Starting phenix.real_space_refine
on Tue Mar  3 19:43:10 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7xjk_33230/03_2026/7xjk_33230.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7xjk_33230/03_2026/7xjk_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_2026/7xjk_33230.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7xjk_33230/03_2026/7xjk_33230.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7xjk_33230/03_2026/7xjk_33230.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7xjk_33230/03_2026/7xjk_33230.cif"
  }
  resolution = 3.3
  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=   0.115
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): 0.01s

  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: 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: {'ARG:plan': 4, 'GLU:plan': 4, 'ASP:plan': 5, 'GLN:plan1': 1}
          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: {'GLU:plan': 4, 'ASP:plan': 6, 'GLN:plan1': 4, 'ARG:plan': 7, 'ASN:plan1': 1, 'HIS:plan': 1}
          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, 'ARG:plan': 1, 'GLU:plan': 2, '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: {'GLU:plan': 7, 'GLN:plan1': 1, '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: 2.12, per 1000 atoms: 0.25
  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: 0.69
  Conformation dependent library (CDL) restraints added in 335.0 milliseconds
  

  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: 0.44
  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: 1.38

  Time building geometry restraints manager: 0.94 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:             0.400
  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:             0.000
  Extract box with map and model:          0.170
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     9.770
  Find NCS groups from input model:        0.040
  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:             0.010
  Load rotamer database and sin/cos tables:1.290
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   11.750
-------------------------------------------------------------------------------
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   8761  Z= 0.215
  Angle     :  0.652   8.197  11932  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 : 11.73
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.32 (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
 ARG   0.006   0.001   ARG C 314 
 TYR   0.029   0.002   TYR F 292 
 PHE   0.016   0.002   PHE E  27 
 TRP   0.015   0.002   TRP F 179 
 HIS   0.009   0.001   HIS F 176 

Details of bonding type rmsd
  covalent geometry    : bond        0.00486 ( 8759)
  covalent geometry    : angle       0.65123 (11928)
  SS BOND              : bond        0.00488 (    2)
  SS BOND              : angle       1.35066 (    4)
  hydrogen bonds       : bond        0.12869 (  455)
  hydrogen bonds       : angle       6.05178 ( 1308)

*********************** 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  : 0.331 
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: 0.0918
  time to fit residues: 20.8599
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  : 0.327 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 108 optimal weight:    1.9990
   chunk 49 optimal weight:    5.9990
   chunk 97 optimal weight:    3.9990
   chunk 53 optimal weight:   10.0000
   chunk 5 optimal weight:    8.9990
   chunk 33 optimal weight:    0.0870
   chunk 65 optimal weight:    5.9990
   chunk 62 optimal weight:    0.7980
   chunk 51 optimal weight:    3.9990
   chunk 100 optimal weight:    1.9990
   chunk 106 optimal weight:    5.9990
   overall best weight:    1.7764

-------------------------------------------------------------------------------
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 = 0.4089 r_free = 0.4089 target = 0.179046 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3752 r_free = 0.3752 target = 0.142073 restraints weight = 10668.007|
|-----------------------------------------------------------------------------|
r_work (start): 0.3711 rms_B_bonded: 2.26
r_work: 0.3469 rms_B_bonded: 3.02 restraints_weight: 0.5000
r_work: 0.3329 rms_B_bonded: 4.82 restraints_weight: 0.2500
r_work (final): 0.3329
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7725
moved from start:          0.0975

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   8761  Z= 0.187
  Angle     :  0.588   8.236  11932  Z= 0.310
  Chirality :  0.043   0.155   1384
  Planarity :  0.004   0.056   1510
  Dihedral  :  4.370  28.262   1228
  Min Nonbonded Distance : 2.478

Molprobity Statistics.
  All-atom Clashscore : 9.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.78 %
    Favored  : 97.22 %
  Rotamer:
    Outliers :  2.06 %
    Allowed  :  9.62 %
    Favored  : 88.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.51 (0.25), residues: 1117
  helix:  1.88 (0.26), residues: 399
  sheet:  0.09 (0.32), residues: 258
  loop : -0.88 (0.27), residues: 460

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C 314 
 TYR   0.023   0.002   TYR F 163 
 PHE   0.020   0.002   PHE F  81 
 TRP   0.012   0.002   TRP C 169 
 HIS   0.011   0.001   HIS F 176 

Details of bonding type rmsd
  covalent geometry    : bond        0.00430 ( 8759)
  covalent geometry    : angle       0.58833 (11928)
  SS BOND              : bond        0.00323 (    2)
  SS BOND              : angle       0.94100 (    4)
  hydrogen bonds       : bond        0.04318 (  455)
  hydrogen bonds       : angle       4.98259 ( 1308)

