Starting phenix.real_space_refine
on Mon Dec 30 20:05:06 2024 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7oo8_13007/12_2024/7oo8_13007.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7oo8_13007/12_2024/7oo8_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_13007/12_2024/7oo8_13007.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7oo8_13007/12_2024/7oo8_13007.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7oo8_13007/12_2024/7oo8_13007.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7oo8_13007/12_2024/7oo8_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-5532/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: 5.89, per 1000 atoms: 0.42
  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: 3.39
  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: 1.46
  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: 4.75

  Time building geometry restraints manager: 3.89 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: 0.00
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'C'
  selection = chain 'D'
  selection = chain 'E'
  selection = chain 'F'
  selection = chain 'G'
}

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:             1.620
  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:          0.490
  Check model and map are aligned:         0.090
  Set scattering table:                    0.110
  Process input model:                     29.960
  Find NCS groups from input model:        0.540
  Set up NCS constraints:                  0.070
  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:             0.010
  Load rotamer database and sin/cos tables:2.950
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   35.850
-------------------------------------------------------------------------------
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= 0.185
  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 

*********************** 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  : 1.649 
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: 0.2518
  time to fit residues: 156.3848
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  : 1.624 
-------------------------------------------------------------------------------
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

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7921
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= 0.236
  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 

*********************** 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  : 1.555 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   50 ASN cc_start: 0.7035 (m-40) cc_final: 0.6760 (t0)
REVERT: A  144 THR cc_start: 0.8969 (m) cc_final: 0.8218 (p)
REVERT: A  199 ASP cc_start: 0.8076 (p0) cc_final: 0.7773 (p0)
REVERT: B   81 THR cc_start: 0.9135 (m) cc_final: 0.8896 (t)
REVERT: C   50 ASN cc_start: 0.7424 (m-40) cc_final: 0.7104 (t0)
REVERT: C   78 ILE cc_start: 0.8099 (pt) cc_final: 0.7757 (mt)
REVERT: C   81 THR cc_start: 0.8997 (m) cc_final: 0.8701 (t)
REVERT: C  273 MET cc_start: 0.8695 (tpp) cc_final: 0.8256 (tpp)
REVERT: D  199 ASP cc_start: 0.8022 (p0) cc_final: 0.7793 (p0)
REVERT: D  247 GLN cc_start: 0.8172 (tp40) cc_final: 0.7831 (tp-100)
REVERT: E   81 THR cc_start: 0.9067 (m) cc_final: 0.8821 (t)
REVERT: F   31 ILE cc_start: 0.9002 (tp) cc_final: 0.8633 (mm)
REVERT: F   78 ILE cc_start: 0.8405 (pt) cc_final: 0.7855 (mt)
REVERT: G   40 VAL cc_start: 0.8580 (t) cc_final: 0.8349 (m)
REVERT: G   81 THR cc_start: 0.9050 (m) cc_final: 0.8814 (t)
  outliers start: 36
  outliers final: 23
  residues processed: 338
  average time/residue: 0.2298
  time to fit residues: 117.2954
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  : 1.664 
-------------------------------------------------------------------------------
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 91 optimal weight:    5.9990
   chunk 51 optimal weight:    0.9990
   chunk 137 optimal weight:    0.7980
   chunk 112 optimal weight:    6.9990
   chunk 45 optimal weight:    0.3980
   chunk 165 optimal weight:    6.9990
   chunk 178 optimal weight:    3.9990
   chunk 147 optimal weight:    3.9990
   chunk 164 optimal weight:    0.8980
   chunk 56 optimal weight:    0.9980
   chunk 132 optimal weight:    0.9990
   overall best weight:    0.8182

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7899
moved from start:          0.1551

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036  14098  Z= 0.147
  Angle     :  0.421   4.609  19117  Z= 0.231
  Chirality :  0.041   0.188   2345
  Planarity :  0.003   0.033   2429
  Dihedral  :  3.744  12.732   1988
  Min Nonbonded Distance : 2.615

Molprobity Statistics.
  All-atom Clashscore : 7.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.43 %
    Favored  : 98.57 %
  Rotamer:
    Outliers :  1.29 %
    Allowed  : 17.33 %
    Favored  : 81.38 %
  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:  2.65 (0.19), residues: 1813
  helix:  3.38 (0.15), residues: 1008
  sheet:  0.63 (0.28), residues: 273
  loop : -0.98 (0.25), residues: 532

