Starting phenix.real_space_refine
on Mon May 12 12:18:22 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8kfx_37207/05_2025/8kfx_37207.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8kfx_37207/05_2025/8kfx_37207.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.96
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8kfx_37207/05_2025/8kfx_37207.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8kfx_37207/05_2025/8kfx_37207.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8kfx_37207/05_2025/8kfx_37207.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8kfx_37207/05_2025/8kfx_37207.cif"
  }
  resolution = 2.96
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.024
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      66      5.16       5
     C    5762      2.51       5
     N    1506      2.21       5
     O    1667      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 5 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 9001
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 1812
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 225, 1812
          Classifications: {'peptide': 225}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 222}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 2
          Planarities with less than four sites: {'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 3
    Chain: "B"
      Number of atoms: 2600
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 338, 2600
          Classifications: {'peptide': 338}
          Link IDs: {'PTRANS': 5, 'TRANS': 332}
    Chain: "C"
      Number of atoms: 429
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 56, 429
          Classifications: {'peptide': 56}
          Link IDs: {'PTRANS': 4, 'TRANS': 51}
    Chain: "R"
      Number of atoms: 2342
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 288, 2342
          Classifications: {'peptide': 288}
          Link IDs: {'PTRANS': 5, 'TRANS': 282}
    Chain: "S"
      Number of atoms: 1783
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 232, 1783
          Classifications: {'peptide': 232}
          Link IDs: {'PTRANS': 10, 'TRANS': 221}
          Chain breaks: 1
    Chain: "R"
      Number of atoms: 35
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 35
          Unusual residues: {'OS9': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 5.35, per 1000 atoms: 0.59
  Number of scatterers: 9001
  At special positions: 0
  Unit cell: (89.44, 121.68, 130, 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      66     16.00
     O    1667      8.00
     N    1506      7.00
     C    5762      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: pdb=" SG  CYS R 106 " - pdb=" SG  CYS R 183 " distance=2.04
    Simple disulfide: pdb=" SG  CYS S  22 " - pdb=" SG  CYS S  96 " distance=2.04
    Simple disulfide: pdb=" SG  CYS S 147 " - pdb=" SG  CYS S 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=0, symmetry=0
  Time building additional restraints: 2.35
  Conformation dependent library (CDL) restraints added in 1.0 seconds
  

  2250 Ramachandran restraints generated.
    1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2138

  Finding SS restraints...
    Secondary structure from input PDB file:
      30 helices and 13 sheets defined
      39.4% alpha, 23.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.95
  Creating SS restraints...
    Processing helix  chain 'A' and resid 6 through 32
    Processing helix  chain 'A' and resid 45 through 54
      removed outlier: 3.534A  pdb=" N   LYS A  54 " --> pdb=" O   VAL A  50 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 207 through 216
      removed outlier: 4.666A  pdb=" N   ILE A 212 " --> pdb=" O   LYS A 209 " (cutoff:3.500A)
      removed outlier: 5.551A  pdb=" N   HIS A 213 " --> pdb=" O   LYS A 210 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 228 through 231
      removed outlier: 3.962A  pdb=" N   ASP A 231 " --> pdb=" O   SER A 228 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 228 through 231'
    Processing helix  chain 'A' and resid 241 through 255
    Processing helix  chain 'A' and resid 270 through 278
    Processing helix  chain 'A' and resid 282 through 286
      removed outlier: 3.727A  pdb=" N   ILE A 285 " --> pdb=" O   PRO A 282 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 295 through 309
    Processing helix  chain 'A' and resid 330 through 351
    Processing helix  chain 'B' and resid 4 through 25
    Processing helix  chain 'B' and resid 29 through 34
    Processing helix  chain 'C' and resid 8 through 24
    Processing helix  chain 'C' and resid 29 through 44
    Processing helix  chain 'C' and resid 45 through 48
      removed outlier: 3.663A  pdb=" N   ASP C  48 " --> pdb=" O   ALA C  45 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 45 through 48'
    Processing helix  chain 'R' and resid 31 through 62
    Processing helix  chain 'R' and resid 68 through 86
    Processing helix  chain 'R' and resid 87 through 97
    Processing helix  chain 'R' and resid 102 through 137
    Processing helix  chain 'R' and resid 137 through 145
      removed outlier: 3.749A  pdb=" N   LYS R 143 " --> pdb=" O   VAL R 139 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 146 through 170
      Proline residue:  R 167  - end of helix
      removed outlier: 3.777A  pdb=" N   VAL R 170 " --> pdb=" O   ILE R 166 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 191 through 205
      removed outlier: 3.537A  pdb=" N   LYS R 195 " --> pdb=" O   THR R 191 " (cutoff:3.500A)
      removed outlier: 3.579A  pdb=" N   MET R 202 " --> pdb=" O   THR R 198 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 207 through 227
      removed outlier: 3.523A  pdb=" N   ARG R 227 " --> pdb=" O   HIS R 223 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 232 through 266
      Proline residue:  R 253  - end of helix
    Processing helix  chain 'R' and resid 271 through 291
    Processing helix  chain 'R' and resid 291 through 301
      Proline residue:  R 297  - end of helix
    Processing helix  chain 'R' and resid 304 through 317
    Processing helix  chain 'S' and resid 53 through 56
      removed outlier: 3.785A  pdb=" N   GLY S  56 " --> pdb=" O   SER S  53 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'S' and resid 53 through 56'
    Processing helix  chain 'S' and resid 62 through 65
      removed outlier: 3.520A  pdb=" N   LYS S  65 " --> pdb=" O   ASP S  62 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'S' and resid 62 through 65'
    Processing helix  chain 'S' and resid 87 through 91
      removed outlier: 3.800A  pdb=" N   THR S  91 " --> pdb=" O   SER S  88 " (cutoff:3.500A)
    Processing helix  chain 'S' and resid 208 through 212
      removed outlier: 3.512A  pdb=" N   VAL S 212 " --> pdb=" O   ALA S 209 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 191
      removed outlier: 3.552A  pdb=" N   PHE A 189 " --> pdb=" O   PHE A 196 " (cutoff:3.500A)
      removed outlier: 6.426A  pdb=" N   LYS A  35 " --> pdb=" O   ALA A 220 " (cutoff:3.500A)
      removed outlier: 7.352A  pdb=" N   ILE A 222 " --> pdb=" O   LYS A  35 " (cutoff:3.500A)
      removed outlier: 6.279A  pdb=" N   LEU A  37 " --> pdb=" O   ILE A 222 " (cutoff:3.500A)
      removed outlier: 7.422A  pdb=" N   CYS A 224 " --> pdb=" O   LEU A  37 " (cutoff:3.500A)
      removed outlier: 6.824A  pdb=" N   LEU A  39 " --> pdb=" O   CYS A 224 " (cutoff:3.500A)
      removed outlier: 8.526A  pdb=" N   ALA A 226 " --> pdb=" O   LEU A  39 " (cutoff:3.500A)
      removed outlier: 6.242A  pdb=" N   ILE A 221 " --> pdb=" O   ILE A 265 " (cutoff:3.500A)
      removed outlier: 7.019A  pdb=" N   PHE A 267 " --> pdb=" O   ILE A 221 " (cutoff:3.500A)
      removed outlier: 6.224A  pdb=" N   PHE A 223 " --> pdb=" O   PHE A 267 " (cutoff:3.500A)
      removed outlier: 7.106A  pdb=" N   ASN A 269 " --> pdb=" O   PHE A 223 " (cutoff:3.500A)
      removed outlier: 6.655A  pdb=" N   VAL A 225 " --> pdb=" O   ASN A 269 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51
      removed outlier: 5.339A  pdb=" N   THR B  47 " --> pdb=" O   ASN B 340 " (cutoff:3.500A)
      removed outlier: 6.789A  pdb=" N   ASN B 340 " --> pdb=" O   THR B  47 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63
      removed outlier: 3.620A  pdb=" N   SER B  74 " --> pdb=" O   LYS B  78 " (cutoff:3.500A)
      removed outlier: 3.908A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 5.868A  pdb=" N   LEU B  79 " --> pdb=" O   ALA B  92 " (cutoff:3.500A)
      removed outlier: 4.198A  pdb=" N   ALA B  92 " --> pdb=" O   LEU B  79 " (cutoff:3.500A)
      removed outlier: 6.573A  pdb=" N   ILE B  81 " --> pdb=" O   VAL B  90 " (cutoff:3.500A)
      removed outlier: 3.504A  pdb=" N   ASN B  88 " --> pdb=" O   ASP B  83 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105
      removed outlier: 6.927A  pdb=" N   GLY B 115 " --> pdb=" O   MET B 101 " (cutoff:3.500A)
      removed outlier: 4.299A  pdb=" N   CYS B 103 " --> pdb=" O   ALA B 113 " (cutoff:3.500A)
      removed outlier: 6.455A  pdb=" N   ALA B 113 " --> pdb=" O   CYS B 103 " (cutoff:3.500A)
      removed outlier: 5.130A  pdb=" N   TYR B 105 " --> pdb=" O   TYR B 111 " (cutoff:3.500A)
      removed outlier: 7.409A  pdb=" N   TYR B 111 " --> pdb=" O   TYR B 105 " (cutoff:3.500A)
      removed outlier: 4.196A  pdb=" N   GLY B 116 " --> pdb=" O   ILE B 120 " (cutoff:3.500A)
      removed outlier: 4.690A  pdb=" N   ILE B 120 " --> pdb=" O   GLY B 116 " (cutoff:3.500A)
      removed outlier: 5.956A  pdb=" N   CYS B 121 " --> pdb=" O   GLU B 138 " (cutoff:3.500A)
      removed outlier: 4.331A  pdb=" N   GLU B 138 " --> pdb=" O   CYS B 121 " (cutoff:3.500A)
      removed outlier: 6.617A  pdb=" N   ILE B 123 " --> pdb=" O   SER B 136 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151
      removed outlier: 3.704A  pdb=" N   CYS B 148 " --> pdb=" O   SER B 160 " (cutoff:3.500A)
      removed outlier: 3.978A  pdb=" N   THR B 165 " --> pdb=" O   SER B 161 " (cutoff:3.500A)
      removed outlier: 6.891A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 6.125A  pdb=" N   GLN B 176 " --> pdb=" O   ASP B 170 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192
      removed outlier: 6.538A  pdb=" N   ALA B 208 " --> pdb=" O   THR B 221 " (cutoff:3.500A)
      removed outlier: 4.598A  pdb=" N   THR B 221 " --> pdb=" O   ALA B 208 " (cutoff:3.500A)
      removed outlier: 6.717A  pdb=" N   LEU B 210 " --> pdb=" O   ARG B 219 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234
      removed outlier: 6.301A  pdb=" N   CYS B 250 " --> pdb=" O   THR B 263 " (cutoff:3.500A)
      removed outlier: 4.384A  pdb=" N   THR B 263 " --> pdb=" O   CYS B 250 " (cutoff:3.500A)
      removed outlier: 6.692A  pdb=" N   LEU B 252 " --> pdb=" O   LEU B 261 " (cutoff:3.500A)
      removed outlier: 3.538A  pdb=" N   GLN B 259 " --> pdb=" O   ASP B 254 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278
      removed outlier: 3.632A  pdb=" N   SER B 275 " --> pdb=" O   GLY B 288 " (cutoff:3.500A)
      removed outlier: 4.007A  pdb=" N   ASN B 293 " --> pdb=" O   TYR B 289 " (cutoff:3.500A)
      removed outlier: 6.081A  pdb=" N   ASP B 298 " --> pdb=" O   ARG B 304 " (cutoff:3.500A)
      removed outlier: 6.455A  pdb=" N   ARG B 304 " --> pdb=" O   ASP B 298 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'R' and resid 172 through 177
    Processing sheet with id=AB1, first strand: chain 'S' and resid 6 through 7
    Processing sheet with id=AB2, first strand: chain 'S' and resid 10 through 12
      removed outlier: 5.814A  pdb=" N   GLY S  10 " --> pdb=" O   THR S 118 " (cutoff:3.500A)
      removed outlier: 3.509A  pdb=" N   ALA S  49 " --> pdb=" O   TRP S  36 " (cutoff:3.500A)
      removed outlier: 6.040A  pdb=" N   ARG S  38 " --> pdb=" O   TRP S  47 " (cutoff:3.500A)
      removed outlier: 6.057A  pdb=" N   TRP S  47 " --> pdb=" O   ARG S  38 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'S' and resid 128 through 129
    Processing sheet with id=AB4, first strand: chain 'S' and resid 134 through 136
      removed outlier: 3.843A  pdb=" N   GLU S 234 " --> pdb=" O   VAL S 135 " (cutoff:3.500A)
      removed outlier: 6.497A  pdb=" N   LEU S 162 " --> pdb=" O   TYR S 178 " (cutoff:3.500A)
      removed outlier: 4.586A  pdb=" N   TYR S 178 " --> pdb=" O   LEU S 162 " (cutoff:3.500A)
      removed outlier: 6.451A  pdb=" N   TRP S 164 " --> pdb=" O   LEU S 176 " (cutoff:3.500A)

