Starting phenix.real_space_refine
on Wed Mar  4 13:16:53 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7oo8_13007/03_2026/7oo8_13007.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7oo8_13007/03_2026/7oo8_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_13007/03_2026/7oo8_13007.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7oo8_13007/03_2026/7oo8_13007.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7oo8_13007/03_2026/7oo8_13007.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7oo8_13007/03_2026/7oo8_13007.cif"
  }
  resolution = 3.7
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.006
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-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/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:
    B, C, D, E, F, G
  Time building chain proxies: 1.62, per 1000 atoms: 0.12
  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: 1.18
  Conformation dependent library (CDL) restraints added in 736.8 milliseconds
  

  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: 0.28
  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: 2.12

  Time building geometry restraints manager: 1.58 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: 0.04
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:             1.900
  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:          0.230
  Check model and map are aligned:         0.050
  Set scattering table:                    0.030
  Process input model:                     11.200
  Find NCS groups from input model:        0.120
  Set up NCS constraints:                  0.010
  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:1.170
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   14.720
-------------------------------------------------------------------------------
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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  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
 ARG   0.002   0.000   ARG F 180 
 TYR   0.006   0.001   TYR D 135 
 PHE   0.005   0.001   PHE G 188 
 TRP   0.004   0.001   TRP C 240 

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

*********************** 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  : 0.545 
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: 0.8502 (t) cc_final: 0.8209 (m)
  outliers start: 0
  outliers final: 0
  residues processed: 426
  average time/residue: 0.1013
  time to fit residues: 64.4681
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  : 0.439 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 182
   random chunks:
   chunk 98 optimal weight:    3.9990
   chunk 107 optimal weight:   10.0000
   chunk 10 optimal weight:    6.9990
   chunk 66 optimal weight:    0.2980
   chunk 130 optimal weight:    0.9980
   chunk 124 optimal weight:    3.9990
   chunk 103 optimal weight:    2.9990
   chunk 77 optimal weight:    0.6980
   chunk 122 optimal weight:    0.9980
   chunk 91 optimal weight:    4.9990
   chunk 149 optimal weight:    2.9990
   overall best weight:    1.1982

-------------------------------------------------------------------------------
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 = 0.3480 r_free = 0.3480 target = 0.110734 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3169 r_free = 0.3169 target = 0.092707 restraints weight = 30543.005|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3207 r_free = 0.3207 target = 0.095182 restraints weight = 14709.869|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 61)----------------|
| r_work = 0.3234 r_free = 0.3234 target = 0.096822 restraints weight = 8900.330|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3250 r_free = 0.3250 target = 0.097806 restraints weight = 6313.512|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 43)----------------|
| r_work = 0.3262 r_free = 0.3262 target = 0.098617 restraints weight = 5092.805|
|-----------------------------------------------------------------------------|
r_work (final): 0.3263
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7880
moved from start:          0.1281

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= 0.129
  Angle     :  0.458   4.728  19117  Z= 0.252
  Chirality :  0.042   0.182   2345
  Planarity :  0.003   0.030   2429
  Dihedral  :  3.787  11.977   1988
  Min Nonbonded Distance : 2.588

Molprobity Statistics.
  All-atom Clashscore : 6.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.99 %
    Favored  : 99.01 %
  Rotamer:
    Outliers :  1.96 %
    Allowed  : 13.54 %
    Favored  : 84.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.66 (0.19), residues: 1813
  helix:  3.40 (0.15), residues: 1008
  sheet: -0.05 (0.27), residues: 308
  loop : -0.62 (0.26), residues: 497

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 279 
 TYR   0.005   0.001   TYR C 250 
 PHE   0.020   0.001   PHE C 277 
 TRP   0.006   0.001   TRP B 251 

Details of bonding type rmsd
  covalent geometry    : bond        0.00280 (14098)
  covalent geometry    : angle       0.45835 (19117)
  hydrogen bonds       : bond        0.03732 ( 1055)
  hydrogen bonds       : angle       4.03891 ( 3081)

*********************** 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
  371 residues out of total 1477 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 342
  time to evaluate  : 0.439 
Fit side-chains
REVERT: A   42 LEU cc_start: 0.7732 (mm) cc_final: 0.7397 (mm)
REVERT: A   50 ASN cc_start: 0.7033 (m-40) cc_final: 0.6775 (t0)
REVERT: A  144 THR cc_start: 0.8988 (m) cc_final: 0.8248 (p)
REVERT: A  199 ASP cc_start: 0.7990 (p0) cc_final: 0.7665 (p0)
REVERT: A  212 GLU cc_start: 0.6798 (tp30) cc_final: 0.6326 (tp30)
REVERT: B   81 THR cc_start: 0.9063 (m) cc_final: 0.8659 (t)
REVERT: C   50 ASN cc_start: 0.7333 (m-40) cc_final: 0.7042 (t0)
REVERT: C   78 ILE cc_start: 0.8132 (pt) cc_final: 0.7730 (mt)
REVERT: C   81 THR cc_start: 0.8976 (m) cc_final: 0.8687 (t)
REVERT: D  199 ASP cc_start: 0.8044 (p0) cc_final: 0.7813 (p0)
REVERT: D  277 PHE cc_start: 0.6358 (m-80) cc_final: 0.6151 (m-80)
REVERT: E   81 THR cc_start: 0.9038 (m) cc_final: 0.8795 (t)
REVERT: E  255 GLU cc_start: 0.8635 (tt0) cc_final: 0.8392 (tt0)
REVERT: E  258 LYS cc_start: 0.9173 (tttp) cc_final: 0.8926 (tptp)
REVERT: F   31 ILE cc_start: 0.8991 (tp) cc_final: 0.8659 (mm)
REVERT: F   78 ILE cc_start: 0.8454 (pt) cc_final: 0.7860 (mt)
REVERT: G   40 VAL cc_start: 0.8489 (t) cc_final: 0.8273 (m)
REVERT: G   81 THR cc_start: 0.8972 (m) cc_final: 0.8747 (t)
REVERT: G  212 GLU cc_start: 0.7093 (tp30) cc_final: 0.6795 (tp30)
  outliers start: 29
  outliers final: 18
  residues processed: 347
  average time/residue: 0.0949
  time to fit residues: 50.8556
Evaluate side-chains
  318 residues out of total 1477 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 300
  time to evaluate  : 0.540 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  148 VAL
Chi-restraints excluded: chain B residue   42 LEU
Chi-restraints excluded: chain B residue  148 VAL
Chi-restraints excluded: chain C residue  122 VAL
Chi-restraints excluded: chain C residue  144 THR
Chi-restraints excluded: chain D residue   35 LEU
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 G residue   73 VAL
Chi-restraints excluded: chain G residue   91 VAL
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 50 optimal weight:    0.9980
   chunk 127 optimal weight:    0.8980
   chunk 139 optimal weight:    0.9990
   chunk 146 optimal weight:    2.9990
   chunk 128 optimal weight:    0.9980
   chunk 72 optimal weight:    4.9990
   chunk 178 optimal weight:    4.9990
   chunk 155 optimal weight:    0.8980
   chunk 49 optimal weight:    0.6980
   chunk 16 optimal weight:    0.4980
   chunk 53 optimal weight:    2.9990
   overall best weight:    0.7980

