234 " --> pdb=" O   ASN F 226 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'G' and resid 183 through 192
      removed outlier: 6.808A  pdb=" N   ASN G 234 " --> pdb=" O   ASN G 226 " (cutoff:3.500A)

    1055 hydrogen bonds defined for protein.
    3081 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: 4.18

  Time building geometry restraints manager: 3.84 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 4654
        1.34 -     1.46: 2133
        1.46 -     1.57: 7227
        1.57 -     1.69: 0
        1.69 -     1.80: 84
  Bond restraints: 14098
  Sorted by residual:
  bond pdb=" C   ARG C 128 "
       pdb=" O   ARG C 128 "
    ideal  model  delta    sigma   weight residual
    1.235  1.231  0.003 4.70e-03 4.53e+04 5.50e-01
  bond pdb=" C   ARG G 128 "
       pdb=" O   ARG G 128 "
    ideal  model  delta    sigma   weight residual
    1.235  1.232  0.003 4.70e-03 4.53e+04 4.64e-01
  bond pdb=" C   ARG E 128 "
       pdb=" O   ARG E 128 "
    ideal  model  delta    sigma   weight residual
    1.235  1.232  0.003 4.70e-03 4.53e+04 4.48e-01
  bond pdb=" N   ILE D 165 "
       pdb=" CA  ILE D 165 "
    ideal  model  delta    sigma   weight residual
    1.460  1.454  0.006 9.30e-03 1.16e+04 4.42e-01
  bond pdb=" C   ARG F 128 "
       pdb=" O   ARG F 128 "
    ideal  model  delta    sigma   weight residual
    1.235  1.232  0.003 4.70e-03 4.53e+04 4.12e-01
  ... (remaining 14093 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     0.91: 18459
        0.91 -     1.83: 595
        1.83 -     2.74: 15
        2.74 -     3.65: 34
        3.65 -     4.56: 14
  Bond angle restraints: 19117
  Sorted by residual:
  angle pdb=" N   ILE B  83 "
        pdb=" CA  ILE B  83 "
        pdb=" CB  ILE B  83 "
      ideal   model   delta    sigma   weight residual
     110.77  113.99   -3.22 1.81e+00 3.05e-01 3.16e+00
  angle pdb=" N   ILE D  83 "
        pdb=" CA  ILE D  83 "
        pdb=" CB  ILE D  83 "
      ideal   model   delta    sigma   weight residual
     110.77  113.96   -3.19 1.81e+00 3.05e-01 3.12e+00
  angle pdb=" N   ILE C  83 "
        pdb=" CA  ILE C  83 "
        pdb=" CB  ILE C  83 "
      ideal   model   delta    sigma   weight residual
     110.77  113.95   -3.18 1.81e+00 3.05e-01 3.08e+00
  angle pdb=" N   ILE E  83 "
        pdb=" CA  ILE E  83 "
        pdb=" CB  ILE E  83 "
      ideal   model   delta    sigma   weight residual
     110.77  113.91   -3.14 1.81e+00 3.05e-01 3.02e+00
  angle pdb=" N   ILE F  83 "
        pdb=" CA  ILE F  83 "
        pdb=" CB  ILE F  83 "
      ideal   model   delta    sigma   weight residual
     110.77  113.91   -3.14 1.81e+00 3.05e-01 3.00e+00
  ... (remaining 19112 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -     9.84: 7336
        9.84 -    19.68: 805
       19.68 -    29.51: 238
       29.51 -    39.35: 91
       39.35 -    49.19: 14
  Dihedral angle restraints: 8484
    sinusoidal: 3248
      harmonic: 5236
  Sorted by residual:
  dihedral pdb=" C   ILE C  83 "
           pdb=" N   ILE C  83 "
           pdb=" CA  ILE C  83 "
           pdb=" CB  ILE C  83 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.00 -130.26    8.26     0      2.50e+00 1.60e-01 1.09e+01
  dihedral pdb=" C   ILE A  83 "
           pdb=" N   ILE A  83 "
           pdb=" CA  ILE A  83 "
           pdb=" CB  ILE A  83 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.00 -130.24    8.24     0      2.50e+00 1.60e-01 1.09e+01
  dihedral pdb=" C   ILE B  83 "
           pdb=" N   ILE B  83 "
           pdb=" CA  ILE B  83 "
           pdb=" CB  ILE B  83 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.00 -130.22    8.22     0      2.50e+00 1.60e-01 1.08e+01
  ... (remaining 8481 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.042: 1774
       0.042 -    0.083: 410
       0.083 -    0.125: 140
       0.125 -    0.166: 14
       0.166 -    0.208: 7
  Chirality restraints: 2345
  Sorted by residual:
  chirality pdb=" CA  ILE C  83 "
            pdb=" N   ILE C  83 "
            pdb=" C   ILE C  83 "
            pdb=" CB  ILE C  83 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.23    0.21 2.00e-01 2.50e+01 1.08e+00
  chirality pdb=" CA  ILE B  83 "
            pdb=" N   ILE B  83 "
            pdb=" C   ILE B  83 "
            pdb=" CB  ILE B  83 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.23    0.21 2.00e-01 2.50e+01 1.06e+00
  chirality pdb=" CA  ILE A  83 "
            pdb=" N   ILE A  83 "
            pdb=" C   ILE A  83 "
            pdb=" CB  ILE A  83 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.23    0.21 2.00e-01 2.50e+01 1.06e+00
  ... (remaining 2342 not shown)

  Planarity restraints: 2429
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL G 275 "    0.004 2.00e-02 2.50e+03   7.56e-03 5.71e-01
        pdb=" C   VAL G 275 "   -0.013 2.00e-02 2.50e+03
        pdb=" O   VAL G 275 "    0.005 2.00e-02 2.50e+03
        pdb=" N   ASN G 276 "    0.004 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL D 275 "    0.004 2.00e-02 2.50e+03   7.54e-03 5.69e-01
        pdb=" C   VAL D 275 "   -0.013 2.00e-02 2.50e+03
        pdb=" O   VAL D 275 "    0.005 2.00e-02 2.50e+03
        pdb=" N   ASN D 276 "    0.004 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL E 275 "    0.004 2.00e-02 2.50e+03   7.52e-03 5.65e-01
        pdb=" C   VAL E 275 "   -0.013 2.00e-02 2.50e+03
        pdb=" O   VAL E 275 "    0.005 2.00e-02 2.50e+03
        pdb=" N   ASN E 276 "    0.004 2.00e-02 2.50e+03
  ... (remaining 2426 not shown)

  Histogram of nonbonded interaction distances:
        2.29 -     2.81: 3570
        2.81 -     3.33: 14071
        3.33 -     3.85: 23177
        3.85 -     4.38: 25652
        4.38 -     4.90: 45696
  Nonbonded interactions: 112166
  Sorted by model distance:
  nonbonded pdb=" NZ  LYS B 202 "
            pdb=" OE1 GLU C 255 "
     model   vdw
     2.286 3.120
  nonbonded pdb=" NH2 ARG E  88 "
            pdb=" O   GLY F  90 "
     model   vdw
     2.291 3.120
  nonbonded pdb=" NH2 ARG D  88 "
            pdb=" O   GLY E  90 "
     model   vdw
     2.292 3.120
  nonbonded pdb=" NH2 ARG C  88 "
            pdb=" O   GLY D  90 "
     model   vdw
     2.293 3.120
  nonbonded pdb=" NH2 ARG F  88 "
            pdb=" O   GLY G  90 "
     model   vdw
     2.310 3.120
  ... (remaining 112161 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: 0.12
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'C'
  selection = chain 'B'
  selection = chain 'E'
  selection = chain 'D'
  selection = chain 'G'
  selection = chain 'F'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.280
  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:          0.560
  Check model and map are aligned:         0.100
  Set scattering table:                    0.140
  Process input model:                     28.660
  Find NCS groups from input model:        0.280
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:3.120
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   34.190
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7895
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      :  0.003   0.017  14098  Z= 0.137
  Angle     :  0.399   4.564  19117  Z= 0.228
  Chirality :  0.041   0.208   2345
  Planarity :  0.002   0.018   2429
  Dihedral  :  9.895  49.189   5110
  Min Nonbonded Distance : 2.286

Molprobity Statistics.
  All-atom Clashscore : 6.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.93 %
    Favored  : 98.07 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  5.75 %
    Favored  : 94.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.79 (0.19), residues: 1813
  helix:  3.46 (0.15), residues: 1008
  sheet:  0.09 (0.28), residues: 294
  loop : -0.47 (0.25), residues: 511

