Starting phenix.real_space_refine
on Mon Nov 17 17:17:54 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6ddf_7869/11_2025/6ddf_7869_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6ddf_7869/11_2025/6ddf_7869.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.5
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/6ddf_7869/11_2025/6ddf_7869_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6ddf_7869/11_2025/6ddf_7869_neut.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/6ddf_7869/11_2025/6ddf_7869.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6ddf_7869/11_2025/6ddf_7869.map"
  }
  resolution = 3.5
  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=   0.021 sd=   0.567
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      52      5.16       5
     C    4342      2.51       5
     N    1165      2.21       5
     O    1249      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 12 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 6808
  Number of models: 1
  Model: ""
    Number of chains: 7
    Chain: "A"
      Number of atoms: 1694
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 217, 1694
          Classifications: {'peptide': 217}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 17}
          Link IDs: {'PTRANS': 2, 'TRANS': 214}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 57
          Unresolved non-hydrogen angles: 70
          Unresolved non-hydrogen dihedrals: 44
          Unresolved non-hydrogen chiralities: 4
          Planarities with less than four sites: {'GLU:plan': 6, 'ASN:plan1': 1, 'ASP:plan': 2}
          Unresolved non-hydrogen planarities: 33
    Chain: "B"
      Number of atoms: 2547
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 336, 2547
          Classifications: {'peptide': 336}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 12}
          Link IDs: {'PTRANS': 5, 'TRANS': 330}
          Unresolved non-hydrogen bonds: 37
          Unresolved non-hydrogen angles: 42
          Unresolved non-hydrogen dihedrals: 32
          Planarities with less than four sites: {'ARG:plan': 2, 'GLU:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 20
    Chain: "C"
      Number of atoms: 396
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 53, 396
          Classifications: {'peptide': 53}
          Incomplete info: {'truncation_to_alanine': 4}
          Link IDs: {'PTRANS': 4, 'TRANS': 48}
          Unresolved non-hydrogen bonds: 11
          Unresolved non-hydrogen angles: 14
          Unresolved non-hydrogen dihedrals: 8
          Planarities with less than four sites: {'ASP:plan': 2, 'GLU:plan': 1}
          Unresolved non-hydrogen planarities: 10
    Chain: "R"
      Number of atoms: 2134
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 281, 2134
          Classifications: {'peptide': 281}
          Incomplete info: {'truncation_to_alanine': 39}
          Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 270}
          Unresolved non-hydrogen bonds: 124
          Unresolved non-hydrogen angles: 154
          Unresolved non-hydrogen dihedrals: 100
          Unresolved non-hydrogen chiralities: 18
          Planarities with less than four sites: {'ARG:plan': 2, 'ASP:plan': 1, 'ASN:plan1': 2, 'GLN:plan1': 1, 'PHE:plan': 3}
          Unresolved non-hydrogen planarities: 41
    Chain: "D"
      Number of atoms: 12
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 12
          Classifications: {'peptide': 1}
    Chain: "D"
      Number of atoms: 21
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 21
          Classifications: {'peptide': 3}
          Modifications used: {'PEPT-D': 1}
          Link IDs: {'TRANS': 2}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Planarities with less than four sites: {'MEA:plan-2': 1}
          Unresolved non-hydrogen planarities: 1
    Chain: "D"
      Number of atoms: 4
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 4
          Unusual residues: {'ETA': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 1.71, per 1000 atoms: 0.25
  Number of scatterers: 6808
  At special positions: 0
  Unit cell: (76.96, 118.56, 112.32, 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      52     16.00
     O    1249      8.00
     N    1165      7.00
     C    4342      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS R 140 " - pdb=" SG  CYS R 217 " 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=1, symmetry=0
  Links applied
    TRANS
      " DAL D   2 " - " TYR D   1 "
  Number of additional bonds: simple=1, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 0.58
  Conformation dependent library (CDL) restraints added in 404.6 milliseconds
  

  1750 Ramachandran restraints generated.
    875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
    Skipped
      Input residue name is d-peptide
        pdb=" CB  DAL D   2 "
  Number of C-beta restraints generated:  1686

  Finding SS restraints...
    Secondary structure from input PDB file:
      23 helices and 10 sheets defined
      40.9% alpha, 14.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.19
  Creating SS restraints...
    Processing helix  chain 'A' and resid 8 through 32
      removed outlier: 4.094A  pdb=" N   ALA A  12 " --> pdb=" O   GLU A   8 " (cutoff:3.500A)
      removed outlier: 3.711A  pdb=" N   ASP A  20 " --> pdb=" O   SER A  16 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 47 through 51
      removed outlier: 3.560A  pdb=" N   VAL A  50 " --> pdb=" O   SER A  47 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 207 through 216
      removed outlier: 3.545A  pdb=" N   LYS A 210 " --> pdb=" O   GLU A 207 " (cutoff:3.500A)
      removed outlier: 3.554A  pdb=" N   TRP A 211 " --> pdb=" O   ARG A 208 " (cutoff:3.500A)
      removed outlier: 4.029A  pdb=" N   ILE A 212 " --> pdb=" O   LYS A 209 " (cutoff:3.500A)
      removed outlier: 5.815A  pdb=" N   HIS A 213 " --> pdb=" O   LYS A 210 " (cutoff:3.500A)
      removed outlier: 3.905A  pdb=" N   GLU A 216 " --> pdb=" O   HIS A 213 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 242 through 255
    Processing helix  chain 'A' and resid 270 through 278
      removed outlier: 5.163A  pdb=" N   GLU A 276 " --> pdb=" O   ASP A 272 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 298 through 309
      removed outlier: 3.834A  pdb=" N   ILE A 303 " --> pdb=" O   ALA A 299 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 330 through 351
      removed outlier: 3.720A  pdb=" N   LYS A 345 " --> pdb=" O   ASP A 341 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 6 through 25
      removed outlier: 3.601A  pdb=" N   ASP B  20 " --> pdb=" O   ASN B  16 " (cutoff:3.500A)
      removed outlier: 3.918A  pdb=" N   ARG B  22 " --> pdb=" O   ILE B  18 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 11 through 24
      removed outlier: 4.323A  pdb=" N   ASN C  24 " --> pdb=" O   LYS C  20 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 34 through 43
      removed outlier: 3.672A  pdb=" N   CYS C  41 " --> pdb=" O   LEU C  37 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 70 through 97
      removed outlier: 3.768A  pdb=" N   LEU R  74 " --> pdb=" O   THR R  70 " (cutoff:3.500A)
      removed outlier: 4.500A  pdb=" N   VAL R  78 " --> pdb=" O   LEU R  74 " (cutoff:3.500A)
      removed outlier: 4.265A  pdb=" N   CYS R  79 " --> pdb=" O   TYR R  75 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 101 through 121
      removed outlier: 3.999A  pdb=" N   ILE R 105 " --> pdb=" O   THR R 101 " (cutoff:3.500A)
      removed outlier: 3.598A  pdb=" N   TYR R 106 " --> pdb=" O   ALA R 102 " (cutoff:3.500A)
      removed outlier: 3.753A  pdb=" N   ALA R 117 " --> pdb=" O   ALA R 113 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 121 through 130
      removed outlier: 3.627A  pdb=" N   SER R 125 " --> pdb=" O   LEU R 121 " (cutoff:3.500A)
      removed outlier: 3.649A  pdb=" N   VAL R 126 " --> pdb=" O   PRO R 122 " (cutoff:3.500A)
      removed outlier: 4.473A  pdb=" N   ASN R 127 " --> pdb=" O   PHE R 123 " (cutoff:3.500A)
      removed outlier: 4.483A  pdb=" N   TYR R 128 " --> pdb=" O   GLN R 124 " (cutoff:3.500A)
      removed outlier: 4.008A  pdb=" N   LEU R 129 " --> pdb=" O   SER R 125 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 136 through 171
      removed outlier: 3.795A  pdb=" N   CYS R 140 " --> pdb=" O   GLY R 136 " (cutoff:3.500A)
      removed outlier: 4.238A  pdb=" N   LYS R 141 " --> pdb=" O   ASN R 137 " (cutoff:3.500A)
      removed outlier: 5.583A  pdb=" N   ILE R 142 " --> pdb=" O   ILE R 138 " (cutoff:3.500A)
      removed outlier: 4.108A  pdb=" N   PHE R 152 " --> pdb=" O   TYR R 148 " (cutoff:3.500A)
      removed outlier: 3.634A  pdb=" N   LEU R 158 " --> pdb=" O   SER R 154 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 174 through 179
    Processing helix  chain 'R' and resid 182 through 204
      removed outlier: 3.612A  pdb=" N   ILE R 198 " --> pdb=" O   LEU R 194 " (cutoff:3.500A)
      Proline residue:  R 201  - end of helix
    Processing helix  chain 'R' and resid 229 through 241
      removed outlier: 3.956A  pdb=" N   LYS R 233 " --> pdb=" O   GLU R 229 " (cutoff:3.500A)
      removed outlier: 3.936A  pdb=" N   ILE R 234 " --> pdb=" O   ASN R 230 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 241 through 249
    Processing helix  chain 'R' and resid 249 through 260
      removed outlier: 4.254A  pdb=" N   MET R 255 " --> pdb=" O   CYS R 251 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 268 through 294
    Processing helix  chain 'R' and resid 294 through 306
      removed outlier: 3.826A  pdb=" N   VAL R 300 " --> pdb=" O   ILE R 296 " (cutoff:3.500A)
      removed outlier: 3.708A  pdb=" N   ALA R 304 " --> pdb=" O   VAL R 300 " (cutoff:3.500A)
      removed outlier: 3.528A  pdb=" N   LEU R 305 " --> pdb=" O   ILE R 301 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 313 through 326
      removed outlier: 4.027A  pdb=" N   SER R 317 " --> pdb=" O   PHE R 313 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 326 through 336
      Proline residue:  R 333  - end of helix
    Processing sheet with id=AA1, first strand: chain 'A' and resid 186 through 190
      removed outlier: 6.911A  pdb=" N   LYS A  35 " --> pdb=" O   ALA A 220 " (cutoff:3.500A)
      removed outlier: 7.751A  pdb=" N   ILE A 222 " --> pdb=" O   LYS A  35 " (cutoff:3.500A)
      removed outlier: 6.240A  pdb=" N   LEU A  37 " --> pdb=" O   ILE A 222 " (cutoff:3.500A)
      removed outlier: 7.437A  pdb=" N   CYS A 224 " --> pdb=" O   LEU A  37 " (cutoff:3.500A)
      removed outlier: 6.901A  pdb=" N   LEU A  39 " --> pdb=" O   CYS A 224 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 266 through 267
      removed outlier: 6.664A  pdb=" N   LEU A 266 " --> pdb=" O   HIS A 322 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA2
    Processing sheet with id=AA3, first strand: chain 'B' and resid 47 through 51
      removed outlier: 3.594A  pdb=" N   ARG B  49 " --> pdb=" O   ILE B 338 " (cutoff:3.500A)
      removed outlier: 3.560A  pdb=" N   LEU B 336 " --> pdb=" O   LEU B  51 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 62 through 63
      removed outlier: 3.617A  pdb=" N   HIS B  62 " --> pdb=" O   VAL B  71 " (cutoff:3.500A)
      removed outlier: 3.627A  pdb=" N   LEU B  70 " --> pdb=" O   TRP B  82 " (cutoff:3.500A)
      removed outlier: 3.615A  pdb=" N   LEU B  79 " --> pdb=" O   ILE B  93 " (cutoff:3.500A)
      removed outlier: 3.706A  pdb=" N   HIS B  91 " --> pdb=" O   ILE B  81 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 104 through 105
      removed outlier: 3.613A  pdb=" N   VAL B 112 " --> pdb=" O   TYR B 124 " (cutoff:3.500A)
      removed outlier: 6.190A  pdb=" N   CYS B 121 " --> pdb=" O   GLU B 138 " (cutoff:3.500A)
      removed outlier: 5.514A  pdb=" N   GLU B 138 " --> pdb=" O   CYS B 121 " (cutoff:3.500A)
      removed outlier: 7.283A  pdb=" N   ILE B 123 " --> pdb=" O   SER B 136 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 146 through 151
      removed outlier: 3.895A  pdb=" N   ILE B 157 " --> pdb=" O   TRP B 169 " (cutoff:3.500A)
      removed outlier: 3.775A  pdb=" N   ALA B 167 " --> pdb=" O   THR B 159 " (cutoff:3.500A)
      removed outlier: 3.688A  pdb=" N   THR B 165 " --> pdb=" O   SER B 161 " (cutoff:3.500A)
      removed outlier: 7.124A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 6.528A  pdb=" N   GLN B 176 " --> pdb=" O   ASP B 170 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 187 through 191
      removed outlier: 6.629A  pdb=" N   GLY B 202 " --> pdb=" O   MET B 188 " (cutoff:3.500A)
      removed outlier: 4.326A  pdb=" N   LEU B 190 " --> pdb=" O   VAL B 200 " (cutoff:3.500A)
      removed outlier: 6.765A  pdb=" N   VAL B 200 " --> pdb=" O   LEU B 190 " (cutoff:3.500A)
      removed outlier: 4.561A  pdb=" N   SER B 207 " --> pdb=" O   ALA B 203 " (cutoff:3.500A)
      removed outlier: 3.987A  pdb=" N   GLN B 220 " --> pdb=" O   LEU B 210 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 229 through 234
      removed outlier: 6.436A  pdb=" N   GLY B 244 " --> pdb=" O   ASN B 230 " (cutoff:3.500A)
      removed outlier: 4.244A  pdb=" N   ILE B 232 " --> pdb=" O   ALA B 242 " (cutoff:3.500A)
      removed outlier: 6.591A  pdb=" N   ALA B 242 " --> pdb=" O   ILE B 232 " (cutoff:3.500A)
      removed outlier: 4.642A  pdb=" N   PHE B 234 " --> pdb=" O   ALA B 240 " (cutoff:3.500A)
      removed outlier: 6.917A  pdb=" N   ALA B 240 " --> pdb=" O   PHE B 234 " (cutoff:3.500A)
      removed outlier: 6.420A  pdb=" N   ASP B 254 " --> pdb=" O   GLU B 260 " (cutoff:3.500A)
      removed outlier: 6.398A  pdb=" N   GLU B 260 " --> pdb=" O   ASP B 254 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 273 through 278
      removed outlier: 3.650A  pdb=" N   SER B 275 " --> pdb=" O   GLY B 288 " (cutoff:3.500A)
      removed outlier: 6.355A  pdb=" N   VAL B 296 " --> pdb=" O   ALA B 305 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'B' and resid 315 through 320
      removed outlier: 3.671A  pdb=" N   CYS B 317 " --> pdb=" O   GLY B 330 " (cutoff:3.500A)

