Starting phenix.real_space_refine
on Tue Apr 29 08:28:43 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9b65_44247/04_2025/9b65_44247_trim.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9b65_44247/04_2025/9b65_44247.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.03
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9b65_44247/04_2025/9b65_44247.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9b65_44247/04_2025/9b65_44247.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9b65_44247/04_2025/9b65_44247_trim.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9b65_44247/04_2025/9b65_44247_trim.cif"
  }
  resolution = 3.03
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.001
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      60      5.16       5
     C    5416      2.51       5
     N    1448      2.21       5
     O    1538      1.98       5
     F       1      1.80       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 22 residue(s): 0.05s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib"
  Total number of atoms: 8463
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 1659
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 218, 1659
          Classifications: {'peptide': 218}
          Incomplete info: {'truncation_to_alanine': 26}
          Link IDs: {'PTRANS': 2, 'TRANS': 215}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 97
          Unresolved non-hydrogen angles: 115
          Unresolved non-hydrogen dihedrals: 79
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLU:plan': 10, 'ARG:plan': 1, 'ASP:plan': 6}
          Unresolved non-hydrogen planarities: 63
    Chain: "B"
      Number of atoms: 2573
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 338, 2573
          Classifications: {'peptide': 338}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 8}
          Link IDs: {'PTRANS': 5, 'TRANS': 332}
          Unresolved non-hydrogen bonds: 28
          Unresolved non-hydrogen angles: 35
          Unresolved non-hydrogen dihedrals: 21
          Planarities with less than four sites: {'GLU:plan': 3, 'ASN:plan1': 2, 'ARG:plan': 1, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 26
    Chain: "C"
      Number of atoms: 438
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 57, 438
          Classifications: {'peptide': 57}
          Link IDs: {'PTRANS': 4, 'TRANS': 52}
    Chain: "R"
      Number of atoms: 2013
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 266, 2013
          Classifications: {'peptide': 266}
          Incomplete info: {'truncation_to_alanine': 33}
          Link IDs: {'CIS': 1, 'PTRANS': 8, 'TRANS': 256}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 120
          Unresolved non-hydrogen angles: 147
          Unresolved non-hydrogen dihedrals: 97
          Unresolved non-hydrogen chiralities: 11
          Planarities with less than four sites: {'GLN:plan1': 3, 'ASN:plan1': 3, 'ASP:plan': 1, 'PHE:plan': 2, 'GLU:plan': 1, 'ARG:plan': 4}
          Unresolved non-hydrogen planarities: 60
    Chain: "S"
      Number of atoms: 1751
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 232, 1751
          Classifications: {'peptide': 232}
          Incomplete info: {'truncation_to_alanine': 11}
          Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 221}
          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': 5, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 23
    Chain: "R"
      Number of atoms: 29
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 29
          Classifications: {'peptide': 1}
  Time building chain proxies: 5.40, per 1000 atoms: 0.64
  Number of scatterers: 8463
  At special positions: 0
  Unit cell: (103.96, 119.6, 104.88, 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      60     16.00
     F       1      9.00
     O    1538      8.00
     N    1448      7.00
     C    5416      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS S 147 " - pdb=" SG  CYS S 217 " distance=2.02

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=1, symmetry=0
  Number of additional bonds: simple=1, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 2.08
  Conformation dependent library (CDL) restraints added in 945.8 milliseconds
  

  2182 Ramachandran restraints generated.
    1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2084

  Finding SS restraints...
    Secondary structure from input PDB file:
      33 helices and 14 sheets defined
      32.3% alpha, 23.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.34
  Creating SS restraints...
    Processing helix  chain 'A' and resid 6 through 29
      removed outlier: 3.510A  pdb=" N   ALA A  11 " --> pdb=" O   ALA A   7 " (cutoff:3.500A)
      removed outlier: 3.517A  pdb=" N   VAL A  13 " --> pdb=" O   ASP A   9 " (cutoff:3.500A)
      removed outlier: 3.588A  pdb=" N   ASN A  22 " --> pdb=" O   MET A  18 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 45 through 50
      removed outlier: 3.626A  pdb=" N   VAL A  50 " --> pdb=" O   LYS A  46 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 207 through 212
      removed outlier: 4.032A  pdb=" N   TRP A 211 " --> pdb=" O   GLU A 207 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 213 through 216
    Processing helix  chain 'A' and resid 228 through 230
      No H-bonds generated for 'chain 'A' and resid 228 through 230'
    Processing helix  chain 'A' and resid 242 through 254
      removed outlier: 3.566A  pdb=" N   LYS A 248 " --> pdb=" O   HIS A 244 " (cutoff:3.500A)
      removed outlier: 3.583A  pdb=" N   SER A 252 " --> pdb=" O   LYS A 248 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 272 through 281
      removed outlier: 3.531A  pdb=" N   GLU A 276 " --> pdb=" O   ASP A 272 " (cutoff:3.500A)
      removed outlier: 3.700A  pdb=" N   ILE A 278 " --> pdb=" O   PHE A 274 " (cutoff:3.500A)
      removed outlier: 3.630A  pdb=" N   LYS A 280 " --> pdb=" O   GLU A 276 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 296 through 311
      removed outlier: 3.596A  pdb=" N   ALA A 300 " --> pdb=" O   TYR A 296 " (cutoff:3.500A)
      removed outlier: 3.886A  pdb=" N   ALA A 301 " --> pdb=" O   GLU A 297 " (cutoff:3.500A)
      removed outlier: 3.706A  pdb=" N   ILE A 303 " --> pdb=" O   ALA A 299 " (cutoff:3.500A)
      removed outlier: 3.566A  pdb=" N   GLU A 308 " --> pdb=" O   GLN A 304 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 329 through 351
      removed outlier: 3.892A  pdb=" N   GLN A 333 " --> pdb=" O   THR A 329 " (cutoff:3.500A)
      removed outlier: 3.728A  pdb=" N   ASP A 341 " --> pdb=" O   ASP A 337 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 4 through 8
      removed outlier: 3.619A  pdb=" N   ARG B   8 " --> pdb=" O   LEU B   4 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 4 through 8'
    Processing helix  chain 'B' and resid 10 through 25
      removed outlier: 4.044A  pdb=" N   ASN B  16 " --> pdb=" O   GLU B  12 " (cutoff:3.500A)
      removed outlier: 3.612A  pdb=" N   ARG B  19 " --> pdb=" O   LYS B  15 " (cutoff:3.500A)
      removed outlier: 3.878A  pdb=" N   LYS B  23 " --> pdb=" O   ARG B  19 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 29 through 34
    Processing helix  chain 'C' and resid 8 through 22
      removed outlier: 3.743A  pdb=" N   VAL C  16 " --> pdb=" O   ALA C  12 " (cutoff:3.500A)
      removed outlier: 3.519A  pdb=" N   GLU C  17 " --> pdb=" O   ARG C  13 " (cutoff:3.500A)
      removed outlier: 3.749A  pdb=" N   MET C  21 " --> pdb=" O   GLU C  17 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 29 through 42
      removed outlier: 3.921A  pdb=" N   ASP C  36 " --> pdb=" O   LYS C  32 " (cutoff:3.500A)
      removed outlier: 3.697A  pdb=" N   LEU C  37 " --> pdb=" O   ALA C  33 " (cutoff:3.500A)
      removed outlier: 4.053A  pdb=" N   TYR C  40 " --> pdb=" O   ASP C  36 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 112 through 114
      No H-bonds generated for 'chain 'R' and resid 112 through 114'
    Processing helix  chain 'R' and resid 115 through 121
      removed outlier: 3.538A  pdb=" N   ALA R 120 " --> pdb=" O   GLN R 116 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 121 through 127
      removed outlier: 3.753A  pdb=" N   THR R 125 " --> pdb=" O   VAL R 121 " (cutoff:3.500A)
      removed outlier: 3.692A  pdb=" N   GLY R 127 " --> pdb=" O   SER R 123 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 133 through 138
      removed outlier: 3.794A  pdb=" N   LEU R 138 " --> pdb=" O   ASN R 134 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 139 through 142
    Processing helix  chain 'R' and resid 154 through 172
      removed outlier: 3.809A  pdb=" N   LEU R 164 " --> pdb=" O   ALA R 160 " (cutoff:3.500A)
      removed outlier: 3.658A  pdb=" N   VAL R 171 " --> pdb=" O   SER R 167 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 172 through 177
    Processing helix  chain 'R' and resid 189 through 220
      removed outlier: 3.514A  pdb=" N   VAL R 204 " --> pdb=" O   PHE R 200 " (cutoff:3.500A)
      removed outlier: 3.560A  pdb=" N   ARG R 214 " --> pdb=" O   THR R 210 " (cutoff:3.500A)
      removed outlier: 3.516A  pdb=" N   TYR R 215 " --> pdb=" O   ALA R 211 " (cutoff:3.500A)
      removed outlier: 3.842A  pdb=" N   ILE R 216 " --> pdb=" O   ILE R 212 " (cutoff:3.500A)
      removed outlier: 3.823A  pdb=" N   ILE R 218 " --> pdb=" O   ARG R 214 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 234 through 247
      removed outlier: 4.151A  pdb=" N   ILE R 245 " --> pdb=" O   TRP R 241 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 275 through 287
      removed outlier: 3.755A  pdb=" N   ILE R 280 " --> pdb=" O   LEU R 276 " (cutoff:3.500A)
      removed outlier: 4.099A  pdb=" N   VAL R 285 " --> pdb=" O   GLY R 281 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 290 through 311
      removed outlier: 3.675A  pdb=" N   TYR R 294 " --> pdb=" O   ILE R 290 " (cutoff:3.500A)
      removed outlier: 3.796A  pdb=" N   ILE R 309 " --> pdb=" O   ALA R 305 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 341 through 357
      removed outlier: 5.321A  pdb=" N   LEU R 347 " --> pdb=" O   LYS R 343 " (cutoff:3.500A)
      removed outlier: 3.713A  pdb=" N   ILE R 348 " --> pdb=" O   THR R 344 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 357 through 366
      removed outlier: 3.874A  pdb=" N   ASP R 366 " --> pdb=" O   ILE R 362 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 378 through 383
    Processing helix  chain 'R' and resid 384 through 397
      removed outlier: 3.994A  pdb=" N   SER R 390 " --> pdb=" O   CYS R 386 " (cutoff:3.500A)
      removed outlier: 3.658A  pdb=" N   THR R 391 " --> pdb=" O   LEU R 387 " (cutoff:3.500A)
      removed outlier: 3.617A  pdb=" N   VAL R 392 " --> pdb=" O   LEU R 388 " (cutoff:3.500A)
      Proline residue:  R 394  - end of helix
    Processing helix  chain 'S' and resid 28 through 32
    Processing helix  chain 'S' and resid 53 through 56
      removed outlier: 4.097A  pdb=" N   GLY S  56 " --> pdb=" O   SER S  53 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'S' and resid 53 through 56'
    Processing helix  chain 'S' and resid 62 through 65
      removed outlier: 3.777A  pdb=" N   LYS S  65 " --> pdb=" O   ASP S  62 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'S' and resid 62 through 65'
    Processing helix  chain 'S' and resid 87 through 91
    Processing sheet with id=AA1, first strand: chain 'A' and resid 188 through 190
      removed outlier: 5.888A  pdb=" N   VAL A  34 " --> pdb=" O   LYS A 197 " (cutoff:3.500A)
      removed outlier: 7.274A  pdb=" N   PHE A 199 " --> pdb=" O   VAL A  34 " (cutoff:3.500A)
      removed outlier: 6.564A  pdb=" N   LEU A  36 " --> pdb=" O   PHE A 199 " (cutoff:3.500A)
      removed outlier: 3.836A  pdb=" N   ALA A 220 " --> pdb=" O   LYS A  35 " (cutoff:3.500A)
      removed outlier: 6.780A  pdb=" N   PHE A 267 " --> pdb=" O   ILE A 221 " (cutoff:3.500A)
      removed outlier: 6.213A  pdb=" N   PHE A 223 " --> pdb=" O   PHE A 267 " (cutoff:3.500A)
      removed outlier: 7.249A  pdb=" N   ASN A 269 " --> pdb=" O   PHE A 223 " (cutoff:3.500A)
      removed outlier: 6.817A  pdb=" N   VAL A 225 " --> pdb=" O   ASN A 269 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 52
      removed outlier: 5.840A  pdb=" N   THR B  47 " --> pdb=" O   ASN B 340 " (cutoff:3.500A)
      removed outlier: 6.790A  pdb=" N   ASN B 340 " --> pdb=" O   THR B  47 " (cutoff:3.500A)
      removed outlier: 3.560A  pdb=" N   CYS B 317 " --> pdb=" O   GLY B 330 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63
      removed outlier: 4.400A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 6.437A  pdb=" N   ASP B  83 " --> pdb=" O   LYS B  89 " (cutoff:3.500A)
      removed outlier: 5.916A  pdb=" N   LYS B  89 " --> pdb=" O   ASP B  83 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105
      removed outlier: 3.892A  pdb=" N   GLY B 116 " --> pdb=" O   ILE B 120 " (cutoff:3.500A)
      removed outlier: 4.735A  pdb=" N   ILE B 120 " --> pdb=" O   GLY B 116 " (cutoff:3.500A)
      removed outlier: 6.214A  pdb=" N   ASN B 125 " --> pdb=" O   VAL B 135 " (cutoff:3.500A)
      removed outlier: 6.041A  pdb=" N   VAL B 135 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 153
      removed outlier: 3.574A  pdb=" N   CYS B 148 " --> pdb=" O   SER B 160 " (cutoff:3.500A)
      removed outlier: 6.362A  pdb=" N   GLN B 156 " --> pdb=" O   LEU B 152 " (cutoff:3.500A)
      removed outlier: 3.851A  pdb=" N   THR B 178 " --> pdb=" O   LEU B 168 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192
      removed outlier: 4.172A  pdb=" N   SER B 207 " --> pdb=" O   ALA B 203 " (cutoff:3.500A)
      removed outlier: 3.501A  pdb=" N   GLN B 220 " --> pdb=" O   LEU B 210 " (cutoff:3.500A)
      removed outlier: 6.906A  pdb=" N   ASP B 212 " --> pdb=" O   CYS B 218 " (cutoff:3.500A)
      removed outlier: 6.385A  pdb=" N   CYS B 218 " --> pdb=" O   ASP B 212 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234
      removed outlier: 6.562A  pdb=" N   CYS B 250 " --> pdb=" O   THR B 263 " (cutoff:3.500A)
      removed outlier: 4.522A  pdb=" N   THR B 263 " --> pdb=" O   CYS B 250 " (cutoff:3.500A)
      removed outlier: 6.463A  pdb=" N   LEU B 252 " --> pdb=" O   LEU B 261 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278
      removed outlier: 6.624A  pdb=" N   CYS B 294 " --> pdb=" O   VAL B 307 " (cutoff:3.500A)
      removed outlier: 4.734A  pdb=" N   VAL B 307 " --> pdb=" O   CYS B 294 " (cutoff:3.500A)
      removed outlier: 6.089A  pdb=" N   VAL B 296 " --> pdb=" O   ALA B 305 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'S' and resid 3 through 7
      removed outlier: 3.587A  pdb=" N   VAL S   5 " --> pdb=" O   SER S  23 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'S' and resid 11 through 12
      removed outlier: 6.754A  pdb=" N   MET S  34 " --> pdb=" O   TYR S  50 " (cutoff:3.500A)
      removed outlier: 4.495A  pdb=" N   TYR S  50 " --> pdb=" O   MET S  34 " (cutoff:3.500A)
      removed outlier: 6.451A  pdb=" N   TRP S  36 " --> pdb=" O   VAL S  48 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'S' and resid 11 through 12
      removed outlier: 3.962A  pdb=" N   PHE S 110 " --> pdb=" O   ARG S  98 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'S' and resid 128 through 129
      removed outlier: 3.594A  pdb=" N   PHE S 200 " --> pdb=" O   CYS S 147 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'S' and resid 182 through 183
      removed outlier: 3.663A  pdb=" N   ASN S 182 " --> pdb=" O   TYR S 178 " (cutoff:3.500A)
      removed outlier: 6.546A  pdb=" N   TRP S 164 " --> pdb=" O   LEU S 176 " (cutoff:3.500A)
      removed outlier: 4.797A  pdb=" N   TYR S 178 " --> pdb=" O   LEU S 162 " (cutoff:3.500A)
      removed outlier: 5.809A  pdb=" N   LEU S 162 " --> pdb=" O   TYR S 178 " (cutoff:3.500A)
      removed outlier: 4.048A  pdb=" N   THR S 226 " --> pdb=" O   GLN S 219 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'S' and resid 182 through 183
      removed outlier: 3.663A  pdb=" N   ASN S 182 " --> pdb=" O   TYR S 178 " (cutoff:3.500A)
      removed outlier: 6.546A  pdb=" N   TRP S 164 " --> pdb=" O   LEU S 176 " (cutoff:3.500A)
      removed outlier: 4.797A  pdb=" N   TYR S 178 " --> pdb=" O   LEU S 162 " (cutoff:3.500A)
      removed outlier: 5.809A  pdb=" N   LEU S 162 " --> pdb=" O   TYR S 178 " (cutoff:3.500A)
      removed outlier: 3.534A  pdb=" N   GLY S 213 " --> pdb=" O   LEU S 233 " (cutoff:3.500A)