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP A 251 
 PHE   0.026   0.001   PHE C 277 
 TYR   0.005   0.001   TYR B 135 
 ARG   0.010   0.000   ARG C 279 

*********************** 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
  361 residues out of total 1477 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 342
  time to evaluate  : 1.583 
Fit side-chains
REVERT: A   50 ASN cc_start: 0.7066 (m-40) cc_final: 0.6762 (t0)
REVERT: A  144 THR cc_start: 0.8933 (m) cc_final: 0.8217 (p)
REVERT: A  199 ASP cc_start: 0.7983 (p0) cc_final: 0.7697 (p0)
REVERT: B   44 ILE cc_start: 0.8559 (mt) cc_final: 0.8334 (mm)
REVERT: C   50 ASN cc_start: 0.7340 (m-40) cc_final: 0.7073 (t0)
REVERT: C   78 ILE cc_start: 0.8177 (pt) cc_final: 0.7794 (mt)
REVERT: C   81 THR cc_start: 0.8997 (m) cc_final: 0.8763 (t)
REVERT: C  273 MET cc_start: 0.8702 (tpp) cc_final: 0.8264 (tpp)
REVERT: D  199 ASP cc_start: 0.8067 (p0) cc_final: 0.7804 (p0)
REVERT: D  247 GLN cc_start: 0.8162 (tp40) cc_final: 0.7846 (tp-100)
REVERT: E   81 THR cc_start: 0.8998 (m) cc_final: 0.8713 (t)
REVERT: F   78 ILE cc_start: 0.8371 (pt) cc_final: 0.7848 (mt)
REVERT: G   46 ARG cc_start: 0.5671 (ttp-170) cc_final: 0.5229 (mtm180)
REVERT: G   81 THR cc_start: 0.9058 (m) cc_final: 0.8834 (t)
  outliers start: 19
  outliers final: 12
  residues processed: 346
  average time/residue: 0.2211
  time to fit residues: 116.0319
Evaluate side-chains
  308 residues out of total 1477 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 296
  time to evaluate  : 1.590 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  148 VAL
Chi-restraints excluded: chain B residue   38 ILE
Chi-restraints excluded: chain B residue   42 LEU
Chi-restraints excluded: chain B residue  148 VAL
Chi-restraints excluded: chain B residue  227 GLU
Chi-restraints excluded: chain C residue  122 VAL
Chi-restraints excluded: chain D residue  227 GLU
Chi-restraints excluded: chain E residue   82 LEU
Chi-restraints excluded: chain E residue  227 GLU
Chi-restraints excluded: chain F residue   83 ILE
Chi-restraints excluded: chain G residue  100 LEU
Chi-restraints excluded: chain G residue  105 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 182
   random chunks:
   chunk 163 optimal weight:    0.8980
   chunk 124 optimal weight:    4.9990
   chunk 85 optimal weight:    6.9990
   chunk 18 optimal weight:    0.9990
   chunk 79 optimal weight:    2.9990
   chunk 111 optimal weight:    1.9990
   chunk 166 optimal weight:    5.9990
   chunk 175 optimal weight:    0.9980
   chunk 86 optimal weight:    3.9990
   chunk 157 optimal weight:    0.9980
   chunk 47 optimal weight:    4.9990
   overall best weight:    1.1784

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7911
moved from start:          0.1693

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049  14098  Z= 0.183
  Angle     :  0.430   4.899  19117  Z= 0.235
  Chirality :  0.041   0.196   2345
  Planarity :  0.003   0.047   2429
  Dihedral  :  3.796  15.628   1988
  Min Nonbonded Distance : 2.608

Molprobity Statistics.
  All-atom Clashscore : 8.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.16 %
    Favored  : 98.84 %
  Rotamer:
    Outliers :  2.30 %
    Allowed  : 19.16 %
    Favored  : 78.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.63 (0.19), residues: 1813
  helix:  3.29 (0.15), residues: 1015
  sheet:  0.71 (0.28), residues: 273
  loop : -0.97 (0.26), residues: 525

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP B 251 
 PHE   0.029   0.002   PHE A 277 
 TYR   0.005   0.001   TYR C 250 
 ARG   0.011   0.000   ARG E 279 

