Starting phenix.real_space_refine
on Fri Jun  6 02:09:55 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8zmd_60243/06_2025/8zmd_60243.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8zmd_60243/06_2025/8zmd_60243.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.25
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8zmd_60243/06_2025/8zmd_60243.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8zmd_60243/06_2025/8zmd_60243.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8zmd_60243/06_2025/8zmd_60243.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8zmd_60243/06_2025/8zmd_60243.cif"
  }
  resolution = 3.25
  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=   0.001 sd=   0.021
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      46      5.16       5
     C    4498      2.51       5
     N    1179      2.21       5
     O    1289      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 2 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib"
  Total number of atoms: 7012
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 1804
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 230, 1804
          Classifications: {'peptide': 230}
          Incomplete info: {'truncation_to_alanine': 21}
          Link IDs: {'PTRANS': 6, 'TRANS': 223}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 89
          Unresolved non-hydrogen angles: 104
          Unresolved non-hydrogen dihedrals: 74
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLU:plan': 5, 'ARG:plan': 5, 'ASP:plan': 4}
          Unresolved non-hydrogen planarities: 57
    Chain: "B"
      Number of atoms: 2486
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 338, 2486
          Classifications: {'peptide': 338}
          Incomplete info: {'truncation_to_alanine': 26}
          Link IDs: {'PTRANS': 5, 'TRANS': 332}
          Unresolved non-hydrogen bonds: 114
          Unresolved non-hydrogen angles: 135
          Unresolved non-hydrogen dihedrals: 93
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'GLN:plan1': 6, 'GLU:plan': 5, 'ARG:plan': 7, 'ASN:plan1': 1}
          Unresolved non-hydrogen planarities: 82
    Chain: "G"
      Number of atoms: 321
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 50, 321
          Classifications: {'peptide': 50}
          Incomplete info: {'truncation_to_alanine': 17}
          Link IDs: {'PTRANS': 4, 'TRANS': 45}
          Unresolved non-hydrogen bonds: 64
          Unresolved non-hydrogen angles: 76
          Unresolved non-hydrogen dihedrals: 52
          Unresolved non-hydrogen chiralities: 4
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ARG:plan': 2, 'ASN:plan1': 2}
          Unresolved non-hydrogen planarities: 32
    Chain: "R"
      Number of atoms: 2401
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 309, 2401
          Classifications: {'peptide': 309}
          Incomplete info: {'truncation_to_alanine': 15}
          Link IDs: {'PTRANS': 11, 'TRANS': 297}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 64
          Unresolved non-hydrogen angles: 76
          Unresolved non-hydrogen dihedrals: 58
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLN:plan1': 1, 'HIS:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 2, 'PHE:plan': 1, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 34
  Time building chain proxies: 5.60, per 1000 atoms: 0.80
  Number of scatterers: 7012
  At special positions: 0
  Unit cell: (90.2, 101.2, 134.2, 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      46     16.00
     O    1289      8.00
     N    1179      7.00
     C    4498      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS R 148 " - pdb=" SG  CYS R 226 " 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: 2.25
  Conformation dependent library (CDL) restraints added in 1.2 seconds
  