    340 hydrogen bonds defined for protein.
    963 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: 2.48

  Time building geometry restraints manager: 2.44 seconds

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

  Histogram of bond lengths:
        1.18 -     1.31: 1340
        1.31 -     1.43: 2408
        1.43 -     1.56: 4805
        1.56 -     1.68: 0
        1.68 -     1.81: 87
  Bond restraints: 8640
  Sorted by residual:
  bond pdb=" N   KCA R 501 "
       pdb=" CAB KCA R 501 "
    ideal  model  delta    sigma   weight residual
    1.345  1.462 -0.117 2.00e-02 2.50e+03 3.41e+01
  bond pdb=" C   KCA R 501 "
       pdb=" OAF KCA R 501 "
    ideal  model  delta    sigma   weight residual
    1.320  1.391 -0.071 2.00e-02 2.50e+03 1.27e+01
  bond pdb=" CAB KCA R 501 "
       pdb=" CAM KCA R 501 "
    ideal  model  delta    sigma   weight residual
    1.476  1.526 -0.050 2.00e-02 2.50e+03 6.26e+00
  bond pdb=" CAG KCA R 501 "
       pdb=" OAF KCA R 501 "
    ideal  model  delta    sigma   weight residual
    1.430  1.392  0.038 2.00e-02 2.50e+03 3.68e+00
  bond pdb=" CAB KCA R 501 "
       pdb=" OAA KCA R 501 "
    ideal  model  delta    sigma   weight residual
    1.223  1.185  0.038 2.00e-02 2.50e+03 3.61e+00
  ... (remaining 8635 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     4.03: 11687
        4.03 -     8.06: 43
        8.06 -    12.09: 1
       12.09 -    16.13: 0
       16.13 -    20.16: 1
  Bond angle restraints: 11732
  Sorted by residual:
  angle pdb=" C   SER R 146 "
        pdb=" N   LEU R 147 "
        pdb=" CA  LEU R 147 "
      ideal   model   delta    sigma   weight residual
     121.70  129.32   -7.62 1.80e+00 3.09e-01 1.79e+01
  angle pdb=" C   HIS R 178 "
        pdb=" N   VAL R 179 "
        pdb=" CA  VAL R 179 "
      ideal   model   delta    sigma   weight residual
     122.77  118.51    4.26 1.05e+00 9.07e-01 1.65e+01
  angle pdb=" N   THR R 130 "
        pdb=" CA  THR R 130 "
        pdb=" C   THR R 130 "
      ideal   model   delta    sigma   weight residual
     113.56  108.27    5.29 1.39e+00 5.18e-01 1.45e+01
  angle pdb=" C   ILE R 271 "
        pdb=" N   ASP R 272 "
        pdb=" CA  ASP R 272 "
      ideal   model   delta    sigma   weight residual
     120.82  126.25   -5.43 1.47e+00 4.63e-01 1.36e+01
  angle pdb=" C   GLU C  58 "
        pdb=" N   ASN C  59 "
        pdb=" CA  ASN C  59 "
      ideal   model   delta    sigma   weight residual
     121.41  101.25   20.16 5.58e+00 3.21e-02 1.30e+01
  ... (remaining 11727 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    25.30: 4997
       25.30 -    50.60: 82
       50.60 -    75.90: 4
       75.90 -   101.20: 1
      101.20 -   126.49: 1
  Dihedral angle restraints: 5085
    sinusoidal: 1861
      harmonic: 3224
  Sorted by residual:
  dihedral pdb=" CA  TYR S 178 "
           pdb=" C   TYR S 178 "
           pdb=" N   ARG S 179 "
           pdb=" CA  ARG S 179 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -136.91  -43.09     0      5.00e+00 4.00e-02 7.43e+01
  dihedral pdb=" CA  HIS R 270 "
           pdb=" C   HIS R 270 "
           pdb=" N   ILE R 271 "
           pdb=" CA  ILE R 271 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -153.89  -26.11     0      5.00e+00 4.00e-02 2.73e+01
  dihedral pdb=" CA  PHE R 174 "
           pdb=" C   PHE R 174 "
           pdb=" N   ILE R 175 "
           pdb=" CA  ILE R 175 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  155.74   24.26     0      5.00e+00 4.00e-02 2.35e+01
  ... (remaining 5082 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.038: 796
       0.038 -    0.075: 407
       0.075 -    0.113: 133
       0.113 -    0.151: 24
       0.151 -    0.188: 3
  Chirality restraints: 1363
  Sorted by residual:
  chirality pdb=" CA  ASP B   5 "
            pdb=" N   ASP B   5 "
            pdb=" C   ASP B   5 "
            pdb=" CB  ASP B   5 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.32    0.19 2.00e-01 2.50e+01 8.86e-01
  chirality pdb=" CG  LEU S 162 "
            pdb=" CB  LEU S 162 "
            pdb=" CD1 LEU S 162 "
            pdb=" CD2 LEU S 162 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.41   -0.18 2.00e-01 2.50e+01 7.98e-01
  chirality pdb=" CA  KCA R 501 "
            pdb=" N   KCA R 501 "
            pdb=" C   KCA R 501 "
            pdb=" CB  KCA R 501 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.47    2.62   -0.16 2.00e-01 2.50e+01 6.11e-01
  ... (remaining 1360 not shown)