-------------------------------------------------------------------------------
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 = 0.3492 r_free = 0.3492 target = 0.111473 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3184 r_free = 0.3184 target = 0.093577 restraints weight = 30801.213|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3220 r_free = 0.3220 target = 0.096035 restraints weight = 14776.541|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3246 r_free = 0.3246 target = 0.097715 restraints weight = 8971.726|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3264 r_free = 0.3264 target = 0.098846 restraints weight = 6369.055|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3271 r_free = 0.3271 target = 0.099288 restraints weight = 5028.815|
|-----------------------------------------------------------------------------|
r_work (final): 0.3271
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7874
moved from start:          0.1497

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029  14098  Z= 0.107
  Angle     :  0.420   4.646  19117  Z= 0.231
  Chirality :  0.041   0.187   2345
  Planarity :  0.003   0.037   2429
  Dihedral  :  3.723  12.905   1988
  Min Nonbonded Distance : 2.624

Molprobity Statistics.
  All-atom Clashscore : 7.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.49 %
    Favored  : 98.51 %
  Rotamer:
    Outliers :  1.69 %
    Allowed  : 16.05 %
    Favored  : 82.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.68 (0.19), residues: 1813
  helix:  3.41 (0.15), residues: 1008
  sheet:  0.64 (0.28), residues: 273
  loop : -0.99 (0.25), residues: 532

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG E 279 
 TYR   0.005   0.001   TYR B 135 
 PHE   0.030   0.002   PHE A 277 
 TRP   0.003   0.001   TRP A 251 

Details of bonding type rmsd
  covalent geometry    : bond        0.00228 (14098)
  covalent geometry    : angle       0.42018 (19117)
  hydrogen bonds       : bond        0.03271 ( 1055)
  hydrogen bonds       : angle       3.86983 ( 3081)

*********************** 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
  365 residues out of total 1477 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 340
  time to evaluate  : 0.563 
Fit side-chains
REVERT: A   50 ASN cc_start: 0.7013 (m-40) cc_final: 0.6728 (t0)
REVERT: A   81 THR cc_start: 0.9157 (OUTLIER) cc_final: 0.8823 (t)
REVERT: A  144 THR cc_start: 0.8930 (m) cc_final: 0.8204 (p)
REVERT: A  199 ASP cc_start: 0.7973 (p0) cc_final: 0.7689 (p0)
REVERT: B   44 ILE cc_start: 0.8564 (mt) cc_final: 0.8330 (mm)
REVERT: B   81 THR cc_start: 0.9174 (m) cc_final: 0.8968 (t)
REVERT: C   50 ASN cc_start: 0.7285 (m-40) cc_final: 0.7037 (t0)
REVERT: C   78 ILE cc_start: 0.8170 (pt) cc_final: 0.7770 (mt)
REVERT: C   81 THR cc_start: 0.8992 (m) cc_final: 0.8753 (t)
REVERT: C  273 MET cc_start: 0.8780 (tpp) cc_final: 0.8467 (tpp)
REVERT: D  199 ASP cc_start: 0.8032 (p0) cc_final: 0.7767 (p0)
REVERT: D  277 PHE cc_start: 0.5933 (m-10) cc_final: 0.5549 (m-10)
REVERT: E   81 THR cc_start: 0.8980 (m) cc_final: 0.8692 (t)
REVERT: E  258 LYS cc_start: 0.9216 (tttp) cc_final: 0.8999 (tptp)
REVERT: F   78 ILE cc_start: 0.8412 (pt) cc_final: 0.7870 (mt)
REVERT: G   46 ARG cc_start: 0.5659 (ttp-170) cc_final: 0.5222 (mtm180)
REVERT: G   81 THR cc_start: 0.9020 (m) cc_final: 0.8803 (t)
  outliers start: 25
  outliers final: 14
  residues processed: 344
  average time/residue: 0.0957
  time to fit residues: 51.2848
Evaluate side-chains
  311 residues out of total 1477 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 296
  time to evaluate  : 0.546 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   81 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 B residue  227 GLU
Chi-restraints excluded: chain C residue   91 VAL
Chi-restraints excluded: chain C residue  227 GLU
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  227 GLU
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 82 optimal weight:    0.0570
   chunk 68 optimal weight:    1.9990
   chunk 109 optimal weight:    3.9990
   chunk 152 optimal weight:    0.9980
   chunk 121 optimal weight:    8.9990
   chunk 105 optimal weight:    1.9990
   chunk 81 optimal weight:    2.9990
   chunk 6 optimal weight:    4.9990
   chunk 93 optimal weight:    4.9990
   chunk 125 optimal weight:    4.9990
   chunk 175 optimal weight:    0.8980
   overall best weight:    1.1902

-------------------------------------------------------------------------------
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

