Starting phenix.real_space_refine
on Wed Mar 12 23:23:04 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7xjk_33230/03_2025/7xjk_33230.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7xjk_33230/03_2025/7xjk_33230.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.3
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7xjk_33230/03_2025/7xjk_33230.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7xjk_33230/03_2025/7xjk_33230.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7xjk_33230/03_2025/7xjk_33230.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7xjk_33230/03_2025/7xjk_33230.cif"
  }
  resolution = 3.3
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.115
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      53      5.16       5
     C    5478      2.51       5
     N    1472      2.21       5
     O    1567      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 6 residue(s): 0.05s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 8570
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 112
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 16, 112
          Classifications: {'peptide': 16}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 14}
          Unresolved non-hydrogen bonds: 6
          Unresolved non-hydrogen angles: 8
          Unresolved non-hydrogen dihedrals: 6
          Planarities with less than four sites: {'HIS:plan': 1}
          Unresolved non-hydrogen planarities: 5
    Chain: "B"
      Number of atoms: 1750
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 226, 1750
          Classifications: {'peptide': 226}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 23}
          Link IDs: {'PTRANS': 6, 'TRANS': 219}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 95
          Unresolved non-hydrogen angles: 109
          Unresolved non-hydrogen dihedrals: 81
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 4, 'ARG:plan': 4, 'ASP:plan': 5}
          Unresolved non-hydrogen planarities: 55
    Chain: "C"
      Number of atoms: 2477
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 338, 2477
          Classifications: {'peptide': 338}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 34}
          Link IDs: {'PTRANS': 5, 'TRANS': 332}
          Unresolved non-hydrogen bonds: 125
          Unresolved non-hydrogen angles: 153
          Unresolved non-hydrogen dihedrals: 99
          Unresolved non-hydrogen chiralities: 4
          Planarities with less than four sites: {'GLN:plan1': 4, 'ASP:plan': 6, 'ASN:plan1': 1, 'HIS:plan': 1, 'GLU:plan': 4, 'ARG:plan': 7}
          Unresolved non-hydrogen planarities: 93
    Chain: "D"
      Number of atoms: 353
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 51, 353
          Classifications: {'peptide': 51}
          Incomplete info: {'truncation_to_alanine': 11}
          Link IDs: {'PTRANS': 4, 'TRANS': 46}
          Unresolved non-hydrogen bonds: 41
          Unresolved non-hydrogen angles: 48
          Unresolved non-hydrogen dihedrals: 34
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 1, 'ASN:plan1': 1}
          Unresolved non-hydrogen planarities: 20
    Chain: "E"
      Number of atoms: 1712
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 230, 1712
          Classifications: {'peptide': 230}
          Incomplete info: {'truncation_to_alanine': 17}
          Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 219}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 58
          Unresolved non-hydrogen angles: 71
          Unresolved non-hydrogen dihedrals: 45
          Unresolved non-hydrogen chiralities: 4
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 7, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 37
    Chain: "F"
      Number of atoms: 2166
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 278, 2166
          Classifications: {'peptide': 278}
          Incomplete info: {'truncation_to_alanine': 5}
          Link IDs: {'PTRANS': 11, 'TRANS': 266}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 30
          Unresolved non-hydrogen angles: 35
          Unresolved non-hydrogen dihedrals: 25
          Planarities with less than four sites: {'ARG:plan': 5}
          Unresolved non-hydrogen planarities: 25
  Time building chain proxies: 5.28, per 1000 atoms: 0.62
  Number of scatterers: 8570
  At special positions: 0
  Unit cell: (91.308, 119.57, 120.657, 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      53     16.00
     O    1567      8.00
     N    1472      7.00
     C    5478      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS E 147 " - pdb=" SG  CYS E 217 " distance=2.04
    Simple disulfide: pdb=" SG  CYS F  98 " - pdb=" SG  CYS F 175 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.27
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  2234 Ramachandran restraints generated.
    1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2122