  Planarity restraints: 1470
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP S 111 "   -0.019 2.00e-02 2.50e+03   1.84e-02 8.49e+00
        pdb=" CG  TRP S 111 "    0.048 2.00e-02 2.50e+03
        pdb=" CD1 TRP S 111 "   -0.025 2.00e-02 2.50e+03
        pdb=" CD2 TRP S 111 "    0.001 2.00e-02 2.50e+03
        pdb=" NE1 TRP S 111 "    0.001 2.00e-02 2.50e+03
        pdb=" CE2 TRP S 111 "    0.005 2.00e-02 2.50e+03
        pdb=" CE3 TRP S 111 "    0.000 2.00e-02 2.50e+03
        pdb=" CZ2 TRP S 111 "   -0.002 2.00e-02 2.50e+03
        pdb=" CZ3 TRP S 111 "   -0.008 2.00e-02 2.50e+03
        pdb=" CH2 TRP S 111 "   -0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR B  59 "   -0.016 2.00e-02 2.50e+03   1.85e-02 6.83e+00
        pdb=" CG  TYR B  59 "    0.045 2.00e-02 2.50e+03
        pdb=" CD1 TYR B  59 "   -0.017 2.00e-02 2.50e+03
        pdb=" CD2 TYR B  59 "   -0.011 2.00e-02 2.50e+03
        pdb=" CE1 TYR B  59 "    0.003 2.00e-02 2.50e+03
        pdb=" CE2 TYR B  59 "   -0.003 2.00e-02 2.50e+03
        pdb=" CZ  TYR B  59 "   -0.003 2.00e-02 2.50e+03
        pdb=" OH  TYR B  59 "    0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR S  94 "   -0.010 2.00e-02 2.50e+03   1.39e-02 3.84e+00
        pdb=" CG  TYR S  94 "    0.033 2.00e-02 2.50e+03
        pdb=" CD1 TYR S  94 "   -0.016 2.00e-02 2.50e+03
        pdb=" CD2 TYR S  94 "   -0.006 2.00e-02 2.50e+03
        pdb=" CE1 TYR S  94 "    0.004 2.00e-02 2.50e+03
        pdb=" CE2 TYR S  94 "   -0.006 2.00e-02 2.50e+03
        pdb=" CZ  TYR S  94 "   -0.000 2.00e-02 2.50e+03
        pdb=" OH  TYR S  94 "    0.001 2.00e-02 2.50e+03
  ... (remaining 1467 not shown)

  Histogram of nonbonded interaction distances:
        2.00 -     2.58: 101
        2.58 -     3.16: 7596
        3.16 -     3.74: 12648
        3.74 -     4.32: 19767
        4.32 -     4.90: 31492
  Nonbonded interactions: 71604
  Sorted by model distance:
  nonbonded pdb=" OG  SER B  74 "
            pdb=" OD1 ASP B  76 "
     model   vdw
     2.000 3.040
  nonbonded pdb=" OG  SER B 245 "
            pdb=" OD1 ASP B 247 "
     model   vdw
     2.008 3.040
  nonbonded pdb=" OE2 GLU A   8 "
            pdb=" OH  TYR S 163 "
     model   vdw
     2.038 3.040
  nonbonded pdb=" OH  TYR A 320 "
            pdb=" OD2 ASP A 341 "
     model   vdw
     2.047 3.040
  nonbonded pdb=" OG1 THR B 274 "
            pdb=" O   VAL B 315 "
     model   vdw
     2.130 3.040
  ... (remaining 71599 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.950
  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:          0.300
  Check model and map are aligned:         0.060
  Set scattering table:                    0.070
  Process input model:                     22.570
  Find NCS groups from input model:        0.100
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.990
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   28.080
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7605
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      :  0.007   0.117   8642  Z= 0.332
  Angle     :  0.824  20.157  11734  Z= 0.464
  Chirality :  0.048   0.188   1363
  Planarity :  0.004   0.047   1470
  Dihedral  :  9.879 126.494   2998
  Min Nonbonded Distance : 2.000

Molprobity Statistics.
  All-atom Clashscore : 29.36
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  7.61 %
    Favored  : 92.30 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.40 %
    Favored  : 97.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    Cis-general     : 0.09 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.23 (0.22), residues: 1091
  helix: -4.13 (0.17), residues: 314
  sheet: -2.01 (0.29), residues: 262
  loop : -2.22 (0.26), residues: 515

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.048   0.003   TRP S 111 
 HIS   0.014   0.002   HIS S  35 
 PHE   0.029   0.003   PHE A 354 
 TYR   0.045   0.003   TYR B  59 
 ARG   0.008   0.001   ARG B 314 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.26462 (  325)
  hydrogen bonds       : angle      11.14333 (  963)
  SS BOND              : bond        0.00801 (    1)
  SS BOND              : angle       1.14394 (    2)
  covalent geometry    : bond        0.00729 ( 8640)
  covalent geometry    : angle       0.82369 (11732)
  Misc. bond           : bond        0.00184 (    1)

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

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

  2182 Ramachandran restraints generated.
    1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2182 Ramachandran restraints generated.
    1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  195 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 195
  time to evaluate  : 1.030 
Fit side-chains
REVERT: A   17 LYS cc_start: 0.8113 (mttt) cc_final: 0.7686 (mtpt)
REVERT: A   29 LYS cc_start: 0.8429 (ttpp) cc_final: 0.8065 (ttmt)
REVERT: A  200 ASP cc_start: 0.8185 (t70) cc_final: 0.7883 (t0)
REVERT: A  231 ASP cc_start: 0.7871 (t70) cc_final: 0.7558 (t0)
REVERT: A  242 ARG cc_start: 0.4932 (mpt180) cc_final: 0.3666 (ttm-80)
REVERT: A  251 ASP cc_start: 0.8222 (t0) cc_final: 0.7930 (t0)
REVERT: B  155 ASN cc_start: 0.8204 (t0) cc_final: 0.8001 (t0)
REVERT: B  337 LYS cc_start: 0.8526 (mttm) cc_final: 0.8321 (mttt)
REVERT: C   20 LYS cc_start: 0.7604 (mtpp) cc_final: 0.7371 (mtmm)
REVERT: R  226 ARG cc_start: 0.5958 (mtm110) cc_final: 0.5318 (ttp-110)
REVERT: R  240 MET cc_start: 0.5162 (mmp) cc_final: 0.4225 (mmp)
REVERT: S   23 SER cc_start: 0.8653 (m) cc_final: 0.8361 (t)
REVERT: S  142 SER cc_start: 0.8281 (t) cc_final: 0.7843 (p)
REVERT: S  194 SER cc_start: 0.8140 (t) cc_final: 0.7863 (m)
  outliers start: 0
  outliers final: 0
  residues processed: 195
  average time/residue: 0.2695
  time to fit residues: 66.9586
Evaluate side-chains
  159 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 159
  time to evaluate  : 1.112 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 91 optimal weight:    0.5980
   chunk 81 optimal weight:    0.6980
   chunk 45 optimal weight:    0.9980
   chunk 27 optimal weight:    0.6980
   chunk 55 optimal weight:    0.9990
   chunk 43 optimal weight:    0.6980
   chunk 84 optimal weight:    0.9980
   chunk 32 optimal weight:    0.9990
   chunk 51 optimal weight:    0.9980
   chunk 63 optimal weight:    0.7980
   chunk 98 optimal weight:    2.9990
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 333 GLN
B  62 HIS
B  91 HIS
B 110 ASN
B 225 HIS
B 230 ASN
** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 266 HIS
B 295 ASN
S  39 GLN

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3866 r_free = 0.3866 target = 0.170598 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3214 r_free = 0.3214 target = 0.115116 restraints weight = 9122.920|
|-----------------------------------------------------------------------------|
r_work (start): 0.3209 rms_B_bonded: 2.30
r_work: 0.3061 rms_B_bonded: 2.92 restraints_weight: 0.5000
r_work: 0.2911 rms_B_bonded: 4.66 restraints_weight: 0.2500
r_work (final): 0.2911
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7681
moved from start:          0.2175

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   8642  Z= 0.178
  Angle     :  0.692  15.280  11734  Z= 0.363
  Chirality :  0.047   0.166   1363
  Planarity :  0.005   0.051   1470
  Dihedral  :  7.248 122.809   1211
  Min Nonbonded Distance : 2.443

Molprobity Statistics.
  All-atom Clashscore : 10.07
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  4.95 %
    Favored  : 94.96 %
  Rotamer:
    Outliers :  2.05 %
    Allowed  :  7.08 %
    Favored  : 90.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    Cis-general     : 0.09 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.39 (0.23), residues: 1091
  helix: -3.09 (0.21), residues: 342
  sheet: -1.66 (0.27), residues: 280
  loop : -1.73 (0.28), residues: 469

