Starting phenix.real_space_refine
on Thu Jul 31 18:00:51 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8pzu_18045/07_2025/8pzu_18045.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8pzu_18045/07_2025/8pzu_18045.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.5
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8pzu_18045/07_2025/8pzu_18045.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8pzu_18045/07_2025/8pzu_18045.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8pzu_18045/07_2025/8pzu_18045.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8pzu_18045/07_2025/8pzu_18045.cif"
  }
  resolution = 3.5
  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
     Mg      1      5.21       5
     S      43      5.16       5
     C    8660      2.51       5
     N    2375      2.21       5
     O    2703      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 8 residue(s): 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 13782
  Number of models: 1
  Model: ""
    Number of chains: 8
    Chain: "A"
      Number of atoms: 6183
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 783, 6183
          Classifications: {'peptide': 783}
          Link IDs: {'PTRANS': 29, 'TRANS': 753}
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 1
    Chain: "B"
      Number of atoms: 2761
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 367, 2761
          Classifications: {'peptide': 367}
          Link IDs: {'PTRANS': 11, 'TRANS': 355}
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 1
    Chain: "C"
      Number of atoms: 398
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 56, 398
          Classifications: {'peptide': 56}
          Link IDs: {'PTRANS': 6, 'TRANS': 49}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 1
    Chain: "D"
      Number of atoms: 1754
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 217, 1754
          Classifications: {'peptide': 217}
          Link IDs: {'PTRANS': 12, 'TRANS': 204}
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 1
    Chain: "E"
      Number of atoms: 657
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 84, 657
          Classifications: {'peptide': 84}
          Link IDs: {'PTRANS': 5, 'TRANS': 78}
    Chain: "F"
      Number of atoms: 1952
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 252, 1952
          Classifications: {'peptide': 252}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 7, 'TRANS': 244}
          Chain breaks: 6
          Unresolved chain link angles: 2
          Unresolved non-hydrogen bonds: 7
          Unresolved non-hydrogen angles: 8
          Unresolved non-hydrogen dihedrals: 4
          Unresolved non-hydrogen chiralities: 1
    Chain: "I"
      Number of atoms: 76
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 7, 76
          Classifications: {'peptide': 7}
          Modifications used: {'COO': 1}
          Link IDs: {'TRANS': 6}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Planarities with less than four sites: {'UX8:plan-2': 1}
          Unresolved non-hydrogen planarities: 1
    Chain: "B"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' MG': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 8.36, per 1000 atoms: 0.61
  Number of scatterers: 13782
  At special positions: 0
  Unit cell: (110.11, 146.51, 123.76, 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      43     16.00
     Mg      1     11.99
     O    2703      8.00
     N    2375      7.00
     C    8660      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 690 " - pdb=" SG  CYS A 700 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=3, symmetry=0
  Number of additional bonds: simple=3, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 3.62
  Conformation dependent library (CDL) restraints added in 1.9 seconds
  

  3474 Ramachandran restraints generated.
    1737 Oldfield, 0 Emsley, 1737 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3240

  Finding SS restraints...
    Secondary structure from input PDB file:
      37 helices and 18 sheets defined
      28.5% alpha, 26.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.55
  Creating SS restraints...