  Finding SS restraints...
    Secondary structure from input PDB file:
      28 helices and 14 sheets defined
      38.5% alpha, 22.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.19
  Creating SS restraints...
    Processing helix  chain 'A' and resid 3 through 12
    Processing helix  chain 'B' and resid 6 through 31
    Processing helix  chain 'B' and resid 45 through 54
    Processing helix  chain 'B' and resid 95 through 99
    Processing helix  chain 'B' and resid 117 through 130
    Processing helix  chain 'B' and resid 145 through 156
    Processing helix  chain 'B' and resid 159 through 164
      removed outlier: 3.956A  pdb=" N   TYR B 163 " --> pdb=" O   LYS B 159 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 165 through 168
    Processing helix  chain 'B' and resid 183 through 204
      removed outlier: 3.533A  pdb=" N   PHE B 197 " --> pdb=" O   ILE B 193 " (cutoff:3.500A)
      removed outlier: 4.585A  pdb=" N   SER B 204 " --> pdb=" O   ILE B 200 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 222 through 243
      removed outlier: 4.045A  pdb=" N   ARG B 226 " --> pdb=" O   GLU B 222 " (cutoff:3.500A)
      removed outlier: 3.870A  pdb=" N   ILE B 227 " --> pdb=" O   ASN B 223 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 4 through 25
    Processing helix  chain 'C' and resid 29 through 34
    Processing helix  chain 'D' and resid 12 through 24
      removed outlier: 3.693A  pdb=" N   ASN D  24 " --> pdb=" O   LYS D  20 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 29 through 44
      removed outlier: 3.505A  pdb=" N   HIS D  44 " --> pdb=" O   TYR D  40 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 45 through 48
      removed outlier: 3.803A  pdb=" N   ASP D  48 " --> pdb=" O   ALA D  45 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'D' and resid 45 through 48'
    Processing helix  chain 'E' and resid 53 through 56
      removed outlier: 4.092A  pdb=" N   GLY E  56 " --> pdb=" O   SER E  53 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'E' and resid 53 through 56'
    Processing helix  chain 'E' and resid 87 through 91
      removed outlier: 4.073A  pdb=" N   THR E  91 " --> pdb=" O   SER E  88 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 27 through 53
    Processing helix  chain 'F' and resid 58 through 88
      Proline residue:  F  80  - end of helix
    Processing helix  chain 'F' and resid 95 through 129
      removed outlier: 3.505A  pdb=" N   LYS F  99 " --> pdb=" O   SER F  95 " (cutoff:3.500A)
      removed outlier: 4.655A  pdb=" N   HIS F 102 " --> pdb=" O   CYS F  98 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 132 through 137
    Processing helix  chain 'F' and resid 138 through 157
    Processing helix  chain 'F' and resid 159 through 163
    Processing helix  chain 'F' and resid 180 through 196
    Processing helix  chain 'F' and resid 196 through 215
    Processing helix  chain 'F' and resid 225 through 262
      removed outlier: 4.196A  pdb=" N   TRP F 249 " --> pdb=" O   PHE F 245 " (cutoff:3.500A)
      Proline residue:  F 251  - end of helix
    Processing helix  chain 'F' and resid 267 through 293
      removed outlier: 3.912A  pdb=" N   SER F 285 " --> pdb=" O   SER F 281 " (cutoff:3.500A)
      Proline residue:  F 289  - end of helix
    Processing helix  chain 'F' and resid 296 through 307
    Processing sheet with id=AA1, first strand: chain 'B' and resid 69 through 76
      removed outlier: 3.942A  pdb=" N   PHE B  84 " --> pdb=" O   LEU B  36 " (cutoff:3.500A)
      removed outlier: 4.780A  pdb=" N   VAL B  86 " --> pdb=" O   LEU B  38 " (cutoff:3.500A)
      removed outlier: 8.005A  pdb=" N   ILE B 107 " --> pdb=" O   ARG B  35 " (cutoff:3.500A)
      removed outlier: 5.998A  pdb=" N   LEU B  37 " --> pdb=" O   ILE B 107 " (cutoff:3.500A)
      removed outlier: 7.239A  pdb=" N   VAL B 109 " --> pdb=" O   LEU B  37 " (cutoff:3.500A)
      removed outlier: 6.397A  pdb=" N   LEU B  39 " --> pdb=" O   VAL B 109 " (cutoff:3.500A)
      removed outlier: 8.411A  pdb=" N   ASP B 111 " --> pdb=" O   LEU B  39 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'C' and resid 47 through 51
      removed outlier: 3.666A  pdb=" N   ARG C  49 " --> pdb=" O   ILE C 338 " (cutoff:3.500A)
      removed outlier: 3.805A  pdb=" N   LEU C 336 " --> pdb=" O   LEU C  51 " (cutoff:3.500A)
      removed outlier: 6.621A  pdb=" N   ALA C 328 " --> pdb=" O   LEU C 318 " (cutoff:3.500A)
      removed outlier: 4.299A  pdb=" N   LEU C 318 " --> pdb=" O   ALA C 328 " (cutoff:3.500A)
      removed outlier: 6.585A  pdb=" N   GLY C 330 " --> pdb=" O   SER C 316 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'C' and resid 62 through 63
      removed outlier: 6.546A  pdb=" N   ILE C  81 " --> pdb=" O   VAL C  90 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'C' and resid 100 through 105
      removed outlier: 6.702A  pdb=" N   GLY C 115 " --> pdb=" O   MET C 101 " (cutoff:3.500A)
      removed outlier: 4.380A  pdb=" N   CYS C 103 " --> pdb=" O   ALA C 113 " (cutoff:3.500A)
      removed outlier: 6.548A  pdb=" N   ALA C 113 " --> pdb=" O   CYS C 103 " (cutoff:3.500A)
      removed outlier: 5.002A  pdb=" N   TYR C 105 " --> pdb=" O   TYR C 111 " (cutoff:3.500A)
      removed outlier: 7.219A  pdb=" N   TYR C 111 " --> pdb=" O   TYR C 105 " (cutoff:3.500A)
      removed outlier: 4.402A  pdb=" N   GLY C 116 " --> pdb=" O   ILE C 120 " (cutoff:3.500A)
      removed outlier: 5.153A  pdb=" N   ILE C 120 " --> pdb=" O   GLY C 116 " (cutoff:3.500A)
      removed outlier: 5.799A  pdb=" N   CYS C 121 " --> pdb=" O   GLU C 138 " (cutoff:3.500A)
      removed outlier: 4.488A  pdb=" N   GLU C 138 " --> pdb=" O   CYS C 121 " (cutoff:3.500A)
      removed outlier: 6.632A  pdb=" N   ILE C 123 " --> pdb=" O   SER C 136 " (cutoff:3.500A)
      removed outlier: 3.611A  pdb=" N   ARG C 134 " --> pdb=" O   ASN C 125 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'C' and resid 146 through 151
      removed outlier: 6.756A  pdb=" N   SER C 160 " --> pdb=" O   SER C 147 " (cutoff:3.500A)
      removed outlier: 4.306A  pdb=" N   CYS C 149 " --> pdb=" O   VAL C 158 " (cutoff:3.500A)
      removed outlier: 6.653A  pdb=" N   VAL C 158 " --> pdb=" O   CYS C 149 " (cutoff:3.500A)
      removed outlier: 5.117A  pdb=" N   PHE C 151 " --> pdb=" O   GLN C 156 " (cutoff:3.500A)
      removed outlier: 7.580A  pdb=" N   GLN C 156 " --> pdb=" O   PHE C 151 " (cutoff:3.500A)
      removed outlier: 4.059A  pdb=" N   THR C 165 " --> pdb=" O   SER C 161 " (cutoff:3.500A)
      removed outlier: 6.094A  pdb=" N   ASP C 170 " --> pdb=" O   GLN C 176 " (cutoff:3.500A)
      removed outlier: 5.955A  pdb=" N   GLN C 176 " --> pdb=" O   ASP C 170 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'C' and resid 187 through 192
      removed outlier: 3.844A  pdb=" N   GLN C 220 " --> pdb=" O   LEU C 210 " (cutoff:3.500A)
      removed outlier: 6.703A  pdb=" N   ASP C 212 " --> pdb=" O   CYS C 218 " (cutoff:3.500A)
      removed outlier: 6.398A  pdb=" N   CYS C 218 " --> pdb=" O   ASP C 212 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'C' and resid 229 through 234
      removed outlier: 6.403A  pdb=" N   CYS C 250 " --> pdb=" O   THR C 263 " (cutoff:3.500A)
      removed outlier: 4.478A  pdb=" N   THR C 263 " --> pdb=" O   CYS C 250 " (cutoff:3.500A)
      removed outlier: 6.607A  pdb=" N   LEU C 252 " --> pdb=" O   LEU C 261 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'C' and resid 273 through 278
      removed outlier: 6.950A  pdb=" N   GLY C 288 " --> pdb=" O   THR C 274 " (cutoff:3.500A)
      removed outlier: 5.448A  pdb=" N   VAL C 276 " --> pdb=" O   LEU C 286 " (cutoff:3.500A)
      removed outlier: 7.133A  pdb=" N   LEU C 286 " --> pdb=" O   VAL C 276 " (cutoff:3.500A)
      removed outlier: 5.147A  pdb=" N   PHE C 278 " --> pdb=" O   LEU C 284 " (cutoff:3.500A)
      removed outlier: 7.008A  pdb=" N   LEU C 284 " --> pdb=" O   PHE C 278 " (cutoff:3.500A)
      removed outlier: 3.647A  pdb=" N   ASN C 295 " --> pdb=" O   ALA C 287 " (cutoff:3.500A)
      removed outlier: 6.455A  pdb=" N   CYS C 294 " --> pdb=" O   VAL C 307 " (cutoff:3.500A)
      removed outlier: 4.469A  pdb=" N   VAL C 307 " --> pdb=" O   CYS C 294 " (cutoff:3.500A)
      removed outlier: 6.312A  pdb=" N   VAL C 296 " --> pdb=" O   ALA C 305 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'E' and resid 3 through 7
    Processing sheet with id=AB1, first strand: chain 'E' and resid 58 through 60
      removed outlier: 5.156A  pdb=" N   TRP E  47 " --> pdb=" O   ARG E  38 " (cutoff:3.500A)
      removed outlier: 5.639A  pdb=" N   ARG E  38 " --> pdb=" O   TRP E  47 " (cutoff:3.500A)
      removed outlier: 4.242A  pdb=" N   PHE E 110 " --> pdb=" O   ARG E  98 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'E' and resid 128 through 130
    Processing sheet with id=AB3, first strand: chain 'E' and resid 134 through 136
      removed outlier: 6.463A  pdb=" N   LEU E 162 " --> pdb=" O   TYR E 178 " (cutoff:3.500A)
      removed outlier: 4.620A  pdb=" N   TYR E 178 " --> pdb=" O   LEU E 162 " (cutoff:3.500A)
      removed outlier: 6.583A  pdb=" N   TRP E 164 " --> pdb=" O   LEU E 176 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'E' and resid 134 through 136
      removed outlier: 4.115A  pdb=" N   THR E 226 " --> pdb=" O   GLN E 219 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'F' and resid 164 through 169

    459 hydrogen bonds defined for protein.
    1308 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 3.10