*********************** 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
  174 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 156
  time to evaluate  : 0.315 
Fit side-chains
REVERT: A   11 LEU cc_start: 0.8979 (mm) cc_final: 0.8698 (mm)
REVERT: E   38 ARG cc_start: 0.7741 (ptp90) cc_final: 0.7297 (ptp90)
REVERT: E   46 GLU cc_start: 0.8387 (pt0) cc_final: 0.8118 (mt-10)
REVERT: E  202 LEU cc_start: 0.8766 (tp) cc_final: 0.8360 (tp)
REVERT: F  187 MET cc_start: 0.8486 (tpp) cc_final: 0.8014 (tpp)
  outliers start: 18
  outliers final: 15
  residues processed: 160
  average time/residue: 0.0877
  time to fit residues: 19.7403
Evaluate side-chains
  147 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 132
  time to evaluate  : 0.295 
-------------------------------------------------------------------------------
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 84 optimal weight:   10.0000
   chunk 54 optimal weight:    5.9990
   chunk 96 optimal weight:    0.9990
   chunk 24 optimal weight:    6.9990
   chunk 83 optimal weight:    6.9990
   chunk 94 optimal weight:    1.9990
   chunk 31 optimal weight:    1.9990
   chunk 11 optimal weight:    0.9980
   chunk 15 optimal weight:    0.9990
   chunk 53 optimal weight:    3.9990
   chunk 20 optimal weight:    4.9990
   overall best weight:    1.3988

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

Flipped N/Q/H residues before XYZ refinement:
C 239 ASN
F 284 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4099 r_free = 0.4099 target = 0.180168 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3760 r_free = 0.3760 target = 0.142942 restraints weight = 10648.280|
|-----------------------------------------------------------------------------|
r_work (start): 0.3717 rms_B_bonded: 2.22
r_work: 0.3480 rms_B_bonded: 3.00 restraints_weight: 0.5000
r_work: 0.3341 rms_B_bonded: 4.77 restraints_weight: 0.2500
r_work (final): 0.3341
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7710
moved from start:          0.1266

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   8761  Z= 0.156
  Angle     :  0.545   6.812  11932  Z= 0.289
  Chirality :  0.042   0.143   1384
  Planarity :  0.004   0.044   1510
  Dihedral  :  4.211  26.613   1228
  Min Nonbonded Distance : 2.538

Molprobity Statistics.
  All-atom Clashscore : 8.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.04 %
    Favored  : 96.96 %
  Rotamer:
    Outliers :  2.29 %
    Allowed  : 14.89 %
    Favored  : 82.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.53 (0.25), residues: 1117
  helix:  1.92 (0.26), residues: 400
  sheet:  0.06 (0.32), residues: 258
  loop : -0.87 (0.28), residues: 459

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C  68 
 TYR   0.021   0.002   TYR F 163 
 PHE   0.021   0.001   PHE F 156 
 TRP   0.013   0.001   TRP C 169 
 HIS   0.010   0.001   HIS F 176 

Details of bonding type rmsd
  covalent geometry    : bond        0.00359 ( 8759)
  covalent geometry    : angle       0.54535 (11928)
  SS BOND              : bond        0.00251 (    2)
  SS BOND              : angle       0.78649 (    4)
  hydrogen bonds       : bond        0.03999 (  455)
  hydrogen bonds       : angle       4.79814 ( 1308)

*********************** 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
  165 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 145
  time to evaluate  : 0.352 
Fit side-chains
REVERT: A   11 LEU cc_start: 0.8974 (mm) cc_final: 0.8680 (mm)
REVERT: B  166 GLU cc_start: 0.8331 (pm20) cc_final: 0.7973 (pm20)
REVERT: C  301 LYS cc_start: 0.7701 (mttp) cc_final: 0.7416 (ttmm)
REVERT: D   48 ASP cc_start: 0.8426 (t0) cc_final: 0.8133 (t0)
REVERT: E   38 ARG cc_start: 0.7726 (ptp90) cc_final: 0.7292 (ptp90)
REVERT: E   46 GLU cc_start: 0.8374 (pt0) cc_final: 0.8137 (mt-10)
REVERT: F  187 MET cc_start: 0.8616 (tpp) cc_final: 0.8058 (tpp)
  outliers start: 20
  outliers final: 12
  residues processed: 154
  average time/residue: 0.0883
  time to fit residues: 19.2790
Evaluate side-chains
  144 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 132
  time to evaluate  : 0.300 
-------------------------------------------------------------------------------
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  210 ILE
Chi-restraints excluded: chain C residue  254 ASP
Chi-restraints excluded: chain C residue  263 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   85 ILE
Chi-restraints excluded: chain F residue  120 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 78 optimal weight:    4.9990
   chunk 41 optimal weight:   10.0000
   chunk 61 optimal weight:    7.9990
   chunk 102 optimal weight:    3.9990
   chunk 17 optimal weight:    0.0570
   chunk 42 optimal weight:    2.9990
   chunk 68 optimal weight:    8.9990
   chunk 84 optimal weight:   10.0000
   chunk 72 optimal weight:    9.9990
   chunk 24 optimal weight:    7.9990
   chunk 63 optimal weight:    0.9980
   overall best weight:    2.6104