  1830 Ramachandran restraints generated.
    915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1758

  Finding SS restraints...
    Secondary structure from input PDB file:
      30 helices and 10 sheets defined
      44.9% alpha, 18.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.86
  Creating SS restraints...
    Processing helix  chain 'A' and resid 17 through 38
      removed outlier: 3.519A  pdb=" N   GLU A  21 " --> pdb=" O   LYS A  17 " (cutoff:3.500A)
      removed outlier: 4.731A  pdb=" N   SER A  23 " --> pdb=" O   ALA A  19 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 52 through 60
    Processing helix  chain 'A' and resid 234 through 238
      removed outlier: 3.560A  pdb=" N   CYS A 237 " --> pdb=" O   TRP A 234 " (cutoff:3.500A)
      removed outlier: 3.669A  pdb=" N   PHE A 238 " --> pdb=" O   ILE A 235 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 234 through 238'
    Processing helix  chain 'A' and resid 265 through 278
    Processing helix  chain 'A' and resid 279 through 283
      removed outlier: 3.618A  pdb=" N   LEU A 282 " --> pdb=" O   ASN A 279 " (cutoff:3.500A)
      removed outlier: 4.056A  pdb=" N   ARG A 283 " --> pdb=" O   ARG A 280 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 279 through 283'
    Processing helix  chain 'A' and resid 293 through 304
      removed outlier: 3.759A  pdb=" N   LEU A 297 " --> pdb=" O   LYS A 293 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 307 through 311
    Processing helix  chain 'A' and resid 312 through 318
    Processing helix  chain 'A' and resid 331 through 351
      removed outlier: 3.577A  pdb=" N   THR A 335 " --> pdb=" O   ASP A 331 " (cutoff:3.500A)
      removed outlier: 3.810A  pdb=" N   PHE A 345 " --> pdb=" O   ILE A 341 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 370 through 391
      removed outlier: 3.507A  pdb=" N   ARG A 374 " --> pdb=" O   GLU A 370 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 4 through 25
      removed outlier: 3.869A  pdb=" N   ARG B   8 " --> pdb=" O   LEU B   4 " (cutoff:3.500A)
      removed outlier: 3.528A  pdb=" N   CYS B  25 " --> pdb=" O   ALA B  21 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 13 through 24
      removed outlier: 3.917A  pdb=" N   ASN G  24 " --> pdb=" O   LYS G  20 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 29 through 44
      removed outlier: 3.739A  pdb=" N   ALA G  33 " --> pdb=" O   LYS G  29 " (cutoff:3.500A)
      removed outlier: 3.643A  pdb=" N   HIS G  44 " --> pdb=" O   TYR G  40 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 55 through 59
      removed outlier: 3.616A  pdb=" N   ASN G  59 " --> pdb=" O   ALA G  56 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 62 through 70
    Processing helix  chain 'R' and resid 76 through 102
      removed outlier: 3.902A  pdb=" N   ILE R  80 " --> pdb=" O   VAL R  76 " (cutoff:3.500A)
      removed outlier: 3.527A  pdb=" N   VAL R  81 " --> pdb=" O   PHE R  77 " (cutoff:3.500A)
      Proline residue:  R  91  - end of helix
    Processing helix  chain 'R' and resid 108 through 125
      removed outlier: 3.720A  pdb=" N   ASN R 116 " --> pdb=" O   ILE R 112 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 127 through 137
      removed outlier: 3.852A  pdb=" N   LYS R 131 " --> pdb=" O   TRP R 127 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 145 through 178
      removed outlier: 3.810A  pdb=" N   ASN R 149 " --> pdb=" O   GLU R 145 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 183 through 203
    Processing helix  chain 'R' and resid 204 through 205
      No H-bonds generated for 'chain 'R' and resid 204 through 205'
    Processing helix  chain 'R' and resid 206 through 210
      removed outlier: 3.538A  pdb=" N   LEU R 209 " --> pdb=" O   THR R 206 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 232 through 236
    Processing helix  chain 'R' and resid 237 through 250
      removed outlier: 3.558A  pdb=" N   ASN R 241 " --> pdb=" O   GLY R 237 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 251 through 270
    Processing helix  chain 'R' and resid 278 through 317
      removed outlier: 3.909A  pdb=" N   ARG R 284 " --> pdb=" O   LYS R 280 " (cutoff:3.500A)
      removed outlier: 4.420A  pdb=" N   CYS R 299 " --> pdb=" O   MET R 295 " (cutoff:3.500A)
      Proline residue:  R 302  - end of helix
    Processing helix  chain 'R' and resid 322 through 334
      removed outlier: 3.570A  pdb=" N   TYR R 326 " --> pdb=" O   VAL R 322 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 335 through 340
    Processing helix  chain 'R' and resid 341 through 343
      No H-bonds generated for 'chain 'R' and resid 341 through 343'
    Processing helix  chain 'R' and resid 349 through 359
      removed outlier: 3.592A  pdb=" N   ASP R 353 " --> pdb=" O   HIS R 349 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 207 through 214
      removed outlier: 4.528A  pdb=" N   VAL A 224 " --> pdb=" O   LEU A  45 " (cutoff:3.500A)
      removed outlier: 7.880A  pdb=" N   GLY A  47 " --> pdb=" O   VAL A 224 " (cutoff:3.500A)
      removed outlier: 9.929A  pdb=" N   ALA A 243 " --> pdb=" O   THR A  40 " (cutoff:3.500A)
      removed outlier: 7.245A  pdb=" N   ARG A  42 " --> pdb=" O   ALA A 243 " (cutoff:3.500A)
      removed outlier: 8.316A  pdb=" N   ILE A 245 " --> pdb=" O   ARG A  42 " (cutoff:3.500A)
      removed outlier: 6.639A  pdb=" N   LEU A  44 " --> pdb=" O   ILE A 245 " (cutoff:3.500A)
      removed outlier: 7.805A  pdb=" N   VAL A 247 " --> pdb=" O   LEU A  44 " (cutoff:3.500A)
      removed outlier: 6.843A  pdb=" N   LEU A  46 " --> pdb=" O   VAL A 247 " (cutoff:3.500A)
      removed outlier: 6.368A  pdb=" N   ILE A 244 " --> pdb=" O   ILE A 288 " (cutoff:3.500A)
      removed outlier: 7.414A  pdb=" N   PHE A 290 " --> pdb=" O   ILE A 244 " (cutoff:3.500A)
      removed outlier: 6.298A  pdb=" N   PHE A 246 " --> pdb=" O   PHE A 290 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51
      removed outlier: 7.044A  pdb=" N   ILE B 338 " --> pdb=" O   ARG B  48 " (cutoff:3.500A)
      removed outlier: 4.721A  pdb=" N   THR B  50 " --> pdb=" O   LEU B 336 " (cutoff:3.500A)
      removed outlier: 6.906A  pdb=" N   LEU B 336 " --> pdb=" O   THR B  50 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63
      removed outlier: 7.272A  pdb=" N   ALA B  73 " --> pdb=" O   TYR B  59 " (cutoff:3.500A)
      removed outlier: 4.618A  pdb=" N   MET B  61 " --> pdb=" O   VAL B  71 " (cutoff:3.500A)
      removed outlier: 6.976A  pdb=" N   VAL B  71 " --> pdb=" O   MET B  61 " (cutoff:3.500A)
      removed outlier: 5.349A  pdb=" N   TRP B  63 " --> pdb=" O   LEU B  69 " (cutoff:3.500A)
      removed outlier: 7.529A  pdb=" N   LEU B  69 " --> pdb=" O   TRP B  63 " (cutoff:3.500A)
      removed outlier: 3.904A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 6.212A  pdb=" N   ASP B  83 " --> pdb=" O   LYS B  89 " (cutoff:3.500A)
      removed outlier: 5.696A  pdb=" N   LYS B  89 " --> pdb=" O   ASP B  83 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 103
      removed outlier: 6.903A  pdb=" N   GLY B 115 " --> pdb=" O   MET B 101 " (cutoff:3.500A)
      removed outlier: 4.633A  pdb=" N   CYS B 103 " --> pdb=" O   ALA B 113 " (cutoff:3.500A)
      removed outlier: 6.485A  pdb=" N   ALA B 113 " --> pdb=" O   CYS B 103 " (cutoff:3.500A)
      removed outlier: 4.093A  pdb=" N   GLY B 116 " --> pdb=" O   ILE B 120 " (cutoff:3.500A)
      removed outlier: 4.789A  pdb=" N   ILE B 120 " --> pdb=" O   GLY B 116 " (cutoff:3.500A)
      removed outlier: 6.205A  pdb=" N   ASN B 125 " --> pdb=" O   VAL B 135 " (cutoff:3.500A)
      removed outlier: 6.198A  pdb=" N   VAL B 135 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 153
      removed outlier: 7.003A  pdb=" N   SER B 160 " --> pdb=" O   SER B 147 " (cutoff:3.500A)
      removed outlier: 4.530A  pdb=" N   CYS B 149 " --> pdb=" O   VAL B 158 " (cutoff:3.500A)
      removed outlier: 6.875A  pdb=" N   VAL B 158 " --> pdb=" O   CYS B 149 " (cutoff:3.500A)
      removed outlier: 5.099A  pdb=" N   PHE B 151 " --> pdb=" O   GLN B 156 " (cutoff:3.500A)
      removed outlier: 7.745A  pdb=" N   GLN B 156 " --> pdb=" O   PHE B 151 " (cutoff:3.500A)
      removed outlier: 4.442A  pdb=" N   THR B 165 " --> pdb=" O   SER B 161 " (cutoff:3.500A)
      removed outlier: 3.649A  pdb=" N   THR B 178 " --> pdb=" O   LEU B 168 " (cutoff:3.500A)
      removed outlier: 6.357A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 6.148A  pdb=" N   GLN B 176 " --> pdb=" O   ASP B 170 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 189 through 192
      removed outlier: 4.161A  pdb=" N   GLN B 220 " --> pdb=" O   LEU B 210 " (cutoff:3.500A)
      removed outlier: 6.847A  pdb=" N   ASP B 212 " --> pdb=" O   CYS B 218 " (cutoff:3.500A)
      removed outlier: 6.923A  pdb=" N   CYS B 218 " --> pdb=" O   ASP B 212 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234
      removed outlier: 6.983A  pdb=" N   GLY B 244 " --> pdb=" O   ASN B 230 " (cutoff:3.500A)
      removed outlier: 4.727A  pdb=" N   ILE B 232 " --> pdb=" O   ALA B 242 " (cutoff:3.500A)
      removed outlier: 6.937A  pdb=" N   ALA B 242 " --> pdb=" O   ILE B 232 " (cutoff:3.500A)
      removed outlier: 4.750A  pdb=" N   PHE B 234 " --> pdb=" O   ALA B 240 " (cutoff:3.500A)
      removed outlier: 7.054A  pdb=" N   ALA B 240 " --> pdb=" O   PHE B 234 " (cutoff:3.500A)
      removed outlier: 4.074A  pdb=" N   MET B 262 " --> pdb=" O   LEU B 252 " (cutoff:3.500A)
      removed outlier: 7.150A  pdb=" N   ASP B 254 " --> pdb=" O   GLU B 260 " (cutoff:3.500A)
      removed outlier: 7.329A  pdb=" N   GLU B 260 " --> pdb=" O   ASP B 254 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278
      removed outlier: 6.796A  pdb=" N   GLY B 288 " --> pdb=" O   THR B 274 " (cutoff:3.500A)
      removed outlier: 4.700A  pdb=" N   VAL B 276 " --> pdb=" O   LEU B 286 " (cutoff:3.500A)
      removed outlier: 7.064A  pdb=" N   LEU B 286 " --> pdb=" O   VAL B 276 " (cutoff:3.500A)
      removed outlier: 4.965A  pdb=" N   PHE B 278 " --> pdb=" O   LEU B 284 " (cutoff:3.500A)
      removed outlier: 7.153A  pdb=" N   LEU B 284 " --> pdb=" O   PHE B 278 " (cutoff:3.500A)
      removed outlier: 6.087A  pdb=" N   ASP B 298 " --> pdb=" O   ARG B 304 " (cutoff:3.500A)
      removed outlier: 6.588A  pdb=" N   ARG B 304 " --> pdb=" O   ASP B 298 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'R' and resid 38 through 40
      removed outlier: 6.050A  pdb=" N   LEU R  38 " --> pdb=" O   LEU R 230 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA9
    Processing sheet with id=AB1, first strand: chain 'R' and resid 215 through 218

    358 hydrogen bonds defined for protein.
    1032 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: 1.92