    465 hydrogen bonds defined for protein.
    1320 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: 2.60

  Time building geometry restraints manager: 2.68 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2861
        1.34 -     1.46: 2235
        1.46 -     1.58: 4001
        1.58 -     1.70: 1
        1.70 -     1.82: 95
  Bond restraints: 9193
  Sorted by residual:
  bond pdb=" N   PRO S 224 "
       pdb=" CD  PRO S 224 "
    ideal  model  delta    sigma   weight residual
    1.473  1.624 -0.151 1.40e-02 5.10e+03 1.17e+02
  bond pdb=" N   ARG S  67 "
       pdb=" CA  ARG S  67 "
    ideal  model  delta    sigma   weight residual
    1.459  1.492 -0.033 1.24e-02 6.50e+03 7.06e+00
  bond pdb=" N   PHE R 290 "
       pdb=" CA  PHE R 290 "
    ideal  model  delta    sigma   weight residual
    1.456  1.491 -0.035 1.31e-02 5.83e+03 7.05e+00
  bond pdb=" N   THR R 291 "
       pdb=" CA  THR R 291 "
    ideal  model  delta    sigma   weight residual
    1.458  1.491 -0.033 1.29e-02 6.01e+03 6.69e+00
  bond pdb=" N   SER R 289 "
       pdb=" CA  SER R 289 "
    ideal  model  delta    sigma   weight residual
    1.459  1.488 -0.028 1.18e-02 7.18e+03 5.73e+00
  ... (remaining 9188 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.29: 12301
        2.29 -     4.57: 119
        4.57 -     6.86: 18
        6.86 -     9.15: 5
        9.15 -    11.43: 1
  Bond angle restraints: 12444
  Sorted by residual:
  angle pdb=" N   THR R 291 "
        pdb=" CA  THR R 291 "
        pdb=" C   THR R 291 "
      ideal   model   delta    sigma   weight residual
     112.34  107.46    4.88 1.30e+00 5.92e-01 1.41e+01
  angle pdb=" CA  GLN A  52 "
        pdb=" CB  GLN A  52 "
        pdb=" CG  GLN A  52 "
      ideal   model   delta    sigma   weight residual
     114.10  121.50   -7.40 2.00e+00 2.50e-01 1.37e+01
  angle pdb=" C   GLU S 222 "
        pdb=" N   TYR S 223 "
        pdb=" CA  TYR S 223 "
      ideal   model   delta    sigma   weight residual
     121.80  113.02    8.78 2.44e+00 1.68e-01 1.29e+01
  angle pdb=" CA  PHE R 290 "
        pdb=" CB  PHE R 290 "
        pdb=" CG  PHE R 290 "
      ideal   model   delta    sigma   weight residual
     113.80  117.11   -3.31 1.00e+00 1.00e+00 1.10e+01
  angle pdb=" CA  LEU R 205 "
        pdb=" CB  LEU R 205 "
        pdb=" CG  LEU R 205 "
      ideal   model   delta    sigma   weight residual
     116.30  127.73  -11.43 3.50e+00 8.16e-02 1.07e+01
  ... (remaining 12439 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.91: 4718
       17.91 -    35.82: 558
       35.82 -    53.73: 162
       53.73 -    71.65: 22
       71.65 -    89.56: 5
  Dihedral angle restraints: 5465
    sinusoidal: 2151
      harmonic: 3314
  Sorted by residual:
  dihedral pdb=" CA  TYR S 223 "
           pdb=" C   TYR S 223 "
           pdb=" N   PRO S 224 "
           pdb=" CA  PRO S 224 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  134.90   45.10     0      5.00e+00 4.00e-02 8.14e+01
  dihedral pdb=" CA  ARG S 179 "
           pdb=" C   ARG S 179 "
           pdb=" N   MET S 180 "
           pdb=" CA  MET S 180 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  158.52   21.48     0      5.00e+00 4.00e-02 1.85e+01
  dihedral pdb=" CA  TRP B  82 "
           pdb=" C   TRP B  82 "
           pdb=" N   ASP B  83 "
           pdb=" CA  ASP B  83 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.86   20.14     0      5.00e+00 4.00e-02 1.62e+01
  ... (remaining 5462 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.028: 821
       0.028 -    0.057: 354
       0.057 -    0.085: 154
       0.085 -    0.114: 71
       0.114 -    0.142: 14
  Chirality restraints: 1414
  Sorted by residual:
  chirality pdb=" CB  ILE S  70 "
            pdb=" CA  ILE S  70 "
            pdb=" CG1 ILE S  70 "
            pdb=" CG2 ILE S  70 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.50    0.14 2.00e-01 2.50e+01 5.05e-01
  chirality pdb=" CA  ILE S 177 "
            pdb=" N   ILE S 177 "
            pdb=" C   ILE S 177 "
            pdb=" CB  ILE S 177 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 4.72e-01
  chirality pdb=" CA  PHE R  41 "
            pdb=" N   PHE R  41 "
            pdb=" C   PHE R  41 "
            pdb=" CB  PHE R  41 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.37    0.14 2.00e-01 2.50e+01 4.70e-01
  ... (remaining 1411 not shown)

  Planarity restraints: 1558
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TYR S 223 "    0.040 5.00e-02 4.00e+02   5.82e-02 5.42e+00
        pdb=" N   PRO S 224 "   -0.101 5.00e-02 4.00e+02
        pdb=" CA  PRO S 224 "    0.030 5.00e-02 4.00e+02
        pdb=" CD  PRO S 224 "    0.030 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE R 186 "   -0.011 2.00e-02 2.50e+03   1.64e-02 4.71e+00
        pdb=" CG  PHE R 186 "    0.037 2.00e-02 2.50e+03
        pdb=" CD1 PHE R 186 "   -0.013 2.00e-02 2.50e+03
        pdb=" CD2 PHE R 186 "   -0.014 2.00e-02 2.50e+03
        pdb=" CE1 PHE R 186 "    0.000 2.00e-02 2.50e+03
        pdb=" CE2 PHE R 186 "    0.001 2.00e-02 2.50e+03
        pdb=" CZ  PHE R 186 "    0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASP B 170 "   -0.010 2.00e-02 2.50e+03   2.03e-02 4.14e+00
        pdb=" CG  ASP B 170 "    0.035 2.00e-02 2.50e+03
        pdb=" OD1 ASP B 170 "   -0.013 2.00e-02 2.50e+03
        pdb=" OD2 ASP B 170 "   -0.012 2.00e-02 2.50e+03
  ... (remaining 1555 not shown)

  Histogram of nonbonded interaction distances:
        2.19 -     2.73: 554
        2.73 -     3.27: 8901
        3.27 -     3.82: 15392
        3.82 -     4.36: 18481
        4.36 -     4.90: 31911
  Nonbonded interactions: 75239
  Sorted by model distance:
  nonbonded pdb=" OG  SER B 331 "
            pdb=" OD1 ASP B 333 "
     model   vdw
     2.189 3.040
  nonbonded pdb=" O   LEU R  50 "
            pdb=" OG  SER R  54 "
     model   vdw
     2.204 3.040
  nonbonded pdb=" OE2 GLU A   8 "
            pdb=" OH  TYR S 163 "
     model   vdw
     2.208 3.040
  nonbonded pdb=" ND1 HIS B  54 "
            pdb=" OG  SER B  74 "
     model   vdw
     2.252 3.120
  nonbonded pdb=" N   GLU A 297 "
            pdb=" OE1 GLU A 297 "
     model   vdw
     2.267 3.120
  ... (remaining 75234 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.040
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.340
  Check model and map are aligned:         0.060
  Set scattering table:                    0.080
  Process input model:                     22.470
  Find NCS groups from input model:        0.100
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:11.610
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   35.740
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7681
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      :  0.004   0.151   9196  Z= 0.207
  Angle     :  0.613  11.433  12450  Z= 0.329
  Chirality :  0.042   0.142   1414
  Planarity :  0.004   0.058   1558
  Dihedral  : 16.545  89.558   3318
  Min Nonbonded Distance : 2.189

Molprobity Statistics.
  All-atom Clashscore : 11.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.49 %
    Favored  : 97.51 %
  Rotamer:
    Outliers :  0.51 %
    Allowed  : 30.16 %
    Favored  : 69.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.85 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.90 (0.25), residues: 1125
  helix:  2.18 (0.27), residues: 398
  sheet:  0.30 (0.30), residues: 286
  loop : -0.64 (0.28), residues: 441

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.002   TRP R 251 
 HIS   0.005   0.001   HIS S  35 
 PHE   0.037   0.002   PHE R 186 
 TYR   0.016   0.001   TYR R  94 
 ARG   0.013   0.001   ARG S 148 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.14760 (  465)
  hydrogen bonds       : angle       5.86794 ( 1320)
  SS BOND              : bond        0.00419 (    3)
  SS BOND              : angle       0.88224 (    6)
  covalent geometry    : bond        0.00395 ( 9193)
  covalent geometry    : angle       0.61294 (12444)

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

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

  2250 Ramachandran restraints generated.
    1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2250 Ramachandran restraints generated.
    1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  257 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 252
  time to evaluate  : 1.079 
Fit side-chains
REVERT: A  231 ASP cc_start: 0.7629 (t0) cc_final: 0.7403 (t0)
REVERT: A  340 THR cc_start: 0.8656 (m) cc_final: 0.8351 (t)
REVERT: B   19 ARG cc_start: 0.7572 (ttp80) cc_final: 0.7279 (mtm110)
REVERT: B   61 MET cc_start: 0.8231 (tmm) cc_final: 0.7993 (ppp)
REVERT: R  117 PHE cc_start: 0.8151 (t80) cc_final: 0.7919 (t80)
REVERT: R  121 MET cc_start: 0.8187 (tpp) cc_final: 0.7617 (mpp)
REVERT: R  216 PHE cc_start: 0.8045 (t80) cc_final: 0.7738 (t80)
  outliers start: 5
  outliers final: 4
  residues processed: 256
  average time/residue: 1.1297
  time to fit residues: 310.4603
Evaluate side-chains
  246 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 242
  time to evaluate  : 0.970 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  119 ASN
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain R residue  183 CYS
Chi-restraints excluded: chain S residue  130 GLN
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 93 optimal weight:    0.7980
   chunk 84 optimal weight:    0.9990
   chunk 46 optimal weight:    1.9990
   chunk 28 optimal weight:    1.9990
   chunk 56 optimal weight:    5.9990
   chunk 44 optimal weight:    0.6980
   chunk 87 optimal weight:    1.9990
   chunk 33 optimal weight:    1.9990
   chunk 52 optimal weight:    4.9990
   chunk 64 optimal weight:    0.9980
   chunk 100 optimal weight:    1.9990
   overall best weight:    1.0984