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP C 240 
 PHE   0.005   0.001   PHE G 188 
 TYR   0.006   0.001   TYR D 135 
 ARG   0.002   0.000   ARG F 180 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.09648 ( 1055)
  hydrogen bonds       : angle       5.03334 ( 3081)
  covalent geometry    : bond        0.00279 (14098)
  covalent geometry    : angle       0.39948 (19117)

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

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

  3626 Ramachandran restraints generated.
    1813 Oldfield, 0 Emsley, 1813 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3626 Ramachandran restraints generated.
    1813 Oldfield, 0 Emsley, 1813 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  426 residues out of total 1477 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 426
  time to evaluate  : 2.610 
Fit side-chains
REVERT: A   43 ILE cc_start: 0.7702 (tp) cc_final: 0.7461 (tp)
REVERT: A   47 MET cc_start: 0.7030 (mmt) cc_final: 0.6676 (mmt)
REVERT: A   50 ASN cc_start: 0.7164 (m-40) cc_final: 0.6843 (t0)
REVERT: A  144 THR cc_start: 0.8965 (m) cc_final: 0.8337 (p)
REVERT: A  199 ASP cc_start: 0.8183 (p0) cc_final: 0.7824 (p0)
REVERT: A  212 GLU cc_start: 0.6741 (tp30) cc_final: 0.6307 (tp30)
REVERT: B   40 VAL cc_start: 0.8419 (t) cc_final: 0.7842 (m)
REVERT: B   78 ILE cc_start: 0.8065 (pt) cc_final: 0.7447 (mt)
REVERT: C   50 ASN cc_start: 0.7503 (m-40) cc_final: 0.7158 (t0)
REVERT: C   78 ILE cc_start: 0.8329 (pt) cc_final: 0.7673 (mt)
REVERT: D  199 ASP cc_start: 0.8112 (p0) cc_final: 0.7859 (p0)
REVERT: E   78 ILE cc_start: 0.8410 (pt) cc_final: 0.7836 (mt)
REVERT: F   31 ILE cc_start: 0.9023 (tp) cc_final: 0.8605 (mm)
REVERT: F   78 ILE cc_start: 0.8463 (pt) cc_final: 0.7859 (mt)
REVERT: F  155 MET cc_start: 0.8772 (ptp) cc_final: 0.8571 (ptm)
REVERT: G   40 VAL cc_start: 0.8501 (t) cc_final: 0.8209 (m)
  outliers start: 0
  outliers final: 0
  residues processed: 426
  average time/residue: 0.3141
  time to fit residues: 195.0001
Evaluate side-chains
  311 residues out of total 1477 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 311
  time to evaluate  : 1.885 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 182
   random chunks:
   chunk 153 optimal weight:    3.9990
   chunk 137 optimal weight:    0.9990
   chunk 76 optimal weight:    2.9990
   chunk 47 optimal weight:    5.9990
   chunk 93 optimal weight:    3.9990
   chunk 73 optimal weight:    5.9990
   chunk 142 optimal weight:    0.7980
   chunk 55 optimal weight:    0.9980
   chunk 86 optimal weight:    3.9990
   chunk 106 optimal weight:    2.9990
   chunk 165 optimal weight:    3.9990
   overall best weight:    1.7586

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

Flipped N/Q/H residues before XYZ refinement:
B 247 GLN
D 149 GLN
E 247 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3459 r_free = 0.3459 target = 0.109359 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3155 r_free = 0.3155 target = 0.091718 restraints weight = 30271.751|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3192 r_free = 0.3192 target = 0.094103 restraints weight = 14401.670|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3220 r_free = 0.3220 target = 0.095826 restraints weight = 8709.199|
|-----------------------------------------------------------------------------|
r_work (final): 0.3223
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7918
moved from start:          0.1370

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039  14098  Z= 0.160
  Angle     :  0.482   4.910  19117  Z= 0.264
  Chirality :  0.042   0.180   2345
  Planarity :  0.004   0.031   2429
  Dihedral  :  3.884  12.352   1988
  Min Nonbonded Distance : 2.601

Molprobity Statistics.
  All-atom Clashscore : 7.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.21 %
    Favored  : 98.79 %
  Rotamer:
    Outliers :  2.44 %
    Allowed  : 14.35 %
    Favored  : 83.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.53 (0.19), residues: 1813
  helix:  3.27 (0.14), residues: 1008
  sheet: -0.11 (0.26), residues: 308
  loop : -0.59 (0.26), residues: 497

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B 251 
 PHE   0.021   0.002   PHE C 277 
 TYR   0.007   0.001   TYR C 250 
 ARG   0.008   0.000   ARG A 279 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03706 ( 1055)
  hydrogen bonds       : angle       4.11262 ( 3081)
  covalent geometry    : bond        0.00358 (14098)
  covalent geometry    : angle       0.48174 (19117)

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

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

  3626 Ramachandran restraints generated.
    1813 Oldfield, 0 Emsley, 1813 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3626 Ramachandran restraints generated.
    1813 Oldfield, 0 Emsley, 1813 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  369 residues out of total 1477 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 333
  time to evaluate  : 1.979 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   50 ASN cc_start: 0.7026 (m-40) cc_final: 0.6758 (t0)
REVERT: A  144 THR cc_start: 0.8970 (m) cc_final: 0.8225 (p)
REVERT: A  199 ASP cc_start: 0.8165 (p0) cc_final: 0.7877 (p0)
REVERT: B   81 THR cc_start: 0.9121 (m) cc_final: 0.8878 (t)
REVERT: C   50 ASN cc_start: 0.7411 (m-40) cc_final: 0.7102 (t0)
REVERT: C   78 ILE cc_start: 0.8103 (pt) cc_final: 0.7756 (mt)
REVERT: C   81 THR cc_start: 0.8989 (m) cc_final: 0.8692 (t)
REVERT: C  273 MET cc_start: 0.8675 (tpp) cc_final: 0.8218 (tpp)
REVERT: D  199 ASP cc_start: 0.8130 (p0) cc_final: 0.7921 (p0)
REVERT: D  247 GLN cc_start: 0.8197 (tp40) cc_final: 0.7831 (tp-100)
REVERT: E   81 THR cc_start: 0.9057 (m) cc_final: 0.8809 (t)
REVERT: F   31 ILE cc_start: 0.9002 (tp) cc_final: 0.8651 (mm)
REVERT: F   78 ILE cc_start: 0.8418 (pt) cc_final: 0.7871 (mt)
REVERT: G   40 VAL cc_start: 0.8592 (t) cc_final: 0.8353 (m)
REVERT: G   81 THR cc_start: 0.9027 (m) cc_final: 0.8792 (t)
  outliers start: 36
  outliers final: 23
  residues processed: 338
  average time/residue: 0.2919
  time to fit residues: 149.8303
Evaluate side-chains
  304 residues out of total 1477 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 281
  time to evaluate  : 2.143 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  148 VAL
Chi-restraints excluded: chain A residue  227 GLU
Chi-restraints excluded: chain B residue   42 LEU
Chi-restraints excluded: chain B residue   91 VAL
Chi-restraints excluded: chain B residue  148 VAL
Chi-restraints excluded: chain C residue   91 VAL
Chi-restraints excluded: chain C residue  122 VAL
Chi-restraints excluded: chain C residue  144 THR
Chi-restraints excluded: chain C residue  227 GLU
Chi-restraints excluded: chain D residue   83 ILE
Chi-restraints excluded: chain D residue   91 VAL
Chi-restraints excluded: chain D residue  122 VAL
Chi-restraints excluded: chain D residue  227 GLU
Chi-restraints excluded: chain E residue   42 LEU
Chi-restraints excluded: chain E residue   82 LEU
Chi-restraints excluded: chain E residue   91 VAL
Chi-restraints excluded: chain E residue  122 VAL
Chi-restraints excluded: chain F residue  122 VAL
Chi-restraints excluded: chain F residue  227 GLU
Chi-restraints excluded: chain G residue   91 VAL
Chi-restraints excluded: chain G residue  105 LEU
Chi-restraints excluded: chain G residue  122 VAL
Chi-restraints excluded: chain G residue  227 GLU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 182
   random chunks:
   chunk 1 optimal weight:    0.9990
   chunk 143 optimal weight:    6.9990
   chunk 41 optimal weight:    2.9990
   chunk 116 optimal weight:    2.9990
   chunk 48 optimal weight:    1.9990
   chunk 173 optimal weight:    6.9990
   chunk 75 optimal weight:    3.9990
   chunk 30 optimal weight:    1.9990
   chunk 50 optimal weight:    0.9990
   chunk 150 optimal weight:    4.9990
   chunk 46 optimal weight:    1.9990
   overall best weight:    1.5990