    Processing helix  chain 'A' and resid 38 through 46
      removed outlier: 3.664A  pdb=" N   ALA A  42 " --> pdb=" O   ALA A  38 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 55 through 69
    Processing helix  chain 'A' and resid 106 through 118
      removed outlier: 3.695A  pdb=" N   LEU A 110 " --> pdb=" O   LYS A 106 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 126 through 145
      removed outlier: 4.355A  pdb=" N   ALA A 131 " --> pdb=" O   ARG A 127 " (cutoff:3.500A)
      removed outlier: 4.244A  pdb=" N   ASP A 132 " --> pdb=" O   THR A 128 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 189 through 196
      removed outlier: 4.109A  pdb=" N   HIS A 196 " --> pdb=" O   GLU A 192 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 215 through 232
    Processing helix  chain 'A' and resid 280 through 288
    Processing helix  chain 'A' and resid 297 through 315
    Processing helix  chain 'A' and resid 361 through 367
      removed outlier: 3.589A  pdb=" N   LEU A 365 " --> pdb=" O   LYS A 361 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 378 through 393
      removed outlier: 3.831A  pdb=" N   GLY A 393 " --> pdb=" O   LEU A 389 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 450 through 452
      No H-bonds generated for 'chain 'A' and resid 450 through 452'
    Processing helix  chain 'A' and resid 542 through 552
    Processing helix  chain 'A' and resid 647 through 651
      removed outlier: 3.506A  pdb=" N   ASN A 651 " --> pdb=" O   PHE A 648 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 686 through 690
      removed outlier: 4.600A  pdb=" N   GLU A 689 " --> pdb=" O   TYR A 686 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 33 through 39
      removed outlier: 3.947A  pdb=" N   GLU C  39 " --> pdb=" O   SER C  36 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 31 through 46
    Processing helix  chain 'D' and resid 48 through 62
    Processing helix  chain 'D' and resid 67 through 82
    Processing helix  chain 'D' and resid 84 through 99
    Processing helix  chain 'D' and resid 104 through 121
    Processing helix  chain 'D' and resid 137 through 154
    Processing helix  chain 'D' and resid 159 through 189
    Processing helix  chain 'D' and resid 190 through 205
    Processing helix  chain 'D' and resid 208 through 225
      Proline residue:  D 216  - end of helix
    Processing helix  chain 'D' and resid 227 through 241
      removed outlier: 4.053A  pdb=" N   LYS D 233 " --> pdb=" O   ALA D 229 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 51 through 59
    Processing helix  chain 'F' and resid 39 through 53
    Processing helix  chain 'F' and resid 62 through 86
      removed outlier: 3.538A  pdb=" N   ILE F  80 " --> pdb=" O   MET F  76 " (cutoff:3.500A)
      removed outlier: 3.513A  pdb=" N   MET F  83 " --> pdb=" O   ILE F  79 " (cutoff:3.500A)
      removed outlier: 4.074A  pdb=" N   GLY F  84 " --> pdb=" O   ILE F  80 " (cutoff:3.500A)
      removed outlier: 4.153A  pdb=" N   LYS F  86 " --> pdb=" O   GLN F  82 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 93 through 103
    Processing helix  chain 'F' and resid 124 through 149
      removed outlier: 3.966A  pdb=" N   ILE F 137 " --> pdb=" O   ARG F 133 " (cutoff:3.500A)
      removed outlier: 3.973A  pdb=" N   ILE F 138 " --> pdb=" O   LYS F 134 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 155 through 159
    Processing helix  chain 'F' and resid 190 through 206
    Processing helix  chain 'F' and resid 213 through 219
      removed outlier: 3.988A  pdb=" N   ILE F 217 " --> pdb=" O   GLY F 213 " (cutoff:3.500A)
      removed outlier: 3.512A  pdb=" N   HIS F 219 " --> pdb=" O   LEU F 215 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 222 through 226