  Time building geometry restraints manager: 2.70 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2772
        1.34 -     1.46: 2196
        1.46 -     1.58: 3719
        1.58 -     1.70: 0
        1.70 -     1.82: 72
  Bond restraints: 8759
  Sorted by residual:
  bond pdb=" CB  ASN F  43 "
       pdb=" CG  ASN F  43 "
    ideal  model  delta    sigma   weight residual
    1.516  1.467  0.049 2.50e-02 1.60e+03 3.90e+00
  bond pdb=" C   VAL F  79 "
       pdb=" N   PRO F  80 "
    ideal  model  delta    sigma   weight residual
    1.333  1.359 -0.026 1.44e-02 4.82e+03 3.16e+00
  bond pdb=" N   LEU F  72 "
       pdb=" CA  LEU F  72 "
    ideal  model  delta    sigma   weight residual
    1.459  1.437  0.022 1.24e-02 6.50e+03 3.11e+00
  bond pdb=" CA  ASP F  71 "
       pdb=" C   ASP F  71 "
    ideal  model  delta    sigma   weight residual
    1.524  1.506  0.017 1.27e-02 6.20e+03 1.86e+00
  bond pdb=" CB  CYS C 103 "
       pdb=" SG  CYS C 103 "
    ideal  model  delta    sigma   weight residual
    1.808  1.765  0.043 3.30e-02 9.18e+02 1.67e+00
  ... (remaining 8754 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.64: 11572
        1.64 -     3.28: 294
        3.28 -     4.92: 47
        4.92 -     6.56: 13
        6.56 -     8.20: 2
  Bond angle restraints: 11928
  Sorted by residual:
  angle pdb=" N   ILE C 270 "
        pdb=" CA  ILE C 270 "
        pdb=" C   ILE C 270 "
      ideal   model   delta    sigma   weight residual
     113.71  109.28    4.43 9.50e-01 1.11e+00 2.17e+01
  angle pdb=" N   HIS F 176 "
        pdb=" CA  HIS F 176 "
        pdb=" C   HIS F 176 "
      ideal   model   delta    sigma   weight residual
     108.25  113.56   -5.31 1.16e+00 7.43e-01 2.10e+01
  angle pdb=" CA  GLU C 130 "
        pdb=" CB  GLU C 130 "
        pdb=" CG  GLU C 130 "
      ideal   model   delta    sigma   weight residual
     114.10  119.22   -5.12 2.00e+00 2.50e-01 6.54e+00
  angle pdb=" CA  TYR F 163 "
        pdb=" CB  TYR F 163 "
        pdb=" CG  TYR F 163 "
      ideal   model   delta    sigma   weight residual
     113.90  118.40   -4.50 1.80e+00 3.09e-01 6.26e+00
  angle pdb=" CA  ILE C 270 "
        pdb=" C   ILE C 270 "
        pdb=" N   CYS C 271 "
      ideal   model   delta    sigma   weight residual
     119.87  116.52    3.35 1.34e+00 5.57e-01 6.24e+00
  ... (remaining 11923 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.90: 4636
       17.90 -    35.80: 408
       35.80 -    53.69: 62
       53.69 -    71.59: 6
       71.59 -    89.49: 4
  Dihedral angle restraints: 5116
    sinusoidal: 1824
      harmonic: 3292
  Sorted by residual:
  dihedral pdb=" CA  TRP C  82 "
           pdb=" C   TRP C  82 "
           pdb=" N   ASP C  83 "
           pdb=" CA  ASP C  83 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  158.15   21.85     0      5.00e+00 4.00e-02 1.91e+01
  dihedral pdb=" CA  ASP F  71 "
           pdb=" C   ASP F  71 "
           pdb=" N   LEU F  72 "
           pdb=" CA  LEU F  72 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -159.72  -20.28     0      5.00e+00 4.00e-02 1.64e+01
  dihedral pdb=" CA  PHE B  81 "
           pdb=" C   PHE B  81 "
           pdb=" N   HIS B  82 "
           pdb=" CA  HIS B  82 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.24   17.76     0      5.00e+00 4.00e-02 1.26e+01
  ... (remaining 5113 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.045: 1011
       0.045 -    0.090: 288
       0.090 -    0.134: 78
       0.134 -    0.179: 5
       0.179 -    0.224: 2
  Chirality restraints: 1384
  Sorted by residual:
  chirality pdb=" CG  LEU F  76 "
            pdb=" CB  LEU F  76 "
            pdb=" CD1 LEU F  76 "
            pdb=" CD2 LEU F  76 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.37   -0.22 2.00e-01 2.50e+01 1.25e+00
  chirality pdb=" CG  LEU F  72 "
            pdb=" CB  LEU F  72 "
            pdb=" CD1 LEU F  72 "
            pdb=" CD2 LEU F  72 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.39   -0.20 2.00e-01 2.50e+01 1.02e+00
  chirality pdb=" CA  LEU F  76 "
            pdb=" N   LEU F  76 "
            pdb=" C   LEU F  76 "
            pdb=" CB  LEU F  76 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.34    0.17 2.00e-01 2.50e+01 7.37e-01
  ... (remaining 1381 not shown)

  Planarity restraints: 1510
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP D  48 "   -0.056 5.00e-02 4.00e+02   8.55e-02 1.17e+01
        pdb=" N   PRO D  49 "    0.148 5.00e-02 4.00e+02
        pdb=" CA  PRO D  49 "   -0.045 5.00e-02 4.00e+02
        pdb=" CD  PRO D  49 "   -0.047 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL F  69 "    0.012 2.00e-02 2.50e+03   2.44e-02 5.98e+00
        pdb=" C   VAL F  69 "   -0.042 2.00e-02 2.50e+03
        pdb=" O   VAL F  69 "    0.016 2.00e-02 2.50e+03
        pdb=" N   ALA F  70 "    0.014 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PHE F 194 "    0.012 2.00e-02 2.50e+03   2.40e-02 5.75e+00
        pdb=" C   PHE F 194 "   -0.041 2.00e-02 2.50e+03
        pdb=" O   PHE F 194 "    0.015 2.00e-02 2.50e+03
        pdb=" N   SER F 195 "    0.014 2.00e-02 2.50e+03
  ... (remaining 1507 not shown)

  Histogram of nonbonded interaction distances:
        2.17 -     2.72: 385
        2.72 -     3.26: 8667
        3.26 -     3.81: 14226
        3.81 -     4.35: 17066
        4.35 -     4.90: 30039
  Nonbonded interactions: 70383
  Sorted by model distance:
  nonbonded pdb=" OD2 ASP F 188 "
            pdb=" NE1 TRP F 260 "
     model   vdw
     2.172 3.120
  nonbonded pdb=" O   SER E  31 "
            pdb=" OG  SER E  53 "
     model   vdw
     2.175 3.040
  nonbonded pdb=" OE2 GLU B   8 "
            pdb=" OH  TYR E 163 "
     model   vdw
     2.204 3.040
  nonbonded pdb=" OE2 GLU C 260 "
            pdb=" OG1 THR C 263 "
     model   vdw
     2.225 3.040
  nonbonded pdb=" OG  SER F  95 "
            pdb=" OE1 GLN F 166 "
     model   vdw
     2.247 3.040
  ... (remaining 70378 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.410
  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:          0.340
  Check model and map are aligned:         0.060
  Set scattering table:                    0.080
  Process input model:                     24.410
  Find NCS groups from input model:        0.100
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.940
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   28.380
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7433
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      :  0.005   0.049   8759  Z= 0.325
  Angle     :  0.651   8.197  11928  Z= 0.353
  Chirality :  0.044   0.224   1384
  Planarity :  0.005   0.086   1510
  Dihedral  : 13.522  89.491   2988
  Min Nonbonded Distance : 2.172

Molprobity Statistics.
  All-atom Clashscore : 11.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.69 %
    Favored  : 97.31 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.23 %
    Favored  : 99.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.32 (0.25), residues: 1117
  helix:  1.58 (0.26), residues: 399
  sheet:  0.07 (0.31), residues: 264
  loop : -0.90 (0.27), residues: 454

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP F 179 
 HIS   0.009   0.001   HIS F 176 
 PHE   0.016   0.002   PHE E  27 
 TYR   0.029   0.002   TYR F 292 
 ARG   0.006   0.001   ARG C 314 

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

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

  2234 Ramachandran restraints generated.
    1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2234 Ramachandran restraints generated.
    1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  163 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 163
  time to evaluate  : 1.001 
Fit side-chains
REVERT: A   11 LEU cc_start: 0.9083 (mm) cc_final: 0.8810 (mm)
REVERT: B  179 GLU cc_start: 0.5497 (pp20) cc_final: 0.5127 (pp20)
  outliers start: 0
  outliers final: 0
  residues processed: 163
  average time/residue: 0.2170
  time to fit residues: 48.7048
Evaluate side-chains
  135 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 135
  time to evaluate  : 0.827 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 93 optimal weight:    0.5980
   chunk 84 optimal weight:    0.2980
   chunk 46 optimal weight:    3.9990
   chunk 28 optimal weight:    3.9990
   chunk 56 optimal weight:    2.9990
   chunk 44 optimal weight:    2.9990
   chunk 87 optimal weight:    5.9990
   chunk 33 optimal weight:    6.9990
   chunk 52 optimal weight:    9.9990
   chunk 64 optimal weight:    2.9990
   chunk 100 optimal weight:    5.9990
   overall best weight:    1.9786