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3457 r_free = 0.3457 target = 0.109265 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3154 r_free = 0.3154 target = 0.091725 restraints weight = 30478.066|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3192 r_free = 0.3192 target = 0.094127 restraints weight = 14632.962|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3217 r_free = 0.3217 target = 0.095780 restraints weight = 8864.986|
|-----------------------------------------------------------------------------|
r_work (final): 0.3220
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7923
moved from start:          0.1575

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  14098  Z= 0.146
  Angle     :  0.441   4.661  19117  Z= 0.243
  Chirality :  0.041   0.185   2345
  Planarity :  0.003   0.030   2429
  Dihedral  :  3.863  12.926   1988
  Min Nonbonded Distance : 2.599

Molprobity Statistics.
  All-atom Clashscore : 8.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.16 %
    Favored  : 98.84 %
  Rotamer:
    Outliers :  2.44 %
    Allowed  : 16.99 %
    Favored  : 80.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.54 (0.19), residues: 1813
  helix:  3.24 (0.14), residues: 1008
  sheet:  0.58 (0.28), residues: 273
  loop : -0.92 (0.25), residues: 532

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP A 251 
 PHE   0.023   0.002   PHE C 277 
 TYR   0.006   0.001   TYR A 250 
 ARG   0.010   0.000   ARG E 279 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03455 ( 1055)
  hydrogen bonds       : angle       4.02206 ( 3081)
  covalent geometry    : bond        0.00324 (14098)
  covalent geometry    : angle       0.44122 (19117)

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

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

  3626 Ramachandran restraints generated.
    1813 Oldfield, 0 Emsley, 1813 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3626 Ramachandran restraints generated.
    1813 Oldfield, 0 Emsley, 1813 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  360 residues out of total 1477 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 324
  time to evaluate  : 1.523 
Fit side-chains
REVERT: A   50 ASN cc_start: 0.7080 (m-40) cc_final: 0.6778 (t0)
REVERT: A  199 ASP cc_start: 0.8068 (p0) cc_final: 0.7810 (p0)
REVERT: B   44 ILE cc_start: 0.8588 (mt) cc_final: 0.8377 (mm)
REVERT: B   81 THR cc_start: 0.9121 (m) cc_final: 0.8868 (t)
REVERT: C   50 ASN cc_start: 0.7353 (m-40) cc_final: 0.7085 (t0)
REVERT: C   78 ILE cc_start: 0.8153 (pt) cc_final: 0.7815 (mt)
REVERT: C   81 THR cc_start: 0.8977 (m) cc_final: 0.8689 (t)
REVERT: C  273 MET cc_start: 0.8710 (tpp) cc_final: 0.8255 (tpp)
REVERT: D  199 ASP cc_start: 0.8209 (p0) cc_final: 0.7967 (p0)
REVERT: E   81 THR cc_start: 0.9038 (m) cc_final: 0.8743 (t)
REVERT: F   31 ILE cc_start: 0.8983 (tp) cc_final: 0.8632 (mm)
REVERT: F   78 ILE cc_start: 0.8412 (pt) cc_final: 0.7862 (mt)
REVERT: G   46 ARG cc_start: 0.5695 (ttp-170) cc_final: 0.5256 (mtm180)
REVERT: G   81 THR cc_start: 0.9024 (m) cc_final: 0.8793 (t)
  outliers start: 36
  outliers final: 29
  residues processed: 334
  average time/residue: 0.2361
  time to fit residues: 120.5697
Evaluate side-chains
  319 residues out of total 1477 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 290
  time to evaluate  : 1.756 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  122 VAL
Chi-restraints excluded: chain A residue  148 VAL
Chi-restraints excluded: chain B residue   42 LEU
Chi-restraints excluded: chain B residue   91 VAL
Chi-restraints excluded: chain B residue  122 VAL
Chi-restraints excluded: chain B residue  148 VAL
Chi-restraints excluded: chain C residue   91 VAL
Chi-restraints excluded: chain C residue  122 VAL
Chi-restraints excluded: chain C residue  148 VAL
Chi-restraints excluded: chain D residue   83 ILE
Chi-restraints excluded: chain D residue   91 VAL
Chi-restraints excluded: chain D residue  122 VAL
Chi-restraints excluded: chain D residue  148 VAL
Chi-restraints excluded: chain D residue  227 GLU
Chi-restraints excluded: chain E residue   42 LEU
Chi-restraints excluded: chain E residue   82 LEU
Chi-restraints excluded: chain E residue   91 VAL
Chi-restraints excluded: chain E residue  122 VAL
Chi-restraints excluded: chain E residue  148 VAL
Chi-restraints excluded: chain E residue  227 GLU
Chi-restraints excluded: chain F residue   83 ILE
Chi-restraints excluded: chain F residue   91 VAL
Chi-restraints excluded: chain F residue  122 VAL
Chi-restraints excluded: chain F residue  148 VAL
Chi-restraints excluded: chain G residue   91 VAL
Chi-restraints excluded: chain G residue  100 LEU
Chi-restraints excluded: chain G residue  105 LEU
Chi-restraints excluded: chain G residue  122 VAL
Chi-restraints excluded: chain G residue  148 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 182
   random chunks:
   chunk 125 optimal weight:    2.9990
   chunk 165 optimal weight:    6.9990
   chunk 129 optimal weight:    0.9980
   chunk 42 optimal weight:    2.9990
   chunk 94 optimal weight:    1.9990
   chunk 150 optimal weight:    0.6980
   chunk 71 optimal weight:    1.9990
   chunk 24 optimal weight:    6.9990
   chunk 139 optimal weight:    0.9980
   chunk 181 optimal weight:    3.9990
   chunk 77 optimal weight:    1.9990
   overall best weight:    1.3384

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3468 r_free = 0.3468 target = 0.109875 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3159 r_free = 0.3159 target = 0.092110 restraints weight = 30430.672|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3194 r_free = 0.3194 target = 0.094485 restraints weight = 14860.902|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 48)----------------|
| r_work = 0.3222 r_free = 0.3222 target = 0.096126 restraints weight = 9151.167|
|-----------------------------------------------------------------------------|
r_work (final): 0.3225
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7921
moved from start:          0.1731

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  14098  Z= 0.130
  Angle     :  0.437   5.024  19117  Z= 0.239
  Chirality :  0.041   0.197   2345
  Planarity :  0.003   0.042   2429
  Dihedral  :  3.862  13.541   1988
  Min Nonbonded Distance : 2.604

Molprobity Statistics.
  All-atom Clashscore : 8.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.27 %
    Favored  : 98.73 %
  Rotamer:
    Outliers :  2.37 %
    Allowed  : 19.77 %
    Favored  : 77.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.56 (0.19), residues: 1813
  helix:  3.22 (0.14), residues: 1015
  sheet:  0.66 (0.28), residues: 273
  loop : -0.96 (0.26), residues: 525

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP F 251 
 PHE   0.036   0.002   PHE A 277 
 TYR   0.006   0.001   TYR C 250 
 ARG   0.011   0.000   ARG C 279 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03309 ( 1055)
  hydrogen bonds       : angle       3.94337 ( 3081)
  covalent geometry    : bond        0.00293 (14098)
  covalent geometry    : angle       0.43660 (19117)

