Starting phenix.real_space_refine
on Tue Apr 29 05:37:04 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8g59_29736/04_2025/8g59_29736.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8g59_29736/04_2025/8g59_29736.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.64
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8g59_29736/04_2025/8g59_29736.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8g59_29736/04_2025/8g59_29736.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8g59_29736/04_2025/8g59_29736.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8g59_29736/04_2025/8g59_29736.cif"
  }
  resolution = 2.64
  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=   0.008 sd=   0.088
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      58      5.16       5
     C    5503      2.51       5
     N    1444      2.21       5
     O    1577      1.98       5
     F       1      1.80       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib"
  Total number of atoms: 8583
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "B"
      Number of atoms: 2509
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 335, 2509
          Classifications: {'peptide': 335}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 16}
          Link IDs: {'PTRANS': 5, 'TRANS': 329}
          Unresolved non-hydrogen bonds: 67
          Unresolved non-hydrogen angles: 81
          Unresolved non-hydrogen dihedrals: 53
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 4, 'ARG:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 53
    Chain: "Y"
      Number of atoms: 365
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 53, 365
          Classifications: {'peptide': 53}
          Incomplete info: {'truncation_to_alanine': 10}
          Link IDs: {'PTRANS': 4, 'TRANS': 48}
          Unresolved non-hydrogen bonds: 42
          Unresolved non-hydrogen angles: 47
          Unresolved non-hydrogen dihedrals: 37
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 21
    Chain: "S"
      Number of atoms: 1739
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 230, 1739
          Classifications: {'peptide': 230}
          Incomplete info: {'truncation_to_alanine': 8}
          Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 219}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 32
          Unresolved non-hydrogen angles: 39
          Unresolved non-hydrogen dihedrals: 25
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLU:plan': 4, 'ARG:plan': 1, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 24
    Chain: "A"
      Number of atoms: 1739
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 219, 1739
          Classifications: {'peptide': 219}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 8}
          Link IDs: {'PTRANS': 2, 'TRANS': 216}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 33
          Unresolved non-hydrogen angles: 38
          Unresolved non-hydrogen dihedrals: 28
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 17
    Chain: "R"
      Number of atoms: 2204
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 281, 2193
          Classifications: {'peptide': 281}
          Incomplete info: {'truncation_to_alanine': 12}
          Link IDs: {'PTRANS': 11, 'TRANS': 269}
          Chain breaks: 4
          Unresolved non-hydrogen bonds: 48
          Unresolved non-hydrogen angles: 61
          Unresolved non-hydrogen dihedrals: 37
          Unresolved non-hydrogen chiralities: 5
          Planarities with less than four sites: {'ARG:plan': 3, 'HIS:plan': 1, 'GLU:plan': 1, 'ASP:plan': 2}
          Unresolved non-hydrogen planarities: 30
      Conformer: "B"
        Number of residues, atoms: 281, 2193
          Classifications: {'peptide': 281}
          Incomplete info: {'truncation_to_alanine': 12}
          Link IDs: {'PTRANS': 11, 'TRANS': 269}
          Chain breaks: 4
          Unresolved non-hydrogen bonds: 48
          Unresolved non-hydrogen angles: 61
          Unresolved non-hydrogen dihedrals: 37
          Unresolved non-hydrogen chiralities: 5
          Planarities with less than four sites: {'ARG:plan': 3, 'HIS:plan': 1, 'GLU:plan': 1, 'ASP:plan': 2}
          Unresolved non-hydrogen planarities: 30
          bond proxies already assigned to first conformer: 2231
    Chain: "R"
      Number of atoms: 27
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 27
          Unusual residues: {'YN9': 1}
          Classifications: {'undetermined': 1}
  Residues with excluded nonbonded symmetry interactions: 1
    residue:
      pdb=" N  APHE R 115 " occ=0.50
      ... (20 atoms not shown)
      pdb=" CZ BPHE R 115 " occ=0.50
  Time building chain proxies: 6.36, per 1000 atoms: 0.74
  Number of scatterers: 8583
  At special positions: 0
  Unit cell: (105.456, 121.68, 115.596, 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)
     S      58     16.00
     F       1      9.00
     O    1577      8.00
     N    1444      7.00
     C    5503      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS S 159 " - pdb=" SG  CYS S 229 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R 111 " - pdb=" SG  CYS R 194 " distance=2.04

  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: 2.45
  Conformation dependent library (CDL) restraints added in 1.4 seconds
  