*********************** 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: 34
    poor density    : 327
  time to evaluate  : 1.504 
Fit side-chains
REVERT: A   50 ASN cc_start: 0.7071 (m-40) cc_final: 0.6772 (t0)
REVERT: A  144 THR cc_start: 0.8932 (m) cc_final: 0.8190 (p)
REVERT: A  199 ASP cc_start: 0.7965 (p0) cc_final: 0.7703 (p0)
REVERT: C   50 ASN cc_start: 0.7347 (m-40) cc_final: 0.7077 (t0)
REVERT: C   78 ILE cc_start: 0.8138 (pt) cc_final: 0.7792 (mt)
REVERT: C   81 THR cc_start: 0.9031 (m) cc_final: 0.8797 (t)
REVERT: C  273 MET cc_start: 0.8694 (tpp) cc_final: 0.8295 (tpp)
REVERT: D  199 ASP cc_start: 0.8150 (p0) cc_final: 0.7944 (p0)
REVERT: E   81 THR cc_start: 0.9086 (m) cc_final: 0.8827 (t)
REVERT: F   78 ILE cc_start: 0.8391 (pt) cc_final: 0.7867 (mt)
REVERT: F  273 MET cc_start: 0.8859 (tpp) cc_final: 0.8440 (tpp)
REVERT: G   46 ARG cc_start: 0.5700 (ttp-170) cc_final: 0.5246 (mtm180)
REVERT: G   81 THR cc_start: 0.9110 (m) cc_final: 0.8879 (t)
  outliers start: 34
  outliers final: 26
  residues processed: 340
  average time/residue: 0.2272
  time to fit residues: 117.1681
Evaluate side-chains
  323 residues out of total 1477 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 297
  time to evaluate  : 1.709 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   91 VAL
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   42 LEU
Chi-restraints excluded: chain B residue   91 VAL
Chi-restraints excluded: chain B residue  148 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 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  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  227 GLU
Chi-restraints excluded: chain G residue   91 VAL
Chi-restraints excluded: chain G residue  100 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=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 182
   random chunks:
   chunk 146 optimal weight:    0.7980
   chunk 99 optimal weight:    2.9990
   chunk 2 optimal weight:    2.9990
   chunk 130 optimal weight:    3.9990
   chunk 72 optimal weight:    3.9990
   chunk 150 optimal weight:    3.9990
   chunk 121 optimal weight:    3.9990
   chunk 0 optimal weight:   10.0000
   chunk 89 optimal weight:    3.9990
   chunk 157 optimal weight:    0.9980
   chunk 44 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:
B 247 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7934
moved from start:          0.1895

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044  14098  Z= 0.244
  Angle     :  0.460   5.121  19117  Z= 0.250
  Chirality :  0.042   0.203   2345
  Planarity :  0.004   0.045   2429
  Dihedral  :  3.937  16.945   1988
  Min Nonbonded Distance : 2.599

Molprobity Statistics.
  All-atom Clashscore : 8.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.16 %
    Favored  : 98.84 %
  Rotamer:
    Outliers :  3.79 %
    Allowed  : 19.36 %
    Favored  : 76.84 %
  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:  2.47 (0.19), residues: 1813
  helix:  3.09 (0.15), residues: 1015
  sheet:  0.75 (0.29), residues: 273
  loop : -0.93 (0.26), residues: 525

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP B 251 
 PHE   0.028   0.002   PHE A 277 
 TYR   0.007   0.001   TYR B 250 
 ARG   0.010   0.000   ARG E 279 