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP B  82 
 HIS   0.005   0.001   HIS B 225 
 PHE   0.021   0.002   PHE A 354 
 TYR   0.027   0.002   TYR B  59 
 ARG   0.007   0.001   ARG R 220 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04690 (  325)
  hydrogen bonds       : angle       6.11546 (  963)
  SS BOND              : bond        0.00703 (    1)
  SS BOND              : angle       1.00267 (    2)
  covalent geometry    : bond        0.00400 ( 8640)
  covalent geometry    : angle       0.69184 (11732)
  Misc. bond           : bond        0.00051 (    1)

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

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

  2182 Ramachandran restraints generated.
    1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2182 Ramachandran restraints generated.
    1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  197 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 179
  time to evaluate  : 0.865 
Fit side-chains
   revert: symmetry clash
REVERT: A   17 LYS cc_start: 0.8155 (mttt) cc_final: 0.7641 (mtpt)
REVERT: A   18 MET cc_start: 0.8717 (ttm) cc_final: 0.8408 (ttm)
REVERT: A   29 LYS cc_start: 0.8331 (ttpp) cc_final: 0.7834 (ttmt)
REVERT: A  231 ASP cc_start: 0.7951 (t70) cc_final: 0.7595 (t0)
REVERT: A  242 ARG cc_start: 0.4599 (mpt180) cc_final: 0.3239 (ttm-80)
REVERT: A  243 MET cc_start: 0.7961 (tpp) cc_final: 0.7421 (tpp)
REVERT: A  244 HIS cc_start: 0.7656 (OUTLIER) cc_final: 0.7312 (m170)
REVERT: A  247 MET cc_start: 0.8154 (mtp) cc_final: 0.7800 (mtt)
REVERT: A  251 ASP cc_start: 0.8416 (t0) cc_final: 0.7925 (t0)
REVERT: A  306 GLN cc_start: 0.7820 (mm-40) cc_final: 0.7557 (mm-40)
REVERT: A  308 GLU cc_start: 0.7512 (OUTLIER) cc_final: 0.6801 (mp0)
REVERT: B   96 ARG cc_start: 0.8751 (mtt-85) cc_final: 0.8491 (mtt-85)
REVERT: B  155 ASN cc_start: 0.8228 (t0) cc_final: 0.7739 (t0)
REVERT: B  197 ARG cc_start: 0.7953 (mtm110) cc_final: 0.7475 (mtt90)
REVERT: B  340 ASN cc_start: 0.8750 (t0) cc_final: 0.8548 (t0)
REVERT: C   20 LYS cc_start: 0.7795 (mtpp) cc_final: 0.7495 (mtmm)
REVERT: R  109 MET cc_start: 0.3735 (pmt) cc_final: 0.3522 (pmm)
REVERT: R  278 PHE cc_start: 0.5973 (t80) cc_final: 0.5739 (t80)
REVERT: R  356 TRP cc_start: 0.7236 (m100) cc_final: 0.6385 (m100)
REVERT: S   23 SER cc_start: 0.8590 (m) cc_final: 0.8252 (t)
REVERT: S  113 GLN cc_start: 0.8122 (mm110) cc_final: 0.7886 (mm-40)
REVERT: S  171 GLN cc_start: 0.8484 (mm-40) cc_final: 0.8009 (mt0)
  outliers start: 18
  outliers final: 8
  residues processed: 185
  average time/residue: 0.3055
  time to fit residues: 74.6531
Evaluate side-chains
  169 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 159
  time to evaluate  : 1.365 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  195 HIS
Chi-restraints excluded: chain A residue  244 HIS
Chi-restraints excluded: chain A residue  305 CYS
Chi-restraints excluded: chain A residue  308 GLU
Chi-restraints excluded: chain C residue   28 ILE
Chi-restraints excluded: chain R residue  218 ILE
Chi-restraints excluded: chain R residue  222 LEU
Chi-restraints excluded: chain R residue  308 MET
Chi-restraints excluded: chain R residue  351 VAL
Chi-restraints excluded: chain S residue    7 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 63 optimal weight:    3.9990
   chunk 76 optimal weight:    0.6980
   chunk 71 optimal weight:    1.9990
   chunk 58 optimal weight:    0.7980
   chunk 80 optimal weight:    0.5980
   chunk 102 optimal weight:    0.7980
   chunk 35 optimal weight:    1.9990
   chunk 30 optimal weight:    0.9990
   chunk 98 optimal weight:    0.4980
   chunk 7 optimal weight:    3.9990
   chunk 33 optimal weight:    0.7980
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 269 ASN
** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3838 r_free = 0.3838 target = 0.167830 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3183 r_free = 0.3183 target = 0.112532 restraints weight = 9425.334|
|-----------------------------------------------------------------------------|
r_work (start): 0.3176 rms_B_bonded: 2.27
r_work: 0.3035 rms_B_bonded: 2.91 restraints_weight: 0.5000
r_work: 0.2888 rms_B_bonded: 4.66 restraints_weight: 0.2500
r_work (final): 0.2888
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7725
moved from start:          0.2572

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   8642  Z= 0.165
  Angle     :  0.644  11.919  11734  Z= 0.334
  Chirality :  0.045   0.168   1363
  Planarity :  0.004   0.050   1470
  Dihedral  :  6.865 118.415   1211
  Min Nonbonded Distance : 2.451

Molprobity Statistics.
  All-atom Clashscore : 7.79
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  4.49 %
    Favored  : 95.42 %
  Rotamer:
    Outliers :  2.40 %
    Allowed  : 11.19 %
    Favored  : 86.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    Cis-general     : 0.09 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.59 (0.24), residues: 1091
  helix: -2.32 (0.24), residues: 334
  sheet: -1.29 (0.28), residues: 277
  loop : -1.32 (0.29), residues: 480

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP B  82 
 HIS   0.003   0.001   HIS R 154 
 PHE   0.016   0.001   PHE A 354 
 TYR   0.026   0.002   TYR S 178 
 ARG   0.004   0.000   ARG B 197 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04189 (  325)
  hydrogen bonds       : angle       5.58861 (  963)
  SS BOND              : bond        0.00481 (    1)
  SS BOND              : angle       1.02543 (    2)
  covalent geometry    : bond        0.00365 ( 8640)
  covalent geometry    : angle       0.64388 (11732)
  Misc. bond           : bond        0.00041 (    1)

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

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

  2182 Ramachandran restraints generated.
    1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2182 Ramachandran restraints generated.
    1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  192 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 171
  time to evaluate  : 0.834 
Fit side-chains
REVERT: A   17 LYS cc_start: 0.8253 (mttt) cc_final: 0.7797 (mtpt)
REVERT: A   18 MET cc_start: 0.8699 (ttm) cc_final: 0.8374 (ttm)
REVERT: A  231 ASP cc_start: 0.8084 (t70) cc_final: 0.7716 (t0)
REVERT: A  243 MET cc_start: 0.8029 (tpp) cc_final: 0.7435 (tpp)
REVERT: A  244 HIS cc_start: 0.7668 (OUTLIER) cc_final: 0.7338 (m170)
REVERT: A  247 MET cc_start: 0.8153 (mtp) cc_final: 0.7813 (mtt)
REVERT: A  251 ASP cc_start: 0.8089 (t0) cc_final: 0.7716 (t0)
REVERT: A  306 GLN cc_start: 0.7593 (mm-40) cc_final: 0.7201 (mm110)
REVERT: A  308 GLU cc_start: 0.7530 (OUTLIER) cc_final: 0.6840 (mp0)
REVERT: B   13 GLN cc_start: 0.6657 (pp30) cc_final: 0.6357 (pp30)
REVERT: B  197 ARG cc_start: 0.7942 (mtm110) cc_final: 0.7687 (mmt-90)
REVERT: B  219 ARG cc_start: 0.7791 (ttm170) cc_final: 0.7548 (mtp85)
REVERT: B  325 MET cc_start: 0.8564 (tpp) cc_final: 0.8083 (tpp)
REVERT: B  337 LYS cc_start: 0.8535 (mttt) cc_final: 0.8093 (mttt)
REVERT: B  340 ASN cc_start: 0.8702 (t0) cc_final: 0.8450 (t0)
REVERT: C   20 LYS cc_start: 0.7847 (mtpp) cc_final: 0.7522 (mtmm)
REVERT: C   42 GLU cc_start: 0.7704 (mt-10) cc_final: 0.7330 (mp0)
REVERT: R  109 MET cc_start: 0.3862 (pmt) cc_final: 0.3633 (pmm)
REVERT: R  278 PHE cc_start: 0.5853 (t80) cc_final: 0.5583 (t80)
REVERT: R  353 ILE cc_start: 0.7377 (mm) cc_final: 0.7038 (mt)
REVERT: R  356 TRP cc_start: 0.7243 (m100) cc_final: 0.6298 (m100)
REVERT: R  404 LEU cc_start: 0.4993 (mm) cc_final: 0.4785 (mm)
REVERT: S   23 SER cc_start: 0.8648 (m) cc_final: 0.8326 (t)
REVERT: S   73 ASP cc_start: 0.7877 (t0) cc_final: 0.7673 (t70)
REVERT: S  171 GLN cc_start: 0.8395 (mm-40) cc_final: 0.8034 (mt0)
  outliers start: 21
  outliers final: 13
  residues processed: 177
  average time/residue: 0.2493
  time to fit residues: 58.1016
Evaluate side-chains
  172 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 157
  time to evaluate  : 0.912 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    6 SER
Chi-restraints excluded: chain A residue  195 HIS
Chi-restraints excluded: chain A residue  244 HIS
Chi-restraints excluded: chain A residue  305 CYS
Chi-restraints excluded: chain A residue  308 GLU
Chi-restraints excluded: chain B residue   38 ASP
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  262 MET
Chi-restraints excluded: chain B residue  322 ASP
Chi-restraints excluded: chain C residue   28 ILE
Chi-restraints excluded: chain R residue  222 LEU
Chi-restraints excluded: chain R residue  308 MET
Chi-restraints excluded: chain R residue  351 VAL
Chi-restraints excluded: chain S residue   84 THR
Chi-restraints excluded: chain S residue  160 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 13 optimal weight:    1.9990
   chunk 80 optimal weight:    0.6980
   chunk 89 optimal weight:    0.8980
   chunk 73 optimal weight:    3.9990
   chunk 104 optimal weight:    1.9990
   chunk 37 optimal weight:    0.8980
   chunk 96 optimal weight:    0.9990
   chunk 91 optimal weight:    0.0670
   chunk 95 optimal weight:    0.0000
   chunk 106 optimal weight:    0.9990
   chunk 75 optimal weight:    2.9990
   overall best weight:    0.5122

