Starting phenix.real_space_refine
on Wed Feb 12 00:33:19 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6ddf_7869/02_2025/6ddf_7869_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6ddf_7869/02_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 {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6ddf_7869/02_2025/6ddf_7869.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6ddf_7869/02_2025/6ddf_7869.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6ddf_7869/02_2025/6ddf_7869_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6ddf_7869/02_2025/6ddf_7869_neut.cif"
  }
  resolution = 3.5
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.021 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): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/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: {'GLU:plan': 1, 'ARG:plan': 2, '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: {'GLU:plan': 1, 'ASP:plan': 2}
          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: {'GLN:plan1': 1, 'PHE:plan': 3, 'ARG:plan': 2, 'ASN:plan1': 2, 'ASP:plan': 1}
          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: 4.68, per 1000 atoms: 0.69
  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: 1.98
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  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: 0.71
  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: 1.76

  Time building geometry restraints manager: 2.14 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:             2.990
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.850
  Check model and map are aligned:         0.000
  Set scattering table:                    0.000
  Process input model:                     18.600
  Find NCS groups from input model:        0.080
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.770
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   25.310
-------------------------------------------------------------------------------
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   6943  Z= 0.399
  Angle     :  1.014  10.968   9427  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 : 7.85
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -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
 TRP   0.042   0.004   TRP B  63 
 HIS   0.011   0.002   HIS B 183 
 PHE   0.031   0.003   PHE B 241 
 TYR   0.031   0.003   TYR R 299 
 ARG   0.004   0.001   ARG A 242 

*********************** 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  : 0.692 
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: 0.2273
  time to fit residues: 71.4284
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  : 0.822 
-------------------------------------------------------------------------------
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 73 optimal weight:    5.9990
   chunk 65 optimal weight:    0.0060
   chunk 36 optimal weight:    0.6980
   chunk 22 optimal weight:    0.9980
   chunk 44 optimal weight:    0.8980
   chunk 35 optimal weight:    0.7980
   chunk 68 optimal weight:    0.5980
   chunk 26 optimal weight:    0.8980
   chunk 41 optimal weight:    2.9990
   chunk 50 optimal weight:    0.7980
   chunk 79 optimal weight:    2.9990
   overall best weight:    0.5796

-------------------------------------------------------------------------------
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 ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3796 r_free = 0.3796 target = 0.145206 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3549 r_free = 0.3549 target = 0.125005 restraints weight = 11762.112|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3599 r_free = 0.3599 target = 0.129051 restraints weight = 6514.128|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3633 r_free = 0.3633 target = 0.131836 restraints weight = 4196.211|
|-----------------------------------------------------------------------------|
r_work (final): 0.3642
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6917
moved from start:          0.2718

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.052   6943  Z= 0.202
  Angle     :  0.673   9.027   9427  Z= 0.345
  Chirality :  0.042   0.135   1098
  Planarity :  0.005   0.044   1189
  Dihedral  :  6.057  64.944    959
  Min Nonbonded Distance : 2.504

Molprobity Statistics.
  All-atom Clashscore : 10.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.37 %
    Favored  : 94.63 %
  Rotamer:
    Outliers :  3.72 %
    Allowed  : 15.31 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.22 (0.26), residues: 875
  helix: -1.12 (0.25), residues: 341
  sheet: -3.17 (0.36), residues: 161
  loop : -2.52 (0.31), residues: 373

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP B 169 
 HIS   0.003   0.001   HIS B 142 
 PHE   0.015   0.001   PHE B 151 
 TYR   0.015   0.001   TYR R 149 
 ARG   0.006   0.001   ARG R 211 

*********************** 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
  222 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 196
  time to evaluate  : 0.751 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   26 ASP cc_start: 0.8880 (t70) cc_final: 0.8240 (t0)
REVERT: B  215 GLU cc_start: 0.7694 (pm20) cc_final: 0.7140 (pm20)
REVERT: B  219 ARG cc_start: 0.8016 (ttm170) cc_final: 0.7715 (mmt90)
REVERT: B  222 PHE cc_start: 0.8508 (m-10) cc_final: 0.8159 (m-10)
REVERT: B  230 ASN cc_start: 0.8804 (t0) cc_final: 0.8321 (m110)
REVERT: B  234 PHE cc_start: 0.8682 (OUTLIER) cc_final: 0.7860 (m-10)
REVERT: B  339 TRP cc_start: 0.8871 (m100) cc_final: 0.8561 (m-10)
REVERT: C   32 LYS cc_start: 0.6960 (tppt) cc_final: 0.6049 (mttm)
REVERT: R  239 PHE cc_start: 0.7918 (OUTLIER) cc_final: 0.7613 (m-80)
REVERT: R  248 ILE cc_start: 0.8185 (pt) cc_final: 0.7953 (mt)
REVERT: R  292 CYS cc_start: 0.8428 (m) cc_final: 0.8186 (m)
REVERT: R  324 LEU cc_start: 0.7437 (OUTLIER) cc_final: 0.7066 (pt)
  outliers start: 26
  outliers final: 17
  residues processed: 214
  average time/residue: 0.2160
  time to fit residues: 59.9221
Evaluate side-chains
  183 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 163
  time to evaluate  : 0.784 
-------------------------------------------------------------------------------
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  168 LEU
Chi-restraints excluded: chain B residue  171 ILE
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  204 CYS
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  284 VAL
Chi-restraints excluded: chain R residue  290 ILE
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 41 optimal weight:    4.9990
   chunk 21 optimal weight:    6.9990
   chunk 9 optimal weight:    0.6980
   chunk 13 optimal weight:    0.1980
   chunk 23 optimal weight:    1.9990
   chunk 68 optimal weight:    0.8980
   chunk 11 optimal weight:    2.9990
   chunk 86 optimal weight:    0.3980
   chunk 3 optimal weight:    0.9990
   chunk 49 optimal weight:    0.9980
   chunk 50 optimal weight:    1.9990
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
A 213 HIS
B  13 GLN
B  32 GLN
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 = 0.3895 r_free = 0.3895 target = 0.151142 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3653 r_free = 0.3653 target = 0.131207 restraints weight = 11581.413|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3707 r_free = 0.3707 target = 0.135469 restraints weight = 6101.067|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3742 r_free = 0.3742 target = 0.138312 restraints weight = 3837.422|
|-----------------------------------------------------------------------------|
r_work (final): 0.3724
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7272
moved from start:          0.3369