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

Flipped N/Q/H residues before XYZ refinement:
B 209 HIS
E   3 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4082 r_free = 0.4082 target = 0.178306 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3739 r_free = 0.3739 target = 0.141097 restraints weight = 10547.190|
|-----------------------------------------------------------------------------|
r_work (start): 0.3699 rms_B_bonded: 2.23
r_work: 0.3461 rms_B_bonded: 2.98 restraints_weight: 0.5000
r_work: 0.3321 rms_B_bonded: 4.77 restraints_weight: 0.2500
r_work (final): 0.3321
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7736
moved from start:          0.0968

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.046   8759  Z= 0.310
  Angle     :  0.599   8.535  11928  Z= 0.315
  Chirality :  0.044   0.161   1384
  Planarity :  0.005   0.057   1510
  Dihedral  :  4.410  28.840   1228
  Min Nonbonded Distance : 2.471

Molprobity Statistics.
  All-atom Clashscore : 9.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.86 %
    Favored  : 97.14 %
  Rotamer:
    Outliers :  2.06 %
    Allowed  :  9.85 %
    Favored  : 88.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.46 (0.25), residues: 1117
  helix:  1.83 (0.26), residues: 399
  sheet:  0.06 (0.32), residues: 258
  loop : -0.90 (0.27), residues: 460

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP F 179 
 HIS   0.011   0.002   HIS F 176 
 PHE   0.020   0.002   PHE F  81 
 TYR   0.024   0.002   TYR F 163 
 ARG   0.004   0.000   ARG C 314 

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

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

  2234 Ramachandran restraints generated.
    1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2234 Ramachandran restraints generated.
    1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  172 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 154
  time to evaluate  : 0.879 
Fit side-chains
REVERT: A   11 LEU cc_start: 0.8997 (mm) cc_final: 0.8728 (mm)
REVERT: B  120 GLU cc_start: 0.8003 (pp20) cc_final: 0.7644 (pp20)
REVERT: E   38 ARG cc_start: 0.7753 (ptp90) cc_final: 0.7299 (ptp90)
REVERT: E   46 GLU cc_start: 0.8387 (pt0) cc_final: 0.8120 (mt-10)
REVERT: E  202 LEU cc_start: 0.8773 (tp) cc_final: 0.8366 (tp)
REVERT: F  187 MET cc_start: 0.8488 (tpp) cc_final: 0.8032 (tpp)
  outliers start: 18
  outliers final: 15
  residues processed: 158
  average time/residue: 0.1937
  time to fit residues: 43.0192
Evaluate side-chains
  146 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 131
  time to evaluate  : 0.958 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   69 ILE
Chi-restraints excluded: chain B residue   75 GLN
Chi-restraints excluded: chain B residue  109 VAL
Chi-restraints excluded: chain B residue  128 ILE
Chi-restraints excluded: chain C residue  254 ASP
Chi-restraints excluded: chain C residue  263 THR
Chi-restraints excluded: chain E residue    2 VAL
Chi-restraints excluded: chain E residue    5 VAL
Chi-restraints excluded: chain E residue   71 SER
Chi-restraints excluded: chain E residue  190 ARG
Chi-restraints excluded: chain E residue  192 SER
Chi-restraints excluded: chain E residue  194 SER
Chi-restraints excluded: chain E residue  212 VAL
Chi-restraints excluded: chain F residue   85 ILE
Chi-restraints excluded: chain F residue  120 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 44 optimal weight:    1.9990
   chunk 107 optimal weight:    0.9990
   chunk 14 optimal weight:    0.0060
   chunk 57 optimal weight:    0.4980
   chunk 89 optimal weight:    0.9980
   chunk 31 optimal weight:    0.9980
   chunk 99 optimal weight:   10.0000
   chunk 91 optimal weight:    2.9990
   chunk 46 optimal weight:    2.9990
   chunk 84 optimal weight:   10.0000
   chunk 47 optimal weight:    1.9990
   overall best weight:    0.6998

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

Flipped N/Q/H residues before XYZ refinement:
** B  82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 239 ASN
E   3 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4131 r_free = 0.4131 target = 0.183275 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3778 r_free = 0.3778 target = 0.144296 restraints weight = 10651.515|
|-----------------------------------------------------------------------------|
r_work (start): 0.3732 rms_B_bonded: 2.13
r_work: 0.3531 rms_B_bonded: 3.00 restraints_weight: 0.5000
r_work: 0.3397 rms_B_bonded: 4.72 restraints_weight: 0.2500
r_work (final): 0.3397
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7655
moved from start:          0.1415

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   8759  Z= 0.174
  Angle     :  0.518   6.059  11928  Z= 0.274
  Chirality :  0.040   0.138   1384
  Planarity :  0.004   0.039   1510
  Dihedral  :  4.048  25.077   1228
  Min Nonbonded Distance : 2.486

Molprobity Statistics.
  All-atom Clashscore : 7.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.04 %
    Favored  : 96.96 %
  Rotamer:
    Outliers :  2.18 %
    Allowed  : 14.78 %
    Favored  : 83.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.67 (0.25), residues: 1117
  helix:  2.08 (0.26), residues: 397
  sheet:  0.15 (0.32), residues: 258
  loop : -0.83 (0.28), residues: 462

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP C 169 
 HIS   0.010   0.001   HIS F 176 
 PHE   0.035   0.002   PHE F 156 
 TYR   0.018   0.001   TYR F 163 
 ARG   0.003   0.000   ARG C 219 

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

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

  2234 Ramachandran restraints generated.
    1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2234 Ramachandran restraints generated.
    1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  174 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 155
  time to evaluate  : 1.099 
Fit side-chains
REVERT: A   11 LEU cc_start: 0.8928 (mm) cc_final: 0.8618 (mm)
REVERT: B  166 GLU cc_start: 0.8321 (pm20) cc_final: 0.7965 (pm20)
REVERT: C  301 LYS cc_start: 0.7711 (mttp) cc_final: 0.7408 (ttmm)
REVERT: D   48 ASP cc_start: 0.8366 (t0) cc_final: 0.8086 (t0)
REVERT: E   19 LYS cc_start: 0.7696 (tttp) cc_final: 0.7495 (tttp)
REVERT: E   38 ARG cc_start: 0.7726 (ptp90) cc_final: 0.7279 (ptp90)
REVERT: E   46 GLU cc_start: 0.8398 (pt0) cc_final: 0.8159 (mt-10)
REVERT: F  187 MET cc_start: 0.8630 (tpp) cc_final: 0.8068 (tpp)
  outliers start: 19
  outliers final: 11
  residues processed: 162
  average time/residue: 0.1926
  time to fit residues: 43.6931
Evaluate side-chains
  150 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 139
  time to evaluate  : 0.853 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   69 ILE
Chi-restraints excluded: chain B residue   75 GLN
Chi-restraints excluded: chain B residue  109 VAL
Chi-restraints excluded: chain C residue  254 ASP
Chi-restraints excluded: chain C residue  263 THR
Chi-restraints excluded: chain E residue    3 GLN
Chi-restraints excluded: chain E residue    5 VAL
Chi-restraints excluded: chain E residue  190 ARG
Chi-restraints excluded: chain E residue  194 SER
Chi-restraints excluded: chain E residue  212 VAL
Chi-restraints excluded: chain F residue   85 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 106 optimal weight:    0.9980
   chunk 12 optimal weight:    4.9990
   chunk 69 optimal weight:   10.0000
   chunk 29 optimal weight:    2.9990
   chunk 39 optimal weight:    7.9990
   chunk 55 optimal weight:    7.9990
   chunk 41 optimal weight:    0.9990
   chunk 71 optimal weight:    0.5980
   chunk 33 optimal weight:    2.9990
   chunk 75 optimal weight:    7.9990
   chunk 47 optimal weight:    9.9990
   overall best weight:    1.7186

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

Flipped N/Q/H residues before XYZ refinement:
E   3 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4097 r_free = 0.4097 target = 0.179870 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3758 r_free = 0.3758 target = 0.142510 restraints weight = 10710.242|
|-----------------------------------------------------------------------------|
r_work (start): 0.3710 rms_B_bonded: 2.25
r_work: 0.3473 rms_B_bonded: 3.03 restraints_weight: 0.5000
r_work: 0.3335 rms_B_bonded: 4.83 restraints_weight: 0.2500
r_work (final): 0.3335
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7725
moved from start:          0.1507