-------------------------------------------------------------------------------
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 = 0.4060 r_free = 0.4060 target = 0.176223 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3713 r_free = 0.3713 target = 0.138623 restraints weight = 10816.617|
|-----------------------------------------------------------------------------|
r_work (start): 0.3666 rms_B_bonded: 2.29
r_work: 0.3414 rms_B_bonded: 3.09 restraints_weight: 0.5000
r_work: 0.3273 rms_B_bonded: 4.91 restraints_weight: 0.2500
r_work (final): 0.3273
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7796
moved from start:          0.1496

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.053   8761  Z= 0.243
  Angle     :  0.622   9.118  11932  Z= 0.325
  Chirality :  0.045   0.173   1384
  Planarity :  0.004   0.045   1510
  Dihedral  :  4.460  29.614   1228
  Min Nonbonded Distance : 2.492

Molprobity Statistics.
  All-atom Clashscore : 9.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.31 %
    Favored  : 96.69 %
  Rotamer:
    Outliers :  3.78 %
    Allowed  : 16.95 %
    Favored  : 79.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.31 (0.25), residues: 1117
  helix:  1.67 (0.26), residues: 400
  sheet: -0.19 (0.32), residues: 260
  loop : -0.84 (0.28), residues: 457

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG C 314 
 TYR   0.026   0.002   TYR F 163 
 PHE   0.025   0.002   PHE F 156 
 TRP   0.014   0.002   TRP F 179 
 HIS   0.010   0.002   HIS F 176 

Details of bonding type rmsd
  covalent geometry    : bond        0.00567 ( 8759)
  covalent geometry    : angle       0.62192 (11928)
  SS BOND              : bond        0.00346 (    2)
  SS BOND              : angle       0.92143 (    4)
  hydrogen bonds       : bond        0.04426 (  455)
  hydrogen bonds       : angle       4.85527 ( 1308)

*********************** 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
  165 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 132
  time to evaluate  : 0.245 
Fit side-chains
REVERT: A   11 LEU cc_start: 0.9042 (mm) cc_final: 0.8760 (mm)
REVERT: D   48 ASP cc_start: 0.8524 (t0) cc_final: 0.8258 (t0)
REVERT: F  187 MET cc_start: 0.8587 (tpp) cc_final: 0.8193 (tpp)
  outliers start: 33
  outliers final: 24
  residues processed: 148
  average time/residue: 0.0889
  time to fit residues: 18.3646
Evaluate side-chains
  149 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 125
  time to evaluate  : 0.319 
-------------------------------------------------------------------------------
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  161 SER
Chi-restraints excluded: chain C residue  247 ASP
Chi-restraints excluded: chain C residue  254 ASP
Chi-restraints excluded: chain C residue  263 THR
Chi-restraints excluded: chain C residue  315 VAL
Chi-restraints excluded: chain C residue  329 THR
Chi-restraints excluded: chain E residue    5 VAL
Chi-restraints excluded: chain E residue   21 SER
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  201 THR
Chi-restraints excluded: chain E residue  212 VAL
Chi-restraints excluded: chain F residue   75 ILE
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=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 25 optimal weight:   20.0000
   chunk 7 optimal weight:    3.9990
   chunk 32 optimal weight:    5.9990
   chunk 17 optimal weight:    1.9990
   chunk 70 optimal weight:    6.9990
   chunk 62 optimal weight:    0.5980
   chunk 71 optimal weight:    0.8980
   chunk 13 optimal weight:    0.5980
   chunk 8 optimal weight:    0.7980
   chunk 80 optimal weight:    8.9990
   chunk 57 optimal weight:   10.0000
   overall best weight:    0.9782