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

Flipped N/Q/H residues before XYZ refinement:
A 256 ASN
A 311 ASN
B  75 GLN
B 220 GLN
R 203 ASN
** R 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
S 167 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3651 r_free = 0.3651 target = 0.125802 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3385 r_free = 0.3385 target = 0.107297 restraints weight = 12953.500|
|-----------------------------------------------------------------------------|
r_work (start): 0.3388 rms_B_bonded: 1.96
r_work: 0.3263 rms_B_bonded: 2.43 restraints_weight: 0.5000
r_work: 0.3109 rms_B_bonded: 4.19 restraints_weight: 0.2500
r_work (final): 0.3109
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7774
moved from start:          0.0872

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.048   9196  Z= 0.236
  Angle     :  0.591  10.234  12450  Z= 0.315
  Chirality :  0.044   0.170   1414
  Planarity :  0.004   0.062   1558
  Dihedral  :  5.530  47.292   1276
  Min Nonbonded Distance : 2.560

Molprobity Statistics.
  All-atom Clashscore : 7.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.58 %
    Favored  : 97.42 %
  Rotamer:
    Outliers :  4.55 %
    Allowed  : 24.80 %
    Favored  : 70.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.85 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.84 (0.25), residues: 1125
  helix:  2.12 (0.26), residues: 399
  sheet:  0.26 (0.30), residues: 288
  loop : -0.66 (0.29), residues: 438

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.002   TRP B 169 
 HIS   0.005   0.001   HIS S  35 
 PHE   0.026   0.002   PHE R 290 
 TYR   0.015   0.002   TYR A 320 
 ARG   0.005   0.001   ARG S 148 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04693 (  465)
  hydrogen bonds       : angle       4.77329 ( 1320)
  SS BOND              : bond        0.00398 (    3)
  SS BOND              : angle       0.88671 (    6)
  covalent geometry    : bond        0.00540 ( 9193)
  covalent geometry    : angle       0.59081 (12444)

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

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

  2250 Ramachandran restraints generated.
    1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2250 Ramachandran restraints generated.
    1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  298 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 253
  time to evaluate  : 0.982 
Fit side-chains
REVERT: A   49 ILE cc_start: 0.6814 (OUTLIER) cc_final: 0.5991 (mp)
REVERT: A  186 GLU cc_start: 0.6966 (mm-30) cc_final: 0.6372 (tm-30)
REVERT: A  193 ASP cc_start: 0.8032 (m-30) cc_final: 0.7800 (t0)
REVERT: A  197 LYS cc_start: 0.8542 (mtmm) cc_final: 0.8223 (mtpp)
REVERT: A  231 ASP cc_start: 0.7938 (t0) cc_final: 0.7685 (t0)
REVERT: A  269 ASN cc_start: 0.8408 (m-40) cc_final: 0.8172 (m110)
REVERT: B   19 ARG cc_start: 0.7714 (ttp80) cc_final: 0.7215 (ttp80)
REVERT: B   22 ARG cc_start: 0.7283 (mtt180) cc_final: 0.7031 (mtp180)
REVERT: B   61 MET cc_start: 0.8210 (tmm) cc_final: 0.7993 (ppp)
REVERT: B  197 ARG cc_start: 0.7854 (mpt-90) cc_final: 0.7623 (mtt-85)
REVERT: B  219 ARG cc_start: 0.8246 (mtp85) cc_final: 0.8005 (mtt-85)
REVERT: B  234 PHE cc_start: 0.8711 (OUTLIER) cc_final: 0.8488 (OUTLIER)
REVERT: B  258 ASP cc_start: 0.8042 (t0) cc_final: 0.7274 (t0)
REVERT: R   37 LEU cc_start: 0.8500 (tp) cc_final: 0.7976 (tm)
REVERT: R   41 PHE cc_start: 0.7826 (m-80) cc_final: 0.7310 (m-80)
REVERT: R   46 PHE cc_start: 0.7732 (t80) cc_final: 0.7385 (t80)
REVERT: R   55 LEU cc_start: 0.8267 (tm) cc_final: 0.7965 (tt)
REVERT: R   95 LEU cc_start: 0.8662 (mt) cc_final: 0.8438 (mm)
REVERT: R  105 MET cc_start: 0.7831 (mmm) cc_final: 0.7439 (tmm)
REVERT: S   39 GLN cc_start: 0.8499 (OUTLIER) cc_final: 0.8007 (tp40)
REVERT: S   69 THR cc_start: 0.8187 (p) cc_final: 0.7952 (t)
REVERT: S  110 PHE cc_start: 0.8658 (t80) cc_final: 0.8330 (t80)
REVERT: S  200 PHE cc_start: 0.8586 (OUTLIER) cc_final: 0.7865 (m-80)
REVERT: S  223 TYR cc_start: 0.7953 (OUTLIER) cc_final: 0.7557 (t80)
  outliers start: 45
  outliers final: 22
  residues processed: 278
  average time/residue: 1.0806
  time to fit residues: 322.0067
Evaluate side-chains
  270 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 244
  time to evaluate  : 1.066 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   29 LYS
Chi-restraints excluded: chain A residue   34 VAL
Chi-restraints excluded: chain A residue   49 ILE
Chi-restraints excluded: chain A residue  295 THR
Chi-restraints excluded: chain A residue  329 THR
Chi-restraints excluded: chain B residue   37 ILE
Chi-restraints excluded: chain B residue  119 ASN
Chi-restraints excluded: chain B residue  134 ARG
Chi-restraints excluded: chain B residue  223 THR
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  322 ASP
Chi-restraints excluded: chain C residue   20 LYS
Chi-restraints excluded: chain C residue   38 MET
Chi-restraints excluded: chain R residue  128 SER
Chi-restraints excluded: chain R residue  180 VAL
Chi-restraints excluded: chain R residue  183 CYS
Chi-restraints excluded: chain R residue  298 VAL
Chi-restraints excluded: chain S residue    4 LEU
Chi-restraints excluded: chain S residue   39 GLN
Chi-restraints excluded: chain S residue  146 SER
Chi-restraints excluded: chain S residue  167 GLN
Chi-restraints excluded: chain S residue  200 PHE
Chi-restraints excluded: chain S residue  202 LEU
Chi-restraints excluded: chain S residue  223 TYR
Chi-restraints excluded: chain S residue  225 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 1 optimal weight:    0.9990
   chunk 93 optimal weight:    0.7980
   chunk 20 optimal weight:    0.6980
   chunk 63 optimal weight:    2.9990
   chunk 67 optimal weight:    0.5980
   chunk 4 optimal weight:    0.8980
   chunk 19 optimal weight:    0.8980
   chunk 100 optimal weight:    1.9990
   chunk 45 optimal weight:    0.9990
   chunk 96 optimal weight:    0.8980
   chunk 76 optimal weight:    0.9980
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
A 256 ASN
A 311 ASN
B  75 GLN
B 220 GLN
R 203 ASN
** R 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
S 167 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3661 r_free = 0.3661 target = 0.126586 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3396 r_free = 0.3396 target = 0.108036 restraints weight = 13097.196|
|-----------------------------------------------------------------------------|
r_work (start): 0.3396 rms_B_bonded: 1.99
r_work: 0.3272 rms_B_bonded: 2.45 restraints_weight: 0.5000
r_work: 0.3118 rms_B_bonded: 4.23 restraints_weight: 0.2500
r_work (final): 0.3118
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7765
moved from start:          0.1086

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   9196  Z= 0.177
  Angle     :  0.544  10.928  12450  Z= 0.288
  Chirality :  0.042   0.149   1414
  Planarity :  0.004   0.062   1558
  Dihedral  :  5.444  53.232   1271
  Min Nonbonded Distance : 2.491

Molprobity Statistics.
  All-atom Clashscore : 7.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.67 %
    Favored  : 97.33 %
  Rotamer:
    Outliers :  4.66 %
    Allowed  : 24.39 %
    Favored  : 70.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.85 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.87 (0.25), residues: 1125
  helix:  2.23 (0.26), residues: 400
  sheet:  0.15 (0.29), residues: 299
  loop : -0.67 (0.29), residues: 426

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.001   TRP B 169 
 HIS   0.005   0.001   HIS S  35 
 PHE   0.028   0.002   PHE R 117 
 TYR   0.016   0.002   TYR S 178 
 ARG   0.007   0.001   ARG S 148 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04256 (  465)
  hydrogen bonds       : angle       4.62619 ( 1320)
  SS BOND              : bond        0.00314 (    3)
  SS BOND              : angle       0.75247 (    6)
  covalent geometry    : bond        0.00405 ( 9193)
  covalent geometry    : angle       0.54432 (12444)

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

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

  2250 Ramachandran restraints generated.
    1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2250 Ramachandran restraints generated.
    1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  297 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 251
  time to evaluate  : 1.044 
Fit side-chains
REVERT: A   49 ILE cc_start: 0.6694 (OUTLIER) cc_final: 0.5744 (mp)
REVERT: A  186 GLU cc_start: 0.6998 (mm-30) cc_final: 0.6766 (mm-30)
REVERT: A  193 ASP cc_start: 0.8001 (m-30) cc_final: 0.7788 (t0)
REVERT: A  197 LYS cc_start: 0.8534 (OUTLIER) cc_final: 0.8302 (mtpp)
REVERT: A  231 ASP cc_start: 0.7956 (t0) cc_final: 0.7681 (t0)
REVERT: A  269 ASN cc_start: 0.8455 (m-40) cc_final: 0.8211 (m110)
REVERT: A  310 LEU cc_start: 0.8712 (mt) cc_final: 0.8504 (mp)
REVERT: B   19 ARG cc_start: 0.7702 (ttp80) cc_final: 0.7216 (ttp80)
REVERT: B   22 ARG cc_start: 0.7271 (mtt180) cc_final: 0.7016 (mtp180)
REVERT: B   61 MET cc_start: 0.8219 (tmm) cc_final: 0.7999 (ppp)
REVERT: B   76 ASP cc_start: 0.7691 (p0) cc_final: 0.7410 (p0)
REVERT: B  197 ARG cc_start: 0.7878 (mpt-90) cc_final: 0.7565 (mtt-85)
REVERT: B  214 ARG cc_start: 0.7825 (OUTLIER) cc_final: 0.7519 (mmt180)
REVERT: B  219 ARG cc_start: 0.8216 (mtp85) cc_final: 0.7999 (mtt-85)
REVERT: B  258 ASP cc_start: 0.8092 (t0) cc_final: 0.7202 (t0)
REVERT: R   37 LEU cc_start: 0.8460 (tp) cc_final: 0.7976 (tm)
REVERT: R   41 PHE cc_start: 0.7910 (m-80) cc_final: 0.7461 (m-80)
REVERT: R   46 PHE cc_start: 0.7745 (t80) cc_final: 0.7396 (t80)
REVERT: R   55 LEU cc_start: 0.8258 (OUTLIER) cc_final: 0.7944 (tt)
REVERT: R   95 LEU cc_start: 0.8656 (mt) cc_final: 0.8447 (mm)
REVERT: R  105 MET cc_start: 0.7866 (mmm) cc_final: 0.7397 (tmm)
REVERT: R  220 LYS cc_start: 0.8316 (mmmm) cc_final: 0.7995 (mmmm)
REVERT: S   39 GLN cc_start: 0.8476 (OUTLIER) cc_final: 0.8005 (tp40)
REVERT: S   69 THR cc_start: 0.8202 (p) cc_final: 0.7963 (t)
REVERT: S  110 PHE cc_start: 0.8637 (t80) cc_final: 0.8335 (t80)
REVERT: S  205 SER cc_start: 0.8001 (m) cc_final: 0.7660 (p)
REVERT: S  223 TYR cc_start: 0.7906 (OUTLIER) cc_final: 0.7545 (t80)
  outliers start: 46
  outliers final: 22
  residues processed: 273
  average time/residue: 1.0966
  time to fit residues: 320.3871
Evaluate side-chains
  269 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 241
  time to evaluate  : 0.981 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   29 LYS
Chi-restraints excluded: chain A residue   34 VAL
Chi-restraints excluded: chain A residue   35 LYS
Chi-restraints excluded: chain A residue   49 ILE
Chi-restraints excluded: chain A residue  197 LYS
Chi-restraints excluded: chain B residue   37 ILE
Chi-restraints excluded: chain B residue   74 SER
Chi-restraints excluded: chain B residue  119 ASN
Chi-restraints excluded: chain B residue  134 ARG
Chi-restraints excluded: chain B residue  150 ARG
Chi-restraints excluded: chain B residue  190 LEU
Chi-restraints excluded: chain B residue  214 ARG
Chi-restraints excluded: chain B residue  223 THR
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain C residue   20 LYS
Chi-restraints excluded: chain C residue   38 MET
Chi-restraints excluded: chain R residue   55 LEU
Chi-restraints excluded: chain R residue   58 LEU
Chi-restraints excluded: chain R residue  128 SER
Chi-restraints excluded: chain R residue  180 VAL
Chi-restraints excluded: chain R residue  183 CYS
Chi-restraints excluded: chain R residue  203 ASN
Chi-restraints excluded: chain R residue  298 VAL
Chi-restraints excluded: chain S residue    4 LEU
Chi-restraints excluded: chain S residue   39 GLN
Chi-restraints excluded: chain S residue  146 SER
Chi-restraints excluded: chain S residue  202 LEU
Chi-restraints excluded: chain S residue  223 TYR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 66 optimal weight:    1.9990
   chunk 100 optimal weight:    0.6980
   chunk 31 optimal weight:    0.4980
   chunk 54 optimal weight:    0.9990
   chunk 85 optimal weight:    0.9990
   chunk 56 optimal weight:    3.9990
   chunk 68 optimal weight:    1.9990
   chunk 105 optimal weight:    0.6980
   chunk 92 optimal weight:    0.9980
   chunk 29 optimal weight:    0.8980
   chunk 5 optimal weight:    0.9990
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
A 311 ASN
B  75 GLN
B 220 GLN
B 259 GLN
R 203 ASN
** R 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
S 167 GLN
S 174 GLN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3662 r_free = 0.3662 target = 0.126606 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3398 r_free = 0.3398 target = 0.108086 restraints weight = 13093.760|
|-----------------------------------------------------------------------------|
r_work (start): 0.3397 rms_B_bonded: 2.00
r_work: 0.3273 rms_B_bonded: 2.46 restraints_weight: 0.5000
r_work: 0.3117 rms_B_bonded: 4.25 restraints_weight: 0.2500
r_work (final): 0.3117
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7762
moved from start:          0.1226