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   8759  Z= 0.270
  Angle     :  0.563   7.268  11928  Z= 0.294
  Chirality :  0.042   0.150   1384
  Planarity :  0.004   0.044   1510
  Dihedral  :  4.133  26.237   1228
  Min Nonbonded Distance : 2.488

Molprobity Statistics.
  All-atom Clashscore : 8.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.13 %
    Favored  : 96.87 %
  Rotamer:
    Outliers :  2.86 %
    Allowed  : 17.30 %
    Favored  : 79.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.53 (0.25), residues: 1117
  helix:  1.95 (0.26), residues: 400
  sheet:  0.00 (0.32), residues: 259
  loop : -0.86 (0.28), residues: 458

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP F 179 
 HIS   0.008   0.001   HIS F 176 
 PHE   0.023   0.002   PHE F 194 
 TYR   0.022   0.002   TYR F 163 
 ARG   0.003   0.000   ARG C  68 

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

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

  2234 Ramachandran restraints generated.
    1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2234 Ramachandran restraints generated.
    1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  169 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 144
  time to evaluate  : 0.956 
Fit side-chains
REVERT: A   11 LEU cc_start: 0.8956 (mm) cc_final: 0.8651 (mm)
REVERT: B  166 GLU cc_start: 0.8373 (pm20) cc_final: 0.7994 (pm20)
REVERT: C  301 LYS cc_start: 0.7716 (mttp) cc_final: 0.7470 (ttmm)
REVERT: D   48 ASP cc_start: 0.8508 (t0) cc_final: 0.8195 (t0)
REVERT: E   38 ARG cc_start: 0.7738 (ptp90) cc_final: 0.7312 (ptp90)
REVERT: E   46 GLU cc_start: 0.8372 (pt0) cc_final: 0.8151 (mt-10)
REVERT: F  187 MET cc_start: 0.8631 (tpp) cc_final: 0.8198 (tpp)
  outliers start: 25
  outliers final: 19
  residues processed: 156
  average time/residue: 0.2010
  time to fit residues: 44.0648
Evaluate side-chains
  152 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 133
  time to evaluate  : 1.106 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   69 ILE
Chi-restraints excluded: chain B residue   75 GLN
Chi-restraints excluded: chain B residue  109 VAL
Chi-restraints excluded: chain B residue  128 ILE
Chi-restraints excluded: chain B residue  210 ILE
Chi-restraints excluded: chain C residue   65 THR
Chi-restraints excluded: chain C residue   67 SER
Chi-restraints excluded: chain C residue  158 VAL
Chi-restraints excluded: chain C residue  254 ASP
Chi-restraints excluded: chain C residue  263 THR
Chi-restraints excluded: chain C residue  329 THR
Chi-restraints excluded: chain E residue    5 VAL
Chi-restraints excluded: chain E residue  190 ARG
Chi-restraints excluded: chain E residue  194 SER
Chi-restraints excluded: chain E residue  212 VAL
Chi-restraints excluded: chain F residue   75 ILE
Chi-restraints excluded: chain F residue   76 LEU
Chi-restraints excluded: chain F residue   85 ILE
Chi-restraints excluded: chain F residue  120 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 67 optimal weight:    4.9990
   chunk 23 optimal weight:    7.9990
   chunk 108 optimal weight:    2.9990
   chunk 90 optimal weight:    2.9990
   chunk 109 optimal weight:    0.9990
   chunk 48 optimal weight:    5.9990
   chunk 92 optimal weight:    0.9980
   chunk 30 optimal weight:    0.9980
   chunk 110 optimal weight:    0.9990
   chunk 35 optimal weight:    5.9990
   chunk 26 optimal weight:   10.0000
   overall best weight:    1.3986

-------------------------------------------------------------------------------
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 = 0.4104 r_free = 0.4104 target = 0.180615 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3766 r_free = 0.3766 target = 0.143269 restraints weight = 10575.362|
|-----------------------------------------------------------------------------|
r_work (start): 0.3719 rms_B_bonded: 2.26
r_work: 0.3485 rms_B_bonded: 3.03 restraints_weight: 0.5000
r_work: 0.3346 rms_B_bonded: 4.86 restraints_weight: 0.2500
r_work (final): 0.3346
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7714
moved from start:          0.1644

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   8759  Z= 0.235
  Angle     :  0.544   8.391  11928  Z= 0.284
  Chirality :  0.042   0.145   1384
  Planarity :  0.004   0.045   1510
  Dihedral  :  4.063  25.513   1228
  Min Nonbonded Distance : 2.505

Molprobity Statistics.
  All-atom Clashscore : 8.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.95 %
    Favored  : 97.05 %
  Rotamer:
    Outliers :  3.44 %
    Allowed  : 19.24 %
    Favored  : 77.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.59 (0.25), residues: 1117
  helix:  2.03 (0.26), residues: 400
  sheet: -0.08 (0.32), residues: 261
  loop : -0.79 (0.28), residues: 456

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP C 169 
 HIS   0.008   0.001   HIS F 176 
 PHE   0.026   0.002   PHE F 156 
 TYR   0.021   0.002   TYR F 163 
 ARG   0.002   0.000   ARG C  68 

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

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

  2234 Ramachandran restraints generated.
    1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2234 Ramachandran restraints generated.
    1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  168 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 138
  time to evaluate  : 0.892 
Fit side-chains
REVERT: A   11 LEU cc_start: 0.8981 (mm) cc_final: 0.8672 (mm)
REVERT: B  179 GLU cc_start: 0.5709 (pp20) cc_final: 0.5325 (pp20)
REVERT: C  301 LYS cc_start: 0.7623 (mttp) cc_final: 0.7356 (ttmm)
REVERT: D   48 ASP cc_start: 0.8536 (t0) cc_final: 0.8216 (t0)
REVERT: E   38 ARG cc_start: 0.7783 (ptp90) cc_final: 0.7331 (ptp90)
REVERT: E   46 GLU cc_start: 0.8366 (pt0) cc_final: 0.8128 (mt-10)
REVERT: E   59 TYR cc_start: 0.7456 (m-10) cc_final: 0.7199 (m-10)
REVERT: F  187 MET cc_start: 0.8606 (tpp) cc_final: 0.8190 (tpp)
  outliers start: 30
  outliers final: 23
  residues processed: 154
  average time/residue: 0.2030
  time to fit residues: 43.5228
Evaluate side-chains
  155 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 132
  time to evaluate  : 0.882 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   69 ILE
Chi-restraints excluded: chain B residue   75 GLN
Chi-restraints excluded: chain B residue  109 VAL
Chi-restraints excluded: chain B residue  128 ILE
Chi-restraints excluded: chain B residue  210 ILE
Chi-restraints excluded: chain C residue   59 TYR
Chi-restraints excluded: chain C residue   65 THR
Chi-restraints excluded: chain C residue   67 SER
Chi-restraints excluded: chain C residue  161 SER
Chi-restraints excluded: chain C residue  254 ASP
Chi-restraints excluded: chain C residue  263 THR
Chi-restraints excluded: chain C residue  329 THR
Chi-restraints excluded: chain D residue   50 LEU
Chi-restraints excluded: chain E residue    5 VAL
Chi-restraints excluded: chain E residue   71 SER
Chi-restraints excluded: chain E residue  190 ARG
Chi-restraints excluded: chain E residue  194 SER
Chi-restraints excluded: chain E residue  201 THR
Chi-restraints excluded: chain E residue  203 THR
Chi-restraints excluded: chain E residue  212 VAL
Chi-restraints excluded: chain F residue   85 ILE
Chi-restraints excluded: chain F residue  119 VAL
Chi-restraints excluded: chain F residue  120 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 16 optimal weight:    2.9990
   chunk 64 optimal weight:    7.9990
   chunk 107 optimal weight:    2.9990
   chunk 56 optimal weight:    0.0570
   chunk 87 optimal weight:    1.9990
   chunk 83 optimal weight:    3.9990
   chunk 47 optimal weight:   10.0000
   chunk 23 optimal weight:    9.9990
   chunk 13 optimal weight:    0.9990
   chunk 6 optimal weight:    6.9990
   chunk 5 optimal weight:    2.9990
   overall best weight:    1.8106