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

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

  3626 Ramachandran restraints generated.
    1813 Oldfield, 0 Emsley, 1813 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3626 Ramachandran restraints generated.
    1813 Oldfield, 0 Emsley, 1813 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  361 residues out of total 1477 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 326
  time to evaluate  : 1.741 
Fit side-chains
REVERT: A   50 ASN cc_start: 0.7060 (m-40) cc_final: 0.6771 (t0)
REVERT: A  199 ASP cc_start: 0.8016 (p0) cc_final: 0.7773 (p0)
REVERT: C   50 ASN cc_start: 0.7337 (m-40) cc_final: 0.7072 (t0)
REVERT: C   78 ILE cc_start: 0.8114 (pt) cc_final: 0.7766 (mt)
REVERT: C   81 THR cc_start: 0.9050 (m) cc_final: 0.8815 (t)
REVERT: C  273 MET cc_start: 0.8693 (tpp) cc_final: 0.8282 (tpp)
REVERT: D  199 ASP cc_start: 0.8176 (p0) cc_final: 0.7966 (p0)
REVERT: E   81 THR cc_start: 0.9003 (m) cc_final: 0.8714 (t)
REVERT: F   31 ILE cc_start: 0.8956 (tp) cc_final: 0.8562 (mm)
REVERT: F   78 ILE cc_start: 0.8402 (pt) cc_final: 0.7842 (mt)
REVERT: F  273 MET cc_start: 0.8791 (tpp) cc_final: 0.8359 (tpp)
REVERT: G   46 ARG cc_start: 0.5731 (ttp-170) cc_final: 0.5274 (mtm180)
REVERT: G   81 THR cc_start: 0.9121 (m) cc_final: 0.8891 (t)
  outliers start: 35
  outliers final: 27
  residues processed: 333
  average time/residue: 0.2419
  time to fit residues: 121.8817
Evaluate side-chains
  322 residues out of total 1477 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 295
  time to evaluate  : 1.612 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  138 LEU
Chi-restraints excluded: chain A residue  144 THR
Chi-restraints excluded: chain A residue  148 VAL
Chi-restraints excluded: chain A residue  227 GLU
Chi-restraints excluded: chain B residue   42 LEU
Chi-restraints excluded: chain B residue   91 VAL
Chi-restraints excluded: chain B residue  148 VAL
Chi-restraints excluded: chain C residue  122 VAL
Chi-restraints excluded: chain C residue  138 LEU
Chi-restraints excluded: chain D residue   91 VAL
Chi-restraints excluded: chain D residue  122 VAL
Chi-restraints excluded: chain D residue  138 LEU
Chi-restraints excluded: chain D residue  227 GLU
Chi-restraints excluded: chain E residue   42 LEU
Chi-restraints excluded: chain E residue   82 LEU
Chi-restraints excluded: chain E residue   91 VAL
Chi-restraints excluded: chain E residue  122 VAL
Chi-restraints excluded: chain E residue  138 LEU
Chi-restraints excluded: chain F residue   83 ILE
Chi-restraints excluded: chain F residue   91 VAL
Chi-restraints excluded: chain F residue  122 VAL
Chi-restraints excluded: chain F residue  227 GLU
Chi-restraints excluded: chain G residue   73 VAL
Chi-restraints excluded: chain G residue   91 VAL
Chi-restraints excluded: chain G residue  100 LEU
Chi-restraints excluded: chain G residue  122 VAL
Chi-restraints excluded: chain G residue  227 GLU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 182
   random chunks:
   chunk 110 optimal weight:    2.9990
   chunk 99 optimal weight:    7.9990
   chunk 155 optimal weight:    0.9980
   chunk 70 optimal weight:    0.9980
   chunk 41 optimal weight:    5.9990
   chunk 161 optimal weight:    8.9990
   chunk 165 optimal weight:    4.9990
   chunk 27 optimal weight:    1.9990
   chunk 43 optimal weight:    3.9990
   chunk 32 optimal weight:    5.9990
   chunk 156 optimal weight:    4.9990
   overall best weight:    2.1986

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3431 r_free = 0.3431 target = 0.107604 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3129 r_free = 0.3129 target = 0.090210 restraints weight = 30695.636|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3165 r_free = 0.3165 target = 0.092528 restraints weight = 14821.227|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3192 r_free = 0.3192 target = 0.094183 restraints weight = 9064.830|
|-----------------------------------------------------------------------------|
r_work (final): 0.3197
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7943
moved from start:          0.1944

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.055  14098  Z= 0.178
  Angle     :  0.465   4.968  19117  Z= 0.255
  Chirality :  0.042   0.204   2345
  Planarity :  0.004   0.054   2429
  Dihedral  :  4.005  14.385   1988
  Min Nonbonded Distance : 2.590

Molprobity Statistics.
  All-atom Clashscore : 8.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.32 %
    Favored  : 98.68 %
  Rotamer:
    Outliers :  4.33 %
    Allowed  : 19.23 %
    Favored  : 76.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.37 (0.19), residues: 1813
  helix:  2.99 (0.14), residues: 1015
  sheet:  0.70 (0.28), residues: 273
  loop : -0.92 (0.26), residues: 525

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP F 240 
 PHE   0.025   0.002   PHE A 277 
 TYR   0.008   0.001   TYR D 250 
 ARG   0.009   0.000   ARG G 279 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03471 ( 1055)
  hydrogen bonds       : angle       4.08965 ( 3081)
  covalent geometry    : bond        0.00405 (14098)
  covalent geometry    : angle       0.46549 (19117)

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

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

  3626 Ramachandran restraints generated.
    1813 Oldfield, 0 Emsley, 1813 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3626 Ramachandran restraints generated.
    1813 Oldfield, 0 Emsley, 1813 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  363 residues out of total 1477 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 64
    poor density    : 299
  time to evaluate  : 1.484 
Fit side-chains
   revert: symmetry clash
REVERT: A  199 ASP cc_start: 0.8163 (p0) cc_final: 0.7926 (p0)
REVERT: C   78 ILE cc_start: 0.8134 (pt) cc_final: 0.7781 (mt)
REVERT: C   81 THR cc_start: 0.9077 (m) cc_final: 0.8809 (t)
REVERT: C  273 MET cc_start: 0.8669 (tpp) cc_final: 0.8031 (tpp)
REVERT: E   81 THR cc_start: 0.9037 (m) cc_final: 0.8751 (t)
REVERT: F   31 ILE cc_start: 0.8955 (tp) cc_final: 0.8540 (mm)
REVERT: F   78 ILE cc_start: 0.8367 (pt) cc_final: 0.7806 (mt)
REVERT: F  273 MET cc_start: 0.8702 (tpp) cc_final: 0.8096 (tpp)
REVERT: G   46 ARG cc_start: 0.5765 (ttp-170) cc_final: 0.5297 (mtm180)
REVERT: G   81 THR cc_start: 0.9117 (m) cc_final: 0.8862 (t)
  outliers start: 64
  outliers final: 45
  residues processed: 329
  average time/residue: 0.2596
  time to fit residues: 130.9407
Evaluate side-chains
  323 residues out of total 1477 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 278
  time to evaluate  : 1.801 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   81 THR
Chi-restraints excluded: chain A residue   91 VAL
Chi-restraints excluded: chain A residue  122 VAL
Chi-restraints excluded: chain A residue  138 LEU
Chi-restraints excluded: chain A residue  144 THR
Chi-restraints excluded: chain A residue  148 VAL
Chi-restraints excluded: chain A residue  171 ILE
Chi-restraints excluded: chain A residue  227 GLU
Chi-restraints excluded: chain B residue   38 ILE
Chi-restraints excluded: chain B residue   42 LEU
Chi-restraints excluded: chain B residue   77 ILE
Chi-restraints excluded: chain B residue   91 VAL
Chi-restraints excluded: chain B residue  122 VAL
Chi-restraints excluded: chain B residue  148 VAL
Chi-restraints excluded: chain C residue   38 ILE
Chi-restraints excluded: chain C residue  122 VAL
Chi-restraints excluded: chain C residue  138 LEU
Chi-restraints excluded: chain C residue  144 THR
Chi-restraints excluded: chain C residue  148 VAL
Chi-restraints excluded: chain C residue  171 ILE
Chi-restraints excluded: chain C residue  227 GLU
Chi-restraints excluded: chain D residue   38 ILE
Chi-restraints excluded: chain D residue   83 ILE
Chi-restraints excluded: chain D residue   91 VAL
Chi-restraints excluded: chain D residue  122 VAL
Chi-restraints excluded: chain D residue  138 LEU
Chi-restraints excluded: chain D residue  148 VAL
Chi-restraints excluded: chain D residue  227 GLU
Chi-restraints excluded: chain E residue   82 LEU
Chi-restraints excluded: chain E residue   91 VAL
Chi-restraints excluded: chain E residue  122 VAL
Chi-restraints excluded: chain E residue  138 LEU
Chi-restraints excluded: chain E residue  148 VAL
Chi-restraints excluded: chain F residue   91 VAL
Chi-restraints excluded: chain F residue  122 VAL
Chi-restraints excluded: chain F residue  148 VAL
Chi-restraints excluded: chain F residue  171 ILE
Chi-restraints excluded: chain F residue  227 GLU
Chi-restraints excluded: chain G residue   73 VAL
Chi-restraints excluded: chain G residue   91 VAL
Chi-restraints excluded: chain G residue  100 LEU
Chi-restraints excluded: chain G residue  105 LEU
Chi-restraints excluded: chain G residue  122 VAL
Chi-restraints excluded: chain G residue  148 VAL
Chi-restraints excluded: chain G residue  227 GLU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 182
   random chunks:
   chunk 172 optimal weight:    5.9990
   chunk 9 optimal weight:    0.9980
   chunk 21 optimal weight:    7.9990
   chunk 46 optimal weight:    0.7980
   chunk 41 optimal weight:    2.9990
   chunk 66 optimal weight:    3.9990
   chunk 39 optimal weight:    5.9990
   chunk 127 optimal weight:    3.9990
   chunk 149 optimal weight:    2.9990
   chunk 126 optimal weight:    5.9990
   chunk 6 optimal weight:    1.9990
   overall best weight:    1.9586