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   6943  Z= 0.189
  Angle     :  0.646   9.196   9427  Z= 0.326
  Chirality :  0.042   0.130   1098
  Planarity :  0.004   0.037   1189
  Dihedral  :  5.579  62.189    959
  Min Nonbonded Distance : 2.484

Molprobity Statistics.
  All-atom Clashscore : 10.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.37 %
    Favored  : 94.63 %
  Rotamer:
    Outliers :  4.86 %
    Allowed  : 18.88 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.64 (0.28), residues: 875
  helix: -0.45 (0.27), residues: 348
  sheet: -3.00 (0.37), residues: 152
  loop : -2.38 (0.33), residues: 375

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP B 169 
 HIS   0.004   0.001   HIS B 183 
 PHE   0.010   0.001   PHE A 189 
 TYR   0.017   0.001   TYR R 149 
 ARG   0.006   0.001   ARG A 313 

*********************** 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
  209 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 175
  time to evaluate  : 0.608 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   26 ASP cc_start: 0.8708 (t70) cc_final: 0.7817 (t0)
REVERT: B   78 LYS cc_start: 0.8964 (mmpt) cc_final: 0.8544 (mmtp)
REVERT: B  234 PHE cc_start: 0.8755 (OUTLIER) cc_final: 0.8158 (m-10)
REVERT: B  297 TRP cc_start: 0.8812 (m100) cc_final: 0.8398 (m100)
REVERT: C   18 GLN cc_start: 0.7870 (tp40) cc_final: 0.7640 (tp40)
REVERT: C   32 LYS cc_start: 0.7237 (tppt) cc_final: 0.6567 (mttm)
REVERT: R  293 TRP cc_start: 0.8286 (OUTLIER) cc_final: 0.7164 (m-10)
REVERT: R  314 GLN cc_start: 0.8653 (OUTLIER) cc_final: 0.8438 (tt0)
REVERT: R  324 LEU cc_start: 0.7536 (OUTLIER) cc_final: 0.7196 (pt)
  outliers start: 34
  outliers final: 16
  residues processed: 195
  average time/residue: 0.2035
  time to fit residues: 51.3748
Evaluate side-chains
  177 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 157
  time to evaluate  : 0.745 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    9 ASP
Chi-restraints excluded: chain A residue   32 ARG
Chi-restraints excluded: chain A residue  185 VAL
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  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  314 GLN
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 85 optimal weight:    0.7980
   chunk 81 optimal weight:    0.9980
   chunk 83 optimal weight:    1.9990
   chunk 50 optimal weight:    1.9990
   chunk 39 optimal weight:    1.9990
   chunk 62 optimal weight:    7.9990
   chunk 53 optimal weight:    0.9990
   chunk 75 optimal weight:    1.9990
   chunk 79 optimal weight:    4.9990
   chunk 58 optimal weight:    4.9990
   chunk 26 optimal weight:    0.8980
   overall best weight:    1.1384

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

Flipped N/Q/H residues before XYZ refinement:
B  13 GLN
B  32 GLN
B 230 ASN
R 150 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3865 r_free = 0.3865 target = 0.148175 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3614 r_free = 0.3614 target = 0.128181 restraints weight = 11459.133|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3668 r_free = 0.3668 target = 0.132306 restraints weight = 6109.211|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3703 r_free = 0.3703 target = 0.135063 restraints weight = 3875.911|
|-----------------------------------------------------------------------------|
r_work (final): 0.3701
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7324
moved from start:          0.3680

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.055   6943  Z= 0.264
  Angle     :  0.656   8.831   9427  Z= 0.336
  Chirality :  0.043   0.124   1098
  Planarity :  0.004   0.034   1189
  Dihedral  :  5.540  59.028    959
  Min Nonbonded Distance : 2.511

Molprobity Statistics.
  All-atom Clashscore : 11.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.40 %
    Favored  : 93.60 %
  Rotamer:
    Outliers :  5.72 %
    Allowed  : 20.03 %
    Favored  : 74.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.40 (0.28), residues: 875
  helix: -0.29 (0.27), residues: 352
  sheet: -2.92 (0.36), residues: 156
  loop : -2.19 (0.34), residues: 367