  Time building geometry restraints manager: 2.67 seconds

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

  Histogram of bond lengths:
        1.20 -     1.32: 1279
        1.32 -     1.45: 2016
        1.45 -     1.58: 3800
        1.58 -     1.71: 0
        1.71 -     1.84: 66
  Bond restraints: 7161
  Sorted by residual:
  bond pdb=" C   ILE B  58 "
       pdb=" O   ILE B  58 "
    ideal  model  delta    sigma   weight residual
    1.238  1.199  0.039 1.17e-02 7.31e+03 1.11e+01
  bond pdb=" C   ALA B  60 "
       pdb=" O   ALA B  60 "
    ideal  model  delta    sigma   weight residual
    1.233  1.195  0.038 1.17e-02 7.31e+03 1.04e+01
  bond pdb=" CA  ALA B  60 "
       pdb=" CB  ALA B  60 "
    ideal  model  delta    sigma   weight residual
    1.532  1.490  0.043 1.68e-02 3.54e+03 6.45e+00
  bond pdb=" C   TYR B  59 "
       pdb=" O   TYR B  59 "
    ideal  model  delta    sigma   weight residual
    1.235  1.204  0.032 1.31e-02 5.83e+03 5.85e+00
  bond pdb=" N   ALA B  60 "
       pdb=" CA  ALA B  60 "
    ideal  model  delta    sigma   weight residual
    1.456  1.478 -0.022 1.16e-02 7.43e+03 3.50e+00
  ... (remaining 7156 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.05: 9458
        2.05 -     4.10: 262
        4.10 -     6.15: 33
        6.15 -     8.21: 5
        8.21 -    10.26: 2
  Bond angle restraints: 9760
  Sorted by residual:
  angle pdb=" N   ALA B 203 "
        pdb=" CA  ALA B 203 "
        pdb=" C   ALA B 203 "
      ideal   model   delta    sigma   weight residual
     110.06  116.99   -6.93 1.43e+00 4.89e-01 2.35e+01
  angle pdb=" C   GLN A  59 "
        pdb=" N   MET A  60 "
        pdb=" CA  MET A  60 "
      ideal   model   delta    sigma   weight residual
     122.66  115.00    7.66 1.63e+00 3.76e-01 2.21e+01
  angle pdb=" CA  ALA B  60 "
        pdb=" C   ALA B  60 "
        pdb=" O   ALA B  60 "
      ideal   model   delta    sigma   weight residual
     121.38  116.58    4.80 1.06e+00 8.90e-01 2.05e+01
  angle pdb=" CA  TYR B  59 "
        pdb=" C   TYR B  59 "
        pdb=" O   TYR B  59 "
      ideal   model   delta    sigma   weight residual
     119.41  114.40    5.01 1.13e+00 7.83e-01 1.96e+01
  angle pdb=" N   VAL R 125 "
        pdb=" CA  VAL R 125 "
        pdb=" CB  VAL R 125 "
      ideal   model   delta    sigma   weight residual
     112.39  107.52    4.87 1.17e+00 7.31e-01 1.73e+01
  ... (remaining 9755 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    13.95: 3797
       13.95 -    27.89: 287
       27.89 -    41.84: 94
       41.84 -    55.78: 21
       55.78 -    69.73: 6
  Dihedral angle restraints: 4205
    sinusoidal: 1494
      harmonic: 2711
  Sorted by residual:
  dihedral pdb=" CB  CYS R 148 "
           pdb=" SG  CYS R 148 "
           pdb=" SG  CYS R 226 "
           pdb=" CB  CYS R 226 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  132.71  -39.71     1      1.00e+01 1.00e-02 2.21e+01
  dihedral pdb=" CA  GLY B 202 "
           pdb=" C   GLY B 202 "
           pdb=" N   ALA B 203 "
           pdb=" CA  ALA B 203 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -156.95  -23.05     0      5.00e+00 4.00e-02 2.13e+01
  dihedral pdb=" CA  TRP B  82 "
           pdb=" C   TRP B  82 "
           pdb=" N   ASP B  83 "
           pdb=" CA  ASP B  83 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.28   19.72     0      5.00e+00 4.00e-02 1.55e+01
  ... (remaining 4202 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.062: 936
       0.062 -    0.125: 196
       0.125 -    0.187: 21
       0.187 -    0.249: 0
       0.249 -    0.311: 1
  Chirality restraints: 1154
  Sorted by residual:
  chirality pdb=" CA  ILE B  58 "
            pdb=" N   ILE B  58 "
            pdb=" C   ILE B  58 "
            pdb=" CB  ILE B  58 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.74   -0.31 2.00e-01 2.50e+01 2.42e+00
  chirality pdb=" CB  VAL B 100 "
            pdb=" CA  VAL B 100 "
            pdb=" CG1 VAL B 100 "
            pdb=" CG2 VAL B 100 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.45   -0.18 2.00e-01 2.50e+01 8.41e-01
  chirality pdb=" CA  MET A  60 "
            pdb=" N   MET A  60 "
            pdb=" C   MET A  60 "
            pdb=" CB  MET A  60 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.34    0.17 2.00e-01 2.50e+01 7.63e-01
  ... (remaining 1151 not shown)

  Planarity restraints: 1232
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP G  48 "    0.044 5.00e-02 4.00e+02   6.66e-02 7.09e+00
        pdb=" N   PRO G  49 "   -0.115 5.00e-02 4.00e+02
        pdb=" CA  PRO G  49 "    0.034 5.00e-02 4.00e+02
        pdb=" CD  PRO G  49 "    0.037 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE B 235 "    0.040 5.00e-02 4.00e+02   6.11e-02 5.96e+00
        pdb=" N   PRO B 236 "   -0.106 5.00e-02 4.00e+02
        pdb=" CA  PRO B 236 "    0.032 5.00e-02 4.00e+02
        pdb=" CD  PRO B 236 "    0.034 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE R 253 "    0.031 5.00e-02 4.00e+02   4.74e-02 3.59e+00
        pdb=" N   PRO R 254 "   -0.082 5.00e-02 4.00e+02
        pdb=" CA  PRO R 254 "    0.024 5.00e-02 4.00e+02
        pdb=" CD  PRO R 254 "    0.027 5.00e-02 4.00e+02
  ... (remaining 1229 not shown)

  Histogram of nonbonded interaction distances:
        2.18 -     2.72: 423
        2.72 -     3.27: 6611
        3.27 -     3.81: 10585
        3.81 -     4.36: 11785
        4.36 -     4.90: 21379
  Nonbonded interactions: 50783
  Sorted by model distance:
  nonbonded pdb=" NE2 GLN A  59 "
            pdb=" O   SER A 366 "
     model   vdw
     2.181 3.120
  nonbonded pdb=" OD1 ASP A 249 "
            pdb=" N   SER A 250 "
     model   vdw
     2.199 3.120
  nonbonded pdb=" OG  SER B 245 "
            pdb=" OD1 ASP B 247 "
     model   vdw
     2.225 3.040
  nonbonded pdb=" OG1 THR B 184 "
            pdb=" OD2 ASP B 205 "
     model   vdw
     2.227 3.040
  nonbonded pdb=" O   ASP B 333 "
            pdb=" OG  SER B 334 "
     model   vdw
     2.235 3.040
  ... (remaining 50778 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:             0.760
  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:          0.310
  Check model and map are aligned:         0.040
  Set scattering table:                    0.060
  Process input model:                     23.260
  Find NCS groups from input model:        0.080
  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:2.850
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   27.400
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7165
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      :  0.007   0.052   7162  Z= 0.300
  Angle     :  0.822  10.256   9762  Z= 0.486
  Chirality :  0.050   0.311   1154
  Planarity :  0.005   0.067   1232
  Dihedral  : 12.138  69.730   2444
  Min Nonbonded Distance : 2.181

Molprobity Statistics.
  All-atom Clashscore : 5.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.37 %
    Favored  : 95.63 %
  Rotamer:
    Outliers :  0.14 %
    Allowed  :  0.28 %
    Favored  : 99.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.04 (0.27), residues: 915
  helix:  0.91 (0.26), residues: 383
  sheet:  0.34 (0.40), residues: 177
  loop : -1.06 (0.31), residues: 355

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.003   TRP B  82 
 HIS   0.006   0.002   HIS R 310 
 PHE   0.026   0.003   PHE B 151 
 TYR   0.019   0.003   TYR A  37 
 ARG   0.006   0.001   ARG A 265 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.15532 (  358)
  hydrogen bonds       : angle       5.56147 ( 1032)
  SS BOND              : bond        0.00383 (    1)
  SS BOND              : angle       4.99470 (    2)
  covalent geometry    : bond        0.00668 ( 7161)
  covalent geometry    : angle       0.81857 ( 9760)

