Starting phenix.real_space_refine
on Wed Mar 12 23:33:58 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8g59_29736/03_2025/8g59_29736.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8g59_29736/03_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_29736/03_2025/8g59_29736.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8g59_29736/03_2025/8g59_29736.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8g59_29736/03_2025/8g59_29736.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8g59_29736/03_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-5624/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: 6.12, per 1000 atoms: 0.71
  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: 2.76
  Conformation dependent library (CDL) restraints added in 1.3 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: 1.00
  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: 2.29

  Time building geometry restraints manager: 3.18 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:             0.460
  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:          0.290
  Check model and map are aligned:         0.050
  Set scattering table:                    0.080
  Process input model:                     25.520
  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:13.300
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   39.840
-------------------------------------------------------------------------------
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   8763  Z= 0.334
  Angle     :  0.728  11.682  11910  Z= 0.430
  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 

*********************** 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  : 0.990 
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: 1.5023
  time to fit residues: 254.4502
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  : 0.993 
-------------------------------------------------------------------------------
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:    3.9990
   chunk 64 optimal weight:    0.7980
   chunk 99 optimal weight:    2.9990
   overall best weight:    0.6280

-------------------------------------------------------------------------------
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 204 GLN
A 357 ASN
R 189 GLN

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4192 r_free = 0.4192 target = 0.157900 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3837 r_free = 0.3837 target = 0.125504 restraints weight = 24006.423|
|-----------------------------------------------------------------------------|
r_work (start): 0.3726 rms_B_bonded: 3.39
r_work: 0.3552 rms_B_bonded: 2.85 restraints_weight: 0.5000
r_work: 0.3386 rms_B_bonded: 4.75 restraints_weight: 0.2500
r_work (final): 0.3386
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3395
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3395 r_free = 0.3395    target_work(ls_wunit_k1) = 0.100         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3395 r_free = 0.3395    target_work(ls_wunit_k1) = 0.100         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3395
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7563
moved from start:          0.1511

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048   8763  Z= 0.194
  Angle     :  0.622  10.650  11910  Z= 0.318
  Chirality :  0.043   0.140   1393
  Planarity :  0.005   0.074   1491
  Dihedral  :  5.137  59.469   1212
  Min Nonbonded Distance : 2.438

Molprobity Statistics.
  All-atom Clashscore : 6.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.66 %
    Favored  : 96.34 %
  Rotamer:
    Outliers :  1.21 %
    Allowed  : 10.46 %
    Favored  : 88.33 %
  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:  0.53 (0.26), residues: 1095
  helix:  1.13 (0.27), residues: 376
  sheet:  0.53 (0.31), residues: 297
  loop : -0.38 (0.31), residues: 422

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 

*********************** 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
  159 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 148
  time to evaluate  : 0.901 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  186 ASP cc_start: 0.7841 (m-30) cc_final: 0.7042 (m-30)
REVERT: B  228 ASP cc_start: 0.8175 (m-30) cc_final: 0.7359 (p0)
REVERT: B  254 ASP cc_start: 0.8045 (t0) cc_final: 0.7682 (t0)
REVERT: B  335 PHE cc_start: 0.8318 (m-80) cc_final: 0.7995 (m-80)
REVERT: A  193 ASP cc_start: 0.8192 (p0) cc_final: 0.7845 (p0)
REVERT: A  248 LYS cc_start: 0.8261 (mppt) cc_final: 0.7851 (mppt)
REVERT: R  155 ARG cc_start: 0.6068 (ptm-80) cc_final: 0.5584 (mtp-110)
REVERT: R  165 TYR cc_start: 0.8040 (t80) cc_final: 0.6572 (t80)
REVERT: R  240 ARG cc_start: 0.7634 (OUTLIER) cc_final: 0.6315 (ptt90)
  outliers start: 11
  outliers final: 2
  residues processed: 151
  average time/residue: 1.4547
  time to fit residues: 231.5231
Evaluate side-chains
  126 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 123
  time to evaluate  : 0.873 
-------------------------------------------------------------------------------
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:    0.8980
   chunk 44 optimal weight:    0.0030
   chunk 31 optimal weight:    4.9990
   chunk 49 optimal weight:    9.9990
   chunk 45 optimal weight:    0.0670
   chunk 78 optimal weight:   10.0000
   chunk 25 optimal weight:    4.9990
   chunk 104 optimal weight:    0.5980
   chunk 82 optimal weight:    2.9990
   chunk 43 optimal weight:    3.9990
   chunk 98 optimal weight:    0.6980
   overall best weight:    0.4528

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

Flipped N/Q/H residues before XYZ refinement:
B  75 GLN
B 259 GLN
B 268 ASN
S 194 ASN
A 188 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4202 r_free = 0.4202 target = 0.158811 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3773 r_free = 0.3773 target = 0.122009 restraints weight = 34158.775|
|-----------------------------------------------------------------------------|
r_work (start): 0.3686 rms_B_bonded: 3.35
r_work: 0.3555 rms_B_bonded: 3.12 restraints_weight: 0.5000
r_work (final): 0.3555
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3560
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3560 r_free = 0.3560    target_work(ls_wunit_k1) = 0.110         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3560 r_free = 0.3560    target_work(ls_wunit_k1) = 0.110         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3560
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7467
moved from start:          0.1883