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

Flipped N/Q/H residues before XYZ refinement:
A  50 ASN
C  50 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3432 r_free = 0.3432 target = 0.107617 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3129 r_free = 0.3129 target = 0.090290 restraints weight = 30739.283|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3166 r_free = 0.3166 target = 0.092700 restraints weight = 14795.758|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3189 r_free = 0.3189 target = 0.094112 restraints weight = 8969.917|
|-----------------------------------------------------------------------------|
r_work (final): 0.3195
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7947
moved from start:          0.2100

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.053  14098  Z= 0.163
  Angle     :  0.462   5.674  19117  Z= 0.253
  Chirality :  0.042   0.213   2345
  Planarity :  0.004   0.063   2429
  Dihedral  :  4.021  15.280   1988
  Min Nonbonded Distance : 2.563

Molprobity Statistics.
  All-atom Clashscore : 8.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.27 %
    Favored  : 98.73 %
  Rotamer:
    Outliers :  4.20 %
    Allowed  : 19.63 %
    Favored  : 76.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.33 (0.19), residues: 1813
  helix:  2.94 (0.14), residues: 1015
  sheet:  0.72 (0.28), residues: 273
  loop : -0.91 (0.26), residues: 525

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP F 240 
 PHE   0.035   0.002   PHE F 277 
 TYR   0.007   0.001   TYR C 250 
 ARG   0.012   0.000   ARG G 279 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03408 ( 1055)
  hydrogen bonds       : angle       4.05858 ( 3081)
  covalent geometry    : bond        0.00370 (14098)
  covalent geometry    : angle       0.46150 (19117)

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

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

  3626 Ramachandran restraints generated.
    1813 Oldfield, 0 Emsley, 1813 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3626 Ramachandran restraints generated.
    1813 Oldfield, 0 Emsley, 1813 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  361 residues out of total 1477 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 62
    poor density    : 299
  time to evaluate  : 1.621 
Fit side-chains
   revert: symmetry clash
REVERT: A   50 ASN cc_start: 0.6725 (OUTLIER) cc_final: 0.6334 (t0)
REVERT: A   81 THR cc_start: 0.9203 (m) cc_final: 0.8999 (t)
REVERT: A  199 ASP cc_start: 0.8166 (p0) cc_final: 0.7924 (p0)
REVERT: B   81 THR cc_start: 0.9114 (m) cc_final: 0.8868 (t)
REVERT: C   50 ASN cc_start: 0.7297 (m-40) cc_final: 0.7097 (t0)
REVERT: C   78 ILE cc_start: 0.8159 (pt) cc_final: 0.7821 (mt)
REVERT: C   81 THR cc_start: 0.9052 (m) cc_final: 0.8808 (t)
REVERT: C  273 MET cc_start: 0.8665 (tpp) cc_final: 0.8005 (tpp)
REVERT: E   81 THR cc_start: 0.9095 (m) cc_final: 0.8826 (t)
REVERT: F   31 ILE cc_start: 0.8953 (tp) cc_final: 0.8538 (mm)
REVERT: F   78 ILE cc_start: 0.8315 (pt) cc_final: 0.7770 (mt)
REVERT: F  273 MET cc_start: 0.8671 (tpp) cc_final: 0.8125 (tpp)
REVERT: G   46 ARG cc_start: 0.5827 (ttp-170) cc_final: 0.5325 (mtm180)
REVERT: G   81 THR cc_start: 0.9105 (m) cc_final: 0.8859 (t)
  outliers start: 62
  outliers final: 48
  residues processed: 328
  average time/residue: 0.2205
  time to fit residues: 109.6308
Evaluate side-chains
  331 residues out of total 1477 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 282
  time to evaluate  : 1.680 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   50 ASN
Chi-restraints excluded: chain A residue  122 VAL
Chi-restraints excluded: chain A residue  138 LEU
Chi-restraints excluded: chain A residue  144 THR
Chi-restraints excluded: chain A residue  148 VAL
Chi-restraints excluded: chain A residue  171 ILE
Chi-restraints excluded: chain A residue  227 GLU
Chi-restraints excluded: chain B residue   42 LEU
Chi-restraints excluded: chain B residue   77 ILE
Chi-restraints excluded: chain B residue   91 VAL
Chi-restraints excluded: chain B residue  111 LEU
Chi-restraints excluded: chain B residue  122 VAL
Chi-restraints excluded: chain B residue  148 VAL
Chi-restraints excluded: chain B residue  217 LYS
Chi-restraints excluded: chain C residue   56 MET
Chi-restraints excluded: chain C residue  122 VAL
Chi-restraints excluded: chain C residue  138 LEU
Chi-restraints excluded: chain C residue  144 THR
Chi-restraints excluded: chain C residue  148 VAL
Chi-restraints excluded: chain C residue  171 ILE
Chi-restraints excluded: chain C residue  227 GLU
Chi-restraints excluded: chain D residue   35 LEU
Chi-restraints excluded: chain D residue   83 ILE
Chi-restraints excluded: chain D residue   91 VAL
Chi-restraints excluded: chain D residue  122 VAL
Chi-restraints excluded: chain D residue  134 GLU
Chi-restraints excluded: chain D residue  138 LEU
Chi-restraints excluded: chain D residue  148 VAL
Chi-restraints excluded: chain D residue  227 GLU
Chi-restraints excluded: chain E residue   82 LEU
Chi-restraints excluded: chain E residue   91 VAL
Chi-restraints excluded: chain E residue  122 VAL
Chi-restraints excluded: chain E residue  138 LEU
Chi-restraints excluded: chain E residue  148 VAL
Chi-restraints excluded: chain F residue   91 VAL
Chi-restraints excluded: chain F residue  122 VAL
Chi-restraints excluded: chain F residue  138 LEU
Chi-restraints excluded: chain F residue  148 VAL
Chi-restraints excluded: chain F residue  171 ILE
Chi-restraints excluded: chain F residue  227 GLU
Chi-restraints excluded: chain G residue   73 VAL
Chi-restraints excluded: chain G residue   82 LEU
Chi-restraints excluded: chain G residue   83 ILE
Chi-restraints excluded: chain G residue   91 VAL
Chi-restraints excluded: chain G residue  100 LEU
Chi-restraints excluded: chain G residue  105 LEU
Chi-restraints excluded: chain G residue  122 VAL
Chi-restraints excluded: chain G residue  148 VAL
Chi-restraints excluded: chain G residue  227 GLU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 182
   random chunks:
   chunk 36 optimal weight:    6.9990
   chunk 180 optimal weight:    0.9980
   chunk 178 optimal weight:    6.9990
   chunk 21 optimal weight:    0.9990
   chunk 116 optimal weight:    3.9990
   chunk 172 optimal weight:    0.9980
   chunk 176 optimal weight:    0.9980
   chunk 170 optimal weight:    5.9990
   chunk 57 optimal weight:    0.5980
   chunk 91 optimal weight:    8.9990
   chunk 70 optimal weight:    3.9990
   overall best weight:    0.9182

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3448 r_free = 0.3448 target = 0.108690 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3147 r_free = 0.3147 target = 0.091309 restraints weight = 30600.283|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 50)----------------|
| r_work = 0.3185 r_free = 0.3185 target = 0.093733 restraints weight = 14681.547|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3210 r_free = 0.3210 target = 0.095362 restraints weight = 8885.853|
|-----------------------------------------------------------------------------|
r_work (final): 0.3218
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7920
moved from start:          0.2138

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031  14098  Z= 0.112
  Angle     :  0.439   4.954  19117  Z= 0.241
  Chirality :  0.042   0.224   2345
  Planarity :  0.003   0.062   2429
  Dihedral  :  3.922  14.648   1988
  Min Nonbonded Distance : 2.588

Molprobity Statistics.
  All-atom Clashscore : 8.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.16 %
    Favored  : 98.84 %
  Rotamer:
    Outliers :  2.91 %
    Allowed  : 21.06 %
    Favored  : 76.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.41 (0.19), residues: 1813
  helix:  3.04 (0.14), residues: 1015
  sheet:  0.75 (0.29), residues: 273
  loop : -0.97 (0.26), residues: 525

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP F 251 
 PHE   0.028   0.001   PHE F 277 
 TYR   0.004   0.001   TYR E 250 
 ARG   0.012   0.000   ARG G 279 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03235 ( 1055)
  hydrogen bonds       : angle       3.92521 ( 3081)
  covalent geometry    : bond        0.00246 (14098)
  covalent geometry    : angle       0.43852 (19117)