-------------------------------------------------------------------------------
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 = 0.4088 r_free = 0.4088 target = 0.179055 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3749 r_free = 0.3749 target = 0.141899 restraints weight = 10546.034|
|-----------------------------------------------------------------------------|
r_work (start): 0.3701 rms_B_bonded: 2.25
r_work: 0.3460 rms_B_bonded: 3.05 restraints_weight: 0.5000
r_work: 0.3324 rms_B_bonded: 4.82 restraints_weight: 0.2500
r_work (final): 0.3324
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7740
moved from start:          0.1722

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   8759  Z= 0.281
  Angle     :  0.563   7.034  11928  Z= 0.295
  Chirality :  0.042   0.149   1384
  Planarity :  0.004   0.049   1510
  Dihedral  :  4.124  25.698   1228
  Min Nonbonded Distance : 2.465

Molprobity Statistics.
  All-atom Clashscore : 8.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.13 %
    Favored  : 96.87 %
  Rotamer:
    Outliers :  3.78 %
    Allowed  : 20.73 %
    Favored  : 75.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.53 (0.25), residues: 1117
  helix:  1.98 (0.26), residues: 400
  sheet: -0.11 (0.32), residues: 260
  loop : -0.81 (0.28), residues: 457

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP C 169 
 HIS   0.008   0.001   HIS F 176 
 PHE   0.019   0.002   PHE F 156 
 TYR   0.023   0.002   TYR F 163 
 ARG   0.003   0.000   ARG B  32 

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

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

  2234 Ramachandran restraints generated.
    1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2234 Ramachandran restraints generated.
    1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  171 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 138
  time to evaluate  : 0.872 
Fit side-chains
REVERT: A   11 LEU cc_start: 0.8986 (mm) cc_final: 0.8678 (mm)
REVERT: D   48 ASP cc_start: 0.8542 (t0) cc_final: 0.8243 (t0)
REVERT: E   38 ARG cc_start: 0.7758 (ptp90) cc_final: 0.7326 (ptp90)
REVERT: E   46 GLU cc_start: 0.8354 (pt0) cc_final: 0.8119 (mt-10)
REVERT: E  180 MET cc_start: 0.7621 (OUTLIER) cc_final: 0.6935 (ptt)
REVERT: F  187 MET cc_start: 0.8610 (tpp) cc_final: 0.8199 (tpp)
  outliers start: 33
  outliers final: 26
  residues processed: 156
  average time/residue: 0.2109
  time to fit residues: 46.0549
Evaluate side-chains
  159 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 132
  time to evaluate  : 0.846 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   69 ILE
Chi-restraints excluded: chain B residue   75 GLN
Chi-restraints excluded: chain B residue  109 VAL
Chi-restraints excluded: chain B residue  128 ILE
Chi-restraints excluded: chain B residue  210 ILE
Chi-restraints excluded: chain C residue   59 TYR
Chi-restraints excluded: chain C residue   65 THR
Chi-restraints excluded: chain C residue   67 SER
Chi-restraints excluded: chain C residue  161 SER
Chi-restraints excluded: chain C residue  247 ASP
Chi-restraints excluded: chain C residue  263 THR
Chi-restraints excluded: chain C residue  318 LEU
Chi-restraints excluded: chain C residue  329 THR
Chi-restraints excluded: chain D residue   50 LEU
Chi-restraints excluded: chain E residue    5 VAL
Chi-restraints excluded: chain E residue   71 SER
Chi-restraints excluded: chain E residue  180 MET
Chi-restraints excluded: chain E residue  190 ARG
Chi-restraints excluded: chain E residue  192 SER
Chi-restraints excluded: chain E residue  194 SER
Chi-restraints excluded: chain E residue  203 THR
Chi-restraints excluded: chain E residue  212 VAL
Chi-restraints excluded: chain F residue   75 ILE
Chi-restraints excluded: chain F residue   76 LEU
Chi-restraints excluded: chain F residue   85 ILE
Chi-restraints excluded: chain F residue  119 VAL
Chi-restraints excluded: chain F residue  120 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 104 optimal weight:    0.8980
   chunk 24 optimal weight:    7.9990
   chunk 76 optimal weight:    5.9990
   chunk 83 optimal weight:    7.9990
   chunk 62 optimal weight:    9.9990
   chunk 11 optimal weight:    0.8980
   chunk 44 optimal weight:    1.9990
   chunk 51 optimal weight:    0.7980
   chunk 94 optimal weight:    0.6980
   chunk 1 optimal weight:    0.7980
   chunk 75 optimal weight:    6.9990
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
B  82 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4124 r_free = 0.4124 target = 0.182665 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3788 r_free = 0.3788 target = 0.145437 restraints weight = 10684.095|
|-----------------------------------------------------------------------------|
r_work (start): 0.3741 rms_B_bonded: 2.19
r_work: 0.3515 rms_B_bonded: 3.03 restraints_weight: 0.5000
r_work: 0.3378 rms_B_bonded: 4.84 restraints_weight: 0.2500
r_work (final): 0.3378
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7676
moved from start:          0.1926

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   8759  Z= 0.180
  Angle     :  0.526   6.843  11928  Z= 0.274
  Chirality :  0.041   0.151   1384
  Planarity :  0.004   0.043   1510
  Dihedral  :  3.935  24.234   1228
  Min Nonbonded Distance : 2.422

Molprobity Statistics.
  All-atom Clashscore : 7.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.04 %
    Favored  : 96.96 %
  Rotamer:
    Outliers :  3.32 %
    Allowed  : 21.99 %
    Favored  : 74.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.72 (0.25), residues: 1117
  helix:  2.20 (0.26), residues: 399
  sheet:  0.02 (0.32), residues: 255
  loop : -0.78 (0.28), residues: 463

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP C 169 
 HIS   0.007   0.001   HIS F 176 
 PHE   0.017   0.001   PHE C 253 
 TYR   0.018   0.001   TYR F 163 
 ARG   0.004   0.000   ARG B  32 

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

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

  2234 Ramachandran restraints generated.
    1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2234 Ramachandran restraints generated.
    1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  175 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 146
  time to evaluate  : 0.967 
Fit side-chains
REVERT: A   11 LEU cc_start: 0.8997 (mm) cc_final: 0.8696 (mm)
REVERT: B  179 GLU cc_start: 0.5776 (pp20) cc_final: 0.5404 (pp20)
REVERT: D   48 ASP cc_start: 0.8483 (t0) cc_final: 0.8174 (t0)
REVERT: E   38 ARG cc_start: 0.7754 (ptp90) cc_final: 0.7311 (ptp90)
REVERT: E   46 GLU cc_start: 0.8371 (pt0) cc_final: 0.8143 (mt-10)
REVERT: E  180 MET cc_start: 0.7660 (OUTLIER) cc_final: 0.7133 (ptt)
REVERT: F  187 MET cc_start: 0.8623 (tpp) cc_final: 0.8194 (tpp)
  outliers start: 29
  outliers final: 23
  residues processed: 162
  average time/residue: 0.1994
  time to fit residues: 45.0960
Evaluate side-chains
  159 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 135
  time to evaluate  : 0.884 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   69 ILE
Chi-restraints excluded: chain B residue   75 GLN
Chi-restraints excluded: chain B residue  109 VAL
Chi-restraints excluded: chain B residue  128 ILE
Chi-restraints excluded: chain B residue  210 ILE
Chi-restraints excluded: chain C residue   59 TYR
Chi-restraints excluded: chain C residue   65 THR
Chi-restraints excluded: chain C residue   67 SER
Chi-restraints excluded: chain C residue  161 SER
Chi-restraints excluded: chain C residue  263 THR
Chi-restraints excluded: chain C residue  318 LEU
Chi-restraints excluded: chain C residue  329 THR
Chi-restraints excluded: chain C residue  336 LEU
Chi-restraints excluded: chain D residue   50 LEU
Chi-restraints excluded: chain E residue    5 VAL
Chi-restraints excluded: chain E residue   71 SER
Chi-restraints excluded: chain E residue  180 MET
Chi-restraints excluded: chain E residue  194 SER
Chi-restraints excluded: chain E residue  203 THR
Chi-restraints excluded: chain F residue   75 ILE
Chi-restraints excluded: chain F residue   76 LEU
Chi-restraints excluded: chain F residue   85 ILE
Chi-restraints excluded: chain F residue  119 VAL
Chi-restraints excluded: chain F residue  120 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 10 optimal weight:    4.9990
   chunk 45 optimal weight:    2.9990
   chunk 24 optimal weight:   10.0000
   chunk 29 optimal weight:    3.9990
   chunk 71 optimal weight:    0.9980
   chunk 106 optimal weight:    3.9990
   chunk 21 optimal weight:    0.9990
   chunk 109 optimal weight:    0.8980
   chunk 43 optimal weight:    7.9990
   chunk 95 optimal weight:    0.0770
   chunk 5 optimal weight:    2.9990
   overall best weight:    1.1942