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.037   8763  Z= 0.161
  Angle     :  0.560   9.924  11910  Z= 0.286
  Chirality :  0.041   0.131   1393
  Planarity :  0.005   0.063   1491
  Dihedral  :  4.360  37.716   1210
  Min Nonbonded Distance : 2.542

Molprobity Statistics.
  All-atom Clashscore : 6.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.02 %
    Favored  : 96.98 %
  Rotamer:
    Outliers :  1.21 %
    Allowed  : 13.33 %
    Favored  : 85.46 %
  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:  0.81 (0.26), residues: 1095
  helix:  1.49 (0.27), residues: 378
  sheet:  0.73 (0.32), residues: 284
  loop : -0.38 (0.31), residues: 433

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP B 169 
 HIS   0.004   0.001   HIS A 195 
 PHE   0.009   0.001   PHE R  51 
 TYR   0.013   0.001   TYR S 190 
 ARG   0.013   0.001   ARG R 261 

*********************** 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
  149 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 138
  time to evaluate  : 1.016 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   78 LYS cc_start: 0.8376 (OUTLIER) cc_final: 0.7914 (mptm)
REVERT: B   96 ARG cc_start: 0.7444 (mtm180) cc_final: 0.7227 (mpp-170)
REVERT: B  188 MET cc_start: 0.7648 (mmm) cc_final: 0.7390 (mmm)
REVERT: B  201 SER cc_start: 0.8298 (m) cc_final: 0.8043 (p)
REVERT: B  228 ASP cc_start: 0.7969 (m-30) cc_final: 0.7456 (p0)
REVERT: B  254 ASP cc_start: 0.7915 (t0) cc_final: 0.7488 (t0)
REVERT: B  335 PHE cc_start: 0.8259 (m-80) cc_final: 0.7976 (m-80)
REVERT: S   46 GLU cc_start: 0.8330 (tt0) cc_final: 0.7934 (tt0)
REVERT: A  240 MET cc_start: 0.6496 (ptt) cc_final: 0.6128 (ptp)
REVERT: R  155 ARG cc_start: 0.5871 (ptm-80) cc_final: 0.5494 (mtp-110)
REVERT: R  165 TYR cc_start: 0.7804 (t80) cc_final: 0.6316 (t80)
REVERT: R  298 ILE cc_start: 0.7906 (OUTLIER) cc_final: 0.7686 (mp)
  outliers start: 11
  outliers final: 2
  residues processed: 141
  average time/residue: 1.4938
  time to fit residues: 221.8101
Evaluate side-chains
  134 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 130
  time to evaluate  : 0.979 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   78 LYS
Chi-restraints excluded: chain S residue  144 THR
Chi-restraints excluded: chain S residue  146 SER
Chi-restraints excluded: chain R residue  298 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 45 optimal weight:    0.2980
   chunk 57 optimal weight:    5.9990
   chunk 94 optimal weight:    0.5980
   chunk 91 optimal weight:    1.9990
   chunk 50 optimal weight:   10.0000
   chunk 23 optimal weight:    0.6980
   chunk 67 optimal weight:   10.0000
   chunk 78 optimal weight:    6.9990
   chunk 9 optimal weight:    3.9990
   chunk 98 optimal weight:    0.7980
   chunk 30 optimal weight:    9.9990
   overall best weight:    0.8782

-------------------------------------------------------------------------------
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  77 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4188 r_free = 0.4188 target = 0.157679 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3779 r_free = 0.3779 target = 0.122681 restraints weight = 18502.184|
|-----------------------------------------------------------------------------|
r_work (start): 0.3699 rms_B_bonded: 2.40
r_work: 0.3594 rms_B_bonded: 2.46 restraints_weight: 0.5000
r_work: 0.3439 rms_B_bonded: 4.12 restraints_weight: 0.2500
r_work (final): 0.3439
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3444
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3444 r_free = 0.3444    target_work(ls_wunit_k1) = 0.103         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3444 r_free = 0.3444    target_work(ls_wunit_k1) = 0.103         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3444
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7579
moved from start:          0.1995

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   8763  Z= 0.188
  Angle     :  0.567  10.910  11910  Z= 0.287
  Chirality :  0.042   0.144   1393
  Planarity :  0.005   0.061   1491
  Dihedral  :  4.467  41.148   1210
  Min Nonbonded Distance : 2.576

Molprobity Statistics.
  All-atom Clashscore : 6.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.85 %
    Favored  : 96.15 %
  Rotamer:
    Outliers :  1.98 %
    Allowed  : 14.54 %
    Favored  : 83.48 %
  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:  0.81 (0.26), residues: 1095
  helix:  1.44 (0.27), residues: 384
  sheet:  0.70 (0.31), residues: 292
  loop : -0.34 (0.32), residues: 419

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP B 169 
 HIS   0.005   0.001   HIS A 195 
 PHE   0.021   0.001   PHE R 260 
 TYR   0.012   0.001   TYR S 190 
 ARG   0.008   0.001   ARG B 129 