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP B 169 
 HIS   0.003   0.001   HIS B 183 
 PHE   0.025   0.002   PHE B 222 
 TYR   0.017   0.002   TYR R 149 
 ARG   0.006   0.001   ARG R 263 

*********************** 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
  201 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 161
  time to evaluate  : 0.769 
Fit side-chains
   revert: symmetry clash
REVERT: A   26 ASP cc_start: 0.8751 (t70) cc_final: 0.8111 (t0)
REVERT: A  198 MET cc_start: 0.8269 (mmp) cc_final: 0.7889 (mmp)
REVERT: A  313 ARG cc_start: 0.8112 (ttm-80) cc_final: 0.7857 (ptm160)
REVERT: B  117 LEU cc_start: 0.7952 (OUTLIER) cc_final: 0.7721 (tt)
REVERT: B  212 ASP cc_start: 0.7297 (p0) cc_final: 0.6891 (p0)
REVERT: B  234 PHE cc_start: 0.8837 (OUTLIER) cc_final: 0.8177 (m-10)
REVERT: B  339 TRP cc_start: 0.8861 (m-10) cc_final: 0.8638 (m-10)
REVERT: C   18 GLN cc_start: 0.7821 (tp40) cc_final: 0.7572 (tp40)
REVERT: C   32 LYS cc_start: 0.7185 (tppt) cc_final: 0.6755 (mtmt)
REVERT: R   83 LEU cc_start: 0.7700 (tm) cc_final: 0.7042 (tm)
REVERT: R   87 PHE cc_start: 0.8013 (m-10) cc_final: 0.7695 (m-80)
REVERT: R   98 LYS cc_start: 0.7019 (mmtt) cc_final: 0.6047 (mmmt)
REVERT: R  179 ARG cc_start: 0.9002 (ptm-80) cc_final: 0.8689 (ptm160)
REVERT: R  293 TRP cc_start: 0.8281 (OUTLIER) cc_final: 0.7048 (m-10)
  outliers start: 40
  outliers final: 25
  residues processed: 187
  average time/residue: 0.2142
  time to fit residues: 51.8663
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  : 0.762 
-------------------------------------------------------------------------------
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  254 CYS
Chi-restraints excluded: chain A residue  273 LEU
Chi-restraints excluded: chain B residue   79 LEU
Chi-restraints excluded: chain B residue   89 LYS
Chi-restraints excluded: chain B residue   97 SER
Chi-restraints excluded: chain B residue  112 VAL
Chi-restraints excluded: chain B residue  117 LEU
Chi-restraints excluded: chain B residue  119 ASN
Chi-restraints excluded: chain B residue  133 VAL
Chi-restraints excluded: chain B residue  148 CYS
Chi-restraints excluded: chain B residue  168 LEU
Chi-restraints excluded: chain B residue  171 ILE
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  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 82 optimal weight:    0.9990
   chunk 71 optimal weight:    4.9990
   chunk 35 optimal weight:    2.9990
   chunk 41 optimal weight:    0.7980
   chunk 53 optimal weight:    0.6980
   chunk 81 optimal weight:    0.6980
   chunk 13 optimal weight:    0.6980
   chunk 4 optimal weight:    0.8980
   chunk 3 optimal weight:    0.9980
   chunk 12 optimal weight:    1.9990
   chunk 44 optimal weight:    1.9990
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
B  13 GLN
B  32 GLN
B 110 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3864 r_free = 0.3864 target = 0.148376 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3614 r_free = 0.3614 target = 0.128409 restraints weight = 11586.001|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3668 r_free = 0.3668 target = 0.132502 restraints weight = 6219.520|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3703 r_free = 0.3703 target = 0.135261 restraints weight = 3953.082|
|-----------------------------------------------------------------------------|
r_work (final): 0.3712
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7312
moved from start:          0.4015

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   6943  Z= 0.207
  Angle     :  0.623   9.726   9427  Z= 0.317
  Chirality :  0.042   0.139   1098
  Planarity :  0.003   0.033   1189
  Dihedral  :  5.384  63.304    959
  Min Nonbonded Distance : 2.535

Molprobity Statistics.
  All-atom Clashscore : 10.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.71 %
    Favored  : 94.29 %
  Rotamer:
    Outliers :  4.86 %
    Allowed  : 22.03 %
    Favored  : 73.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.09 (0.29), residues: 875
  helix:  0.01 (0.28), residues: 343
  sheet: -2.62 (0.38), residues: 155
  loop : -2.10 (0.34), residues: 377

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP B 169 
 HIS   0.004   0.001   HIS B 142 
 PHE   0.024   0.001   PHE B 222 
 TYR   0.018   0.001   TYR R 149 
 ARG   0.006   0.001   ARG B 129 