    290 hydrogen bonds defined for protein.
    849 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: 0.98

  Time building geometry restraints manager: 0.79 seconds

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

  Histogram of bond lengths:
        1.20 -     1.33: 1369
        1.33 -     1.45: 1720
        1.45 -     1.58: 3779
        1.58 -     1.70: 0
        1.70 -     1.82: 75
  Bond restraints: 6943
  Sorted by residual:
  bond pdb=" C   LEU B  79 "
       pdb=" O   LEU B  79 "
    ideal  model  delta    sigma   weight residual
    1.236  1.203  0.033 1.24e-02 6.50e+03 7.30e+00
  bond pdb=" O   ETA D   5 "
       pdb=" CB  ETA D   5 "
    ideal  model  delta    sigma   weight residual
    1.413  1.459 -0.046 2.00e-02 2.50e+03 5.18e+00
  bond pdb=" CA  LEU B  79 "
       pdb=" CB  LEU B  79 "
    ideal  model  delta    sigma   weight residual
    1.528  1.500  0.028 1.35e-02 5.49e+03 4.34e+00
  bond pdb=" CB  PRO R 244 "
       pdb=" CG  PRO R 244 "
    ideal  model  delta    sigma   weight residual
    1.492  1.392  0.100 5.00e-02 4.00e+02 4.01e+00
  bond pdb=" CA  LEU B  79 "
       pdb=" C   LEU B  79 "
    ideal  model  delta    sigma   weight residual
    1.524  1.504  0.021 1.22e-02 6.72e+03 2.88e+00
  ... (remaining 6938 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.19: 9027
        2.19 -     4.39: 331
        4.39 -     6.58: 46
        6.58 -     8.77: 15
        8.77 -    10.97: 8
  Bond angle restraints: 9427
  Sorted by residual:
  angle pdb=" N   LEU R 121 "
        pdb=" CA  LEU R 121 "
        pdb=" C   LEU R 121 "
      ideal   model   delta    sigma   weight residual
     109.81  120.78  -10.97 2.21e+00 2.05e-01 2.46e+01
  angle pdb=" C   SER R 268 "
        pdb=" N   LYS R 269 "
        pdb=" CA  LYS R 269 "
      ideal   model   delta    sigma   weight residual
     121.54  129.84   -8.30 1.91e+00 2.74e-01 1.89e+01
  angle pdb=" N   MEA D   4 "
        pdb=" CA  MEA D   4 "
        pdb=" CB  MEA D   4 "
      ideal   model   delta    sigma   weight residual
     110.50  117.47   -6.97 1.70e+00 3.46e-01 1.68e+01
  angle pdb=" C   ASP B  27 "
        pdb=" N   ALA B  28 "
        pdb=" CA  ALA B  28 "
      ideal   model   delta    sigma   weight residual
     121.19  127.29   -6.10 1.59e+00 3.96e-01 1.47e+01
  angle pdb=" N   LEU B  79 "
        pdb=" CA  LEU B  79 "
        pdb=" C   LEU B  79 "
      ideal   model   delta    sigma   weight residual
     108.96  103.24    5.72 1.59e+00 3.96e-01 1.29e+01
  ... (remaining 9422 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    12.19: 3677
       12.19 -    24.39: 324
       24.39 -    36.58: 74
       36.58 -    48.78: 27
       48.78 -    60.97: 1
  Dihedral angle restraints: 4103
    sinusoidal: 1503
      harmonic: 2600
  Sorted by residual:
  dihedral pdb=" CA  ILE A  49 "
           pdb=" C   ILE A  49 "
           pdb=" N   VAL A  50 "
           pdb=" CA  VAL A  50 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  150.50   29.50     0      5.00e+00 4.00e-02 3.48e+01
  dihedral pdb=" CA  SER R 214 "
           pdb=" C   SER R 214 "
           pdb=" N   ILE R 215 "
           pdb=" CA  ILE R 215 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  151.00   29.00     0      5.00e+00 4.00e-02 3.36e+01
  dihedral pdb=" CA  TRP B 169 "
           pdb=" C   TRP B 169 "
           pdb=" N   ASP B 170 "
           pdb=" CA  ASP B 170 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  151.90   28.10     0      5.00e+00 4.00e-02 3.16e+01
  ... (remaining 4100 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.057: 796
       0.057 -    0.113: 251
       0.113 -    0.170: 41
       0.170 -    0.227: 7
       0.227 -    0.284: 3
  Chirality restraints: 1098
  Sorted by residual:
  chirality pdb=" CB  ILE R 308 "
            pdb=" CA  ILE R 308 "
            pdb=" CG1 ILE R 308 "
            pdb=" CG2 ILE R 308 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.36    0.28 2.00e-01 2.50e+01 2.01e+00
  chirality pdb=" CA  LEU R 121 "
            pdb=" N   LEU R 121 "
            pdb=" C   LEU R 121 "
            pdb=" CB  LEU R 121 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.27    0.24 2.00e-01 2.50e+01 1.47e+00
  chirality pdb=" CB  ILE B  37 "
            pdb=" CA  ILE B  37 "
            pdb=" CG1 ILE B  37 "
            pdb=" CG2 ILE B  37 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.40    0.24 2.00e-01 2.50e+01 1.46e+00
  ... (remaining 1095 not shown)

  Planarity restraints: 1190
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP B  63 "    0.014 2.00e-02 2.50e+03   1.66e-02 6.88e+00
        pdb=" CG  TRP B  63 "   -0.042 2.00e-02 2.50e+03
        pdb=" CD1 TRP B  63 "    0.026 2.00e-02 2.50e+03
        pdb=" CD2 TRP B  63 "   -0.002 2.00e-02 2.50e+03
        pdb=" NE1 TRP B  63 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE2 TRP B  63 "   -0.002 2.00e-02 2.50e+03
        pdb=" CE3 TRP B  63 "    0.001 2.00e-02 2.50e+03
        pdb=" CZ2 TRP B  63 "   -0.003 2.00e-02 2.50e+03
        pdb=" CZ3 TRP B  63 "    0.010 2.00e-02 2.50e+03
        pdb=" CH2 TRP B  63 "   -0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP C  48 "    0.043 5.00e-02 4.00e+02   6.54e-02 6.84e+00
        pdb=" N   PRO C  49 "   -0.113 5.00e-02 4.00e+02
        pdb=" CA  PRO C  49 "    0.035 5.00e-02 4.00e+02
        pdb=" CD  PRO C  49 "    0.036 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR R 180 "   -0.039 5.00e-02 4.00e+02   5.84e-02 5.46e+00
        pdb=" N   PRO R 181 "    0.101 5.00e-02 4.00e+02
        pdb=" CA  PRO R 181 "   -0.030 5.00e-02 4.00e+02
        pdb=" CD  PRO R 181 "   -0.032 5.00e-02 4.00e+02
  ... (remaining 1187 not shown)