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3479 r_free = 0.3479 target = 0.110594 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3172 r_free = 0.3172 target = 0.092820 restraints weight = 30785.629|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3208 r_free = 0.3208 target = 0.095142 restraints weight = 14965.305|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.3236 r_free = 0.3236 target = 0.096849 restraints weight = 9186.908|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3250 r_free = 0.3250 target = 0.097764 restraints weight = 6535.522|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.3262 r_free = 0.3262 target = 0.098597 restraints weight = 5312.553|
|-----------------------------------------------------------------------------|
r_work (final): 0.3261
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7881
moved from start:          0.1681

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     :  0.432   4.980  19117  Z= 0.236
  Chirality :  0.041   0.197   2345
  Planarity :  0.003   0.041   2429
  Dihedral  :  3.752  14.164   1988
  Min Nonbonded Distance : 2.605

Molprobity Statistics.
  All-atom Clashscore : 8.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.16 %
    Favored  : 98.84 %
  Rotamer:
    Outliers :  2.64 %
    Allowed  : 17.20 %
    Favored  : 80.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.64 (0.19), residues: 1813
  helix:  3.31 (0.15), residues: 1015
  sheet:  0.71 (0.28), residues: 273
  loop : -0.99 (0.26), residues: 525

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG E 279 
 TYR   0.006   0.001   TYR A 250 
 PHE   0.037   0.001   PHE A 277 
 TRP   0.003   0.001   TRP A 251 

Details of bonding type rmsd
  covalent geometry    : bond        0.00270 (14098)
  covalent geometry    : angle       0.43249 (19117)
  hydrogen bonds       : bond        0.03214 ( 1055)
  hydrogen bonds       : angle       3.87079 ( 3081)

*********************** 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
  363 residues out of total 1477 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 324
  time to evaluate  : 0.351 
Fit side-chains
   revert: symmetry clash
REVERT: A   50 ASN cc_start: 0.7000 (m-40) cc_final: 0.6725 (t0)
REVERT: A   81 THR cc_start: 0.9178 (OUTLIER) cc_final: 0.8841 (t)
REVERT: A  144 THR cc_start: 0.8915 (m) cc_final: 0.8197 (p)
REVERT: A  199 ASP cc_start: 0.7935 (p0) cc_final: 0.7667 (p0)
REVERT: B   44 ILE cc_start: 0.8576 (mt) cc_final: 0.8373 (mm)
REVERT: B  134 GLU cc_start: 0.7101 (tt0) cc_final: 0.6890 (tt0)
REVERT: C   50 ASN cc_start: 0.7269 (m-40) cc_final: 0.7025 (t0)
REVERT: C   78 ILE cc_start: 0.8173 (pt) cc_final: 0.7766 (mt)
REVERT: C   81 THR cc_start: 0.8989 (m) cc_final: 0.8752 (t)
REVERT: C  273 MET cc_start: 0.8717 (tpp) cc_final: 0.8356 (tpp)
REVERT: D  199 ASP cc_start: 0.8104 (p0) cc_final: 0.7868 (p0)
REVERT: D  277 PHE cc_start: 0.5416 (m-10) cc_final: 0.5002 (m-10)
REVERT: E   44 ILE cc_start: 0.8656 (OUTLIER) cc_final: 0.8443 (mp)
REVERT: E   81 THR cc_start: 0.9065 (m) cc_final: 0.8805 (t)
REVERT: F   78 ILE cc_start: 0.8370 (pt) cc_final: 0.7848 (mt)
REVERT: F  273 MET cc_start: 0.8846 (tpp) cc_final: 0.8471 (tpp)
REVERT: G   46 ARG cc_start: 0.5697 (ttp-170) cc_final: 0.5253 (mtm180)
REVERT: G   81 THR cc_start: 0.9070 (m) cc_final: 0.8852 (t)
  outliers start: 39
  outliers final: 33
  residues processed: 335
  average time/residue: 0.0983
  time to fit residues: 50.5544
Evaluate side-chains
  334 residues out of total 1477 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 299
  time to evaluate  : 0.620 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   81 THR
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  148 VAL
Chi-restraints excluded: chain C residue   56 MET
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  148 VAL
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  138 LEU
Chi-restraints excluded: chain D residue  148 VAL
Chi-restraints excluded: chain D residue  227 GLU
Chi-restraints excluded: chain E residue   44 ILE
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  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=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 182
   random chunks:
   chunk 126 optimal weight:    0.7980
   chunk 56 optimal weight:    0.4980
   chunk 138 optimal weight:    2.9990
   chunk 25 optimal weight:    0.7980
   chunk 75 optimal weight:    5.9990
   chunk 26 optimal weight:    0.0040
   chunk 144 optimal weight:    6.9990
   chunk 128 optimal weight:    0.0970
   chunk 181 optimal weight:    0.7980
   chunk 157 optimal weight:    1.9990
   chunk 156 optimal weight:    2.9990
   overall best weight:    0.4390

-------------------------------------------------------------------------------
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

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3499 r_free = 0.3499 target = 0.111937 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3195 r_free = 0.3195 target = 0.094098 restraints weight = 30559.737|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3232 r_free = 0.3232 target = 0.096582 restraints weight = 14740.534|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3258 r_free = 0.3258 target = 0.098246 restraints weight = 8939.064|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3271 r_free = 0.3271 target = 0.099084 restraints weight = 6366.362|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 50)----------------|
| r_work = 0.3286 r_free = 0.3286 target = 0.099958 restraints weight = 5216.663|
|-----------------------------------------------------------------------------|
r_work (final): 0.3283
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7859
moved from start:          0.1782

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035  14098  Z= 0.096
  Angle     :  0.421   5.979  19117  Z= 0.227
  Chirality :  0.041   0.163   2345
  Planarity :  0.003   0.061   2429
  Dihedral  :  3.691  15.852   1988
  Min Nonbonded Distance : 2.611

Molprobity Statistics.
  All-atom Clashscore : 8.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.32 %
    Favored  : 98.68 %
  Rotamer:
    Outliers :  2.03 %
    Allowed  : 19.36 %
    Favored  : 78.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.67 (0.19), residues: 1813
  helix:  3.37 (0.15), residues: 1015
  sheet:  1.20 (0.31), residues: 238
  loop : -1.18 (0.24), residues: 560

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.000   ARG E 279 
 TYR   0.003   0.001   TYR C 250 
 PHE   0.032   0.001   PHE A 277 
 TRP   0.004   0.001   TRP B 251 