      removed outlier: 4.334A  pdb=" N   LEU F 226 " --> pdb=" O   GLN F 223 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 235 through 239
      removed outlier: 3.832A  pdb=" N   LEU F 239 " --> pdb=" O   ILE F 236 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 240 through 249
      removed outlier: 4.283A  pdb=" N   GLN F 245 " --> pdb=" O   GLY F 241 " (cutoff:3.500A)
      removed outlier: 4.097A  pdb=" N   ALA F 246 " --> pdb=" O   ILE F 242 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 396 through 420
      removed outlier: 3.763A  pdb=" N   MET F 400 " --> pdb=" O   ARG F 396 " (cutoff:3.500A)
      removed outlier: 3.572A  pdb=" N   GLN F 415 " --> pdb=" O   ALA F 411 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 72 through 76
    Processing sheet with id=AA2, first strand: chain 'A' and resid 93 through 100
      removed outlier: 4.040A  pdb=" N   ILE A  94 " --> pdb=" O   VAL A 163 " (cutoff:3.500A)
      removed outlier: 7.774A  pdb=" N   LEU A 165 " --> pdb=" O   ILE A  94 " (cutoff:3.500A)
      removed outlier: 6.625A  pdb=" N   SER A  96 " --> pdb=" O   LEU A 165 " (cutoff:3.500A)
      removed outlier: 8.040A  pdb=" N   LEU A 167 " --> pdb=" O   SER A  96 " (cutoff:3.500A)
      removed outlier: 6.847A  pdb=" N   THR A  98 " --> pdb=" O   LEU A 167 " (cutoff:3.500A)
      removed outlier: 7.449A  pdb=" N   PHE A 169 " --> pdb=" O   THR A  98 " (cutoff:3.500A)
      removed outlier: 6.541A  pdb=" N   SER A 100 " --> pdb=" O   PHE A 169 " (cutoff:3.500A)
      removed outlier: 7.420A  pdb=" N   GLU A 171 " --> pdb=" O   SER A 100 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 93 through 100
      removed outlier: 4.040A  pdb=" N   ILE A  94 " --> pdb=" O   VAL A 163 " (cutoff:3.500A)
      removed outlier: 7.774A  pdb=" N   LEU A 165 " --> pdb=" O   ILE A  94 " (cutoff:3.500A)
      removed outlier: 6.625A  pdb=" N   SER A  96 " --> pdb=" O   LEU A 165 " (cutoff:3.500A)
      removed outlier: 8.040A  pdb=" N   LEU A 167 " --> pdb=" O   SER A  96 " (cutoff:3.500A)
      removed outlier: 6.847A  pdb=" N   THR A  98 " --> pdb=" O   LEU A 167 " (cutoff:3.500A)
      removed outlier: 7.449A  pdb=" N   PHE A 169 " --> pdb=" O   THR A  98 " (cutoff:3.500A)
      removed outlier: 6.541A  pdb=" N   SER A 100 " --> pdb=" O   PHE A 169 " (cutoff:3.500A)
      removed outlier: 7.420A  pdb=" N   GLU A 171 " --> pdb=" O   SER A 100 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 176 through 183
      removed outlier: 5.576A  pdb=" N   ILE A 254 " --> pdb=" O   ILE A 177 " (cutoff:3.500A)
      removed outlier: 3.533A  pdb=" N   GLN A 179 " --> pdb=" O   ILE A 254 " (cutoff:3.500A)
      removed outlier: 6.733A  pdb=" N   GLY A 253 " --> pdb=" O   LEU A 247 " (cutoff:3.500A)
      removed outlier: 4.584A  pdb=" N   LEU A 247 " --> pdb=" O   GLY A 253 " (cutoff:3.500A)
      removed outlier: 6.535A  pdb=" N   TYR A 255 " --> pdb=" O   VAL A 245 " (cutoff:3.500A)
      removed outlier: 4.273A  pdb=" N   VAL A 245 " --> pdb=" O   TYR A 255 " (cutoff:3.500A)
      removed outlier: 6.270A  pdb=" N   THR A 257 " --> pdb=" O   THR A 243 " (cutoff:3.500A)
      removed outlier: 4.319A  pdb=" N   THR A 243 " --> pdb=" O   THR A 257 " (cutoff:3.500A)
      removed outlier: 6.893A  pdb=" N   ASN A 259 " --> pdb=" O   ASP A 241 " (cutoff:3.500A)
      removed outlier: 7.919A  pdb=" N   SER B 193 " --> pdb=" O   THR A 243 " (cutoff:3.500A)
      removed outlier: 6.522A  pdb=" N   VAL A 245 " --> pdb=" O   SER B 193 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 267 through 274
      removed outlier: 4.389A  pdb=" N   LEU A 268 " --> pdb=" O   VAL A 335 " (cutoff:3.500A)
      removed outlier: 7.618A  pdb=" N   LEU A 337 " --> pdb=" O   LEU A 268 " (cutoff:3.500A)
