Starting phenix.real_space_refine
on Wed Feb 12 12:22:24 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8iyw_35831/02_2025/8iyw_35831.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8iyw_35831/02_2025/8iyw_35831.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.45
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8iyw_35831/02_2025/8iyw_35831.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8iyw_35831/02_2025/8iyw_35831.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8iyw_35831/02_2025/8iyw_35831.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8iyw_35831/02_2025/8iyw_35831.cif"
  }
  resolution = 3.45
  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=   0.000 sd=   0.029
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: 5
    Type Number    sf(0)   Gaussians
     S      43      5.16       5
     Cl      1      4.86       5
     C    4980      2.51       5
     N    1381      2.21       5
     O    1444      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 23 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 7849
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "B"
      Number of atoms: 1475
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 202, 1475
          Classifications: {'peptide': 202}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 41}
          Link IDs: {'PTRANS': 4, 'TRANS': 197}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 125
          Unresolved non-hydrogen angles: 154
          Unresolved non-hydrogen dihedrals: 98
          Unresolved non-hydrogen chiralities: 7
          Planarities with less than four sites: {'GLU:plan': 7, 'HIS:plan': 1, 'ASN:plan1': 3, 'ARG:plan': 2, 'ASP:plan': 8}
          Unresolved non-hydrogen planarities: 76
    Chain: "C"
      Number of atoms: 2393
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 338, 2393
          Classifications: {'peptide': 338}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 63}
          Link IDs: {'PTRANS': 5, 'TRANS': 332}
          Unresolved non-hydrogen bonds: 208
          Unresolved non-hydrogen angles: 259
          Unresolved non-hydrogen dihedrals: 157
          Unresolved non-hydrogen chiralities: 20
          Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 7, 'ARG:plan': 8, 'ASN:plan1': 3, 'ASP:plan': 10}
          Unresolved non-hydrogen planarities: 119
    Chain: "G"
      Number of atoms: 379
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 55, 379
          Classifications: {'peptide': 55}
          Incomplete info: {'truncation_to_alanine': 12}
          Link IDs: {'PTRANS': 4, 'TRANS': 50}
          Unresolved non-hydrogen bonds: 45
          Unresolved non-hydrogen angles: 53
          Unresolved non-hydrogen dihedrals: 37
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 2, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 25
    Chain: "H"
      Number of atoms: 1655
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 232, 1655
          Classifications: {'peptide': 232}
          Incomplete info: {'truncation_to_alanine': 38}
          Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 221}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 130
          Unresolved non-hydrogen angles: 158
          Unresolved non-hydrogen dihedrals: 102
          Unresolved non-hydrogen chiralities: 11
          Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 8, 'ARG:plan': 3, 'ASP:plan': 4}
          Unresolved non-hydrogen planarities: 67
    Chain: "R"
      Number of atoms: 1930
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 291, 1930
          Classifications: {'peptide': 291}
          Incomplete info: {'truncation_to_alanine': 120}
          Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 280}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 482
          Unresolved non-hydrogen angles: 617
          Unresolved non-hydrogen dihedrals: 411
          Unresolved non-hydrogen chiralities: 46
          Planarities with less than four sites: {'GLN:plan1': 4, 'HIS:plan': 3, 'TYR:plan': 2, 'ASN:plan1': 6, 'TRP:plan': 4, 'ASP:plan': 9, 'PHE:plan': 12, 'GLU:plan': 5, 'ARG:plan': 9}
          Unresolved non-hydrogen planarities: 263
    Chain: "R"
      Number of atoms: 17
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 17
          Unusual residues: {'OKL': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 5.14, per 1000 atoms: 0.65
  Number of scatterers: 7849
  At special positions: 0
  Unit cell: (87.8, 116.335, 132.797, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     Cl      1     17.00
     S      43     16.00
     O    1444      8.00
     N    1381      7.00
     C    4980      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=5, symmetry=0
    Simple disulfide: pdb=" SG  CYS H  22 " - pdb=" SG  CYS H  96 " distance=2.04
    Simple disulfide: pdb=" SG  CYS H 159 " - pdb=" SG  CYS H 229 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R  18 " - pdb=" SG  CYS R 183 " distance=2.04
    Simple disulfide: pdb=" SG  CYS R  19 " - pdb=" SG  CYS R 266 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R 100 " - pdb=" SG  CYS R 177 " 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: 2.19
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  2200 Ramachandran restraints generated.
    1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2090