-------------------------------------------------------------------------------
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 = 0.4110 r_free = 0.4110 target = 0.180970 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3775 r_free = 0.3775 target = 0.144127 restraints weight = 10713.808|
|-----------------------------------------------------------------------------|
r_work (start): 0.3728 rms_B_bonded: 2.25
r_work: 0.3493 rms_B_bonded: 3.05 restraints_weight: 0.5000
r_work: 0.3356 rms_B_bonded: 4.85 restraints_weight: 0.2500
r_work (final): 0.3356
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7700
moved from start:          0.1946

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   8759  Z= 0.214
  Angle     :  0.551   9.508  11928  Z= 0.284
  Chirality :  0.042   0.152   1384
  Planarity :  0.004   0.043   1510
  Dihedral  :  3.953  24.415   1228
  Min Nonbonded Distance : 2.436

Molprobity Statistics.
  All-atom Clashscore : 7.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.31 %
    Favored  : 96.69 %
  Rotamer:
    Outliers :  3.67 %
    Allowed  : 21.99 %
    Favored  : 74.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.69 (0.25), residues: 1117
  helix:  2.18 (0.26), residues: 399
  sheet: -0.09 (0.32), residues: 260
  loop : -0.75 (0.28), residues: 458

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP F 260 
 HIS   0.007   0.001   HIS F 176 
 PHE   0.020   0.001   PHE C 253 
 TYR   0.021   0.002   TYR F 163 
 ARG   0.006   0.000   ARG B  32 

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

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

  2234 Ramachandran restraints generated.
    1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2234 Ramachandran restraints generated.
    1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  167 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 135
  time to evaluate  : 0.959 
Fit side-chains
REVERT: A   11 LEU cc_start: 0.9022 (mm) cc_final: 0.8714 (mm)
REVERT: B  179 GLU cc_start: 0.5858 (pp20) cc_final: 0.5469 (pp20)
REVERT: D   48 ASP cc_start: 0.8520 (t0) cc_final: 0.8213 (t0)
REVERT: E   38 ARG cc_start: 0.7706 (ptp90) cc_final: 0.7299 (ptp90)
REVERT: E   46 GLU cc_start: 0.8350 (pt0) cc_final: 0.8125 (mt-10)
REVERT: E  180 MET cc_start: 0.7705 (OUTLIER) cc_final: 0.7176 (ptt)
REVERT: F  187 MET cc_start: 0.8630 (tpp) cc_final: 0.8253 (tpp)
  outliers start: 32
  outliers final: 25
  residues processed: 152
  average time/residue: 0.1953
  time to fit residues: 41.4281
Evaluate side-chains
  158 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 132
  time to evaluate  : 0.902 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   69 ILE
Chi-restraints excluded: chain B residue   75 GLN
Chi-restraints excluded: chain B residue  109 VAL
Chi-restraints excluded: chain B residue  128 ILE
Chi-restraints excluded: chain B residue  210 ILE
Chi-restraints excluded: chain C residue   59 TYR
Chi-restraints excluded: chain C residue   65 THR
Chi-restraints excluded: chain C residue   67 SER
Chi-restraints excluded: chain C residue  161 SER
Chi-restraints excluded: chain C residue  263 THR
Chi-restraints excluded: chain C residue  318 LEU
Chi-restraints excluded: chain C residue  329 THR
Chi-restraints excluded: chain C residue  336 LEU
Chi-restraints excluded: chain D residue   50 LEU
Chi-restraints excluded: chain E residue    5 VAL
Chi-restraints excluded: chain E residue   71 SER
Chi-restraints excluded: chain E residue  180 MET
Chi-restraints excluded: chain E residue  190 ARG
Chi-restraints excluded: chain E residue  194 SER
Chi-restraints excluded: chain E residue  203 THR
Chi-restraints excluded: chain E residue  212 VAL
Chi-restraints excluded: chain F residue   75 ILE
Chi-restraints excluded: chain F residue   76 LEU
Chi-restraints excluded: chain F residue   85 ILE
Chi-restraints excluded: chain F residue  119 VAL
Chi-restraints excluded: chain F residue  120 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 81 optimal weight:   10.0000
   chunk 1 optimal weight:    2.9990
   chunk 67 optimal weight:    6.9990
   chunk 31 optimal weight:    3.9990
   chunk 12 optimal weight:    1.9990
   chunk 23 optimal weight:    9.9990
   chunk 77 optimal weight:    2.9990
   chunk 91 optimal weight:    3.9990
   chunk 57 optimal weight:    6.9990
   chunk 78 optimal weight:    1.9990
   chunk 65 optimal weight:    0.7980
   overall best weight:    2.1588

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

Flipped N/Q/H residues before XYZ refinement:
** C  75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4078 r_free = 0.4078 target = 0.177890 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3736 r_free = 0.3736 target = 0.140803 restraints weight = 10769.850|
|-----------------------------------------------------------------------------|
r_work (start): 0.3689 rms_B_bonded: 2.27
r_work: 0.3443 rms_B_bonded: 3.08 restraints_weight: 0.5000
r_work: 0.3306 rms_B_bonded: 4.86 restraints_weight: 0.2500
r_work (final): 0.3306
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7758
moved from start:          0.1908

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.045   8759  Z= 0.318
  Angle     :  0.602   8.874  11928  Z= 0.311
  Chirality :  0.043   0.156   1384
  Planarity :  0.004   0.047   1510
  Dihedral  :  4.172  25.744   1228
  Min Nonbonded Distance : 2.367

Molprobity Statistics.
  All-atom Clashscore : 9.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.40 %
    Favored  : 96.60 %
  Rotamer:
    Outliers :  3.78 %
    Allowed  : 22.45 %
    Favored  : 73.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.55 (0.25), residues: 1117
  helix:  2.01 (0.26), residues: 400
  sheet: -0.17 (0.32), residues: 260
  loop : -0.78 (0.28), residues: 457

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP F 260 
 HIS   0.008   0.001   HIS F 176 
 PHE   0.018   0.002   PHE C 253 
 TYR   0.025   0.002   TYR F 163 
 ARG   0.011   0.000   ARG B  32 