      removed outlier: 6.877A  pdb=" N   GLY A 270 " --> pdb=" O   LEU A 337 " (cutoff:3.500A)
      removed outlier: 7.775A  pdb=" N   VAL A 339 " --> pdb=" O   GLY A 270 " (cutoff:3.500A)
      removed outlier: 6.690A  pdb=" N   GLU A 272 " --> pdb=" O   VAL A 339 " (cutoff:3.500A)
      removed outlier: 7.292A  pdb=" N   VAL A 341 " --> pdb=" O   GLU A 272 " (cutoff:3.500A)
      removed outlier: 5.911A  pdb=" N   SER A 274 " --> pdb=" O   VAL A 341 " (cutoff:3.500A)
      removed outlier: 7.424A  pdb=" N   ALA A 343 " --> pdb=" O   SER A 274 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 348 through 355
      removed outlier: 6.072A  pdb=" N   VAL A 412 " --> pdb=" O   VAL A 349 " (cutoff:3.500A)
      removed outlier: 3.905A  pdb=" N   LYS A 351 " --> pdb=" O   VAL A 412 " (cutoff:3.500A)
      removed outlier: 7.678A  pdb=" N   GLN A 411 " --> pdb=" O   ARG A 404 " (cutoff:3.500A)
      removed outlier: 5.172A  pdb=" N   ARG A 404 " --> pdb=" O   GLN A 411 " (cutoff:3.500A)
      removed outlier: 5.548A  pdb=" N   ASP A 413 " --> pdb=" O   THR A 402 " (cutoff:3.500A)
      removed outlier: 4.297A  pdb=" N   THR A 402 " --> pdb=" O   ASP A 413 " (cutoff:3.500A)
      removed outlier: 6.710A  pdb=" N   VAL A 415 " --> pdb=" O   THR A 400 " (cutoff:3.500A)
      removed outlier: 4.509A  pdb=" N   THR A 400 " --> pdb=" O   VAL A 415 " (cutoff:3.500A)
      removed outlier: 6.598A  pdb=" N   LYS A 417 " --> pdb=" O   VAL A 398 " (cutoff:3.500A)
      removed outlier: 4.395A  pdb=" N   VAL A 398 " --> pdb=" O   LYS A 417 " (cutoff:3.500A)
      removed outlier: 6.598A  pdb=" N   LYS A 419 " --> pdb=" O   GLU A 396 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'I' and resid 4 through 6
      removed outlier: 6.961A  pdb=" N   MET A 768 " --> pdb=" O   PHE A 791 " (cutoff:3.500A)
      removed outlier: 3.692A  pdb=" N   THR A 735 " --> pdb=" O   THR A 720 " (cutoff:3.500A)
      removed outlier: 5.278A  pdb=" N   TYR A 608 " --> pdb=" O   THR A 600 " (cutoff:3.500A)
      removed outlier: 4.540A  pdb=" N   TYR A 454 " --> pdb=" O   TRP A 449 " (cutoff:3.500A)
      removed outlier: 5.498A  pdb=" N   VAL A 456 " --> pdb=" O   ASP A 447 " (cutoff:3.500A)
      removed outlier: 4.517A  pdb=" N   ASP A 447 " --> pdb=" O   VAL A 456 " (cutoff:3.500A)
      removed outlier: 7.170A  pdb=" N   ILE A 458 " --> pdb=" O   GLN A 445 " (cutoff:3.500A)
      removed outlier: 4.804A  pdb=" N   GLN A 445 " --> pdb=" O   ILE A 458 " (cutoff:3.500A)
      removed outlier: 7.065A  pdb=" N   GLY A 460 " --> pdb=" O   GLY A 443 " (cutoff:3.500A)
      removed outlier: 5.309A  pdb=" N   GLY A 443 " --> pdb=" O   GLY A 460 " (cutoff:3.500A)
      removed outlier: 7.195A  pdb=" N   LYS A 462 " --> pdb=" O   GLN A 441 " (cutoff:3.500A)
      removed outlier: 5.531A  pdb=" N   GLN A 441 " --> pdb=" O   LYS A 462 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 45 through 50
      removed outlier: 3.753A  pdb=" N   THR B  45 " --> pdb=" O   THR B 391 " (cutoff:3.500A)
      removed outlier: 6.565A  pdb=" N   SER B 389 " --> pdb=" O   ALA B  47 " (cutoff:3.500A)
      removed outlier: 4.228A  pdb=" N   SER B  49 " --> pdb=" O   VAL B 387 " (cutoff:3.500A)
      removed outlier: 6.525A  pdb=" N   VAL B 387 " --> pdb=" O   SER B  49 " (cutoff:3.500A)
      removed outlier: 3.843A  pdb=" N   LEU B 378 " --> pdb=" O   ILE B 390 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 66 through 67
      removed outlier: 6.100A  pdb=" N   ASN B  85 " --> pdb=" O   GLU B  91 " (cutoff:3.500A)
      removed outlier: 6.543A  pdb=" N   GLU B  91 " --> pdb=" O   ASN B  85 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'B' and resid 116 through 117