  Finding SS restraints...
    Secondary structure from input PDB file:
      31 helices and 14 sheets defined
      37.9% alpha, 22.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.99
  Creating SS restraints...
    Processing helix  chain 'B' and resid 8 through 31
    Processing helix  chain 'B' and resid 208 through 213
      removed outlier: 4.074A  pdb=" N   TRP B 212 " --> pdb=" O   GLU B 208 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 214 through 219
      removed outlier: 4.376A  pdb=" N   ASP B 218 " --> pdb=" O   CYS B 215 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 247 through 256
    Processing helix  chain 'B' and resid 271 through 280
      removed outlier: 3.605A  pdb=" N   LYS B 280 " --> pdb=" O   GLY B 276 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 283 through 287
    Processing helix  chain 'B' and resid 296 through 310
    Processing helix  chain 'B' and resid 329 through 351
      removed outlier: 4.463A  pdb=" N   GLN B 333 " --> pdb=" O   THR B 329 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 4 through 26
      removed outlier: 3.569A  pdb=" N   ALA C  26 " --> pdb=" O   ARG C  22 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 29 through 35
    Processing helix  chain 'G' and resid 9 through 24
    Processing helix  chain 'G' and resid 29 through 44
    Processing helix  chain 'G' and resid 45 through 48
      removed outlier: 4.144A  pdb=" N   ASP G  48 " --> pdb=" O   ALA G  45 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'G' and resid 45 through 48'
    Processing helix  chain 'H' and resid 28 through 32
    Processing helix  chain 'H' and resid 53 through 56
    Processing helix  chain 'H' and resid 74 through 76
      No H-bonds generated for 'chain 'H' and resid 74 through 76'
    Processing helix  chain 'H' and resid 87 through 91
      removed outlier: 3.931A  pdb=" N   THR H  91 " --> pdb=" O   SER H  88 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 220 through 224
    Processing helix  chain 'R' and resid 24 through 55
      Proline residue:  R  31  - end of helix
    Processing helix  chain 'R' and resid 60 through 89
      Proline residue:  R  81  - end of helix
    Processing helix  chain 'R' and resid 96 through 130
    Processing helix  chain 'R' and resid 134 through 139
      removed outlier: 3.690A  pdb=" N   ILE R 139 " --> pdb=" O   LEU R 136 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 140 through 158
    Processing helix  chain 'R' and resid 160 through 165
      removed outlier: 4.092A  pdb=" N   LYS R 164 " --> pdb=" O   VAL R 160 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 187 through 218
      removed outlier: 3.624A  pdb=" N   PHE R 197 " --> pdb=" O   PHE R 193 " (cutoff:3.500A)
      Proline residue:  R 200  - end of helix
    Processing helix  chain 'R' and resid 219 through 222
    Processing helix  chain 'R' and resid 223 through 262
      removed outlier: 4.797A  pdb=" N   ALA R 237 " --> pdb=" O   ILE R 233 " (cutoff:3.500A)
      removed outlier: 3.741A  pdb=" N   ILE R 238 " --> pdb=" O   MET R 234 " (cutoff:3.500A)
      Proline residue:  R 246  - end of helix
      removed outlier: 3.619A  pdb=" N   GLY R 262 " --> pdb=" O   LEU R 258 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 265 through 268
      removed outlier: 3.806A  pdb=" N   VAL R 268 " --> pdb=" O   ASN R 265 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'R' and resid 265 through 268'
    Processing helix  chain 'R' and resid 269 through 281
      removed outlier: 3.787A  pdb=" N   SER R 281 " --> pdb=" O   PHE R 277 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 281 through 290
    Processing helix  chain 'R' and resid 290 through 295
      removed outlier: 4.099A  pdb=" N   TYR R 294 " --> pdb=" O   ASP R 290 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'B' and resid 186 through 189
      removed outlier: 6.314A  pdb=" N   VAL B  34 " --> pdb=" O   ARG B 198 " (cutoff:3.500A)
      removed outlier: 7.662A  pdb=" N   PHE B 200 " --> pdb=" O   VAL B  34 " (cutoff:3.500A)
      removed outlier: 7.220A  pdb=" N   LEU B  36 " --> pdb=" O   PHE B 200 " (cutoff:3.500A)
      removed outlier: 9.864A  pdb=" N   ALA B 221 " --> pdb=" O   ASP B  33 " (cutoff:3.500A)
      removed outlier: 7.123A  pdb=" N   LYS B  35 " --> pdb=" O   ALA B 221 " (cutoff:3.500A)
      removed outlier: 7.970A  pdb=" N   ILE B 223 " --> pdb=" O   LYS B  35 " (cutoff:3.500A)
      removed outlier: 6.537A  pdb=" N   LEU B  37 " --> pdb=" O   ILE B 223 " (cutoff:3.500A)
      removed outlier: 7.899A  pdb=" N   CYS B 225 " --> pdb=" O   LEU B  37 " (cutoff:3.500A)
      removed outlier: 6.913A  pdb=" N   LEU B  39 " --> pdb=" O   CYS B 225 " (cutoff:3.500A)
      removed outlier: 8.432A  pdb=" N   ASP B 227 " --> pdb=" O   LEU B  39 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'C' and resid 47 through 51
      removed outlier: 3.776A  pdb=" N   LEU C 336 " --> pdb=" O   LEU C  51 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'C' and resid 58 through 63
      removed outlier: 6.749A  pdb=" N   ALA C  73 " --> pdb=" O   TYR C  59 " (cutoff:3.500A)
      removed outlier: 4.313A  pdb=" N   MET C  61 " --> pdb=" O   VAL C  71 " (cutoff:3.500A)
      removed outlier: 6.707A  pdb=" N   VAL C  71 " --> pdb=" O   MET C  61 " (cutoff:3.500A)
      removed outlier: 4.874A  pdb=" N   TRP C  63 " --> pdb=" O   LEU C  69 " (cutoff:3.500A)
      removed outlier: 7.179A  pdb=" N   LEU C  69 " --> pdb=" O   TRP C  63 " (cutoff:3.500A)
      removed outlier: 3.777A  pdb=" N   SER C  74 " --> pdb=" O   LYS C  78 " (cutoff:3.500A)
      removed outlier: 3.921A  pdb=" N   LYS C  78 " --> pdb=" O   SER C  74 " (cutoff:3.500A)
      removed outlier: 6.008A  pdb=" N   LEU C  79 " --> pdb=" O   ALA C  92 " (cutoff:3.500A)
      removed outlier: 4.579A  pdb=" N   ALA C  92 " --> pdb=" O   LEU C  79 " (cutoff:3.500A)
      removed outlier: 6.575A  pdb=" N   ILE C  81 " --> pdb=" O   VAL C  90 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'C' and resid 100 through 105
      removed outlier: 6.957A  pdb=" N   GLY C 115 " --> pdb=" O   MET C 101 " (cutoff:3.500A)
      removed outlier: 4.563A  pdb=" N   CYS C 103 " --> pdb=" O   ALA C 113 " (cutoff:3.500A)
      removed outlier: 6.473A  pdb=" N   ALA C 113 " --> pdb=" O   CYS C 103 " (cutoff:3.500A)
      removed outlier: 4.933A  pdb=" N   TYR C 105 " --> pdb=" O   TYR C 111 " (cutoff:3.500A)
      removed outlier: 7.110A  pdb=" N   TYR C 111 " --> pdb=" O   TYR C 105 " (cutoff:3.500A)
      removed outlier: 4.180A  pdb=" N   GLY C 116 " --> pdb=" O   ILE C 120 " (cutoff:3.500A)
      removed outlier: 4.681A  pdb=" N   ILE C 120 " --> pdb=" O   GLY C 116 " (cutoff:3.500A)
      removed outlier: 5.855A  pdb=" N   CYS C 121 " --> pdb=" O   GLU C 138 " (cutoff:3.500A)
      removed outlier: 4.607A  pdb=" N   GLU C 138 " --> pdb=" O   CYS C 121 " (cutoff:3.500A)
      removed outlier: 6.711A  pdb=" N   ILE C 123 " --> pdb=" O   SER C 136 " (cutoff:3.500A)
      removed outlier: 3.525A  pdb=" N   ARG C 134 " --> pdb=" O   ASN C 125 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'C' and resid 146 through 151
      removed outlier: 6.737A  pdb=" N   SER C 160 " --> pdb=" O   SER C 147 " (cutoff:3.500A)
      removed outlier: 4.567A  pdb=" N   CYS C 149 " --> pdb=" O   VAL C 158 " (cutoff:3.500A)
      removed outlier: 6.872A  pdb=" N   VAL C 158 " --> pdb=" O   CYS C 149 " (cutoff:3.500A)
      removed outlier: 3.811A  pdb=" N   THR C 165 " --> pdb=" O   SER C 161 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'C' and resid 187 through 192
      removed outlier: 3.654A  pdb=" N   GLN C 220 " --> pdb=" O   LEU C 210 " (cutoff:3.500A)
      removed outlier: 5.846A  pdb=" N   ASP C 212 " --> pdb=" O   CYS C 218 " (cutoff:3.500A)
      removed outlier: 6.020A  pdb=" N   CYS C 218 " --> pdb=" O   ASP C 212 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'C' and resid 229 through 234
      removed outlier: 6.448A  pdb=" N   CYS C 250 " --> pdb=" O   THR C 263 " (cutoff:3.500A)
      removed outlier: 4.502A  pdb=" N   THR C 263 " --> pdb=" O   CYS C 250 " (cutoff:3.500A)
      removed outlier: 6.752A  pdb=" N   LEU C 252 " --> pdb=" O   LEU C 261 " (cutoff:3.500A)
      removed outlier: 3.584A  pdb=" N   GLN C 259 " --> pdb=" O   ASP C 254 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'C' and resid 273 through 275
      removed outlier: 6.316A  pdb=" N   GLY C 288 " --> pdb=" O   THR C 274 " (cutoff:3.500A)
      removed outlier: 3.508A  pdb=" N   ALA C 287 " --> pdb=" O   ASN C 295 " (cutoff:3.500A)
      removed outlier: 6.765A  pdb=" N   CYS C 294 " --> pdb=" O   VAL C 307 " (cutoff:3.500A)
      removed outlier: 4.775A  pdb=" N   VAL C 307 " --> pdb=" O   CYS C 294 " (cutoff:3.500A)
      removed outlier: 6.683A  pdb=" N   VAL C 296 " --> pdb=" O   ALA C 305 " (cutoff:3.500A)
      removed outlier: 3.798A  pdb=" N   ASP C 303 " --> pdb=" O   ASP C 298 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'H' and resid 3 through 7
    Processing sheet with id=AB1, first strand: chain 'H' and resid 10 through 12
      removed outlier: 5.992A  pdb=" N   GLY H  10 " --> pdb=" O   THR H 118 " (cutoff:3.500A)
      removed outlier: 6.971A  pdb=" N   MET H  34 " --> pdb=" O   TYR H  50 " (cutoff:3.500A)
      removed outlier: 4.766A  pdb=" N   TYR H  50 " --> pdb=" O   MET H  34 " (cutoff:3.500A)
      removed outlier: 6.628A  pdb=" N   TRP H  36 " --> pdb=" O   VAL H  48 " (cutoff:3.500A)
      removed outlier: 3.669A  pdb=" N   TYR H  59 " --> pdb=" O   TYR H  50 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'H' and resid 140 through 141
    Processing sheet with id=AB3, first strand: chain 'H' and resid 146 through 148
      removed outlier: 5.862A  pdb=" N   LEU H 178 " --> pdb=" O   LEU H 187 " (cutoff:3.500A)
      removed outlier: 5.397A  pdb=" N   LEU H 187 " --> pdb=" O   LEU H 178 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'R' and resid 11 through 13
    Processing sheet with id=AB5, first strand: chain 'R' and resid 169 through 170

    424 hydrogen bonds defined for protein.
    1182 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: 2.55