  Histogram of nonbonded interaction distances:
        2.23 -     2.76: 1188
        2.76 -     3.30: 6364
        3.30 -     3.83: 11292
        3.83 -     4.37: 12756
        4.37 -     4.90: 22133
  Nonbonded interactions: 53733
  Sorted by model distance:
  nonbonded pdb=" NZ  LYS A 210 "
            pdb=" OD2 ASP B 246 "
     model   vdw
     2.228 3.120
  nonbonded pdb=" OG  SER B  74 "
            pdb=" OD1 ASP B  76 "
     model   vdw
     2.259 3.040
  nonbonded pdb=" OD1 ASP R 147 "
            pdb=" OH  TYR R 326 "
     model   vdw
     2.283 3.040
  nonbonded pdb=" OH  TYR A 320 "
            pdb=" OD2 ASP A 341 "
     model   vdw
     2.310 3.040
  nonbonded pdb=" N   THR B 143 "
            pdb=" OD2 ASP B 163 "
     model   vdw
     2.313 3.120
  ... (remaining 53728 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 group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.940
  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:          0.120
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     7.710
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.260
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   10.130
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7084
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      :  0.006   0.100   6946  Z= 0.266
  Angle     :  1.014  10.968   9432  Z= 0.540
  Chirality :  0.057   0.284   1098
  Planarity :  0.007   0.065   1189
  Dihedral  : 10.482  60.972   2411
  Min Nonbonded Distance : 2.228

Molprobity Statistics.
  All-atom Clashscore : 7.77
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  8.34 %
    Favored  : 91.54 %
  Rotamer:
    Outliers :  0.72 %
    Allowed  :  5.15 %
    Favored  : 94.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    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: -4.62 (0.23), residues: 875
  helix: -2.94 (0.19), residues: 347
  sheet: -3.53 (0.36), residues: 159
  loop : -2.74 (0.29), residues: 369

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 242 
 TYR   0.031   0.003   TYR R 299 
 PHE   0.031   0.003   PHE B 241 
 TRP   0.042   0.004   TRP B  63 
 HIS   0.011   0.002   HIS B 183 

Details of bonding type rmsd
  covalent geometry    : bond        0.00611 ( 6943)
  covalent geometry    : angle       1.01435 ( 9427)
  SS BOND              : bond        0.00240 (    1)
  SS BOND              : angle       1.45627 (    2)
  hydrogen bonds       : bond        0.15828 (  290)
  hydrogen bonds       : angle       8.20744 (  849)
  Misc. bond           : bond        0.00085 (    1)
  link_TRANS           : bond        0.00163 (    1)
  link_TRANS           : angle       0.98735 (    3)

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

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

  1750 Ramachandran restraints generated.
    875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1750 Ramachandran restraints generated.
    875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  251 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 246
  time to evaluate  : 0.255 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   26 ASP cc_start: 0.7114 (t70) cc_final: 0.6641 (t0)
REVERT: B   65 THR cc_start: 0.7469 (p) cc_final: 0.7212 (p)
REVERT: B   78 LYS cc_start: 0.8230 (mmpt) cc_final: 0.7742 (mmtt)
REVERT: B  123 ILE cc_start: 0.8588 (pp) cc_final: 0.8376 (pt)
REVERT: R  162 SER cc_start: 0.8137 (t) cc_final: 0.7889 (t)
REVERT: R  198 ILE cc_start: 0.3926 (tp) cc_final: 0.3041 (mt)
REVERT: R  216 ASP cc_start: 0.7316 (t0) cc_final: 0.6711 (t0)
REVERT: R  336 TYR cc_start: 0.7601 (m-10) cc_final: 0.7219 (m-80)
  outliers start: 5
  outliers final: 1
  residues processed: 250
  average time/residue: 0.1018
  time to fit residues: 32.2308
Evaluate side-chains
  161 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 160
  time to evaluate  : 0.263 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  168 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 87
   random chunks:
   chunk 49 optimal weight:    0.9990
   chunk 53 optimal weight:    1.9990
   chunk 5 optimal weight:    0.7980
   chunk 33 optimal weight:    0.9990
   chunk 65 optimal weight:    0.0060
   chunk 62 optimal weight:   10.0000
   chunk 51 optimal weight:    4.9990
   chunk 38 optimal weight:    4.9990
   chunk 61 optimal weight:    0.9990
   chunk 45 optimal weight:    0.8980
   chunk 74 optimal weight:    1.9990
   overall best weight:    0.7400

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

Flipped N/Q/H residues before XYZ refinement:
A  52 GLN
A 244 HIS
A 269 ASN
A 294 ASN
B  13 GLN
B  88 ASN
** R 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 297 HIS
R 314 GLN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3791 r_free = 0.3791 target = 0.144454 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3535 r_free = 0.3535 target = 0.123772 restraints weight = 11907.888|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3587 r_free = 0.3587 target = 0.127956 restraints weight = 6494.526|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3623 r_free = 0.3623 target = 0.130832 restraints weight = 4150.022|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3647 r_free = 0.3647 target = 0.132820 restraints weight = 2946.856|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3663 r_free = 0.3663 target = 0.134188 restraints weight = 2256.634|
|-----------------------------------------------------------------------------|
r_work (final): 0.3665
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6822
moved from start:          0.2681

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.054   6946  Z= 0.146
  Angle     :  0.679   8.923   9432  Z= 0.349
  Chirality :  0.043   0.137   1098
  Planarity :  0.005   0.043   1189
  Dihedral  :  6.099  63.499    959
  Min Nonbonded Distance : 2.503

Molprobity Statistics.
  All-atom Clashscore : 10.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.26 %
    Favored  : 94.74 %
  Rotamer:
    Outliers :  3.86 %
    Allowed  : 15.16 %
    Favored  : 80.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    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: -3.23 (0.27), residues: 875
  helix: -1.13 (0.25), residues: 340
  sheet: -3.34 (0.34), residues: 173
  loop : -2.37 (0.32), residues: 362

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B 137 
 TYR   0.015   0.001   TYR R 149 
 PHE   0.014   0.002   PHE B 151 
 TRP   0.019   0.002   TRP B 169 
 HIS   0.003   0.001   HIS B 183 

Details of bonding type rmsd
  covalent geometry    : bond        0.00333 ( 6943)
  covalent geometry    : angle       0.67869 ( 9427)
  SS BOND              : bond        0.00690 (    1)
  SS BOND              : angle       1.25487 (    2)
  hydrogen bonds       : bond        0.03718 (  290)
  hydrogen bonds       : angle       5.62717 (  849)
  Misc. bond           : bond        0.00007 (    1)
  link_TRANS           : bond        0.00032 (    1)
  link_TRANS           : angle       0.31441 (    3)

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

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

  1750 Ramachandran restraints generated.
    875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1750 Ramachandran restraints generated.
    875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  219 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 192
  time to evaluate  : 0.266 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   26 ASP cc_start: 0.8881 (t70) cc_final: 0.8248 (t0)
REVERT: B  117 LEU cc_start: 0.7531 (OUTLIER) cc_final: 0.7279 (tt)
REVERT: B  188 MET cc_start: 0.8247 (mmm) cc_final: 0.8029 (tpp)
REVERT: B  222 PHE cc_start: 0.8517 (m-10) cc_final: 0.8124 (m-10)
REVERT: B  230 ASN cc_start: 0.8842 (t0) cc_final: 0.8294 (m110)
REVERT: B  234 PHE cc_start: 0.8616 (OUTLIER) cc_final: 0.7780 (m-10)
REVERT: B  339 TRP cc_start: 0.8899 (m100) cc_final: 0.8537 (m-10)
REVERT: C   32 LYS cc_start: 0.6826 (tppt) cc_final: 0.6143 (mtmm)
REVERT: R  239 PHE cc_start: 0.7905 (OUTLIER) cc_final: 0.7584 (m-80)
REVERT: R  292 CYS cc_start: 0.8466 (m) cc_final: 0.8224 (m)
REVERT: R  324 LEU cc_start: 0.7426 (OUTLIER) cc_final: 0.7064 (pt)
  outliers start: 27
  outliers final: 15
  residues processed: 213
  average time/residue: 0.0958
  time to fit residues: 26.4161
Evaluate side-chains
  182 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 163
  time to evaluate  : 0.265 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    9 ASP
Chi-restraints excluded: chain A residue   34 VAL
Chi-restraints excluded: chain A residue  185 VAL
Chi-restraints excluded: chain A residue  273 LEU
Chi-restraints excluded: chain A residue  310 LEU
Chi-restraints excluded: chain B residue  117 LEU
Chi-restraints excluded: chain B residue  168 LEU
Chi-restraints excluded: chain B residue  184 THR
Chi-restraints excluded: chain B residue  190 LEU
Chi-restraints excluded: chain B residue  191 SER
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  266 HIS
Chi-restraints excluded: chain R residue  121 LEU
Chi-restraints excluded: chain R residue  231 LEU
Chi-restraints excluded: chain R residue  239 PHE
Chi-restraints excluded: chain R residue  259 LEU
Chi-restraints excluded: chain R residue  290 ILE
Chi-restraints excluded: chain R residue  311 THR
Chi-restraints excluded: chain R residue  324 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 87
   random chunks:
   chunk 70 optimal weight:    4.9990
   chunk 46 optimal weight:    0.5980
   chunk 61 optimal weight:    0.9990
   chunk 79 optimal weight:    5.9990
   chunk 8 optimal weight:    0.6980
   chunk 83 optimal weight:    5.9990
   chunk 39 optimal weight:    1.9990
   chunk 26 optimal weight:    0.8980
   chunk 53 optimal weight:    0.5980
   chunk 59 optimal weight:    0.6980
   chunk 45 optimal weight:    0.1980
   overall best weight:    0.5580

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

Flipped N/Q/H residues before XYZ refinement:
A 213 HIS
A 269 ASN
B 110 ASN
B 119 ASN
R 314 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3731 r_free = 0.3731 target = 0.140243 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3467 r_free = 0.3467 target = 0.118883 restraints weight = 11813.254|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.3520 r_free = 0.3520 target = 0.123034 restraints weight = 6478.155|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3557 r_free = 0.3557 target = 0.125909 restraints weight = 4162.647|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3581 r_free = 0.3581 target = 0.127893 restraints weight = 2968.610|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.3599 r_free = 0.3599 target = 0.129360 restraints weight = 2287.149|
|-----------------------------------------------------------------------------|
r_work (final): 0.3602
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6805
moved from start:          0.3343

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   6946  Z= 0.123
  Angle     :  0.644   9.295   9432  Z= 0.325
  Chirality :  0.042   0.132   1098
  Planarity :  0.004   0.038   1189
  Dihedral  :  5.620  63.284    959
  Min Nonbonded Distance : 2.495