*********************** 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
  357 residues out of total 1477 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 56
    poor density    : 301
  time to evaluate  : 1.709 
Fit side-chains
   revert: symmetry clash
REVERT: A  199 ASP cc_start: 0.8030 (p0) cc_final: 0.7766 (p0)
REVERT: B   81 THR cc_start: 0.9124 (m) cc_final: 0.8871 (t)
REVERT: C   50 ASN cc_start: 0.7372 (m-40) cc_final: 0.7099 (t0)
REVERT: C   78 ILE cc_start: 0.8143 (pt) cc_final: 0.7800 (mt)
REVERT: C   81 THR cc_start: 0.9072 (m) cc_final: 0.8831 (t)
REVERT: C  273 MET cc_start: 0.8712 (tpp) cc_final: 0.8077 (tpp)
REVERT: D  199 ASP cc_start: 0.8144 (p0) cc_final: 0.7939 (p0)
REVERT: E   81 THR cc_start: 0.9104 (m) cc_final: 0.8852 (t)
REVERT: F   78 ILE cc_start: 0.8384 (pt) cc_final: 0.7846 (mt)
REVERT: F  273 MET cc_start: 0.8731 (tpp) cc_final: 0.8141 (tpp)
REVERT: G   46 ARG cc_start: 0.5694 (ttp-170) cc_final: 0.5250 (mtm180)
REVERT: G   81 THR cc_start: 0.9104 (m) cc_final: 0.8850 (t)
  outliers start: 56
  outliers final: 43
  residues processed: 323
  average time/residue: 0.2232
  time to fit residues: 109.9673
Evaluate side-chains
  330 residues out of total 1477 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 287
  time to evaluate  : 1.641 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  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  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   91 VAL
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  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  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  138 LEU
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 59 optimal weight:    3.9990
   chunk 158 optimal weight:    0.8980
   chunk 34 optimal weight:    0.7980
   chunk 103 optimal weight:    4.9990
   chunk 43 optimal weight:    3.9990
   chunk 176 optimal weight:    0.8980
   chunk 146 optimal weight:    0.0570
   chunk 81 optimal weight:    8.9990
   chunk 14 optimal weight:    0.7980
   chunk 58 optimal weight:    5.9990
   chunk 92 optimal weight:    5.9990
   overall best weight:    0.6898

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7906
moved from start:          0.1991

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028  14098  Z= 0.140
  Angle     :  0.428   5.569  19117  Z= 0.231
  Chirality :  0.042   0.216   2345
  Planarity :  0.003   0.053   2429
  Dihedral  :  3.767  16.577   1988
  Min Nonbonded Distance : 2.582

Molprobity Statistics.
  All-atom Clashscore : 8.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.21 %
    Favored  : 98.79 %
  Rotamer:
    Outliers :  2.23 %
    Allowed  : 21.39 %
    Favored  : 76.37 %
  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:  2.62 (0.19), residues: 1813
  helix:  3.25 (0.15), residues: 1015
  sheet:  0.87 (0.29), residues: 273
  loop : -1.01 (0.26), residues: 525

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP B 251 
 PHE   0.030   0.001   PHE A 277 
 TYR   0.003   0.001   TYR B 250 
 ARG   0.010   0.000   ARG G 279 

*********************** 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
  360 residues out of total 1477 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 327
  time to evaluate  : 1.574 
Fit side-chains
   revert: symmetry clash
REVERT: A   50 ASN cc_start: 0.7018 (m-40) cc_final: 0.6600 (t0)
REVERT: A  199 ASP cc_start: 0.7991 (p0) cc_final: 0.7732 (p0)
REVERT: A  217 LYS cc_start: 0.8372 (mmmt) cc_final: 0.8075 (mmmt)
REVERT: C   50 ASN cc_start: 0.7343 (m-40) cc_final: 0.7082 (t0)
REVERT: C   78 ILE cc_start: 0.8132 (pt) cc_final: 0.7790 (mt)
REVERT: C   81 THR cc_start: 0.9160 (m) cc_final: 0.8947 (t)
REVERT: C  111 LEU cc_start: 0.9117 (mm) cc_final: 0.8759 (mt)
REVERT: C  273 MET cc_start: 0.8639 (tpp) cc_final: 0.8019 (tpp)
REVERT: E   81 THR cc_start: 0.9085 (m) cc_final: 0.8819 (t)
REVERT: F   78 ILE cc_start: 0.8291 (pt) cc_final: 0.7776 (mt)
REVERT: F  273 MET cc_start: 0.8646 (tpp) cc_final: 0.8101 (tpp)
REVERT: G   46 ARG cc_start: 0.5685 (ttp-170) cc_final: 0.5240 (mtm180)
REVERT: G   81 THR cc_start: 0.9104 (m) cc_final: 0.8864 (t)
  outliers start: 33
  outliers final: 24
  residues processed: 343
  average time/residue: 0.2236
  time to fit residues: 116.5791
Evaluate side-chains
  322 residues out of total 1477 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 298
  time to evaluate  : 1.597 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  148 VAL
Chi-restraints excluded: chain C residue   56 MET
Chi-restraints excluded: chain C residue   91 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   91 VAL
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  148 VAL
Chi-restraints excluded: chain E residue  227 GLU
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  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=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 182
   random chunks:
   chunk 169 optimal weight:    0.1980
   chunk 19 optimal weight:    0.4980
   chunk 100 optimal weight:    0.9990
   chunk 128 optimal weight:    1.9990
   chunk 99 optimal weight:    0.0870
   chunk 148 optimal weight:    0.7980
   chunk 98 optimal weight:    4.9990
   chunk 175 optimal weight:    6.9990
   chunk 109 optimal weight:    1.9990
   chunk 106 optimal weight:    0.9980
   chunk 80 optimal weight:    0.5980
   overall best weight:    0.4358