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

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

  2234 Ramachandran restraints generated.
    1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2234 Ramachandran restraints generated.
    1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  171 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 138
  time to evaluate  : 0.883 
Fit side-chains
REVERT: A   11 LEU cc_start: 0.9074 (mm) cc_final: 0.8777 (mm)
REVERT: B  179 GLU cc_start: 0.5907 (pp20) cc_final: 0.5523 (pp20)
REVERT: D   48 ASP cc_start: 0.8541 (t0) cc_final: 0.8245 (t0)
REVERT: E   38 ARG cc_start: 0.7784 (ptp90) cc_final: 0.7355 (ptp90)
REVERT: E   46 GLU cc_start: 0.8324 (pt0) cc_final: 0.8096 (mt-10)
REVERT: E  180 MET cc_start: 0.7822 (OUTLIER) cc_final: 0.7310 (ptt)
REVERT: F  187 MET cc_start: 0.8575 (tpp) cc_final: 0.8254 (tpp)
REVERT: F  267 THR cc_start: 0.6109 (OUTLIER) cc_final: 0.5850 (p)
  outliers start: 33
  outliers final: 27
  residues processed: 157
  average time/residue: 0.1896
  time to fit residues: 42.3820
Evaluate side-chains
  166 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 137
  time to evaluate  : 0.884 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   69 ILE
Chi-restraints excluded: chain B residue   75 GLN
Chi-restraints excluded: chain B residue  109 VAL
Chi-restraints excluded: chain B residue  128 ILE
Chi-restraints excluded: chain B residue  210 ILE
Chi-restraints excluded: chain C residue   59 TYR
Chi-restraints excluded: chain C residue   65 THR
Chi-restraints excluded: chain C residue   67 SER
Chi-restraints excluded: chain C residue  161 SER
Chi-restraints excluded: chain C residue  263 THR
Chi-restraints excluded: chain C residue  318 LEU
Chi-restraints excluded: chain C residue  329 THR
Chi-restraints excluded: chain C residue  336 LEU
Chi-restraints excluded: chain D residue   50 LEU
Chi-restraints excluded: chain E residue    5 VAL
Chi-restraints excluded: chain E residue   58 ILE
Chi-restraints excluded: chain E residue   71 SER
Chi-restraints excluded: chain E residue  180 MET
Chi-restraints excluded: chain E residue  190 ARG
Chi-restraints excluded: chain E residue  194 SER
Chi-restraints excluded: chain E residue  202 LEU
Chi-restraints excluded: chain E residue  203 THR
Chi-restraints excluded: chain E residue  212 VAL
Chi-restraints excluded: chain F residue   75 ILE
Chi-restraints excluded: chain F residue   76 LEU
Chi-restraints excluded: chain F residue   85 ILE
Chi-restraints excluded: chain F residue  119 VAL
Chi-restraints excluded: chain F residue  120 SER
Chi-restraints excluded: chain F residue  267 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 73 optimal weight:    2.9990
   chunk 72 optimal weight:    2.9990
   chunk 25 optimal weight:    0.3980
   chunk 82 optimal weight:    7.9990
   chunk 97 optimal weight:    0.1980
   chunk 81 optimal weight:    1.9990
   chunk 24 optimal weight:   20.0000
   chunk 61 optimal weight:    8.9990
   chunk 2 optimal weight:    3.9990
   chunk 21 optimal weight:    0.1980
   chunk 80 optimal weight:    2.9990
   overall best weight:    1.1584

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

Flipped N/Q/H residues before XYZ refinement:
B 116 ASN
C  75 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4107 r_free = 0.4107 target = 0.180798 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3776 r_free = 0.3776 target = 0.144141 restraints weight = 10678.804|
|-----------------------------------------------------------------------------|
r_work (start): 0.3729 rms_B_bonded: 2.22
r_work: 0.3491 rms_B_bonded: 3.04 restraints_weight: 0.5000
r_work: 0.3353 rms_B_bonded: 4.84 restraints_weight: 0.2500
r_work (final): 0.3353
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7705
moved from start:          0.2013

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   8759  Z= 0.212
  Angle     :  0.558   9.176  11928  Z= 0.288
  Chirality :  0.042   0.155   1384
  Planarity :  0.004   0.047   1510
  Dihedral  :  4.028  24.849   1228
  Min Nonbonded Distance : 2.386

Molprobity Statistics.
  All-atom Clashscore : 8.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.31 %
    Favored  : 96.69 %
  Rotamer:
    Outliers :  3.78 %
    Allowed  : 22.45 %
    Favored  : 73.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.63 (0.26), residues: 1117
  helix:  2.16 (0.26), residues: 399
  sheet: -0.12 (0.33), residues: 253
  loop : -0.80 (0.28), residues: 465

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP F 260 
 HIS   0.008   0.001   HIS F 176 
 PHE   0.020   0.001   PHE C 253 
 TYR   0.020   0.002   TYR F 163 
 ARG   0.007   0.000   ARG B  32 

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

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

  2234 Ramachandran restraints generated.
    1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2234 Ramachandran restraints generated.
    1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  174 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 141
  time to evaluate  : 0.957 
Fit side-chains
REVERT: B  179 GLU cc_start: 0.5874 (pp20) cc_final: 0.5513 (pp20)
REVERT: D   48 ASP cc_start: 0.8496 (t0) cc_final: 0.8180 (t0)
REVERT: E   38 ARG cc_start: 0.7738 (ptp90) cc_final: 0.7317 (ptp90)
REVERT: E   46 GLU cc_start: 0.8350 (pt0) cc_final: 0.8121 (mt-10)
REVERT: E  180 MET cc_start: 0.7843 (OUTLIER) cc_final: 0.7316 (ptt)
REVERT: F  187 MET cc_start: 0.8585 (tpp) cc_final: 0.8162 (tpp)
  outliers start: 33
  outliers final: 25
  residues processed: 157
  average time/residue: 0.1917
  time to fit residues: 42.6193
Evaluate side-chains
  163 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 137
  time to evaluate  : 1.010 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   69 ILE
Chi-restraints excluded: chain B residue   75 GLN
Chi-restraints excluded: chain B residue  109 VAL
Chi-restraints excluded: chain B residue  128 ILE
Chi-restraints excluded: chain B residue  210 ILE
Chi-restraints excluded: chain C residue   59 TYR
Chi-restraints excluded: chain C residue   65 THR
Chi-restraints excluded: chain C residue   67 SER
Chi-restraints excluded: chain C residue  161 SER
Chi-restraints excluded: chain C residue  263 THR
Chi-restraints excluded: chain C residue  318 LEU
Chi-restraints excluded: chain C residue  329 THR
Chi-restraints excluded: chain C residue  336 LEU
Chi-restraints excluded: chain E residue    5 VAL
Chi-restraints excluded: chain E residue   71 SER
Chi-restraints excluded: chain E residue  180 MET
Chi-restraints excluded: chain E residue  190 ARG
Chi-restraints excluded: chain E residue  194 SER
Chi-restraints excluded: chain E residue  202 LEU
Chi-restraints excluded: chain E residue  203 THR
Chi-restraints excluded: chain E residue  212 VAL
Chi-restraints excluded: chain F residue   75 ILE
Chi-restraints excluded: chain F residue   76 LEU
Chi-restraints excluded: chain F residue   85 ILE
Chi-restraints excluded: chain F residue  119 VAL
Chi-restraints excluded: chain F residue  120 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 76 optimal weight:    5.9990
   chunk 101 optimal weight:    0.7980
   chunk 36 optimal weight:    0.9990
   chunk 96 optimal weight:    0.9980
   chunk 42 optimal weight:    0.9980
   chunk 47 optimal weight:    0.9990
   chunk 90 optimal weight:    4.9990
   chunk 27 optimal weight:    0.7980
   chunk 89 optimal weight:    0.7980
   chunk 100 optimal weight:    0.8980
   chunk 106 optimal weight:    0.9980
   overall best weight:    0.8580

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

Flipped N/Q/H residues before XYZ refinement:
B 223 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4121 r_free = 0.4121 target = 0.182237 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3767 r_free = 0.3767 target = 0.143281 restraints weight = 10619.373|
|-----------------------------------------------------------------------------|
r_work (start): 0.3718 rms_B_bonded: 2.15
r_work: 0.3512 rms_B_bonded: 3.04 restraints_weight: 0.5000
r_work: 0.3375 rms_B_bonded: 4.86 restraints_weight: 0.2500
r_work (final): 0.3375
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7679
moved from start:          0.2128

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   8759  Z= 0.186
  Angle     :  0.548   9.004  11928  Z= 0.283
  Chirality :  0.041   0.177   1384
  Planarity :  0.004   0.043   1510
  Dihedral  :  3.918  23.961   1228
  Min Nonbonded Distance : 2.382

Molprobity Statistics.
  All-atom Clashscore : 8.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.95 %
    Favored  : 97.05 %
  Rotamer:
    Outliers :  3.09 %
    Allowed  : 23.71 %
    Favored  : 73.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.73 (0.26), residues: 1117
  helix:  2.22 (0.26), residues: 398
  sheet: -0.00 (0.33), residues: 255
  loop : -0.76 (0.28), residues: 464

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.001   TRP F 260 
 HIS   0.007   0.001   HIS F 176 
 PHE   0.019   0.001   PHE C 253 
 TYR   0.020   0.001   TYR F 129 
 ARG   0.005   0.000   ARG B  32 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5251.75 seconds
wall clock time: 90 minutes 45.00 seconds (5445.00 seconds total)