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

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

  3626 Ramachandran restraints generated.
    1813 Oldfield, 0 Emsley, 1813 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3626 Ramachandran restraints generated.
    1813 Oldfield, 0 Emsley, 1813 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  365 residues out of total 1477 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 322
  time to evaluate  : 1.983 
Fit side-chains
REVERT: A   50 ASN cc_start: 0.6900 (OUTLIER) cc_final: 0.6694 (p0)
REVERT: A   81 THR cc_start: 0.9206 (OUTLIER) cc_final: 0.8867 (t)
REVERT: A  111 LEU cc_start: 0.9008 (mm) cc_final: 0.8751 (mt)
REVERT: A  199 ASP cc_start: 0.8144 (p0) cc_final: 0.7909 (p0)
REVERT: B   81 THR cc_start: 0.9209 (m) cc_final: 0.8992 (t)
REVERT: C   50 ASN cc_start: 0.7435 (m-40) cc_final: 0.7144 (t0)
REVERT: C   78 ILE cc_start: 0.8129 (pt) cc_final: 0.7775 (mt)
REVERT: C   81 THR cc_start: 0.9146 (m) cc_final: 0.8939 (t)
REVERT: C  111 LEU cc_start: 0.9139 (mm) cc_final: 0.8839 (mt)
REVERT: C  273 MET cc_start: 0.8611 (tpp) cc_final: 0.7970 (tpp)
REVERT: E   81 THR cc_start: 0.9104 (m) cc_final: 0.8819 (t)
REVERT: F   31 ILE cc_start: 0.8950 (tp) cc_final: 0.8544 (mm)
REVERT: F   78 ILE cc_start: 0.8346 (pt) cc_final: 0.7794 (mt)
REVERT: F  273 MET cc_start: 0.8644 (tpp) cc_final: 0.8213 (tpp)
REVERT: G   46 ARG cc_start: 0.5742 (ttp-170) cc_final: 0.5266 (mtm180)
REVERT: G   81 THR cc_start: 0.9089 (m) cc_final: 0.8844 (t)
REVERT: G  279 ARG cc_start: 0.5821 (mtm110) cc_final: 0.5549 (mtp-110)
  outliers start: 43
  outliers final: 31
  residues processed: 342
  average time/residue: 0.2343
  time to fit residues: 121.6862
Evaluate side-chains
  337 residues out of total 1477 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 304
  time to evaluate  : 1.635 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   50 ASN
Chi-restraints excluded: chain A residue   81 THR
Chi-restraints excluded: chain A residue  138 LEU
Chi-restraints excluded: chain A residue  148 VAL
Chi-restraints excluded: chain A residue  227 GLU
Chi-restraints excluded: chain B residue   77 ILE
Chi-restraints excluded: chain B residue  138 LEU
Chi-restraints excluded: chain B residue  148 VAL
Chi-restraints excluded: chain C residue   56 MET
Chi-restraints excluded: chain C residue  122 VAL
Chi-restraints excluded: chain C residue  138 LEU
Chi-restraints excluded: chain C residue  148 VAL
Chi-restraints excluded: chain C residue  171 ILE
Chi-restraints excluded: chain C residue  227 GLU
Chi-restraints excluded: chain D residue  138 LEU
Chi-restraints excluded: chain D residue  148 VAL
Chi-restraints excluded: chain D residue  227 GLU
Chi-restraints excluded: chain E residue   82 LEU
Chi-restraints excluded: chain E residue  138 LEU
Chi-restraints excluded: chain E residue  148 VAL
Chi-restraints excluded: chain F residue   91 VAL
Chi-restraints excluded: chain F residue  122 VAL
Chi-restraints excluded: chain F residue  138 LEU
Chi-restraints excluded: chain F residue  148 VAL
Chi-restraints excluded: chain F residue  171 ILE
Chi-restraints excluded: chain F residue  227 GLU
Chi-restraints excluded: chain G residue   82 LEU
Chi-restraints excluded: chain G residue   83 ILE
Chi-restraints excluded: chain G residue  100 LEU
Chi-restraints excluded: chain G residue  105 LEU
Chi-restraints excluded: chain G residue  138 LEU
Chi-restraints excluded: chain G residue  148 VAL
Chi-restraints excluded: chain G residue  227 GLU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 182
   random chunks:
   chunk 83 optimal weight:    1.9990
   chunk 154 optimal weight:    1.9990
   chunk 143 optimal weight:    8.9990
   chunk 168 optimal weight:    0.9980
   chunk 118 optimal weight:    8.9990
   chunk 131 optimal weight:    0.9990
   chunk 128 optimal weight:    2.9990
   chunk 106 optimal weight:    0.7980
   chunk 142 optimal weight:    1.9990
   chunk 58 optimal weight:    5.9990
   chunk 127 optimal weight:    0.9990
   overall best weight:    1.1586

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

Flipped N/Q/H residues before XYZ refinement:
A  50 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3454 r_free = 0.3454 target = 0.109087 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3157 r_free = 0.3157 target = 0.091851 restraints weight = 30304.673|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3193 r_free = 0.3193 target = 0.094202 restraints weight = 14819.786|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 48)----------------|
| r_work = 0.3219 r_free = 0.3219 target = 0.095813 restraints weight = 9118.200|
|-----------------------------------------------------------------------------|
r_work (final): 0.3219
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7922
moved from start:          0.2202

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046  14098  Z= 0.121
  Angle     :  0.443   6.110  19117  Z= 0.241
  Chirality :  0.042   0.227   2345
  Planarity :  0.003   0.042   2429
  Dihedral  :  3.915  18.029   1988
  Min Nonbonded Distance : 2.592

Molprobity Statistics.
  All-atom Clashscore : 9.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.16 %
    Favored  : 98.84 %
  Rotamer:
    Outliers :  2.78 %
    Allowed  : 21.60 %
    Favored  : 75.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.41 (0.19), residues: 1813
  helix:  3.04 (0.15), residues: 1015
  sheet:  0.77 (0.29), residues: 273
  loop : -0.98 (0.26), residues: 525

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP F 251 
 PHE   0.036   0.002   PHE G 277 
 TYR   0.005   0.001   TYR C 250 
 ARG   0.011   0.000   ARG G 279 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03197 ( 1055)
  hydrogen bonds       : angle       3.92926 ( 3081)
  covalent geometry    : bond        0.00273 (14098)
  covalent geometry    : angle       0.44251 (19117)