Details of bonding type rmsd
  covalent geometry    : bond        0.00200 (14098)
  covalent geometry    : angle       0.42092 (19117)
  hydrogen bonds       : bond        0.03076 ( 1055)
  hydrogen bonds       : angle       3.74540 ( 3081)

*********************** 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
  362 residues out of total 1477 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 332
  time to evaluate  : 0.530 
Fit side-chains
   revert: symmetry clash
REVERT: A   50 ASN cc_start: 0.7037 (m-40) cc_final: 0.6769 (t0)
REVERT: A   81 THR cc_start: 0.9179 (m) cc_final: 0.8851 (t)
REVERT: A  144 THR cc_start: 0.8901 (m) cc_final: 0.8175 (p)
REVERT: A  199 ASP cc_start: 0.7914 (p0) cc_final: 0.7648 (p0)
REVERT: B  134 GLU cc_start: 0.7097 (tt0) cc_final: 0.6837 (tt0)
REVERT: B  155 MET cc_start: 0.8510 (ptm) cc_final: 0.8243 (ptm)
REVERT: C   50 ASN cc_start: 0.7359 (m-40) cc_final: 0.7059 (t0)
REVERT: C   78 ILE cc_start: 0.8161 (pt) cc_final: 0.7754 (mt)
REVERT: C  273 MET cc_start: 0.8679 (tpp) cc_final: 0.8405 (tpp)
REVERT: D  199 ASP cc_start: 0.8097 (p0) cc_final: 0.7890 (p0)
REVERT: D  277 PHE cc_start: 0.5121 (m-10) cc_final: 0.4502 (m-10)
REVERT: E   81 THR cc_start: 0.9070 (m) cc_final: 0.8813 (t)
REVERT: F   78 ILE cc_start: 0.8298 (pt) cc_final: 0.7778 (mt)
REVERT: F  273 MET cc_start: 0.8846 (tpp) cc_final: 0.8494 (tpp)
REVERT: G   46 ARG cc_start: 0.5702 (ttp-170) cc_final: 0.5252 (mtm180)
REVERT: G   81 THR cc_start: 0.9048 (m) cc_final: 0.8821 (t)
  outliers start: 30
  outliers final: 21
  residues processed: 339
  average time/residue: 0.0951
  time to fit residues: 49.5542
Evaluate side-chains
  325 residues out of total 1477 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 304
  time to evaluate  : 0.508 
-------------------------------------------------------------------------------
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   42 LEU
Chi-restraints excluded: chain B residue  148 VAL
Chi-restraints excluded: chain B residue  227 GLU
Chi-restraints excluded: chain C residue  138 LEU
Chi-restraints excluded: chain C residue  227 GLU
Chi-restraints excluded: chain D residue   83 ILE
Chi-restraints excluded: chain D residue  138 LEU
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  227 GLU
Chi-restraints excluded: chain F residue  138 LEU
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=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 182
   random chunks:
   chunk 11 optimal weight:    5.9990
   chunk 120 optimal weight:    5.9990
   chunk 128 optimal weight:    0.0870
   chunk 31 optimal weight:    6.9990
   chunk 29 optimal weight:    3.9990
   chunk 90 optimal weight:    0.0060
   chunk 138 optimal weight:    0.9990
   chunk 28 optimal weight:    8.9990
   chunk 169 optimal weight:    7.9990
   chunk 7 optimal weight:    5.9990
   chunk 38 optimal weight:    5.9990
   overall best weight:    2.2180

-------------------------------------------------------------------------------
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 = 0.3456 r_free = 0.3456 target = 0.109150 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3148 r_free = 0.3148 target = 0.091403 restraints weight = 30728.910|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3185 r_free = 0.3185 target = 0.093789 restraints weight = 15139.165|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3208 r_free = 0.3208 target = 0.095269 restraints weight = 9315.419|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3227 r_free = 0.3227 target = 0.096459 restraints weight = 6775.637|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3236 r_free = 0.3236 target = 0.097034 restraints weight = 5386.867|
|-----------------------------------------------------------------------------|
r_work (final): 0.3237
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7908
moved from start:          0.1937

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.093  14098  Z= 0.173
  Angle     :  0.463   5.502  19117  Z= 0.251
  Chirality :  0.042   0.206   2345
  Planarity :  0.003   0.050   2429
  Dihedral  :  3.874  14.918   1988
  Min Nonbonded Distance : 2.544

Molprobity Statistics.
  All-atom Clashscore : 8.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.21 %
    Favored  : 98.79 %
  Rotamer:
    Outliers :  3.11 %
    Allowed  : 19.70 %
    Favored  : 77.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.44 (0.19), residues: 1813
  helix:  3.09 (0.15), residues: 1015
  sheet:  1.18 (0.31), residues: 238
  loop : -1.11 (0.25), residues: 560

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG G 279 
 TYR   0.007   0.001   TYR A 250 
 PHE   0.024   0.002   PHE A 277 
 TRP   0.004   0.001   TRP B 251 

Details of bonding type rmsd
  covalent geometry    : bond        0.00396 (14098)
  covalent geometry    : angle       0.46303 (19117)
  hydrogen bonds       : bond        0.03319 ( 1055)
  hydrogen bonds       : angle       3.96840 ( 3081)