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

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

  1830 Ramachandran restraints generated.
    915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1830 Ramachandran restraints generated.
    915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  164 residues out of total 803 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 163
  time to evaluate  : 0.860 
Fit side-chains
REVERT: A   34 LYS cc_start: 0.7783 (tttt) cc_final: 0.7432 (ttmm)
REVERT: A  252 ASP cc_start: 0.7409 (t70) cc_final: 0.6931 (t70)
REVERT: A  292 ASN cc_start: 0.8245 (t0) cc_final: 0.8014 (t0)
REVERT: A  381 ASP cc_start: 0.8064 (t70) cc_final: 0.7598 (t70)
REVERT: B   76 ASP cc_start: 0.7319 (m-30) cc_final: 0.6932 (m-30)
REVERT: B  300 LEU cc_start: 0.8534 (mt) cc_final: 0.8266 (mp)
REVERT: R  212 VAL cc_start: 0.8151 (t) cc_final: 0.7941 (t)
  outliers start: 1
  outliers final: 1
  residues processed: 163
  average time/residue: 0.2303
  time to fit residues: 48.2069
Evaluate side-chains
  150 residues out of total 803 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 149
  time to evaluate  : 0.766 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   59 TYR
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 76 optimal weight:    1.9990
   chunk 68 optimal weight:    0.8980
   chunk 38 optimal weight:    2.9990
   chunk 23 optimal weight:    4.9990
   chunk 46 optimal weight:    0.8980
   chunk 36 optimal weight:    0.7980
   chunk 71 optimal weight:    0.5980
   chunk 27 optimal weight:    2.9990
   chunk 43 optimal weight:    0.8980
   chunk 53 optimal weight:    0.9990
   chunk 82 optimal weight:    0.6980
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
A 392 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3799 r_free = 0.3799 target = 0.138818 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3485 r_free = 0.3485 target = 0.115538 restraints weight = 10297.797|
|-----------------------------------------------------------------------------|
r_work (start): 0.3461 rms_B_bonded: 2.61
r_work: 0.3333 rms_B_bonded: 2.95 restraints_weight: 0.5000
r_work (final): 0.3333
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7388
moved from start:          0.0903

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   7162  Z= 0.192
  Angle     :  0.631   8.409   9762  Z= 0.341
  Chirality :  0.046   0.177   1154
  Planarity :  0.005   0.062   1232
  Dihedral  :  5.038  50.465    991
  Min Nonbonded Distance : 2.526

Molprobity Statistics.
  All-atom Clashscore : 4.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.39 %
    Favored  : 96.61 %
  Rotamer:
    Outliers :  1.80 %
    Allowed  :  6.63 %
    Favored  : 91.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.34 (0.28), residues: 915
  helix:  1.34 (0.26), residues: 392
  sheet:  0.19 (0.37), residues: 194
  loop : -1.07 (0.32), residues: 329

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.002   TRP B  82 
 HIS   0.004   0.001   HIS R 310 
 PHE   0.019   0.002   PHE B 151 
 TYR   0.023   0.002   TYR R 296 
 ARG   0.004   0.000   ARG A 265 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.07984 (  358)
  hydrogen bonds       : angle       4.33831 ( 1032)
  SS BOND              : bond        0.00153 (    1)
  SS BOND              : angle       3.48291 (    2)
  covalent geometry    : bond        0.00432 ( 7161)
  covalent geometry    : angle       0.62861 ( 9760)

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

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

  1830 Ramachandran restraints generated.
    915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1830 Ramachandran restraints generated.
    915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  164 residues out of total 803 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 151
  time to evaluate  : 0.771 
Fit side-chains
REVERT: A  221 MET cc_start: 0.8463 (ttp) cc_final: 0.8215 (ttp)
REVERT: A  252 ASP cc_start: 0.7684 (t70) cc_final: 0.7184 (t70)
REVERT: A  381 ASP cc_start: 0.8335 (t70) cc_final: 0.7984 (t70)
REVERT: B   76 ASP cc_start: 0.7548 (m-30) cc_final: 0.7306 (m-30)
REVERT: R  112 ILE cc_start: 0.7579 (mm) cc_final: 0.7274 (tt)
  outliers start: 13
  outliers final: 10
  residues processed: 158
  average time/residue: 0.2153
  time to fit residues: 43.5485
Evaluate side-chains
  150 residues out of total 803 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 140
  time to evaluate  : 0.707 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   51 SER
Chi-restraints excluded: chain A residue   60 MET
Chi-restraints excluded: chain A residue  248 VAL
Chi-restraints excluded: chain A residue  349 SER
Chi-restraints excluded: chain A residue  358 ILE
Chi-restraints excluded: chain B residue  221 THR
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  296 VAL
Chi-restraints excluded: chain R residue  216 ILE
Chi-restraints excluded: chain R residue  347 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 16 optimal weight:    6.9990
   chunk 82 optimal weight:    0.4980
   chunk 66 optimal weight:    3.9990
   chunk 67 optimal weight:    0.8980
   chunk 28 optimal weight:    3.9990
   chunk 86 optimal weight:    0.6980
   chunk 37 optimal weight:    1.9990
   chunk 24 optimal weight:    6.9990
   chunk 59 optimal weight:    0.7980
   chunk 75 optimal weight:    0.6980
   chunk 85 optimal weight:    0.5980
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
B 340 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3797 r_free = 0.3797 target = 0.138092 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3482 r_free = 0.3482 target = 0.114784 restraints weight = 10298.803|
|-----------------------------------------------------------------------------|
r_work (start): 0.3472 rms_B_bonded: 2.56
r_work: 0.3355 rms_B_bonded: 2.85 restraints_weight: 0.5000
r_work: 0.3184 rms_B_bonded: 4.92 restraints_weight: 0.2500
r_work (final): 0.3184
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7485
moved from start:          0.1247

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   7162  Z= 0.167
  Angle     :  0.581   6.598   9762  Z= 0.314
  Chirality :  0.044   0.162   1154
  Planarity :  0.004   0.061   1232
  Dihedral  :  4.467  24.448    989
  Min Nonbonded Distance : 2.578

Molprobity Statistics.
  All-atom Clashscore : 4.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.28 %
    Favored  : 96.72 %
  Rotamer:
    Outliers :  2.35 %
    Allowed  :  9.25 %
    Favored  : 88.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.58 (0.28), residues: 915
  helix:  1.63 (0.26), residues: 391
  sheet:  0.21 (0.37), residues: 196
  loop : -1.01 (0.33), residues: 328

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.002   TRP B  82 
 HIS   0.003   0.001   HIS R 310 
 PHE   0.019   0.002   PHE R  77 
 TYR   0.019   0.002   TYR R 296 
 ARG   0.003   0.000   ARG A 265 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.07188 (  358)
  hydrogen bonds       : angle       4.09975 ( 1032)
  SS BOND              : bond        0.00074 (    1)
  SS BOND              : angle       3.23054 (    2)
  covalent geometry    : bond        0.00372 ( 7161)
  covalent geometry    : angle       0.57947 ( 9760)