      removed outlier: 6.188A  pdb=" N   ASN B 135 " --> pdb=" O   VAL B 141 " (cutoff:3.500A)
      removed outlier: 6.646A  pdb=" N   VAL B 141 " --> pdb=" O   ASN B 135 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'B' and resid 156 through 158
      removed outlier: 5.894A  pdb=" N   ASN B 175 " --> pdb=" O   VAL B 181 " (cutoff:3.500A)
      removed outlier: 6.694A  pdb=" N   VAL B 181 " --> pdb=" O   ASN B 175 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'B' and resid 201 through 203
      removed outlier: 6.524A  pdb=" N   LEU B 220 " --> pdb=" O   MET B 226 " (cutoff:3.500A)
      removed outlier: 7.359A  pdb=" N   MET B 226 " --> pdb=" O   LEU B 220 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'B' and resid 252 through 254
      removed outlier: 5.900A  pdb=" N   ASP B 271 " --> pdb=" O   ILE B 277 " (cutoff:3.500A)
      removed outlier: 6.433A  pdb=" N   ILE B 277 " --> pdb=" O   ASP B 271 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'B' and resid 290 through 292
      removed outlier: 6.204A  pdb=" N   THR B 309 " --> pdb=" O   THR B 315 " (cutoff:3.500A)
      removed outlier: 6.356A  pdb=" N   THR B 315 " --> pdb=" O   THR B 309 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'B' and resid 331 through 332
    Processing sheet with id=AB7, first strand: chain 'E' and resid 32 through 34
    Processing sheet with id=AB8, first strand: chain 'F' and resid 28 through 32
    Processing sheet with id=AB9, first strand: chain 'F' and resid 230 through 234
      removed outlier: 5.510A  pdb=" N   GLN F 230 " --> pdb=" O   HIS F 178 " (cutoff:3.500A)
      removed outlier: 6.549A  pdb=" N   HIS F 178 " --> pdb=" O   GLN F 230 " (cutoff:3.500A)
      removed outlier: 4.826A  pdb=" N   GLY F 232 " --> pdb=" O   LEU F 176 " (cutoff:3.500A)
      removed outlier: 3.973A  pdb=" N   LEU F 176 " --> pdb=" O   GLY F 232 " (cutoff:3.500A)
      removed outlier: 6.329A  pdb=" N   ASN F 175 " --> pdb=" O   ASN F 271 " (cutoff:3.500A)
      removed outlier: 5.797A  pdb=" N   HIS F 266 " --> pdb=" O   PRO F 258 " (cutoff:3.500A)
      removed outlier: 3.664A  pdb=" N   LEU F 268 " --> pdb=" O   VAL F 256 " (cutoff:3.500A)

    640 hydrogen bonds defined for protein.
    1794 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: 5.06

  Time building geometry restraints manager: 4.21 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 4592
        1.34 -     1.46: 2353
        1.46 -     1.58: 7027
        1.58 -     1.70: 1
        1.70 -     1.82: 83
  Bond restraints: 14056
  Sorted by residual:
  bond pdb=" CA  UX8 I   3 "
       pdb=" CB  UX8 I   3 "
    ideal  model  delta    sigma   weight residual
    1.530  1.714 -0.184 2.00e-02 2.50e+03 8.43e+01
  bond pdb=" CA  UX8 I   3 "
       pdb=" C   UX8 I   3 "
    ideal  model  delta    sigma   weight residual
    1.525  1.334  0.191 2.10e-02 2.27e+03 8.31e+01
  bond pdb=" CB  UX8 I   3 "
       pdb=" CG  UX8 I   3 "
    ideal  model  delta    sigma   weight residual
    1.493  1.648 -0.155 2.00e-02 2.50e+03 6.01e+01
  bond pdb=" CG  UX8 I   3 "
       pdb=" CD2 UX8 I   3 "
    ideal  model  delta    sigma   weight residual
    1.433  1.575 -0.142 2.00e-02 2.50e+03 5.06e+01
  bond pdb=" N   UX8 I   3 "
       pdb=" CA  UX8 I   3 "
    ideal  model  delta    sigma   weight residual
    1.458  1.337  0.121 1.90e-02 2.77e+03 4.08e+01
  ... (remaining 14051 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     5.24: 19062
        5.24 -    10.48: 15
       10.48 -    15.72: 0
       15.72 -    20.97: 1
       20.97 -    26.21: 1
  Bond angle restraints: 19079
  Sorted by residual:
  angle pdb=" CA  UX8 I   3 "
        pdb=" C   UX8 I   3 "
        pdb=" O   UX8 I   3 "
      ideal   model   delta    sigma   weight residual
     120.80  147.01  -26.21 1.70e+00 3.46e-01 2.38e+02