-------------------------------------------------------------------------------
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 = 0.4111 r_free = 0.4111 target = 0.181305 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3773 r_free = 0.3773 target = 0.144022 restraints weight = 10715.874|
|-----------------------------------------------------------------------------|
r_work (start): 0.3726 rms_B_bonded: 2.24
r_work: 0.3493 rms_B_bonded: 3.03 restraints_weight: 0.5000
r_work: 0.3356 rms_B_bonded: 4.81 restraints_weight: 0.2500
r_work (final): 0.3356
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7697
moved from start:          0.1683

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   8761  Z= 0.132
  Angle     :  0.539   8.607  11932  Z= 0.283
  Chirality :  0.041   0.140   1384
  Planarity :  0.004   0.061   1510
  Dihedral  :  4.135  25.677   1228
  Min Nonbonded Distance : 2.501

Molprobity Statistics.
  All-atom Clashscore : 8.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.04 %
    Favored  : 96.96 %
  Rotamer:
    Outliers :  2.98 %
    Allowed  : 20.05 %
    Favored  : 76.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.61 (0.25), residues: 1117
  helix:  2.02 (0.26), residues: 400
  sheet: -0.10 (0.32), residues: 260
  loop : -0.71 (0.28), residues: 457

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B  32 
 TYR   0.019   0.001   TYR F 163 
 PHE   0.028   0.001   PHE F 156 
 TRP   0.016   0.001   TRP C 169 
 HIS   0.008   0.001   HIS F 176 

Details of bonding type rmsd
  covalent geometry    : bond        0.00299 ( 8759)
  covalent geometry    : angle       0.53853 (11928)
  SS BOND              : bond        0.00243 (    2)
  SS BOND              : angle       0.54209 (    4)
  hydrogen bonds       : bond        0.03723 (  455)
  hydrogen bonds       : angle       4.63399 ( 1308)

*********************** 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
  174 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 148
  time to evaluate  : 0.269 
Fit side-chains
REVERT: A   11 LEU cc_start: 0.8945 (mm) cc_final: 0.8637 (mm)
REVERT: B  179 GLU cc_start: 0.5697 (pp20) cc_final: 0.5312 (pp20)
REVERT: D   48 ASP cc_start: 0.8523 (t0) cc_final: 0.8245 (t0)
REVERT: E   38 ARG cc_start: 0.7836 (ptp90) cc_final: 0.7360 (ptp90)
REVERT: F  187 MET cc_start: 0.8564 (tpp) cc_final: 0.8155 (tpp)
  outliers start: 26
  outliers final: 18
  residues processed: 158
  average time/residue: 0.0885
  time to fit residues: 19.6721
Evaluate side-chains
  146 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 128
  time to evaluate  : 0.314 
-------------------------------------------------------------------------------
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  254 ASP
Chi-restraints excluded: chain C residue  263 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  190 ARG
Chi-restraints excluded: chain E residue  194 SER
Chi-restraints excluded: chain E residue  201 THR
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=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 70 optimal weight:    6.9990
   chunk 40 optimal weight:    8.9990
   chunk 29 optimal weight:    0.7980
   chunk 52 optimal weight:    8.9990
   chunk 65 optimal weight:    6.9990
   chunk 110 optimal weight:    0.7980
   chunk 49 optimal weight:    4.9990
   chunk 9 optimal weight:    0.9980
   chunk 97 optimal weight:    0.9990
   chunk 63 optimal weight:    0.7980
   chunk 109 optimal weight:    0.9980
   overall best weight:    0.8780

-------------------------------------------------------------------------------
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 = 0.4118 r_free = 0.4118 target = 0.182058 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3785 r_free = 0.3785 target = 0.145032 restraints weight = 10686.243|
|-----------------------------------------------------------------------------|
r_work (start): 0.3736 rms_B_bonded: 2.27
r_work: 0.3504 rms_B_bonded: 3.03 restraints_weight: 0.5000
r_work: 0.3365 rms_B_bonded: 4.87 restraints_weight: 0.2500
r_work (final): 0.3365
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7684
moved from start:          0.1861

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   8761  Z= 0.126
  Angle     :  0.526   7.811  11932  Z= 0.278
  Chirality :  0.041   0.141   1384
  Planarity :  0.004   0.044   1510
  Dihedral  :  4.004  24.717   1228
  Min Nonbonded Distance : 2.453

Molprobity Statistics.
  All-atom Clashscore : 8.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.13 %
    Favored  : 96.87 %
  Rotamer:
    Outliers :  3.67 %
    Allowed  : 20.16 %
    Favored  : 76.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.75 (0.25), residues: 1117
  helix:  2.17 (0.26), residues: 400
  sheet:  0.03 (0.32), residues: 256
  loop : -0.70 (0.28), residues: 461