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

Flipped N/Q/H residues before XYZ refinement:
A 331 ASN
** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
S  82 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3857 r_free = 0.3857 target = 0.169634 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.3209 r_free = 0.3209 target = 0.114631 restraints weight = 9359.667|
|-----------------------------------------------------------------------------|
r_work (start): 0.3201 rms_B_bonded: 2.27
r_work: 0.3064 rms_B_bonded: 2.90 restraints_weight: 0.5000
r_work: 0.2917 rms_B_bonded: 4.67 restraints_weight: 0.2500
r_work (final): 0.2917
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7726
moved from start:          0.2952

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   8642  Z= 0.135
  Angle     :  0.602  11.066  11734  Z= 0.312
  Chirality :  0.043   0.151   1363
  Planarity :  0.004   0.054   1470
  Dihedral  :  6.540 115.735   1211
  Min Nonbonded Distance : 2.443

Molprobity Statistics.
  All-atom Clashscore : 7.49
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  4.49 %
    Favored  : 95.42 %
  Rotamer:
    Outliers :  3.20 %
    Allowed  : 12.79 %
    Favored  : 84.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    Cis-general     : 0.09 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.14 (0.25), residues: 1091
  helix: -1.78 (0.26), residues: 336
  sheet: -1.02 (0.28), residues: 274
  loop : -1.20 (0.30), residues: 481

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP B  82 
 HIS   0.003   0.001   HIS R 154 
 PHE   0.013   0.001   PHE A 189 
 TYR   0.026   0.001   TYR S 178 
 ARG   0.003   0.000   ARG B 134 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03715 (  325)
  hydrogen bonds       : angle       5.21684 (  963)
  SS BOND              : bond        0.00360 (    1)
  SS BOND              : angle       0.89662 (    2)
  covalent geometry    : bond        0.00297 ( 8640)
  covalent geometry    : angle       0.60208 (11732)
  Misc. bond           : bond        0.00042 (    1)

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

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

  2182 Ramachandran restraints generated.
    1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2182 Ramachandran restraints generated.
    1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  190 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 162
  time to evaluate  : 0.837 
Fit side-chains
REVERT: A   17 LYS cc_start: 0.8198 (mttt) cc_final: 0.7813 (mtpt)
REVERT: A   18 MET cc_start: 0.8655 (ttm) cc_final: 0.8304 (ttm)
REVERT: A  232 LEU cc_start: 0.7313 (mt) cc_final: 0.7007 (mp)
REVERT: A  243 MET cc_start: 0.8040 (tpp) cc_final: 0.7504 (tpp)
REVERT: A  244 HIS cc_start: 0.7705 (OUTLIER) cc_final: 0.7388 (m170)
REVERT: A  247 MET cc_start: 0.8134 (mtp) cc_final: 0.7900 (mtt)
REVERT: A  306 GLN cc_start: 0.7554 (mm-40) cc_final: 0.7182 (mm110)
REVERT: A  308 GLU cc_start: 0.7496 (OUTLIER) cc_final: 0.6915 (mp0)
REVERT: B   13 GLN cc_start: 0.6791 (pp30) cc_final: 0.6489 (pp30)
REVERT: B  197 ARG cc_start: 0.7878 (mtm110) cc_final: 0.7627 (mpt180)
REVERT: B  219 ARG cc_start: 0.7762 (ttm170) cc_final: 0.7545 (mtp85)
REVERT: B  325 MET cc_start: 0.8593 (tpp) cc_final: 0.8174 (tpp)
REVERT: B  337 LYS cc_start: 0.8553 (mttt) cc_final: 0.8188 (mttt)
REVERT: C   14 LYS cc_start: 0.7985 (OUTLIER) cc_final: 0.7690 (ttpp)
REVERT: R  109 MET cc_start: 0.3691 (pmt) cc_final: 0.3466 (pmm)
REVERT: R  164 LEU cc_start: 0.6307 (OUTLIER) cc_final: 0.6018 (tt)
REVERT: R  353 ILE cc_start: 0.7351 (mm) cc_final: 0.7014 (mt)
REVERT: R  356 TRP cc_start: 0.7213 (m100) cc_final: 0.6297 (m100)
REVERT: R  404 LEU cc_start: 0.5065 (mm) cc_final: 0.4849 (mm)
REVERT: S   18 ARG cc_start: 0.7815 (mmt-90) cc_final: 0.7554 (tpt170)
REVERT: S   23 SER cc_start: 0.8623 (m) cc_final: 0.8315 (t)
REVERT: S   77 ASN cc_start: 0.8324 (m-40) cc_final: 0.8078 (m110)
REVERT: S  171 GLN cc_start: 0.8362 (mm-40) cc_final: 0.8072 (mt0)
  outliers start: 28
  outliers final: 14
  residues processed: 176
  average time/residue: 0.2411
  time to fit residues: 55.6711
Evaluate side-chains
  172 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 154
  time to evaluate  : 0.875 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    6 SER
Chi-restraints excluded: chain A residue  244 HIS
Chi-restraints excluded: chain A residue  305 CYS
Chi-restraints excluded: chain A residue  308 GLU
Chi-restraints excluded: chain B residue   38 ASP
Chi-restraints excluded: chain B residue   98 SER
Chi-restraints excluded: chain B residue  114 CYS
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  262 MET
Chi-restraints excluded: chain B residue  322 ASP
Chi-restraints excluded: chain C residue   14 LYS
Chi-restraints excluded: chain C residue   28 ILE
Chi-restraints excluded: chain R residue  164 LEU
Chi-restraints excluded: chain R residue  222 LEU
Chi-restraints excluded: chain R residue  308 MET
Chi-restraints excluded: chain R residue  346 VAL
Chi-restraints excluded: chain R residue  351 VAL
Chi-restraints excluded: chain S residue  160 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 64 optimal weight:    0.6980
   chunk 45 optimal weight:    0.6980
   chunk 100 optimal weight:    0.1980
   chunk 84 optimal weight:    0.1980
   chunk 31 optimal weight:    0.9990
   chunk 58 optimal weight:    0.0570
   chunk 80 optimal weight:    0.9980
   chunk 8 optimal weight:    0.9990
   chunk 6 optimal weight:    3.9990
   chunk 28 optimal weight:    0.6980
   chunk 88 optimal weight:    1.9990
   overall best weight:    0.3698

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

Flipped N/Q/H residues before XYZ refinement:
A 269 ASN
** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  18 GLN
S  39 GLN
S  82 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3870 r_free = 0.3870 target = 0.170952 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3226 r_free = 0.3226 target = 0.115944 restraints weight = 9315.342|
|-----------------------------------------------------------------------------|
r_work (start): 0.3220 rms_B_bonded: 2.30
r_work: 0.3084 rms_B_bonded: 2.93 restraints_weight: 0.5000
r_work: 0.2934 rms_B_bonded: 4.74 restraints_weight: 0.2500
r_work (final): 0.2934
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7686
moved from start:          0.3237

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   8642  Z= 0.118
  Angle     :  0.583  10.694  11734  Z= 0.301
  Chirality :  0.043   0.148   1363
  Planarity :  0.004   0.063   1470
  Dihedral  :  6.305 114.589   1211
  Min Nonbonded Distance : 2.451

Molprobity Statistics.
  All-atom Clashscore : 7.55
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  4.31 %
    Favored  : 95.60 %
  Rotamer:
    Outliers :  2.74 %
    Allowed  : 14.38 %
    Favored  : 82.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    Cis-general     : 0.09 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

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: -1.78 (0.25), residues: 1091
  helix: -1.39 (0.27), residues: 337
  sheet: -0.94 (0.28), residues: 290
  loop : -0.95 (0.31), residues: 464

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP B  82 
 HIS   0.003   0.001   HIS A 195 
 PHE   0.013   0.001   PHE R 237 
 TYR   0.026   0.001   TYR S 178 
 ARG   0.006   0.000   ARG C  27 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03516 (  325)
  hydrogen bonds       : angle       4.93058 (  963)
  SS BOND              : bond        0.00295 (    1)
  SS BOND              : angle       1.01630 (    2)
  covalent geometry    : bond        0.00253 ( 8640)
  covalent geometry    : angle       0.58330 (11732)
  Misc. bond           : bond        0.00049 (    1)

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

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

  2182 Ramachandran restraints generated.
    1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2182 Ramachandran restraints generated.
    1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  195 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 171
  time to evaluate  : 0.946 
Fit side-chains
REVERT: A   17 LYS cc_start: 0.8142 (mttt) cc_final: 0.7676 (mtpt)
REVERT: A   18 MET cc_start: 0.8593 (ttm) cc_final: 0.8238 (ttm)
REVERT: A  232 LEU cc_start: 0.7159 (mt) cc_final: 0.6800 (mp)
REVERT: A  243 MET cc_start: 0.8006 (tpp) cc_final: 0.7474 (tpp)
REVERT: A  244 HIS cc_start: 0.7572 (OUTLIER) cc_final: 0.7291 (m170)
REVERT: A  247 MET cc_start: 0.8064 (mtp) cc_final: 0.7812 (mtt)
REVERT: A  306 GLN cc_start: 0.7428 (mm-40) cc_final: 0.7061 (mm110)
REVERT: A  308 GLU cc_start: 0.7412 (OUTLIER) cc_final: 0.6917 (mp0)
REVERT: B   13 GLN cc_start: 0.6808 (pp30) cc_final: 0.6502 (pp30)
REVERT: B  197 ARG cc_start: 0.7859 (mtm110) cc_final: 0.7580 (mpt180)
REVERT: C   14 LYS cc_start: 0.7958 (OUTLIER) cc_final: 0.7678 (ttpp)
REVERT: R  109 MET cc_start: 0.3642 (pmt) cc_final: 0.3223 (pmm)
REVERT: R  164 LEU cc_start: 0.6262 (OUTLIER) cc_final: 0.5989 (tt)
REVERT: R  220 ARG cc_start: 0.7119 (mmm160) cc_final: 0.6653 (mmp80)
REVERT: R  336 ARG cc_start: 0.5541 (tpm-80) cc_final: 0.3313 (mmt-90)
REVERT: R  340 ARG cc_start: 0.6494 (ttm110) cc_final: 0.6193 (ptm-80)
REVERT: R  404 LEU cc_start: 0.5011 (mm) cc_final: 0.4792 (mm)
REVERT: S   23 SER cc_start: 0.8581 (m) cc_final: 0.8272 (t)
REVERT: S  194 SER cc_start: 0.8633 (t) cc_final: 0.8379 (m)
  outliers start: 24
  outliers final: 15
  residues processed: 184
  average time/residue: 0.2593
  time to fit residues: 61.6623
Evaluate side-chains
  181 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 162
  time to evaluate  : 0.856 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    6 SER
Chi-restraints excluded: chain A residue  190 THR
Chi-restraints excluded: chain A residue  244 HIS
Chi-restraints excluded: chain A residue  308 GLU
Chi-restraints excluded: chain B residue   38 ASP
Chi-restraints excluded: chain B residue   98 SER
Chi-restraints excluded: chain B residue  114 CYS
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  262 MET
Chi-restraints excluded: chain B residue  322 ASP
Chi-restraints excluded: chain C residue   14 LYS
Chi-restraints excluded: chain C residue   28 ILE
Chi-restraints excluded: chain C residue   38 MET
Chi-restraints excluded: chain R residue  164 LEU
Chi-restraints excluded: chain R residue  222 LEU
Chi-restraints excluded: chain R residue  308 MET
Chi-restraints excluded: chain R residue  351 VAL
Chi-restraints excluded: chain S residue   84 THR
Chi-restraints excluded: chain S residue  160 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 76 optimal weight:    2.9990
   chunk 77 optimal weight:    1.9990
   chunk 48 optimal weight:    1.9990
   chunk 78 optimal weight:    0.8980
   chunk 17 optimal weight:    3.9990
   chunk 66 optimal weight:    5.9990
   chunk 90 optimal weight:    0.7980
   chunk 9 optimal weight:    0.7980
   chunk 2 optimal weight:    0.9980
   chunk 13 optimal weight:    0.3980
   chunk 88 optimal weight:    1.9990
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
B  75 GLN
B 220 GLN
B 239 ASN
B 259 GLN
S  82 GLN
S 171 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3837 r_free = 0.3837 target = 0.168026 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3181 r_free = 0.3181 target = 0.112691 restraints weight = 9300.291|
|-----------------------------------------------------------------------------|
r_work (start): 0.3175 rms_B_bonded: 2.27
r_work: 0.3034 rms_B_bonded: 2.92 restraints_weight: 0.5000
r_work: 0.2886 rms_B_bonded: 4.67 restraints_weight: 0.2500
r_work (final): 0.2886
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7715
moved from start:          0.3196