  Time building geometry restraints manager: 2.45 seconds

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

  Histogram of bond lengths:
        1.20 -     1.33: 1407
        1.33 -     1.45: 2209
        1.45 -     1.58: 4347
        1.58 -     1.71: 0
        1.71 -     1.83: 55
  Bond restraints: 8018
  Sorted by residual:
  bond pdb=" C   PHE R 282 "
       pdb=" N   THR R 283 "
    ideal  model  delta    sigma   weight residual
    1.335  1.218  0.117 1.38e-02 5.25e+03 7.15e+01
  bond pdb=" C   VAL R  88 "
       pdb=" N   ARG R  89 "
    ideal  model  delta    sigma   weight residual
    1.332  1.400 -0.068 1.52e-02 4.33e+03 2.02e+01
  bond pdb=" CA  ILE R  98 "
       pdb=" CB  ILE R  98 "
    ideal  model  delta    sigma   weight residual
    1.539  1.521  0.018 5.40e-03 3.43e+04 1.07e+01
  bond pdb=" N   ILE R 212 "
       pdb=" CA  ILE R 212 "
    ideal  model  delta    sigma   weight residual
    1.459  1.497 -0.038 1.33e-02 5.65e+03 7.98e+00
  bond pdb=" N   CYS B 287 "
       pdb=" CA  CYS B 287 "
    ideal  model  delta    sigma   weight residual
    1.456  1.493 -0.038 1.35e-02 5.49e+03 7.75e+00
  ... (remaining 8013 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.74: 10465
        1.74 -     3.48: 385
        3.48 -     5.22: 70
        5.22 -     6.96: 21
        6.96 -     8.69: 13
  Bond angle restraints: 10954
  Sorted by residual:
  angle pdb=" CA  CYS R 177 "
        pdb=" C   CYS R 177 "
        pdb=" O   CYS R 177 "
      ideal   model   delta    sigma   weight residual
     120.40  113.07    7.33 1.05e+00 9.07e-01 4.88e+01
  angle pdb=" N   TYR R 284 "
        pdb=" CA  TYR R 284 "
        pdb=" C   TYR R 284 "
      ideal   model   delta    sigma   weight residual
     111.36  104.59    6.77 1.09e+00 8.42e-01 3.86e+01
  angle pdb=" N   LEU R  83 "
        pdb=" CA  LEU R  83 "
        pdb=" C   LEU R  83 "
      ideal   model   delta    sigma   weight residual
     111.14  104.57    6.57 1.08e+00 8.57e-01 3.70e+01
  angle pdb=" C   PHE R 282 "
        pdb=" N   THR R 283 "
        pdb=" CA  THR R 283 "
      ideal   model   delta    sigma   weight residual
     120.31  111.62    8.69 1.52e+00 4.33e-01 3.27e+01
  angle pdb=" C   ILE R 116 "
        pdb=" N   PHE R 117 "
        pdb=" CA  PHE R 117 "
      ideal   model   delta    sigma   weight residual
     120.65  113.16    7.49 1.32e+00 5.74e-01 3.22e+01
  ... (remaining 10949 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    23.42: 4453
       23.42 -    46.83: 176
       46.83 -    70.25: 18
       70.25 -    93.67: 4
       93.67 -   117.08: 1
  Dihedral angle restraints: 4652
    sinusoidal: 1421
      harmonic: 3231
  Sorted by residual:
  dihedral pdb=" CA  GLN H  82 "
           pdb=" C   GLN H  82 "
           pdb=" N   MET H  83 "
           pdb=" CA  MET H  83 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -159.40  -20.60     0      5.00e+00 4.00e-02 1.70e+01
  dihedral pdb=" CA  ALA B   7 "
           pdb=" C   ALA B   7 "
           pdb=" N   GLU B   8 "
           pdb=" CA  GLU B   8 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.63   20.37     0      5.00e+00 4.00e-02 1.66e+01
  dihedral pdb=" C03 OKL R 401 "
           pdb=" C04 OKL R 401 "
           pdb=" C05 OKL R 401 "
           pdb=" N06 OKL R 401 "
      ideal   model   delta sinusoidal    sigma   weight residual
     183.45   66.37  117.08     1      3.00e+01 1.11e-03 1.55e+01
  ... (remaining 4649 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.050: 962
       0.050 -    0.100: 245
       0.100 -    0.150: 66
       0.150 -    0.200: 4
       0.200 -    0.250: 4
  Chirality restraints: 1281
  Sorted by residual:
  chirality pdb=" CA  HIS B 196 "
            pdb=" N   HIS B 196 "
            pdb=" C   HIS B 196 "
            pdb=" CB  HIS B 196 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.76   -0.25 2.00e-01 2.50e+01 1.56e+00
  chirality pdb=" CA  PHE R 105 "
            pdb=" N   PHE R 105 "
            pdb=" C   PHE R 105 "
            pdb=" CB  PHE R 105 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.74   -0.23 2.00e-01 2.50e+01 1.35e+00
  chirality pdb=" CA  HIS R 161 "
            pdb=" N   HIS R 161 "
            pdb=" C   HIS R 161 "
            pdb=" CB  HIS R 161 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.73   -0.22 2.00e-01 2.50e+01 1.23e+00
  ... (remaining 1278 not shown)

  Planarity restraints: 1415
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C05 OKL R 401 "   -0.012 2.00e-02 2.50e+03   4.04e-02 5.30e+01
        pdb=" C07 OKL R 401 "   -0.020 2.00e-02 2.50e+03
        pdb=" C10 OKL R 401 "    0.006 2.00e-02 2.50e+03
        pdb=" C12 OKL R 401 "    0.041 2.00e-02 2.50e+03
        pdb=" C13 OKL R 401 "    0.053 2.00e-02 2.50e+03
        pdb=" C15 OKL R 401 "    0.015 2.00e-02 2.50e+03
        pdb=" N06 OKL R 401 "    0.018 2.00e-02 2.50e+03
        pdb=" N09 OKL R 401 "   -0.020 2.00e-02 2.50e+03
        pdb=" N14 OKL R 401 "    0.054 2.00e-02 2.50e+03
        pdb=" N16 OKL R 401 "    0.024 2.00e-02 2.50e+03
        pdb=" O08 OKL R 401 "   -0.041 2.00e-02 2.50e+03
        pdb=" O11 OKL R 401 "   -0.016 2.00e-02 2.50e+03
        pdb="CL17 OKL R 401 "   -0.099 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  CYS R 177 "   -0.018 2.00e-02 2.50e+03   3.82e-02 1.46e+01
        pdb=" C   CYS R 177 "    0.066 2.00e-02 2.50e+03
        pdb=" O   CYS R 177 "   -0.025 2.00e-02 2.50e+03
        pdb=" N   SER R 178 "   -0.023 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LYS B 210 "   -0.014 2.00e-02 2.50e+03   2.87e-02 8.26e+00
        pdb=" C   LYS B 210 "    0.050 2.00e-02 2.50e+03
        pdb=" O   LYS B 210 "   -0.019 2.00e-02 2.50e+03
        pdb=" N   LYS B 211 "   -0.017 2.00e-02 2.50e+03
  ... (remaining 1412 not shown)

  Histogram of nonbonded interaction distances:
        2.25 -     2.78: 1783
        2.78 -     3.31: 7637
        3.31 -     3.84: 12456
        3.84 -     4.37: 14149
        4.37 -     4.90: 25163
  Nonbonded interactions: 61188
  Sorted by model distance:
  nonbonded pdb=" O   LYS B 193 "
            pdb=" ND2 ASN B 194 "
     model   vdw
     2.252 3.120
  nonbonded pdb=" OG  SER C 331 "
            pdb=" OD1 ASP C 333 "
     model   vdw
     2.260 3.040
  nonbonded pdb=" O   ARG R 228 "
            pdb=" OG1 THR R 231 "
     model   vdw
     2.278 3.040
  nonbonded pdb=" NE  ARG H  98 "
            pdb=" OD1 ASP H 109 "
     model   vdw
     2.295 3.120
  nonbonded pdb=" O   ASN R  17 "
            pdb=" ND2 ASN R  17 "
     model   vdw
     2.298 3.120
  ... (remaining 61183 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:             1.210
  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:          0.270
  Check model and map are aligned:         0.050
  Set scattering table:                    0.060
  Process input model:                     21.710
  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:2.870
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   26.310
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7665
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.117   8018  Z= 0.311
  Angle     :  0.837   8.695  10954  Z= 0.518
  Chirality :  0.049   0.250   1281
  Planarity :  0.005   0.047   1415
  Dihedral  : 12.733 117.085   2547
  Min Nonbonded Distance : 2.252

Molprobity Statistics.
  All-atom Clashscore : 5.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.27 %
    Favored  : 96.73 %
  Rotamer:
    Outliers :  1.45 %
    Allowed  : 11.76 %
    Favored  : 86.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.06 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.09 (0.25), residues: 1100
  helix:  0.47 (0.27), residues: 353
  sheet:  0.06 (0.32), residues: 250
  loop : -0.09 (0.29), residues: 497

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.002   TRP R 152 
 HIS   0.006   0.001   HIS H  35 
 PHE   0.017   0.002   PHE C 199 
 TYR   0.025   0.002   TYR R 284 
 ARG   0.003   0.001   ARG H 191 