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C  68 
 TYR   0.019   0.001   TYR F 163 
 PHE   0.018   0.001   PHE F 156 
 TRP   0.014   0.001   TRP C 169 
 HIS   0.007   0.001   HIS F 176 

Details of bonding type rmsd
  covalent geometry    : bond        0.00285 ( 8759)
  covalent geometry    : angle       0.52646 (11928)
  SS BOND              : bond        0.00239 (    2)
  SS BOND              : angle       0.57648 (    4)
  hydrogen bonds       : bond        0.03605 (  455)
  hydrogen bonds       : angle       4.55725 ( 1308)

*********************** 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
  178 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 146
  time to evaluate  : 0.307 
Fit side-chains
REVERT: A   11 LEU cc_start: 0.8980 (mm) cc_final: 0.8687 (mm)
REVERT: B  179 GLU cc_start: 0.5749 (pp20) cc_final: 0.5379 (pp20)
REVERT: D   48 ASP cc_start: 0.8489 (t0) cc_final: 0.8211 (t0)
REVERT: E   38 ARG cc_start: 0.7862 (ptp90) cc_final: 0.7390 (ptp90)
REVERT: E   82 GLN cc_start: 0.7165 (OUTLIER) cc_final: 0.6252 (mm-40)
REVERT: F  187 MET cc_start: 0.8616 (tpp) cc_final: 0.8214 (tpp)
  outliers start: 32
  outliers final: 21
  residues processed: 164
  average time/residue: 0.0803
  time to fit residues: 18.8241
Evaluate side-chains
  159 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 137
  time to evaluate  : 0.285 
-------------------------------------------------------------------------------
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  161 SER
Chi-restraints excluded: chain C residue  263 THR
Chi-restraints excluded: chain C residue  318 LEU
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   82 GLN
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   60 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
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 21 optimal weight:    0.9990
   chunk 50 optimal weight:    6.9990
   chunk 12 optimal weight:    0.8980
   chunk 6 optimal weight:   10.0000
   chunk 76 optimal weight:    5.9990
   chunk 55 optimal weight:    9.9990
   chunk 25 optimal weight:    2.9990
   chunk 64 optimal weight:    1.9990
   chunk 29 optimal weight:    1.9990
   chunk 81 optimal weight:   30.0000
   chunk 8 optimal weight:    1.9990
   overall best weight:    1.5788

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

Flipped N/Q/H residues before XYZ refinement:
C 237 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4093 r_free = 0.4093 target = 0.179527 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3755 r_free = 0.3755 target = 0.142400 restraints weight = 10819.674|
|-----------------------------------------------------------------------------|
r_work (start): 0.3707 rms_B_bonded: 2.25
r_work: 0.3467 rms_B_bonded: 3.05 restraints_weight: 0.5000
r_work: 0.3329 rms_B_bonded: 4.86 restraints_weight: 0.2500
r_work (final): 0.3329
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7732
moved from start:          0.1848

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   8761  Z= 0.166
  Angle     :  0.565   8.982  11932  Z= 0.294
  Chirality :  0.042   0.150   1384
  Planarity :  0.004   0.044   1510
  Dihedral  :  4.087  25.403   1228
  Min Nonbonded Distance : 2.438

Molprobity Statistics.
  All-atom Clashscore : 8.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.31 %
    Favored  : 96.69 %
  Rotamer:
    Outliers :  3.32 %
    Allowed  : 20.96 %
    Favored  : 75.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.66 (0.25), residues: 1117
  helix:  2.08 (0.26), residues: 400
  sheet: -0.07 (0.32), residues: 261
  loop : -0.71 (0.28), residues: 456

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG E  18 
 TYR   0.022   0.002   TYR F 163 
 PHE   0.016   0.001   PHE F 194 
 TRP   0.012   0.001   TRP F 260 
 HIS   0.007   0.001   HIS F 176 

Details of bonding type rmsd
  covalent geometry    : bond        0.00386 ( 8759)
  covalent geometry    : angle       0.56501 (11928)
  SS BOND              : bond        0.00320 (    2)
  SS BOND              : angle       0.81544 (    4)
  hydrogen bonds       : bond        0.03823 (  455)
  hydrogen bonds       : angle       4.60388 ( 1308)