  2190 Ramachandran restraints generated.
    1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2102

  Finding SS restraints...
    Secondary structure from input PDB file:
      27 helices and 13 sheets defined
      37.4% alpha, 23.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.95
  Creating SS restraints...
    Processing helix  chain 'B' and resid 6 through 24
    Processing helix  chain 'B' and resid 29 through 35
    Processing helix  chain 'Y' and resid 10 through 24
    Processing helix  chain 'Y' and resid 29 through 44
    Processing helix  chain 'Y' and resid 45 through 48
    Processing helix  chain 'Y' and resid 55 through 59
    Processing helix  chain 'S' and resid 28 through 32
    Processing helix  chain 'S' and resid 87 through 91
      removed outlier: 3.619A  pdb=" N   THR S  91 " --> pdb=" O   SER S  88 " (cutoff:3.500A)
    Processing helix  chain 'S' and resid 220 through 224
      removed outlier: 3.985A  pdb=" N   VAL S 224 " --> pdb=" O   ALA S 221 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 6 through 31
    Processing helix  chain 'A' and resid 45 through 51
    Processing helix  chain 'A' and resid 207 through 216
      removed outlier: 4.388A  pdb=" N   ILE A 212 " --> pdb=" O   LYS A 209 " (cutoff:3.500A)
      removed outlier: 5.773A  pdb=" N   HIS A 213 " --> pdb=" O   LYS A 210 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 228 through 231
      removed outlier: 4.367A  pdb=" N   ASP A 231 " --> pdb=" O   SER A 228 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 228 through 231'
    Processing helix  chain 'A' and resid 241 through 255
    Processing helix  chain 'A' and resid 256 through 260
      removed outlier: 3.940A  pdb=" N   THR A 260 " --> pdb=" O   LYS A 257 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 270 through 279
    Processing helix  chain 'A' and resid 295 through 309
    Processing helix  chain 'A' and resid 335 through 355
    Processing helix  chain 'R' and resid 42 through 70
    Processing helix  chain 'R' and resid 78 through 91
      removed outlier: 3.956A  pdb=" N   ALA R  91 " --> pdb=" O   LEU R  87 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 91 through 101
      removed outlier: 3.628A  pdb=" N   VAL R  95 " --> pdb=" O   ALA R  91 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 109 through 142
      removed outlier: 4.695A  pdb=" N  APHE R 115 " --> pdb=" O   CYS R 111 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 152 through 169
    Processing helix  chain 'R' and resid 171 through 176
      removed outlier: 3.658A  pdb=" N   PHE R 176 " --> pdb=" O   PRO R 172 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 201 through 244
      removed outlier: 3.556A  pdb=" N   TRP R 207 " --> pdb=" O   GLY R 203 " (cutoff:3.500A)
      removed outlier: 3.840A  pdb=" N   VAL R 209 " --> pdb=" O   ILE R 205 " (cutoff:3.500A)
      removed outlier: 5.301A  pdb=" N   VAL R 218 " --> pdb=" O   LEU R 214 " (cutoff:3.500A)
      Proline residue:  R 219  - end of helix
      removed outlier: 3.958A  pdb=" N   ARG R 238 " --> pdb=" O   THR R 234 " (cutoff:3.500A)
      removed outlier: 3.566A  pdb=" N   VAL R 243 " --> pdb=" O   LYS R 239 " (cutoff:3.500A)
      removed outlier: 4.017A  pdb=" N   SER R 244 " --> pdb=" O   ARG R 240 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 248 through 292
      removed outlier: 3.614A  pdb=" N   LEU R 262 " --> pdb=" O   GLN R 258 " (cutoff:3.500A)
      removed outlier: 4.442A  pdb=" N   PHE R 263 " --> pdb=" O   ASP R 259 " (cutoff:3.500A)
      Proline residue:  R 279  - end of helix
    Processing helix  chain 'R' and resid 299 through 321
      removed outlier: 3.903A  pdb=" N   TRP R 305 " --> pdb=" O   SER R 301 " (cutoff:3.500A)
      removed outlier: 3.937A  pdb=" N   ASN R 313 " --> pdb=" O   PHE R 309 " (cutoff:3.500A)
      removed outlier: 4.397A  pdb=" N   SER R 314 " --> pdb=" O   THR R 310 " (cutoff:3.500A)
      removed outlier: 4.036A  pdb=" N   ALA R 315 " --> pdb=" O   PHE R 311 " (cutoff:3.500A)
      Proline residue:  R 318  - end of helix
    Processing sheet with id=AA1, first strand: chain 'B' and resid 47 through 51
      removed outlier: 3.541A  pdb=" N   ARG B  49 " --> pdb=" O   ILE B 338 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 58 through 63
      removed outlier: 3.627A  pdb=" N   ALA B  60 " --> pdb=" O   ALA B  73 " (cutoff:3.500A)
      removed outlier: 3.773A  pdb=" N   SER B  74 " --> pdb=" O   LYS B  78 " (cutoff:3.500A)
      removed outlier: 4.157A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 3.617A  pdb=" N   HIS B  91 " --> pdb=" O   ILE B  81 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 100 through 105
      removed outlier: 6.826A  pdb=" N   GLY B 115 " --> pdb=" O   MET B 101 " (cutoff:3.500A)
      removed outlier: 4.444A  pdb=" N   CYS B 103 " --> pdb=" O   ALA B 113 " (cutoff:3.500A)
      removed outlier: 6.474A  pdb=" N   ALA B 113 " --> pdb=" O   CYS B 103 " (cutoff:3.500A)
      removed outlier: 5.165A  pdb=" N   TYR B 105 " --> pdb=" O   TYR B 111 " (cutoff:3.500A)
      removed outlier: 7.203A  pdb=" N   TYR B 111 " --> pdb=" O   TYR B 105 " (cutoff:3.500A)
      removed outlier: 4.261A  pdb=" N   GLY B 116 " --> pdb=" O   ILE B 120 " (cutoff:3.500A)
      removed outlier: 4.840A  pdb=" N   ILE B 120 " --> pdb=" O   GLY B 116 " (cutoff:3.500A)
      removed outlier: 6.605A  pdb=" N   CYS B 121 " --> pdb=" O   GLU B 138 " (cutoff:3.500A)
      removed outlier: 5.003A  pdb=" N   GLU B 138 " --> pdb=" O   CYS B 121 " (cutoff:3.500A)
      removed outlier: 6.911A  pdb=" N   ILE B 123 " --> pdb=" O   SER B 136 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 146 through 153
      removed outlier: 3.600A  pdb=" N   CYS B 148 " --> pdb=" O   SER B 160 " (cutoff:3.500A)
      removed outlier: 7.199A  pdb=" N   GLN B 156 " --> pdb=" O   LEU B 152 " (cutoff:3.500A)
      removed outlier: 4.300A  pdb=" N   THR B 165 " --> pdb=" O   SER B 161 " (cutoff:3.500A)
      removed outlier: 6.227A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 6.001A  pdb=" N   GLN B 176 " --> pdb=" O   ASP B 170 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 187 through 192
      removed outlier: 6.484A  pdb=" N   GLY B 202 " --> pdb=" O   MET B 188 " (cutoff:3.500A)
      removed outlier: 4.679A  pdb=" N   LEU B 190 " --> pdb=" O   VAL B 200 " (cutoff:3.500A)
      removed outlier: 7.043A  pdb=" N   VAL B 200 " --> pdb=" O   LEU B 190 " (cutoff:3.500A)
      removed outlier: 5.133A  pdb=" N   LEU B 192 " --> pdb=" O   LEU B 198 " (cutoff:3.500A)
      removed outlier: 7.125A  pdb=" N   LEU B 198 " --> pdb=" O   LEU B 192 " (cutoff:3.500A)
      removed outlier: 3.632A  pdb=" N   ALA B 203 " --> pdb=" O   SER B 207 " (cutoff:3.500A)
      removed outlier: 4.548A  pdb=" N   SER B 207 " --> pdb=" O   ALA B 203 " (cutoff:3.500A)
      removed outlier: 3.814A  pdb=" N   GLN B 220 " --> pdb=" O   LEU B 210 " (cutoff:3.500A)
      removed outlier: 7.017A  pdb=" N   ASP B 212 " --> pdb=" O   CYS B 218 " (cutoff:3.500A)
      removed outlier: 6.612A  pdb=" N   CYS B 218 " --> pdb=" O   ASP B 212 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 229 through 234
      removed outlier: 3.593A  pdb=" N   SER B 245 " --> pdb=" O   THR B 249 " (cutoff:3.500A)
      removed outlier: 4.499A  pdb=" N   THR B 249 " --> pdb=" O   SER B 245 " (cutoff:3.500A)
      removed outlier: 3.597A  pdb=" N   MET B 262 " --> pdb=" O   LEU B 252 " (cutoff:3.500A)
      removed outlier: 6.464A  pdb=" N   ASP B 254 " --> pdb=" O   GLU B 260 " (cutoff:3.500A)
      removed outlier: 6.395A  pdb=" N   GLU B 260 " --> pdb=" O   ASP B 254 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 273 through 278
      removed outlier: 3.714A  pdb=" N   CYS B 294 " --> pdb=" O   LEU B 308 " (cutoff:3.500A)
      removed outlier: 3.555A  pdb=" N   GLY B 306 " --> pdb=" O   VAL B 296 " (cutoff:3.500A)
      removed outlier: 6.237A  pdb=" N   ASP B 298 " --> pdb=" O   ARG B 304 " (cutoff:3.500A)
      removed outlier: 6.347A  pdb=" N   ARG B 304 " --> pdb=" O   ASP B 298 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'S' and resid 3 through 7
      removed outlier: 3.527A  pdb=" N   SER S  21 " --> pdb=" O   SER S   7 " (cutoff:3.500A)
      removed outlier: 3.682A  pdb=" N   CYS S  22 " --> pdb=" O   LEU S  79 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'S' and resid 11 through 12
      removed outlier: 3.572A  pdb=" N   THR S 115 " --> pdb=" O   TYR S  94 " (cutoff:3.500A)
      removed outlier: 6.800A  pdb=" N   MET S  34 " --> pdb=" O   TYR S  50 " (cutoff:3.500A)
      removed outlier: 4.414A  pdb=" N   TYR S  50 " --> pdb=" O   MET S  34 " (cutoff:3.500A)
      removed outlier: 6.630A  pdb=" N   TRP S  36 " --> pdb=" O   VAL S  48 " (cutoff:3.500A)
      removed outlier: 3.809A  pdb=" N   GLY S  44 " --> pdb=" O   ALA S  40 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'S' and resid 140 through 142
      removed outlier: 3.559A  pdb=" N   ALA S 211 " --> pdb=" O   SER S 208 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'S' and resid 146 through 148
      removed outlier: 3.624A  pdb=" N   ILE S 189 " --> pdb=" O   TRP S 176 " (cutoff:3.500A)
      removed outlier: 6.015A  pdb=" N   LEU S 178 " --> pdb=" O   LEU S 187 " (cutoff:3.500A)
      removed outlier: 5.630A  pdb=" N   LEU S 187 " --> pdb=" O   LEU S 178 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'A' and resid 185 through 190
      removed outlier: 3.697A  pdb=" N   PHE A 189 " --> pdb=" O   PHE A 196 " (cutoff:3.500A)
      removed outlier: 9.010A  pdb=" N   ALA A 220 " --> pdb=" O   GLU A  33 " (cutoff:3.500A)
      removed outlier: 6.792A  pdb=" N   LYS A  35 " --> pdb=" O   ALA A 220 " (cutoff:3.500A)
      removed outlier: 7.581A  pdb=" N   ILE A 222 " --> pdb=" O   LYS A  35 " (cutoff:3.500A)
      removed outlier: 6.370A  pdb=" N   LEU A  37 " --> pdb=" O   ILE A 222 " (cutoff:3.500A)
      removed outlier: 7.703A  pdb=" N   CYS A 224 " --> pdb=" O   LEU A  37 " (cutoff:3.500A)
      removed outlier: 6.885A  pdb=" N   LEU A  39 " --> pdb=" O   CYS A 224 " (cutoff:3.500A)
      removed outlier: 8.796A  pdb=" N   ALA A 226 " --> pdb=" O   LEU A  39 " (cutoff:3.500A)
      removed outlier: 6.340A  pdb=" N   ILE A 221 " --> pdb=" O   ILE A 265 " (cutoff:3.500A)
      removed outlier: 7.078A  pdb=" N   PHE A 267 " --> pdb=" O   ILE A 221 " (cutoff:3.500A)
      removed outlier: 6.237A  pdb=" N   PHE A 223 " --> pdb=" O   PHE A 267 " (cutoff:3.500A)
      removed outlier: 7.180A  pdb=" N   ASN A 269 " --> pdb=" O   PHE A 223 " (cutoff:3.500A)
      removed outlier: 6.768A  pdb=" N   VAL A 225 " --> pdb=" O   ASN A 269 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'R' and resid 177 through 182

    437 hydrogen bonds defined for protein.
    1231 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: 2.51