*********************** 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
  194 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 160
  time to evaluate  : 0.898 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   26 ASP cc_start: 0.8749 (t70) cc_final: 0.7916 (t0)
REVERT: A   32 ARG cc_start: 0.7919 (ttp-110) cc_final: 0.7525 (ttm-80)
REVERT: A  310 LEU cc_start: 0.8542 (OUTLIER) cc_final: 0.7914 (tp)
REVERT: B   34 THR cc_start: 0.6421 (m) cc_final: 0.6148 (p)
REVERT: B   78 LYS cc_start: 0.8985 (mmtm) cc_final: 0.8591 (mmtp)
REVERT: B  164 THR cc_start: 0.8744 (OUTLIER) cc_final: 0.8330 (p)
REVERT: B  212 ASP cc_start: 0.7223 (p0) cc_final: 0.6728 (p0)
REVERT: B  219 ARG cc_start: 0.8066 (mmt90) cc_final: 0.7750 (mmt90)
REVERT: B  234 PHE cc_start: 0.8871 (OUTLIER) cc_final: 0.8128 (m-10)
REVERT: B  339 TRP cc_start: 0.8938 (m100) cc_final: 0.8656 (m-10)
REVERT: C   32 LYS cc_start: 0.7136 (tppt) cc_final: 0.6637 (mtmt)
REVERT: R   83 LEU cc_start: 0.7726 (tm) cc_final: 0.7515 (tm)
REVERT: R   98 LYS cc_start: 0.6918 (mmtt) cc_final: 0.6165 (mmmt)
REVERT: R  177 ASP cc_start: 0.8462 (t0) cc_final: 0.7945 (t0)
REVERT: R  179 ARG cc_start: 0.8975 (ptm-80) cc_final: 0.8690 (ptm160)
REVERT: R  293 TRP cc_start: 0.8179 (OUTLIER) cc_final: 0.6850 (m-10)
  outliers start: 34
  outliers final: 21
  residues processed: 183
  average time/residue: 0.2062
  time to fit residues: 48.9736
Evaluate side-chains
  178 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 153
  time to evaluate  : 0.869 
-------------------------------------------------------------------------------
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 A residue  310 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  119 ASN
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  171 ILE
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  231 LEU
Chi-restraints excluded: chain R residue  284 VAL
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=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 87
   random chunks:
   chunk 28 optimal weight:    1.9990
   chunk 27 optimal weight:    0.6980
   chunk 39 optimal weight:    0.6980
   chunk 29 optimal weight:    0.9990
   chunk 45 optimal weight:    0.6980
   chunk 84 optimal weight:    0.9990
   chunk 11 optimal weight:    1.9990
   chunk 75 optimal weight:    2.9990
   chunk 31 optimal weight:    0.9980
   chunk 40 optimal weight:    0.9990
   chunk 80 optimal weight:    2.9990
   overall best weight:    0.8182

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

Flipped N/Q/H residues before XYZ refinement:
C  18 GLN
R  86 ASN
R 150 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3862 r_free = 0.3862 target = 0.147775 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3616 r_free = 0.3616 target = 0.128273 restraints weight = 11532.534|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3671 r_free = 0.3671 target = 0.132437 restraints weight = 6117.589|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3706 r_free = 0.3706 target = 0.135185 restraints weight = 3836.468|
|-----------------------------------------------------------------------------|
r_work (final): 0.3706
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7313
moved from start:          0.4238

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048   6943  Z= 0.216
  Angle     :  0.629   9.663   9427  Z= 0.319
  Chirality :  0.043   0.152   1098
  Planarity :  0.004   0.034   1189
  Dihedral  :  5.370  62.810    959
  Min Nonbonded Distance : 2.544

Molprobity Statistics.
  All-atom Clashscore : 10.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.60 %
    Favored  : 94.40 %
  Rotamer:
    Outliers :  4.72 %
    Allowed  : 23.61 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.91 (0.29), residues: 875
  helix:  0.16 (0.28), residues: 344
  sheet: -2.43 (0.39), residues: 156
  loop : -2.05 (0.34), residues: 375

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP B 169 
 HIS   0.004   0.001   HIS B 183 
 PHE   0.026   0.001   PHE B 222 
 TYR   0.019   0.001   TYR R 149 
 ARG   0.007   0.001   ARG B 129 

*********************** 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
  196 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 163
  time to evaluate  : 0.763 
Fit side-chains
   revert: symmetry clash
REVERT: A   26 ASP cc_start: 0.8752 (t70) cc_final: 0.7981 (t0)
REVERT: A  310 LEU cc_start: 0.8525 (OUTLIER) cc_final: 0.7900 (tp)
REVERT: B   75 GLN cc_start: 0.8671 (mm110) cc_final: 0.7640 (mm110)
REVERT: B   78 LYS cc_start: 0.8939 (mmtm) cc_final: 0.8611 (mmtp)
REVERT: B  117 LEU cc_start: 0.7941 (OUTLIER) cc_final: 0.7335 (tt)
REVERT: B  118 ASP cc_start: 0.8221 (p0) cc_final: 0.7557 (p0)
REVERT: B  164 THR cc_start: 0.8775 (OUTLIER) cc_final: 0.8322 (p)
REVERT: B  212 ASP cc_start: 0.7224 (p0) cc_final: 0.6991 (p0)
REVERT: B  234 PHE cc_start: 0.8899 (OUTLIER) cc_final: 0.8154 (m-10)
REVERT: B  339 TRP cc_start: 0.9001 (m100) cc_final: 0.8666 (m-10)
REVERT: C   32 LYS cc_start: 0.6982 (tppt) cc_final: 0.6507 (mtmm)
REVERT: R   83 LEU cc_start: 0.7713 (tm) cc_final: 0.7021 (tm)
REVERT: R   87 PHE cc_start: 0.7844 (m-10) cc_final: 0.7584 (m-80)
REVERT: R  179 ARG cc_start: 0.8968 (ptm-80) cc_final: 0.8686 (ptm160)
REVERT: R  211 ARG cc_start: 0.6312 (mtt90) cc_final: 0.5868 (mtt90)
REVERT: R  293 TRP cc_start: 0.8093 (OUTLIER) cc_final: 0.7112 (m-10)
  outliers start: 33
  outliers final: 22
  residues processed: 185
  average time/residue: 0.2009
  time to fit residues: 48.3987
Evaluate side-chains
  174 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 147
  time to evaluate  : 0.789 
-------------------------------------------------------------------------------
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  273 LEU
Chi-restraints excluded: chain A residue  310 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  119 ASN
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  171 ILE
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  231 LEU
Chi-restraints excluded: chain R residue  259 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 42 optimal weight:    1.9990
   chunk 15 optimal weight:    2.9990
   chunk 24 optimal weight:    0.0970
   chunk 9 optimal weight:    1.9990
   chunk 43 optimal weight:    0.6980
   chunk 53 optimal weight:    4.9990
   chunk 3 optimal weight:    0.6980
   chunk 27 optimal weight:    0.8980
   chunk 0 optimal weight:    4.9990
   chunk 64 optimal weight:    6.9990
   chunk 58 optimal weight:    0.4980
   overall best weight:    0.5778