*********************** 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
  170 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 141
  time to evaluate  : 0.308 
Fit side-chains
REVERT: A   11 LEU cc_start: 0.9044 (mm) cc_final: 0.8749 (mm)
REVERT: C  289 TYR cc_start: 0.8582 (m-80) cc_final: 0.8367 (m-80)
REVERT: D   48 ASP cc_start: 0.8566 (t0) cc_final: 0.8262 (t0)
REVERT: E   38 ARG cc_start: 0.7829 (ptp90) cc_final: 0.7378 (ptp90)
REVERT: F  187 MET cc_start: 0.8602 (tpp) cc_final: 0.8190 (tpp)
  outliers start: 29
  outliers final: 25
  residues processed: 156
  average time/residue: 0.0881
  time to fit residues: 19.2690
Evaluate side-chains
  163 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 138
  time to evaluate  : 0.319 
-------------------------------------------------------------------------------
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  161 SER
Chi-restraints excluded: chain C residue  237 ASN
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  190 ARG
Chi-restraints excluded: chain E residue  194 SER
Chi-restraints excluded: chain E residue  202 LEU
Chi-restraints excluded: chain E residue  212 VAL
Chi-restraints excluded: chain F residue   60 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 82 optimal weight:    4.9990
   chunk 29 optimal weight:    0.7980
   chunk 0 optimal weight:    6.9990
   chunk 20 optimal weight:    0.6980
   chunk 77 optimal weight:    0.8980
   chunk 9 optimal weight:    0.7980
   chunk 90 optimal weight:    0.9980
   chunk 105 optimal weight:    0.8980
   chunk 74 optimal weight:    0.0060
   chunk 37 optimal weight:    8.9990
   chunk 24 optimal weight:    8.9990
   overall best weight:    0.6396

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

Flipped N/Q/H residues before XYZ refinement:
B  82 HIS
B 223 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4127 r_free = 0.4127 target = 0.182945 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3773 r_free = 0.3773 target = 0.143929 restraints weight = 10617.602|
|-----------------------------------------------------------------------------|
r_work (start): 0.3723 rms_B_bonded: 2.16
r_work: 0.3522 rms_B_bonded: 3.02 restraints_weight: 0.5000
r_work: 0.3384 rms_B_bonded: 4.84 restraints_weight: 0.2500
r_work (final): 0.3384
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7668
moved from start:          0.2018

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   8761  Z= 0.116
  Angle     :  0.527   8.879  11932  Z= 0.275
  Chirality :  0.041   0.145   1384
  Planarity :  0.004   0.054   1510
  Dihedral  :  3.930  23.987   1228
  Min Nonbonded Distance : 2.411

Molprobity Statistics.
  All-atom Clashscore : 7.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.31 %
    Favored  : 96.69 %
  Rotamer:
    Outliers :  2.98 %
    Allowed  : 21.99 %
    Favored  : 75.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.81 (0.26), residues: 1117
  helix:  2.32 (0.26), residues: 393
  sheet: -0.04 (0.32), residues: 258
  loop : -0.65 (0.28), residues: 466

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG E  18 
 TYR   0.016   0.001   TYR F 163 
 PHE   0.012   0.001   PHE F 194 
 TRP   0.016   0.001   TRP C 169 
 HIS   0.007   0.001   HIS F 176 

Details of bonding type rmsd
  covalent geometry    : bond        0.00255 ( 8759)
  covalent geometry    : angle       0.52691 (11928)
  SS BOND              : bond        0.00274 (    2)
  SS BOND              : angle       0.69509 (    4)
  hydrogen bonds       : bond        0.03496 (  455)
  hydrogen bonds       : angle       4.53949 ( 1308)

*********************** 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
  181 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 155
  time to evaluate  : 0.276 
Fit side-chains
REVERT: A   11 LEU cc_start: 0.9023 (mm) cc_final: 0.8723 (mm)
REVERT: B  179 GLU cc_start: 0.5740 (pp20) cc_final: 0.5416 (pp20)
REVERT: E   38 ARG cc_start: 0.7783 (ptp90) cc_final: 0.7351 (ptp90)
REVERT: F  187 MET cc_start: 0.8590 (tpp) cc_final: 0.8169 (tpp)
  outliers start: 26
  outliers final: 21
  residues processed: 169
  average time/residue: 0.0866
  time to fit residues: 20.9074
Evaluate side-chains
  161 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 140
  time to evaluate  : 0.296 
-------------------------------------------------------------------------------
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  263 THR
Chi-restraints excluded: chain C residue  318 LEU
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  190 ARG
Chi-restraints excluded: chain E residue  194 SER
Chi-restraints excluded: chain E residue  202 LEU
Chi-restraints excluded: chain E residue  212 VAL
Chi-restraints excluded: chain F residue   60 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
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 8 optimal weight:    1.9990
   chunk 5 optimal weight:    0.8980
   chunk 109 optimal weight:    2.9990
   chunk 60 optimal weight:    0.0050
   chunk 104 optimal weight:    0.6980
   chunk 30 optimal weight:    0.0030
   chunk 89 optimal weight:    2.9990
   chunk 61 optimal weight:    5.9990
   chunk 97 optimal weight:    3.9990
   chunk 3 optimal weight:    3.9990
   chunk 65 optimal weight:    2.9990
   overall best weight:    0.7206