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

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

  3626 Ramachandran restraints generated.
    1813 Oldfield, 0 Emsley, 1813 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3626 Ramachandran restraints generated.
    1813 Oldfield, 0 Emsley, 1813 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  344 residues out of total 1477 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 303
  time to evaluate  : 1.577 
Fit side-chains
REVERT: A   50 ASN cc_start: 0.6817 (OUTLIER) cc_final: 0.6428 (t0)
REVERT: A   81 THR cc_start: 0.9213 (m) cc_final: 0.8886 (t)
REVERT: A  111 LEU cc_start: 0.9012 (mm) cc_final: 0.8766 (mt)
REVERT: A  199 ASP cc_start: 0.8112 (p0) cc_final: 0.7856 (p0)
REVERT: A  217 LYS cc_start: 0.8423 (mmmt) cc_final: 0.8125 (mmmt)
REVERT: B   81 THR cc_start: 0.9231 (m) cc_final: 0.8969 (t)
REVERT: C   50 ASN cc_start: 0.7548 (m-40) cc_final: 0.7222 (t0)
REVERT: C   78 ILE cc_start: 0.8110 (pt) cc_final: 0.7751 (mt)
REVERT: C  111 LEU cc_start: 0.9133 (mm) cc_final: 0.8848 (mt)
REVERT: C  273 MET cc_start: 0.8591 (tpp) cc_final: 0.7968 (tpp)
REVERT: E   81 THR cc_start: 0.9101 (m) cc_final: 0.8816 (t)
REVERT: F   31 ILE cc_start: 0.8944 (tp) cc_final: 0.8520 (mm)
REVERT: F   78 ILE cc_start: 0.8333 (pt) cc_final: 0.7774 (mt)
REVERT: F  273 MET cc_start: 0.8625 (tpp) cc_final: 0.8227 (tpp)
REVERT: G   46 ARG cc_start: 0.5750 (ttp-170) cc_final: 0.5271 (mtm180)
REVERT: G   81 THR cc_start: 0.9110 (m) cc_final: 0.8858 (t)
  outliers start: 41
  outliers final: 33
  residues processed: 323
  average time/residue: 0.2268
  time to fit residues: 110.4396
Evaluate side-chains
  329 residues out of total 1477 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 295
  time to evaluate  : 1.510 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   50 ASN
Chi-restraints excluded: chain A residue  138 LEU
Chi-restraints excluded: chain A residue  144 THR
Chi-restraints excluded: chain A residue  148 VAL
Chi-restraints excluded: chain A residue  227 GLU
Chi-restraints excluded: chain B residue   42 LEU
Chi-restraints excluded: chain B residue   77 ILE
Chi-restraints excluded: chain B residue  105 LEU
Chi-restraints excluded: chain B residue  138 LEU
Chi-restraints excluded: chain B residue  148 VAL
Chi-restraints excluded: chain C residue   56 MET
Chi-restraints excluded: chain C residue  122 VAL
Chi-restraints excluded: chain C residue  138 LEU
Chi-restraints excluded: chain C residue  148 VAL
Chi-restraints excluded: chain C residue  227 GLU
Chi-restraints excluded: chain D residue  138 LEU
Chi-restraints excluded: chain D residue  148 VAL
Chi-restraints excluded: chain E residue   82 LEU
Chi-restraints excluded: chain E residue  138 LEU
Chi-restraints excluded: chain E residue  148 VAL
Chi-restraints excluded: chain F residue   91 VAL
Chi-restraints excluded: chain F residue  122 VAL
Chi-restraints excluded: chain F residue  138 LEU
Chi-restraints excluded: chain F residue  148 VAL
Chi-restraints excluded: chain F residue  171 ILE
Chi-restraints excluded: chain F residue  227 GLU
Chi-restraints excluded: chain G residue   73 VAL
Chi-restraints excluded: chain G residue   82 LEU
Chi-restraints excluded: chain G residue   83 ILE
Chi-restraints excluded: chain G residue  100 LEU
Chi-restraints excluded: chain G residue  105 LEU
Chi-restraints excluded: chain G residue  138 LEU
Chi-restraints excluded: chain G residue  148 VAL
Chi-restraints excluded: chain G residue  227 GLU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 182
   random chunks:
   chunk 108 optimal weight:    6.9990
   chunk 113 optimal weight:    8.9990
   chunk 126 optimal weight:    3.9990
   chunk 101 optimal weight:    0.4980
   chunk 41 optimal weight:    0.6980
   chunk 66 optimal weight:    2.9990
   chunk 79 optimal weight:    1.9990
   chunk 125 optimal weight:    0.9990
   chunk 60 optimal weight:    6.9990
   chunk 170 optimal weight:    8.9990
   chunk 176 optimal weight:    6.9990
   overall best weight:    1.4386

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3449 r_free = 0.3449 target = 0.108781 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3150 r_free = 0.3150 target = 0.091472 restraints weight = 30380.535|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3186 r_free = 0.3186 target = 0.093843 restraints weight = 14798.238|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3212 r_free = 0.3212 target = 0.095488 restraints weight = 9057.392|
|-----------------------------------------------------------------------------|
r_work (final): 0.3214
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7926
moved from start:          0.2260

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.053  14098  Z= 0.136
  Angle     :  0.453   5.110  19117  Z= 0.248
  Chirality :  0.042   0.233   2345
  Planarity :  0.003   0.062   2429
  Dihedral  :  3.946  17.948   1988
  Min Nonbonded Distance : 2.589

Molprobity Statistics.
  All-atom Clashscore : 9.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.38 %
    Favored  : 98.62 %
  Rotamer:
    Outliers :  2.98 %
    Allowed  : 21.39 %
    Favored  : 75.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.35 (0.19), residues: 1813
  helix:  2.98 (0.15), residues: 1015
  sheet:  0.77 (0.29), residues: 273
  loop : -1.00 (0.26), residues: 525

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.002   0.001   TRP B 240 
 PHE   0.038   0.002   PHE G 277 
 TYR   0.005   0.001   TYR E 250 
 ARG   0.014   0.000   ARG G 279 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03234 ( 1055)
  hydrogen bonds       : angle       3.95679 ( 3081)
  covalent geometry    : bond        0.00309 (14098)
  covalent geometry    : angle       0.45321 (19117)

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

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

  3626 Ramachandran restraints generated.
    1813 Oldfield, 0 Emsley, 1813 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3626 Ramachandran restraints generated.
    1813 Oldfield, 0 Emsley, 1813 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  344 residues out of total 1477 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 300
  time to evaluate  : 1.626 
Fit side-chains
REVERT: A   81 THR cc_start: 0.9199 (m) cc_final: 0.8861 (t)
REVERT: A  111 LEU cc_start: 0.9012 (mm) cc_final: 0.8748 (mt)
REVERT: A  199 ASP cc_start: 0.8155 (p0) cc_final: 0.7905 (p0)
REVERT: A  217 LYS cc_start: 0.8436 (mmmt) cc_final: 0.8218 (mmmt)
REVERT: B   81 THR cc_start: 0.9239 (m) cc_final: 0.8973 (t)
REVERT: C   50 ASN cc_start: 0.7584 (m-40) cc_final: 0.7257 (t0)
REVERT: C   78 ILE cc_start: 0.8339 (pt) cc_final: 0.7812 (mt)
REVERT: C  111 LEU cc_start: 0.9131 (mm) cc_final: 0.8857 (mt)
REVERT: C  273 MET cc_start: 0.8597 (tpp) cc_final: 0.7784 (ttm)
REVERT: E   81 THR cc_start: 0.9092 (m) cc_final: 0.8803 (t)
REVERT: F   78 ILE cc_start: 0.8352 (pt) cc_final: 0.7807 (mt)
REVERT: F  273 MET cc_start: 0.8638 (tpp) cc_final: 0.8239 (tpp)
REVERT: G   46 ARG cc_start: 0.5746 (ttp-170) cc_final: 0.5256 (mtm180)
REVERT: G   81 THR cc_start: 0.9088 (m) cc_final: 0.8826 (t)
REVERT: G  279 ARG cc_start: 0.5764 (mtm110) cc_final: 0.5449 (mtp-110)
  outliers start: 44
  outliers final: 40
  residues processed: 318
  average time/residue: 0.2225
  time to fit residues: 106.3174
Evaluate side-chains
  337 residues out of total 1477 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 297
  time to evaluate  : 1.966 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  138 LEU
Chi-restraints excluded: chain A residue  144 THR
Chi-restraints excluded: chain A residue  148 VAL
Chi-restraints excluded: chain A residue  227 GLU
Chi-restraints excluded: chain B residue   42 LEU
Chi-restraints excluded: chain B residue   77 ILE
Chi-restraints excluded: chain B residue  105 LEU
Chi-restraints excluded: chain B residue  122 VAL
Chi-restraints excluded: chain B residue  138 LEU
Chi-restraints excluded: chain B residue  148 VAL
Chi-restraints excluded: chain C residue   56 MET
Chi-restraints excluded: chain C residue  122 VAL
Chi-restraints excluded: chain C residue  138 LEU
Chi-restraints excluded: chain C residue  148 VAL
Chi-restraints excluded: chain C residue  227 GLU
Chi-restraints excluded: chain D residue   35 LEU
Chi-restraints excluded: chain D residue   91 VAL
Chi-restraints excluded: chain D residue  134 GLU
Chi-restraints excluded: chain D residue  138 LEU
Chi-restraints excluded: chain D residue  148 VAL
Chi-restraints excluded: chain D residue  227 GLU
Chi-restraints excluded: chain E residue   82 LEU
Chi-restraints excluded: chain E residue  122 VAL
Chi-restraints excluded: chain E residue  138 LEU
Chi-restraints excluded: chain E residue  148 VAL
Chi-restraints excluded: chain F residue   91 VAL
Chi-restraints excluded: chain F residue  122 VAL
Chi-restraints excluded: chain F residue  138 LEU
Chi-restraints excluded: chain F residue  148 VAL
Chi-restraints excluded: chain F residue  171 ILE
Chi-restraints excluded: chain F residue  227 GLU
Chi-restraints excluded: chain G residue   73 VAL
Chi-restraints excluded: chain G residue   82 LEU
Chi-restraints excluded: chain G residue   83 ILE
Chi-restraints excluded: chain G residue   91 VAL
Chi-restraints excluded: chain G residue  100 LEU
Chi-restraints excluded: chain G residue  105 LEU
Chi-restraints excluded: chain G residue  138 LEU
Chi-restraints excluded: chain G residue  148 VAL
Chi-restraints excluded: chain G residue  227 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 182
   random chunks:
   chunk 120 optimal weight:    6.9990
   chunk 135 optimal weight:    5.9990
   chunk 142 optimal weight:    5.9990
   chunk 167 optimal weight:    0.6980
   chunk 154 optimal weight:    0.9990
   chunk 125 optimal weight:    2.9990
   chunk 62 optimal weight:    5.9990
   chunk 122 optimal weight:    0.7980
   chunk 81 optimal weight:    4.9990
   chunk 170 optimal weight:    6.9990
   chunk 96 optimal weight:    0.7980
   overall best weight:    1.2584