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

Flipped N/Q/H residues before XYZ refinement:
A 255 ASN
A 269 ASN
C  18 GLN
R  86 ASN
R 332 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3885 r_free = 0.3885 target = 0.150485 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3631 r_free = 0.3631 target = 0.130168 restraints weight = 11498.949|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3685 r_free = 0.3685 target = 0.134397 restraints weight = 6141.722|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3721 r_free = 0.3721 target = 0.137241 restraints weight = 3893.962|
|-----------------------------------------------------------------------------|
r_work (final): 0.3707
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7281
moved from start:          0.4472

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   6943  Z= 0.191
  Angle     :  0.626   8.882   9427  Z= 0.316
  Chirality :  0.043   0.262   1098
  Planarity :  0.004   0.036   1189
  Dihedral  :  5.259  64.939    959
  Min Nonbonded Distance : 2.462

Molprobity Statistics.
  All-atom Clashscore : 10.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.26 %
    Favored  : 94.74 %
  Rotamer:
    Outliers :  5.01 %
    Allowed  : 25.04 %
    Favored  : 69.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.68 (0.29), residues: 875
  helix:  0.38 (0.28), residues: 343
  sheet: -2.24 (0.40), residues: 155
  loop : -2.00 (0.34), residues: 377

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP B  82 
 HIS   0.003   0.001   HIS B 183 
 PHE   0.026   0.001   PHE B 222 
 TYR   0.018   0.001   TYR R 149 
 ARG   0.004   0.000   ARG R 211 

*********************** 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
  199 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 164
  time to evaluate  : 0.730 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   26 ASP cc_start: 0.8776 (t70) cc_final: 0.7955 (t0)
REVERT: A  247 MET cc_start: 0.7827 (mtm) cc_final: 0.7570 (mtt)
REVERT: A  276 GLU cc_start: 0.6173 (OUTLIER) cc_final: 0.5501 (tp30)
REVERT: A  310 LEU cc_start: 0.8445 (OUTLIER) cc_final: 0.7877 (tp)
REVERT: B   34 THR cc_start: 0.6212 (m) cc_final: 0.5949 (p)
REVERT: B   59 TYR cc_start: 0.8789 (m-80) cc_final: 0.8522 (m-80)
REVERT: B  164 THR cc_start: 0.8809 (OUTLIER) cc_final: 0.8458 (p)
REVERT: B  170 ASP cc_start: 0.7908 (t0) cc_final: 0.7666 (t0)
REVERT: B  200 VAL cc_start: 0.9227 (m) cc_final: 0.8836 (m)
REVERT: B  234 PHE cc_start: 0.8885 (OUTLIER) cc_final: 0.8072 (m-10)
REVERT: B  339 TRP cc_start: 0.9017 (m100) cc_final: 0.8723 (m-10)
REVERT: C   11 GLN cc_start: 0.6580 (pm20) cc_final: 0.6002 (tm-30)
REVERT: C   32 LYS cc_start: 0.6889 (tppt) cc_final: 0.6445 (mtmm)
REVERT: R   83 LEU cc_start: 0.7646 (OUTLIER) cc_final: 0.6930 (tm)
REVERT: R   87 PHE cc_start: 0.7833 (m-10) cc_final: 0.7413 (m-10)
REVERT: R   98 LYS cc_start: 0.6982 (mmtt) cc_final: 0.6074 (mmmt)
REVERT: R  179 ARG cc_start: 0.8960 (ptm-80) cc_final: 0.8681 (ptm160)
REVERT: R  293 TRP cc_start: 0.8095 (OUTLIER) cc_final: 0.6670 (m-10)
REVERT: R  329 SER cc_start: 0.8085 (t) cc_final: 0.7858 (p)
  outliers start: 35
  outliers final: 22
  residues processed: 187
  average time/residue: 0.1961
  time to fit residues: 48.5901
Evaluate side-chains
  180 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 152
  time to evaluate  : 0.900 
-------------------------------------------------------------------------------
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  273 LEU
Chi-restraints excluded: chain A residue  276 GLU
Chi-restraints excluded: chain A residue  310 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  171 ILE
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 C residue   18 GLN
Chi-restraints excluded: chain R residue   79 CYS
Chi-restraints excluded: chain R residue   83 LEU
Chi-restraints excluded: chain R residue   86 ASN
Chi-restraints excluded: chain R residue  121 LEU
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=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 87
   random chunks:
   chunk 30 optimal weight:    3.9990
   chunk 69 optimal weight:    0.7980
   chunk 15 optimal weight:    0.6980
   chunk 76 optimal weight:    3.9990
   chunk 10 optimal weight:    0.3980
   chunk 65 optimal weight:    0.1980
   chunk 51 optimal weight:    9.9990
   chunk 38 optimal weight:    1.9990
   chunk 53 optimal weight:    2.9990
   chunk 26 optimal weight:    0.6980
   chunk 48 optimal weight:    0.7980
   overall best weight:    0.5580