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7891
moved from start:          0.2093

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.041  14098  Z= 0.128
  Angle     :  0.429   5.914  19117  Z= 0.231
  Chirality :  0.042   0.222   2345
  Planarity :  0.003   0.056   2429
  Dihedral  :  3.708  15.591   1988
  Min Nonbonded Distance : 2.597

Molprobity Statistics.
  All-atom Clashscore : 8.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.16 %
    Favored  : 98.84 %
  Rotamer:
    Outliers :  2.44 %
    Allowed  : 20.58 %
    Favored  : 76.98 %
  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:  2.62 (0.19), residues: 1813
  helix:  3.28 (0.15), residues: 1015
  sheet:  1.35 (0.31), residues: 238
  loop : -1.20 (0.25), residues: 560

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.002   0.001   TRP F 251 
 PHE   0.024   0.001   PHE A 277 
 TYR   0.003   0.000   TYR C 250 
 ARG   0.012   0.000   ARG G 279 

*********************** 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
  364 residues out of total 1477 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 328
  time to evaluate  : 1.694 
Fit side-chains
REVERT: A   50 ASN cc_start: 0.6978 (m-40) cc_final: 0.6577 (t0)
REVERT: A  199 ASP cc_start: 0.8013 (p0) cc_final: 0.7763 (p0)
REVERT: A  217 LYS cc_start: 0.8349 (mmmt) cc_final: 0.8126 (mmmt)
REVERT: C   50 ASN cc_start: 0.7358 (m-40) cc_final: 0.7089 (t0)
REVERT: C   78 ILE cc_start: 0.8133 (pt) cc_final: 0.7789 (mt)
REVERT: C   81 THR cc_start: 0.9077 (m) cc_final: 0.8869 (t)
REVERT: C  273 MET cc_start: 0.8608 (tpp) cc_final: 0.8016 (tpp)
REVERT: E   81 THR cc_start: 0.9027 (m) cc_final: 0.8787 (t)
REVERT: F   78 ILE cc_start: 0.8304 (pt) cc_final: 0.7792 (mt)
REVERT: F  273 MET cc_start: 0.8636 (tpp) cc_final: 0.8107 (tpp)
REVERT: G   46 ARG cc_start: 0.5658 (ttp-170) cc_final: 0.5199 (mtm180)
REVERT: G   81 THR cc_start: 0.9116 (m) cc_final: 0.8893 (t)
  outliers start: 36
  outliers final: 22
  residues processed: 344
  average time/residue: 0.2222
  time to fit residues: 116.2304
Evaluate side-chains
  326 residues out of total 1477 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 304
  time to evaluate  : 1.627 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  148 VAL
Chi-restraints excluded: chain B residue  227 GLU
Chi-restraints excluded: chain C residue   56 MET
Chi-restraints excluded: chain C residue   91 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   91 VAL
Chi-restraints excluded: chain D residue  148 VAL
Chi-restraints excluded: chain E residue  138 LEU
Chi-restraints excluded: chain E residue  148 VAL
Chi-restraints excluded: chain E residue  227 GLU
Chi-restraints excluded: chain F residue  138 LEU
Chi-restraints excluded: chain F residue  148 VAL
Chi-restraints excluded: chain F residue  227 GLU
Chi-restraints excluded: chain G residue  100 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 108 optimal weight:    4.9990
   chunk 70 optimal weight:    0.6980
   chunk 104 optimal weight:    7.9990
   chunk 52 optimal weight:    0.4980
   chunk 34 optimal weight:    5.9990
   chunk 33 optimal weight:    0.7980
   chunk 111 optimal weight:    0.7980
   chunk 119 optimal weight:    5.9990
   chunk 86 optimal weight:    6.9990
   chunk 16 optimal weight:    0.4980
   chunk 137 optimal weight:    5.9990
   overall best weight:    0.6580