*********************** 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
  155 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 137
  time to evaluate  : 1.020 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   52 ARG cc_start: 0.8644 (OUTLIER) cc_final: 0.8349 (mtp85)
REVERT: B   78 LYS cc_start: 0.8521 (OUTLIER) cc_final: 0.7936 (mptm)
REVERT: B   96 ARG cc_start: 0.7563 (mtm180) cc_final: 0.7330 (mpp-170)
REVERT: B  170 ASP cc_start: 0.8279 (t70) cc_final: 0.7956 (t70)
REVERT: B  188 MET cc_start: 0.7754 (mmm) cc_final: 0.7544 (mmm)
REVERT: B  201 SER cc_start: 0.8472 (m) cc_final: 0.8207 (p)
REVERT: B  228 ASP cc_start: 0.8119 (m-30) cc_final: 0.7562 (p0)
REVERT: B  254 ASP cc_start: 0.8038 (t0) cc_final: 0.7587 (t0)
REVERT: S   46 GLU cc_start: 0.8448 (tt0) cc_final: 0.8073 (tt0)
REVERT: A  193 ASP cc_start: 0.8347 (p0) cc_final: 0.7981 (p0)
REVERT: A  240 MET cc_start: 0.6463 (ptt) cc_final: 0.6014 (ptp)
REVERT: A  309 ASP cc_start: 0.8238 (m-30) cc_final: 0.7839 (m-30)
REVERT: R  155 ARG cc_start: 0.6136 (ptm-80) cc_final: 0.5744 (mtp-110)
REVERT: R  165 TYR cc_start: 0.8009 (t80) cc_final: 0.6500 (t80)
REVERT: R  298 ILE cc_start: 0.8084 (OUTLIER) cc_final: 0.7821 (mp)
  outliers start: 18
  outliers final: 5
  residues processed: 143
  average time/residue: 1.4077
  time to fit residues: 212.6560
Evaluate side-chains
  137 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 129
  time to evaluate  : 0.911 
-------------------------------------------------------------------------------
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   78 LYS
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  298 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 45 optimal weight:    0.7980
   chunk 32 optimal weight:   10.0000
   chunk 51 optimal weight:    0.0060
   chunk 24 optimal weight:    8.9990
   chunk 75 optimal weight:    2.9990
   chunk 31 optimal weight:    2.9990
   chunk 21 optimal weight:   10.0000
   chunk 59 optimal weight:    8.9990
   chunk 2 optimal weight:    4.9990
   chunk 25 optimal weight:    0.6980
   chunk 50 optimal weight:    4.9990
   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

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4170 r_free = 0.4170 target = 0.156071 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3757 r_free = 0.3757 target = 0.121413 restraints weight = 16239.572|
|-----------------------------------------------------------------------------|
r_work (start): 0.3664 rms_B_bonded: 2.20
r_work: 0.3564 rms_B_bonded: 2.30 restraints_weight: 0.5000
r_work: 0.3414 rms_B_bonded: 3.81 restraints_weight: 0.2500
r_work (final): 0.3414
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3420
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3420 r_free = 0.3420    target_work(ls_wunit_k1) = 0.102         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3420 r_free = 0.3420    target_work(ls_wunit_k1) = 0.102         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3420
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7605
moved from start:          0.2114

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   8763  Z= 0.263
  Angle     :  0.601  10.990  11910  Z= 0.305
  Chirality :  0.043   0.145   1393
  Planarity :  0.005   0.060   1491
  Dihedral  :  4.681  44.972   1210
  Min Nonbonded Distance : 2.545

Molprobity Statistics.
  All-atom Clashscore : 6.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.85 %
    Favored  : 96.15 %
  Rotamer:
    Outliers :  2.09 %
    Allowed  : 15.09 %
    Favored  : 82.82 %
  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:  1.30 (0.27), residues: 384
  sheet:  0.69 (0.31), residues: 292
  loop : -0.38 (0.31), residues: 419

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.002   TRP R 104 
 HIS   0.004   0.001   HIS A 188 
 PHE   0.015   0.002   PHE R 260 
 TYR   0.011   0.001   TYR S 190 
 ARG   0.009   0.001   ARG B 129 

*********************** 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
  155 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 136
  time to evaluate  : 0.967 
Fit side-chains
   revert: symmetry clash
REVERT: B   52 ARG cc_start: 0.8585 (OUTLIER) cc_final: 0.8288 (mtp85)
REVERT: B  254 ASP cc_start: 0.7996 (t0) cc_final: 0.7486 (t0)
REVERT: B  262 MET cc_start: 0.8434 (OUTLIER) cc_final: 0.7830 (ptm)
REVERT: S   46 GLU cc_start: 0.8360 (tt0) cc_final: 0.7978 (tt0)
REVERT: A  240 MET cc_start: 0.6488 (ptt) cc_final: 0.6016 (ptp)
REVERT: A  309 ASP cc_start: 0.8230 (m-30) cc_final: 0.7829 (m-30)
REVERT: R  155 ARG cc_start: 0.6075 (ptm-80) cc_final: 0.5653 (mtp-110)
REVERT: R  165 TYR cc_start: 0.8022 (t80) cc_final: 0.6447 (t80)
REVERT: R  298 ILE cc_start: 0.8161 (OUTLIER) cc_final: 0.7853 (mp)
  outliers start: 19
  outliers final: 5
  residues processed: 143
  average time/residue: 1.4653
  time to fit residues: 220.6282
Evaluate side-chains
  143 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 135
  time to evaluate  : 0.873 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   52 ARG
Chi-restraints excluded: chain B residue  262 MET
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
Chi-restraints excluded: chain R residue  298 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 34 optimal weight:    2.9990
   chunk 32 optimal weight:    8.9990
   chunk 60 optimal weight:   10.0000
   chunk 42 optimal weight:    1.9990
   chunk 81 optimal weight:    0.8980
   chunk 8 optimal weight:    0.5980
   chunk 40 optimal weight:    0.6980
   chunk 28 optimal weight:    0.9990
   chunk 23 optimal weight:    0.6980
   chunk 31 optimal weight:    2.9990
   chunk 0 optimal weight:   40.0000
   overall best weight:    0.7782