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

Flipped N/Q/H residues before XYZ refinement:
B  32 GLN
R  86 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3899 r_free = 0.3899 target = 0.150887 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3657 r_free = 0.3657 target = 0.131411 restraints weight = 11384.749|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3711 r_free = 0.3711 target = 0.135565 restraints weight = 6065.753|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3746 r_free = 0.3746 target = 0.138352 restraints weight = 3816.402|
|-----------------------------------------------------------------------------|
r_work (final): 0.3724
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7301
moved from start:          0.4609

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   6943  Z= 0.192
  Angle     :  0.630   9.039   9427  Z= 0.317
  Chirality :  0.043   0.298   1098
  Planarity :  0.004   0.035   1189
  Dihedral  :  5.152  65.235    957
  Min Nonbonded Distance : 2.474

Molprobity Statistics.
  All-atom Clashscore : 11.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.49 %
    Favored  : 94.51 %
  Rotamer:
    Outliers :  4.29 %
    Allowed  : 26.18 %
    Favored  : 69.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.49 (0.30), residues: 875
  helix:  0.51 (0.29), residues: 343
  sheet: -2.09 (0.41), residues: 146
  loop : -1.91 (0.34), residues: 386

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.002   TRP B  82 
 HIS   0.002   0.001   HIS B 142 
 PHE   0.012   0.001   PHE B 199 
 TYR   0.019   0.001   TYR R 149 
 ARG   0.004   0.000   ARG A 313 

*********************** 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
  182 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 152
  time to evaluate  : 0.825 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   26 ASP cc_start: 0.8657 (t70) cc_final: 0.7941 (t0)
REVERT: A   32 ARG cc_start: 0.7727 (ttm110) cc_final: 0.7408 (ttm110)
REVERT: A  247 MET cc_start: 0.7839 (mtm) cc_final: 0.7607 (mtt)
REVERT: A  276 GLU cc_start: 0.6110 (OUTLIER) cc_final: 0.5495 (tp30)
REVERT: A  310 LEU cc_start: 0.8516 (OUTLIER) cc_final: 0.8196 (tp)
REVERT: B   32 GLN cc_start: 0.6233 (OUTLIER) cc_final: 0.5940 (tm130)
REVERT: B   59 TYR cc_start: 0.8726 (m-80) cc_final: 0.8468 (m-80)
REVERT: B  164 THR cc_start: 0.8795 (OUTLIER) cc_final: 0.8388 (p)
REVERT: B  170 ASP cc_start: 0.7911 (t0) cc_final: 0.7679 (t0)
REVERT: B  200 VAL cc_start: 0.9262 (OUTLIER) cc_final: 0.8886 (m)
REVERT: B  234 PHE cc_start: 0.8877 (OUTLIER) cc_final: 0.8084 (m-10)
REVERT: B  339 TRP cc_start: 0.8957 (m100) cc_final: 0.8697 (m-10)
REVERT: C   32 LYS cc_start: 0.6908 (tppt) cc_final: 0.6388 (mttt)
REVERT: R   98 LYS cc_start: 0.6983 (mmtt) cc_final: 0.6127 (mmmt)
REVERT: R  179 ARG cc_start: 0.8914 (ptm-80) cc_final: 0.8601 (ptm160)
REVERT: R  293 TRP cc_start: 0.8058 (OUTLIER) cc_final: 0.7080 (m-10)
  outliers start: 30
  outliers final: 20
  residues processed: 174
  average time/residue: 0.2023
  time to fit residues: 45.8264
Evaluate side-chains
  171 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 144
  time to evaluate  : 0.817 
-------------------------------------------------------------------------------
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  273 LEU
Chi-restraints excluded: chain A residue  276 GLU
Chi-restraints excluded: chain A residue  310 LEU
Chi-restraints excluded: chain B residue   32 GLN
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  171 ILE
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   86 ASN
Chi-restraints excluded: chain R residue  121 LEU
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  322 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 87
   random chunks:
   chunk 79 optimal weight:    2.9990
   chunk 59 optimal weight:    0.5980
   chunk 47 optimal weight:    0.0070
   chunk 36 optimal weight:    0.9980
   chunk 21 optimal weight:    8.9990
   chunk 34 optimal weight:    0.8980
   chunk 38 optimal weight:    0.9980
   chunk 15 optimal weight:    0.0770
   chunk 54 optimal weight:    2.9990
   chunk 32 optimal weight:    3.9990
   chunk 27 optimal weight:    1.9990
   overall best weight:    0.5156