*********************** 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
  346 residues out of total 1477 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 300
  time to evaluate  : 0.516 
Fit side-chains
REVERT: A   50 ASN cc_start: 0.6970 (m-40) cc_final: 0.6708 (t0)
REVERT: A   81 THR cc_start: 0.9202 (OUTLIER) cc_final: 0.8994 (t)
REVERT: A  199 ASP cc_start: 0.7998 (p0) cc_final: 0.7720 (p0)
REVERT: B  134 GLU cc_start: 0.7130 (tt0) cc_final: 0.6801 (tt0)
REVERT: C   50 ASN cc_start: 0.7312 (m-40) cc_final: 0.7056 (t0)
REVERT: C   78 ILE cc_start: 0.8260 (pt) cc_final: 0.7729 (mt)
REVERT: C  273 MET cc_start: 0.8655 (tpp) cc_final: 0.8228 (tpp)
REVERT: C  279 ARG cc_start: 0.5393 (ttp-110) cc_final: 0.4646 (mtm110)
REVERT: D  247 GLN cc_start: 0.8045 (tp40) cc_final: 0.7742 (tp-100)
REVERT: D  277 PHE cc_start: 0.5688 (m-10) cc_final: 0.5036 (m-10)
REVERT: E   44 ILE cc_start: 0.8674 (OUTLIER) cc_final: 0.8472 (mp)
REVERT: E   81 THR cc_start: 0.9110 (m) cc_final: 0.8848 (t)
REVERT: E  279 ARG cc_start: 0.5570 (ttp-110) cc_final: 0.5062 (mtm110)
REVERT: F   78 ILE cc_start: 0.8372 (pt) cc_final: 0.7818 (mt)
REVERT: F  273 MET cc_start: 0.8806 (tpp) cc_final: 0.8420 (tpp)
REVERT: G   46 ARG cc_start: 0.5675 (ttp-170) cc_final: 0.5240 (mtm180)
REVERT: G   81 THR cc_start: 0.9091 (m) cc_final: 0.8833 (t)
  outliers start: 46
  outliers final: 33
  residues processed: 319
  average time/residue: 0.0940
  time to fit residues: 46.5561
Evaluate side-chains
  321 residues out of total 1477 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 286
  time to evaluate  : 0.510 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   81 THR
Chi-restraints excluded: chain A residue   83 ILE
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 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  148 VAL
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  138 LEU
Chi-restraints excluded: chain D residue  148 VAL
Chi-restraints excluded: chain E residue   44 ILE
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  122 VAL
Chi-restraints excluded: chain F residue  138 LEU
Chi-restraints excluded: chain F residue  148 VAL
Chi-restraints excluded: chain G residue   73 VAL
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  138 LEU
Chi-restraints excluded: chain G residue  148 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 182
   random chunks:
   chunk 56 optimal weight:    5.9990
   chunk 165 optimal weight:    2.9990
   chunk 116 optimal weight:    2.9990
   chunk 99 optimal weight:    0.8980
   chunk 176 optimal weight:    0.5980
   chunk 10 optimal weight:    5.9990
   chunk 167 optimal weight:    0.0980
   chunk 30 optimal weight:    0.9990
   chunk 158 optimal weight:    1.9990
   chunk 115 optimal weight:    3.9990
   chunk 118 optimal weight:    7.9990
   overall best weight:    0.9184

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

Flipped N/Q/H residues before XYZ refinement:
A 276 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3477 r_free = 0.3477 target = 0.110502 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3172 r_free = 0.3172 target = 0.092755 restraints weight = 30741.715|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3210 r_free = 0.3210 target = 0.095213 restraints weight = 15005.699|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3232 r_free = 0.3232 target = 0.096687 restraints weight = 9148.352|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 44)----------------|
| r_work = 0.3251 r_free = 0.3251 target = 0.097887 restraints weight = 6642.872|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3259 r_free = 0.3259 target = 0.098422 restraints weight = 5281.559|
|-----------------------------------------------------------------------------|
r_work (final): 0.3260
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7883
moved from start:          0.2025

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029  14098  Z= 0.105
  Angle     :  0.427   5.692  19117  Z= 0.231
  Chirality :  0.042   0.222   2345
  Planarity :  0.003   0.021   2429
  Dihedral  :  3.750  16.101   1988
  Min Nonbonded Distance : 2.588

Molprobity Statistics.
  All-atom Clashscore : 8.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.16 %
    Favored  : 98.84 %
  Rotamer:
    Outliers :  2.17 %
    Allowed  : 20.85 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.54 (0.19), residues: 1813
  helix:  3.20 (0.15), residues: 1015
  sheet:  1.26 (0.31), residues: 238
  loop : -1.17 (0.25), residues: 560

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 279 
 TYR   0.003   0.001   TYR B 250 
 PHE   0.019   0.001   PHE A 277 
 TRP   0.003   0.001   TRP F 251 

Details of bonding type rmsd
  covalent geometry    : bond        0.00227 (14098)
  covalent geometry    : angle       0.42680 (19117)
  hydrogen bonds       : bond        0.03096 ( 1055)
  hydrogen bonds       : angle       3.78046 ( 3081)

*********************** 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
  356 residues out of total 1477 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 324
  time to evaluate  : 0.607 
Fit side-chains
REVERT: A   50 ASN cc_start: 0.7050 (m-40) cc_final: 0.6810 (t0)
REVERT: A   81 THR cc_start: 0.9199 (m) cc_final: 0.8868 (t)
REVERT: A  199 ASP cc_start: 0.8023 (p0) cc_final: 0.7744 (p0)
REVERT: A  217 LYS cc_start: 0.8379 (mmmt) cc_final: 0.8138 (mmmt)
REVERT: B   81 THR cc_start: 0.9189 (m) cc_final: 0.8980 (t)
REVERT: B  134 GLU cc_start: 0.7060 (tt0) cc_final: 0.6684 (tt0)
REVERT: C   50 ASN cc_start: 0.7289 (m-40) cc_final: 0.7039 (t0)
REVERT: C   78 ILE cc_start: 0.8208 (pt) cc_final: 0.7623 (mt)
REVERT: C  111 LEU cc_start: 0.9063 (mm) cc_final: 0.8753 (mt)
REVERT: C  273 MET cc_start: 0.8588 (tpp) cc_final: 0.8253 (tpp)
REVERT: C  279 ARG cc_start: 0.5358 (ttp-110) cc_final: 0.4814 (mtm110)
REVERT: D  247 GLN cc_start: 0.8109 (tp40) cc_final: 0.7808 (tp-100)
REVERT: D  277 PHE cc_start: 0.5794 (m-10) cc_final: 0.5260 (m-10)
REVERT: E   44 ILE cc_start: 0.8633 (OUTLIER) cc_final: 0.8405 (mp)
REVERT: E   81 THR cc_start: 0.9077 (m) cc_final: 0.8808 (t)
REVERT: E  279 ARG cc_start: 0.5636 (ttp-110) cc_final: 0.5358 (mtm110)
REVERT: F   78 ILE cc_start: 0.8281 (pt) cc_final: 0.7749 (mt)
REVERT: F  273 MET cc_start: 0.8783 (tpp) cc_final: 0.8451 (tpp)
REVERT: G   46 ARG cc_start: 0.5695 (ttp-170) cc_final: 0.5229 (mtm180)
REVERT: G   81 THR cc_start: 0.9062 (m) cc_final: 0.8818 (t)
  outliers start: 32
  outliers final: 24
  residues processed: 339
  average time/residue: 0.0961
  time to fit residues: 50.3809
Evaluate side-chains
  327 residues out of total 1477 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 302
  time to evaluate  : 0.511 
-------------------------------------------------------------------------------
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   91 VAL
Chi-restraints excluded: chain B residue  138 LEU
Chi-restraints excluded: chain B residue  148 VAL
Chi-restraints excluded: chain B residue  227 GLU
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   83 ILE
Chi-restraints excluded: chain D residue  138 LEU
Chi-restraints excluded: chain D residue  148 VAL
Chi-restraints excluded: chain E residue   44 ILE
Chi-restraints excluded: chain E residue   82 LEU
Chi-restraints excluded: chain E residue  148 VAL
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  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 12 optimal weight:    0.7980
   chunk 71 optimal weight:    2.9990
   chunk 72 optimal weight:    0.7980
   chunk 8 optimal weight:    0.9980
   chunk 128 optimal weight:    0.9990
   chunk 15 optimal weight:    4.9990
   chunk 165 optimal weight:    6.9990
   chunk 170 optimal weight:    6.9990
   chunk 158 optimal weight:    0.9980
   chunk 87 optimal weight:    3.9990
   chunk 145 optimal weight:    0.8980
   overall best weight:    0.8980