  Time building geometry restraints manager: 2.80 seconds

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

  Histogram of bond lengths:
        1.12 -     1.26: 1365
        1.26 -     1.40: 2177
        1.40 -     1.53: 4857
        1.53 -     1.67: 280
        1.67 -     1.81: 84
  Bond restraints: 8763
  Sorted by residual:
  bond pdb=" C   PHE R 260 "
       pdb=" O   PHE R 260 "
    ideal  model  delta    sigma   weight residual
    1.233  1.117  0.116 1.46e-02 4.69e+03 6.29e+01
  bond pdb=" N   GLN R 258 "
       pdb=" CA  GLN R 258 "
    ideal  model  delta    sigma   weight residual
    1.458  1.383  0.074 1.33e-02 5.65e+03 3.12e+01
  bond pdb=" N   ASP R 259 "
       pdb=" CA  ASP R 259 "
    ideal  model  delta    sigma   weight residual
    1.456  1.393  0.063 1.18e-02 7.18e+03 2.84e+01
  bond pdb=" C   ARG R  36 "
       pdb=" O   ARG R  36 "
    ideal  model  delta    sigma   weight residual
    1.235  1.172  0.063 1.25e-02 6.40e+03 2.54e+01
  bond pdb=" C1  YN9 R 401 "
       pdb=" C3  YN9 R 401 "
    ideal  model  delta    sigma   weight residual
    1.481  1.581 -0.100 2.00e-02 2.50e+03 2.50e+01
  ... (remaining 8758 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.34: 11696
        2.34 -     4.67: 178
        4.67 -     7.01: 27
        7.01 -     9.35: 5
        9.35 -    11.68: 4
  Bond angle restraints: 11910
  Sorted by residual:
  angle pdb=" N   PHE R 260 "
        pdb=" CA  PHE R 260 "
        pdb=" C   PHE R 260 "
      ideal   model   delta    sigma   weight residual
     114.04  102.67   11.37 1.24e+00 6.50e-01 8.41e+01
  angle pdb=" C   ALA R  91 "
        pdb=" N   ILE R  92 "
        pdb=" CA  ILE R  92 "
      ideal   model   delta    sigma   weight residual
     120.24  124.87   -4.63 6.30e-01 2.52e+00 5.39e+01
  angle pdb=" N   ILE R  89 "
        pdb=" CA  ILE R  89 "
        pdb=" C   ILE R  89 "
      ideal   model   delta    sigma   weight residual
     110.62  117.17   -6.55 1.02e+00 9.61e-01 4.13e+01
  angle pdb=" N   LEU A 358 "
        pdb=" CA  LEU A 358 "
        pdb=" C   LEU A 358 "
      ideal   model   delta    sigma   weight residual
     111.36  118.33   -6.97 1.09e+00 8.42e-01 4.09e+01
  angle pdb=" C   ASP R 259 "
        pdb=" CA  ASP R 259 "
        pdb=" CB  ASP R 259 "
      ideal   model   delta    sigma   weight residual
     110.94  120.06   -9.12 1.65e+00 3.67e-01 3.05e+01
  ... (remaining 11905 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.94: 4695
       15.94 -    31.87: 368
       31.87 -    47.81: 62
       47.81 -    63.75: 16
       63.75 -    79.68: 7
  Dihedral angle restraints: 5148
    sinusoidal: 1904
      harmonic: 3244
  Sorted by residual:
  dihedral pdb=" C   ASP R 259 "
           pdb=" N   ASP R 259 "
           pdb=" CA  ASP R 259 "
           pdb=" CB  ASP R 259 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -144.58   21.98     0      2.50e+00 1.60e-01 7.73e+01
  dihedral pdb=" N   ASP R 259 "
           pdb=" C   ASP R 259 "
           pdb=" CA  ASP R 259 "
           pdb=" CB  ASP R 259 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80  142.49  -19.69     0      2.50e+00 1.60e-01 6.21e+01
  dihedral pdb=" CB  CYS R 111 "
           pdb=" SG  CYS R 111 "
           pdb=" SG  CYS R 194 "
           pdb=" CB  CYS R 194 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   27.64   65.36     1      1.00e+01 1.00e-02 5.60e+01
  ... (remaining 5145 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.197: 1389
       0.197 -    0.394: 3
       0.394 -    0.591: 0
       0.591 -    0.788: 0
       0.788 -    0.985: 1
  Chirality restraints: 1393
  Sorted by residual:
  chirality pdb=" CA  ASP R 259 "
            pdb=" N   ASP R 259 "
            pdb=" C   ASP R 259 "
            pdb=" CB  ASP R 259 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.53    0.99 2.00e-01 2.50e+01 2.43e+01
  chirality pdb=" CA  ARG R 254 "
            pdb=" N   ARG R 254 "
            pdb=" C   ARG R 254 "
            pdb=" CB  ARG R 254 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.18    0.33 2.00e-01 2.50e+01 2.67e+00
  chirality pdb=" CA  GLN R 258 "
            pdb=" N   GLN R 258 "
            pdb=" C   GLN R 258 "
            pdb=" CB  GLN R 258 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.23    0.28 2.00e-01 2.50e+01 1.91e+00
  ... (remaining 1390 not shown)

  Planarity restraints: 1491
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLN R 257 "   -0.028 2.00e-02 2.50e+03   5.65e-02 3.19e+01
        pdb=" C   GLN R 257 "    0.098 2.00e-02 2.50e+03
        pdb=" O   GLN R 257 "   -0.037 2.00e-02 2.50e+03
        pdb=" N   GLN R 258 "   -0.033 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP S  74 "   -0.075 5.00e-02 4.00e+02   1.12e-01 2.01e+01
        pdb=" N   PRO S  75 "    0.194 5.00e-02 4.00e+02
        pdb=" CA  PRO S  75 "   -0.058 5.00e-02 4.00e+02
        pdb=" CD  PRO S  75 "   -0.061 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TRP R 299 "    0.040 5.00e-02 4.00e+02   6.13e-02 6.01e+00
        pdb=" N   PRO R 300 "   -0.106 5.00e-02 4.00e+02
        pdb=" CA  PRO R 300 "    0.032 5.00e-02 4.00e+02
        pdb=" CD  PRO R 300 "    0.034 5.00e-02 4.00e+02
  ... (remaining 1488 not shown)

  Histogram of nonbonded interaction distances:
        1.93 -     2.52: 57
        2.52 -     3.12: 6315
        3.12 -     3.71: 13279
        3.71 -     4.31: 19213
        4.31 -     4.90: 32205
  Nonbonded interactions: 71069
  Sorted by model distance:
  nonbonded pdb=" NH2 ARG R 238 "
            pdb=" OD2 ASP R 259 "
     model   vdw
     1.930 3.120
  nonbonded pdb=" O   CYS R  60 "
            pdb=" CD2 LEU R  64 "
     model   vdw
     1.953 3.460
  nonbonded pdb=" O   ALA A  41 "
            pdb=" OG  SER A  44 "
     model   vdw
     2.183 3.040
  nonbonded pdb=" OG  SER B 331 "
            pdb=" OD1 ASP B 333 "
     model   vdw
     2.222 3.040
  nonbonded pdb=" O   CYS A 254 "
            pdb=" NZ  LYS A 317 "
     model   vdw
     2.255 3.120
  ... (remaining 71064 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=0.50 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.500
  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:          0.380
  Check model and map are aligned:         0.080
  Set scattering table:                    0.090
  Process input model:                     25.160
  Find NCS groups from input model:        0.090
  Set up NCS constraints:                  0.040
  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:13.040
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   39.390
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7237
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   0.116   8765  Z= 0.293
  Angle     :  0.731  11.682  11914  Z= 0.431
  Chirality :  0.053   0.985   1393
  Planarity :  0.006   0.112   1491
  Dihedral  : 12.174  79.684   3040
  Min Nonbonded Distance : 1.930

Molprobity Statistics.
  All-atom Clashscore : 10.26
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  3.85 %
    Favored  : 96.06 %
  Rotamer:
    Outliers :  0.22 %
    Allowed  :  0.88 %
    Favored  : 98.90 %
  Cbeta Deviations :  0.10 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    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: -0.15 (0.25), residues: 1095
  helix:  0.23 (0.25), residues: 387
  sheet:  0.39 (0.30), residues: 301
  loop : -0.65 (0.30), residues: 407

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP B  63 
 HIS   0.004   0.001   HIS R 251 
 PHE   0.016   0.001   PHE R 311 
 TYR   0.017   0.001   TYR A 302 
 ARG   0.007   0.000   ARG R  36 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.19869 (  437)
  hydrogen bonds       : angle       7.15701 ( 1231)
  SS BOND              : bond        0.00460 (    2)
  SS BOND              : angle       4.13992 (    4)
  covalent geometry    : bond        0.00524 ( 8763)
  covalent geometry    : angle       0.72755 (11910)

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

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

  2190 Ramachandran restraints generated.
    1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2190 Ramachandran restraints generated.
    1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  161 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 159
  time to evaluate  : 1.010 
Fit side-chains
   revert: symmetry clash
REVERT: B  209 LYS cc_start: 0.9253 (mttm) cc_final: 0.9006 (mttp)
REVERT: R  165 TYR cc_start: 0.7006 (t80) cc_final: 0.6178 (t80)
  outliers start: 2
  outliers final: 1
  residues processed: 161
  average time/residue: 1.5671
  time to fit residues: 265.2506
Evaluate side-chains
  135 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 134
  time to evaluate  : 0.931 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  259 ASP
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 92 optimal weight:    0.6980
   chunk 83 optimal weight:    0.9990
   chunk 46 optimal weight:    9.9990
   chunk 28 optimal weight:    7.9990
   chunk 56 optimal weight:    0.0470
   chunk 44 optimal weight:    5.9990
   chunk 86 optimal weight:    0.5980
   chunk 33 optimal weight:    8.9990
   chunk 52 optimal weight:    0.7980
   chunk 64 optimal weight:    0.7980
   chunk 99 optimal weight:    2.9990
   overall best weight:    0.5878

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

Flipped N/Q/H residues before XYZ refinement:
B  75 GLN
B 230 ASN
B 268 ASN
B 340 ASN
S 179 GLN
S 186 GLN
A 188 HIS
A 204 GLN
A 357 ASN
R 189 GLN