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   9196  Z= 0.174
  Angle     :  0.538   9.680  12450  Z= 0.284
  Chirality :  0.041   0.144   1414
  Planarity :  0.004   0.063   1558
  Dihedral  :  5.431  54.685   1271
  Min Nonbonded Distance : 2.558

Molprobity Statistics.
  All-atom Clashscore : 7.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.67 %
    Favored  : 97.33 %
  Rotamer:
    Outliers :  5.77 %
    Allowed  : 23.79 %
    Favored  : 70.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.85 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.92 (0.25), residues: 1125
  helix:  2.29 (0.26), residues: 400
  sheet:  0.18 (0.29), residues: 297
  loop : -0.67 (0.30), residues: 428

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP B 169 
 HIS   0.005   0.001   HIS S  35 
 PHE   0.026   0.002   PHE R 117 
 TYR   0.015   0.002   TYR S 178 
 ARG   0.010   0.001   ARG B  49 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04079 (  465)
  hydrogen bonds       : angle       4.58668 ( 1320)
  SS BOND              : bond        0.00319 (    3)
  SS BOND              : angle       0.74944 (    6)
  covalent geometry    : bond        0.00398 ( 9193)
  covalent geometry    : angle       0.53805 (12444)

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

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

  2250 Ramachandran restraints generated.
    1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2250 Ramachandran restraints generated.
    1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  304 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 57
    poor density    : 247
  time to evaluate  : 1.066 
Fit side-chains
   revert: symmetry clash
REVERT: A   49 ILE cc_start: 0.6693 (OUTLIER) cc_final: 0.5791 (mp)
REVERT: A  193 ASP cc_start: 0.8012 (m-30) cc_final: 0.7780 (t0)
REVERT: A  231 ASP cc_start: 0.7983 (t0) cc_final: 0.7684 (t0)
REVERT: A  269 ASN cc_start: 0.8479 (m-40) cc_final: 0.8232 (m110)
REVERT: B   22 ARG cc_start: 0.7261 (mtt180) cc_final: 0.7000 (mtp180)
REVERT: B   61 MET cc_start: 0.8233 (tmm) cc_final: 0.8010 (ppp)
REVERT: B   76 ASP cc_start: 0.7647 (p0) cc_final: 0.7359 (p0)
REVERT: B  130 GLU cc_start: 0.8180 (mp0) cc_final: 0.7705 (mp0)
REVERT: B  197 ARG cc_start: 0.7921 (mpt-90) cc_final: 0.7602 (mtt-85)
REVERT: B  214 ARG cc_start: 0.7849 (OUTLIER) cc_final: 0.7537 (mmt180)
REVERT: B  219 ARG cc_start: 0.8210 (mtp85) cc_final: 0.7966 (mtt-85)
REVERT: B  258 ASP cc_start: 0.8092 (t0) cc_final: 0.7144 (t0)
REVERT: R   37 LEU cc_start: 0.8435 (tp) cc_final: 0.8036 (tm)
REVERT: R   41 PHE cc_start: 0.7958 (m-80) cc_final: 0.7533 (m-80)
REVERT: R   46 PHE cc_start: 0.7683 (t80) cc_final: 0.7352 (t80)
REVERT: R   55 LEU cc_start: 0.8231 (OUTLIER) cc_final: 0.7922 (tt)
REVERT: R   95 LEU cc_start: 0.8657 (mt) cc_final: 0.8431 (mm)
REVERT: R  105 MET cc_start: 0.7899 (mmm) cc_final: 0.7431 (mmm)
REVERT: R  235 LYS cc_start: 0.8205 (OUTLIER) cc_final: 0.7377 (mmmm)
REVERT: S   39 GLN cc_start: 0.8479 (OUTLIER) cc_final: 0.8003 (tp40)
REVERT: S   69 THR cc_start: 0.8237 (p) cc_final: 0.7995 (t)
REVERT: S  110 PHE cc_start: 0.8615 (t80) cc_final: 0.8325 (t80)
REVERT: S  205 SER cc_start: 0.7997 (m) cc_final: 0.7641 (p)
REVERT: S  223 TYR cc_start: 0.7912 (OUTLIER) cc_final: 0.7572 (t80)
  outliers start: 57
  outliers final: 24
  residues processed: 278
  average time/residue: 1.0278
  time to fit residues: 306.3968
Evaluate side-chains
  271 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 241
  time to evaluate  : 0.920 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   29 LYS
Chi-restraints excluded: chain A residue   34 VAL
Chi-restraints excluded: chain A residue   35 LYS
Chi-restraints excluded: chain A residue   49 ILE
Chi-restraints excluded: chain A residue  197 LYS
Chi-restraints excluded: chain B residue   33 ILE
Chi-restraints excluded: chain B residue   37 ILE
Chi-restraints excluded: chain B residue   74 SER
Chi-restraints excluded: chain B residue  119 ASN
Chi-restraints excluded: chain B residue  134 ARG
Chi-restraints excluded: chain B residue  190 LEU
Chi-restraints excluded: chain B residue  214 ARG
Chi-restraints excluded: chain B residue  223 THR
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  322 ASP
Chi-restraints excluded: chain C residue   20 LYS
Chi-restraints excluded: chain C residue   38 MET
Chi-restraints excluded: chain R residue   55 LEU
Chi-restraints excluded: chain R residue   58 LEU
Chi-restraints excluded: chain R residue  128 SER
Chi-restraints excluded: chain R residue  180 VAL
Chi-restraints excluded: chain R residue  183 CYS
Chi-restraints excluded: chain R residue  235 LYS
Chi-restraints excluded: chain R residue  298 VAL
Chi-restraints excluded: chain S residue    4 LEU
Chi-restraints excluded: chain S residue   39 GLN
Chi-restraints excluded: chain S residue  146 SER
Chi-restraints excluded: chain S residue  167 GLN
Chi-restraints excluded: chain S residue  202 LEU
Chi-restraints excluded: chain S residue  223 TYR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 52 optimal weight:    3.9990
   chunk 32 optimal weight:    0.8980
   chunk 65 optimal weight:    0.5980
   chunk 59 optimal weight:    0.8980
   chunk 66 optimal weight:    0.8980
   chunk 108 optimal weight:    0.9980
   chunk 90 optimal weight:    0.9980
   chunk 4 optimal weight:    0.4980
   chunk 58 optimal weight:    0.9980
   chunk 74 optimal weight:    0.9980
   chunk 100 optimal weight:    0.7980
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
A 311 ASN
B  75 GLN
B 220 GLN
** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
S 167 GLN
S 174 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3666 r_free = 0.3666 target = 0.126927 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3402 r_free = 0.3402 target = 0.108412 restraints weight = 12949.178|
|-----------------------------------------------------------------------------|
r_work (start): 0.3398 rms_B_bonded: 1.98
r_work: 0.3277 rms_B_bonded: 2.43 restraints_weight: 0.5000
r_work: 0.3122 rms_B_bonded: 4.20 restraints_weight: 0.2500
r_work (final): 0.3122
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7757
moved from start:          0.1333

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   9196  Z= 0.170
  Angle     :  0.538   8.160  12450  Z= 0.284
  Chirality :  0.041   0.144   1414
  Planarity :  0.004   0.063   1558
  Dihedral  :  5.490  59.780   1271
  Min Nonbonded Distance : 2.546

Molprobity Statistics.
  All-atom Clashscore : 7.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.76 %
    Favored  : 97.24 %
  Rotamer:
    Outliers :  5.36 %
    Allowed  : 24.70 %
    Favored  : 69.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.85 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.94 (0.25), residues: 1125
  helix:  2.29 (0.26), residues: 402
  sheet:  0.17 (0.29), residues: 297
  loop : -0.64 (0.30), residues: 426

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP B 169 
 HIS   0.005   0.001   HIS S  35 
 PHE   0.024   0.002   PHE R 117 
 TYR   0.015   0.001   TYR S 178 
 ARG   0.009   0.001   ARG S 148 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04006 (  465)
  hydrogen bonds       : angle       4.56554 ( 1320)
  SS BOND              : bond        0.00315 (    3)
  SS BOND              : angle       0.76129 (    6)
  covalent geometry    : bond        0.00390 ( 9193)
  covalent geometry    : angle       0.53768 (12444)