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4131 r_free = 0.4131 target = 0.183228 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3780 r_free = 0.3780 target = 0.145029 restraints weight = 10591.406|
|-----------------------------------------------------------------------------|
r_work (start): 0.3737 rms_B_bonded: 2.06
r_work: 0.3532 rms_B_bonded: 2.99 restraints_weight: 0.5000
r_work: 0.3394 rms_B_bonded: 4.79 restraints_weight: 0.2500
r_work (final): 0.3394
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7661
moved from start:          0.2144

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   8761  Z= 0.117
  Angle     :  0.532   8.731  11932  Z= 0.278
  Chirality :  0.041   0.151   1384
  Planarity :  0.004   0.039   1510
  Dihedral  :  3.891  23.262   1228
  Min Nonbonded Distance : 2.397

Molprobity Statistics.
  All-atom Clashscore : 7.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.86 %
    Favored  : 97.14 %
  Rotamer:
    Outliers :  3.44 %
    Allowed  : 22.45 %
    Favored  : 74.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.87 (0.26), residues: 1117
  helix:  2.43 (0.26), residues: 393
  sheet:  0.03 (0.32), residues: 256
  loop : -0.71 (0.28), residues: 468

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B  32 
 TYR   0.018   0.001   TYR E  59 
 PHE   0.012   0.001   PHE F 106 
 TRP   0.014   0.001   TRP C 169 
 HIS   0.006   0.001   HIS F 176 

Details of bonding type rmsd
  covalent geometry    : bond        0.00261 ( 8759)
  covalent geometry    : angle       0.53193 (11928)
  SS BOND              : bond        0.00292 (    2)
  SS BOND              : angle       0.68628 (    4)
  hydrogen bonds       : bond        0.03455 (  455)
  hydrogen bonds       : angle       4.51185 ( 1308)

*********************** 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
  175 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 145
  time to evaluate  : 0.305 
Fit side-chains
REVERT: B  122 LEU cc_start: 0.8762 (OUTLIER) cc_final: 0.8553 (mp)
REVERT: B  179 GLU cc_start: 0.5754 (pp20) cc_final: 0.5392 (pp20)
REVERT: E   38 ARG cc_start: 0.7777 (ptp90) cc_final: 0.7376 (ptp90)
REVERT: F  187 MET cc_start: 0.8655 (tpp) cc_final: 0.8211 (tpp)
  outliers start: 30
  outliers final: 23
  residues processed: 162
  average time/residue: 0.0862
  time to fit residues: 19.8721
Evaluate side-chains
  164 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 140
  time to evaluate  : 0.304 
-------------------------------------------------------------------------------
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  122 LEU
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  161 SER
Chi-restraints excluded: chain C residue  263 THR
Chi-restraints excluded: chain C residue  307 VAL
Chi-restraints excluded: chain C residue  318 LEU
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  194 SER
Chi-restraints excluded: chain E residue  202 LEU
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 97 optimal weight:    3.9990
   chunk 76 optimal weight:    5.9990
   chunk 99 optimal weight:    1.9990
   chunk 65 optimal weight:    0.8980
   chunk 90 optimal weight:    0.7980
   chunk 43 optimal weight:    7.9990
   chunk 37 optimal weight:    6.9990
   chunk 8 optimal weight:    0.7980
   chunk 85 optimal weight:    0.6980
   chunk 12 optimal weight:    4.9990
   chunk 39 optimal weight:    3.9990
   overall best weight:    1.0382

-------------------------------------------------------------------------------
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 = 0.4121 r_free = 0.4121 target = 0.182314 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3764 r_free = 0.3764 target = 0.143175 restraints weight = 10607.836|
|-----------------------------------------------------------------------------|
r_work (start): 0.3718 rms_B_bonded: 2.14
r_work: 0.3514 rms_B_bonded: 3.03 restraints_weight: 0.5000
r_work: 0.3375 rms_B_bonded: 4.87 restraints_weight: 0.2500
r_work (final): 0.3375
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7684
moved from start:          0.2141

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   8761  Z= 0.132
  Angle     :  0.547   8.631  11932  Z= 0.285
  Chirality :  0.042   0.152   1384
  Planarity :  0.004   0.040   1510
  Dihedral  :  3.932  23.675   1228
  Min Nonbonded Distance : 2.378