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

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

  2200 Ramachandran restraints generated.
    1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2200 Ramachandran restraints generated.
    1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  141 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 131
  time to evaluate  : 0.837 
Fit side-chains
REVERT: H   68 PHE cc_start: 0.7828 (m-10) cc_final: 0.7427 (m-10)
REVERT: R  216 ARG cc_start: 0.7355 (mtt180) cc_final: 0.7067 (mtt-85)
  outliers start: 10
  outliers final: 3
  residues processed: 136
  average time/residue: 0.2044
  time to fit residues: 37.5872
Evaluate side-chains
  119 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 116
  time to evaluate  : 0.818 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  211 LYS
Chi-restraints excluded: chain R residue   17 ASN
Chi-restraints excluded: chain R residue  255 PHE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 92 optimal weight:    0.7980
   chunk 83 optimal weight:    7.9990
   chunk 46 optimal weight:    0.3980
   chunk 28 optimal weight:    1.9990
   chunk 56 optimal weight:    0.7980
   chunk 44 optimal weight:    3.9990
   chunk 86 optimal weight:    0.8980
   chunk 33 optimal weight:    0.1980
   chunk 52 optimal weight:    0.5980
   chunk 64 optimal weight:    0.5980
   chunk 99 optimal weight:    2.9990
   overall best weight:    0.5180

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

Flipped N/Q/H residues before XYZ refinement:
B 194 ASN
** B 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 295 ASN
H 113 GLN
R 112 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4113 r_free = 0.4113 target = 0.176563 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3682 r_free = 0.3682 target = 0.132808 restraints weight = 9663.354|
|-----------------------------------------------------------------------------|
r_work (start): 0.3660 rms_B_bonded: 3.39
r_work: 0.3328 rms_B_bonded: 3.67 restraints_weight: 0.5000
r_work (final): 0.3328
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7259
moved from start:          0.1245

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   8018  Z= 0.190
  Angle     :  0.576   6.598  10954  Z= 0.313
  Chirality :  0.044   0.148   1281
  Planarity :  0.004   0.037   1415
  Dihedral  :  6.916 146.988   1192
  Min Nonbonded Distance : 2.295

Molprobity Statistics.
  All-atom Clashscore : 3.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.73 %
    Favored  : 97.27 %
  Rotamer:
    Outliers :  2.76 %
    Allowed  : 12.92 %
    Favored  : 84.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.06 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.70 (0.26), residues: 1100
  helix:  1.59 (0.28), residues: 360
  sheet:  0.05 (0.31), residues: 249
  loop : -0.05 (0.29), residues: 491

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP C 169 
 HIS   0.005   0.001   HIS H  35 
 PHE   0.014   0.001   PHE C 199 
 TYR   0.020   0.001   TYR R 269 
 ARG   0.003   0.000   ARG R 218 

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

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

  2200 Ramachandran restraints generated.
    1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2200 Ramachandran restraints generated.
    1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  141 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 122
  time to evaluate  : 0.865 
Fit side-chains
   revert: symmetry clash
REVERT: G   44 HIS cc_start: 0.7978 (m-70) cc_final: 0.7573 (m-70)
REVERT: G   48 ASP cc_start: 0.7683 (t0) cc_final: 0.7124 (t0)
REVERT: R  198 PHE cc_start: 0.7986 (OUTLIER) cc_final: 0.7625 (m-10)
REVERT: R  213 TRP cc_start: 0.8095 (t60) cc_final: 0.7881 (t60)
REVERT: R  216 ARG cc_start: 0.7328 (mtt180) cc_final: 0.6955 (mtt-85)
REVERT: R  284 TYR cc_start: 0.7825 (m-80) cc_final: 0.7327 (m-80)
  outliers start: 19
  outliers final: 12
  residues processed: 133
  average time/residue: 0.1815
  time to fit residues: 33.7560
Evaluate side-chains
  127 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 114
  time to evaluate  : 0.853 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  185 ILE
Chi-restraints excluded: chain B residue  194 ASN
Chi-restraints excluded: chain B residue  253 SER
Chi-restraints excluded: chain B residue  274 LEU
Chi-restraints excluded: chain B residue  296 THR
Chi-restraints excluded: chain C residue  143 THR
Chi-restraints excluded: chain C residue  233 CYS
Chi-restraints excluded: chain G residue   51 LEU
Chi-restraints excluded: chain H residue  139 VAL
Chi-restraints excluded: chain H residue  178 LEU
Chi-restraints excluded: chain R residue  119 THR
Chi-restraints excluded: chain R residue  198 PHE
Chi-restraints excluded: chain R residue  255 PHE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 102 optimal weight:    0.8980
   chunk 50 optimal weight:    3.9990
   chunk 11 optimal weight:    2.9990
   chunk 87 optimal weight:    6.9990
   chunk 6 optimal weight:    0.9990
   chunk 25 optimal weight:    4.9990
   chunk 41 optimal weight:    0.2980
   chunk 100 optimal weight:    0.5980
   chunk 18 optimal weight:    0.8980
   chunk 84 optimal weight:   10.0000
   chunk 56 optimal weight:    3.9990
   overall best weight:    0.7382

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

Flipped N/Q/H residues before XYZ refinement:
** B 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4093 r_free = 0.4093 target = 0.174531 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3648 r_free = 0.3648 target = 0.129531 restraints weight = 9961.223|
|-----------------------------------------------------------------------------|
r_work (start): 0.3626 rms_B_bonded: 3.49
r_work: 0.3293 rms_B_bonded: 3.81 restraints_weight: 0.5000
r_work (final): 0.3293
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7221
moved from start:          0.1614

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   8018  Z= 0.223
  Angle     :  0.551   6.416  10954  Z= 0.298
  Chirality :  0.043   0.160   1281
  Planarity :  0.004   0.037   1415
  Dihedral  :  6.553 138.670   1186
  Min Nonbonded Distance : 2.540

Molprobity Statistics.
  All-atom Clashscore : 3.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.73 %
    Favored  : 97.27 %
  Rotamer:
    Outliers :  3.63 %
    Allowed  : 13.06 %
    Favored  : 83.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.06 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.82 (0.26), residues: 1100
  helix:  1.96 (0.28), residues: 363
  sheet: -0.10 (0.30), residues: 253
  loop : -0.10 (0.30), residues: 484

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP C 169 
 HIS   0.004   0.001   HIS H  35 
 PHE   0.016   0.001   PHE C 199 
 TYR   0.017   0.002   TYR B 297 
 ARG   0.003   0.000   ARG R 218 

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

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

  2200 Ramachandran restraints generated.
    1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2200 Ramachandran restraints generated.
    1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  140 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 115
  time to evaluate  : 0.916 
Fit side-chains
   revert: symmetry clash
REVERT: B  290 GLU cc_start: 0.8199 (pm20) cc_final: 0.7811 (pm20)
REVERT: C   98 SER cc_start: 0.8084 (m) cc_final: 0.7509 (t)
REVERT: G   44 HIS cc_start: 0.7928 (m-70) cc_final: 0.7578 (m-70)
REVERT: G   48 ASP cc_start: 0.7995 (t0) cc_final: 0.7237 (t0)
REVERT: H  237 LEU cc_start: 0.8578 (OUTLIER) cc_final: 0.8358 (mp)
REVERT: R  198 PHE cc_start: 0.7921 (OUTLIER) cc_final: 0.7544 (m-10)
REVERT: R  216 ARG cc_start: 0.7253 (mtt180) cc_final: 0.6820 (mtt-85)
  outliers start: 25
  outliers final: 18
  residues processed: 128
  average time/residue: 0.1664
  time to fit residues: 30.0298
Evaluate side-chains
  133 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 113
  time to evaluate  : 0.772 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  185 ILE
Chi-restraints excluded: chain B residue  228 LEU
Chi-restraints excluded: chain B residue  253 SER
Chi-restraints excluded: chain B residue  274 LEU
Chi-restraints excluded: chain B residue  296 THR
Chi-restraints excluded: chain C residue  143 THR
Chi-restraints excluded: chain C residue  191 SER
Chi-restraints excluded: chain C residue  233 CYS
Chi-restraints excluded: chain G residue   51 LEU
Chi-restraints excluded: chain H residue   52 SER
Chi-restraints excluded: chain H residue   83 MET
Chi-restraints excluded: chain H residue  139 VAL
Chi-restraints excluded: chain H residue  178 LEU
Chi-restraints excluded: chain H residue  237 LEU
Chi-restraints excluded: chain R residue   71 VAL
Chi-restraints excluded: chain R residue  119 THR
Chi-restraints excluded: chain R residue  156 ILE
Chi-restraints excluded: chain R residue  198 PHE
Chi-restraints excluded: chain R residue  255 PHE
Chi-restraints excluded: chain R residue  269 TYR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 38 optimal weight:    3.9990
   chunk 48 optimal weight:    0.0170
   chunk 16 optimal weight:    0.8980
   chunk 62 optimal weight:    0.7980
   chunk 37 optimal weight:    0.2980
   chunk 61 optimal weight:    0.8980
   chunk 26 optimal weight:    0.6980
   chunk 53 optimal weight:    2.9990
   chunk 39 optimal weight:    0.8980
   chunk 36 optimal weight:    0.8980
   chunk 75 optimal weight:    1.9990
   overall best weight:    0.5418