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

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

  2250 Ramachandran restraints generated.
    1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2250 Ramachandran restraints generated.
    1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  307 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 53
    poor density    : 254
  time to evaluate  : 1.080 
Fit side-chains
REVERT: A   49 ILE cc_start: 0.6638 (OUTLIER) cc_final: 0.5672 (mp)
REVERT: A  193 ASP cc_start: 0.8003 (m-30) cc_final: 0.7782 (t0)
REVERT: A  197 LYS cc_start: 0.8511 (OUTLIER) cc_final: 0.8271 (mtpp)
REVERT: A  231 ASP cc_start: 0.7966 (t0) cc_final: 0.7683 (t0)
REVERT: A  269 ASN cc_start: 0.8481 (m-40) cc_final: 0.8227 (m110)
REVERT: B   19 ARG cc_start: 0.7767 (ttp80) cc_final: 0.7379 (mtm-85)
REVERT: B   22 ARG cc_start: 0.7278 (mtt180) cc_final: 0.7049 (mtp180)
REVERT: B   61 MET cc_start: 0.8213 (tmm) cc_final: 0.8000 (ppp)
REVERT: B   76 ASP cc_start: 0.7627 (p0) cc_final: 0.7351 (p0)
REVERT: B  130 GLU cc_start: 0.8170 (mp0) cc_final: 0.7702 (mp0)
REVERT: B  150 ARG cc_start: 0.8457 (mmt-90) cc_final: 0.8242 (mpt180)
REVERT: B  197 ARG cc_start: 0.7887 (mpt-90) cc_final: 0.7573 (mtt-85)
REVERT: B  214 ARG cc_start: 0.7838 (OUTLIER) cc_final: 0.7524 (mmt180)
REVERT: B  219 ARG cc_start: 0.8197 (mtp85) cc_final: 0.7940 (mtt-85)
REVERT: B  258 ASP cc_start: 0.8075 (t0) cc_final: 0.7195 (t0)
REVERT: R   37 LEU cc_start: 0.8426 (tp) cc_final: 0.7986 (tm)
REVERT: R   41 PHE cc_start: 0.7970 (m-80) cc_final: 0.7572 (m-80)
REVERT: R   46 PHE cc_start: 0.7678 (t80) cc_final: 0.7268 (t80)
REVERT: R   49 SER cc_start: 0.8683 (OUTLIER) cc_final: 0.8351 (p)
REVERT: R   55 LEU cc_start: 0.8238 (OUTLIER) cc_final: 0.7924 (tt)
REVERT: R   95 LEU cc_start: 0.8667 (mt) cc_final: 0.8434 (mm)
REVERT: R  105 MET cc_start: 0.7852 (mmm) cc_final: 0.7416 (mmm)
REVERT: R  127 MET cc_start: 0.8684 (OUTLIER) cc_final: 0.8464 (mtp)
REVERT: R  219 ILE cc_start: 0.8568 (mm) cc_final: 0.8352 (mt)
REVERT: R  220 LYS cc_start: 0.8307 (mmmm) cc_final: 0.7980 (mmmm)
REVERT: R  235 LYS cc_start: 0.8200 (OUTLIER) cc_final: 0.7365 (mmmm)
REVERT: R  298 VAL cc_start: 0.8582 (OUTLIER) cc_final: 0.8266 (t)
REVERT: S   39 GLN cc_start: 0.8472 (OUTLIER) cc_final: 0.7984 (tp40)
REVERT: S   69 THR cc_start: 0.8249 (p) cc_final: 0.8001 (t)
REVERT: S  200 PHE cc_start: 0.8603 (OUTLIER) cc_final: 0.7954 (m-80)
REVERT: S  205 SER cc_start: 0.7995 (m) cc_final: 0.7640 (p)
REVERT: S  223 TYR cc_start: 0.7922 (OUTLIER) cc_final: 0.7532 (t80)
  outliers start: 53
  outliers final: 23
  residues processed: 278
  average time/residue: 1.0458
  time to fit residues: 311.9820
Evaluate side-chains
  283 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 249
  time to evaluate  : 0.945 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   33 GLU
Chi-restraints excluded: chain A residue   34 VAL
Chi-restraints excluded: chain A residue   49 ILE
Chi-restraints excluded: chain A residue  185 VAL
Chi-restraints excluded: chain A residue  197 LYS
Chi-restraints excluded: chain A residue  295 THR
Chi-restraints excluded: chain B residue   13 GLN
Chi-restraints excluded: chain B residue   33 ILE
Chi-restraints excluded: chain B residue   37 ILE
Chi-restraints excluded: chain B residue   74 SER
Chi-restraints excluded: chain B residue  119 ASN
Chi-restraints excluded: chain B residue  134 ARG
Chi-restraints excluded: chain B residue  190 LEU
Chi-restraints excluded: chain B residue  214 ARG
Chi-restraints excluded: chain B residue  223 THR
Chi-restraints excluded: chain B residue  252 LEU
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain C residue   20 LYS
Chi-restraints excluded: chain C residue   38 MET
Chi-restraints excluded: chain R residue   49 SER
Chi-restraints excluded: chain R residue   55 LEU
Chi-restraints excluded: chain R residue   58 LEU
Chi-restraints excluded: chain R residue  127 MET
Chi-restraints excluded: chain R residue  128 SER
Chi-restraints excluded: chain R residue  180 VAL
Chi-restraints excluded: chain R residue  183 CYS
Chi-restraints excluded: chain R residue  235 LYS
Chi-restraints excluded: chain R residue  298 VAL
Chi-restraints excluded: chain S residue    4 LEU
Chi-restraints excluded: chain S residue   39 GLN
Chi-restraints excluded: chain S residue  146 SER
Chi-restraints excluded: chain S residue  167 GLN
Chi-restraints excluded: chain S residue  200 PHE
Chi-restraints excluded: chain S residue  223 TYR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 85 optimal weight:    1.9990
   chunk 47 optimal weight:    1.9990
   chunk 54 optimal weight:    0.9980
   chunk 77 optimal weight:    0.5980
   chunk 98 optimal weight:    1.9990
   chunk 29 optimal weight:    0.6980
   chunk 12 optimal weight:    0.4980
   chunk 36 optimal weight:    0.9980
   chunk 70 optimal weight:    0.5980
   chunk 95 optimal weight:    0.5980
   chunk 27 optimal weight:    0.9990
   overall best weight:    0.5980

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

Flipped N/Q/H residues before XYZ refinement:
B  75 GLN
B 220 GLN
** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
S 167 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3672 r_free = 0.3672 target = 0.127294 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 25)----------------|
| r_work = 0.3408 r_free = 0.3408 target = 0.108790 restraints weight = 12928.695|
|-----------------------------------------------------------------------------|
r_work (start): 0.3400 rms_B_bonded: 1.97
r_work: 0.3279 rms_B_bonded: 2.43 restraints_weight: 0.5000
r_work: 0.3125 rms_B_bonded: 4.20 restraints_weight: 0.2500
r_work (final): 0.3125
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7750
moved from start:          0.1392

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   9196  Z= 0.148
  Angle     :  0.531   7.634  12450  Z= 0.278
  Chirality :  0.041   0.143   1414
  Planarity :  0.004   0.062   1558
  Dihedral  :  5.407  58.960   1271
  Min Nonbonded Distance : 2.533

Molprobity Statistics.
  All-atom Clashscore : 7.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.76 %
    Favored  : 97.24 %
  Rotamer:
    Outliers :  5.77 %
    Allowed  : 26.01 %
    Favored  : 68.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.85 %
    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:  1.00 (0.25), residues: 1125
  helix:  2.37 (0.26), residues: 402
  sheet:  0.16 (0.29), residues: 297
  loop : -0.61 (0.30), residues: 426

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP B 169 
 HIS   0.005   0.001   HIS S  35 
 PHE   0.025   0.002   PHE R 186 
 TYR   0.015   0.001   TYR S 178 
 ARG   0.010   0.000   ARG S 148 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03883 (  465)
  hydrogen bonds       : angle       4.51991 ( 1320)
  SS BOND              : bond        0.00292 (    3)
  SS BOND              : angle       0.71377 (    6)
  covalent geometry    : bond        0.00337 ( 9193)
  covalent geometry    : angle       0.53110 (12444)

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

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

  2250 Ramachandran restraints generated.
    1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2250 Ramachandran restraints generated.
    1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  315 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 57
    poor density    : 258
  time to evaluate  : 1.059 
Fit side-chains
REVERT: A   49 ILE cc_start: 0.6623 (OUTLIER) cc_final: 0.5747 (mp)
REVERT: A  193 ASP cc_start: 0.8014 (m-30) cc_final: 0.7797 (t0)
REVERT: A  197 LYS cc_start: 0.8488 (OUTLIER) cc_final: 0.8257 (mtpp)
REVERT: A  231 ASP cc_start: 0.7918 (t0) cc_final: 0.7619 (t0)
REVERT: A  269 ASN cc_start: 0.8477 (m-40) cc_final: 0.8232 (m110)
REVERT: A  328 ASP cc_start: 0.7847 (m-30) cc_final: 0.7562 (m-30)
REVERT: B   19 ARG cc_start: 0.7733 (ttp80) cc_final: 0.7326 (mtm-85)
REVERT: B   22 ARG cc_start: 0.7255 (mtt180) cc_final: 0.7030 (mtp180)
REVERT: B   61 MET cc_start: 0.8199 (tmm) cc_final: 0.7979 (ppp)
REVERT: B   76 ASP cc_start: 0.7619 (p0) cc_final: 0.7350 (p0)
REVERT: B  130 GLU cc_start: 0.8150 (mp0) cc_final: 0.7677 (mp0)
REVERT: B  150 ARG cc_start: 0.8457 (mmt-90) cc_final: 0.8251 (mpt180)
REVERT: B  197 ARG cc_start: 0.7899 (mpt-90) cc_final: 0.7579 (mtt-85)
REVERT: B  214 ARG cc_start: 0.7833 (OUTLIER) cc_final: 0.7502 (mmt180)
REVERT: B  258 ASP cc_start: 0.8046 (t0) cc_final: 0.7211 (t0)
REVERT: R   37 LEU cc_start: 0.8408 (tp) cc_final: 0.7941 (tm)
REVERT: R   41 PHE cc_start: 0.7959 (m-80) cc_final: 0.7489 (m-80)
REVERT: R   46 PHE cc_start: 0.7703 (t80) cc_final: 0.7296 (t80)
REVERT: R   49 SER cc_start: 0.8691 (OUTLIER) cc_final: 0.8358 (p)
REVERT: R   55 LEU cc_start: 0.8229 (OUTLIER) cc_final: 0.7917 (tt)
REVERT: R   95 LEU cc_start: 0.8635 (mt) cc_final: 0.8388 (mm)
REVERT: R  105 MET cc_start: 0.7862 (mmm) cc_final: 0.7420 (mmm)
REVERT: R  168 LEU cc_start: 0.7990 (OUTLIER) cc_final: 0.7674 (mp)
REVERT: R  220 LYS cc_start: 0.8302 (mmmm) cc_final: 0.7984 (mmmm)
REVERT: R  235 LYS cc_start: 0.8190 (OUTLIER) cc_final: 0.7357 (mmmm)
REVERT: R  298 VAL cc_start: 0.8566 (OUTLIER) cc_final: 0.8250 (t)
REVERT: S   39 GLN cc_start: 0.8455 (OUTLIER) cc_final: 0.7999 (tp40)
REVERT: S   69 THR cc_start: 0.8199 (p) cc_final: 0.7960 (t)
REVERT: S  200 PHE cc_start: 0.8608 (OUTLIER) cc_final: 0.7942 (m-80)
REVERT: S  205 SER cc_start: 0.7996 (m) cc_final: 0.7640 (p)
REVERT: S  223 TYR cc_start: 0.7920 (OUTLIER) cc_final: 0.7541 (t80)
  outliers start: 57
  outliers final: 24
  residues processed: 287
  average time/residue: 1.0066
  time to fit residues: 310.7844
Evaluate side-chains
  283 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 248
  time to evaluate  : 1.056 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   33 GLU
Chi-restraints excluded: chain A residue   34 VAL
Chi-restraints excluded: chain A residue   49 ILE
Chi-restraints excluded: chain A residue  197 LYS
Chi-restraints excluded: chain A residue  295 THR
Chi-restraints excluded: chain B residue   13 GLN
Chi-restraints excluded: chain B residue   33 ILE
Chi-restraints excluded: chain B residue   37 ILE
Chi-restraints excluded: chain B residue   74 SER
Chi-restraints excluded: chain B residue  134 ARG
Chi-restraints excluded: chain B residue  190 LEU
Chi-restraints excluded: chain B residue  214 ARG
Chi-restraints excluded: chain B residue  223 THR
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  252 LEU
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  322 ASP
Chi-restraints excluded: chain C residue   20 LYS
Chi-restraints excluded: chain C residue   38 MET
Chi-restraints excluded: chain R residue   49 SER
Chi-restraints excluded: chain R residue   55 LEU
Chi-restraints excluded: chain R residue   58 LEU
Chi-restraints excluded: chain R residue   85 VAL
Chi-restraints excluded: chain R residue  128 SER
Chi-restraints excluded: chain R residue  168 LEU
Chi-restraints excluded: chain R residue  180 VAL
Chi-restraints excluded: chain R residue  183 CYS
Chi-restraints excluded: chain R residue  235 LYS
Chi-restraints excluded: chain R residue  287 ILE
Chi-restraints excluded: chain R residue  298 VAL
Chi-restraints excluded: chain S residue    4 LEU
Chi-restraints excluded: chain S residue   39 GLN
Chi-restraints excluded: chain S residue  146 SER
Chi-restraints excluded: chain S residue  200 PHE
Chi-restraints excluded: chain S residue  223 TYR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 77 optimal weight:    0.9990
   chunk 48 optimal weight:    2.9990
   chunk 96 optimal weight:    0.0070
   chunk 17 optimal weight:    0.9980
   chunk 66 optimal weight:    1.9990
   chunk 51 optimal weight:    0.7980
   chunk 18 optimal weight:    0.4980
   chunk 7 optimal weight:    1.9990
   chunk 31 optimal weight:    0.7980
   chunk 46 optimal weight:    0.9990
   chunk 45 optimal weight:    0.9980
   overall best weight:    0.6198