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3451 r_free = 0.3451 target = 0.108807 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3153 r_free = 0.3153 target = 0.091600 restraints weight = 30396.699|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3190 r_free = 0.3190 target = 0.093981 restraints weight = 14864.643|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3212 r_free = 0.3212 target = 0.095452 restraints weight = 9096.333|
|-----------------------------------------------------------------------------|
r_work (final): 0.3217
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7925
moved from start:          0.2311

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  14098  Z= 0.126
  Angle     :  0.453   5.723  19117  Z= 0.248
  Chirality :  0.042   0.239   2345
  Planarity :  0.003   0.059   2429
  Dihedral  :  3.948  18.519   1988
  Min Nonbonded Distance : 2.589

Molprobity Statistics.
  All-atom Clashscore : 9.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.32 %
    Favored  : 98.68 %
  Rotamer:
    Outliers :  2.91 %
    Allowed  : 21.26 %
    Favored  : 75.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.32 (0.19), residues: 1813
  helix:  2.96 (0.15), residues: 1015
  sheet:  0.76 (0.29), residues: 273
  loop : -1.03 (0.26), residues: 525

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP E 251 
 PHE   0.026   0.001   PHE G 277 
 TYR   0.005   0.001   TYR E 250 
 ARG   0.014   0.000   ARG G 279 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03202 ( 1055)
  hydrogen bonds       : angle       3.94433 ( 3081)
  covalent geometry    : bond        0.00284 (14098)
  covalent geometry    : angle       0.45313 (19117)

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

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

  3626 Ramachandran restraints generated.
    1813 Oldfield, 0 Emsley, 1813 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3626 Ramachandran restraints generated.
    1813 Oldfield, 0 Emsley, 1813 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  338 residues out of total 1477 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 295
  time to evaluate  : 1.696 
Fit side-chains
REVERT: A   81 THR cc_start: 0.9207 (m) cc_final: 0.8856 (t)
REVERT: A  111 LEU cc_start: 0.9037 (mm) cc_final: 0.8775 (mt)
REVERT: A  199 ASP cc_start: 0.8122 (p0) cc_final: 0.7871 (p0)
REVERT: A  217 LYS cc_start: 0.8426 (mmmt) cc_final: 0.8150 (mmmt)
REVERT: A  277 PHE cc_start: 0.5399 (m-80) cc_final: 0.4996 (m-80)
REVERT: A  279 ARG cc_start: 0.6002 (mtm110) cc_final: 0.5782 (mtp-110)
REVERT: B   81 THR cc_start: 0.9289 (m) cc_final: 0.9029 (t)
REVERT: C   50 ASN cc_start: 0.7717 (m-40) cc_final: 0.7356 (t0)
REVERT: C   78 ILE cc_start: 0.8201 (pt) cc_final: 0.7656 (mt)
REVERT: C  111 LEU cc_start: 0.9134 (mm) cc_final: 0.8867 (mt)
REVERT: C  273 MET cc_start: 0.8599 (tpp) cc_final: 0.7921 (ttm)
REVERT: E   81 THR cc_start: 0.9078 (m) cc_final: 0.8794 (t)
REVERT: F   78 ILE cc_start: 0.8345 (pt) cc_final: 0.7791 (mt)
REVERT: F   80 PHE cc_start: 0.8563 (m-10) cc_final: 0.8257 (m-10)
REVERT: F  273 MET cc_start: 0.8595 (tpp) cc_final: 0.8142 (tpp)
REVERT: G   46 ARG cc_start: 0.5734 (ttp-170) cc_final: 0.5255 (mtm180)
REVERT: G   81 THR cc_start: 0.9127 (m) cc_final: 0.8889 (t)
REVERT: G  279 ARG cc_start: 0.5711 (mtm110) cc_final: 0.5391 (mtp-110)
  outliers start: 43
  outliers final: 41
  residues processed: 312
  average time/residue: 0.2293
  time to fit residues: 108.7604
Evaluate side-chains
  329 residues out of total 1477 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 288
  time to evaluate  : 1.591 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  138 LEU
Chi-restraints excluded: chain A residue  144 THR
Chi-restraints excluded: chain A residue  148 VAL
Chi-restraints excluded: chain A residue  227 GLU
Chi-restraints excluded: chain B residue   42 LEU
Chi-restraints excluded: chain B residue   77 ILE
Chi-restraints excluded: chain B residue  105 LEU
Chi-restraints excluded: chain B residue  122 VAL
Chi-restraints excluded: chain B residue  138 LEU
Chi-restraints excluded: chain B residue  148 VAL
Chi-restraints excluded: chain B residue  217 LYS
Chi-restraints excluded: chain C residue   56 MET
Chi-restraints excluded: chain C residue  122 VAL
Chi-restraints excluded: chain C residue  138 LEU
Chi-restraints excluded: chain C residue  148 VAL
Chi-restraints excluded: chain C residue  227 GLU
Chi-restraints excluded: chain D residue   35 LEU
Chi-restraints excluded: chain D residue   91 VAL
Chi-restraints excluded: chain D residue  138 LEU
Chi-restraints excluded: chain D residue  148 VAL
Chi-restraints excluded: chain D residue  227 GLU
Chi-restraints excluded: chain E residue   82 LEU
Chi-restraints excluded: chain E residue   91 VAL
Chi-restraints excluded: chain E residue  122 VAL
Chi-restraints excluded: chain E residue  138 LEU
Chi-restraints excluded: chain E residue  148 VAL
Chi-restraints excluded: chain F residue   91 VAL
Chi-restraints excluded: chain F residue  122 VAL
Chi-restraints excluded: chain F residue  138 LEU
Chi-restraints excluded: chain F residue  148 VAL
Chi-restraints excluded: chain F residue  171 ILE
Chi-restraints excluded: chain F residue  227 GLU
Chi-restraints excluded: chain G residue   73 VAL
Chi-restraints excluded: chain G residue   82 LEU
Chi-restraints excluded: chain G residue   83 ILE
Chi-restraints excluded: chain G residue   91 VAL
Chi-restraints excluded: chain G residue  100 LEU
Chi-restraints excluded: chain G residue  105 LEU
Chi-restraints excluded: chain G residue  138 LEU
Chi-restraints excluded: chain G residue  148 VAL
Chi-restraints excluded: chain G residue  227 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 182
   random chunks:
   chunk 56 optimal weight:   10.0000
   chunk 15 optimal weight:    0.9980
   chunk 118 optimal weight:    0.9990
   chunk 62 optimal weight:    5.9990
   chunk 115 optimal weight:    0.7980
   chunk 13 optimal weight:    5.9990
   chunk 122 optimal weight:    0.8980
   chunk 65 optimal weight:    5.9990
   chunk 67 optimal weight:    8.9990
   chunk 152 optimal weight:    8.9990
   chunk 60 optimal weight:    0.9990
   overall best weight:    0.9384

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3461 r_free = 0.3461 target = 0.109442 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3163 r_free = 0.3163 target = 0.092182 restraints weight = 30790.730|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 50)----------------|
| r_work = 0.3200 r_free = 0.3200 target = 0.094565 restraints weight = 14978.439|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3224 r_free = 0.3224 target = 0.096157 restraints weight = 9129.048|
|-----------------------------------------------------------------------------|
r_work (final): 0.3229
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7915
moved from start:          0.2350

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.075  14098  Z= 0.113
  Angle     :  0.456   6.321  19117  Z= 0.249
  Chirality :  0.042   0.237   2345
  Planarity :  0.003   0.060   2429
  Dihedral  :  3.900  18.627   1988
  Min Nonbonded Distance : 2.589

Molprobity Statistics.
  All-atom Clashscore : 9.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.27 %
    Favored  : 98.73 %
  Rotamer:
    Outliers :  2.51 %
    Allowed  : 21.73 %
    Favored  : 75.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.37 (0.19), residues: 1813
  helix:  3.03 (0.15), residues: 1015
  sheet:  0.80 (0.29), residues: 273
  loop : -1.06 (0.26), residues: 525

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP E 251 
 PHE   0.024   0.001   PHE G 277 
 TYR   0.004   0.001   TYR E 250 
 ARG   0.013   0.000   ARG A 279 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03146 ( 1055)
  hydrogen bonds       : angle       3.90032 ( 3081)
  covalent geometry    : bond        0.00255 (14098)
  covalent geometry    : angle       0.45567 (19117)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4489.80 seconds
wall clock time: 82 minutes 7.94 seconds (4927.94 seconds total)