Molprobity Statistics.
  All-atom Clashscore : 10.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.03 %
    Favored  : 94.97 %
  Rotamer:
    Outliers :  3.86 %
    Allowed  : 19.89 %
    Favored  : 76.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.67 (0.28), residues: 875
  helix: -0.47 (0.27), residues: 348
  sheet: -3.06 (0.36), residues: 152
  loop : -2.40 (0.32), residues: 375

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 313 
 TYR   0.017   0.001   TYR R 149 
 PHE   0.011   0.001   PHE B 151 
 TRP   0.017   0.001   TRP B 169 
 HIS   0.004   0.001   HIS B 183 

Details of bonding type rmsd
  covalent geometry    : bond        0.00280 ( 6943)
  covalent geometry    : angle       0.64366 ( 9427)
  SS BOND              : bond        0.00076 (    1)
  SS BOND              : angle       0.62905 (    2)
  hydrogen bonds       : bond        0.03387 (  290)
  hydrogen bonds       : angle       5.17596 (  849)
  Misc. bond           : bond        0.00003 (    1)
  link_TRANS           : bond        0.00004 (    1)
  link_TRANS           : angle       0.16267 (    3)

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

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

  1750 Ramachandran restraints generated.
    875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1750 Ramachandran restraints generated.
    875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  207 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 180
  time to evaluate  : 0.260 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   26 ASP cc_start: 0.8870 (t70) cc_final: 0.8041 (t0)
REVERT: A  230 TYR cc_start: 0.4005 (t80) cc_final: 0.3767 (t80)
REVERT: B   75 GLN cc_start: 0.8471 (mm110) cc_final: 0.7702 (mm110)
REVERT: B  188 MET cc_start: 0.8241 (mmm) cc_final: 0.7980 (tpp)
REVERT: B  219 ARG cc_start: 0.8014 (ttm170) cc_final: 0.7496 (mmt90)
REVERT: B  222 PHE cc_start: 0.8507 (m-80) cc_final: 0.8269 (m-10)
REVERT: B  230 ASN cc_start: 0.8717 (t0) cc_final: 0.8197 (m110)
REVERT: B  234 PHE cc_start: 0.8587 (OUTLIER) cc_final: 0.7840 (m-10)
REVERT: B  297 TRP cc_start: 0.8744 (m100) cc_final: 0.8177 (m100)
REVERT: B  339 TRP cc_start: 0.8946 (m100) cc_final: 0.8529 (m-10)
REVERT: C   32 LYS cc_start: 0.6649 (tppt) cc_final: 0.5951 (mttm)
REVERT: R   87 PHE cc_start: 0.8094 (m-10) cc_final: 0.7857 (m-10)
REVERT: R  211 ARG cc_start: 0.7378 (ttm110) cc_final: 0.6925 (mtt90)
REVERT: R  239 PHE cc_start: 0.7859 (OUTLIER) cc_final: 0.7633 (m-80)
REVERT: R  293 TRP cc_start: 0.8099 (OUTLIER) cc_final: 0.6953 (m-10)
REVERT: R  324 LEU cc_start: 0.7283 (OUTLIER) cc_final: 0.6904 (pt)
  outliers start: 27
  outliers final: 15
  residues processed: 195
  average time/residue: 0.0983
  time to fit residues: 24.7658
Evaluate side-chains
  179 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 160
  time to evaluate  : 0.255 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    9 ASP
Chi-restraints excluded: chain A residue  185 VAL
Chi-restraints excluded: chain A residue  193 ASP
Chi-restraints excluded: chain A residue  216 GLU
Chi-restraints excluded: chain A residue  273 LEU
Chi-restraints excluded: chain B residue   79 LEU
Chi-restraints excluded: chain B residue  148 CYS
Chi-restraints excluded: chain B residue  168 LEU
Chi-restraints excluded: chain B residue  190 LEU
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain C residue   16 VAL
Chi-restraints excluded: chain R residue   79 CYS
Chi-restraints excluded: chain R residue  121 LEU
Chi-restraints excluded: chain R residue  162 SER
Chi-restraints excluded: chain R residue  231 LEU
Chi-restraints excluded: chain R residue  239 PHE
Chi-restraints excluded: chain R residue  293 TRP
Chi-restraints excluded: chain R residue  322 ILE
Chi-restraints excluded: chain R residue  324 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 87
   random chunks:
   chunk 68 optimal weight:    0.8980
   chunk 39 optimal weight:    1.9990
   chunk 58 optimal weight:    0.9980
   chunk 45 optimal weight:    0.0170
   chunk 18 optimal weight:    1.9990
   chunk 23 optimal weight:    1.9990
   chunk 21 optimal weight:    8.9990
   chunk 32 optimal weight:    3.9990
   chunk 33 optimal weight:    0.9980
   chunk 82 optimal weight:    0.9990
   chunk 79 optimal weight:    3.9990
   overall best weight:    0.7820

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

Flipped N/Q/H residues before XYZ refinement:
B  13 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3759 r_free = 0.3759 target = 0.141659 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3499 r_free = 0.3499 target = 0.121074 restraints weight = 11819.204|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3551 r_free = 0.3551 target = 0.124996 restraints weight = 6661.747|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3585 r_free = 0.3585 target = 0.127750 restraints weight = 4368.762|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3609 r_free = 0.3609 target = 0.129677 restraints weight = 3149.659|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3625 r_free = 0.3625 target = 0.130970 restraints weight = 2438.679|
|-----------------------------------------------------------------------------|
r_work (final): 0.3623
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6939
moved from start:          0.3724

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050   6946  Z= 0.138
  Angle     :  0.623   9.117   9432  Z= 0.320
  Chirality :  0.042   0.124   1098
  Planarity :  0.004   0.036   1189
  Dihedral  :  5.443  62.374    959
  Min Nonbonded Distance : 2.509

Molprobity Statistics.
  All-atom Clashscore : 9.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.60 %
    Favored  : 94.40 %
  Rotamer:
    Outliers :  6.15 %
    Allowed  : 19.46 %
    Favored  : 74.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.36 (0.28), residues: 875
  helix: -0.21 (0.27), residues: 349
  sheet: -2.88 (0.36), residues: 156
  loop : -2.21 (0.34), residues: 370

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG R 182 
 TYR   0.018   0.001   TYR R 149 
 PHE   0.010   0.001   PHE B 234 
 TRP   0.019   0.001   TRP B 169 
 HIS   0.003   0.001   HIS B 183 

Details of bonding type rmsd
  covalent geometry    : bond        0.00320 ( 6943)
  covalent geometry    : angle       0.62284 ( 9427)
  SS BOND              : bond        0.00151 (    1)
  SS BOND              : angle       0.90018 (    2)
  hydrogen bonds       : bond        0.03310 (  290)
  hydrogen bonds       : angle       5.04563 (  849)
  Misc. bond           : bond        0.00004 (    1)
  link_TRANS           : bond        0.00000 (    1)
  link_TRANS           : angle       0.13694 (    3)

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

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

  1750 Ramachandran restraints generated.
    875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1750 Ramachandran restraints generated.
    875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  205 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 162
  time to evaluate  : 0.258 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   32 ARG cc_start: 0.7839 (ttp-110) cc_final: 0.7273 (ttm-80)
REVERT: A  230 TYR cc_start: 0.4353 (t80) cc_final: 0.4089 (t80)
REVERT: A  313 ARG cc_start: 0.8446 (ttm-80) cc_final: 0.7840 (ptm160)
REVERT: B   32 GLN cc_start: 0.6325 (tp40) cc_final: 0.5915 (tp-100)
REVERT: B  117 LEU cc_start: 0.7814 (OUTLIER) cc_final: 0.7540 (tt)
REVERT: B  163 ASP cc_start: 0.7021 (p0) cc_final: 0.6808 (p0)
REVERT: B  212 ASP cc_start: 0.6987 (p0) cc_final: 0.6191 (p0)
REVERT: B  222 PHE cc_start: 0.8590 (m-80) cc_final: 0.8354 (m-10)
REVERT: B  233 CYS cc_start: 0.8767 (t) cc_final: 0.8373 (t)
REVERT: B  234 PHE cc_start: 0.8715 (OUTLIER) cc_final: 0.7869 (m-10)
REVERT: B  260 GLU cc_start: 0.8650 (tt0) cc_final: 0.8416 (tt0)
REVERT: B  339 TRP cc_start: 0.9014 (m100) cc_final: 0.8564 (m-10)
REVERT: C   32 LYS cc_start: 0.6670 (tppt) cc_final: 0.6157 (mtmm)
REVERT: R   87 PHE cc_start: 0.8070 (m-10) cc_final: 0.7780 (m-10)
REVERT: R  177 ASP cc_start: 0.8474 (t0) cc_final: 0.7953 (t0)
REVERT: R  179 ARG cc_start: 0.9065 (ptm-80) cc_final: 0.8705 (ptm160)
REVERT: R  211 ARG cc_start: 0.7252 (ttm110) cc_final: 0.6780 (mtt90)
REVERT: R  293 TRP cc_start: 0.8157 (OUTLIER) cc_final: 0.6865 (m-10)
  outliers start: 43
  outliers final: 25
  residues processed: 188
  average time/residue: 0.0907
  time to fit residues: 22.1930
Evaluate side-chains
  178 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 150
  time to evaluate  : 0.263 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    9 ASP
Chi-restraints excluded: chain A residue   34 VAL
Chi-restraints excluded: chain A residue  185 VAL
Chi-restraints excluded: chain A residue  193 ASP
Chi-restraints excluded: chain A residue  216 GLU
Chi-restraints excluded: chain A residue  273 LEU
Chi-restraints excluded: chain B residue   38 ASP
Chi-restraints excluded: chain B residue   74 SER
Chi-restraints excluded: chain B residue   79 LEU
Chi-restraints excluded: chain B residue   89 LYS
Chi-restraints excluded: chain B residue  112 VAL
Chi-restraints excluded: chain B residue  117 LEU
Chi-restraints excluded: chain B residue  148 CYS
Chi-restraints excluded: chain B residue  168 LEU
Chi-restraints excluded: chain B residue  184 THR
Chi-restraints excluded: chain B residue  190 LEU
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  329 THR
Chi-restraints excluded: chain C residue   16 VAL
Chi-restraints excluded: chain R residue   79 CYS
Chi-restraints excluded: chain R residue  121 LEU
Chi-restraints excluded: chain R residue  157 THR
Chi-restraints excluded: chain R residue  162 SER
Chi-restraints excluded: chain R residue  231 LEU
Chi-restraints excluded: chain R residue  259 LEU
Chi-restraints excluded: chain R residue  290 ILE
Chi-restraints excluded: chain R residue  293 TRP
Chi-restraints excluded: chain R residue  322 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 87
   random chunks:
   chunk 39 optimal weight:    1.9990
   chunk 17 optimal weight:    4.9990
   chunk 8 optimal weight:    0.9990
   chunk 81 optimal weight:    0.7980
   chunk 25 optimal weight:    0.9990
   chunk 78 optimal weight:    0.8980
   chunk 37 optimal weight:    2.9990
   chunk 20 optimal weight:    0.9990
   chunk 5 optimal weight:    4.9990
   chunk 32 optimal weight:    0.5980
   chunk 16 optimal weight:    0.9990
   overall best weight:    0.8584