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

Flipped N/Q/H residues before XYZ refinement:
** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 220 GLN
** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
S 167 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3665 r_free = 0.3665 target = 0.126913 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3405 r_free = 0.3405 target = 0.108482 restraints weight = 13088.662|
|-----------------------------------------------------------------------------|
r_work (start): 0.3401 rms_B_bonded: 1.98
r_work: 0.3280 rms_B_bonded: 2.45 restraints_weight: 0.5000
r_work: 0.3126 rms_B_bonded: 4.22 restraints_weight: 0.2500
r_work (final): 0.3126
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7753
moved from start:          0.1482

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   9196  Z= 0.152
  Angle     :  0.540  11.598  12450  Z= 0.281
  Chirality :  0.041   0.144   1414
  Planarity :  0.004   0.062   1558
  Dihedral  :  5.296  59.613   1269
  Min Nonbonded Distance : 2.531

Molprobity Statistics.
  All-atom Clashscore : 7.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.93 %
    Favored  : 97.07 %
  Rotamer:
    Outliers :  5.16 %
    Allowed  : 26.01 %
    Favored  : 68.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.85 %
    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:  1.02 (0.26), residues: 1125
  helix:  2.40 (0.26), residues: 402
  sheet:  0.16 (0.29), residues: 297
  loop : -0.57 (0.30), residues: 426

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP B 169 
 HIS   0.005   0.001   HIS S  35 
 PHE   0.021   0.002   PHE R 117 
 TYR   0.014   0.001   TYR S 178 
 ARG   0.011   0.000   ARG S 148 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03851 (  465)
  hydrogen bonds       : angle       4.50902 ( 1320)
  SS BOND              : bond        0.00289 (    3)
  SS BOND              : angle       0.71062 (    6)
  covalent geometry    : bond        0.00348 ( 9193)
  covalent geometry    : angle       0.53962 (12444)

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

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

  2250 Ramachandran restraints generated.
    1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2250 Ramachandran restraints generated.
    1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  306 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 51
    poor density    : 255
  time to evaluate  : 0.922 
Fit side-chains
REVERT: A   49 ILE cc_start: 0.6610 (OUTLIER) cc_final: 0.5747 (mp)
REVERT: A  193 ASP cc_start: 0.7966 (m-30) cc_final: 0.7750 (t0)
REVERT: A  231 ASP cc_start: 0.7910 (t0) cc_final: 0.7610 (t0)
REVERT: A  269 ASN cc_start: 0.8444 (m-40) cc_final: 0.8194 (m110)
REVERT: A  328 ASP cc_start: 0.7817 (m-30) cc_final: 0.7537 (m-30)
REVERT: B   19 ARG cc_start: 0.7765 (ttp80) cc_final: 0.7341 (mtm-85)
REVERT: B   22 ARG cc_start: 0.7272 (mtt180) cc_final: 0.7032 (mtp180)
REVERT: B   61 MET cc_start: 0.8190 (tmm) cc_final: 0.7970 (ppp)
REVERT: B   76 ASP cc_start: 0.7603 (p0) cc_final: 0.7366 (p0)
REVERT: B  130 GLU cc_start: 0.8168 (mp0) cc_final: 0.7726 (mp0)
REVERT: B  197 ARG cc_start: 0.7858 (mpt-90) cc_final: 0.7525 (mtt-85)
REVERT: B  214 ARG cc_start: 0.7896 (OUTLIER) cc_final: 0.7547 (mmt180)
REVERT: B  258 ASP cc_start: 0.8043 (t0) cc_final: 0.7201 (t0)
REVERT: R   37 LEU cc_start: 0.8391 (tp) cc_final: 0.7967 (tm)
REVERT: R   41 PHE cc_start: 0.7969 (m-80) cc_final: 0.7578 (m-80)
REVERT: R   46 PHE cc_start: 0.7703 (t80) cc_final: 0.7328 (t80)
REVERT: R   49 SER cc_start: 0.8668 (OUTLIER) cc_final: 0.8362 (p)
REVERT: R   55 LEU cc_start: 0.8241 (OUTLIER) cc_final: 0.7937 (tt)
REVERT: R   95 LEU cc_start: 0.8627 (mt) cc_final: 0.8351 (mm)
REVERT: R  105 MET cc_start: 0.7888 (mmm) cc_final: 0.7465 (mmm)
REVERT: R  168 LEU cc_start: 0.7970 (OUTLIER) cc_final: 0.7655 (mp)
REVERT: R  204 ILE cc_start: 0.8376 (pp) cc_final: 0.8176 (pt)
REVERT: R  219 ILE cc_start: 0.8555 (mm) cc_final: 0.8345 (mt)
REVERT: R  235 LYS cc_start: 0.8205 (OUTLIER) cc_final: 0.7387 (mmmm)
REVERT: R  298 VAL cc_start: 0.8566 (OUTLIER) cc_final: 0.8257 (t)
REVERT: S   39 GLN cc_start: 0.8471 (OUTLIER) cc_final: 0.7995 (tp40)
REVERT: S   69 THR cc_start: 0.8160 (p) cc_final: 0.7941 (t)
REVERT: S  200 PHE cc_start: 0.8625 (OUTLIER) cc_final: 0.7959 (m-80)
REVERT: S  205 SER cc_start: 0.7991 (m) cc_final: 0.7574 (p)
REVERT: S  223 TYR cc_start: 0.7943 (OUTLIER) cc_final: 0.7492 (t80)
  outliers start: 51
  outliers final: 27
  residues processed: 282
  average time/residue: 1.0411
  time to fit residues: 315.5659
Evaluate side-chains
  283 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 246
  time to evaluate  : 0.944 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   29 LYS
Chi-restraints excluded: chain A residue   33 GLU
Chi-restraints excluded: chain A residue   49 ILE
Chi-restraints excluded: chain A residue  295 THR
Chi-restraints excluded: chain B residue   13 GLN
Chi-restraints excluded: chain B residue   33 ILE
Chi-restraints excluded: chain B residue   37 ILE
Chi-restraints excluded: chain B residue   74 SER
Chi-restraints excluded: chain B residue  114 CYS
Chi-restraints excluded: chain B residue  134 ARG
Chi-restraints excluded: chain B residue  190 LEU
Chi-restraints excluded: chain B residue  214 ARG
Chi-restraints excluded: chain B residue  223 THR
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  252 LEU
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  322 ASP
Chi-restraints excluded: chain C residue   20 LYS
Chi-restraints excluded: chain C residue   38 MET
Chi-restraints excluded: chain R residue   49 SER
Chi-restraints excluded: chain R residue   55 LEU
Chi-restraints excluded: chain R residue   58 LEU
Chi-restraints excluded: chain R residue   85 VAL
Chi-restraints excluded: chain R residue  128 SER
Chi-restraints excluded: chain R residue  168 LEU
Chi-restraints excluded: chain R residue  180 VAL
Chi-restraints excluded: chain R residue  183 CYS
Chi-restraints excluded: chain R residue  235 LYS
Chi-restraints excluded: chain R residue  287 ILE
Chi-restraints excluded: chain R residue  298 VAL
Chi-restraints excluded: chain S residue    4 LEU
Chi-restraints excluded: chain S residue   39 GLN
Chi-restraints excluded: chain S residue  146 SER
Chi-restraints excluded: chain S residue  167 GLN
Chi-restraints excluded: chain S residue  200 PHE
Chi-restraints excluded: chain S residue  223 TYR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 27 optimal weight:    0.5980
   chunk 79 optimal weight:    0.5980
   chunk 39 optimal weight:    0.4980
   chunk 101 optimal weight:    5.9990
   chunk 89 optimal weight:    4.9990
   chunk 21 optimal weight:    0.5980
   chunk 31 optimal weight:    0.4980
   chunk 72 optimal weight:    1.9990
   chunk 66 optimal weight:    1.9990
   chunk 23 optimal weight:    0.8980
   chunk 85 optimal weight:    0.5980
   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  75 GLN
B 220 GLN
** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
S 167 GLN
S 174 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3665 r_free = 0.3665 target = 0.126959 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3406 r_free = 0.3406 target = 0.108588 restraints weight = 13218.984|
|-----------------------------------------------------------------------------|
r_work (start): 0.3412 rms_B_bonded: 1.98
r_work: 0.3290 rms_B_bonded: 2.44 restraints_weight: 0.5000
r_work: 0.3136 rms_B_bonded: 4.22 restraints_weight: 0.2500
r_work (final): 0.3136
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7751
moved from start:          0.1569

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   9196  Z= 0.144
  Angle     :  0.540  11.487  12450  Z= 0.281
  Chirality :  0.041   0.153   1414
  Planarity :  0.004   0.061   1558
  Dihedral  :  5.241  58.758   1269
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 7.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.76 %
    Favored  : 97.24 %
  Rotamer:
    Outliers :  4.25 %
    Allowed  : 26.52 %
    Favored  : 69.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.85 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.03 (0.26), residues: 1125
  helix:  2.34 (0.26), residues: 408
  sheet:  0.14 (0.29), residues: 297
  loop : -0.54 (0.30), residues: 420

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP R 251 
 HIS   0.005   0.001   HIS S  35 
 PHE   0.024   0.002   PHE R 186 
 TYR   0.015   0.001   TYR S 178 
 ARG   0.013   0.000   ARG S 148 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03806 (  465)
  hydrogen bonds       : angle       4.49789 ( 1320)
  SS BOND              : bond        0.00297 (    3)
  SS BOND              : angle       0.70054 (    6)
  covalent geometry    : bond        0.00330 ( 9193)
  covalent geometry    : angle       0.53993 (12444)