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

Flipped N/Q/H residues before XYZ refinement:
B  32 GLN
C  18 GLN
R  86 ASN
** R 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3901 r_free = 0.3901 target = 0.150943 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3658 r_free = 0.3658 target = 0.131405 restraints weight = 11426.117|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3712 r_free = 0.3712 target = 0.135554 restraints weight = 6088.566|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3748 r_free = 0.3748 target = 0.138365 restraints weight = 3829.734|
|-----------------------------------------------------------------------------|
r_work (final): 0.3751
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7295
moved from start:          0.4738

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   6943  Z= 0.191
  Angle     :  0.657  12.044   9427  Z= 0.323
  Chirality :  0.043   0.171   1098
  Planarity :  0.004   0.041   1189
  Dihedral  :  5.031  65.642    957
  Min Nonbonded Distance : 2.478

Molprobity Statistics.
  All-atom Clashscore : 11.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.26 %
    Favored  : 94.74 %
  Rotamer:
    Outliers :  4.15 %
    Allowed  : 26.90 %
    Favored  : 68.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.45 (0.29), residues: 875
  helix:  0.48 (0.28), residues: 344
  sheet: -1.96 (0.41), residues: 150
  loop : -1.86 (0.34), residues: 381

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP B  82 
 HIS   0.005   0.001   HIS B 183 
 PHE   0.011   0.001   PHE B 199 
 TYR   0.018   0.001   TYR D   1 
 ARG   0.009   0.001   ARG R 211 

*********************** 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
  180 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 151
  time to evaluate  : 0.814 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   22 ASN cc_start: 0.8918 (m-40) cc_final: 0.8438 (t0)
REVERT: A   26 ASP cc_start: 0.8650 (t70) cc_final: 0.7938 (t0)
REVERT: A   32 ARG cc_start: 0.7630 (ttm110) cc_final: 0.7408 (ttm110)
REVERT: A  198 MET cc_start: 0.7893 (mmp) cc_final: 0.7660 (mmp)
REVERT: A  247 MET cc_start: 0.7792 (mtm) cc_final: 0.7538 (mtt)
REVERT: A  276 GLU cc_start: 0.6117 (OUTLIER) cc_final: 0.5453 (tp30)
REVERT: B  164 THR cc_start: 0.8807 (OUTLIER) cc_final: 0.8402 (p)
REVERT: B  170 ASP cc_start: 0.7913 (t0) cc_final: 0.7687 (t0)
REVERT: B  200 VAL cc_start: 0.9269 (OUTLIER) cc_final: 0.8883 (m)
REVERT: B  222 PHE cc_start: 0.8677 (m-80) cc_final: 0.8448 (m-80)
REVERT: B  234 PHE cc_start: 0.8844 (OUTLIER) cc_final: 0.8076 (m-10)
REVERT: B  339 TRP cc_start: 0.8955 (m100) cc_final: 0.8706 (m-10)
REVERT: C   11 GLN cc_start: 0.6538 (pm20) cc_final: 0.6007 (tm-30)
REVERT: C   32 LYS cc_start: 0.6897 (tppt) cc_final: 0.6402 (mttt)
REVERT: R   98 LYS cc_start: 0.7005 (mmtt) cc_final: 0.6168 (mmmt)
REVERT: R  177 ASP cc_start: 0.8335 (t0) cc_final: 0.7988 (t0)
REVERT: R  179 ARG cc_start: 0.8903 (ptm-80) cc_final: 0.8686 (ptm160)
REVERT: R  293 TRP cc_start: 0.8046 (OUTLIER) cc_final: 0.7094 (m-10)
  outliers start: 29
  outliers final: 21
  residues processed: 172
  average time/residue: 0.1908
  time to fit residues: 43.0924
Evaluate side-chains
  168 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 142
  time to evaluate  : 0.722 
-------------------------------------------------------------------------------
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  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  171 ILE
Chi-restraints excluded: chain B residue  184 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   18 GLN
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  290 ILE
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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 87
   random chunks:
   chunk 17 optimal weight:    0.0010
   chunk 85 optimal weight:    0.6980
   chunk 23 optimal weight:    0.7980
   chunk 26 optimal weight:    4.9990
   chunk 48 optimal weight:    0.9990
   chunk 57 optimal weight:    0.8980
   chunk 20 optimal weight:    2.9990
   chunk 32 optimal weight:    1.9990
   chunk 58 optimal weight:    0.0970
   chunk 3 optimal weight:    0.0870
   chunk 39 optimal weight:    2.9990
   overall best weight:    0.3362

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

Flipped N/Q/H residues before XYZ refinement:
C  18 GLN
** R 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4011 r_free = 0.4011 target = 0.158236 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3774 r_free = 0.3774 target = 0.138464 restraints weight = 11190.321|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3827 r_free = 0.3827 target = 0.142745 restraints weight = 5812.101|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3863 r_free = 0.3863 target = 0.145642 restraints weight = 3611.881|
|-----------------------------------------------------------------------------|
r_work (final): 0.3866
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7253
moved from start:          0.4905

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   6943  Z= 0.172
  Angle     :  0.632   9.101   9427  Z= 0.315
  Chirality :  0.042   0.171   1098
  Planarity :  0.004   0.036   1189
  Dihedral  :  5.014  67.362    957
  Min Nonbonded Distance : 2.464

Molprobity Statistics.
  All-atom Clashscore : 10.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.91 %
    Favored  : 95.09 %
  Rotamer:
    Outliers :  4.29 %
    Allowed  : 26.47 %
    Favored  : 69.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.30 (0.29), residues: 875
  helix:  0.61 (0.29), residues: 344
  sheet: -1.91 (0.41), residues: 150
  loop : -1.76 (0.34), residues: 381