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

Flipped N/Q/H residues before XYZ refinement:
B 194 ASN
** B 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4108 r_free = 0.4108 target = 0.175778 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3673 r_free = 0.3673 target = 0.131927 restraints weight = 9815.228|
|-----------------------------------------------------------------------------|
r_work (start): 0.3650 rms_B_bonded: 3.33
r_work: 0.3320 rms_B_bonded: 3.65 restraints_weight: 0.5000
r_work (final): 0.3320
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7283
moved from start:          0.1957

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   8018  Z= 0.181
  Angle     :  0.514   6.359  10954  Z= 0.277
  Chirality :  0.042   0.163   1281
  Planarity :  0.004   0.038   1415
  Dihedral  :  6.372 140.637   1186
  Min Nonbonded Distance : 2.253

Molprobity Statistics.
  All-atom Clashscore : 3.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.64 %
    Favored  : 97.36 %
  Rotamer:
    Outliers :  3.77 %
    Allowed  : 13.35 %
    Favored  : 82.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.06 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.90 (0.26), residues: 1100
  helix:  2.17 (0.28), residues: 370
  sheet: -0.23 (0.30), residues: 258
  loop : -0.12 (0.30), residues: 472

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP C 169 
 HIS   0.004   0.001   HIS H  35 
 PHE   0.012   0.001   PHE C 199 
 TYR   0.019   0.001   TYR B 297 
 ARG   0.002   0.000   ARG R 218 

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

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

  2200 Ramachandran restraints generated.
    1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2200 Ramachandran restraints generated.
    1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  148 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 122
  time to evaluate  : 0.829 
Fit side-chains
   revert: symmetry clash
REVERT: C   98 SER cc_start: 0.8072 (m) cc_final: 0.7503 (t)
REVERT: G   44 HIS cc_start: 0.7958 (m-70) cc_final: 0.7606 (m-70)
REVERT: G   48 ASP cc_start: 0.8091 (t0) cc_final: 0.7321 (t0)
REVERT: R  111 ARG cc_start: 0.5511 (mtm-85) cc_final: 0.5074 (mtm-85)
REVERT: R  198 PHE cc_start: 0.7893 (OUTLIER) cc_final: 0.7525 (m-10)
REVERT: R  216 ARG cc_start: 0.7316 (mtt180) cc_final: 0.6873 (mtt-85)
  outliers start: 26
  outliers final: 19
  residues processed: 139
  average time/residue: 0.1839
  time to fit residues: 35.3118
Evaluate side-chains
  132 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 112
  time to evaluate  : 0.841 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  185 ILE
Chi-restraints excluded: chain B residue  194 ASN
Chi-restraints excluded: chain B residue  228 LEU
Chi-restraints excluded: chain B residue  254 ILE
Chi-restraints excluded: chain B residue  274 LEU
Chi-restraints excluded: chain B residue  296 THR
Chi-restraints excluded: chain C residue  100 VAL
Chi-restraints excluded: chain C residue  143 THR
Chi-restraints excluded: chain C residue  157 ILE
Chi-restraints excluded: chain C residue  191 SER
Chi-restraints excluded: chain C residue  233 CYS
Chi-restraints excluded: chain G residue   51 LEU
Chi-restraints excluded: chain H residue   83 MET
Chi-restraints excluded: chain H residue  116 THR
Chi-restraints excluded: chain H residue  139 VAL
Chi-restraints excluded: chain R residue   71 VAL
Chi-restraints excluded: chain R residue  119 THR
Chi-restraints excluded: chain R residue  198 PHE
Chi-restraints excluded: chain R residue  232 PHE
Chi-restraints excluded: chain R residue  255 PHE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 107 optimal weight:    0.7980
   chunk 40 optimal weight:    0.8980
   chunk 29 optimal weight:    0.0040
   chunk 53 optimal weight:    3.9990
   chunk 36 optimal weight:    1.9990
   chunk 3 optimal weight:    0.8980
   chunk 80 optimal weight:    0.9980
   chunk 82 optimal weight:   20.0000
   chunk 91 optimal weight:    0.7980
   chunk 98 optimal weight:    1.9990
   chunk 43 optimal weight:    0.8980
   overall best weight:    0.6792

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

Flipped N/Q/H residues before XYZ refinement:
B 194 ASN
** B 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4098 r_free = 0.4098 target = 0.174938 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3652 r_free = 0.3652 target = 0.129822 restraints weight = 9772.519|
|-----------------------------------------------------------------------------|
r_work (start): 0.3620 rms_B_bonded: 3.44
r_work: 0.3315 rms_B_bonded: 3.69 restraints_weight: 0.5000
r_work (final): 0.3315
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7258
moved from start:          0.2100

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   8018  Z= 0.211
  Angle     :  0.531   8.603  10954  Z= 0.283
  Chirality :  0.043   0.173   1281
  Planarity :  0.004   0.038   1415
  Dihedral  :  6.346 140.531   1186
  Min Nonbonded Distance : 2.288

Molprobity Statistics.
  All-atom Clashscore : 4.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.18 %
    Favored  : 96.82 %
  Rotamer:
    Outliers :  4.06 %
    Allowed  : 14.80 %
    Favored  : 81.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.06 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.93 (0.26), residues: 1100
  helix:  2.30 (0.28), residues: 369
  sheet: -0.31 (0.30), residues: 257
  loop : -0.11 (0.30), residues: 474

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP C 169 
 HIS   0.004   0.001   HIS H  35 
 PHE   0.015   0.001   PHE C 199 
 TYR   0.019   0.001   TYR B 297 
 ARG   0.006   0.000   ARG R 218 

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

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

  2200 Ramachandran restraints generated.
    1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2200 Ramachandran restraints generated.
    1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  141 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 113
  time to evaluate  : 0.860 
Fit side-chains
   revert: symmetry clash
REVERT: B  290 GLU cc_start: 0.8272 (pm20) cc_final: 0.7884 (pm20)
REVERT: C   98 SER cc_start: 0.8149 (m) cc_final: 0.7493 (t)
REVERT: G   44 HIS cc_start: 0.8012 (m-70) cc_final: 0.7679 (m-70)
REVERT: G   48 ASP cc_start: 0.8119 (t0) cc_final: 0.7272 (t0)
REVERT: H  231 GLN cc_start: 0.8540 (pp30) cc_final: 0.8209 (pp30)
REVERT: R  111 ARG cc_start: 0.5681 (mtm-85) cc_final: 0.5219 (mtm-85)
REVERT: R  198 PHE cc_start: 0.7931 (OUTLIER) cc_final: 0.7607 (m-10)
REVERT: R  216 ARG cc_start: 0.7331 (mtt180) cc_final: 0.6890 (mtt-85)
  outliers start: 28
  outliers final: 23
  residues processed: 131
  average time/residue: 0.1869
  time to fit residues: 34.6142
Evaluate side-chains
  132 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 108
  time to evaluate  : 1.198 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  185 ILE
Chi-restraints excluded: chain B residue  194 ASN
Chi-restraints excluded: chain B residue  228 LEU
Chi-restraints excluded: chain B residue  254 ILE
Chi-restraints excluded: chain B residue  274 LEU
Chi-restraints excluded: chain B residue  296 THR
Chi-restraints excluded: chain C residue  100 VAL
Chi-restraints excluded: chain C residue  143 THR
Chi-restraints excluded: chain C residue  157 ILE
Chi-restraints excluded: chain C residue  191 SER
Chi-restraints excluded: chain C residue  233 CYS
Chi-restraints excluded: chain C residue  234 PHE
Chi-restraints excluded: chain G residue   51 LEU
Chi-restraints excluded: chain H residue   52 SER
Chi-restraints excluded: chain H residue   83 MET
Chi-restraints excluded: chain H residue  116 THR
Chi-restraints excluded: chain H residue  139 VAL
Chi-restraints excluded: chain H residue  199 VAL
Chi-restraints excluded: chain R residue   71 VAL
Chi-restraints excluded: chain R residue  119 THR
Chi-restraints excluded: chain R residue  156 ILE
Chi-restraints excluded: chain R residue  198 PHE
Chi-restraints excluded: chain R residue  232 PHE
Chi-restraints excluded: chain R residue  255 PHE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 94 optimal weight:   20.0000
   chunk 96 optimal weight:   20.0000
   chunk 107 optimal weight:    5.9990
   chunk 20 optimal weight:    6.9990
   chunk 31 optimal weight:    0.9980
   chunk 0 optimal weight:    5.9990
   chunk 67 optimal weight:    0.9990
   chunk 108 optimal weight:    0.9990
   chunk 28 optimal weight:    1.9990
   chunk 60 optimal weight:    0.4980
   chunk 4 optimal weight:    0.9980
   overall best weight:    0.8984