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

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

  2250 Ramachandran restraints generated.
    1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2250 Ramachandran restraints generated.
    1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  298 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 256
  time to evaluate  : 0.950 
Fit side-chains
REVERT: A   49 ILE cc_start: 0.6649 (OUTLIER) cc_final: 0.5758 (mp)
REVERT: A  193 ASP cc_start: 0.7961 (m-30) cc_final: 0.7745 (t0)
REVERT: A  231 ASP cc_start: 0.7861 (t0) cc_final: 0.7555 (t0)
REVERT: A  269 ASN cc_start: 0.8435 (m-40) cc_final: 0.8197 (m110)
REVERT: A  328 ASP cc_start: 0.7817 (m-30) cc_final: 0.7533 (m-30)
REVERT: A  340 THR cc_start: 0.8618 (m) cc_final: 0.8294 (t)
REVERT: B   22 ARG cc_start: 0.7257 (mtt180) cc_final: 0.7038 (mtp180)
REVERT: B   30 LEU cc_start: 0.7891 (tp) cc_final: 0.7599 (tt)
REVERT: B   61 MET cc_start: 0.8176 (tmm) cc_final: 0.7958 (ppp)
REVERT: B   76 ASP cc_start: 0.7594 (p0) cc_final: 0.7336 (p0)
REVERT: B  130 GLU cc_start: 0.8177 (mp0) cc_final: 0.7746 (mp0)
REVERT: B  197 ARG cc_start: 0.7893 (mpt-90) cc_final: 0.7558 (mtt-85)
REVERT: B  214 ARG cc_start: 0.7920 (OUTLIER) cc_final: 0.7558 (mmt180)
REVERT: B  258 ASP cc_start: 0.8030 (t0) cc_final: 0.7207 (t0)
REVERT: R   37 LEU cc_start: 0.8349 (tp) cc_final: 0.7920 (tm)
REVERT: R   41 PHE cc_start: 0.7964 (m-80) cc_final: 0.7579 (m-80)
REVERT: R   46 PHE cc_start: 0.7706 (t80) cc_final: 0.7320 (t80)
REVERT: R   49 SER cc_start: 0.8673 (OUTLIER) cc_final: 0.8369 (p)
REVERT: R   55 LEU cc_start: 0.8259 (OUTLIER) cc_final: 0.7959 (tt)
REVERT: R   95 LEU cc_start: 0.8634 (mt) cc_final: 0.8394 (mm)
REVERT: R  105 MET cc_start: 0.7860 (mmm) cc_final: 0.7470 (mmm)
REVERT: R  121 MET cc_start: 0.8056 (tpp) cc_final: 0.7473 (mpp)
REVERT: R  168 LEU cc_start: 0.7978 (OUTLIER) cc_final: 0.7695 (mp)
REVERT: R  204 ILE cc_start: 0.8384 (pp) cc_final: 0.8179 (pt)
REVERT: R  219 ILE cc_start: 0.8565 (mm) cc_final: 0.8351 (mt)
REVERT: R  298 VAL cc_start: 0.8556 (OUTLIER) cc_final: 0.8261 (t)
REVERT: S   39 GLN cc_start: 0.8455 (OUTLIER) cc_final: 0.7982 (tp40)
REVERT: S   69 THR cc_start: 0.8172 (p) cc_final: 0.7950 (t)
REVERT: S   98 ARG cc_start: 0.8678 (ptm160) cc_final: 0.8380 (ptm160)
REVERT: S  200 PHE cc_start: 0.8619 (OUTLIER) cc_final: 0.7972 (m-80)
REVERT: S  205 SER cc_start: 0.7999 (m) cc_final: 0.7579 (p)
REVERT: S  223 TYR cc_start: 0.7913 (OUTLIER) cc_final: 0.7475 (t80)
  outliers start: 42
  outliers final: 26
  residues processed: 279
  average time/residue: 1.0145
  time to fit residues: 304.0532
Evaluate side-chains
  288 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 253
  time to evaluate  : 0.914 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   33 GLU
Chi-restraints excluded: chain A residue   34 VAL
Chi-restraints excluded: chain A residue   49 ILE
Chi-restraints excluded: chain A residue  295 THR
Chi-restraints excluded: chain B residue   13 GLN
Chi-restraints excluded: chain B residue   33 ILE
Chi-restraints excluded: chain B residue   37 ILE
Chi-restraints excluded: chain B residue   74 SER
Chi-restraints excluded: chain B residue  114 CYS
Chi-restraints excluded: chain B residue  134 ARG
Chi-restraints excluded: chain B residue  190 LEU
Chi-restraints excluded: chain B residue  214 ARG
Chi-restraints excluded: chain B residue  223 THR
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  252 LEU
Chi-restraints excluded: chain B residue  262 MET
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain C residue   38 MET
Chi-restraints excluded: chain R residue   49 SER
Chi-restraints excluded: chain R residue   55 LEU
Chi-restraints excluded: chain R residue   58 LEU
Chi-restraints excluded: chain R residue   85 VAL
Chi-restraints excluded: chain R residue  128 SER
Chi-restraints excluded: chain R residue  168 LEU
Chi-restraints excluded: chain R residue  180 VAL
Chi-restraints excluded: chain R residue  183 CYS
Chi-restraints excluded: chain R residue  258 LEU
Chi-restraints excluded: chain R residue  287 ILE
Chi-restraints excluded: chain R residue  298 VAL
Chi-restraints excluded: chain S residue    4 LEU
Chi-restraints excluded: chain S residue   39 GLN
Chi-restraints excluded: chain S residue  167 GLN
Chi-restraints excluded: chain S residue  200 PHE
Chi-restraints excluded: chain S residue  223 TYR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 19 optimal weight:    0.6980
   chunk 2 optimal weight:    0.8980
   chunk 47 optimal weight:    0.6980
   chunk 42 optimal weight:    0.8980
   chunk 34 optimal weight:    0.2980
   chunk 21 optimal weight:    0.9980
   chunk 15 optimal weight:    0.8980
   chunk 84 optimal weight:    0.8980
   chunk 89 optimal weight:    3.9990
   chunk 26 optimal weight:    0.6980
   chunk 86 optimal weight:    0.6980
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
B 220 GLN
B 259 GLN
** R 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
S  82 GLN
S 167 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3666 r_free = 0.3666 target = 0.127097 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3412 r_free = 0.3412 target = 0.108966 restraints weight = 12942.363|
|-----------------------------------------------------------------------------|
r_work (start): 0.3416 rms_B_bonded: 1.93
r_work: 0.3295 rms_B_bonded: 2.40 restraints_weight: 0.5000
r_work: 0.3144 rms_B_bonded: 4.14 restraints_weight: 0.2500
r_work (final): 0.3144
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7751
moved from start:          0.1590

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   9196  Z= 0.153
  Angle     :  0.546  11.251  12450  Z= 0.284
  Chirality :  0.041   0.143   1414
  Planarity :  0.004   0.062   1558
  Dihedral  :  5.251  58.935   1269
  Min Nonbonded Distance : 2.519

Molprobity Statistics.
  All-atom Clashscore : 7.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.93 %
    Favored  : 97.07 %
  Rotamer:
    Outliers :  4.45 %
    Allowed  : 26.72 %
    Favored  : 68.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.85 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.03 (0.26), residues: 1125
  helix:  2.32 (0.26), residues: 408
  sheet:  0.14 (0.29), residues: 297
  loop : -0.51 (0.31), residues: 420

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP R 251 
 HIS   0.005   0.001   HIS S  35 
 PHE   0.022   0.002   PHE R 216 
 TYR   0.014   0.001   TYR S 178 
 ARG   0.014   0.000   ARG S 148 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03811 (  465)
  hydrogen bonds       : angle       4.51146 ( 1320)
  SS BOND              : bond        0.00314 (    3)
  SS BOND              : angle       0.76522 (    6)
  covalent geometry    : bond        0.00352 ( 9193)
  covalent geometry    : angle       0.54585 (12444)

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

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

  2250 Ramachandran restraints generated.
    1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2250 Ramachandran restraints generated.
    1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  301 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 257
  time to evaluate  : 1.077 
Fit side-chains
REVERT: A   49 ILE cc_start: 0.6646 (OUTLIER) cc_final: 0.5792 (mp)
REVERT: A  193 ASP cc_start: 0.7949 (m-30) cc_final: 0.7737 (t0)
REVERT: A  231 ASP cc_start: 0.7804 (t0) cc_final: 0.7504 (t0)
REVERT: A  269 ASN cc_start: 0.8434 (m-40) cc_final: 0.8198 (m110)
REVERT: A  328 ASP cc_start: 0.7826 (m-30) cc_final: 0.7515 (m-30)
REVERT: A  340 THR cc_start: 0.8628 (m) cc_final: 0.8294 (t)
REVERT: B   19 ARG cc_start: 0.7737 (ttp80) cc_final: 0.7406 (mtm-85)
REVERT: B   22 ARG cc_start: 0.7283 (mtt180) cc_final: 0.7061 (mtp180)
REVERT: B   30 LEU cc_start: 0.7927 (tp) cc_final: 0.7621 (tt)
REVERT: B   61 MET cc_start: 0.8176 (tmm) cc_final: 0.7954 (ppp)
REVERT: B   76 ASP cc_start: 0.7576 (p0) cc_final: 0.7343 (p0)
REVERT: B  130 GLU cc_start: 0.8174 (mp0) cc_final: 0.7746 (mp0)
REVERT: B  197 ARG cc_start: 0.7853 (mpt-90) cc_final: 0.7509 (mtt-85)
REVERT: B  214 ARG cc_start: 0.7910 (OUTLIER) cc_final: 0.7550 (mmt180)
REVERT: B  258 ASP cc_start: 0.8032 (t0) cc_final: 0.7207 (t0)
REVERT: R   37 LEU cc_start: 0.8341 (tp) cc_final: 0.7909 (tm)
REVERT: R   41 PHE cc_start: 0.7970 (m-80) cc_final: 0.7575 (m-80)
REVERT: R   46 PHE cc_start: 0.7716 (t80) cc_final: 0.7327 (t80)
REVERT: R   49 SER cc_start: 0.8669 (OUTLIER) cc_final: 0.8368 (p)
REVERT: R   55 LEU cc_start: 0.8266 (OUTLIER) cc_final: 0.7969 (tt)
REVERT: R   95 LEU cc_start: 0.8646 (mt) cc_final: 0.8401 (mm)
REVERT: R  105 MET cc_start: 0.7859 (mmm) cc_final: 0.7472 (mmm)
REVERT: R  121 MET cc_start: 0.8088 (tpp) cc_final: 0.7400 (mpp)
REVERT: R  168 LEU cc_start: 0.7979 (OUTLIER) cc_final: 0.7684 (mp)
REVERT: R  204 ILE cc_start: 0.8371 (pp) cc_final: 0.8162 (pt)
REVERT: R  298 VAL cc_start: 0.8562 (OUTLIER) cc_final: 0.8268 (t)
REVERT: S   39 GLN cc_start: 0.8466 (OUTLIER) cc_final: 0.8003 (tp40)
REVERT: S   69 THR cc_start: 0.8184 (p) cc_final: 0.7959 (t)
REVERT: S   98 ARG cc_start: 0.8706 (ptm160) cc_final: 0.8401 (ptm160)
REVERT: S  110 PHE cc_start: 0.8546 (t80) cc_final: 0.8273 (t80)
REVERT: S  200 PHE cc_start: 0.8633 (OUTLIER) cc_final: 0.7996 (m-80)
REVERT: S  205 SER cc_start: 0.8004 (m) cc_final: 0.7588 (p)
REVERT: S  223 TYR cc_start: 0.7915 (OUTLIER) cc_final: 0.7487 (t80)
  outliers start: 44
  outliers final: 29
  residues processed: 281
  average time/residue: 1.0140
  time to fit residues: 305.9175
Evaluate side-chains
  290 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 252
  time to evaluate  : 0.935 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   29 LYS
Chi-restraints excluded: chain A residue   33 GLU
Chi-restraints excluded: chain A residue   34 VAL
Chi-restraints excluded: chain A residue   49 ILE
Chi-restraints excluded: chain A residue  251 ASP
Chi-restraints excluded: chain A residue  295 THR
Chi-restraints excluded: chain B residue   13 GLN
Chi-restraints excluded: chain B residue   33 ILE
Chi-restraints excluded: chain B residue   37 ILE
Chi-restraints excluded: chain B residue   74 SER
Chi-restraints excluded: chain B residue  114 CYS
Chi-restraints excluded: chain B residue  134 ARG
Chi-restraints excluded: chain B residue  190 LEU
Chi-restraints excluded: chain B residue  214 ARG
Chi-restraints excluded: chain B residue  223 THR
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  252 LEU
Chi-restraints excluded: chain B residue  259 GLN
Chi-restraints excluded: chain B residue  262 MET
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  322 ASP
Chi-restraints excluded: chain R residue   49 SER
Chi-restraints excluded: chain R residue   55 LEU
Chi-restraints excluded: chain R residue   58 LEU
Chi-restraints excluded: chain R residue   85 VAL
Chi-restraints excluded: chain R residue  128 SER
Chi-restraints excluded: chain R residue  168 LEU
Chi-restraints excluded: chain R residue  180 VAL
Chi-restraints excluded: chain R residue  183 CYS
Chi-restraints excluded: chain R residue  287 ILE
Chi-restraints excluded: chain R residue  298 VAL
Chi-restraints excluded: chain S residue    4 LEU
Chi-restraints excluded: chain S residue   12 VAL
Chi-restraints excluded: chain S residue   39 GLN
Chi-restraints excluded: chain S residue  146 SER
Chi-restraints excluded: chain S residue  167 GLN
Chi-restraints excluded: chain S residue  200 PHE
Chi-restraints excluded: chain S residue  223 TYR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 110 optimal weight:    0.9990
   chunk 95 optimal weight:    0.9990
   chunk 44 optimal weight:    1.9990
   chunk 67 optimal weight:    0.9980
   chunk 3 optimal weight:    0.6980
   chunk 23 optimal weight:    1.9990
   chunk 14 optimal weight:    0.9980
   chunk 28 optimal weight:    0.6980
   chunk 102 optimal weight:    0.0010
   chunk 5 optimal weight:    1.9990
   chunk 88 optimal weight:    0.6980
   overall best weight:    0.6186