Molprobity Statistics.
  All-atom Clashscore : 8.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.22 %
    Favored  : 96.78 %
  Rotamer:
    Outliers :  3.09 %
    Allowed  : 23.02 %
    Favored  : 73.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.73 (0.25), residues: 1117
  helix:  2.30 (0.26), residues: 399
  sheet: -0.01 (0.32), residues: 249
  loop : -0.83 (0.28), residues: 469

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B  32 
 TYR   0.018   0.001   TYR F 163 
 PHE   0.012   0.001   PHE F 106 
 TRP   0.013   0.001   TRP C 169 
 HIS   0.006   0.001   HIS F 176 

Details of bonding type rmsd
  covalent geometry    : bond        0.00300 ( 8759)
  covalent geometry    : angle       0.54730 (11928)
  SS BOND              : bond        0.00333 (    2)
  SS BOND              : angle       0.82481 (    4)
  hydrogen bonds       : bond        0.03535 (  455)
  hydrogen bonds       : angle       4.52163 ( 1308)

********************** 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
  166 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 139
  time to evaluate  : 0.314 
Fit side-chains
REVERT: B  122 LEU cc_start: 0.8720 (OUTLIER) cc_final: 0.8507 (mp)
REVERT: B  179 GLU cc_start: 0.5801 (pp20) cc_final: 0.5480 (pp20)
REVERT: E   38 ARG cc_start: 0.7744 (ptp90) cc_final: 0.7350 (ptp90)
REVERT: F  187 MET cc_start: 0.8621 (tpp) cc_final: 0.8193 (tpp)
  outliers start: 27
  outliers final: 22
  residues processed: 153
  average time/residue: 0.0870
  time to fit residues: 18.9114
Evaluate side-chains
  160 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 137
  time to evaluate  : 0.322 
-------------------------------------------------------------------------------
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  122 LEU
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  161 SER
Chi-restraints excluded: chain C residue  263 THR
Chi-restraints excluded: chain C residue  307 VAL
Chi-restraints excluded: chain C residue  318 LEU
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  194 SER
Chi-restraints excluded: chain E residue  202 LEU
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 92 optimal weight:    0.7980
   chunk 38 optimal weight:    0.8980
   chunk 79 optimal weight:    9.9990
   chunk 37 optimal weight:    0.9980
   chunk 100 optimal weight:    7.9990
   chunk 36 optimal weight:    0.0770
   chunk 10 optimal weight:    4.9990
   chunk 56 optimal weight:    4.9990
   chunk 68 optimal weight:    0.0870
   chunk 98 optimal weight:    1.9990
   chunk 3 optimal weight:    6.9990
   overall best weight:    0.5716

-------------------------------------------------------------------------------
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 = 0.4151 r_free = 0.4151 target = 0.185301 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3808 r_free = 0.3808 target = 0.147240 restraints weight = 10518.680|
|-----------------------------------------------------------------------------|
r_work (start): 0.3764 rms_B_bonded: 2.09
r_work: 0.3561 rms_B_bonded: 3.01 restraints_weight: 0.5000
r_work: 0.3424 rms_B_bonded: 4.84 restraints_weight: 0.2500
r_work (final): 0.3424
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7630
moved from start:          0.2336

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033   8761  Z= 0.110
  Angle     :  0.544   8.640  11932  Z= 0.278
  Chirality :  0.041   0.184   1384
  Planarity :  0.004   0.035   1510
  Dihedral  :  3.811  22.049   1228
  Min Nonbonded Distance : 2.393

Molprobity Statistics.
  All-atom Clashscore : 8.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.86 %
    Favored  : 97.14 %
  Rotamer:
    Outliers :  2.52 %
    Allowed  : 23.71 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.80 (0.26), residues: 1117
  helix:  2.40 (0.26), residues: 398
  sheet:  0.02 (0.32), residues: 249
  loop : -0.82 (0.28), residues: 470

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B  32 
 TYR   0.017   0.001   TYR F 129 
 PHE   0.012   0.001   PHE F 106 
 TRP   0.015   0.001   TRP C 169 
 HIS   0.006   0.001   HIS F 176 

Details of bonding type rmsd
  covalent geometry    : bond        0.00240 ( 8759)
  covalent geometry    : angle       0.54357 (11928)
  SS BOND              : bond        0.00295 (    2)
  SS BOND              : angle       0.72172 (    4)
  hydrogen bonds       : bond        0.03334 (  455)
  hydrogen bonds       : angle       4.48260 ( 1308)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2672.81 seconds
wall clock time: 46 minutes 26.35 seconds (2786.35 seconds total)