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP B  82 
 HIS   0.004   0.001   HIS B 183 
 PHE   0.011   0.001   PHE A 189 
 TYR   0.019   0.001   TYR R 149 
 ARG   0.007   0.001   ARG C  13 

********************** 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
  184 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 154
  time to evaluate  : 0.766 
Fit side-chains
   revert: symmetry clash
REVERT: A   22 ASN cc_start: 0.8927 (m-40) cc_final: 0.8524 (t0)
REVERT: A   26 ASP cc_start: 0.8640 (t70) cc_final: 0.7940 (t0)
REVERT: A  247 MET cc_start: 0.7805 (mtm) cc_final: 0.7573 (mtt)
REVERT: A  276 GLU cc_start: 0.6077 (OUTLIER) cc_final: 0.5379 (tp30)
REVERT: B   32 GLN cc_start: 0.6306 (OUTLIER) cc_final: 0.5832 (tm-30)
REVERT: B   38 ASP cc_start: 0.7780 (OUTLIER) cc_final: 0.7231 (m-30)
REVERT: B  164 THR cc_start: 0.8855 (OUTLIER) cc_final: 0.8444 (p)
REVERT: B  170 ASP cc_start: 0.7952 (t0) cc_final: 0.7706 (t0)
REVERT: B  200 VAL cc_start: 0.9254 (OUTLIER) cc_final: 0.8842 (m)
REVERT: B  222 PHE cc_start: 0.8594 (m-80) cc_final: 0.8349 (m-80)
REVERT: B  234 PHE cc_start: 0.8810 (OUTLIER) cc_final: 0.7961 (m-10)
REVERT: C   18 GLN cc_start: 0.7791 (OUTLIER) cc_final: 0.6322 (tm130)
REVERT: C   32 LYS cc_start: 0.6870 (tppt) cc_final: 0.6421 (mttt)
REVERT: R   98 LYS cc_start: 0.7036 (mmtt) cc_final: 0.6220 (mmmt)
REVERT: R  177 ASP cc_start: 0.8272 (t0) cc_final: 0.7928 (t0)
REVERT: R  179 ARG cc_start: 0.8914 (ptm-80) cc_final: 0.8619 (ptm160)
REVERT: R  247 ILE cc_start: 0.8412 (tt) cc_final: 0.8204 (tt)
REVERT: R  293 TRP cc_start: 0.7975 (OUTLIER) cc_final: 0.7104 (m-10)
  outliers start: 30
  outliers final: 19
  residues processed: 174
  average time/residue: 0.1932
  time to fit residues: 44.3020
Evaluate side-chains
  173 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 146
  time to evaluate  : 0.711 
-------------------------------------------------------------------------------
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  273 LEU
Chi-restraints excluded: chain A residue  276 GLU
Chi-restraints excluded: chain B residue   32 GLN
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  171 ILE
Chi-restraints excluded: chain B residue  184 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 B residue  329 THR
Chi-restraints excluded: chain C residue   16 VAL
Chi-restraints excluded: chain C residue   18 GLN
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  290 ILE
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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 87
   random chunks:
   chunk 56 optimal weight:    0.0770
   chunk 36 optimal weight:    2.9990
   chunk 55 optimal weight:    6.9990
   chunk 33 optimal weight:    0.0570
   chunk 5 optimal weight:    6.9990
   chunk 32 optimal weight:    2.9990
   chunk 31 optimal weight:    0.8980
   chunk 13 optimal weight:    0.9980
   chunk 26 optimal weight:    2.9990
   chunk 84 optimal weight:    1.9990
   chunk 12 optimal weight:    0.0570
   overall best weight:    0.4174

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

Flipped N/Q/H residues before XYZ refinement:
** R 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4009 r_free = 0.4009 target = 0.158377 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3776 r_free = 0.3776 target = 0.138979 restraints weight = 11199.041|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3828 r_free = 0.3828 target = 0.143147 restraints weight = 5909.620|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3862 r_free = 0.3862 target = 0.145900 restraints weight = 3683.649|
|-----------------------------------------------------------------------------|
r_work (final): 0.3863
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7257
moved from start:          0.5050

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   6943  Z= 0.182
  Angle     :  0.656   9.152   9427  Z= 0.325
  Chirality :  0.043   0.171   1098
  Planarity :  0.004   0.036   1189
  Dihedral  :  4.967  66.749    957
  Min Nonbonded Distance : 2.433

Molprobity Statistics.
  All-atom Clashscore : 11.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.14 %
    Favored  : 94.86 %
  Rotamer:
    Outliers :  3.72 %
    Allowed  : 27.32 %
    Favored  : 68.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.32 (0.29), residues: 875
  helix:  0.56 (0.28), residues: 350
  sheet: -1.97 (0.42), residues: 148
  loop : -1.74 (0.34), residues: 377

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.030   0.002   TRP B 339 
 HIS   0.004   0.001   HIS B 183 
 PHE   0.016   0.001   PHE R  87 
 TYR   0.020   0.001   TYR R 149 
 ARG   0.007   0.001   ARG C  13 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2421.14 seconds
wall clock time: 44 minutes 27.86 seconds (2667.86 seconds total)