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

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

  1830 Ramachandran restraints generated.
    915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1830 Ramachandran restraints generated.
    915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  169 residues out of total 803 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 152
  time to evaluate  : 0.709 
Fit side-chains
REVERT: A   41 LEU cc_start: 0.8245 (mt) cc_final: 0.8042 (mt)
REVERT: A  252 ASP cc_start: 0.7860 (t70) cc_final: 0.7325 (t70)
REVERT: A  381 ASP cc_start: 0.8448 (t70) cc_final: 0.8136 (t70)
REVERT: R  112 ILE cc_start: 0.7659 (mm) cc_final: 0.7277 (tt)
REVERT: R  295 MET cc_start: 0.8064 (mmm) cc_final: 0.7748 (mmm)
  outliers start: 17
  outliers final: 13
  residues processed: 161
  average time/residue: 0.2190
  time to fit residues: 45.5948
Evaluate side-chains
  159 residues out of total 803 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 146
  time to evaluate  : 0.835 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   51 SER
Chi-restraints excluded: chain A residue   54 SER
Chi-restraints excluded: chain A residue  248 VAL
Chi-restraints excluded: chain A residue  286 SER
Chi-restraints excluded: chain A residue  349 SER
Chi-restraints excluded: chain A residue  358 ILE
Chi-restraints excluded: chain B residue  221 THR
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  294 CYS
Chi-restraints excluded: chain B residue  296 VAL
Chi-restraints excluded: chain R residue  216 ILE
Chi-restraints excluded: chain R residue  276 GLU
Chi-restraints excluded: chain R residue  347 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 33 optimal weight:    0.9980
   chunk 85 optimal weight:    0.5980
   chunk 52 optimal weight:    0.8980
   chunk 5 optimal weight:    0.2980
   chunk 37 optimal weight:    0.6980
   chunk 9 optimal weight:    0.9990
   chunk 56 optimal weight:    8.9990
   chunk 47 optimal weight:    2.9990
   chunk 51 optimal weight:    0.8980
   chunk 54 optimal weight:    0.9990
   chunk 14 optimal weight:    1.9990
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
A 213 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3802 r_free = 0.3802 target = 0.139216 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3487 r_free = 0.3487 target = 0.115774 restraints weight = 10382.363|
|-----------------------------------------------------------------------------|
r_work (start): 0.3474 rms_B_bonded: 2.65
r_work: 0.3353 rms_B_bonded: 2.94 restraints_weight: 0.5000
r_work (final): 0.3353
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7374
moved from start:          0.1462

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   7162  Z= 0.167
  Angle     :  0.572   6.650   9762  Z= 0.309
  Chirality :  0.044   0.161   1154
  Planarity :  0.004   0.060   1232
  Dihedral  :  4.379  24.413    989
  Min Nonbonded Distance : 2.601

Molprobity Statistics.
  All-atom Clashscore : 3.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.39 %
    Favored  : 96.61 %
  Rotamer:
    Outliers :  3.18 %
    Allowed  : 10.22 %
    Favored  : 86.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.71 (0.28), residues: 915
  helix:  1.82 (0.27), residues: 391
  sheet:  0.27 (0.37), residues: 196
  loop : -1.04 (0.33), residues: 328

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.002   TRP B  82 
 HIS   0.003   0.001   HIS R 310 
 PHE   0.019   0.002   PHE B 199 
 TYR   0.019   0.002   TYR R 296 
 ARG   0.002   0.000   ARG B 150 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.07114 (  358)
  hydrogen bonds       : angle       4.03111 ( 1032)
  SS BOND              : bond        0.00200 (    1)
  SS BOND              : angle       3.36093 (    2)
  covalent geometry    : bond        0.00373 ( 7161)
  covalent geometry    : angle       0.56984 ( 9760)

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

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

  1830 Ramachandran restraints generated.
    915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1830 Ramachandran restraints generated.
    915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  171 residues out of total 803 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 148
  time to evaluate  : 0.860 
Fit side-chains
REVERT: A   41 LEU cc_start: 0.8225 (mt) cc_final: 0.8021 (mt)
REVERT: A  252 ASP cc_start: 0.7699 (t70) cc_final: 0.7240 (t70)
REVERT: A  381 ASP cc_start: 0.8333 (t70) cc_final: 0.8023 (t70)
REVERT: R  112 ILE cc_start: 0.7554 (mm) cc_final: 0.7254 (tt)
  outliers start: 23
  outliers final: 18
  residues processed: 160
  average time/residue: 0.2099
  time to fit residues: 43.6492
Evaluate side-chains
  166 residues out of total 803 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 148
  time to evaluate  : 0.766 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   51 SER
Chi-restraints excluded: chain A residue   54 SER
Chi-restraints excluded: chain A residue   60 MET
Chi-restraints excluded: chain A residue  248 VAL
Chi-restraints excluded: chain A residue  349 SER
Chi-restraints excluded: chain A residue  358 ILE
Chi-restraints excluded: chain B residue  221 THR
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  294 CYS
Chi-restraints excluded: chain B residue  296 VAL
Chi-restraints excluded: chain B residue  300 LEU
Chi-restraints excluded: chain R residue  136 ILE
Chi-restraints excluded: chain R residue  216 ILE
Chi-restraints excluded: chain R residue  235 LEU
Chi-restraints excluded: chain R residue  244 LEU
Chi-restraints excluded: chain R residue  276 GLU
Chi-restraints excluded: chain R residue  298 ILE
Chi-restraints excluded: chain R residue  347 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 77 optimal weight:    0.0000
   chunk 65 optimal weight:    0.9990
   chunk 76 optimal weight:    0.0980
   chunk 63 optimal weight:    0.9980
   chunk 15 optimal weight:    1.9990
   chunk 10 optimal weight:    0.9980
   chunk 53 optimal weight:    0.0050
   chunk 30 optimal weight:    1.9990
   chunk 66 optimal weight:    0.7980
   chunk 43 optimal weight:    0.8980
   chunk 3 optimal weight:    0.6980
   overall best weight:    0.3198

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

Flipped N/Q/H residues before XYZ refinement:
B 230 ASN
B 340 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3842 r_free = 0.3842 target = 0.142045 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3538 r_free = 0.3538 target = 0.118909 restraints weight = 10232.179|
|-----------------------------------------------------------------------------|
r_work (start): 0.3522 rms_B_bonded: 2.52
r_work: 0.3409 rms_B_bonded: 2.82 restraints_weight: 0.5000
r_work: 0.3243 rms_B_bonded: 4.87 restraints_weight: 0.2500
r_work (final): 0.3243
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7408
moved from start:          0.1854

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033   7162  Z= 0.116
  Angle     :  0.517   7.282   9762  Z= 0.278
  Chirality :  0.043   0.165   1154
  Planarity :  0.004   0.059   1232
  Dihedral  :  4.051  21.334    989
  Min Nonbonded Distance : 2.611

Molprobity Statistics.
  All-atom Clashscore : 3.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.51 %
    Favored  : 97.49 %
  Rotamer:
    Outliers :  2.49 %
    Allowed  : 12.29 %
    Favored  : 85.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.04 (0.29), residues: 915
  helix:  2.12 (0.27), residues: 393
  sheet:  0.45 (0.38), residues: 196
  loop : -0.94 (0.33), residues: 326

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.001   TRP B  82 
 HIS   0.004   0.001   HIS R 310 
 PHE   0.017   0.001   PHE R  77 
 TYR   0.011   0.001   TYR R 296 
 ARG   0.002   0.000   ARG A 265 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05553 (  358)
  hydrogen bonds       : angle       3.79096 ( 1032)
  SS BOND              : bond        0.00342 (    1)
  SS BOND              : angle       3.64279 (    2)
  covalent geometry    : bond        0.00235 ( 7161)
  covalent geometry    : angle       0.51402 ( 9760)

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

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

  1830 Ramachandran restraints generated.
    915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1830 Ramachandran restraints generated.
    915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  170 residues out of total 803 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 152
  time to evaluate  : 0.769 
Fit side-chains
REVERT: A  252 ASP cc_start: 0.7666 (t70) cc_final: 0.7222 (t70)
REVERT: A  344 GLU cc_start: 0.7855 (mm-30) cc_final: 0.7374 (tm-30)
REVERT: A  381 ASP cc_start: 0.8417 (t70) cc_final: 0.8098 (t70)
REVERT: B  199 PHE cc_start: 0.7952 (p90) cc_final: 0.7668 (p90)
REVERT: R  295 MET cc_start: 0.7938 (mmm) cc_final: 0.7683 (mmm)
REVERT: R  307 LEU cc_start: 0.8292 (tp) cc_final: 0.7950 (tt)
  outliers start: 18
  outliers final: 12
  residues processed: 160
  average time/residue: 0.2112
  time to fit residues: 43.8470
Evaluate side-chains
  160 residues out of total 803 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 148
  time to evaluate  : 0.765 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   60 MET
Chi-restraints excluded: chain A residue  286 SER
Chi-restraints excluded: chain A residue  349 SER
Chi-restraints excluded: chain A residue  358 ILE
Chi-restraints excluded: chain B residue   40 VAL
Chi-restraints excluded: chain B residue  221 THR
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  294 CYS
Chi-restraints excluded: chain B residue  296 VAL
Chi-restraints excluded: chain R residue  216 ILE
Chi-restraints excluded: chain R residue  235 LEU
Chi-restraints excluded: chain R residue  347 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 50 optimal weight:    1.9990
   chunk 78 optimal weight:    2.9990
   chunk 6 optimal weight:    1.9990
   chunk 16 optimal weight:    0.7980
   chunk 3 optimal weight:    0.5980
   chunk 35 optimal weight:    1.9990
   chunk 49 optimal weight:    2.9990
   chunk 76 optimal weight:    0.0670
   chunk 77 optimal weight:    0.5980
   chunk 56 optimal weight:   20.0000
   chunk 80 optimal weight:    0.7980
   overall best weight:    0.5718