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

Flipped N/Q/H residues before XYZ refinement:
B  75 GLN
** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 220 GLN
** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
S 167 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3664 r_free = 0.3664 target = 0.126893 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3404 r_free = 0.3404 target = 0.108476 restraints weight = 13133.153|
|-----------------------------------------------------------------------------|
r_work (start): 0.3404 rms_B_bonded: 1.99
r_work: 0.3281 rms_B_bonded: 2.46 restraints_weight: 0.5000
r_work: 0.3128 rms_B_bonded: 4.24 restraints_weight: 0.2500
r_work (final): 0.3128
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7751
moved from start:          0.1628

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   9196  Z= 0.154
  Angle     :  0.551  11.105  12450  Z= 0.287
  Chirality :  0.041   0.143   1414
  Planarity :  0.004   0.061   1558
  Dihedral  :  5.259  59.057   1269
  Min Nonbonded Distance : 2.520

Molprobity Statistics.
  All-atom Clashscore : 7.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.58 %
    Favored  : 97.42 %
  Rotamer:
    Outliers :  4.15 %
    Allowed  : 27.23 %
    Favored  : 68.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.85 %
    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:  1.02 (0.26), residues: 1125
  helix:  2.32 (0.26), residues: 408
  sheet:  0.14 (0.29), residues: 297
  loop : -0.51 (0.31), residues: 420

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.001   TRP R 251 
 HIS   0.004   0.001   HIS S  35 
 PHE   0.025   0.002   PHE R 186 
 TYR   0.014   0.001   TYR S 178 
 ARG   0.013   0.000   ARG S 148 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03804 (  465)
  hydrogen bonds       : angle       4.51795 ( 1320)
  SS BOND              : bond        0.00305 (    3)
  SS BOND              : angle       0.78221 (    6)
  covalent geometry    : bond        0.00354 ( 9193)
  covalent geometry    : angle       0.55044 (12444)

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

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

  2250 Ramachandran restraints generated.
    1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2250 Ramachandran restraints generated.
    1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  293 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 252
  time to evaluate  : 1.039 
Fit side-chains
REVERT: A   49 ILE cc_start: 0.6611 (OUTLIER) cc_final: 0.5774 (mp)
REVERT: A  193 ASP cc_start: 0.7973 (m-30) cc_final: 0.7755 (t0)
REVERT: A  231 ASP cc_start: 0.7816 (t0) cc_final: 0.7518 (t0)
REVERT: A  269 ASN cc_start: 0.8444 (m-40) cc_final: 0.8205 (m110)
REVERT: A  328 ASP cc_start: 0.7828 (m-30) cc_final: 0.7518 (m-30)
REVERT: A  340 THR cc_start: 0.8619 (m) cc_final: 0.8281 (t)
REVERT: B   19 ARG cc_start: 0.7739 (ttp80) cc_final: 0.7408 (mtm-85)
REVERT: B   22 ARG cc_start: 0.7235 (mtt180) cc_final: 0.7028 (mtp180)
REVERT: B   30 LEU cc_start: 0.7860 (tp) cc_final: 0.7546 (tt)
REVERT: B   61 MET cc_start: 0.8189 (tmm) cc_final: 0.7967 (ppp)
REVERT: B   76 ASP cc_start: 0.7586 (p0) cc_final: 0.7333 (p0)
REVERT: B  130 GLU cc_start: 0.8187 (mp0) cc_final: 0.7759 (mp0)
REVERT: B  197 ARG cc_start: 0.7884 (mpt-90) cc_final: 0.7543 (mtt-85)
REVERT: B  214 ARG cc_start: 0.7909 (OUTLIER) cc_final: 0.7545 (mmt180)
REVERT: B  258 ASP cc_start: 0.7967 (t0) cc_final: 0.7239 (t0)
REVERT: R   37 LEU cc_start: 0.8344 (tp) cc_final: 0.7911 (tm)
REVERT: R   41 PHE cc_start: 0.7969 (m-80) cc_final: 0.7571 (m-80)
REVERT: R   46 PHE cc_start: 0.7716 (t80) cc_final: 0.7312 (t80)
REVERT: R   49 SER cc_start: 0.8678 (OUTLIER) cc_final: 0.8377 (p)
REVERT: R   55 LEU cc_start: 0.8252 (OUTLIER) cc_final: 0.7955 (tt)
REVERT: R   95 LEU cc_start: 0.8645 (mt) cc_final: 0.8407 (mm)
REVERT: R  105 MET cc_start: 0.7883 (mmm) cc_final: 0.7510 (mmm)
REVERT: R  121 MET cc_start: 0.8139 (tpp) cc_final: 0.7490 (mpp)
REVERT: R  204 ILE cc_start: 0.8373 (pp) cc_final: 0.8161 (pt)
REVERT: R  298 VAL cc_start: 0.8560 (OUTLIER) cc_final: 0.8269 (t)
REVERT: S   39 GLN cc_start: 0.8468 (OUTLIER) cc_final: 0.8010 (tp40)
REVERT: S   69 THR cc_start: 0.8190 (p) cc_final: 0.7960 (t)
REVERT: S   98 ARG cc_start: 0.8718 (ptm160) cc_final: 0.8404 (ptm160)
REVERT: S  200 PHE cc_start: 0.8620 (OUTLIER) cc_final: 0.7991 (m-80)
REVERT: S  205 SER cc_start: 0.7984 (m) cc_final: 0.7562 (p)
REVERT: S  223 TYR cc_start: 0.7929 (OUTLIER) cc_final: 0.7496 (t80)
  outliers start: 41
  outliers final: 27
  residues processed: 274
  average time/residue: 0.9934
  time to fit residues: 292.6711
Evaluate side-chains
  285 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 250
  time to evaluate  : 0.939 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   29 LYS
Chi-restraints excluded: chain A residue   33 GLU
Chi-restraints excluded: chain A residue   34 VAL
Chi-restraints excluded: chain A residue   49 ILE
Chi-restraints excluded: chain A residue  251 ASP
Chi-restraints excluded: chain A residue  295 THR
Chi-restraints excluded: chain B residue   13 GLN
Chi-restraints excluded: chain B residue   33 ILE
Chi-restraints excluded: chain B residue   37 ILE
Chi-restraints excluded: chain B residue   74 SER
Chi-restraints excluded: chain B residue  114 CYS
Chi-restraints excluded: chain B residue  134 ARG
Chi-restraints excluded: chain B residue  190 LEU
Chi-restraints excluded: chain B residue  214 ARG
Chi-restraints excluded: chain B residue  223 THR
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  252 LEU
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  322 ASP
Chi-restraints excluded: chain R residue   49 SER
Chi-restraints excluded: chain R residue   55 LEU
Chi-restraints excluded: chain R residue   58 LEU
Chi-restraints excluded: chain R residue   85 VAL
Chi-restraints excluded: chain R residue  128 SER
Chi-restraints excluded: chain R residue  180 VAL
Chi-restraints excluded: chain R residue  183 CYS
Chi-restraints excluded: chain R residue  287 ILE
Chi-restraints excluded: chain R residue  298 VAL
Chi-restraints excluded: chain S residue    4 LEU
Chi-restraints excluded: chain S residue   12 VAL
Chi-restraints excluded: chain S residue   39 GLN
Chi-restraints excluded: chain S residue  146 SER
Chi-restraints excluded: chain S residue  167 GLN
Chi-restraints excluded: chain S residue  200 PHE
Chi-restraints excluded: chain S residue  223 TYR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 52 optimal weight:    3.9990
   chunk 103 optimal weight:    0.6980
   chunk 24 optimal weight:    0.9980
   chunk 110 optimal weight:    0.8980
   chunk 15 optimal weight:    0.9990
   chunk 86 optimal weight:    0.9980
   chunk 31 optimal weight:    1.9990
   chunk 78 optimal weight:    0.5980
   chunk 93 optimal weight:    0.9980
   chunk 73 optimal weight:    0.8980
   chunk 37 optimal weight:    0.6980
   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 220 GLN
** R 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
S  77 ASN
S 167 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3662 r_free = 0.3662 target = 0.126785 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3407 r_free = 0.3407 target = 0.108618 restraints weight = 13014.864|
|-----------------------------------------------------------------------------|
r_work (start): 0.3412 rms_B_bonded: 1.94
r_work: 0.3291 rms_B_bonded: 2.40 restraints_weight: 0.5000
r_work: 0.3140 rms_B_bonded: 4.14 restraints_weight: 0.2500
r_work (final): 0.3140
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7755
moved from start:          0.1643

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   9196  Z= 0.175
  Angle     :  0.562  11.076  12450  Z= 0.293
  Chirality :  0.041   0.142   1414
  Planarity :  0.004   0.062   1558
  Dihedral  :  5.170  50.552   1269
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 7.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.76 %
    Favored  : 97.24 %
  Rotamer:
    Outliers :  3.64 %
    Allowed  : 27.94 %
    Favored  : 68.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.85 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.99 (0.26), residues: 1125
  helix:  2.32 (0.26), residues: 402
  sheet:  0.12 (0.29), residues: 297
  loop : -0.54 (0.30), residues: 426

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.002   TRP R 251 
 HIS   0.005   0.001   HIS S  35 
 PHE   0.023   0.002   PHE R 216 
 TYR   0.014   0.002   TYR S 178 
 ARG   0.012   0.001   ARG S 148 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03918 (  465)
  hydrogen bonds       : angle       4.54853 ( 1320)
  SS BOND              : bond        0.00330 (    3)
  SS BOND              : angle       0.85502 (    6)
  covalent geometry    : bond        0.00405 ( 9193)
  covalent geometry    : angle       0.56165 (12444)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 7481.06 seconds
wall clock time: 129 minutes 38.15 seconds (7778.15 seconds total)