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7892
moved from start:          0.2161

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.047  14098  Z= 0.143
  Angle     :  0.438   5.917  19117  Z= 0.236
  Chirality :  0.042   0.229   2345
  Planarity :  0.003   0.030   2429
  Dihedral  :  3.697  17.005   1988
  Min Nonbonded Distance : 2.583

Molprobity Statistics.
  All-atom Clashscore : 8.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.21 %
    Favored  : 98.79 %
  Rotamer:
    Outliers :  2.37 %
    Allowed  : 20.58 %
    Favored  : 77.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.60 (0.19), residues: 1813
  helix:  3.26 (0.15), residues: 1015
  sheet:  1.37 (0.31), residues: 238
  loop : -1.21 (0.25), residues: 560

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP B 251 
 PHE   0.023   0.001   PHE A 277 
 TYR   0.003   0.001   TYR B 250 
 ARG   0.007   0.000   ARG C 279 

*********************** 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
  341 residues out of total 1477 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 306
  time to evaluate  : 1.717 
Fit side-chains
REVERT: A   50 ASN cc_start: 0.6891 (m-40) cc_final: 0.6491 (t0)
REVERT: A   81 THR cc_start: 0.9205 (m) cc_final: 0.8870 (t)
REVERT: A  199 ASP cc_start: 0.8039 (p0) cc_final: 0.7774 (p0)
REVERT: A  217 LYS cc_start: 0.8336 (mmmt) cc_final: 0.8109 (mmmt)
REVERT: B   81 THR cc_start: 0.9189 (m) cc_final: 0.8974 (t)
REVERT: C   50 ASN cc_start: 0.7443 (m-40) cc_final: 0.7123 (t0)
REVERT: C   78 ILE cc_start: 0.8137 (pt) cc_final: 0.7788 (mt)
REVERT: C  273 MET cc_start: 0.8630 (tpp) cc_final: 0.8040 (tpp)
REVERT: E   81 THR cc_start: 0.9051 (m) cc_final: 0.8799 (t)
REVERT: F   78 ILE cc_start: 0.8304 (pt) cc_final: 0.7792 (mt)
REVERT: F  273 MET cc_start: 0.8601 (tpp) cc_final: 0.8071 (tpp)
REVERT: G   46 ARG cc_start: 0.5641 (ttp-170) cc_final: 0.5196 (mtm180)
REVERT: G   81 THR cc_start: 0.9111 (m) cc_final: 0.8892 (t)
  outliers start: 35
  outliers final: 26
  residues processed: 321
  average time/residue: 0.2252
  time to fit residues: 109.4571
Evaluate side-chains
  327 residues out of total 1477 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 301
  time to evaluate  : 1.578 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  138 LEU
Chi-restraints excluded: chain B residue  148 VAL
Chi-restraints excluded: chain C residue   56 MET
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   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  138 LEU
Chi-restraints excluded: chain E residue  148 VAL
Chi-restraints excluded: chain E residue  227 GLU
Chi-restraints excluded: chain F residue   91 VAL
Chi-restraints excluded: chain F residue  138 LEU
Chi-restraints excluded: chain F residue  148 VAL
Chi-restraints excluded: chain F residue  227 GLU
Chi-restraints excluded: chain G residue   73 VAL
Chi-restraints excluded: chain G residue  100 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 159 optimal weight:   10.0000
   chunk 168 optimal weight:    0.9980
   chunk 153 optimal weight:    4.9990
   chunk 163 optimal weight:    2.9990
   chunk 98 optimal weight:    4.9990
   chunk 71 optimal weight:    0.7980
   chunk 128 optimal weight:    7.9990
   chunk 50 optimal weight:    2.9990
   chunk 147 optimal weight:    4.9990
   chunk 154 optimal weight:    2.9990
   chunk 162 optimal weight:    0.9990
   overall best weight:    1.7586

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7927
moved from start:          0.2219

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.055  14098  Z= 0.233
  Angle     :  0.475   5.591  19117  Z= 0.257
  Chirality :  0.042   0.228   2345
  Planarity :  0.004   0.053   2429
  Dihedral  :  3.890  21.908   1988
  Min Nonbonded Distance : 2.594