-------------------------------------------------------------------------------
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 = 0.3818 r_free = 0.3818 target = 0.140147 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3506 r_free = 0.3506 target = 0.116922 restraints weight = 10283.618|
|-----------------------------------------------------------------------------|
r_work (start): 0.3495 rms_B_bonded: 2.56
r_work: 0.3381 rms_B_bonded: 2.84 restraints_weight: 0.5000
r_work: 0.3212 rms_B_bonded: 4.91 restraints_weight: 0.2500
r_work (final): 0.3212
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7462
moved from start:          0.1829

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   7162  Z= 0.146
  Angle     :  0.542   6.765   9762  Z= 0.292
  Chirality :  0.043   0.154   1154
  Planarity :  0.004   0.058   1232
  Dihedral  :  4.107  23.248    989
  Min Nonbonded Distance : 2.562

Molprobity Statistics.
  All-atom Clashscore : 3.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.72 %
    Favored  : 96.28 %
  Rotamer:
    Outliers :  2.49 %
    Allowed  : 14.64 %
    Favored  : 82.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.03 (0.29), residues: 915
  helix:  2.15 (0.27), residues: 391
  sheet:  0.43 (0.38), residues: 196
  loop : -0.99 (0.33), residues: 328

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP B  82 
 HIS   0.004   0.001   HIS R 310 
 PHE   0.018   0.002   PHE B 199 
 TYR   0.017   0.002   TYR R 296 
 ARG   0.001   0.000   ARG B 150 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06446 (  358)
  hydrogen bonds       : angle       3.86155 ( 1032)
  SS BOND              : bond        0.00266 (    1)
  SS BOND              : angle       3.17678 (    2)
  covalent geometry    : bond        0.00324 ( 7161)
  covalent geometry    : angle       0.53970 ( 9760)

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

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

  1830 Ramachandran restraints generated.
    915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1830 Ramachandran restraints generated.
    915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  167 residues out of total 803 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 149
  time to evaluate  : 0.714 
Fit side-chains
REVERT: A  252 ASP cc_start: 0.7669 (t70) cc_final: 0.7240 (t70)
REVERT: A  344 GLU cc_start: 0.7898 (mm-30) cc_final: 0.7409 (tm-30)
REVERT: A  381 ASP cc_start: 0.8424 (t70) cc_final: 0.8131 (t70)
REVERT: B  199 PHE cc_start: 0.8032 (p90) cc_final: 0.7713 (p90)
REVERT: R  203 LEU cc_start: 0.8235 (OUTLIER) cc_final: 0.7935 (mp)
REVERT: R  295 MET cc_start: 0.7982 (mmm) cc_final: 0.7663 (mmm)
  outliers start: 18
  outliers final: 15
  residues processed: 158
  average time/residue: 0.2278
  time to fit residues: 46.2630
Evaluate side-chains
  161 residues out of total 803 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 145
  time to evaluate  : 0.822 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   51 SER
Chi-restraints excluded: chain A residue   54 SER
Chi-restraints excluded: chain A residue   60 MET
Chi-restraints excluded: chain A residue  286 SER
Chi-restraints excluded: chain A residue  349 SER
Chi-restraints excluded: chain A residue  358 ILE
Chi-restraints excluded: chain B residue  221 THR
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  294 CYS
Chi-restraints excluded: chain B residue  296 VAL
Chi-restraints excluded: chain B residue  300 LEU
Chi-restraints excluded: chain R residue  203 LEU
Chi-restraints excluded: chain R residue  216 ILE
Chi-restraints excluded: chain R residue  235 LEU
Chi-restraints excluded: chain R residue  244 LEU
Chi-restraints excluded: chain R residue  347 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 61 optimal weight:    0.8980
   chunk 81 optimal weight:    0.8980
   chunk 33 optimal weight:    0.0020
   chunk 39 optimal weight:    0.9990
   chunk 88 optimal weight:    0.9980
   chunk 84 optimal weight:    0.3980
   chunk 4 optimal weight:    0.5980
   chunk 58 optimal weight:    0.9990
   chunk 26 optimal weight:    0.8980
   chunk 15 optimal weight:    0.8980
   chunk 43 optimal weight:    2.9990
   overall best weight:    0.5588

-------------------------------------------------------------------------------
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 = 0.3822 r_free = 0.3822 target = 0.140530 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3511 r_free = 0.3511 target = 0.117322 restraints weight = 10199.172|
|-----------------------------------------------------------------------------|
r_work (start): 0.3496 rms_B_bonded: 2.61
r_work: 0.3374 rms_B_bonded: 2.93 restraints_weight: 0.5000
r_work (final): 0.3374
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7361
moved from start:          0.1902

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   7162  Z= 0.145
  Angle     :  0.541   8.116   9762  Z= 0.292
  Chirality :  0.043   0.157   1154
  Planarity :  0.004   0.058   1232
  Dihedral  :  4.099  23.594    989
  Min Nonbonded Distance : 2.562

Molprobity Statistics.
  All-atom Clashscore : 3.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.39 %
    Favored  : 96.61 %
  Rotamer:
    Outliers :  2.76 %
    Allowed  : 14.64 %
    Favored  : 82.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.03 (0.29), residues: 915
  helix:  2.14 (0.27), residues: 391
  sheet:  0.44 (0.38), residues: 196
  loop : -0.98 (0.33), residues: 328

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.001   TRP B  82 
 HIS   0.004   0.001   HIS R 310 
 PHE   0.017   0.002   PHE B 199 
 TYR   0.016   0.002   TYR R 296 
 ARG   0.002   0.000   ARG B 283 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06359 (  358)
  hydrogen bonds       : angle       3.86758 ( 1032)
  SS BOND              : bond        0.00139 (    1)
  SS BOND              : angle       3.93148 (    2)
  covalent geometry    : bond        0.00320 ( 7161)
  covalent geometry    : angle       0.53852 ( 9760)