-------------------------------------------------------------------------------
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

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3464 r_free = 0.3464 target = 0.109337 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3167 r_free = 0.3167 target = 0.092202 restraints weight = 30209.229|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3203 r_free = 0.3203 target = 0.094477 restraints weight = 14603.041|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 50)----------------|
| r_work = 0.3231 r_free = 0.3231 target = 0.096146 restraints weight = 8854.260|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3244 r_free = 0.3244 target = 0.096958 restraints weight = 6245.573|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3257 r_free = 0.3257 target = 0.097760 restraints weight = 5073.306|
|-----------------------------------------------------------------------------|
r_work (final): 0.3261
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7877
moved from start:          0.2110

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.038  14098  Z= 0.107
  Angle     :  0.434   6.057  19117  Z= 0.234
  Chirality :  0.042   0.233   2345
  Planarity :  0.003   0.057   2429
  Dihedral  :  3.740  16.332   1988
  Min Nonbonded Distance : 2.587

Molprobity Statistics.
  All-atom Clashscore : 8.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.16 %
    Favored  : 98.84 %
  Rotamer:
    Outliers :  2.51 %
    Allowed  : 20.11 %
    Favored  : 77.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.54 (0.19), residues: 1813
  helix:  3.20 (0.15), residues: 1015
  sheet:  1.27 (0.31), residues: 238
  loop : -1.17 (0.25), residues: 560

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.000   ARG A 279 
 TYR   0.004   0.001   TYR B 250 
 PHE   0.017   0.001   PHE B 277 
 TRP   0.003   0.001   TRP B 251 

Details of bonding type rmsd
  covalent geometry    : bond        0.00234 (14098)
  covalent geometry    : angle       0.43424 (19117)
  hydrogen bonds       : bond        0.03077 ( 1055)
  hydrogen bonds       : angle       3.77736 ( 3081)

*********************** 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
  354 residues out of total 1477 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 317
  time to evaluate  : 0.389 
Fit side-chains
REVERT: A   50 ASN cc_start: 0.7021 (m-40) cc_final: 0.6794 (t0)
REVERT: A   81 THR cc_start: 0.9170 (m) cc_final: 0.8849 (t)
REVERT: A  199 ASP cc_start: 0.8009 (p0) cc_final: 0.7727 (p0)
REVERT: A  217 LYS cc_start: 0.8350 (mmmt) cc_final: 0.8141 (mmmt)
REVERT: B   81 THR cc_start: 0.9208 (m) cc_final: 0.8965 (t)
REVERT: B  134 GLU cc_start: 0.6976 (tt0) cc_final: 0.6594 (tt0)
REVERT: C   50 ASN cc_start: 0.7283 (m-40) cc_final: 0.7036 (t0)
REVERT: C   78 ILE cc_start: 0.8213 (pt) cc_final: 0.7504 (mt)
REVERT: C  111 LEU cc_start: 0.9074 (mm) cc_final: 0.8784 (mt)
REVERT: C  273 MET cc_start: 0.8576 (tpp) cc_final: 0.8169 (tpp)
REVERT: C  279 ARG cc_start: 0.5350 (ttp-110) cc_final: 0.4798 (mtm110)
REVERT: D  247 GLN cc_start: 0.8123 (tp40) cc_final: 0.7793 (tp-100)
REVERT: D  277 PHE cc_start: 0.5818 (m-10) cc_final: 0.5150 (m-10)
REVERT: E   81 THR cc_start: 0.9063 (m) cc_final: 0.8796 (t)
REVERT: E  279 ARG cc_start: 0.5674 (ttp-110) cc_final: 0.5437 (mtm110)
REVERT: F   78 ILE cc_start: 0.8293 (pt) cc_final: 0.7756 (mt)
REVERT: F  273 MET cc_start: 0.8733 (tpp) cc_final: 0.8412 (tpp)
REVERT: G   46 ARG cc_start: 0.5696 (ttp-170) cc_final: 0.5224 (mtm180)
REVERT: G   81 THR cc_start: 0.9095 (m) cc_final: 0.8869 (t)
  outliers start: 37
  outliers final: 31
  residues processed: 331
  average time/residue: 0.0981
  time to fit residues: 49.9817
Evaluate side-chains
  337 residues out of total 1477 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 306
  time to evaluate  : 0.488 
-------------------------------------------------------------------------------
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   91 VAL
Chi-restraints excluded: chain B residue  138 LEU
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   35 LEU
Chi-restraints excluded: chain D residue   83 ILE
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   91 VAL
Chi-restraints excluded: chain E residue  138 LEU
Chi-restraints excluded: chain E residue  148 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  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 128 optimal weight:    0.8980
   chunk 154 optimal weight:    3.9990
   chunk 104 optimal weight:    6.9990
   chunk 105 optimal weight:    0.9980
   chunk 29 optimal weight:    2.9990
   chunk 113 optimal weight:    6.9990
   chunk 72 optimal weight:    4.9990
   chunk 101 optimal weight:    0.9990
   chunk 108 optimal weight:    5.9990
   chunk 3 optimal weight:    2.9990
   chunk 97 optimal weight:    8.9990
   overall best weight:    1.7786