-------------------------------------------------------------------------------
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 = 0.4181 r_free = 0.4181 target = 0.157182 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3837 r_free = 0.3837 target = 0.124638 restraints weight = 26933.328|
|-----------------------------------------------------------------------------|
r_work (start): 0.3719 rms_B_bonded: 3.23
r_work: 0.3519 rms_B_bonded: 3.05 restraints_weight: 0.5000
r_work (final): 0.3519
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3525
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3525 r_free = 0.3525    target_work(ls_wunit_k1) = 0.108         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3525 r_free = 0.3525    target_work(ls_wunit_k1) = 0.108         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3525
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7466
moved from start:          0.2266

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   8763  Z= 0.181
  Angle     :  0.556   7.899  11910  Z= 0.284
  Chirality :  0.041   0.138   1393
  Planarity :  0.005   0.059   1491
  Dihedral  :  4.388  39.793   1210
  Min Nonbonded Distance : 2.554

Molprobity Statistics.
  All-atom Clashscore : 5.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.57 %
    Favored  : 96.43 %
  Rotamer:
    Outliers :  1.98 %
    Allowed  : 16.85 %
    Favored  : 81.17 %
  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:  0.87 (0.26), residues: 1095
  helix:  1.52 (0.27), residues: 389
  sheet:  0.66 (0.30), residues: 292
  loop : -0.30 (0.32), residues: 414

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP B 169 
 HIS   0.005   0.001   HIS A 188 
 PHE   0.018   0.001   PHE R 263 
 TYR   0.011   0.001   TYR S 190 
 ARG   0.009   0.001   ARG R 254 

*********************** 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
  165 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 147
  time to evaluate  : 0.912 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   52 ARG cc_start: 0.8446 (OUTLIER) cc_final: 0.8146 (mtp85)
REVERT: B  201 SER cc_start: 0.8457 (m) cc_final: 0.8094 (p)
REVERT: B  212 ASP cc_start: 0.8092 (t70) cc_final: 0.7667 (t0)
REVERT: B  254 ASP cc_start: 0.7862 (t0) cc_final: 0.7167 (t0)
REVERT: B  262 MET cc_start: 0.8317 (OUTLIER) cc_final: 0.7756 (ptm)
REVERT: S   46 GLU cc_start: 0.8275 (tt0) cc_final: 0.7853 (tt0)
REVERT: A  193 ASP cc_start: 0.8317 (p0) cc_final: 0.7930 (p0)
REVERT: A  240 MET cc_start: 0.6601 (ptt) cc_final: 0.6142 (ptp)
REVERT: A  309 ASP cc_start: 0.8089 (m-30) cc_final: 0.7661 (m-30)
REVERT: R  155 ARG cc_start: 0.5917 (ptm-80) cc_final: 0.5553 (mtp-110)
REVERT: R  165 TYR cc_start: 0.7920 (t80) cc_final: 0.6347 (t80)
REVERT: R  175 VAL cc_start: 0.8347 (m) cc_final: 0.8032 (p)
REVERT: R  298 ILE cc_start: 0.8070 (OUTLIER) cc_final: 0.7812 (mp)
  outliers start: 18
  outliers final: 5
  residues processed: 154
  average time/residue: 1.5900
  time to fit residues: 257.9665
Evaluate side-chains
  137 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 129
  time to evaluate  : 0.879 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   52 ARG
Chi-restraints excluded: chain B residue  262 MET
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 R residue  298 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 46 optimal weight:   10.0000
   chunk 96 optimal weight:    0.0020
   chunk 67 optimal weight:   10.0000
   chunk 57 optimal weight:    8.9990
   chunk 13 optimal weight:    7.9990
   chunk 81 optimal weight:    0.8980
   chunk 0 optimal weight:   40.0000
   chunk 61 optimal weight:    0.0670
   chunk 105 optimal weight:    0.9990
   chunk 33 optimal weight:   30.0000
   chunk 59 optimal weight:    8.9990
   overall best weight:    1.9930

-------------------------------------------------------------------------------
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
A 306 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4142 r_free = 0.4142 target = 0.154269 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3750 r_free = 0.3750 target = 0.120262 restraints weight = 27288.590|
|-----------------------------------------------------------------------------|
r_work (start): 0.3653 rms_B_bonded: 3.05
r_work: 0.3489 rms_B_bonded: 2.74 restraints_weight: 0.5000
r_work: 0.3314 rms_B_bonded: 4.66 restraints_weight: 0.2500
r_work (final): 0.3314
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3320
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3320 r_free = 0.3320    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3320 r_free = 0.3320    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3320
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7661
moved from start:          0.2358