Total number of N/Q/H flips: 10

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4195 r_free = 0.4195 target = 0.158102 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3835 r_free = 0.3835 target = 0.124755 restraints weight = 24024.603|
|-----------------------------------------------------------------------------|
r_work (start): 0.3721 rms_B_bonded: 3.11
r_work: 0.3569 rms_B_bonded: 2.72 restraints_weight: 0.5000
r_work: 0.3404 rms_B_bonded: 4.55 restraints_weight: 0.2500
r_work (final): 0.3404
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3414
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3414 r_free = 0.3414    target_work(ls_wunit_k1) = 0.102         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3414 r_free = 0.3414    target_work(ls_wunit_k1) = 0.102         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3414
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7550
moved from start:          0.1560

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048   8765  Z= 0.135
  Angle     :  0.622  10.636  11914  Z= 0.318
  Chirality :  0.043   0.134   1393
  Planarity :  0.005   0.074   1491
  Dihedral  :  5.110  58.836   1212
  Min Nonbonded Distance : 2.438

Molprobity Statistics.
  All-atom Clashscore : 6.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.66 %
    Favored  : 96.34 %
  Rotamer:
    Outliers :  1.21 %
    Allowed  : 10.68 %
    Favored  : 88.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.58 (0.26), residues: 1095
  helix:  1.16 (0.27), residues: 375
  sheet:  0.58 (0.31), residues: 297
  loop : -0.36 (0.31), residues: 423

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP B 169 
 HIS   0.004   0.001   HIS A 195 
 PHE   0.017   0.001   PHE R 263 
 TYR   0.015   0.001   TYR S 190 
 ARG   0.007   0.001   ARG B 129 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04097 (  437)
  hydrogen bonds       : angle       5.14976 ( 1231)
  SS BOND              : bond        0.00386 (    2)
  SS BOND              : angle       3.08655 (    4)
  covalent geometry    : bond        0.00290 ( 8763)
  covalent geometry    : angle       0.61916 (11910)

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

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

  2190 Ramachandran restraints generated.
    1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2190 Ramachandran restraints generated.
    1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  158 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 147
  time to evaluate  : 0.952 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  228 ASP cc_start: 0.8157 (m-30) cc_final: 0.7393 (p0)
REVERT: B  254 ASP cc_start: 0.8045 (t0) cc_final: 0.7687 (t0)
REVERT: B  335 PHE cc_start: 0.8327 (m-80) cc_final: 0.8007 (m-80)
REVERT: A  193 ASP cc_start: 0.8218 (p0) cc_final: 0.7877 (p0)
REVERT: A  248 LYS cc_start: 0.8294 (mppt) cc_final: 0.7883 (mppt)
REVERT: R  155 ARG cc_start: 0.6038 (ptm-80) cc_final: 0.5576 (mtp-110)
REVERT: R  165 TYR cc_start: 0.8020 (t80) cc_final: 0.6571 (t80)
REVERT: R  240 ARG cc_start: 0.7596 (OUTLIER) cc_final: 0.6266 (ptt90)
  outliers start: 11
  outliers final: 2
  residues processed: 150
  average time/residue: 1.4518
  time to fit residues: 229.6563
Evaluate side-chains
  125 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 122
  time to evaluate  : 0.900 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   78 LYS
Chi-restraints excluded: chain S residue  144 THR
Chi-restraints excluded: chain R residue  240 ARG
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 62 optimal weight:    3.9990
   chunk 44 optimal weight:    0.0030
   chunk 31 optimal weight:    3.9990
   chunk 49 optimal weight:    9.9990
   chunk 45 optimal weight:    0.0770
   chunk 78 optimal weight:    0.9980
   chunk 25 optimal weight:    0.1980
   chunk 104 optimal weight:    0.8980
   chunk 82 optimal weight:    4.9990
   chunk 43 optimal weight:    0.7980
   chunk 98 optimal weight:    0.0770
   overall best weight:    0.2306

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

Flipped N/Q/H residues before XYZ refinement:
B  75 GLN
B 268 ASN
S 194 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4218 r_free = 0.4218 target = 0.160004 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 64)----------------|
| r_work = 0.3806 r_free = 0.3806 target = 0.123896 restraints weight = 34053.245|
|-----------------------------------------------------------------------------|
r_work (start): 0.3717 rms_B_bonded: 3.30
r_work: 0.3589 rms_B_bonded: 3.12 restraints_weight: 0.5000
r_work (final): 0.3589
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3596
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3596 r_free = 0.3596    target_work(ls_wunit_k1) = 0.111         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3596 r_free = 0.3596    target_work(ls_wunit_k1) = 0.111         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3596
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7432
moved from start:          0.2023

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033   8765  Z= 0.104
  Angle     :  0.547   9.723  11914  Z= 0.280
  Chirality :  0.041   0.133   1393
  Planarity :  0.005   0.063   1491
  Dihedral  :  4.235  34.915   1210
  Min Nonbonded Distance : 2.549

Molprobity Statistics.
  All-atom Clashscore : 6.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.93 %
    Favored  : 97.07 %
  Rotamer:
    Outliers :  1.32 %
    Allowed  : 13.77 %
    Favored  : 84.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    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:  0.86 (0.26), residues: 1095
  helix:  1.55 (0.27), residues: 383
  sheet:  0.74 (0.31), residues: 284
  loop : -0.38 (0.31), residues: 428

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP B 169 
 HIS   0.005   0.001   HIS A 188 
 PHE   0.024   0.001   PHE R 260 
 TYR   0.012   0.001   TYR S 190 
 ARG   0.012   0.001   ARG R 261 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03369 (  437)
  hydrogen bonds       : angle       4.63551 ( 1231)
  SS BOND              : bond        0.00439 (    2)
  SS BOND              : angle       2.45164 (    4)
  covalent geometry    : bond        0.00221 ( 8763)
  covalent geometry    : angle       0.54540 (11910)

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

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

  2190 Ramachandran restraints generated.
    1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2190 Ramachandran restraints generated.
    1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  153 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 141
  time to evaluate  : 0.945 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   61 MET cc_start: 0.8245 (tmm) cc_final: 0.8021 (ppp)
REVERT: B   96 ARG cc_start: 0.7467 (mtm180) cc_final: 0.7264 (mpp-170)
REVERT: B  124 TYR cc_start: 0.8522 (m-80) cc_final: 0.8216 (m-80)
REVERT: B  170 ASP cc_start: 0.8158 (t70) cc_final: 0.7843 (t70)
REVERT: B  186 ASP cc_start: 0.7394 (m-30) cc_final: 0.7087 (m-30)
REVERT: B  201 SER cc_start: 0.8182 (m) cc_final: 0.7939 (p)
REVERT: B  228 ASP cc_start: 0.7935 (m-30) cc_final: 0.7461 (p0)
REVERT: B  254 ASP cc_start: 0.7886 (t0) cc_final: 0.7407 (t0)
REVERT: B  335 PHE cc_start: 0.8133 (m-80) cc_final: 0.7854 (m-80)
REVERT: S   46 GLU cc_start: 0.8318 (tt0) cc_final: 0.7943 (tt0)
REVERT: R  155 ARG cc_start: 0.5967 (ptm-80) cc_final: 0.5580 (mtp-110)
REVERT: R  165 TYR cc_start: 0.7742 (t80) cc_final: 0.6211 (t80)
  outliers start: 12
  outliers final: 2
  residues processed: 145
  average time/residue: 1.5143
  time to fit residues: 231.0578
Evaluate side-chains
  139 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 137
  time to evaluate  : 0.963 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain S residue  144 THR
Chi-restraints excluded: chain S residue  146 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 45 optimal weight:    0.9980
   chunk 57 optimal weight:    9.9990
   chunk 94 optimal weight:    0.4980
   chunk 91 optimal weight:    1.9990
   chunk 50 optimal weight:    8.9990
   chunk 23 optimal weight:    3.9990
   chunk 67 optimal weight:    5.9990
   chunk 78 optimal weight:    6.9990
   chunk 9 optimal weight:    4.9990
   chunk 98 optimal weight:    0.0060
   chunk 30 optimal weight:    9.9990
   overall best weight:    1.5000

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

Flipped N/Q/H residues before XYZ refinement:
B  75 GLN
B 268 ASN
B 340 ASN
S  77 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4166 r_free = 0.4166 target = 0.156246 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3740 r_free = 0.3740 target = 0.120438 restraints weight = 18509.228|
|-----------------------------------------------------------------------------|
r_work (start): 0.3658 rms_B_bonded: 2.44
r_work: 0.3552 rms_B_bonded: 2.47 restraints_weight: 0.5000
r_work: 0.3400 rms_B_bonded: 4.04 restraints_weight: 0.2500
r_work (final): 0.3400
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3407
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3407 r_free = 0.3407    target_work(ls_wunit_k1) = 0.101         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3407 r_free = 0.3407    target_work(ls_wunit_k1) = 0.101         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3407
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7615
moved from start:          0.2058

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   8765  Z= 0.171
  Angle     :  0.612  11.280  11914  Z= 0.309
  Chirality :  0.043   0.149   1393
  Planarity :  0.005   0.061   1491
  Dihedral  :  4.667  46.693   1210
  Min Nonbonded Distance : 2.572