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

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

  1830 Ramachandran restraints generated.
    915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1830 Ramachandran restraints generated.
    915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  169 residues out of total 803 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 149
  time to evaluate  : 0.731 
Fit side-chains
REVERT: A  252 ASP cc_start: 0.7506 (t70) cc_final: 0.7100 (t70)
REVERT: A  344 GLU cc_start: 0.7811 (mm-30) cc_final: 0.7310 (tm-30)
REVERT: A  381 ASP cc_start: 0.8305 (t70) cc_final: 0.7996 (t70)
REVERT: B  199 PHE cc_start: 0.7925 (p90) cc_final: 0.7618 (p90)
REVERT: R  127 TRP cc_start: 0.8192 (OUTLIER) cc_final: 0.7372 (m-90)
REVERT: R  295 MET cc_start: 0.7905 (mmm) cc_final: 0.7594 (mmm)
REVERT: R  307 LEU cc_start: 0.8243 (tp) cc_final: 0.7871 (tt)
  outliers start: 20
  outliers final: 17
  residues processed: 161
  average time/residue: 0.2147
  time to fit residues: 44.7714
Evaluate side-chains
  164 residues out of total 803 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 146
  time to evaluate  : 0.720 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   54 SER
Chi-restraints excluded: chain A residue   60 MET
Chi-restraints excluded: chain A residue  286 SER
Chi-restraints excluded: chain A residue  306 SER
Chi-restraints excluded: chain A residue  349 SER
Chi-restraints excluded: chain A residue  358 ILE
Chi-restraints excluded: chain B residue  221 THR
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  294 CYS
Chi-restraints excluded: chain B residue  296 VAL
Chi-restraints excluded: chain B residue  300 LEU
Chi-restraints excluded: chain R residue  127 TRP
Chi-restraints excluded: chain R residue  216 ILE
Chi-restraints excluded: chain R residue  235 LEU
Chi-restraints excluded: chain R residue  244 LEU
Chi-restraints excluded: chain R residue  276 GLU
Chi-restraints excluded: chain R residue  298 ILE
Chi-restraints excluded: chain R residue  347 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 62 optimal weight:    0.8980
   chunk 66 optimal weight:    1.9990
   chunk 83 optimal weight:    0.6980
   chunk 70 optimal weight:    0.7980
   chunk 30 optimal weight:    0.7980
   chunk 12 optimal weight:    0.9990
   chunk 2 optimal weight:    1.9990
   chunk 29 optimal weight:    0.9980
   chunk 4 optimal weight:    0.3980
   chunk 49 optimal weight:    2.9990
   chunk 89 optimal weight:    0.9980
   overall best weight:    0.7180

-------------------------------------------------------------------------------
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 = 0.3803 r_free = 0.3803 target = 0.138822 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3485 r_free = 0.3485 target = 0.115414 restraints weight = 10300.739|
|-----------------------------------------------------------------------------|
r_work (start): 0.3479 rms_B_bonded: 2.59
r_work: 0.3361 rms_B_bonded: 2.87 restraints_weight: 0.5000
r_work: 0.3189 rms_B_bonded: 4.96 restraints_weight: 0.2500
r_work (final): 0.3189
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7489
moved from start:          0.1891

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   7162  Z= 0.171
  Angle     :  0.567   7.972   9762  Z= 0.305
  Chirality :  0.044   0.156   1154
  Planarity :  0.004   0.059   1232
  Dihedral  :  4.181  24.126    989
  Min Nonbonded Distance : 2.493

Molprobity Statistics.
  All-atom Clashscore : 4.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.93 %
    Favored  : 96.07 %
  Rotamer:
    Outliers :  3.04 %
    Allowed  : 14.09 %
    Favored  : 82.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.93 (0.28), residues: 915
  helix:  2.07 (0.27), residues: 391
  sheet:  0.35 (0.37), residues: 196
  loop : -1.01 (0.33), residues: 328

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP B  82 
 HIS   0.004   0.001   HIS R 310 
 PHE   0.020   0.002   PHE B 199 
 TYR   0.019   0.002   TYR R 296 
 ARG   0.004   0.000   ARG B 283 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06891 (  358)
  hydrogen bonds       : angle       3.97358 ( 1032)
  SS BOND              : bond        0.00371 (    1)
  SS BOND              : angle       3.51042 (    2)
  covalent geometry    : bond        0.00390 ( 7161)
  covalent geometry    : angle       0.56464 ( 9760)

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

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

  1830 Ramachandran restraints generated.
    915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1830 Ramachandran restraints generated.
    915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  173 residues out of total 803 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 151
  time to evaluate  : 0.845 
Fit side-chains
REVERT: A  252 ASP cc_start: 0.7653 (t70) cc_final: 0.7201 (t70)
REVERT: A  344 GLU cc_start: 0.7947 (mm-30) cc_final: 0.7435 (tm-30)
REVERT: R  127 TRP cc_start: 0.8271 (OUTLIER) cc_final: 0.7427 (m-90)
  outliers start: 22
  outliers final: 20
  residues processed: 162
  average time/residue: 0.2264
  time to fit residues: 47.1571
Evaluate side-chains
  169 residues out of total 803 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 148
  time to evaluate  : 0.733 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   51 SER
Chi-restraints excluded: chain A residue   54 SER
Chi-restraints excluded: chain A residue   60 MET
Chi-restraints excluded: chain A residue  286 SER
Chi-restraints excluded: chain A residue  306 SER
Chi-restraints excluded: chain A residue  349 SER
Chi-restraints excluded: chain A residue  358 ILE
Chi-restraints excluded: chain B residue  221 THR
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  294 CYS
Chi-restraints excluded: chain B residue  296 VAL
Chi-restraints excluded: chain B residue  300 LEU
Chi-restraints excluded: chain R residue  127 TRP
Chi-restraints excluded: chain R residue  203 LEU
Chi-restraints excluded: chain R residue  216 ILE
Chi-restraints excluded: chain R residue  235 LEU
Chi-restraints excluded: chain R residue  244 LEU
Chi-restraints excluded: chain R residue  270 ARG
Chi-restraints excluded: chain R residue  276 GLU
Chi-restraints excluded: chain R residue  298 ILE
Chi-restraints excluded: chain R residue  347 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 33 optimal weight:    0.0170
   chunk 30 optimal weight:    0.5980
   chunk 25 optimal weight:    5.9990
   chunk 36 optimal weight:    0.4980
   chunk 49 optimal weight:    2.9990
   chunk 78 optimal weight:    1.9990
   chunk 19 optimal weight:    0.9980
   chunk 14 optimal weight:    0.6980
   chunk 56 optimal weight:   20.0000
   chunk 74 optimal weight:    0.9980
   chunk 29 optimal weight:    0.7980
   overall best weight:    0.5218

-------------------------------------------------------------------------------
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 = 0.3820 r_free = 0.3820 target = 0.140212 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3503 r_free = 0.3503 target = 0.116672 restraints weight = 10416.177|
|-----------------------------------------------------------------------------|
r_work (start): 0.3490 rms_B_bonded: 2.62
r_work: 0.3370 rms_B_bonded: 2.91 restraints_weight: 0.5000
r_work (final): 0.3370
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7333
moved from start:          0.2041

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   7162  Z= 0.141
  Angle     :  0.542   7.789   9762  Z= 0.293
  Chirality :  0.043   0.163   1154
  Planarity :  0.004   0.060   1232
  Dihedral  :  4.078  23.197    989
  Min Nonbonded Distance : 2.535

Molprobity Statistics.
  All-atom Clashscore : 4.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.39 %
    Favored  : 96.61 %
  Rotamer:
    Outliers :  2.76 %
    Allowed  : 15.19 %
    Favored  : 82.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.01 (0.28), residues: 915
  helix:  2.14 (0.27), residues: 391
  sheet:  0.38 (0.37), residues: 200
  loop : -0.99 (0.33), residues: 324

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.001   TRP B  82 
 HIS   0.004   0.001   HIS R 310 
 PHE   0.017   0.002   PHE B 199 
 TYR   0.016   0.001   TYR R 296 
 ARG   0.003   0.000   ARG B 283 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06221 (  358)
  hydrogen bonds       : angle       3.89011 ( 1032)
  SS BOND              : bond        0.00258 (    1)
  SS BOND              : angle       3.65578 (    2)
  covalent geometry    : bond        0.00311 ( 7161)
  covalent geometry    : angle       0.53978 ( 9760)