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   8642  Z= 0.171
  Angle     :  0.622  12.464  11734  Z= 0.320
  Chirality :  0.044   0.150   1363
  Planarity :  0.004   0.068   1470
  Dihedral  :  6.300 109.562   1211
  Min Nonbonded Distance : 2.459

Molprobity Statistics.
  All-atom Clashscore : 7.67
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  4.77 %
    Favored  : 95.14 %
  Rotamer:
    Outliers :  3.31 %
    Allowed  : 15.87 %
    Favored  : 80.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    Cis-general     : 0.09 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

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: -1.76 (0.25), residues: 1091
  helix: -1.29 (0.27), residues: 343
  sheet: -0.87 (0.29), residues: 285
  loop : -1.06 (0.30), residues: 463

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B  82 
 HIS   0.004   0.001   HIS A 195 
 PHE   0.013   0.002   PHE A 189 
 TYR   0.024   0.001   TYR S 178 
 ARG   0.006   0.001   ARG B 314 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03691 (  325)
  hydrogen bonds       : angle       5.03409 (  963)
  SS BOND              : bond        0.00247 (    1)
  SS BOND              : angle       1.42451 (    2)
  covalent geometry    : bond        0.00383 ( 8640)
  covalent geometry    : angle       0.62201 (11732)
  Misc. bond           : bond        0.00046 (    1)

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

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

  2182 Ramachandran restraints generated.
    1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2182 Ramachandran restraints generated.
    1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  197 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 168
  time to evaluate  : 0.882 
Fit side-chains
REVERT: A   17 LYS cc_start: 0.8150 (mttt) cc_final: 0.7881 (mmtp)
REVERT: A  231 ASP cc_start: 0.7990 (t70) cc_final: 0.7768 (t0)
REVERT: A  232 LEU cc_start: 0.7232 (mt) cc_final: 0.6926 (mp)
REVERT: A  243 MET cc_start: 0.8040 (tpp) cc_final: 0.7468 (tpp)
REVERT: A  247 MET cc_start: 0.8088 (mtp) cc_final: 0.7821 (mtt)
REVERT: A  306 GLN cc_start: 0.7428 (mm-40) cc_final: 0.7095 (mm110)
REVERT: A  308 GLU cc_start: 0.7470 (OUTLIER) cc_final: 0.6865 (mp0)
REVERT: B   13 GLN cc_start: 0.6758 (pp30) cc_final: 0.6484 (pp30)
REVERT: B  197 ARG cc_start: 0.7903 (mtm110) cc_final: 0.7562 (mpt180)
REVERT: B  217 MET cc_start: 0.8264 (OUTLIER) cc_final: 0.7899 (ppp)
REVERT: B  325 MET cc_start: 0.8503 (tpp) cc_final: 0.8101 (mmt)
REVERT: C   14 LYS cc_start: 0.7940 (OUTLIER) cc_final: 0.7636 (ttpp)
REVERT: R  109 MET cc_start: 0.3727 (pmt) cc_final: 0.3485 (pmm)
REVERT: R  164 LEU cc_start: 0.6283 (OUTLIER) cc_final: 0.6020 (tt)
REVERT: R  336 ARG cc_start: 0.5510 (tpm-80) cc_final: 0.3202 (mmt-90)
REVERT: R  340 ARG cc_start: 0.6451 (ttm110) cc_final: 0.6127 (ptm-80)
REVERT: R  356 TRP cc_start: 0.7228 (m100) cc_final: 0.6313 (m100)
REVERT: R  404 LEU cc_start: 0.5158 (mm) cc_final: 0.4953 (mm)
REVERT: R  405 ARG cc_start: 0.5873 (mtm-85) cc_final: 0.5226 (mtm-85)
REVERT: S   23 SER cc_start: 0.8740 (m) cc_final: 0.8405 (t)
REVERT: S  194 SER cc_start: 0.8693 (t) cc_final: 0.8408 (m)
  outliers start: 29
  outliers final: 18
  residues processed: 184
  average time/residue: 0.3091
  time to fit residues: 73.4524
Evaluate side-chains
  184 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 162
  time to evaluate  : 0.874 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    6 SER
Chi-restraints excluded: chain A residue  244 HIS
Chi-restraints excluded: chain A residue  256 ASN
Chi-restraints excluded: chain A residue  305 CYS
Chi-restraints excluded: chain A residue  308 GLU
Chi-restraints excluded: chain B residue   38 ASP
Chi-restraints excluded: chain B residue   98 SER
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  217 MET
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  262 MET
Chi-restraints excluded: chain B residue  322 ASP
Chi-restraints excluded: chain C residue   14 LYS
Chi-restraints excluded: chain C residue   28 ILE
Chi-restraints excluded: chain C residue   38 MET
Chi-restraints excluded: chain R residue  164 LEU
Chi-restraints excluded: chain R residue  216 ILE
Chi-restraints excluded: chain R residue  222 LEU
Chi-restraints excluded: chain R residue  308 MET
Chi-restraints excluded: chain R residue  351 VAL
Chi-restraints excluded: chain S residue  129 THR
Chi-restraints excluded: chain S residue  160 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 47 optimal weight:    0.9980
   chunk 3 optimal weight:    0.4980
   chunk 48 optimal weight:    1.9990
   chunk 34 optimal weight:    0.0010
   chunk 58 optimal weight:    0.2980
   chunk 104 optimal weight:    4.9990
   chunk 94 optimal weight:    1.9990
   chunk 91 optimal weight:    0.0870
   chunk 2 optimal weight:    0.3980
   chunk 12 optimal weight:    0.6980
   chunk 67 optimal weight:    5.9990
   overall best weight:    0.2564

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

Flipped N/Q/H residues before XYZ refinement:
A 195 HIS
B 220 GLN
B 239 ASN
** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3885 r_free = 0.3885 target = 0.172524 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3381 r_free = 0.3381 target = 0.127735 restraints weight = 9346.961|
|-----------------------------------------------------------------------------|
r_work (start): 0.3364 rms_B_bonded: 2.29
r_work: 0.3126 rms_B_bonded: 2.73 restraints_weight: 0.5000
r_work: 0.2982 rms_B_bonded: 4.37 restraints_weight: 0.2500
r_work (final): 0.2982
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7573
moved from start:          0.3617

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031   8642  Z= 0.106
  Angle     :  0.574   9.549  11734  Z= 0.295
  Chirality :  0.042   0.151   1363
  Planarity :  0.004   0.075   1470
  Dihedral  :  5.932 105.709   1211
  Min Nonbonded Distance : 2.496

Molprobity Statistics.
  All-atom Clashscore : 7.73
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  3.48 %
    Favored  : 96.43 %
  Rotamer:
    Outliers :  2.85 %
    Allowed  : 17.01 %
    Favored  : 80.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    Cis-general     : 0.09 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

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: -1.44 (0.25), residues: 1091
  helix: -0.85 (0.28), residues: 341
  sheet: -0.83 (0.29), residues: 288
  loop : -0.92 (0.30), residues: 462

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP B  82 
 HIS   0.002   0.001   HIS R 154 
 PHE   0.012   0.001   PHE R 237 
 TYR   0.027   0.001   TYR S 178 
 ARG   0.007   0.001   ARG C  27 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03309 (  325)
  hydrogen bonds       : angle       4.71744 (  963)
  SS BOND              : bond        0.00313 (    1)
  SS BOND              : angle       0.95041 (    2)
  covalent geometry    : bond        0.00224 ( 8640)
  covalent geometry    : angle       0.57440 (11732)
  Misc. bond           : bond        0.00042 (    1)