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

Flipped N/Q/H residues before XYZ refinement:
** B 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  54 HIS
H 113 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4086 r_free = 0.4086 target = 0.173738 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3639 r_free = 0.3639 target = 0.128798 restraints weight = 9820.013|
|-----------------------------------------------------------------------------|
r_work (start): 0.3615 rms_B_bonded: 3.45
r_work: 0.3280 rms_B_bonded: 3.79 restraints_weight: 0.5000
r_work (final): 0.3280
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7259
moved from start:          0.2250

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   8018  Z= 0.255
  Angle     :  0.545   7.036  10954  Z= 0.292
  Chirality :  0.043   0.172   1281
  Planarity :  0.004   0.037   1415
  Dihedral  :  6.448 142.379   1186
  Min Nonbonded Distance : 2.475

Molprobity Statistics.
  All-atom Clashscore : 4.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.18 %
    Favored  : 96.82 %
  Rotamer:
    Outliers :  4.35 %
    Allowed  : 14.95 %
    Favored  : 80.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.06 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.87 (0.26), residues: 1100
  helix:  2.37 (0.28), residues: 369
  sheet: -0.46 (0.31), residues: 257
  loop : -0.19 (0.30), residues: 474

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP C 169 
 HIS   0.004   0.001   HIS C  91 
 PHE   0.017   0.002   PHE C 199 
 TYR   0.019   0.002   TYR B 297 
 ARG   0.006   0.000   ARG R 218 

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

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

  2200 Ramachandran restraints generated.
    1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2200 Ramachandran restraints generated.
    1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  142 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 112
  time to evaluate  : 0.892 
Fit side-chains
   revert: symmetry clash
REVERT: C   98 SER cc_start: 0.8161 (m) cc_final: 0.7510 (t)
REVERT: G   44 HIS cc_start: 0.7976 (m-70) cc_final: 0.7632 (m-70)
REVERT: G   48 ASP cc_start: 0.8242 (t0) cc_final: 0.7365 (t0)
REVERT: H  231 GLN cc_start: 0.8621 (pp30) cc_final: 0.8230 (pp30)
REVERT: R  111 ARG cc_start: 0.5541 (mtm-85) cc_final: 0.5104 (mtm-85)
REVERT: R  198 PHE cc_start: 0.7816 (OUTLIER) cc_final: 0.7488 (m-10)
REVERT: R  216 ARG cc_start: 0.7283 (mtt180) cc_final: 0.6869 (mtt-85)
  outliers start: 30
  outliers final: 24
  residues processed: 133
  average time/residue: 0.1699
  time to fit residues: 31.9142
Evaluate side-chains
  132 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 107
  time to evaluate  : 0.956 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  185 ILE
Chi-restraints excluded: chain B residue  228 LEU
Chi-restraints excluded: chain B residue  254 ILE
Chi-restraints excluded: chain B residue  274 LEU
Chi-restraints excluded: chain B residue  296 THR
Chi-restraints excluded: chain C residue  100 VAL
Chi-restraints excluded: chain C residue  143 THR
Chi-restraints excluded: chain C residue  157 ILE
Chi-restraints excluded: chain C residue  191 SER
Chi-restraints excluded: chain C residue  232 ILE
Chi-restraints excluded: chain C residue  233 CYS
Chi-restraints excluded: chain C residue  234 PHE
Chi-restraints excluded: chain G residue   51 LEU
Chi-restraints excluded: chain H residue   52 SER
Chi-restraints excluded: chain H residue   83 MET
Chi-restraints excluded: chain H residue  116 THR
Chi-restraints excluded: chain H residue  139 VAL
Chi-restraints excluded: chain H residue  199 VAL
Chi-restraints excluded: chain R residue   71 VAL
Chi-restraints excluded: chain R residue  119 THR
Chi-restraints excluded: chain R residue  130 VAL
Chi-restraints excluded: chain R residue  156 ILE
Chi-restraints excluded: chain R residue  198 PHE
Chi-restraints excluded: chain R residue  232 PHE
Chi-restraints excluded: chain R residue  255 PHE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 13 optimal weight:    0.8980
   chunk 7 optimal weight:    0.0070
   chunk 0 optimal weight:    5.9990
   chunk 16 optimal weight:    0.9990
   chunk 47 optimal weight:    0.9980
   chunk 65 optimal weight:    3.9990
   chunk 6 optimal weight:    0.6980
   chunk 69 optimal weight:    1.9990
   chunk 89 optimal weight:    2.9990
   chunk 59 optimal weight:    3.9990
   chunk 26 optimal weight:    0.6980
   overall best weight:    0.6598

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

Flipped N/Q/H residues before XYZ refinement:
** B 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4085 r_free = 0.4085 target = 0.173825 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3654 r_free = 0.3654 target = 0.130534 restraints weight = 9844.495|
|-----------------------------------------------------------------------------|
r_work (start): 0.3628 rms_B_bonded: 3.39
r_work: 0.3295 rms_B_bonded: 3.80 restraints_weight: 0.5000
r_work (final): 0.3295
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7292
moved from start:          0.2382

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   8018  Z= 0.207
  Angle     :  0.532   9.189  10954  Z= 0.283
  Chirality :  0.042   0.162   1281
  Planarity :  0.004   0.037   1415
  Dihedral  :  6.413 143.906   1186
  Min Nonbonded Distance : 2.524

Molprobity Statistics.
  All-atom Clashscore : 4.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.18 %
    Favored  : 96.82 %
  Rotamer:
    Outliers :  3.92 %
    Allowed  : 15.67 %
    Favored  : 80.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.06 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.91 (0.26), residues: 1100
  helix:  2.47 (0.28), residues: 369
  sheet: -0.50 (0.31), residues: 257
  loop : -0.17 (0.30), residues: 474

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP C 169 
 HIS   0.004   0.001   HIS H  35 
 PHE   0.017   0.001   PHE B 336 
 TYR   0.020   0.001   TYR B 297 
 ARG   0.006   0.000   ARG R 218 