-------------------------------------------------------------------------------
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 = 0.3453 r_free = 0.3453 target = 0.108860 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3154 r_free = 0.3154 target = 0.091463 restraints weight = 30739.574|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3189 r_free = 0.3189 target = 0.093834 restraints weight = 15029.756|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3214 r_free = 0.3214 target = 0.095437 restraints weight = 9236.188|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 50)----------------|
| r_work = 0.3232 r_free = 0.3232 target = 0.096531 restraints weight = 6626.622|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 41)----------------|
| r_work = 0.3241 r_free = 0.3241 target = 0.097129 restraints weight = 5254.045|
|-----------------------------------------------------------------------------|
r_work (final): 0.3243
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7902
moved from start:          0.2183

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.057  14098  Z= 0.152
  Angle     :  0.467   6.093  19117  Z= 0.252
  Chirality :  0.042   0.232   2345
  Planarity :  0.003   0.049   2429
  Dihedral  :  3.878  16.745   1988
  Min Nonbonded Distance : 2.590

Molprobity Statistics.
  All-atom Clashscore : 8.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.32 %
    Favored  : 98.68 %
  Rotamer:
    Outliers :  2.44 %
    Allowed  : 20.24 %
    Favored  : 77.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.39 (0.19), residues: 1813
  helix:  3.03 (0.15), residues: 1015
  sheet:  1.18 (0.31), residues: 238
  loop : -1.13 (0.25), residues: 560

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.000   ARG A 279 
 TYR   0.006   0.001   TYR D 250 
 PHE   0.020   0.001   PHE E 277 
 TRP   0.006   0.001   TRP B 251 

Details of bonding type rmsd
  covalent geometry    : bond        0.00344 (14098)
  covalent geometry    : angle       0.46665 (19117)
  hydrogen bonds       : bond        0.03254 ( 1055)
  hydrogen bonds       : angle       3.94367 ( 3081)

*********************** 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
  330 residues out of total 1477 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 294
  time to evaluate  : 0.422 
Fit side-chains
REVERT: A   81 THR cc_start: 0.9209 (m) cc_final: 0.8868 (t)
REVERT: A  199 ASP cc_start: 0.8068 (p0) cc_final: 0.7793 (p0)
REVERT: A  217 LYS cc_start: 0.8406 (mmmt) cc_final: 0.8175 (mmmt)
REVERT: B   81 THR cc_start: 0.9249 (m) cc_final: 0.8970 (t)
REVERT: B  134 GLU cc_start: 0.7108 (tt0) cc_final: 0.6748 (tt0)
REVERT: C   50 ASN cc_start: 0.7302 (m-40) cc_final: 0.7053 (t0)
REVERT: C   78 ILE cc_start: 0.8102 (pt) cc_final: 0.7727 (mt)
REVERT: C   81 THR cc_start: 0.9110 (m) cc_final: 0.8816 (t)
REVERT: C  273 MET cc_start: 0.8607 (tpp) cc_final: 0.8164 (tpp)
REVERT: C  279 ARG cc_start: 0.5400 (ttp-110) cc_final: 0.4858 (mtm110)
REVERT: D  277 PHE cc_start: 0.6057 (m-10) cc_final: 0.5623 (m-10)
REVERT: E   81 THR cc_start: 0.9095 (m) cc_final: 0.8822 (t)
REVERT: F   78 ILE cc_start: 0.8318 (pt) cc_final: 0.7767 (mt)
REVERT: F  273 MET cc_start: 0.8761 (tpp) cc_final: 0.8472 (tpp)
REVERT: G   46 ARG cc_start: 0.5773 (ttp-170) cc_final: 0.5264 (mtm180)
REVERT: G   81 THR cc_start: 0.9080 (m) cc_final: 0.8817 (t)
  outliers start: 36
  outliers final: 31
  residues processed: 307
  average time/residue: 0.0973
  time to fit residues: 45.4758
Evaluate side-chains
  318 residues out of total 1477 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 287
  time to evaluate  : 0.415 
-------------------------------------------------------------------------------
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   91 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  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   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   56 MET
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  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  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 160 optimal weight:    7.9990
   chunk 86 optimal weight:    0.8980
   chunk 76 optimal weight:    0.9990
   chunk 84 optimal weight:    5.9990
   chunk 37 optimal weight:    0.8980
   chunk 19 optimal weight:    4.9990
   chunk 90 optimal weight:    3.9990
   chunk 101 optimal weight:    2.9990
   chunk 177 optimal weight:    0.9980
   chunk 94 optimal weight:    6.9990
   chunk 181 optimal weight:    0.9990
   overall best weight:    0.9584

-------------------------------------------------------------------------------
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 = 0.3469 r_free = 0.3469 target = 0.109880 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3168 r_free = 0.3168 target = 0.092389 restraints weight = 30346.194|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 50)----------------|
| r_work = 0.3204 r_free = 0.3204 target = 0.094807 restraints weight = 14658.145|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3227 r_free = 0.3227 target = 0.096272 restraints weight = 8921.262|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3245 r_free = 0.3245 target = 0.097498 restraints weight = 6471.113|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.3257 r_free = 0.3257 target = 0.098256 restraints weight = 5135.306|
|-----------------------------------------------------------------------------|
r_work (final): 0.3260
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7882
moved from start:          0.2231