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

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

  2182 Ramachandran restraints generated.
    1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2182 Ramachandran restraints generated.
    1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  192 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 167
  time to evaluate  : 1.175 
Fit side-chains
REVERT: A   17 LYS cc_start: 0.8036 (mttt) cc_final: 0.7706 (mmtp)
REVERT: A   22 ASN cc_start: 0.8126 (m-40) cc_final: 0.7588 (m110)
REVERT: A  195 HIS cc_start: 0.7528 (OUTLIER) cc_final: 0.7136 (m-70)
REVERT: A  243 MET cc_start: 0.7958 (tpp) cc_final: 0.7414 (tpp)
REVERT: A  247 MET cc_start: 0.7942 (mtp) cc_final: 0.7686 (mtt)
REVERT: A  306 GLN cc_start: 0.7334 (mm-40) cc_final: 0.6990 (mm110)
REVERT: A  308 GLU cc_start: 0.7385 (OUTLIER) cc_final: 0.6891 (mp0)
REVERT: B   13 GLN cc_start: 0.6691 (pp30) cc_final: 0.6389 (pp30)
REVERT: B   96 ARG cc_start: 0.8648 (mtt-85) cc_final: 0.8398 (mtt-85)
REVERT: B  197 ARG cc_start: 0.7787 (mtm110) cc_final: 0.7531 (mpt180)
REVERT: B  217 MET cc_start: 0.8074 (ptt) cc_final: 0.7783 (ppp)
REVERT: B  227 SER cc_start: 0.8966 (t) cc_final: 0.8748 (m)
REVERT: B  325 MET cc_start: 0.8428 (tpp) cc_final: 0.8187 (mmt)
REVERT: B  337 LYS cc_start: 0.8509 (mttt) cc_final: 0.8258 (mttt)
REVERT: C   14 LYS cc_start: 0.7918 (OUTLIER) cc_final: 0.7647 (ttpp)
REVERT: C   20 LYS cc_start: 0.8032 (mtpt) cc_final: 0.7739 (mtpt)
REVERT: R  109 MET cc_start: 0.3558 (pmt) cc_final: 0.3166 (pmm)
REVERT: R  164 LEU cc_start: 0.6039 (OUTLIER) cc_final: 0.5794 (tt)
REVERT: S   23 SER cc_start: 0.8552 (m) cc_final: 0.8232 (t)
REVERT: S  194 SER cc_start: 0.8654 (t) cc_final: 0.8377 (m)
  outliers start: 25
  outliers final: 15
  residues processed: 181
  average time/residue: 0.2695
  time to fit residues: 66.6722
Evaluate side-chains
  173 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 154
  time to evaluate  : 0.998 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    6 SER
Chi-restraints excluded: chain A residue   38 LEU
Chi-restraints excluded: chain A residue  195 HIS
Chi-restraints excluded: chain A residue  244 HIS
Chi-restraints excluded: chain A residue  305 CYS
Chi-restraints excluded: chain A residue  308 GLU
Chi-restraints excluded: chain B residue   38 ASP
Chi-restraints excluded: chain B residue   98 SER
Chi-restraints excluded: chain B residue  262 MET
Chi-restraints excluded: chain C residue   14 LYS
Chi-restraints excluded: chain C residue   28 ILE
Chi-restraints excluded: chain C residue   38 MET
Chi-restraints excluded: chain R residue  164 LEU
Chi-restraints excluded: chain R residue  222 LEU
Chi-restraints excluded: chain R residue  308 MET
Chi-restraints excluded: chain R residue  351 VAL
Chi-restraints excluded: chain S residue   69 THR
Chi-restraints excluded: chain S residue  129 THR
Chi-restraints excluded: chain S residue  160 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 46 optimal weight:    0.8980
   chunk 76 optimal weight:    3.9990
   chunk 48 optimal weight:    0.7980
   chunk 45 optimal weight:    3.9990
   chunk 93 optimal weight:    2.9990
   chunk 23 optimal weight:    0.0770
   chunk 53 optimal weight:    0.5980
   chunk 0 optimal weight:    4.9990
   chunk 62 optimal weight:    0.5980
   chunk 33 optimal weight:    0.5980
   chunk 35 optimal weight:    1.9990
   overall best weight:    0.5338

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

Flipped N/Q/H residues before XYZ refinement:
A 195 HIS
A 269 ASN
B 239 ASN
** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
S 171 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3862 r_free = 0.3862 target = 0.170317 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.3213 r_free = 0.3213 target = 0.115127 restraints weight = 9482.536|
|-----------------------------------------------------------------------------|
r_work (start): 0.3206 rms_B_bonded: 2.31
r_work: 0.3071 rms_B_bonded: 2.92 restraints_weight: 0.5000
r_work: 0.2924 rms_B_bonded: 4.68 restraints_weight: 0.2500
r_work (final): 0.2924
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7672
moved from start:          0.3570

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   8642  Z= 0.136
  Angle     :  0.609  10.998  11734  Z= 0.308
  Chirality :  0.043   0.147   1363
  Planarity :  0.004   0.077   1470
  Dihedral  :  5.914 102.523   1211
  Min Nonbonded Distance : 2.473

Molprobity Statistics.
  All-atom Clashscore : 7.91
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  4.40 %
    Favored  : 95.51 %
  Rotamer:
    Outliers :  2.85 %
    Allowed  : 17.58 %
    Favored  : 79.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    Cis-general     : 0.09 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

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: -1.36 (0.25), residues: 1091
  helix: -0.72 (0.28), residues: 340
  sheet: -0.73 (0.29), residues: 284
  loop : -0.97 (0.30), residues: 467

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP B  82 
 HIS   0.005   0.001   HIS A 195 
 PHE   0.013   0.001   PHE R 237 
 TYR   0.025   0.001   TYR S 178 
 ARG   0.009   0.001   ARG C  27 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03431 (  325)
  hydrogen bonds       : angle       4.75993 (  963)
  SS BOND              : bond        0.00208 (    1)
  SS BOND              : angle       1.15896 (    2)
  covalent geometry    : bond        0.00301 ( 8640)
  covalent geometry    : angle       0.60851 (11732)
  Misc. bond           : bond        0.00022 (    1)

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

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

  2182 Ramachandran restraints generated.
    1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2182 Ramachandran restraints generated.
    1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  185 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 160
  time to evaluate  : 1.054 
Fit side-chains
REVERT: A   17 LYS cc_start: 0.8129 (mttt) cc_final: 0.7811 (mmtp)
REVERT: A  244 HIS cc_start: 0.7434 (OUTLIER) cc_final: 0.7081 (m170)
REVERT: A  247 MET cc_start: 0.8026 (mtp) cc_final: 0.7745 (mtt)
REVERT: A  308 GLU cc_start: 0.7418 (OUTLIER) cc_final: 0.6948 (mp0)
REVERT: B  197 ARG cc_start: 0.7940 (mtm110) cc_final: 0.7692 (mpt180)
REVERT: B  217 MET cc_start: 0.8164 (ptt) cc_final: 0.7839 (ppp)
REVERT: B  337 LYS cc_start: 0.8512 (mttt) cc_final: 0.8190 (mttt)
REVERT: C   14 LYS cc_start: 0.7941 (OUTLIER) cc_final: 0.7648 (ttpp)
REVERT: C   20 LYS cc_start: 0.8094 (mtpt) cc_final: 0.7803 (mtpt)
REVERT: R  109 MET cc_start: 0.3638 (pmt) cc_final: 0.3199 (pmm)
REVERT: R  164 LEU cc_start: 0.6082 (OUTLIER) cc_final: 0.5823 (tt)
REVERT: S   23 SER cc_start: 0.8654 (m) cc_final: 0.8324 (t)
REVERT: S  194 SER cc_start: 0.8681 (t) cc_final: 0.8400 (m)
  outliers start: 25
  outliers final: 18
  residues processed: 175
  average time/residue: 0.2475
  time to fit residues: 56.9984
Evaluate side-chains
  180 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 158
  time to evaluate  : 0.862 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    6 SER
Chi-restraints excluded: chain A residue   38 LEU
Chi-restraints excluded: chain A residue  244 HIS
Chi-restraints excluded: chain A residue  256 ASN
Chi-restraints excluded: chain A residue  305 CYS
Chi-restraints excluded: chain A residue  308 GLU
Chi-restraints excluded: chain B residue   38 ASP
Chi-restraints excluded: chain B residue   98 SER
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  262 MET
Chi-restraints excluded: chain C residue   14 LYS
Chi-restraints excluded: chain C residue   28 ILE
Chi-restraints excluded: chain C residue   38 MET
Chi-restraints excluded: chain R residue  164 LEU
Chi-restraints excluded: chain R residue  222 LEU
Chi-restraints excluded: chain R residue  308 MET
Chi-restraints excluded: chain R residue  351 VAL
Chi-restraints excluded: chain S residue   69 THR
Chi-restraints excluded: chain S residue  129 THR
Chi-restraints excluded: chain S residue  160 THR
Chi-restraints excluded: chain S residue  210 GLU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 31 optimal weight:    1.9990
   chunk 75 optimal weight:    2.9990
   chunk 60 optimal weight:    0.9980
   chunk 11 optimal weight:    0.9980
   chunk 22 optimal weight:    1.9990
   chunk 29 optimal weight:    1.9990
   chunk 64 optimal weight:    5.9990
   chunk 14 optimal weight:    4.9990
   chunk 28 optimal weight:    0.5980
   chunk 74 optimal weight:    0.8980
   chunk 82 optimal weight:    0.8980
   overall best weight:    0.8780

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

Flipped N/Q/H residues before XYZ refinement:
** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3829 r_free = 0.3829 target = 0.167340 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3172 r_free = 0.3172 target = 0.112053 restraints weight = 9505.118|
|-----------------------------------------------------------------------------|
r_work (start): 0.3166 rms_B_bonded: 2.29
r_work: 0.3026 rms_B_bonded: 2.92 restraints_weight: 0.5000
r_work: 0.2877 rms_B_bonded: 4.68 restraints_weight: 0.2500
r_work (final): 0.2877
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7738
moved from start:          0.3423

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   8642  Z= 0.186
  Angle     :  0.649  12.124  11734  Z= 0.331
  Chirality :  0.045   0.156   1363
  Planarity :  0.005   0.077   1470
  Dihedral  :  6.032  95.710   1211
  Min Nonbonded Distance : 2.491

Molprobity Statistics.
  All-atom Clashscore : 8.15
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  4.86 %
    Favored  : 95.05 %
  Rotamer:
    Outliers :  2.63 %
    Allowed  : 17.92 %
    Favored  : 79.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    Cis-general     : 0.09 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

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: -1.39 (0.25), residues: 1091
  helix: -0.81 (0.28), residues: 340
  sheet: -0.82 (0.29), residues: 287
  loop : -0.87 (0.30), residues: 464

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B  82 
 HIS   0.003   0.001   HIS B 311 
 PHE   0.013   0.002   PHE B 199 
 TYR   0.024   0.002   TYR S 178 
 ARG   0.009   0.001   ARG C  27 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03702 (  325)
  hydrogen bonds       : angle       4.95663 (  963)
  SS BOND              : bond        0.00217 (    1)
  SS BOND              : angle       1.49426 (    2)
  covalent geometry    : bond        0.00421 ( 8640)
  covalent geometry    : angle       0.64903 (11732)
  Misc. bond           : bond        0.00002 (    1)