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.047   8763  Z= 0.319
  Angle     :  0.646  11.000  11910  Z= 0.327
  Chirality :  0.044   0.151   1393
  Planarity :  0.005   0.065   1491
  Dihedral  :  4.865  43.362   1210
  Min Nonbonded Distance : 2.511

Molprobity Statistics.
  All-atom Clashscore : 6.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.21 %
    Favored  : 95.79 %
  Rotamer:
    Outliers :  2.09 %
    Allowed  : 17.07 %
    Favored  : 80.84 %
  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:  0.67 (0.26), residues: 1095
  helix:  1.22 (0.27), residues: 383
  sheet:  0.64 (0.30), residues: 294
  loop : -0.32 (0.31), residues: 418

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP R 104 
 HIS   0.005   0.001   HIS R 251 
 PHE   0.015   0.002   PHE R 177 
 TYR   0.014   0.002   TYR B  59 
 ARG   0.009   0.001   ARG B 129 

*********************** 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
  153 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 134
  time to evaluate  : 0.879 
Fit side-chains
   revert: symmetry clash
REVERT: B   52 ARG cc_start: 0.8680 (OUTLIER) cc_final: 0.8383 (mtp85)
REVERT: B   78 LYS cc_start: 0.8435 (OUTLIER) cc_final: 0.7828 (mptm)
REVERT: B  254 ASP cc_start: 0.8092 (t0) cc_final: 0.7475 (t0)
REVERT: B  259 GLN cc_start: 0.8409 (tt0) cc_final: 0.7707 (mt0)
REVERT: B  262 MET cc_start: 0.8484 (OUTLIER) cc_final: 0.7896 (ptm)
REVERT: S   46 GLU cc_start: 0.8410 (tt0) cc_final: 0.8029 (tt0)
REVERT: A  240 MET cc_start: 0.6534 (ptt) cc_final: 0.6118 (ptp)
REVERT: A  248 LYS cc_start: 0.8294 (mppt) cc_final: 0.7854 (mtmm)
REVERT: A  306 GLN cc_start: 0.7200 (mt0) cc_final: 0.6973 (mt0)
REVERT: A  309 ASP cc_start: 0.8127 (m-30) cc_final: 0.7686 (m-30)
REVERT: R  155 ARG cc_start: 0.6031 (ptm-80) cc_final: 0.5608 (mtp-110)
REVERT: R  165 TYR cc_start: 0.8209 (t80) cc_final: 0.7739 (t80)
REVERT: R  175 VAL cc_start: 0.8482 (m) cc_final: 0.8092 (p)
REVERT: R  178 ARG cc_start: 0.8151 (OUTLIER) cc_final: 0.7403 (mmp80)
REVERT: R  240 ARG cc_start: 0.7891 (OUTLIER) cc_final: 0.6900 (ptp90)
REVERT: R  259 ASP cc_start: 0.7349 (m-30) cc_final: 0.7130 (t0)
REVERT: R  298 ILE cc_start: 0.8248 (OUTLIER) cc_final: 0.7904 (mp)
  outliers start: 19
  outliers final: 7
  residues processed: 142
  average time/residue: 1.7376
  time to fit residues: 258.7868
Evaluate side-chains
  147 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 134
  time to evaluate  : 0.929 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   52 ARG
Chi-restraints excluded: chain B residue   61 MET
Chi-restraints excluded: chain B residue   78 LYS
Chi-restraints excluded: chain B residue  262 MET
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 R residue   89 ILE
Chi-restraints excluded: chain R residue  178 ARG
Chi-restraints excluded: chain R residue  240 ARG
Chi-restraints excluded: chain R residue  298 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 10 optimal weight:    0.5980
   chunk 56 optimal weight:    7.9990
   chunk 102 optimal weight:    2.9990
   chunk 96 optimal weight:    0.7980
   chunk 106 optimal weight:    1.9990
   chunk 19 optimal weight:    4.9990
   chunk 45 optimal weight:    6.9990
   chunk 99 optimal weight:    0.9990
   chunk 20 optimal weight:    2.9990
   chunk 2 optimal weight:    0.0980
   chunk 82 optimal weight:    0.8980
   overall best weight:    0.6782

-------------------------------------------------------------------------------
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 = 0.4196 r_free = 0.4196 target = 0.150482 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3820 r_free = 0.3820 target = 0.118177 restraints weight = 25990.291|
|-----------------------------------------------------------------------------|
r_work (start): 0.3739 rms_B_bonded: 3.31
r_work: 0.3525 rms_B_bonded: 2.98 restraints_weight: 0.5000
r_work: 0.3358 rms_B_bonded: 4.97 restraints_weight: 0.2500
r_work (final): 0.3358
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3367
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3367 r_free = 0.3367    target_work(ls_wunit_k1) = 0.093         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3367 r_free = 0.3367    target_work(ls_wunit_k1) = 0.093         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3367
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7679
moved from start:          0.2415

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   8763  Z= 0.174
  Angle     :  0.565   8.677  11910  Z= 0.289
  Chirality :  0.041   0.143   1393
  Planarity :  0.005   0.060   1491
  Dihedral  :  4.352  33.600   1210
  Min Nonbonded Distance : 2.533