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

Flipped N/Q/H residues before XYZ refinement:
A 269 ASN
B  13 GLN
R  86 ASN
R 332 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3743 r_free = 0.3743 target = 0.140370 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3484 r_free = 0.3484 target = 0.119741 restraints weight = 11877.588|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3537 r_free = 0.3537 target = 0.123807 restraints weight = 6517.744|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3572 r_free = 0.3572 target = 0.126568 restraints weight = 4190.133|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3596 r_free = 0.3596 target = 0.128555 restraints weight = 2998.743|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.3614 r_free = 0.3614 target = 0.129977 restraints weight = 2293.061|
|-----------------------------------------------------------------------------|
r_work (final): 0.3610
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6859
moved from start:          0.4028

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048   6946  Z= 0.145
  Angle     :  0.628   9.547   9432  Z= 0.321
  Chirality :  0.043   0.142   1098
  Planarity :  0.004   0.034   1189
  Dihedral  :  5.370  62.113    959
  Min Nonbonded Distance : 2.551

Molprobity Statistics.
  All-atom Clashscore : 10.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.94 %
    Favored  : 94.06 %
  Rotamer:
    Outliers :  5.29 %
    Allowed  : 21.17 %
    Favored  : 73.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.06 (0.29), residues: 875
  helix:  0.06 (0.28), residues: 344
  sheet: -2.59 (0.38), residues: 156
  loop : -2.11 (0.34), residues: 375

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG R 182 
 TYR   0.016   0.001   TYR R 149 
 PHE   0.011   0.001   PHE B 199 
 TRP   0.018   0.001   TRP B 169 
 HIS   0.003   0.001   HIS B 183 

Details of bonding type rmsd
  covalent geometry    : bond        0.00334 ( 6943)
  covalent geometry    : angle       0.62833 ( 9427)
  SS BOND              : bond        0.00137 (    1)
  SS BOND              : angle       0.81074 (    2)
  hydrogen bonds       : bond        0.03273 (  290)
  hydrogen bonds       : angle       5.02656 (  849)
  Misc. bond           : bond        0.00007 (    1)
  link_TRANS           : bond        0.00074 (    1)
  link_TRANS           : angle       0.15767 (    3)

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

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

  1750 Ramachandran restraints generated.
    875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1750 Ramachandran restraints generated.
    875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  196 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 159
  time to evaluate  : 0.259 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   32 ARG cc_start: 0.7915 (ttp-110) cc_final: 0.7360 (ttm-80)
REVERT: A  214 CYS cc_start: 0.8965 (t) cc_final: 0.8667 (m)
REVERT: A  313 ARG cc_start: 0.8567 (ttm-80) cc_final: 0.7952 (ptm160)
REVERT: B   32 GLN cc_start: 0.6348 (tp40) cc_final: 0.5881 (tp40)
REVERT: B  117 LEU cc_start: 0.7829 (OUTLIER) cc_final: 0.7519 (tt)
REVERT: B  164 THR cc_start: 0.8960 (OUTLIER) cc_final: 0.8607 (p)
REVERT: B  212 ASP cc_start: 0.7298 (p0) cc_final: 0.6495 (p0)
REVERT: B  219 ARG cc_start: 0.8012 (ttm170) cc_final: 0.7526 (tpp80)
REVERT: B  222 PHE cc_start: 0.8590 (m-80) cc_final: 0.8314 (m-10)
REVERT: B  233 CYS cc_start: 0.8751 (t) cc_final: 0.8316 (t)
REVERT: B  234 PHE cc_start: 0.8675 (OUTLIER) cc_final: 0.7826 (m-10)
REVERT: B  260 GLU cc_start: 0.8641 (tt0) cc_final: 0.8346 (tt0)
REVERT: B  339 TRP cc_start: 0.9082 (m100) cc_final: 0.8528 (m-10)
REVERT: C   32 LYS cc_start: 0.6497 (tppt) cc_final: 0.5954 (mtmt)
REVERT: R  177 ASP cc_start: 0.8578 (t0) cc_final: 0.8071 (t0)
REVERT: R  179 ARG cc_start: 0.9062 (ptm-80) cc_final: 0.8665 (ptm160)
REVERT: R  211 ARG cc_start: 0.7100 (ttm110) cc_final: 0.6419 (mtt90)
REVERT: R  241 PHE cc_start: 0.7247 (t80) cc_final: 0.6983 (t80)
REVERT: R  293 TRP cc_start: 0.8030 (OUTLIER) cc_final: 0.6365 (m-10)
  outliers start: 37
  outliers final: 22
  residues processed: 186
  average time/residue: 0.0916
  time to fit residues: 22.2586
Evaluate side-chains
  174 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 148
  time to evaluate  : 0.257 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    9 ASP
Chi-restraints excluded: chain A residue   34 VAL
Chi-restraints excluded: chain A residue  193 ASP
Chi-restraints excluded: chain A residue  254 CYS
Chi-restraints excluded: chain A residue  273 LEU
Chi-restraints excluded: chain B residue   38 ASP
Chi-restraints excluded: chain B residue   79 LEU
Chi-restraints excluded: chain B residue   89 LYS
Chi-restraints excluded: chain B residue  112 VAL
Chi-restraints excluded: chain B residue  117 LEU
Chi-restraints excluded: chain B residue  133 VAL
Chi-restraints excluded: chain B residue  148 CYS
Chi-restraints excluded: chain B residue  164 THR
Chi-restraints excluded: chain B residue  168 LEU
Chi-restraints excluded: chain B residue  184 THR
Chi-restraints excluded: chain B residue  190 LEU
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain C residue   16 VAL
Chi-restraints excluded: chain R residue   79 CYS
Chi-restraints excluded: chain R residue  121 LEU
Chi-restraints excluded: chain R residue  162 SER
Chi-restraints excluded: chain R residue  231 LEU
Chi-restraints excluded: chain R residue  259 LEU
Chi-restraints excluded: chain R residue  290 ILE
Chi-restraints excluded: chain R residue  293 TRP
Chi-restraints excluded: chain R residue  322 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 87
   random chunks:
   chunk 33 optimal weight:    0.0670
   chunk 12 optimal weight:    0.0870
   chunk 80 optimal weight:    1.9990
   chunk 68 optimal weight:    0.5980
   chunk 10 optimal weight:    2.9990
   chunk 20 optimal weight:    0.8980
   chunk 83 optimal weight:    0.9990
   chunk 8 optimal weight:    0.7980
   chunk 9 optimal weight:    0.8980
   chunk 7 optimal weight:    1.9990
   chunk 1 optimal weight:    1.9990
   overall best weight:    0.4896

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

Flipped N/Q/H residues before XYZ refinement:
R 150 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3724 r_free = 0.3724 target = 0.139740 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3461 r_free = 0.3461 target = 0.118741 restraints weight = 12015.636|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3515 r_free = 0.3515 target = 0.122802 restraints weight = 6623.364|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3551 r_free = 0.3551 target = 0.125654 restraints weight = 4269.164|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3575 r_free = 0.3575 target = 0.127635 restraints weight = 3055.147|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3593 r_free = 0.3593 target = 0.129085 restraints weight = 2354.508|
|-----------------------------------------------------------------------------|
r_work (final): 0.3642
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6833
moved from start:          0.4329

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   6946  Z= 0.114
  Angle     :  0.613   9.871   9432  Z= 0.310
  Chirality :  0.042   0.148   1098
  Planarity :  0.003   0.035   1189
  Dihedral  :  5.204  65.595    959
  Min Nonbonded Distance : 2.565

Molprobity Statistics.
  All-atom Clashscore : 9.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.57 %
    Favored  : 95.43 %
  Rotamer:
    Outliers :  4.29 %
    Allowed  : 24.03 %
    Favored  : 71.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    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: -1.82 (0.29), residues: 875
  helix:  0.25 (0.28), residues: 349
  sheet: -2.38 (0.39), residues: 155
  loop : -2.04 (0.34), residues: 371

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A  21 
 TYR   0.018   0.001   TYR R 149 
 PHE   0.010   0.001   PHE A 274 
 TRP   0.016   0.001   TRP B 169 
 HIS   0.004   0.001   HIS B 142 

Details of bonding type rmsd
  covalent geometry    : bond        0.00260 ( 6943)
  covalent geometry    : angle       0.61266 ( 9427)
  SS BOND              : bond        0.00155 (    1)
  SS BOND              : angle       0.68106 (    2)
  hydrogen bonds       : bond        0.03233 (  290)
  hydrogen bonds       : angle       4.91281 (  849)
  Misc. bond           : bond        0.00006 (    1)
  link_TRANS           : bond        0.00023 (    1)
  link_TRANS           : angle       0.25252 (    3)