Molprobity Statistics.
  All-atom Clashscore : 7.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.30 %
    Favored  : 95.70 %
  Rotamer:
    Outliers :  1.65 %
    Allowed  : 15.31 %
    Favored  : 83.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.71 (0.26), residues: 1095
  helix:  1.25 (0.27), residues: 384
  sheet:  0.73 (0.31), residues: 292
  loop : -0.35 (0.31), residues: 419

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.002   TRP R 104 
 HIS   0.006   0.001   HIS R 251 
 PHE   0.017   0.002   PHE R 260 
 TYR   0.012   0.001   TYR R 165 
 ARG   0.008   0.001   ARG B 129 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04052 (  437)
  hydrogen bonds       : angle       4.73301 ( 1231)
  SS BOND              : bond        0.00317 (    2)
  SS BOND              : angle       3.11197 (    4)
  covalent geometry    : bond        0.00400 ( 8763)
  covalent geometry    : angle       0.60979 (11910)

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

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

  2190 Ramachandran restraints generated.
    1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2190 Ramachandran restraints generated.
    1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  150 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 135
  time to evaluate  : 0.990 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  254 ASP cc_start: 0.8070 (t0) cc_final: 0.7596 (t0)
REVERT: S   46 GLU cc_start: 0.8343 (tt0) cc_final: 0.8002 (tt0)
REVERT: A  193 ASP cc_start: 0.8281 (p0) cc_final: 0.7884 (p0)
REVERT: A  240 MET cc_start: 0.6577 (ptt) cc_final: 0.6201 (ptp)
REVERT: R  155 ARG cc_start: 0.6092 (ptm-80) cc_final: 0.5662 (mtp-110)
REVERT: R  165 TYR cc_start: 0.8068 (t80) cc_final: 0.6491 (t80)
  outliers start: 15
  outliers final: 5
  residues processed: 142
  average time/residue: 1.5250
  time to fit residues: 228.7780
Evaluate side-chains
  131 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 126
  time to evaluate  : 0.966 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain Y residue   41 CYS
Chi-restraints excluded: chain S residue   22 CYS
Chi-restraints excluded: chain S residue  144 THR
Chi-restraints excluded: chain S residue  146 SER
Chi-restraints excluded: chain R residue  141 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 45 optimal weight:    0.0470
   chunk 32 optimal weight:    8.9990
   chunk 51 optimal weight:    1.9990
   chunk 24 optimal weight:    7.9990
   chunk 75 optimal weight:    8.9990
   chunk 31 optimal weight:    0.8980
   chunk 21 optimal weight:    9.9990
   chunk 59 optimal weight:    0.0870
   chunk 2 optimal weight:   10.0000
   chunk 25 optimal weight:    0.8980
   chunk 50 optimal weight:    8.9990
   overall best weight:    0.7858

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

Flipped N/Q/H residues before XYZ refinement:
B  75 GLN
B 268 ASN
B 340 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4186 r_free = 0.4186 target = 0.157638 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 68)----------------|
| r_work = 0.3777 r_free = 0.3777 target = 0.122722 restraints weight = 16389.928|
|-----------------------------------------------------------------------------|
r_work (start): 0.3696 rms_B_bonded: 2.28
r_work: 0.3597 rms_B_bonded: 2.37 restraints_weight: 0.5000
r_work: 0.3449 rms_B_bonded: 3.89 restraints_weight: 0.2500
r_work (final): 0.3449
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3454
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3454 r_free = 0.3454    target_work(ls_wunit_k1) = 0.104         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3454 r_free = 0.3454    target_work(ls_wunit_k1) = 0.104         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3454
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7570
moved from start:          0.2256

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   8765  Z= 0.122
  Angle     :  0.571   8.300  11914  Z= 0.290
  Chirality :  0.041   0.134   1393
  Planarity :  0.005   0.060   1491
  Dihedral  :  4.393  40.631   1210
  Min Nonbonded Distance : 2.477

Molprobity Statistics.
  All-atom Clashscore : 5.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.48 %
    Favored  : 96.52 %
  Rotamer:
    Outliers :  1.43 %
    Allowed  : 16.41 %
    Favored  : 82.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    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:  0.85 (0.26), residues: 1095
  helix:  1.45 (0.27), residues: 389
  sheet:  0.71 (0.31), residues: 292
  loop : -0.32 (0.32), residues: 414

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP B 169 
 HIS   0.004   0.001   HIS A 188 
 PHE   0.014   0.001   PHE R 260 
 TYR   0.011   0.001   TYR S 190 
 ARG   0.010   0.001   ARG R 254 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03502 (  437)
  hydrogen bonds       : angle       4.55009 ( 1231)
  SS BOND              : bond        0.00277 (    2)
  SS BOND              : angle       2.28601 (    4)
  covalent geometry    : bond        0.00278 ( 8763)
  covalent geometry    : angle       0.56982 (11910)

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

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

  2190 Ramachandran restraints generated.
    1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2190 Ramachandran restraints generated.
    1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  150 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 137
  time to evaluate  : 0.917 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   52 ARG cc_start: 0.8542 (OUTLIER) cc_final: 0.8310 (mtp85)
REVERT: B  170 ASP cc_start: 0.8236 (t70) cc_final: 0.7766 (OUTLIER)
REVERT: B  201 SER cc_start: 0.8487 (m) cc_final: 0.8174 (p)
REVERT: B  254 ASP cc_start: 0.7972 (t0) cc_final: 0.7449 (t0)
REVERT: B  262 MET cc_start: 0.8350 (ttp) cc_final: 0.7879 (ptm)
REVERT: B  325 MET cc_start: 0.8741 (ttp) cc_final: 0.8431 (mtp)
REVERT: S   46 GLU cc_start: 0.8370 (tt0) cc_final: 0.8026 (tt0)
REVERT: A  186 GLU cc_start: 0.7829 (tm-30) cc_final: 0.7602 (tm-30)
REVERT: A  240 MET cc_start: 0.6287 (ptt) cc_final: 0.5909 (ptp)
REVERT: A  243 MET cc_start: 0.7636 (tpt) cc_final: 0.7348 (tpt)
REVERT: A  248 LYS cc_start: 0.8328 (mppt) cc_final: 0.7886 (mtmm)
REVERT: A  283 LEU cc_start: 0.8560 (OUTLIER) cc_final: 0.8257 (tt)
REVERT: A  309 ASP cc_start: 0.8268 (t0) cc_final: 0.7839 (m-30)
REVERT: R  155 ARG cc_start: 0.6115 (ptm-80) cc_final: 0.5740 (mtp-110)
REVERT: R  165 TYR cc_start: 0.8009 (t80) cc_final: 0.6451 (t80)
REVERT: R  175 VAL cc_start: 0.8420 (m) cc_final: 0.8090 (p)
  outliers start: 13
  outliers final: 6
  residues processed: 142
  average time/residue: 1.6281
  time to fit residues: 242.9266
Evaluate side-chains
  146 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 139
  time to evaluate  : 1.024 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   44 GLN
Chi-restraints excluded: chain B residue   52 ARG
Chi-restraints excluded: chain S residue   22 CYS
Chi-restraints excluded: chain S residue  144 THR
Chi-restraints excluded: chain S residue  146 SER
Chi-restraints excluded: chain A residue  283 LEU
Chi-restraints excluded: chain A residue  354 LYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 34 optimal weight:    0.8980
   chunk 32 optimal weight:    9.9990
   chunk 60 optimal weight:    8.9990
   chunk 42 optimal weight:    2.9990
   chunk 81 optimal weight:    0.7980
   chunk 8 optimal weight:    2.9990
   chunk 40 optimal weight:    0.6980
   chunk 28 optimal weight:    1.9990
   chunk 23 optimal weight:    1.9990
   chunk 31 optimal weight:    0.8980
   chunk 0 optimal weight:   40.0000
   overall best weight:    1.0582

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

Flipped N/Q/H residues before XYZ refinement:
B  75 GLN
B 268 ASN
B 340 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4177 r_free = 0.4177 target = 0.156852 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3791 r_free = 0.3791 target = 0.123855 restraints weight = 26868.504|
|-----------------------------------------------------------------------------|
r_work (start): 0.3711 rms_B_bonded: 2.92
r_work: 0.3526 rms_B_bonded: 2.88 restraints_weight: 0.5000
r_work: 0.3350 rms_B_bonded: 4.87 restraints_weight: 0.2500
r_work (final): 0.3350
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3356
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3356 r_free = 0.3356    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3356 r_free = 0.3356    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3356
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7650
moved from start:          0.2327

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   8765  Z= 0.136
  Angle     :  0.576  10.318  11914  Z= 0.292
  Chirality :  0.042   0.138   1393
  Planarity :  0.005   0.061   1491
  Dihedral  :  4.440  40.254   1210
  Min Nonbonded Distance : 2.524

Molprobity Statistics.
  All-atom Clashscore : 6.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.85 %
    Favored  : 96.15 %
  Rotamer:
    Outliers :  1.87 %
    Allowed  : 17.18 %
    Favored  : 80.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    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: 1095
  helix:  1.49 (0.27), residues: 389
  sheet:  0.70 (0.31), residues: 292
  loop : -0.26 (0.32), residues: 414