Molprobity Statistics.
  All-atom Clashscore : 6.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.30 %
    Favored  : 96.70 %
  Rotamer:
    Outliers :  2.20 %
    Allowed  : 17.40 %
    Favored  : 80.40 %
  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:  0.90 (0.26), residues: 1095
  helix:  1.53 (0.27), residues: 389
  sheet:  0.69 (0.31), residues: 292
  loop : -0.29 (0.32), residues: 414

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP B 169 
 HIS   0.004   0.001   HIS A 188 
 PHE   0.021   0.001   PHE R 263 
 TYR   0.011   0.001   TYR S 190 
 ARG   0.009   0.001   ARG B 129 

*********************** 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
  158 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 138
  time to evaluate  : 0.994 
Fit side-chains
   revert: symmetry clash
REVERT: B   52 ARG cc_start: 0.8724 (OUTLIER) cc_final: 0.8469 (mtp85)
REVERT: B  201 SER cc_start: 0.8592 (m) cc_final: 0.8328 (p)
REVERT: B  212 ASP cc_start: 0.8322 (t70) cc_final: 0.7895 (t0)
REVERT: B  254 ASP cc_start: 0.8099 (t0) cc_final: 0.7699 (t0)
REVERT: B  259 GLN cc_start: 0.8411 (tt0) cc_final: 0.7562 (mt0)
REVERT: B  262 MET cc_start: 0.8454 (OUTLIER) cc_final: 0.8035 (ptm)
REVERT: S   46 GLU cc_start: 0.8564 (tt0) cc_final: 0.8217 (tt0)
REVERT: A  240 MET cc_start: 0.6510 (ptt) cc_final: 0.6093 (ptp)
REVERT: A  248 LYS cc_start: 0.8368 (mppt) cc_final: 0.7928 (mtmm)
REVERT: A  306 GLN cc_start: 0.7223 (mt0) cc_final: 0.6964 (mt0)
REVERT: A  309 ASP cc_start: 0.8174 (m-30) cc_final: 0.7741 (m-30)
REVERT: R  155 ARG cc_start: 0.6133 (ptm-80) cc_final: 0.5739 (mtp-110)
REVERT: R  165 TYR cc_start: 0.8108 (t80) cc_final: 0.6596 (t80)
REVERT: R  175 VAL cc_start: 0.8393 (m) cc_final: 0.8082 (p)
REVERT: R  240 ARG cc_start: 0.7950 (OUTLIER) cc_final: 0.6965 (ptp90)
REVERT: R  298 ILE cc_start: 0.8110 (OUTLIER) cc_final: 0.7870 (mp)
REVERT: R  323 MET cc_start: 0.5948 (mmm) cc_final: 0.5350 (mtm)
  outliers start: 20
  outliers final: 6
  residues processed: 149
  average time/residue: 1.5038
  time to fit residues: 236.1811
Evaluate side-chains
  141 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 131
  time to evaluate  : 0.879 
-------------------------------------------------------------------------------
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  262 MET
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 R residue  240 ARG
Chi-restraints excluded: chain R residue  298 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 97 optimal weight:    0.8980
   chunk 61 optimal weight:    0.9990
   chunk 95 optimal weight:    0.6980
   chunk 47 optimal weight:    0.9990
   chunk 90 optimal weight:    0.8980
   chunk 57 optimal weight:    7.9990
   chunk 26 optimal weight:    5.9990
   chunk 104 optimal weight:    0.6980
   chunk 32 optimal weight:    8.9990
   chunk 102 optimal weight:    2.9990
   chunk 74 optimal weight:    6.9990
   overall best weight:    0.8382

-------------------------------------------------------------------------------
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
A 294 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4187 r_free = 0.4187 target = 0.157025 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3824 r_free = 0.3824 target = 0.124248 restraints weight = 27211.150|
|-----------------------------------------------------------------------------|
r_work (start): 0.3699 rms_B_bonded: 3.36
r_work: 0.3514 rms_B_bonded: 3.03 restraints_weight: 0.5000
r_work (final): 0.3514
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3519
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3519 r_free = 0.3519    target_work(ls_wunit_k1) = 0.107         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3519 r_free = 0.3519    target_work(ls_wunit_k1) = 0.107         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3519
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7462
moved from start:          0.2511

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   8763  Z= 0.193
  Angle     :  0.595  11.156  11910  Z= 0.302
  Chirality :  0.041   0.141   1393
  Planarity :  0.005   0.060   1491
  Dihedral  :  4.301  31.890   1210
  Min Nonbonded Distance : 2.491

Molprobity Statistics.
  All-atom Clashscore : 6.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.03 %
    Favored  : 95.97 %
  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:  0.97 (0.26), residues: 1095
  helix:  1.63 (0.27), residues: 388
  sheet:  0.69 (0.31), residues: 292
  loop : -0.25 (0.32), residues: 415

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   0.014   0.001   PHE R 260 
 TYR   0.011   0.001   TYR S 190 
 ARG   0.010   0.001   ARG B 129 