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

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

  2200 Ramachandran restraints generated.
    1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2200 Ramachandran restraints generated.
    1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  142 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 115
  time to evaluate  : 0.833 
Fit side-chains
   revert: symmetry clash
REVERT: B  290 GLU cc_start: 0.8329 (pm20) cc_final: 0.7922 (pm20)
REVERT: C   98 SER cc_start: 0.8188 (m) cc_final: 0.7495 (t)
REVERT: G   44 HIS cc_start: 0.8025 (m-70) cc_final: 0.7710 (m-70)
REVERT: G   48 ASP cc_start: 0.8275 (t0) cc_final: 0.7424 (t0)
REVERT: H  106 SER cc_start: 0.9220 (t) cc_final: 0.8673 (p)
REVERT: H  231 GLN cc_start: 0.8512 (pp30) cc_final: 0.8098 (pp30)
REVERT: R  111 ARG cc_start: 0.5564 (mtm-85) cc_final: 0.5134 (mtm-85)
REVERT: R  198 PHE cc_start: 0.7807 (OUTLIER) cc_final: 0.7492 (m-10)
REVERT: R  216 ARG cc_start: 0.7280 (mtt180) cc_final: 0.6866 (mtt-85)
  outliers start: 27
  outliers final: 21
  residues processed: 133
  average time/residue: 0.2013
  time to fit residues: 37.6053
Evaluate side-chains
  134 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 112
  time to evaluate  : 0.865 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  185 ILE
Chi-restraints excluded: chain B residue  228 LEU
Chi-restraints excluded: chain B residue  254 ILE
Chi-restraints excluded: chain B residue  274 LEU
Chi-restraints excluded: chain B residue  296 THR
Chi-restraints excluded: chain C residue   71 VAL
Chi-restraints excluded: chain C residue  100 VAL
Chi-restraints excluded: chain C residue  157 ILE
Chi-restraints excluded: chain C residue  191 SER
Chi-restraints excluded: chain C residue  233 CYS
Chi-restraints excluded: chain C residue  234 PHE
Chi-restraints excluded: chain G residue   51 LEU
Chi-restraints excluded: chain H residue   52 SER
Chi-restraints excluded: chain H residue   83 MET
Chi-restraints excluded: chain H residue  116 THR
Chi-restraints excluded: chain H residue  139 VAL
Chi-restraints excluded: chain H residue  199 VAL
Chi-restraints excluded: chain R residue   71 VAL
Chi-restraints excluded: chain R residue  119 THR
Chi-restraints excluded: chain R residue  130 VAL
Chi-restraints excluded: chain R residue  198 PHE
Chi-restraints excluded: chain R residue  255 PHE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 93 optimal weight:    0.0030
   chunk 24 optimal weight:    2.9990
   chunk 5 optimal weight:    1.9990
   chunk 20 optimal weight:    6.9990
   chunk 6 optimal weight:    1.9990
   chunk 23 optimal weight:    0.2980
   chunk 104 optimal weight:    2.9990
   chunk 45 optimal weight:    0.9990
   chunk 103 optimal weight:    1.9990
   chunk 44 optimal weight:    0.9980
   chunk 69 optimal weight:    0.5980
   overall best weight:    0.5792

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

Flipped N/Q/H residues before XYZ refinement:
** B 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4088 r_free = 0.4088 target = 0.174050 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3658 r_free = 0.3658 target = 0.130838 restraints weight = 9882.073|
|-----------------------------------------------------------------------------|
r_work (start): 0.3634 rms_B_bonded: 3.41
r_work: 0.3298 rms_B_bonded: 3.83 restraints_weight: 0.5000
r_work (final): 0.3298
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7291
moved from start:          0.2522

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   8018  Z= 0.194
  Angle     :  0.529   8.397  10954  Z= 0.281
  Chirality :  0.042   0.163   1281
  Planarity :  0.004   0.037   1415
  Dihedral  :  6.335 144.402   1186
  Min Nonbonded Distance : 2.524

Molprobity Statistics.
  All-atom Clashscore : 4.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.36 %
    Favored  : 96.64 %
  Rotamer:
    Outliers :  3.48 %
    Allowed  : 16.55 %
    Favored  : 79.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.06 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.93 (0.26), residues: 1100
  helix:  2.52 (0.28), residues: 369
  sheet: -0.52 (0.31), residues: 252
  loop : -0.19 (0.29), residues: 479

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.001   TRP C 339 
 HIS   0.004   0.001   HIS H  35 
 PHE   0.014   0.001   PHE B 336 
 TYR   0.020   0.001   TYR B 297 
 ARG   0.007   0.000   ARG R 218 

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

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

  2200 Ramachandran restraints generated.
    1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2200 Ramachandran restraints generated.
    1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 113
  time to evaluate  : 0.871 
Fit side-chains
   revert: symmetry clash
REVERT: B   38 LEU cc_start: 0.8025 (OUTLIER) cc_final: 0.7738 (tt)
REVERT: B  290 GLU cc_start: 0.8439 (pm20) cc_final: 0.8036 (pm20)
REVERT: C   98 SER cc_start: 0.8234 (m) cc_final: 0.7535 (t)
REVERT: G   44 HIS cc_start: 0.7999 (m-70) cc_final: 0.7663 (m-70)
REVERT: G   48 ASP cc_start: 0.8380 (t0) cc_final: 0.7578 (t0)
REVERT: H  106 SER cc_start: 0.9247 (t) cc_final: 0.8691 (p)
REVERT: H  183 GLN cc_start: 0.7814 (mt0) cc_final: 0.7330 (tt0)
REVERT: H  231 GLN cc_start: 0.8473 (pp30) cc_final: 0.8057 (pp30)
REVERT: R  111 ARG cc_start: 0.5519 (mtm-85) cc_final: 0.5088 (mtm-85)
REVERT: R  216 ARG cc_start: 0.7209 (mtt180) cc_final: 0.6799 (mtt-85)
  outliers start: 24
  outliers final: 21
  residues processed: 130
  average time/residue: 0.1866
  time to fit residues: 33.8041
Evaluate side-chains
  133 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 111
  time to evaluate  : 0.932 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   38 LEU
Chi-restraints excluded: chain B residue  185 ILE
Chi-restraints excluded: chain B residue  228 LEU
Chi-restraints excluded: chain B residue  254 ILE
Chi-restraints excluded: chain B residue  274 LEU
Chi-restraints excluded: chain B residue  296 THR
Chi-restraints excluded: chain C residue  100 VAL
Chi-restraints excluded: chain C residue  143 THR
Chi-restraints excluded: chain C residue  157 ILE
Chi-restraints excluded: chain C residue  191 SER
Chi-restraints excluded: chain C residue  233 CYS
Chi-restraints excluded: chain C residue  234 PHE
Chi-restraints excluded: chain G residue   51 LEU
Chi-restraints excluded: chain H residue   52 SER
Chi-restraints excluded: chain H residue   83 MET
Chi-restraints excluded: chain H residue  116 THR
Chi-restraints excluded: chain H residue  139 VAL
Chi-restraints excluded: chain H residue  199 VAL
Chi-restraints excluded: chain R residue   71 VAL
Chi-restraints excluded: chain R residue  119 THR
Chi-restraints excluded: chain R residue  130 VAL
Chi-restraints excluded: chain R residue  255 PHE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 5 optimal weight:    0.9990
   chunk 44 optimal weight:    1.9990
   chunk 94 optimal weight:    5.9990
   chunk 11 optimal weight:    2.9990
   chunk 100 optimal weight:    0.3980
   chunk 48 optimal weight:    0.9980
   chunk 46 optimal weight:    1.9990
   chunk 76 optimal weight:    2.9990
   chunk 96 optimal weight:    2.9990
   chunk 92 optimal weight:    0.6980
   chunk 91 optimal weight:    0.9980
   overall best weight:    0.8182

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

Flipped N/Q/H residues before XYZ refinement:
** B 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3999 r_free = 0.3999 target = 0.171100 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.3375 r_free = 0.3375 target = 0.113692 restraints weight = 9787.898|
|-----------------------------------------------------------------------------|
r_work (start): 0.3365 rms_B_bonded: 2.86
r_work: 0.3224 rms_B_bonded: 3.32 restraints_weight: 0.5000
r_work (final): 0.3224
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6932
moved from start:          0.2582

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   8018  Z= 0.240
  Angle     :  0.548   9.381  10954  Z= 0.294
  Chirality :  0.043   0.162   1281
  Planarity :  0.004   0.037   1415
  Dihedral  :  6.383 144.254   1186
  Min Nonbonded Distance : 2.495

Molprobity Statistics.
  All-atom Clashscore : 4.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.45 %
    Favored  : 96.55 %
  Rotamer:
    Outliers :  3.48 %
    Allowed  : 16.69 %
    Favored  : 79.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.06 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.89 (0.26), residues: 1100
  helix:  2.55 (0.28), residues: 369
  sheet: -0.54 (0.31), residues: 252
  loop : -0.26 (0.29), residues: 479

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP C 169 
 HIS   0.004   0.001   HIS H  35 
 PHE   0.016   0.002   PHE C 199 
 TYR   0.020   0.002   TYR B 297 
 ARG   0.007   0.000   ARG R 218 