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

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

  2182 Ramachandran restraints generated.
    1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2182 Ramachandran restraints generated.
    1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  180 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 157
  time to evaluate  : 0.854 
Fit side-chains
REVERT: A   17 LYS cc_start: 0.8171 (mttt) cc_final: 0.7854 (mmtp)
REVERT: A  244 HIS cc_start: 0.7471 (OUTLIER) cc_final: 0.7105 (m170)
REVERT: A  247 MET cc_start: 0.8044 (mtp) cc_final: 0.7776 (mtt)
REVERT: A  306 GLN cc_start: 0.7220 (mm-40) cc_final: 0.7002 (mm110)
REVERT: A  308 GLU cc_start: 0.7490 (OUTLIER) cc_final: 0.6891 (mp0)
REVERT: B   52 ARG cc_start: 0.8567 (OUTLIER) cc_final: 0.7783 (mtp85)
REVERT: B  197 ARG cc_start: 0.7865 (mtm110) cc_final: 0.7587 (mpt180)
REVERT: B  217 MET cc_start: 0.8210 (ptt) cc_final: 0.7820 (ppp)
REVERT: B  337 LYS cc_start: 0.8570 (mttt) cc_final: 0.8237 (mttt)
REVERT: C   14 LYS cc_start: 0.7891 (OUTLIER) cc_final: 0.7599 (ttpp)
REVERT: C   20 LYS cc_start: 0.8029 (mtpt) cc_final: 0.7776 (mtpt)
REVERT: R  109 MET cc_start: 0.3797 (pmt) cc_final: 0.3314 (pmm)
REVERT: R  356 TRP cc_start: 0.7227 (m100) cc_final: 0.6261 (m100)
REVERT: S    6 GLU cc_start: 0.8213 (pm20) cc_final: 0.7864 (pm20)
REVERT: S   23 SER cc_start: 0.8764 (m) cc_final: 0.8447 (t)
REVERT: S  194 SER cc_start: 0.8720 (t) cc_final: 0.8430 (m)
  outliers start: 23
  outliers final: 15
  residues processed: 172
  average time/residue: 0.2403
  time to fit residues: 54.4956
Evaluate side-chains
  175 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 156
  time to evaluate  : 0.847 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    6 SER
Chi-restraints excluded: chain A residue  244 HIS
Chi-restraints excluded: chain A residue  305 CYS
Chi-restraints excluded: chain A residue  308 GLU
Chi-restraints excluded: chain B residue   38 ASP
Chi-restraints excluded: chain B residue   52 ARG
Chi-restraints excluded: chain B residue   98 SER
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  262 MET
Chi-restraints excluded: chain C residue   14 LYS
Chi-restraints excluded: chain C residue   28 ILE
Chi-restraints excluded: chain C residue   38 MET
Chi-restraints excluded: chain R residue  222 LEU
Chi-restraints excluded: chain R residue  308 MET
Chi-restraints excluded: chain R residue  351 VAL
Chi-restraints excluded: chain S residue   69 THR
Chi-restraints excluded: chain S residue  129 THR
Chi-restraints excluded: chain S residue  160 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 19 optimal weight:    0.9990
   chunk 16 optimal weight:    0.7980
   chunk 36 optimal weight:    0.7980
   chunk 6 optimal weight:    0.1980
   chunk 95 optimal weight:    0.3980
   chunk 70 optimal weight:    0.9980
   chunk 89 optimal weight:    0.5980
   chunk 13 optimal weight:    0.8980
   chunk 97 optimal weight:    0.9990
   chunk 0 optimal weight:    2.9990
   chunk 26 optimal weight:    0.7980
   overall best weight:    0.5580

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

Flipped N/Q/H residues before XYZ refinement:
** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3850 r_free = 0.3850 target = 0.169310 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3350 r_free = 0.3350 target = 0.125156 restraints weight = 9394.158|
|-----------------------------------------------------------------------------|
r_work (start): 0.3319 rms_B_bonded: 2.44
r_work: 0.3060 rms_B_bonded: 2.84 restraints_weight: 0.5000
r_work: 0.2913 rms_B_bonded: 4.55 restraints_weight: 0.2500
r_work (final): 0.2913
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7623
moved from start:          0.3576

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   8642  Z= 0.142
  Angle     :  0.622  10.834  11734  Z= 0.315
  Chirality :  0.044   0.148   1363
  Planarity :  0.004   0.078   1470
  Dihedral  :  5.806  91.010   1211
  Min Nonbonded Distance : 2.493

Molprobity Statistics.
  All-atom Clashscore : 8.15
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  4.49 %
    Favored  : 95.42 %
  Rotamer:
    Outliers :  2.51 %
    Allowed  : 18.72 %
    Favored  : 78.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    Cis-general     : 0.09 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

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: -1.24 (0.25), residues: 1091
  helix: -0.70 (0.28), residues: 340
  sheet: -0.65 (0.30), residues: 272
  loop : -0.85 (0.30), residues: 479

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP B  82 
 HIS   0.003   0.001   HIS B  62 
 PHE   0.012   0.001   PHE R 237 
 TYR   0.025   0.001   TYR S 178 
 ARG   0.009   0.001   ARG C  27 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03525 (  325)
  hydrogen bonds       : angle       4.88031 (  963)
  SS BOND              : bond        0.00255 (    1)
  SS BOND              : angle       1.27020 (    2)
  covalent geometry    : bond        0.00317 ( 8640)
  covalent geometry    : angle       0.62195 (11732)
  Misc. bond           : bond        0.00000 (    1)

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

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

  2182 Ramachandran restraints generated.
    1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2182 Ramachandran restraints generated.
    1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  184 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 162
  time to evaluate  : 0.922 
Fit side-chains
REVERT: A   17 LYS cc_start: 0.8000 (mttt) cc_final: 0.7730 (mmtp)
REVERT: A  244 HIS cc_start: 0.7389 (OUTLIER) cc_final: 0.7030 (m170)
REVERT: A  247 MET cc_start: 0.7905 (mtp) cc_final: 0.7637 (mtt)
REVERT: A  306 GLN cc_start: 0.7240 (mm-40) cc_final: 0.7001 (mm110)
REVERT: A  308 GLU cc_start: 0.7443 (OUTLIER) cc_final: 0.6817 (mp0)
REVERT: B   52 ARG cc_start: 0.8472 (OUTLIER) cc_final: 0.7620 (mtp85)
REVERT: B  197 ARG cc_start: 0.7864 (mtm110) cc_final: 0.7601 (mpt180)
REVERT: B  217 MET cc_start: 0.8181 (OUTLIER) cc_final: 0.7739 (ppp)
REVERT: B  337 LYS cc_start: 0.8514 (mttt) cc_final: 0.8175 (mttt)
REVERT: C   14 LYS cc_start: 0.7863 (OUTLIER) cc_final: 0.7571 (ttpp)
REVERT: C   20 LYS cc_start: 0.8080 (mtpt) cc_final: 0.7798 (mtpt)
REVERT: R  109 MET cc_start: 0.3703 (pmt) cc_final: 0.3245 (pmm)
REVERT: R  356 TRP cc_start: 0.7191 (m100) cc_final: 0.6292 (m100)
REVERT: S   23 SER cc_start: 0.8603 (m) cc_final: 0.8269 (t)
  outliers start: 22
  outliers final: 15
  residues processed: 175
  average time/residue: 0.2700
  time to fit residues: 63.6937
Evaluate side-chains
  175 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 155
  time to evaluate  : 1.184 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    6 SER
Chi-restraints excluded: chain A residue  244 HIS
Chi-restraints excluded: chain A residue  305 CYS
Chi-restraints excluded: chain A residue  308 GLU
Chi-restraints excluded: chain B residue   38 ASP
Chi-restraints excluded: chain B residue   52 ARG
Chi-restraints excluded: chain B residue   98 SER
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  217 MET
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  262 MET
Chi-restraints excluded: chain C residue   14 LYS
Chi-restraints excluded: chain C residue   28 ILE
Chi-restraints excluded: chain C residue   38 MET
Chi-restraints excluded: chain R residue  222 LEU
Chi-restraints excluded: chain R residue  308 MET
Chi-restraints excluded: chain R residue  351 VAL
Chi-restraints excluded: chain S residue   69 THR
Chi-restraints excluded: chain S residue  129 THR
Chi-restraints excluded: chain S residue  160 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 17 optimal weight:    0.1980
   chunk 26 optimal weight:    1.9990
   chunk 93 optimal weight:    1.9990
   chunk 38 optimal weight:    1.9990
   chunk 53 optimal weight:    0.8980
   chunk 59 optimal weight:    0.0770
   chunk 22 optimal weight:    1.9990
   chunk 42 optimal weight:    0.6980
   chunk 48 optimal weight:    0.4980
   chunk 2 optimal weight:    0.5980
   chunk 106 optimal weight:    0.9990
   overall best weight:    0.4138

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

Flipped N/Q/H residues before XYZ refinement:
B  13 GLN
** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3867 r_free = 0.3867 target = 0.170833 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 66)----------------|
| r_work = 0.3222 r_free = 0.3222 target = 0.115817 restraints weight = 9504.839|
|-----------------------------------------------------------------------------|
r_work (start): 0.3213 rms_B_bonded: 2.32
r_work: 0.3072 rms_B_bonded: 2.97 restraints_weight: 0.5000
r_work: 0.2925 rms_B_bonded: 4.75 restraints_weight: 0.2500
r_work (final): 0.2925
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7674
moved from start:          0.3722

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   8642  Z= 0.125
  Angle     :  0.612  10.137  11734  Z= 0.309
  Chirality :  0.043   0.164   1363
  Planarity :  0.004   0.078   1470
  Dihedral  :  5.603  86.542   1211
  Min Nonbonded Distance : 2.488

Molprobity Statistics.
  All-atom Clashscore : 7.97
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  4.58 %
    Favored  : 95.33 %
  Rotamer:
    Outliers :  2.63 %
    Allowed  : 18.84 %
    Favored  : 78.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    Cis-general     : 0.09 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

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: -1.10 (0.26), residues: 1091
  helix: -0.47 (0.28), residues: 339
  sheet: -0.63 (0.30), residues: 279
  loop : -0.81 (0.30), residues: 473

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP B  82 
 HIS   0.002   0.001   HIS S  35 
 PHE   0.012   0.001   PHE R 237 
 TYR   0.026   0.001   TYR S 178 
 ARG   0.009   0.001   ARG C  27 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03380 (  325)
  hydrogen bonds       : angle       4.78016 (  963)
  SS BOND              : bond        0.00204 (    1)
  SS BOND              : angle       1.28303 (    2)
  covalent geometry    : bond        0.00275 ( 8640)
  covalent geometry    : angle       0.61166 (11732)
  Misc. bond           : bond        0.00009 (    1)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 6330.35 seconds
wall clock time: 110 minutes 58.07 seconds (6658.07 seconds total)