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP R 104 
 HIS   0.005   0.001   HIS A 188 
 PHE   0.017   0.001   PHE R 263 
 TYR   0.011   0.001   TYR S 190 
 ARG   0.010   0.001   ARG B 129 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03624 (  437)
  hydrogen bonds       : angle       4.52582 ( 1231)
  SS BOND              : bond        0.00263 (    2)
  SS BOND              : angle       2.62056 (    4)
  covalent geometry    : bond        0.00314 ( 8763)
  covalent geometry    : angle       0.57387 (11910)

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

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

  2190 Ramachandran restraints generated.
    1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2190 Ramachandran restraints generated.
    1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  161 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 144
  time to evaluate  : 1.053 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   52 ARG cc_start: 0.8620 (OUTLIER) cc_final: 0.8372 (mtp85)
REVERT: B  201 SER cc_start: 0.8573 (m) cc_final: 0.8244 (p)
REVERT: B  254 ASP cc_start: 0.8085 (t0) cc_final: 0.7320 (t0)
REVERT: B  262 MET cc_start: 0.8440 (ttp) cc_final: 0.7962 (ptm)
REVERT: B  325 MET cc_start: 0.8789 (ttp) cc_final: 0.8541 (mtp)
REVERT: S   46 GLU cc_start: 0.8447 (tt0) cc_final: 0.8110 (tt0)
REVERT: A  186 GLU cc_start: 0.7851 (tm-30) cc_final: 0.7578 (tm-30)
REVERT: A  193 ASP cc_start: 0.8331 (p0) cc_final: 0.7926 (p0)
REVERT: A  240 MET cc_start: 0.6396 (ptt) cc_final: 0.6006 (ptp)
REVERT: A  248 LYS cc_start: 0.8334 (mppt) cc_final: 0.7893 (mtmm)
REVERT: R  155 ARG cc_start: 0.6191 (ptm-80) cc_final: 0.5773 (mtp-110)
REVERT: R  165 TYR cc_start: 0.8168 (t80) cc_final: 0.6584 (t80)
REVERT: R  175 VAL cc_start: 0.8471 (m) cc_final: 0.8133 (p)
REVERT: R  240 ARG cc_start: 0.7925 (OUTLIER) cc_final: 0.6821 (ptp90)
REVERT: R  259 ASP cc_start: 0.7161 (m-30) cc_final: 0.6857 (t0)
  outliers start: 17
  outliers final: 7
  residues processed: 154
  average time/residue: 1.6707
  time to fit residues: 271.5813
Evaluate side-chains
  148 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 139
  time to evaluate  : 1.034 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   44 GLN
Chi-restraints excluded: chain B residue   52 ARG
Chi-restraints excluded: chain B residue  317 CYS
Chi-restraints excluded: chain Y residue   41 CYS
Chi-restraints excluded: chain S residue   22 CYS
Chi-restraints excluded: chain S residue  144 THR
Chi-restraints excluded: chain S residue  146 SER
Chi-restraints excluded: chain A residue  354 LYS
Chi-restraints excluded: chain R residue  240 ARG
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 46 optimal weight:    6.9990
   chunk 96 optimal weight:    0.9990
   chunk 67 optimal weight:    0.4980
   chunk 57 optimal weight:    9.9990
   chunk 13 optimal weight:    3.9990
   chunk 81 optimal weight:    1.9990
   chunk 0 optimal weight:   40.0000
   chunk 61 optimal weight:    2.9990
   chunk 105 optimal weight:    0.8980
   chunk 33 optimal weight:   20.0000
   chunk 59 optimal weight:    3.9990
   overall best weight:    1.4786

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

Flipped N/Q/H residues before XYZ refinement:
B  75 GLN
B  88 ASN
B 268 ASN
B 340 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4176 r_free = 0.4176 target = 0.148995 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3796 r_free = 0.3796 target = 0.115200 restraints weight = 27367.801|
|-----------------------------------------------------------------------------|
r_work (start): 0.3679 rms_B_bonded: 2.92
r_work: 0.3514 rms_B_bonded: 2.68 restraints_weight: 0.5000
r_work: 0.3341 rms_B_bonded: 4.58 restraints_weight: 0.2500
r_work (final): 0.3341
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3352
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3352 r_free = 0.3352    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3352 r_free = 0.3352    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3352
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7664
moved from start:          0.2417

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   8765  Z= 0.168
  Angle     :  0.608  11.269  11914  Z= 0.308
  Chirality :  0.043   0.141   1393
  Planarity :  0.005   0.061   1491
  Dihedral  :  4.530  37.728   1210
  Min Nonbonded Distance : 2.530

Molprobity Statistics.
  All-atom Clashscore : 6.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.75 %
    Favored  : 96.25 %
  Rotamer:
    Outliers :  2.42 %
    Allowed  : 16.85 %
    Favored  : 80.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    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:  0.79 (0.26), residues: 1095
  helix:  1.38 (0.27), residues: 388
  sheet:  0.69 (0.31), residues: 292
  loop : -0.32 (0.32), residues: 415

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP R 104 
 HIS   0.005   0.001   HIS A 188 
 PHE   0.012   0.002   PHE R 260 
 TYR   0.013   0.001   TYR B  59 
 ARG   0.010   0.001   ARG R 254 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03907 (  437)
  hydrogen bonds       : angle       4.62880 ( 1231)
  SS BOND              : bond        0.00287 (    2)
  SS BOND              : angle       2.69957 (    4)
  covalent geometry    : bond        0.00394 ( 8763)
  covalent geometry    : angle       0.60636 (11910)

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

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

  2190 Ramachandran restraints generated.
    1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2190 Ramachandran restraints generated.
    1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  162 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 140
  time to evaluate  : 0.945 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   52 ARG cc_start: 0.8626 (OUTLIER) cc_final: 0.8374 (mtp85)
REVERT: B  254 ASP cc_start: 0.8053 (t0) cc_final: 0.7500 (t0)
REVERT: B  259 GLN cc_start: 0.8363 (tt0) cc_final: 0.7747 (mt0)
REVERT: B  262 MET cc_start: 0.8402 (ttp) cc_final: 0.7845 (ptm)
REVERT: B  325 MET cc_start: 0.8799 (ttp) cc_final: 0.8582 (mtp)
REVERT: S   46 GLU cc_start: 0.8419 (tt0) cc_final: 0.8049 (tt0)
REVERT: A  193 ASP cc_start: 0.8365 (p0) cc_final: 0.7984 (p0)
REVERT: A  240 MET cc_start: 0.6583 (ptt) cc_final: 0.6220 (ptp)
REVERT: A  248 LYS cc_start: 0.8352 (mppt) cc_final: 0.7911 (mtmm)
REVERT: A  283 LEU cc_start: 0.8607 (OUTLIER) cc_final: 0.8364 (tt)
REVERT: R  155 ARG cc_start: 0.6112 (ptm-80) cc_final: 0.5685 (mtp-110)
REVERT: R  165 TYR cc_start: 0.8168 (t80) cc_final: 0.7711 (t80)
REVERT: R  175 VAL cc_start: 0.8470 (m) cc_final: 0.8127 (p)
REVERT: R  240 ARG cc_start: 0.7898 (OUTLIER) cc_final: 0.6805 (ptp90)
REVERT: R  290 GLN cc_start: 0.7939 (OUTLIER) cc_final: 0.7697 (pt0)
  outliers start: 22
  outliers final: 12
  residues processed: 151
  average time/residue: 1.6367
  time to fit residues: 260.8171
Evaluate side-chains
  150 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 134
  time to evaluate  : 0.898 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   44 GLN
Chi-restraints excluded: chain B residue   52 ARG
Chi-restraints excluded: chain B residue  112 VAL
Chi-restraints excluded: chain B residue  317 CYS
Chi-restraints excluded: chain Y residue   41 CYS
Chi-restraints excluded: chain S residue   22 CYS
Chi-restraints excluded: chain S residue  144 THR
Chi-restraints excluded: chain S residue  146 SER
Chi-restraints excluded: chain A residue  283 LEU
Chi-restraints excluded: chain A residue  333 ASP
Chi-restraints excluded: chain A residue  354 LYS
Chi-restraints excluded: chain R residue   49 LEU
Chi-restraints excluded: chain R residue   89 ILE
Chi-restraints excluded: chain R residue  180 VAL
Chi-restraints excluded: chain R residue  240 ARG
Chi-restraints excluded: chain R residue  290 GLN
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 10 optimal weight:    3.9990
   chunk 56 optimal weight:    7.9990
   chunk 102 optimal weight:    0.9990
   chunk 96 optimal weight:    0.6980
   chunk 106 optimal weight:    0.9990
   chunk 19 optimal weight:    4.9990
   chunk 45 optimal weight:    1.9990
   chunk 99 optimal weight:    0.6980
   chunk 20 optimal weight:    2.9990
   chunk 2 optimal weight:    2.9990
   chunk 82 optimal weight:    1.9990
   overall best weight:    1.0786