Molprobity Statistics.
  All-atom Clashscore : 9.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.32 %
    Favored  : 98.68 %
  Rotamer:
    Outliers :  2.03 %
    Allowed  : 21.06 %
    Favored  : 76.91 %
  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:  3.00 (0.15), residues: 1015
  sheet:  1.26 (0.31), residues: 238
  loop : -1.16 (0.25), residues: 560

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B 251 
 PHE   0.029   0.002   PHE D 277 
 TYR   0.006   0.001   TYR D 250 
 ARG   0.014   0.000   ARG A 279 

*********************** 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
  325 residues out of total 1477 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 295
  time to evaluate  : 1.564 
Fit side-chains
REVERT: A   50 ASN cc_start: 0.6919 (m110) cc_final: 0.6513 (t0)
REVERT: A   81 THR cc_start: 0.9216 (m) cc_final: 0.8858 (t)
REVERT: A  199 ASP cc_start: 0.8106 (p0) cc_final: 0.7838 (p0)
REVERT: B   81 THR cc_start: 0.9218 (m) cc_final: 0.8930 (t)
REVERT: C   50 ASN cc_start: 0.7388 (m-40) cc_final: 0.7112 (t0)
REVERT: C   78 ILE cc_start: 0.8232 (pt) cc_final: 0.7614 (mt)
REVERT: C  273 MET cc_start: 0.8659 (tpp) cc_final: 0.8035 (tpp)
REVERT: E   81 THR cc_start: 0.9086 (m) cc_final: 0.8805 (t)
REVERT: E  279 ARG cc_start: 0.5116 (ttp-110) cc_final: 0.4740 (mtm110)
REVERT: F   78 ILE cc_start: 0.8329 (pt) cc_final: 0.7796 (mt)
REVERT: F  273 MET cc_start: 0.8601 (tpp) cc_final: 0.8067 (tpp)
REVERT: G   46 ARG cc_start: 0.5736 (ttp-170) cc_final: 0.5249 (mtm180)
REVERT: G   81 THR cc_start: 0.9100 (m) cc_final: 0.8834 (t)
  outliers start: 30
  outliers final: 24
  residues processed: 307
  average time/residue: 0.2310
  time to fit residues: 106.7266
Evaluate side-chains
  307 residues out of total 1477 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 283
  time to evaluate  : 1.759 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   91 VAL
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  138 LEU
Chi-restraints excluded: chain B residue  148 VAL
Chi-restraints excluded: chain C residue  138 LEU
Chi-restraints excluded: chain C residue  148 VAL
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  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  138 LEU
Chi-restraints excluded: chain F residue  148 VAL
Chi-restraints excluded: chain F residue  227 GLU
Chi-restraints excluded: chain G residue   73 VAL
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 107 optimal weight:    5.9990
   chunk 172 optimal weight:    6.9990
   chunk 105 optimal weight:    4.9990
   chunk 82 optimal weight:    7.9990
   chunk 120 optimal weight:    6.9990
   chunk 181 optimal weight:    5.9990
   chunk 166 optimal weight:    2.9990
   chunk 144 optimal weight:    0.9990
   chunk 14 optimal weight:    0.9990
   chunk 111 optimal weight:    0.5980
   chunk 88 optimal weight:    0.7980
   overall best weight:    1.2786

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7917
moved from start:          0.2281

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047  14098  Z= 0.186
  Angle     :  0.455   5.763  19117  Z= 0.247
  Chirality :  0.042   0.233   2345
  Planarity :  0.003   0.067   2429
  Dihedral  :  3.860  23.295   1988
  Min Nonbonded Distance : 2.583

Molprobity Statistics.
  All-atom Clashscore : 9.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.21 %
    Favored  : 98.79 %
  Rotamer:
    Outliers :  1.76 %
    Allowed  : 21.67 %
    Favored  : 76.57 %
  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:  2.37 (0.19), residues: 1813
  helix:  3.03 (0.15), residues: 1015
  sheet:  1.25 (0.31), residues: 238
  loop : -1.19 (0.25), residues: 560

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP B 251 
 PHE   0.024   0.001   PHE G 277 
 TYR   0.005   0.001   TYR B 250 
 ARG   0.013   0.000   ARG A 279 