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

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

  1750 Ramachandran restraints generated.
    875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1750 Ramachandran restraints generated.
    875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  192 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 162
  time to evaluate  : 0.271 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   22 ASN cc_start: 0.8589 (m-40) cc_final: 0.8126 (t0)
REVERT: A  198 MET cc_start: 0.8257 (mmp) cc_final: 0.7961 (mmp)
REVERT: A  214 CYS cc_start: 0.9069 (t) cc_final: 0.8719 (m)
REVERT: A  247 MET cc_start: 0.7854 (mtm) cc_final: 0.7466 (mtt)
REVERT: A  313 ARG cc_start: 0.8559 (ttm-80) cc_final: 0.8026 (ptm160)
REVERT: B   32 GLN cc_start: 0.6136 (tp40) cc_final: 0.5699 (tp40)
REVERT: B   34 THR cc_start: 0.5540 (m) cc_final: 0.5338 (p)
REVERT: B  164 THR cc_start: 0.8847 (OUTLIER) cc_final: 0.8490 (p)
REVERT: B  212 ASP cc_start: 0.6950 (p0) cc_final: 0.5844 (p0)
REVERT: B  222 PHE cc_start: 0.8547 (m-80) cc_final: 0.8259 (m-10)
REVERT: B  233 CYS cc_start: 0.8688 (t) cc_final: 0.8232 (t)
REVERT: B  234 PHE cc_start: 0.8666 (OUTLIER) cc_final: 0.7753 (m-10)
REVERT: B  339 TRP cc_start: 0.9078 (m100) cc_final: 0.8521 (m-10)
REVERT: C   32 LYS cc_start: 0.6378 (tppt) cc_final: 0.5755 (mttt)
REVERT: R   87 PHE cc_start: 0.7998 (m-10) cc_final: 0.7780 (m-10)
REVERT: R  179 ARG cc_start: 0.9043 (ptm-80) cc_final: 0.8683 (ptm160)
REVERT: R  211 ARG cc_start: 0.6974 (ttm110) cc_final: 0.6428 (mtt90)
REVERT: R  293 TRP cc_start: 0.7931 (OUTLIER) cc_final: 0.6536 (m-10)
  outliers start: 30
  outliers final: 21
  residues processed: 183
  average time/residue: 0.0911
  time to fit residues: 21.8986
Evaluate side-chains
  174 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 150
  time to evaluate  : 0.197 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    9 ASP
Chi-restraints excluded: chain A residue   34 VAL
Chi-restraints excluded: chain A residue  193 ASP
Chi-restraints excluded: chain A residue  254 CYS
Chi-restraints excluded: chain A residue  273 LEU
Chi-restraints excluded: chain B residue   38 ASP
Chi-restraints excluded: chain B residue   79 LEU
Chi-restraints excluded: chain B residue   89 LYS
Chi-restraints excluded: chain B residue  112 VAL
Chi-restraints excluded: chain B residue  148 CYS
Chi-restraints excluded: chain B residue  164 THR
Chi-restraints excluded: chain B residue  168 LEU
Chi-restraints excluded: chain B residue  190 LEU
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain C residue   16 VAL
Chi-restraints excluded: chain R residue   79 CYS
Chi-restraints excluded: chain R residue  121 LEU
Chi-restraints excluded: chain R residue  162 SER
Chi-restraints excluded: chain R residue  231 LEU
Chi-restraints excluded: chain R residue  284 VAL
Chi-restraints excluded: chain R residue  290 ILE
Chi-restraints excluded: chain R residue  293 TRP
Chi-restraints excluded: chain R residue  300 VAL
Chi-restraints excluded: chain R residue  322 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 87
   random chunks:
   chunk 9 optimal weight:    3.9990
   chunk 42 optimal weight:    0.0570
   chunk 69 optimal weight:    1.9990
   chunk 62 optimal weight:   20.0000
   chunk 36 optimal weight:    1.9990
   chunk 68 optimal weight:    0.6980
   chunk 51 optimal weight:    9.9990
   chunk 30 optimal weight:    3.9990
   chunk 77 optimal weight:    0.7980
   chunk 50 optimal weight:    0.4980
   chunk 6 optimal weight:    1.9990
   overall best weight:    0.8100

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

Flipped N/Q/H residues before XYZ refinement:
A 255 ASN
B  13 GLN
B  17 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3693 r_free = 0.3693 target = 0.137278 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3432 r_free = 0.3432 target = 0.116495 restraints weight = 11881.707|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3486 r_free = 0.3486 target = 0.120595 restraints weight = 6482.493|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3522 r_free = 0.3522 target = 0.123415 restraints weight = 4152.819|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3547 r_free = 0.3547 target = 0.125411 restraints weight = 2959.091|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3565 r_free = 0.3565 target = 0.126811 restraints weight = 2267.868|
|-----------------------------------------------------------------------------|
r_work (final): 0.3613
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6830
moved from start:          0.4454

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   6946  Z= 0.139
  Angle     :  0.637   9.673   9432  Z= 0.319
  Chirality :  0.044   0.316   1098
  Planarity :  0.004   0.035   1189
  Dihedral  :  5.183  63.125    959
  Min Nonbonded Distance : 2.580

Molprobity Statistics.
  All-atom Clashscore : 10.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.71 %
    Favored  : 94.29 %
  Rotamer:
    Outliers :  4.43 %
    Allowed  : 24.32 %
    Favored  : 71.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    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: -1.65 (0.29), residues: 875
  helix:  0.44 (0.28), residues: 343
  sheet: -2.36 (0.40), residues: 146
  loop : -1.96 (0.34), residues: 386

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG R 182 
 TYR   0.015   0.001   TYR R 149 
 PHE   0.011   0.001   PHE B 199 
 TRP   0.016   0.002   TRP B  82 
 HIS   0.003   0.001   HIS B 142 

Details of bonding type rmsd
  covalent geometry    : bond        0.00321 ( 6943)
  covalent geometry    : angle       0.63732 ( 9427)
  SS BOND              : bond        0.00162 (    1)
  SS BOND              : angle       0.82039 (    2)
  hydrogen bonds       : bond        0.03217 (  290)
  hydrogen bonds       : angle       4.90284 (  849)
  Misc. bond           : bond        0.00005 (    1)
  link_TRANS           : bond        0.00068 (    1)
  link_TRANS           : angle       0.35502 (    3)

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

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

  1750 Ramachandran restraints generated.
    875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1750 Ramachandran restraints generated.
    875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  179 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 148
  time to evaluate  : 0.324 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   22 ASN cc_start: 0.8503 (m-40) cc_final: 0.8021 (t0)
REVERT: A  214 CYS cc_start: 0.9107 (t) cc_final: 0.8732 (t)
REVERT: A  247 MET cc_start: 0.7817 (mtm) cc_final: 0.7452 (mtt)
REVERT: A  313 ARG cc_start: 0.8430 (ttm-80) cc_final: 0.7937 (ptm160)
REVERT: B   32 GLN cc_start: 0.6185 (tp40) cc_final: 0.5716 (tp40)
REVERT: B   59 TYR cc_start: 0.8894 (m-80) cc_final: 0.8661 (m-80)
REVERT: B  163 ASP cc_start: 0.7238 (p0) cc_final: 0.6998 (p0)
REVERT: B  164 THR cc_start: 0.8878 (OUTLIER) cc_final: 0.8472 (p)
REVERT: B  212 ASP cc_start: 0.7287 (p0) cc_final: 0.6685 (p0)
REVERT: B  222 PHE cc_start: 0.8577 (m-80) cc_final: 0.8261 (m-10)
REVERT: B  230 ASN cc_start: 0.8591 (t0) cc_final: 0.8206 (t0)
REVERT: B  233 CYS cc_start: 0.8707 (t) cc_final: 0.8247 (t)
REVERT: B  234 PHE cc_start: 0.8669 (OUTLIER) cc_final: 0.7825 (m-10)
REVERT: B  260 GLU cc_start: 0.8570 (tt0) cc_final: 0.8244 (tt0)
REVERT: B  339 TRP cc_start: 0.9083 (m100) cc_final: 0.8471 (m-10)
REVERT: C   11 GLN cc_start: 0.6628 (pm20) cc_final: 0.5961 (tm-30)
REVERT: C   32 LYS cc_start: 0.6379 (tppt) cc_final: 0.5870 (mtmm)
REVERT: R  179 ARG cc_start: 0.9055 (ptm-80) cc_final: 0.8684 (ptm160)
REVERT: R  211 ARG cc_start: 0.6865 (ttm110) cc_final: 0.6347 (mtt90)
REVERT: R  251 CYS cc_start: 0.8772 (OUTLIER) cc_final: 0.8138 (t)
REVERT: R  255 MET cc_start: 0.8651 (ttt) cc_final: 0.8296 (ttt)
REVERT: R  293 TRP cc_start: 0.7908 (OUTLIER) cc_final: 0.6561 (m-10)
  outliers start: 31
  outliers final: 21
  residues processed: 171
  average time/residue: 0.0904
  time to fit residues: 20.3784
Evaluate side-chains
  166 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 141
  time to evaluate  : 0.268 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    9 ASP
Chi-restraints excluded: chain A residue   34 VAL
Chi-restraints excluded: chain A residue  193 ASP
Chi-restraints excluded: chain A residue  254 CYS
Chi-restraints excluded: chain A residue  273 LEU
Chi-restraints excluded: chain B residue   38 ASP
Chi-restraints excluded: chain B residue   79 LEU
Chi-restraints excluded: chain B residue  112 VAL
Chi-restraints excluded: chain B residue  148 CYS
Chi-restraints excluded: chain B residue  164 THR
Chi-restraints excluded: chain B residue  168 LEU
Chi-restraints excluded: chain B residue  190 LEU
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain C residue   16 VAL
Chi-restraints excluded: chain R residue   79 CYS
Chi-restraints excluded: chain R residue   88 LEU
Chi-restraints excluded: chain R residue  121 LEU
Chi-restraints excluded: chain R residue  162 SER
Chi-restraints excluded: chain R residue  231 LEU
Chi-restraints excluded: chain R residue  251 CYS
Chi-restraints excluded: chain R residue  284 VAL
Chi-restraints excluded: chain R residue  290 ILE
Chi-restraints excluded: chain R residue  293 TRP
Chi-restraints excluded: chain R residue  300 VAL
Chi-restraints excluded: chain R residue  322 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 87
   random chunks:
   chunk 68 optimal weight:    0.9990
   chunk 62 optimal weight:   20.0000
   chunk 61 optimal weight:    0.8980
   chunk 50 optimal weight:    0.0770
   chunk 25 optimal weight:    0.8980
   chunk 63 optimal weight:    0.8980
   chunk 41 optimal weight:    2.9990
   chunk 38 optimal weight:    1.9990
   chunk 54 optimal weight:    0.5980
   chunk 45 optimal weight:    3.9990
   chunk 1 optimal weight:    0.8980
   overall best weight:    0.6738

-------------------------------------------------------------------------------
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 = 0.3697 r_free = 0.3697 target = 0.137636 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3448 r_free = 0.3448 target = 0.117792 restraints weight = 11982.930|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3499 r_free = 0.3499 target = 0.121666 restraints weight = 6654.255|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3533 r_free = 0.3533 target = 0.124376 restraints weight = 4303.817|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3557 r_free = 0.3557 target = 0.126293 restraints weight = 3079.016|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3573 r_free = 0.3573 target = 0.127575 restraints weight = 2362.531|
|-----------------------------------------------------------------------------|
r_work (final): 0.3628
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6884
moved from start:          0.4582

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   6946  Z= 0.127
  Angle     :  0.633   9.162   9432  Z= 0.316
  Chirality :  0.043   0.337   1098
  Planarity :  0.003   0.035   1189
  Dihedral  :  5.147  64.626    959
  Min Nonbonded Distance : 2.588

Molprobity Statistics.
  All-atom Clashscore : 10.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.03 %
    Favored  : 94.97 %
  Rotamer:
    Outliers :  4.01 %
    Allowed  : 24.46 %
    Favored  : 71.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    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: -1.53 (0.29), residues: 875
  helix:  0.48 (0.28), residues: 344
  sheet: -2.36 (0.40), residues: 140
  loop : -1.83 (0.34), residues: 391