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

Flipped N/Q/H residues before XYZ refinement:
B  75 GLN
B 340 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4169 r_free = 0.4169 target = 0.156126 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3806 r_free = 0.3806 target = 0.123266 restraints weight = 25702.905|
|-----------------------------------------------------------------------------|
r_work (start): 0.3695 rms_B_bonded: 3.26
r_work: 0.3504 rms_B_bonded: 2.98 restraints_weight: 0.5000
r_work: 0.3331 rms_B_bonded: 4.95 restraints_weight: 0.2500
r_work (final): 0.3331
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3338
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3338 r_free = 0.3338    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3338 r_free = 0.3338    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3338
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7625
moved from start:          0.2490

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   8765  Z= 0.141
  Angle     :  0.589   7.895  11914  Z= 0.300
  Chirality :  0.042   0.144   1393
  Planarity :  0.005   0.060   1491
  Dihedral  :  4.379  34.700   1210
  Min Nonbonded Distance : 2.492

Molprobity Statistics.
  All-atom Clashscore : 6.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.12 %
    Favored  : 95.88 %
  Rotamer:
    Outliers :  2.09 %
    Allowed  : 17.40 %
    Favored  : 80.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    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:  0.86 (0.26), residues: 1095
  helix:  1.49 (0.27), residues: 389
  sheet:  0.67 (0.31), residues: 292
  loop : -0.31 (0.32), residues: 414

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP R 104 
 HIS   0.004   0.001   HIS A 188 
 PHE   0.018   0.001   PHE R 263 
 TYR   0.015   0.001   TYR B  59 
 ARG   0.009   0.001   ARG R 254 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03663 (  437)
  hydrogen bonds       : angle       4.56174 ( 1231)
  SS BOND              : bond        0.00277 (    2)
  SS BOND              : angle       2.57215 (    4)
  covalent geometry    : bond        0.00328 ( 8763)
  covalent geometry    : angle       0.58769 (11910)

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

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

  2190 Ramachandran restraints generated.
    1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2190 Ramachandran restraints generated.
    1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  154 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 135
  time to evaluate  : 1.216 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   52 ARG cc_start: 0.8667 (OUTLIER) cc_final: 0.8406 (mtp85)
REVERT: B  201 SER cc_start: 0.8571 (m) cc_final: 0.8244 (p)
REVERT: B  254 ASP cc_start: 0.8043 (t0) cc_final: 0.7616 (t0)
REVERT: B  259 GLN cc_start: 0.8280 (tt0) cc_final: 0.7493 (mt0)
REVERT: B  262 MET cc_start: 0.8387 (ttp) cc_final: 0.7769 (ptm)
REVERT: B  325 MET cc_start: 0.8758 (ttp) cc_final: 0.8525 (mtp)
REVERT: S   22 CYS cc_start: 0.8353 (OUTLIER) cc_final: 0.8036 (t)
REVERT: S   46 GLU cc_start: 0.8435 (tt0) cc_final: 0.8061 (tt0)
REVERT: A  240 MET cc_start: 0.6489 (ptt) cc_final: 0.6149 (ptp)
REVERT: A  243 MET cc_start: 0.7512 (tpt) cc_final: 0.7090 (tpt)
REVERT: A  248 LYS cc_start: 0.8312 (mppt) cc_final: 0.7849 (mtmm)
REVERT: A  309 ASP cc_start: 0.8260 (t0) cc_final: 0.7911 (m-30)
REVERT: R  155 ARG cc_start: 0.5939 (ptm-80) cc_final: 0.5469 (mtp-110)
REVERT: R  165 TYR cc_start: 0.8202 (t80) cc_final: 0.6591 (t80)
REVERT: R  175 VAL cc_start: 0.8435 (m) cc_final: 0.8094 (p)
REVERT: R  240 ARG cc_start: 0.7899 (OUTLIER) cc_final: 0.6880 (ptp90)
  outliers start: 19
  outliers final: 10
  residues processed: 145
  average time/residue: 1.8404
  time to fit residues: 281.3844
Evaluate side-chains
  154 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 141
  time to evaluate  : 1.109 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   44 GLN
Chi-restraints excluded: chain B residue   52 ARG
Chi-restraints excluded: chain B residue  112 VAL
Chi-restraints excluded: chain B residue  317 CYS
Chi-restraints excluded: chain Y residue   41 CYS
Chi-restraints excluded: chain S residue   22 CYS
Chi-restraints excluded: chain S residue  144 THR
Chi-restraints excluded: chain S residue  146 SER
Chi-restraints excluded: chain A residue  333 ASP
Chi-restraints excluded: chain A residue  354 LYS
Chi-restraints excluded: chain R residue   49 LEU
Chi-restraints excluded: chain R residue  180 VAL
Chi-restraints excluded: chain R residue  240 ARG
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 97 optimal weight:    0.4980
   chunk 61 optimal weight:    7.9990
   chunk 95 optimal weight:    0.8980
   chunk 47 optimal weight:    0.9990
   chunk 90 optimal weight:    0.1980
   chunk 57 optimal weight:   10.0000
   chunk 26 optimal weight:   20.0000
   chunk 104 optimal weight:    0.8980
   chunk 32 optimal weight:   10.0000
   chunk 102 optimal weight:    0.9990
   chunk 74 optimal weight:    6.9990
   overall best weight:    0.6982

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

Flipped N/Q/H residues before XYZ refinement:
B  75 GLN
B 268 ASN
B 340 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4199 r_free = 0.4199 target = 0.150656 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3830 r_free = 0.3830 target = 0.117275 restraints weight = 27370.702|
|-----------------------------------------------------------------------------|
r_work (start): 0.3717 rms_B_bonded: 2.93
r_work: 0.3541 rms_B_bonded: 2.80 restraints_weight: 0.5000
r_work: 0.3384 rms_B_bonded: 4.57 restraints_weight: 0.2500
r_work (final): 0.3384
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3397
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3397 r_free = 0.3397    target_work(ls_wunit_k1) = 0.100         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3397 r_free = 0.3397    target_work(ls_wunit_k1) = 0.100         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3397
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7621
moved from start:          0.2555

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   8765  Z= 0.121
  Angle     :  0.582  10.988  11914  Z= 0.294
  Chirality :  0.041   0.139   1393
  Planarity :  0.005   0.060   1491
  Dihedral  :  4.223  32.219   1210
  Min Nonbonded Distance : 2.528

Molprobity Statistics.
  All-atom Clashscore : 6.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.66 %
    Favored  : 96.34 %
  Rotamer:
    Outliers :  1.76 %
    Allowed  : 17.95 %
    Favored  : 80.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    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:  0.98 (0.26), residues: 1095
  helix:  1.65 (0.27), residues: 390
  sheet:  0.69 (0.31), residues: 292
  loop : -0.26 (0.32), residues: 413

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP B 169 
 HIS   0.004   0.001   HIS A 188 
 PHE   0.011   0.001   PHE R 260 
 TYR   0.011   0.001   TYR S 190 
 ARG   0.009   0.001   ARG B 129 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03426 (  437)
  hydrogen bonds       : angle       4.47599 ( 1231)
  SS BOND              : bond        0.00259 (    2)
  SS BOND              : angle       2.11107 (    4)
  covalent geometry    : bond        0.00275 ( 8763)
  covalent geometry    : angle       0.58054 (11910)

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

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

  2190 Ramachandran restraints generated.
    1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2190 Ramachandran restraints generated.
    1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  168 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 152
  time to evaluate  : 2.148 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   52 ARG cc_start: 0.8580 (OUTLIER) cc_final: 0.8341 (mtp85)
REVERT: B  170 ASP cc_start: 0.8203 (t70) cc_final: 0.7734 (OUTLIER)
REVERT: B  201 SER cc_start: 0.8546 (m) cc_final: 0.8283 (p)
REVERT: B  254 ASP cc_start: 0.8034 (t0) cc_final: 0.7691 (t0)
REVERT: B  259 GLN cc_start: 0.8337 (tt0) cc_final: 0.7597 (mt0)
REVERT: B  262 MET cc_start: 0.8336 (ttp) cc_final: 0.7807 (ptm)
REVERT: B  325 MET cc_start: 0.8796 (ttp) cc_final: 0.8582 (mtp)
REVERT: S   22 CYS cc_start: 0.8331 (OUTLIER) cc_final: 0.8063 (t)
REVERT: S   46 GLU cc_start: 0.8378 (tt0) cc_final: 0.8046 (tt0)
REVERT: S  192 MET cc_start: 0.8886 (ttp) cc_final: 0.8424 (tmm)
REVERT: A  240 MET cc_start: 0.6429 (ptt) cc_final: 0.6023 (ptp)
REVERT: A  243 MET cc_start: 0.7634 (tpt) cc_final: 0.7254 (tpt)
REVERT: A  248 LYS cc_start: 0.8370 (mppt) cc_final: 0.7911 (mtmm)
REVERT: A  297 GLU cc_start: 0.8138 (mp0) cc_final: 0.7836 (mp0)
REVERT: A  309 ASP cc_start: 0.8274 (t0) cc_final: 0.8004 (m-30)
REVERT: R  155 ARG cc_start: 0.6008 (ptm-80) cc_final: 0.5590 (mtp-110)
REVERT: R  165 TYR cc_start: 0.8126 (t80) cc_final: 0.6531 (t80)
REVERT: R  175 VAL cc_start: 0.8404 (m) cc_final: 0.8104 (p)
REVERT: R  240 ARG cc_start: 0.7909 (OUTLIER) cc_final: 0.6849 (ptp90)
REVERT: R  323 MET cc_start: 0.5846 (mmm) cc_final: 0.5321 (mtm)
  outliers start: 16
  outliers final: 10
  residues processed: 161
  average time/residue: 1.8008
  time to fit residues: 305.5761
Evaluate side-chains
  151 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 139
  time to evaluate  : 0.917 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   44 GLN
Chi-restraints excluded: chain B residue   52 ARG
Chi-restraints excluded: chain B residue  112 VAL
Chi-restraints excluded: chain B residue  317 CYS
Chi-restraints excluded: chain Y residue   41 CYS
Chi-restraints excluded: chain S residue   22 CYS
Chi-restraints excluded: chain S residue  144 THR
Chi-restraints excluded: chain S residue  146 SER
Chi-restraints excluded: chain A residue  333 ASP
Chi-restraints excluded: chain A residue  354 LYS
Chi-restraints excluded: chain R residue  180 VAL
Chi-restraints excluded: chain R residue  240 ARG
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 79 optimal weight:    5.9990
   chunk 43 optimal weight:    2.9990
   chunk 107 optimal weight:    0.2980
   chunk 72 optimal weight:    2.9990
   chunk 39 optimal weight:   10.0000
   chunk 52 optimal weight:    0.8980
   chunk 23 optimal weight:   10.0000
   chunk 51 optimal weight:    9.9990
   chunk 2 optimal weight:   10.0000
   chunk 94 optimal weight:    0.4980
   chunk 106 optimal weight:    1.9990
   overall best weight:    1.3384