*********************** 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
  152 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 136
  time to evaluate  : 0.756 
Fit side-chains
   revert: symmetry clash
REVERT: B   52 ARG cc_start: 0.8455 (OUTLIER) cc_final: 0.8176 (mtp85)
REVERT: B   78 LYS cc_start: 0.8270 (OUTLIER) cc_final: 0.7688 (mptm)
REVERT: B  170 ASP cc_start: 0.8057 (t70) cc_final: 0.7565 (OUTLIER)
REVERT: B  201 SER cc_start: 0.8455 (m) cc_final: 0.8116 (p)
REVERT: B  212 ASP cc_start: 0.8100 (t70) cc_final: 0.7680 (t0)
REVERT: B  254 ASP cc_start: 0.7847 (t0) cc_final: 0.7510 (t0)
REVERT: B  259 GLN cc_start: 0.8338 (tt0) cc_final: 0.7514 (mt0)
REVERT: B  262 MET cc_start: 0.8208 (OUTLIER) cc_final: 0.7725 (ptm)
REVERT: S   22 CYS cc_start: 0.8179 (OUTLIER) cc_final: 0.7921 (t)
REVERT: S   46 GLU cc_start: 0.8208 (tt0) cc_final: 0.7820 (tt0)
REVERT: S  192 MET cc_start: 0.8812 (ttp) cc_final: 0.8450 (tmm)
REVERT: A  197 LYS cc_start: 0.8448 (mmmm) cc_final: 0.8124 (mmtp)
REVERT: A  240 MET cc_start: 0.6535 (ptt) cc_final: 0.6127 (ptp)
REVERT: A  248 LYS cc_start: 0.8259 (mppt) cc_final: 0.7834 (mtmm)
REVERT: A  283 LEU cc_start: 0.8713 (OUTLIER) cc_final: 0.8486 (tt)
REVERT: A  306 GLN cc_start: 0.7077 (mt0) cc_final: 0.6817 (mt0)
REVERT: A  309 ASP cc_start: 0.8068 (m-30) cc_final: 0.7621 (m-30)
REVERT: R  155 ARG cc_start: 0.5805 (ptm-80) cc_final: 0.5407 (mtp-110)
REVERT: R  165 TYR cc_start: 0.7954 (t80) cc_final: 0.6336 (t80)
REVERT: R  175 VAL cc_start: 0.8305 (m) cc_final: 0.8023 (p)
REVERT: R  240 ARG cc_start: 0.7734 (OUTLIER) cc_final: 0.6761 (ptp90)
REVERT: R  298 ILE cc_start: 0.8009 (OUTLIER) cc_final: 0.7752 (mp)
  outliers start: 16
  outliers final: 6
  residues processed: 143
  average time/residue: 1.6156
  time to fit residues: 242.6764
Evaluate side-chains
  152 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 140
  time to evaluate  : 0.836 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   52 ARG
Chi-restraints excluded: chain B residue   78 LYS
Chi-restraints excluded: chain B residue  112 VAL
Chi-restraints excluded: chain B residue  262 MET
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 R residue  240 ARG
Chi-restraints excluded: chain R residue  298 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 79 optimal weight:    4.9990
   chunk 43 optimal weight:    2.9990
   chunk 107 optimal weight:    0.8980
   chunk 72 optimal weight:    4.9990
   chunk 39 optimal weight:    0.8980
   chunk 52 optimal weight:    0.0470
   chunk 23 optimal weight:    9.9990
   chunk 51 optimal weight:    0.0470
   chunk 2 optimal weight:    1.9990
   chunk 94 optimal weight:    0.5980
   chunk 106 optimal weight:    0.8980
   overall best weight:    0.4976

-------------------------------------------------------------------------------
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
R 112 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4215 r_free = 0.4215 target = 0.151814 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3849 r_free = 0.3849 target = 0.118509 restraints weight = 29602.850|
|-----------------------------------------------------------------------------|
r_work (start): 0.3740 rms_B_bonded: 3.07
r_work: 0.3562 rms_B_bonded: 2.89 restraints_weight: 0.5000
r_work: 0.3403 rms_B_bonded: 4.72 restraints_weight: 0.2500
r_work (final): 0.3403
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3414
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3414 r_free = 0.3414    target_work(ls_wunit_k1) = 0.101         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3414 r_free = 0.3414    target_work(ls_wunit_k1) = 0.101         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3414
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7600
moved from start:          0.2617

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.044   8763  Z= 0.161
  Angle     :  0.569  11.581  11910  Z= 0.288
  Chirality :  0.041   0.141   1393
  Planarity :  0.005   0.059   1491
  Dihedral  :  4.084  29.935   1210
  Min Nonbonded Distance : 2.497

Molprobity Statistics.
  All-atom Clashscore : 5.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.48 %
    Favored  : 96.52 %
  Rotamer:
    Outliers :  1.43 %
    Allowed  : 18.83 %
    Favored  : 79.74 %
  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:  1.08 (0.26), residues: 1095
  helix:  1.78 (0.27), residues: 394
  sheet:  0.69 (0.31), residues: 287
  loop : -0.22 (0.32), residues: 414

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP B 169 
 HIS   0.004   0.001   HIS R 112 
 PHE   0.026   0.001   PHE R 263 
 TYR   0.011   0.001   TYR S 190 
 ARG   0.010   0.001   ARG B 214 