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

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

  1830 Ramachandran restraints generated.
    915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1830 Ramachandran restraints generated.
    915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  167 residues out of total 803 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 147
  time to evaluate  : 0.765 
Fit side-chains
REVERT: A  252 ASP cc_start: 0.7493 (t70) cc_final: 0.7058 (t70)
REVERT: A  344 GLU cc_start: 0.7786 (mm-30) cc_final: 0.7281 (tm-30)
REVERT: A  381 ASP cc_start: 0.8283 (t70) cc_final: 0.7972 (t70)
REVERT: R  127 TRP cc_start: 0.8187 (OUTLIER) cc_final: 0.7369 (m-90)
REVERT: R  295 MET cc_start: 0.7894 (mmm) cc_final: 0.7576 (mmm)
REVERT: R  307 LEU cc_start: 0.8184 (tp) cc_final: 0.7822 (tt)
  outliers start: 20
  outliers final: 18
  residues processed: 157
  average time/residue: 0.2242
  time to fit residues: 45.5330
Evaluate side-chains
  167 residues out of total 803 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 148
  time to evaluate  : 0.762 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   51 SER
Chi-restraints excluded: chain A residue   54 SER
Chi-restraints excluded: chain A residue   60 MET
Chi-restraints excluded: chain A residue  286 SER
Chi-restraints excluded: chain A residue  306 SER
Chi-restraints excluded: chain A residue  349 SER
Chi-restraints excluded: chain A residue  358 ILE
Chi-restraints excluded: chain B residue  221 THR
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  294 CYS
Chi-restraints excluded: chain B residue  296 VAL
Chi-restraints excluded: chain B residue  300 LEU
Chi-restraints excluded: chain R residue  127 TRP
Chi-restraints excluded: chain R residue  216 ILE
Chi-restraints excluded: chain R residue  235 LEU
Chi-restraints excluded: chain R residue  244 LEU
Chi-restraints excluded: chain R residue  276 GLU
Chi-restraints excluded: chain R residue  298 ILE
Chi-restraints excluded: chain R residue  347 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 81 optimal weight:    0.8980
   chunk 40 optimal weight:    0.6980
   chunk 34 optimal weight:    0.8980
   chunk 24 optimal weight:    0.9980
   chunk 55 optimal weight:    5.9990
   chunk 43 optimal weight:    2.9990
   chunk 21 optimal weight:    0.9990
   chunk 19 optimal weight:    0.0570
   chunk 7 optimal weight:    1.9990
   chunk 86 optimal weight:    0.2980
   chunk 36 optimal weight:    5.9990
   overall best weight:    0.5698

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

Flipped N/Q/H residues before XYZ refinement:
** A 220 HIS ** 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 = 0.3805 r_free = 0.3805 target = 0.138861 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3487 r_free = 0.3487 target = 0.115402 restraints weight = 10460.674|
|-----------------------------------------------------------------------------|
r_work (start): 0.3493 rms_B_bonded: 2.60
r_work: 0.3377 rms_B_bonded: 2.87 restraints_weight: 0.5000
r_work: 0.3205 rms_B_bonded: 4.97 restraints_weight: 0.2500
r_work (final): 0.3205
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7474
moved from start:          0.2052

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   7162  Z= 0.149
  Angle     :  0.557   7.756   9762  Z= 0.300
  Chirality :  0.044   0.160   1154
  Planarity :  0.004   0.060   1232
  Dihedral  :  4.084  22.647    989
  Min Nonbonded Distance : 2.531

Molprobity Statistics.
  All-atom Clashscore : 4.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.93 %
    Favored  : 96.07 %
  Rotamer:
    Outliers :  2.76 %
    Allowed  : 15.61 %
    Favored  : 81.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.96 (0.28), residues: 915
  helix:  2.12 (0.27), residues: 391
  sheet:  0.30 (0.37), residues: 198
  loop : -1.00 (0.33), residues: 326

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.001   TRP B  82 
 HIS   0.004   0.001   HIS R 310 
 PHE   0.016   0.002   PHE A 212 
 TYR   0.016   0.002   TYR R 296 
 ARG   0.001   0.000   ARG B 150 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06406 (  358)
  hydrogen bonds       : angle       3.91819 ( 1032)
  SS BOND              : bond        0.00309 (    1)
  SS BOND              : angle       3.57610 (    2)
  covalent geometry    : bond        0.00332 ( 7161)
  covalent geometry    : angle       0.55425 ( 9760)

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

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

  1830 Ramachandran restraints generated.
    915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1830 Ramachandran restraints generated.
    915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  165 residues out of total 803 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 145
  time to evaluate  : 0.709 
Fit side-chains
REVERT: A  211 LYS cc_start: 0.8336 (mtpp) cc_final: 0.8066 (mmtt)
REVERT: A  252 ASP cc_start: 0.7660 (t70) cc_final: 0.7253 (t70)
REVERT: A  344 GLU cc_start: 0.7915 (mm-30) cc_final: 0.7420 (tm-30)
REVERT: A  381 ASP cc_start: 0.8419 (t70) cc_final: 0.8137 (t70)
REVERT: R  127 TRP cc_start: 0.8295 (OUTLIER) cc_final: 0.7446 (m-90)
REVERT: R  295 MET cc_start: 0.7967 (mmm) cc_final: 0.7630 (mmm)
REVERT: R  307 LEU cc_start: 0.8326 (tp) cc_final: 0.7958 (tt)
  outliers start: 20
  outliers final: 18
  residues processed: 155
  average time/residue: 0.2138
  time to fit residues: 42.6559
Evaluate side-chains
  165 residues out of total 803 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 146
  time to evaluate  : 0.700 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   51 SER
Chi-restraints excluded: chain A residue   54 SER
Chi-restraints excluded: chain A residue   60 MET
Chi-restraints excluded: chain A residue  286 SER
Chi-restraints excluded: chain A residue  306 SER
Chi-restraints excluded: chain A residue  349 SER
Chi-restraints excluded: chain A residue  358 ILE
Chi-restraints excluded: chain B residue  221 THR
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  294 CYS
Chi-restraints excluded: chain B residue  296 VAL
Chi-restraints excluded: chain B residue  300 LEU
Chi-restraints excluded: chain R residue  127 TRP
Chi-restraints excluded: chain R residue  216 ILE
Chi-restraints excluded: chain R residue  235 LEU
Chi-restraints excluded: chain R residue  244 LEU
Chi-restraints excluded: chain R residue  276 GLU
Chi-restraints excluded: chain R residue  298 ILE
Chi-restraints excluded: chain R residue  347 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 8 optimal weight:    1.9990
   chunk 13 optimal weight:    0.8980
   chunk 38 optimal weight:    0.7980
   chunk 9 optimal weight:    0.9980
   chunk 36 optimal weight:    4.9990
   chunk 58 optimal weight:    0.9990
   chunk 15 optimal weight:    0.7980
   chunk 50 optimal weight:    1.9990
   chunk 73 optimal weight:    0.9980
   chunk 25 optimal weight:    4.9990
   chunk 10 optimal weight:    0.9990
   overall best weight:    0.8980

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

Flipped N/Q/H residues before XYZ refinement:
** A 220 HIS ** 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 = 0.3790 r_free = 0.3790 target = 0.137888 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3471 r_free = 0.3471 target = 0.114469 restraints weight = 10370.480|
|-----------------------------------------------------------------------------|
r_work (start): 0.3457 rms_B_bonded: 2.64
r_work: 0.3332 rms_B_bonded: 2.92 restraints_weight: 0.5000
r_work (final): 0.3332
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7392
moved from start:          0.1956

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.037   7162  Z= 0.201
  Angle     :  0.601   8.274   9762  Z= 0.324
  Chirality :  0.045   0.159   1154
  Planarity :  0.004   0.062   1232
  Dihedral  :  4.290  24.360    989
  Min Nonbonded Distance : 2.528

Molprobity Statistics.
  All-atom Clashscore : 4.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.70 %
    Favored  : 95.30 %
  Rotamer:
    Outliers :  2.76 %
    Allowed  : 15.33 %
    Favored  : 81.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.76 (0.28), residues: 915
  helix:  1.95 (0.27), residues: 391
  sheet:  0.21 (0.36), residues: 195
  loop : -1.09 (0.33), residues: 329

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.002   TRP B  82 
 HIS   0.004   0.001   HIS A 220 
 PHE   0.023   0.002   PHE R  77 
 TYR   0.023   0.002   TYR R 296 
 ARG   0.002   0.000   ARG B 150 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.07493 (  358)
  hydrogen bonds       : angle       4.08102 ( 1032)
  SS BOND              : bond        0.00375 (    1)
  SS BOND              : angle       3.58364 (    2)
  covalent geometry    : bond        0.00466 ( 7161)
  covalent geometry    : angle       0.59879 ( 9760)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3974.68 seconds
wall clock time: 68 minutes 49.30 seconds (4129.30 seconds total)