********************** 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
  317 residues out of total 1477 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 291
  time to evaluate  : 1.582 
Fit side-chains
REVERT: A   50 ASN cc_start: 0.6953 (m110) cc_final: 0.6565 (t0)
REVERT: A   81 THR cc_start: 0.9205 (m) cc_final: 0.8855 (t)
REVERT: A  199 ASP cc_start: 0.8095 (p0) cc_final: 0.7827 (p0)
REVERT: B   81 THR cc_start: 0.9246 (m) cc_final: 0.8948 (t)
REVERT: C   50 ASN cc_start: 0.7391 (m-40) cc_final: 0.7120 (t0)
REVERT: C   78 ILE cc_start: 0.8068 (pt) cc_final: 0.7708 (mt)
REVERT: C   81 THR cc_start: 0.9043 (m) cc_final: 0.8778 (t)
REVERT: C  273 MET cc_start: 0.8637 (tpp) cc_final: 0.8039 (tpp)
REVERT: D  277 PHE cc_start: 0.4387 (m-10) cc_final: 0.4075 (m-10)
REVERT: E   81 THR cc_start: 0.9061 (m) cc_final: 0.8782 (t)
REVERT: E  279 ARG cc_start: 0.5214 (ttp-110) cc_final: 0.4799 (mtm110)
REVERT: F   78 ILE cc_start: 0.8327 (pt) cc_final: 0.7797 (mt)
REVERT: F   80 PHE cc_start: 0.8624 (m-10) cc_final: 0.8318 (m-10)
REVERT: F  273 MET cc_start: 0.8589 (tpp) cc_final: 0.8083 (tpp)
REVERT: G   46 ARG cc_start: 0.5701 (ttp-170) cc_final: 0.5222 (mtm180)
REVERT: G   81 THR cc_start: 0.9125 (m) cc_final: 0.8880 (t)
  outliers start: 26
  outliers final: 25
  residues processed: 300
  average time/residue: 0.2201
  time to fit residues: 100.0361
Evaluate side-chains
  311 residues out of total 1477 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 286
  time to evaluate  : 1.705 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  100 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 D residue   91 VAL
Chi-restraints excluded: chain D residue  138 LEU
Chi-restraints excluded: chain D residue  148 VAL
Chi-restraints excluded: chain E residue   56 MET
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  138 LEU
Chi-restraints excluded: chain F residue  148 VAL
Chi-restraints excluded: chain F residue  227 GLU
Chi-restraints excluded: chain G residue   73 VAL
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 114 optimal weight:    5.9990
   chunk 153 optimal weight:    0.9980
   chunk 44 optimal weight:    0.8980
   chunk 133 optimal weight:    7.9990
   chunk 21 optimal weight:    7.9990
   chunk 40 optimal weight:    1.9990
   chunk 144 optimal weight:    1.9990
   chunk 60 optimal weight:    0.9990
   chunk 148 optimal weight:    0.6980
   chunk 18 optimal weight:    0.6980
   chunk 26 optimal weight:    3.9990
   overall best weight:    0.8582

-------------------------------------------------------------------------------
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 = 0.3464 r_free = 0.3464 target = 0.109293 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3169 r_free = 0.3169 target = 0.092212 restraints weight = 30110.894|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3203 r_free = 0.3203 target = 0.094452 restraints weight = 14562.376|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3230 r_free = 0.3230 target = 0.096110 restraints weight = 8851.404|
|-----------------------------------------------------------------------------|
r_work (final): 0.3233
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7900
moved from start:          0.2318

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.043  14098  Z= 0.156
  Angle     :  0.452   6.465  19117  Z= 0.243
  Chirality :  0.042   0.234   2345
  Planarity :  0.003   0.061   2429
  Dihedral  :  3.811  21.760   1988
  Min Nonbonded Distance : 2.595

Molprobity Statistics.
  All-atom Clashscore : 9.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.32 %
    Favored  : 98.68 %
  Rotamer:
    Outliers :  1.62 %
    Allowed  : 21.73 %
    Favored  : 76.64 %
  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:  3.09 (0.15), residues: 1015
  sheet:  1.25 (0.31), residues: 238
  loop : -1.24 (0.25), residues: 560

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP B 251 
 PHE   0.015   0.001   PHE G 277 
 TYR   0.004   0.001   TYR B 250 
 ARG   0.018   0.000   ARG G 279 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2806.55 seconds
wall clock time: 52 minutes 0.22 seconds (3120.22 seconds total)