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG R 182 
 TYR   0.015   0.001   TYR D   1 
 PHE   0.010   0.001   PHE B 199 
 TRP   0.016   0.002   TRP B 169 
 HIS   0.003   0.001   HIS B 183 

Details of bonding type rmsd
  covalent geometry    : bond        0.00294 ( 6943)
  covalent geometry    : angle       0.63335 ( 9427)
  SS BOND              : bond        0.00237 (    1)
  SS BOND              : angle       0.80125 (    2)
  hydrogen bonds       : bond        0.03134 (  290)
  hydrogen bonds       : angle       4.84613 (  849)
  Misc. bond           : bond        0.00007 (    1)
  link_TRANS           : bond        0.00117 (    1)
  link_TRANS           : angle       0.47455 (    3)

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

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

  1750 Ramachandran restraints generated.
    875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1750 Ramachandran restraints generated.
    875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  179 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 151
  time to evaluate  : 0.166 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   22 ASN cc_start: 0.8612 (m-40) cc_final: 0.8140 (t0)
REVERT: A   32 ARG cc_start: 0.7422 (ttm110) cc_final: 0.7196 (ttm110)
REVERT: A  198 MET cc_start: 0.8171 (mmp) cc_final: 0.7956 (mmp)
REVERT: A  214 CYS cc_start: 0.9146 (t) cc_final: 0.8803 (t)
REVERT: A  247 MET cc_start: 0.7869 (mtm) cc_final: 0.7511 (mtt)
REVERT: A  276 GLU cc_start: 0.6065 (OUTLIER) cc_final: 0.5202 (tp30)
REVERT: B   32 GLN cc_start: 0.6278 (tp40) cc_final: 0.5879 (tp40)
REVERT: B   59 TYR cc_start: 0.8962 (m-80) cc_final: 0.8760 (m-80)
REVERT: B  164 THR cc_start: 0.8901 (OUTLIER) cc_final: 0.8562 (p)
REVERT: B  200 VAL cc_start: 0.8983 (OUTLIER) cc_final: 0.8770 (m)
REVERT: B  212 ASP cc_start: 0.7376 (p0) cc_final: 0.6912 (p0)
REVERT: B  222 PHE cc_start: 0.8588 (m-80) cc_final: 0.8361 (m-10)
REVERT: B  230 ASN cc_start: 0.8605 (t0) cc_final: 0.8207 (t0)
REVERT: B  233 CYS cc_start: 0.8703 (t) cc_final: 0.8258 (t)
REVERT: B  234 PHE cc_start: 0.8703 (OUTLIER) cc_final: 0.7799 (m-10)
REVERT: B  339 TRP cc_start: 0.9059 (m100) cc_final: 0.8482 (m-10)
REVERT: C   11 GLN cc_start: 0.6604 (pm20) cc_final: 0.5956 (tm-30)
REVERT: C   32 LYS cc_start: 0.6287 (tppt) cc_final: 0.5700 (mttt)
REVERT: R  179 ARG cc_start: 0.9044 (ptm-80) cc_final: 0.8683 (ptm160)
REVERT: R  211 ARG cc_start: 0.6826 (ttm110) cc_final: 0.6279 (mtt90)
REVERT: R  251 CYS cc_start: 0.8820 (OUTLIER) cc_final: 0.8243 (t)
REVERT: R  293 TRP cc_start: 0.7951 (OUTLIER) cc_final: 0.6967 (m-10)
  outliers start: 28
  outliers final: 20
  residues processed: 173
  average time/residue: 0.0978
  time to fit residues: 21.9054
Evaluate side-chains
  169 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 143
  time to evaluate  : 0.266 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    9 ASP
Chi-restraints excluded: chain A residue   34 VAL
Chi-restraints excluded: chain A residue  193 ASP
Chi-restraints excluded: chain A residue  254 CYS
Chi-restraints excluded: chain A residue  273 LEU
Chi-restraints excluded: chain A residue  276 GLU
Chi-restraints excluded: chain B residue   38 ASP
Chi-restraints excluded: chain B residue   79 LEU
Chi-restraints excluded: chain B residue  112 VAL
Chi-restraints excluded: chain B residue  148 CYS
Chi-restraints excluded: chain B residue  164 THR
Chi-restraints excluded: chain B residue  190 LEU
Chi-restraints excluded: chain B residue  200 VAL
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain C residue   16 VAL
Chi-restraints excluded: chain C residue   37 LEU
Chi-restraints excluded: chain R residue   79 CYS
Chi-restraints excluded: chain R residue   88 LEU
Chi-restraints excluded: chain R residue  121 LEU
Chi-restraints excluded: chain R residue  162 SER
Chi-restraints excluded: chain R residue  231 LEU
Chi-restraints excluded: chain R residue  251 CYS
Chi-restraints excluded: chain R residue  290 ILE
Chi-restraints excluded: chain R residue  293 TRP
Chi-restraints excluded: chain R residue  300 VAL
Chi-restraints excluded: chain R residue  322 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 87
   random chunks:
   chunk 5 optimal weight:    0.5980
   chunk 27 optimal weight:    1.9990
   chunk 40 optimal weight:    0.0980
   chunk 74 optimal weight:    0.9980
   chunk 83 optimal weight:    2.9990
   chunk 81 optimal weight:    0.9990
   chunk 26 optimal weight:    0.8980
   chunk 84 optimal weight:    0.8980
   chunk 72 optimal weight:    3.9990
   chunk 19 optimal weight:    0.5980
   chunk 49 optimal weight:    2.9990
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
B  13 GLN
C  18 GLN
** R 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3710 r_free = 0.3710 target = 0.138498 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3457 r_free = 0.3457 target = 0.118366 restraints weight = 12044.324|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3509 r_free = 0.3509 target = 0.122347 restraints weight = 6695.937|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3543 r_free = 0.3543 target = 0.125094 restraints weight = 4328.401|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3568 r_free = 0.3568 target = 0.127054 restraints weight = 3094.084|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3585 r_free = 0.3585 target = 0.128416 restraints weight = 2365.288|
|-----------------------------------------------------------------------------|
r_work (final): 0.3584
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6861
moved from start:          0.4707

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   6946  Z= 0.123
  Angle     :  0.623   8.768   9432  Z= 0.312
  Chirality :  0.043   0.329   1098
  Planarity :  0.004   0.042   1189
  Dihedral  :  5.013  65.464    957
  Min Nonbonded Distance : 2.448

Molprobity Statistics.
  All-atom Clashscore : 11.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.14 %
    Favored  : 94.86 %
  Rotamer:
    Outliers :  4.01 %
    Allowed  : 24.75 %
    Favored  : 71.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    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: -1.38 (0.30), residues: 875
  helix:  0.62 (0.29), residues: 345
  sheet: -2.33 (0.41), residues: 140
  loop : -1.75 (0.34), residues: 390

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A 313 
 TYR   0.016   0.001   TYR R 149 
 PHE   0.010   0.001   PHE A 274 
 TRP   0.014   0.001   TRP B 169 
 HIS   0.004   0.001   HIS B 142 

Details of bonding type rmsd
  covalent geometry    : bond        0.00283 ( 6943)
  covalent geometry    : angle       0.62253 ( 9427)
  SS BOND              : bond        0.00204 (    1)
  SS BOND              : angle       0.78544 (    2)
  hydrogen bonds       : bond        0.03094 (  290)
  hydrogen bonds       : angle       4.78872 (  849)
  Misc. bond           : bond        0.00008 (    1)
  link_TRANS           : bond        0.00034 (    1)
  link_TRANS           : angle       0.70334 (    3)

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

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

  1750 Ramachandran restraints generated.
    875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1750 Ramachandran restraints generated.
    875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  175 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 147
  time to evaluate  : 0.307 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   22 ASN cc_start: 0.8596 (m-40) cc_final: 0.8134 (t0)
REVERT: A   32 ARG cc_start: 0.7444 (ttm110) cc_final: 0.7172 (ttm110)
REVERT: A  214 CYS cc_start: 0.9150 (t) cc_final: 0.8865 (t)
REVERT: A  247 MET cc_start: 0.7894 (mtm) cc_final: 0.7554 (mtt)
REVERT: A  276 GLU cc_start: 0.6027 (OUTLIER) cc_final: 0.5114 (tp30)
REVERT: B   32 GLN cc_start: 0.6291 (tp40) cc_final: 0.5878 (tp40)
REVERT: B   51 LEU cc_start: 0.8935 (mt) cc_final: 0.8689 (mp)
REVERT: B  164 THR cc_start: 0.8988 (OUTLIER) cc_final: 0.8658 (p)
REVERT: B  212 ASP cc_start: 0.7324 (p0) cc_final: 0.6859 (p0)
REVERT: B  222 PHE cc_start: 0.8586 (m-80) cc_final: 0.8357 (m-10)
REVERT: B  230 ASN cc_start: 0.8527 (t0) cc_final: 0.7689 (t0)
REVERT: B  233 CYS cc_start: 0.8669 (t) cc_final: 0.8238 (t)
REVERT: B  234 PHE cc_start: 0.8692 (OUTLIER) cc_final: 0.7739 (m-10)
REVERT: B  339 TRP cc_start: 0.9030 (m100) cc_final: 0.8449 (m-10)
REVERT: C   11 GLN cc_start: 0.6641 (pm20) cc_final: 0.5986 (tm-30)
REVERT: C   32 LYS cc_start: 0.6308 (tppt) cc_final: 0.5721 (mttt)
REVERT: R   99 MET cc_start: 0.6776 (mmp) cc_final: 0.6453 (mmp)
REVERT: R  177 ASP cc_start: 0.8388 (t0) cc_final: 0.7913 (t0)
REVERT: R  179 ARG cc_start: 0.9037 (ptm-80) cc_final: 0.8754 (ptm160)
REVERT: R  211 ARG cc_start: 0.6827 (ttm110) cc_final: 0.6353 (mtt90)
REVERT: R  251 CYS cc_start: 0.8852 (OUTLIER) cc_final: 0.8310 (t)
REVERT: R  255 MET cc_start: 0.8621 (ttt) cc_final: 0.8394 (ttt)
REVERT: R  293 TRP cc_start: 0.7939 (OUTLIER) cc_final: 0.6992 (m-10)
  outliers start: 28
  outliers final: 19
  residues processed: 170
  average time/residue: 0.0939
  time to fit residues: 20.7652
Evaluate side-chains
  168 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 144
  time to evaluate  : 0.270 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 VAL
Chi-restraints excluded: chain A residue  193 ASP
Chi-restraints excluded: chain A residue  254 CYS
Chi-restraints excluded: chain A residue  273 LEU
Chi-restraints excluded: chain A residue  276 GLU
Chi-restraints excluded: chain B residue   38 ASP
Chi-restraints excluded: chain B residue   79 LEU
Chi-restraints excluded: chain B residue  112 VAL
Chi-restraints excluded: chain B residue  148 CYS
Chi-restraints excluded: chain B residue  164 THR
Chi-restraints excluded: chain B residue  184 THR
Chi-restraints excluded: chain B residue  190 LEU
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain C residue   16 VAL
Chi-restraints excluded: chain C residue   37 LEU
Chi-restraints excluded: chain R residue   79 CYS
Chi-restraints excluded: chain R residue  121 LEU
Chi-restraints excluded: chain R residue  231 LEU
Chi-restraints excluded: chain R residue  251 CYS
Chi-restraints excluded: chain R residue  290 ILE
Chi-restraints excluded: chain R residue  293 TRP
Chi-restraints excluded: chain R residue  315 THR
Chi-restraints excluded: chain R residue  322 ILE
Chi-restraints excluded: chain R residue  324 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 87
   random chunks:
   chunk 33 optimal weight:    0.7980
   chunk 11 optimal weight:    0.9980
   chunk 39 optimal weight:    0.8980
   chunk 64 optimal weight:    0.8980
   chunk 5 optimal weight:    6.9990
   chunk 50 optimal weight:    0.2980
   chunk 10 optimal weight:    0.6980
   chunk 68 optimal weight:    0.8980
   chunk 26 optimal weight:    0.6980
   chunk 41 optimal weight:    0.4980
   chunk 23 optimal weight:    0.7980
   overall best weight:    0.5980