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

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

  2200 Ramachandran restraints generated.
    1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2200 Ramachandran restraints generated.
    1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 113
  time to evaluate  : 0.917 
Fit side-chains
   revert: symmetry clash
REVERT: B   38 LEU cc_start: 0.7638 (OUTLIER) cc_final: 0.7350 (tt)
REVERT: B  331 ASN cc_start: 0.7471 (m-40) cc_final: 0.7143 (p0)
REVERT: C   98 SER cc_start: 0.8042 (m) cc_final: 0.7258 (t)
REVERT: G   44 HIS cc_start: 0.7888 (m-70) cc_final: 0.7537 (m-70)
REVERT: G   48 ASP cc_start: 0.8378 (t0) cc_final: 0.7460 (t0)
REVERT: H  106 SER cc_start: 0.9326 (t) cc_final: 0.9019 (t)
REVERT: H  231 GLN cc_start: 0.8602 (pp30) cc_final: 0.8095 (pp30)
REVERT: R  111 ARG cc_start: 0.5235 (mtm-85) cc_final: 0.4806 (mtm-85)
REVERT: R  216 ARG cc_start: 0.7047 (mtt180) cc_final: 0.6662 (mtt-85)
  outliers start: 24
  outliers final: 22
  residues processed: 131
  average time/residue: 0.1864
  time to fit residues: 34.0861
Evaluate side-chains
  133 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 110
  time to evaluate  : 0.870 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   38 LEU
Chi-restraints excluded: chain B residue  185 ILE
Chi-restraints excluded: chain B residue  228 LEU
Chi-restraints excluded: chain B residue  254 ILE
Chi-restraints excluded: chain B residue  274 LEU
Chi-restraints excluded: chain B residue  296 THR
Chi-restraints excluded: chain C residue   71 VAL
Chi-restraints excluded: chain C residue  100 VAL
Chi-restraints excluded: chain C residue  143 THR
Chi-restraints excluded: chain C residue  157 ILE
Chi-restraints excluded: chain C residue  191 SER
Chi-restraints excluded: chain C residue  233 CYS
Chi-restraints excluded: chain C residue  234 PHE
Chi-restraints excluded: chain G residue   51 LEU
Chi-restraints excluded: chain H residue   52 SER
Chi-restraints excluded: chain H residue   83 MET
Chi-restraints excluded: chain H residue  116 THR
Chi-restraints excluded: chain H residue  139 VAL
Chi-restraints excluded: chain H residue  199 VAL
Chi-restraints excluded: chain R residue   71 VAL
Chi-restraints excluded: chain R residue  119 THR
Chi-restraints excluded: chain R residue  130 VAL
Chi-restraints excluded: chain R residue  255 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 101 optimal weight:    0.8980
   chunk 14 optimal weight:    7.9990
   chunk 88 optimal weight:    7.9990
   chunk 10 optimal weight:    0.7980
   chunk 31 optimal weight:    1.9990
   chunk 0 optimal weight:    5.9990
   chunk 36 optimal weight:    1.9990
   chunk 92 optimal weight:    0.7980
   chunk 35 optimal weight:    0.6980
   chunk 22 optimal weight:    8.9990
   chunk 91 optimal weight:    0.8980
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
** B 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4077 r_free = 0.4077 target = 0.172941 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3644 r_free = 0.3644 target = 0.129498 restraints weight = 9919.895|
|-----------------------------------------------------------------------------|
r_work (start): 0.3619 rms_B_bonded: 3.40
r_work: 0.3284 rms_B_bonded: 3.81 restraints_weight: 0.5000
r_work (final): 0.3284
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7298
moved from start:          0.2707

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   8018  Z= 0.241
  Angle     :  0.554   9.464  10954  Z= 0.297
  Chirality :  0.043   0.161   1281
  Planarity :  0.004   0.039   1415
  Dihedral  :  6.410 144.135   1186
  Min Nonbonded Distance : 2.460

Molprobity Statistics.
  All-atom Clashscore : 4.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.45 %
    Favored  : 96.55 %
  Rotamer:
    Outliers :  3.48 %
    Allowed  : 16.98 %
    Favored  : 79.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.06 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.87 (0.26), residues: 1100
  helix:  2.54 (0.28), residues: 369
  sheet: -0.62 (0.31), residues: 252
  loop : -0.25 (0.29), residues: 479

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP C 169 
 HIS   0.004   0.001   HIS H  35 
 PHE   0.016   0.001   PHE C 199 
 TYR   0.020   0.002   TYR B 297 
 ARG   0.007   0.000   ARG R 218 

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

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

  2200 Ramachandran restraints generated.
    1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2200 Ramachandran restraints generated.
    1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  134 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 110
  time to evaluate  : 0.810 
Fit side-chains
   revert: symmetry clash
REVERT: B   38 LEU cc_start: 0.8029 (OUTLIER) cc_final: 0.7766 (tt)
REVERT: B  290 GLU cc_start: 0.8592 (pm20) cc_final: 0.8201 (pm20)
REVERT: B  331 ASN cc_start: 0.7499 (m-40) cc_final: 0.7219 (p0)
REVERT: C   98 SER cc_start: 0.8113 (m) cc_final: 0.7461 (t)
REVERT: G   44 HIS cc_start: 0.8030 (m-70) cc_final: 0.7684 (m-70)
REVERT: G   48 ASP cc_start: 0.8380 (t0) cc_final: 0.7553 (t0)
REVERT: H  106 SER cc_start: 0.9243 (t) cc_final: 0.8893 (t)
REVERT: H  231 GLN cc_start: 0.8515 (pp30) cc_final: 0.8070 (pp30)
REVERT: R  111 ARG cc_start: 0.5499 (mtm-85) cc_final: 0.5054 (mtm-85)
REVERT: R  216 ARG cc_start: 0.7217 (mtt180) cc_final: 0.6812 (mtt-85)
  outliers start: 24
  outliers final: 22
  residues processed: 128
  average time/residue: 0.1803
  time to fit residues: 32.1588
Evaluate side-chains
  131 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 108
  time to evaluate  : 0.793 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   38 LEU
Chi-restraints excluded: chain B residue  185 ILE
Chi-restraints excluded: chain B residue  228 LEU
Chi-restraints excluded: chain B residue  254 ILE
Chi-restraints excluded: chain B residue  274 LEU
Chi-restraints excluded: chain B residue  296 THR
Chi-restraints excluded: chain C residue   71 VAL
Chi-restraints excluded: chain C residue  100 VAL
Chi-restraints excluded: chain C residue  143 THR
Chi-restraints excluded: chain C residue  157 ILE
Chi-restraints excluded: chain C residue  191 SER
Chi-restraints excluded: chain C residue  233 CYS
Chi-restraints excluded: chain C residue  234 PHE
Chi-restraints excluded: chain G residue   51 LEU
Chi-restraints excluded: chain H residue   52 SER
Chi-restraints excluded: chain H residue   83 MET
Chi-restraints excluded: chain H residue  116 THR
Chi-restraints excluded: chain H residue  139 VAL
Chi-restraints excluded: chain H residue  199 VAL
Chi-restraints excluded: chain R residue   71 VAL
Chi-restraints excluded: chain R residue  119 THR
Chi-restraints excluded: chain R residue  130 VAL
Chi-restraints excluded: chain R residue  255 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 87 optimal weight:    4.9990
   chunk 85 optimal weight:    1.9990
   chunk 4 optimal weight:    0.3980
   chunk 99 optimal weight:    1.9990
   chunk 43 optimal weight:    0.9980
   chunk 56 optimal weight:    3.9990
   chunk 72 optimal weight:    1.9990
   chunk 29 optimal weight:    0.6980
   chunk 6 optimal weight:    0.9980
   chunk 100 optimal weight:    0.6980
   chunk 33 optimal weight:    1.9990
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
** B 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
H 113 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4078 r_free = 0.4078 target = 0.173136 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3651 r_free = 0.3651 target = 0.130129 restraints weight = 9946.920|
|-----------------------------------------------------------------------------|
r_work (start): 0.3627 rms_B_bonded: 3.37
r_work: 0.3292 rms_B_bonded: 3.75 restraints_weight: 0.5000
r_work (final): 0.3292
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7277
moved from start:          0.2766

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   8018  Z= 0.229
  Angle     :  0.550   9.462  10954  Z= 0.293
  Chirality :  0.043   0.161   1281
  Planarity :  0.004   0.037   1415
  Dihedral  :  6.379 145.586   1186
  Min Nonbonded Distance : 2.473

Molprobity Statistics.
  All-atom Clashscore : 4.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.55 %
    Favored  : 96.45 %
  Rotamer:
    Outliers :  3.48 %
    Allowed  : 16.98 %
    Favored  : 79.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.06 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.88 (0.26), residues: 1100
  helix:  2.58 (0.28), residues: 369
  sheet: -0.66 (0.31), residues: 252
  loop : -0.24 (0.29), residues: 479

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP C 169 
 HIS   0.004   0.001   HIS H  35 
 PHE   0.015   0.001   PHE C 199 
 TYR   0.020   0.001   TYR B 297 
 ARG   0.007   0.000   ARG R 218 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3679.83 seconds
wall clock time: 66 minutes 8.22 seconds (3968.22 seconds total)