********************** 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
  156 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 143
  time to evaluate  : 0.946 
Fit side-chains
   revert: symmetry clash
REVERT: B   52 ARG cc_start: 0.8643 (OUTLIER) cc_final: 0.8379 (mtp85)
REVERT: B   78 LYS cc_start: 0.8433 (OUTLIER) cc_final: 0.7860 (mptm)
REVERT: B  170 ASP cc_start: 0.8112 (t70) cc_final: 0.7674 (OUTLIER)
REVERT: B  201 SER cc_start: 0.8497 (m) cc_final: 0.8247 (p)
REVERT: B  212 ASP cc_start: 0.8212 (t70) cc_final: 0.7803 (t0)
REVERT: B  254 ASP cc_start: 0.7959 (t0) cc_final: 0.7648 (t0)
REVERT: B  259 GLN cc_start: 0.8337 (tt0) cc_final: 0.7546 (mt0)
REVERT: B  262 MET cc_start: 0.8269 (ttp) cc_final: 0.7977 (ptm)
REVERT: S   22 CYS cc_start: 0.8311 (OUTLIER) cc_final: 0.7999 (t)
REVERT: S   46 GLU cc_start: 0.8433 (tt0) cc_final: 0.8124 (tt0)
REVERT: S  192 MET cc_start: 0.8878 (ttp) cc_final: 0.8487 (tmm)
REVERT: A  186 GLU cc_start: 0.7867 (tm-30) cc_final: 0.7662 (tm-30)
REVERT: A  197 LYS cc_start: 0.8592 (mmmm) cc_final: 0.8293 (mmmm)
REVERT: A  240 MET cc_start: 0.6511 (ptt) cc_final: 0.6057 (ptp)
REVERT: A  248 LYS cc_start: 0.8343 (OUTLIER) cc_final: 0.7924 (mtmm)
REVERT: A  306 GLN cc_start: 0.7187 (mt0) cc_final: 0.6916 (mt0)
REVERT: A  309 ASP cc_start: 0.8164 (m-30) cc_final: 0.7725 (m-30)
REVERT: R  155 ARG cc_start: 0.5895 (ptm-80) cc_final: 0.5518 (mtp-110)
REVERT: R  165 TYR cc_start: 0.8116 (t80) cc_final: 0.6531 (t80)
REVERT: R  175 VAL cc_start: 0.8417 (m) cc_final: 0.8146 (p)
REVERT: R  240 ARG cc_start: 0.7799 (OUTLIER) cc_final: 0.6782 (ptp90)
REVERT: R  298 ILE cc_start: 0.8059 (OUTLIER) cc_final: 0.7805 (mp)
  outliers start: 13
  outliers final: 6
  residues processed: 150
  average time/residue: 1.5930
  time to fit residues: 252.3792
Evaluate side-chains
  144 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 133
  time to evaluate  : 1.273 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   52 ARG
Chi-restraints excluded: chain B residue   78 LYS
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 A residue  248 LYS
Chi-restraints excluded: chain A residue  333 ASP
Chi-restraints excluded: chain R residue  240 ARG
Chi-restraints excluded: chain R residue  298 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 28 optimal weight:    3.9990
   chunk 4 optimal weight:    7.9990
   chunk 88 optimal weight:    0.9990
   chunk 31 optimal weight:    0.9990
   chunk 56 optimal weight:    7.9990
   chunk 63 optimal weight:    0.9990
   chunk 36 optimal weight:    5.9990
   chunk 1 optimal weight:    9.9990
   chunk 106 optimal weight:    1.9990
   chunk 0 optimal weight:   30.0000
   chunk 103 optimal weight:    0.9980
   overall best weight:    1.1988

-------------------------------------------------------------------------------
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 = 0.4192 r_free = 0.4192 target = 0.150052 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3813 r_free = 0.3813 target = 0.116163 restraints weight = 30408.396|
|-----------------------------------------------------------------------------|
r_work (start): 0.3704 rms_B_bonded: 3.22
r_work: 0.3525 rms_B_bonded: 2.88 restraints_weight: 0.5000
r_work: 0.3356 rms_B_bonded: 4.79 restraints_weight: 0.2500
r_work (final): 0.3356
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3368
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3368 r_free = 0.3368    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 = 0.3368 r_free = 0.3368    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3368
-------------------------------------------------------------------------------
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      :  0.004   0.046   8763  Z= 0.229
  Angle     :  0.612  11.897  11910  Z= 0.309
  Chirality :  0.042   0.143   1393
  Planarity :  0.005   0.059   1491
  Dihedral  :  4.279  30.150   1210
  Min Nonbonded Distance : 2.471

Molprobity Statistics.
  All-atom Clashscore : 6.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.94 %
    Favored  : 96.06 %
  Rotamer:
    Outliers :  1.65 %
    Allowed  : 18.61 %
    Favored  : 79.74 %
  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:  1.00 (0.26), residues: 1095
  helix:  1.62 (0.27), residues: 393
  sheet:  0.74 (0.31), residues: 286
  loop : -0.23 (0.32), residues: 416

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP B  63 
 HIS   0.004   0.001   HIS A 188 
 PHE   0.011   0.001   PHE R 260 
 TYR   0.010   0.001   TYR S 190 
 ARG   0.010   0.001   ARG R 254 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 10640.80 seconds
wall clock time: 184 minutes 24.38 seconds (11064.38 seconds total)