  angle pdb=" CA  UX8 I   3 "
        pdb=" C   UX8 I   3 "
        pdb=" N   THR I   4 "
      ideal   model   delta    sigma   weight residual
     116.20   95.86   20.34 2.00e+00 2.50e-01 1.03e+02
  angle pdb=" O   UX8 I   3 "
        pdb=" C   UX8 I   3 "
        pdb=" N   THR I   4 "
      ideal   model   delta    sigma   weight residual
     123.00  117.13    5.87 1.60e+00 3.91e-01 1.35e+01
  angle pdb=" C   UX8 I   3 "
        pdb=" N   THR I   4 "
        pdb=" CA  THR I   4 "
      ideal   model   delta    sigma   weight residual
     121.70  128.19   -6.49 1.80e+00 3.09e-01 1.30e+01
  angle pdb=" CD1 UX8 I   3 "
        pdb=" NE1 UX8 I   3 "
        pdb=" CE2 UX8 I   3 "
      ideal   model   delta    sigma   weight residual
     109.40  119.72  -10.32 3.00e+00 1.11e-01 1.18e+01
  ... (remaining 19074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    18.19: 7618
       18.19 -    36.39: 627
       36.39 -    54.58: 82
       54.58 -    72.78: 23
       72.78 -    90.97: 13
  Dihedral angle restraints: 8363
    sinusoidal: 3289
      harmonic: 5074
  Sorted by residual:
  dihedral pdb=" CB  CYS A 690 "
           pdb=" SG  CYS A 690 "
           pdb=" SG  CYS A 700 "
           pdb=" CB  CYS A 700 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  133.35  -40.35     1      1.00e+01 1.00e-02 2.28e+01
  dihedral pdb=" CA  GLU A 521 "
           pdb=" C   GLU A 521 "
           pdb=" N   TYR A 522 "
           pdb=" CA  TYR A 522 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -160.03  -19.97     0      5.00e+00 4.00e-02 1.60e+01
  dihedral pdb=" CA  THR A 288 "
           pdb=" C   THR A 288 "
           pdb=" N   LYS A 289 "
           pdb=" CA  LYS A 289 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.19   18.81     0      5.00e+00 4.00e-02 1.41e+01
  ... (remaining 8360 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.092: 1957
       0.092 -    0.185: 136
       0.185 -    0.277: 2
       0.277 -    0.370: 1
       0.370 -    0.462: 1
  Chirality restraints: 2097
  Sorted by residual:
  chirality pdb=" CB  UX8 I   3 "
            pdb=" CA  UX8 I   3 "
            pdb=" CG  UX8 I   3 "
            pdb=" O9  UX8 I   3 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.38   -2.84    0.46 2.00e-01 2.50e+01 5.34e+00
  chirality pdb=" CA  UX8 I   3 "
            pdb=" N   UX8 I   3 "
            pdb=" C   UX8 I   3 "
            pdb=" CB  UX8 I   3 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.20    0.31 2.00e-01 2.50e+01 2.37e+00
  chirality pdb=" CB  THR B 386 "
            pdb=" CA  THR B 386 "
            pdb=" OG1 THR B 386 "
            pdb=" CG2 THR B 386 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.33    0.23 2.00e-01 2.50e+01 1.27e+00
  ... (remaining 2094 not shown)

  Planarity restraints: 2514
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   MET A  46 "    0.033 5.00e-02 4.00e+02   4.99e-02 3.98e+00
        pdb=" N   PRO A  47 "   -0.086 5.00e-02 4.00e+02
        pdb=" CA  PRO A  47 "    0.026 5.00e-02 4.00e+02
        pdb=" CD  PRO A  47 "    0.028 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER A 778 "    0.030 5.00e-02 4.00e+02   4.49e-02 3.23e+00
        pdb=" N   PRO A 779 "   -0.078 5.00e-02 4.00e+02
        pdb=" CA  PRO A 779 "    0.023 5.00e-02 4.00e+02
        pdb=" CD  PRO A 779 "    0.025 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU F 239 "    0.026 5.00e-02 4.00e+02   3.98e-02 2.54e+00
        pdb=" N   PRO F 240 "   -0.069 5.00e-02 4.00e+02
        pdb=" CA  PRO F 240 "    0.021 5.00e-02 4.00e+02
        pdb=" CD  PRO F 240 "    0.022 5.00e-02 4.00e+02
  ... (remaining 2511 not shown)

  Histogram of nonbonded interaction distances:
        2.01 -     2.59: 166
        2.59 -     3.16: 11854