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.057  14098  Z= 0.113
  Angle     :  0.454   5.987  19117  Z= 0.246
  Chirality :  0.042   0.239   2345
  Planarity :  0.003   0.054   2429
  Dihedral  :  3.822  20.714   1988
  Min Nonbonded Distance : 2.591

Molprobity Statistics.
  All-atom Clashscore : 9.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.21 %
    Favored  : 98.79 %
  Rotamer:
    Outliers :  2.37 %
    Allowed  : 20.38 %
    Favored  : 77.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.40 (0.19), residues: 1813
  helix:  3.06 (0.15), residues: 1015
  sheet:  1.22 (0.31), residues: 238
  loop : -1.17 (0.25), residues: 560

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.015   0.000   ARG E 279 
 TYR   0.004   0.001   TYR B 250 
 PHE   0.020   0.001   PHE B  80 
 TRP   0.005   0.001   TRP B 251 

Details of bonding type rmsd
  covalent geometry    : bond        0.00248 (14098)
  covalent geometry    : angle       0.45357 (19117)
  hydrogen bonds       : bond        0.03136 ( 1055)
  hydrogen bonds       : angle       3.85742 ( 3081)

********************** 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
  339 residues out of total 1477 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 304
  time to evaluate  : 0.509 
Fit side-chains
REVERT: A   50 ASN cc_start: 0.6791 (m-40) cc_final: 0.6307 (t0)
REVERT: A   81 THR cc_start: 0.9213 (m) cc_final: 0.8892 (t)
REVERT: A  199 ASP cc_start: 0.8077 (p0) cc_final: 0.7806 (p0)
REVERT: A  217 LYS cc_start: 0.8399 (mmmt) cc_final: 0.8195 (mmmt)
REVERT: A  273 MET cc_start: 0.8445 (tpp) cc_final: 0.8086 (tpp)
REVERT: B   81 THR cc_start: 0.9204 (m) cc_final: 0.8913 (t)
REVERT: B  134 GLU cc_start: 0.7133 (tt0) cc_final: 0.6793 (tt0)
REVERT: C   50 ASN cc_start: 0.7385 (m-40) cc_final: 0.7093 (t0)
REVERT: C   78 ILE cc_start: 0.8174 (pt) cc_final: 0.7754 (mt)
REVERT: C   81 THR cc_start: 0.9053 (m) cc_final: 0.8773 (t)
REVERT: C  111 LEU cc_start: 0.9082 (mm) cc_final: 0.8757 (mt)
REVERT: C  273 MET cc_start: 0.8566 (tpp) cc_final: 0.8121 (tpp)
REVERT: C  279 ARG cc_start: 0.5410 (ttp-110) cc_final: 0.4873 (mtm110)
REVERT: D  277 PHE cc_start: 0.6141 (m-10) cc_final: 0.5687 (m-10)
REVERT: E   81 THR cc_start: 0.9038 (m) cc_final: 0.8770 (t)
REVERT: F   78 ILE cc_start: 0.8346 (pt) cc_final: 0.7791 (mt)
REVERT: F   80 PHE cc_start: 0.8579 (m-10) cc_final: 0.8327 (m-10)
REVERT: F  273 MET cc_start: 0.8738 (tpp) cc_final: 0.8436 (tpp)
REVERT: G   46 ARG cc_start: 0.5736 (ttp-170) cc_final: 0.5235 (mtm180)
REVERT: G   81 THR cc_start: 0.9085 (m) cc_final: 0.8858 (t)
  outliers start: 35
  outliers final: 33
  residues processed: 316
  average time/residue: 0.0941
  time to fit residues: 45.9257
Evaluate side-chains
  326 residues out of total 1477 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 293
  time to evaluate  : 0.439 
-------------------------------------------------------------------------------
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   91 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  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   56 MET
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   56 MET
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  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  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 149 optimal weight:    0.9990
   chunk 115 optimal weight:    0.0040
   chunk 90 optimal weight:    5.9990
   chunk 101 optimal weight:    5.9990
   chunk 123 optimal weight:    0.0030
   chunk 117 optimal weight:    4.9990
   chunk 50 optimal weight:    0.9990
   chunk 104 optimal weight:    2.9990
   chunk 47 optimal weight:    8.9990
   chunk 174 optimal weight:    4.9990
   chunk 40 optimal weight:    1.9990
   overall best weight:    0.8008

-------------------------------------------------------------------------------
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 = 0.3478 r_free = 0.3478 target = 0.110449 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3179 r_free = 0.3179 target = 0.092979 restraints weight = 30198.075|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3214 r_free = 0.3214 target = 0.095390 restraints weight = 14566.836|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3240 r_free = 0.3240 target = 0.097068 restraints weight = 8885.892|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3255 r_free = 0.3255 target = 0.098025 restraints weight = 6294.352|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3267 r_free = 0.3267 target = 0.098802 restraints weight = 5092.853|
|-----------------------------------------------------------------------------|
r_work (final): 0.3276
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7876
moved from start:          0.2290

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= 0.105
  Angle     :  0.448   6.033  19117  Z= 0.241
  Chirality :  0.042   0.232   2345
  Planarity :  0.003   0.063   2429
  Dihedral  :  3.771  18.535   1988
  Min Nonbonded Distance : 2.595

Molprobity Statistics.
  All-atom Clashscore : 8.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.32 %
    Favored  : 98.68 %
  Rotamer:
    Outliers :  2.23 %
    Allowed  : 20.72 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.48 (0.19), residues: 1813
  helix:  3.15 (0.15), residues: 1015
  sheet:  1.27 (0.31), residues: 238
  loop : -1.21 (0.25), residues: 560

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.015   0.000   ARG E 279 
 TYR   0.004   0.001   TYR B 250 
 PHE   0.013   0.001   PHE G 277 
 TRP   0.005   0.001   TRP B 251 

Details of bonding type rmsd
  covalent geometry    : bond        0.00229 (14098)
  covalent geometry    : angle       0.44818 (19117)
  hydrogen bonds       : bond        0.03068 ( 1055)
  hydrogen bonds       : angle       3.79843 ( 3081)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2043.94 seconds
wall clock time: 36 minutes 1.26 seconds (2161.26 seconds total)