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

Flipped N/Q/H residues before XYZ refinement:
B 266 HIS
C  18 GLN
** R 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3714 r_free = 0.3714 target = 0.138889 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3454 r_free = 0.3454 target = 0.118045 restraints weight = 12009.658|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3507 r_free = 0.3507 target = 0.122219 restraints weight = 6582.790|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3544 r_free = 0.3544 target = 0.125112 restraints weight = 4215.665|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3570 r_free = 0.3570 target = 0.127159 restraints weight = 2989.200|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3586 r_free = 0.3586 target = 0.128488 restraints weight = 2277.779|
|-----------------------------------------------------------------------------|
r_work (final): 0.3650
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6780
moved from start:          0.4806

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   6946  Z= 0.123
  Angle     :  0.630   8.749   9432  Z= 0.316
  Chirality :  0.043   0.301   1098
  Planarity :  0.004   0.040   1189
  Dihedral  :  4.981  65.689    957
  Min Nonbonded Distance : 2.439

Molprobity Statistics.
  All-atom Clashscore : 11.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.91 %
    Favored  : 95.09 %
  Rotamer:
    Outliers :  3.86 %
    Allowed  : 25.32 %
    Favored  : 70.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    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: -1.30 (0.30), residues: 875
  helix:  0.69 (0.28), residues: 345
  sheet: -2.33 (0.41), residues: 140
  loop : -1.68 (0.34), residues: 390

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG C  13 
 TYR   0.016   0.001   TYR R 149 
 PHE   0.011   0.001   PHE B 234 
 TRP   0.013   0.001   TRP B 169 
 HIS   0.003   0.001   HIS B 142 

Details of bonding type rmsd
  covalent geometry    : bond        0.00284 ( 6943)
  covalent geometry    : angle       0.62971 ( 9427)
  SS BOND              : bond        0.00102 (    1)
  SS BOND              : angle       0.79057 (    2)
  hydrogen bonds       : bond        0.03097 (  290)
  hydrogen bonds       : angle       4.78110 (  849)
  Misc. bond           : bond        0.00007 (    1)
  link_TRANS           : bond        0.00032 (    1)
  link_TRANS           : angle       0.41702 (    3)

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

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

  1750 Ramachandran restraints generated.
    875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1750 Ramachandran restraints generated.
    875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  175 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 148
  time to evaluate  : 0.248 
Fit side-chains
   revert: symmetry clash
REVERT: A   22 ASN cc_start: 0.8530 (m-40) cc_final: 0.8070 (t0)
REVERT: A   32 ARG cc_start: 0.7427 (ttm110) cc_final: 0.7129 (ttm110)
REVERT: A  214 CYS cc_start: 0.9177 (t) cc_final: 0.8939 (t)
REVERT: A  276 GLU cc_start: 0.5987 (OUTLIER) cc_final: 0.5036 (tp30)
REVERT: A  313 ARG cc_start: 0.8519 (ttm-80) cc_final: 0.8304 (mtp85)
REVERT: B   32 GLN cc_start: 0.6495 (tp40) cc_final: 0.6050 (tp40)
REVERT: B   82 TRP cc_start: 0.8704 (m100) cc_final: 0.7750 (m100)
REVERT: B  164 THR cc_start: 0.9035 (OUTLIER) cc_final: 0.8691 (p)
REVERT: B  169 TRP cc_start: 0.7854 (OUTLIER) cc_final: 0.7000 (m-90)
REVERT: B  212 ASP cc_start: 0.7157 (p0) cc_final: 0.5948 (p0)
REVERT: B  215 GLU cc_start: 0.7607 (pm20) cc_final: 0.7156 (pm20)
REVERT: B  219 ARG cc_start: 0.8027 (ttm170) cc_final: 0.7306 (mmt90)
REVERT: B  222 PHE cc_start: 0.8622 (m-80) cc_final: 0.8344 (m-10)
REVERT: B  230 ASN cc_start: 0.8521 (t0) cc_final: 0.7748 (t0)
REVERT: B  234 PHE cc_start: 0.8625 (OUTLIER) cc_final: 0.7801 (m-10)
REVERT: B  339 TRP cc_start: 0.9045 (m100) cc_final: 0.8437 (m-10)
REVERT: C   11 GLN cc_start: 0.6620 (pm20) cc_final: 0.5957 (tm-30)
REVERT: C   32 LYS cc_start: 0.6125 (tppt) cc_final: 0.5608 (mttt)
REVERT: R   99 MET cc_start: 0.6544 (mmp) cc_final: 0.6149 (mmp)
REVERT: R  179 ARG cc_start: 0.9066 (ptm-80) cc_final: 0.8659 (ptm160)
REVERT: R  211 ARG cc_start: 0.6811 (ttm110) cc_final: 0.6287 (mtt90)
REVERT: R  251 CYS cc_start: 0.8819 (OUTLIER) cc_final: 0.8149 (t)
REVERT: R  255 MET cc_start: 0.8589 (ttt) cc_final: 0.8353 (ttt)
REVERT: R  293 TRP cc_start: 0.7867 (OUTLIER) cc_final: 0.6940 (m-10)
  outliers start: 27
  outliers final: 20
  residues processed: 170
  average time/residue: 0.0891
  time to fit residues: 19.9935
Evaluate side-chains
  170 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 144
  time to evaluate  : 0.295 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    9 ASP
Chi-restraints excluded: chain A residue   34 VAL
Chi-restraints excluded: chain A residue  193 ASP
Chi-restraints excluded: chain A residue  254 CYS
Chi-restraints excluded: chain A residue  273 LEU
Chi-restraints excluded: chain A residue  276 GLU
Chi-restraints excluded: chain B residue   38 ASP
Chi-restraints excluded: chain B residue   79 LEU
Chi-restraints excluded: chain B residue  112 VAL
Chi-restraints excluded: chain B residue  148 CYS
Chi-restraints excluded: chain B residue  164 THR
Chi-restraints excluded: chain B residue  168 LEU
Chi-restraints excluded: chain B residue  169 TRP
Chi-restraints excluded: chain B residue  190 LEU
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain C residue   16 VAL
Chi-restraints excluded: chain C residue   37 LEU
Chi-restraints excluded: chain R residue   79 CYS
Chi-restraints excluded: chain R residue  121 LEU
Chi-restraints excluded: chain R residue  231 LEU
Chi-restraints excluded: chain R residue  251 CYS
Chi-restraints excluded: chain R residue  290 ILE
Chi-restraints excluded: chain R residue  293 TRP
Chi-restraints excluded: chain R residue  315 THR
Chi-restraints excluded: chain R residue  322 ILE
Chi-restraints excluded: chain R residue  324 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 87
   random chunks:
   chunk 76 optimal weight:    1.9990
   chunk 13 optimal weight:    0.5980
   chunk 59 optimal weight:    0.0970
   chunk 82 optimal weight:    1.9990
   chunk 22 optimal weight:    0.9980
   chunk 64 optimal weight:    1.9990
   chunk 21 optimal weight:    2.9990
   chunk 18 optimal weight:    2.9990
   chunk 34 optimal weight:    1.9990
   chunk 32 optimal weight:    0.8980
   chunk 71 optimal weight:    0.7980
   overall best weight:    0.6778

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

Flipped N/Q/H residues before XYZ refinement:
B 266 HIS
C  18 GLN
** R 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3776 r_free = 0.3776 target = 0.142945 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3527 r_free = 0.3527 target = 0.122797 restraints weight = 11798.253|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3579 r_free = 0.3579 target = 0.126922 restraints weight = 6427.367|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3615 r_free = 0.3615 target = 0.129775 restraints weight = 4105.572|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3638 r_free = 0.3638 target = 0.131644 restraints weight = 2902.347|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3656 r_free = 0.3656 target = 0.133116 restraints weight = 2227.507|
|-----------------------------------------------------------------------------|
r_work (final): 0.3650
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6861
moved from start:          0.4890

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   6946  Z= 0.129
  Angle     :  0.636   8.839   9432  Z= 0.317
  Chirality :  0.043   0.172   1098
  Planarity :  0.004   0.057   1189
  Dihedral  :  4.956  65.161    957
  Min Nonbonded Distance : 2.453

Molprobity Statistics.
  All-atom Clashscore : 10.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.37 %
    Favored  : 94.63 %
  Rotamer:
    Outliers :  4.15 %
    Allowed  : 25.46 %
    Favored  : 70.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    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: -1.27 (0.30), residues: 875
  helix:  0.69 (0.28), residues: 345
  sheet: -2.33 (0.41), residues: 140
  loop : -1.64 (0.34), residues: 390

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.015   0.001   ARG C  13 
 TYR   0.016   0.001   TYR R 149 
 PHE   0.012   0.001   PHE B 234 
 TRP   0.013   0.001   TRP B 169 
 HIS   0.003   0.001   HIS B 142 

Details of bonding type rmsd
  covalent geometry    : bond        0.00301 ( 6943)
  covalent geometry    : angle       0.63569 ( 9427)
  SS BOND              : bond        0.00187 (    1)
  SS BOND              : angle       0.81694 (    2)
  hydrogen bonds       : bond        0.03094 (  290)
  hydrogen bonds       : angle       4.79259 (  849)
  Misc. bond           : bond        0.00006 (    1)
  link_TRANS           : bond        0.00053 (    1)
  link_TRANS           : angle       0.40138 (    3)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1320.94 seconds
wall clock time: 23 minutes 35.53 seconds (1415.53 seconds total)