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

Flipped N/Q/H residues before XYZ refinement:
B  75 GLN
B 175 GLN
B 268 ASN
B 340 ASN
A 306 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4183 r_free = 0.4183 target = 0.149358 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3798 r_free = 0.3798 target = 0.115273 restraints weight = 29370.642|
|-----------------------------------------------------------------------------|
r_work (start): 0.3680 rms_B_bonded: 3.07
r_work: 0.3505 rms_B_bonded: 2.83 restraints_weight: 0.5000
r_work: 0.3340 rms_B_bonded: 4.69 restraints_weight: 0.2500
r_work (final): 0.3340
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3354
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3354 r_free = 0.3354    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3354 r_free = 0.3354    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3354
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7654
moved from start:          0.2594

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   8765  Z= 0.159
  Angle     :  0.622  11.860  11914  Z= 0.314
  Chirality :  0.042   0.145   1393
  Planarity :  0.005   0.060   1491
  Dihedral  :  4.358  31.955   1210
  Min Nonbonded Distance : 2.489

Molprobity Statistics.
  All-atom Clashscore : 6.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.12 %
    Favored  : 95.88 %
  Rotamer:
    Outliers :  1.76 %
    Allowed  : 18.61 %
    Favored  : 79.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    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:  0.92 (0.26), residues: 1095
  helix:  1.49 (0.27), residues: 389
  sheet:  0.74 (0.31), residues: 292
  loop : -0.25 (0.32), residues: 414

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP R 104 
 HIS   0.004   0.001   HIS R 112 
 PHE   0.019   0.002   PHE R 263 
 TYR   0.011   0.001   TYR S 190 
 ARG   0.009   0.001   ARG B 129 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03788 (  437)
  hydrogen bonds       : angle       4.56203 ( 1231)
  SS BOND              : bond        0.00338 (    2)
  SS BOND              : angle       2.35372 (    4)
  covalent geometry    : bond        0.00376 ( 8763)
  covalent geometry    : angle       0.62098 (11910)

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

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

  2190 Ramachandran restraints generated.
    1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2190 Ramachandran restraints generated.
    1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  157 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 141
  time to evaluate  : 1.005 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   52 ARG cc_start: 0.8667 (OUTLIER) cc_final: 0.8428 (mtp85)
REVERT: B  201 SER cc_start: 0.8615 (m) cc_final: 0.8349 (p)
REVERT: B  212 ASP cc_start: 0.8255 (t0) cc_final: 0.7827 (t0)
REVERT: B  254 ASP cc_start: 0.8019 (t0) cc_final: 0.7686 (t0)
REVERT: B  259 GLN cc_start: 0.8310 (tt0) cc_final: 0.7576 (mt0)
REVERT: B  262 MET cc_start: 0.8313 (ttp) cc_final: 0.7782 (ptm)
REVERT: S   22 CYS cc_start: 0.8350 (OUTLIER) cc_final: 0.8048 (t)
REVERT: S   46 GLU cc_start: 0.8401 (tt0) cc_final: 0.8041 (tt0)
REVERT: S  192 MET cc_start: 0.8916 (ttp) cc_final: 0.8553 (tmm)
REVERT: A  240 MET cc_start: 0.6543 (ptt) cc_final: 0.6176 (ptp)
REVERT: A  243 MET cc_start: 0.7674 (tpt) cc_final: 0.7268 (tpt)
REVERT: A  248 LYS cc_start: 0.8362 (mppt) cc_final: 0.7905 (mtmm)
REVERT: A  283 LEU cc_start: 0.8719 (OUTLIER) cc_final: 0.8447 (tt)
REVERT: R  155 ARG cc_start: 0.6049 (ptm-80) cc_final: 0.5625 (mtp-110)
REVERT: R  165 TYR cc_start: 0.8197 (t80) cc_final: 0.6607 (t80)
REVERT: R  175 VAL cc_start: 0.8450 (m) cc_final: 0.8148 (p)
REVERT: R  178 ARG cc_start: 0.8144 (OUTLIER) cc_final: 0.7238 (mmp80)
REVERT: R  240 ARG cc_start: 0.7893 (OUTLIER) cc_final: 0.6771 (ptp90)
  outliers start: 16
  outliers final: 7
  residues processed: 149
  average time/residue: 1.7118
  time to fit residues: 268.6112
Evaluate side-chains
  149 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 137
  time to evaluate  : 0.927 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   52 ARG
Chi-restraints excluded: chain B residue  112 VAL
Chi-restraints excluded: chain B residue  317 CYS
Chi-restraints excluded: chain Y residue   41 CYS
Chi-restraints excluded: chain S residue   22 CYS
Chi-restraints excluded: chain S residue  144 THR
Chi-restraints excluded: chain S residue  146 SER
Chi-restraints excluded: chain A residue  283 LEU
Chi-restraints excluded: chain A residue  354 LYS
Chi-restraints excluded: chain R residue  178 ARG
Chi-restraints excluded: chain R residue  180 VAL
Chi-restraints excluded: chain R residue  240 ARG
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 28 optimal weight:    0.8980
   chunk 4 optimal weight:    1.9990
   chunk 88 optimal weight:    0.0670
   chunk 31 optimal weight:    1.9990
   chunk 56 optimal weight:    0.9990
   chunk 63 optimal weight:    3.9990
   chunk 36 optimal weight:    5.9990
   chunk 1 optimal weight:    8.9990
   chunk 106 optimal weight:    0.8980
   chunk 0 optimal weight:   30.0000
   chunk 103 optimal weight:    1.9990
   overall best weight:    0.9722

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

Flipped N/Q/H residues before XYZ refinement:
B  75 GLN
B 175 GLN
B 268 ASN
B 340 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4192 r_free = 0.4192 target = 0.150076 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3809 r_free = 0.3809 target = 0.116111 restraints weight = 30363.682|
|-----------------------------------------------------------------------------|
r_work (start): 0.3701 rms_B_bonded: 3.18
r_work: 0.3521 rms_B_bonded: 2.84 restraints_weight: 0.5000
r_work: 0.3358 rms_B_bonded: 4.71 restraints_weight: 0.2500
r_work (final): 0.3358
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3370
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3370 r_free = 0.3370    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3370 r_free = 0.3370    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3370
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7641
moved from start:          0.2597

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   8765  Z= 0.135
  Angle     :  0.600   9.131  11914  Z= 0.304
  Chirality :  0.042   0.141   1393
  Planarity :  0.005   0.056   1491
  Dihedral  :  4.254  29.737   1210
  Min Nonbonded Distance : 2.524

Molprobity Statistics.
  All-atom Clashscore : 6.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.85 %
    Favored  : 96.15 %
  Rotamer:
    Outliers :  1.76 %
    Allowed  : 18.28 %
    Favored  : 79.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.96 (0.26), residues: 1095
  helix:  1.57 (0.27), residues: 389
  sheet:  0.70 (0.31), residues: 292
  loop : -0.21 (0.32), residues: 414

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B 169 
 HIS   0.004   0.001   HIS A 188 
 PHE   0.010   0.001   PHE R 260 
 TYR   0.011   0.001   TYR S 190 
 ARG   0.010   0.001   ARG B 129 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03584 (  437)
  hydrogen bonds       : angle       4.51987 ( 1231)
  SS BOND              : bond        0.00264 (    2)
  SS BOND              : angle       2.12252 (    4)
  covalent geometry    : bond        0.00315 ( 8763)
  covalent geometry    : angle       0.59875 (11910)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 11543.11 seconds
wall clock time: 200 minutes 16.47 seconds (12016.47 seconds total)