        3.16 -     3.74: 22625
        3.74 -     4.32: 31581
        4.32 -     4.90: 51811
  Nonbonded interactions: 118037
  Sorted by model distance:
  nonbonded pdb=" OD1 ASP B 212 "
            pdb="MG    MG B 401 "
     model   vdw
     2.007 2.170
  nonbonded pdb=" OD1 ASP B 248 "
            pdb="MG    MG B 401 "
     model   vdw
     2.060 2.170
  nonbonded pdb=" O   GLY B 196 "
            pdb="MG    MG B 401 "
     model   vdw
     2.065 2.170
  nonbonded pdb=" OG  SER B 126 "
            pdb=" O   GLN B 130 "
     model   vdw
     2.158 3.040
  nonbonded pdb=" OH  TYR D 110 "
            pdb=" OD2 ASP D 162 "
     model   vdw
     2.197 3.040
  ... (remaining 118032 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
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:             1.320
  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:          0.630
  Check model and map are aligned:         0.110
  Set scattering table:                    0.150
  Process input model:                     34.500
  Find NCS groups from input model:        0.180
  Set up NCS constraints:                  0.060
  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:2.920
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   39.880
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7664
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.191  14060  Z= 0.228
  Angle     :  0.640  26.208  19081  Z= 0.344
  Chirality :  0.045   0.462   2097
  Planarity :  0.004   0.050   2514
  Dihedral  : 13.738  90.973   5120
  Min Nonbonded Distance : 2.007

Molprobity Statistics.
  All-atom Clashscore : 13.31
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  4.55 %
    Favored  : 95.34 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.34 %
    Favored  : 99.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.37 (0.20), residues: 1737
  helix:  1.42 (0.24), residues: 451
  sheet: -0.80 (0.23), residues: 473
  loop : -0.78 (0.23), residues: 813

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B  93 
 HIS   0.003   0.001   HIS A 555 
 PHE   0.024   0.001   PHE A 140 
 TYR   0.013   0.001   TYR A 522 
 ARG   0.010   0.000   ARG D  97 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.12496 (  640)
  hydrogen bonds       : angle       6.06648 ( 1794)
  SS BOND              : bond        0.00234 (    1)
  SS BOND              : angle       0.85899 (    2)
  covalent geometry    : bond        0.00457 (14056)
  covalent geometry    : angle       0.63985 (19079)
  Misc. bond           : bond        0.00601 (    3)

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

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

  3474 Ramachandran restraints generated.
    1737 Oldfield, 0 Emsley, 1737 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3474 Ramachandran restraints generated.
    1737 Oldfield, 0 Emsley, 1737 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  176 residues out of total 1479 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 176
  time to evaluate  : 1.704 
Fit side-chains
   revert: symmetry clash
TARDY: cannot create tardy model for: "LYS A 808 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "GLN B 234 " (corrupted residue). Skipping it.
   revert: symmetry clash
   revert: symmetry clash
TARDY: cannot create tardy model for: "SER F 427 " (corrupted residue). Skipping it.
REVERT: A  413 ASP cc_start: 0.7769 (m-30) cc_final: 0.7551 (m-30)
REVERT: D  128 PHE cc_start: 0.3921 (t80) cc_final: 0.3674 (m-10)
REVERT: D  201 MET cc_start: 0.8037 (mmm) cc_final: 0.7575 (mtt)
  outliers start: 0
  outliers final: 0
  residues processed: 176
  average time/residue: 0.2595
  time to fit residues: 66.8857
Evaluate side-chains
  137 residues out of total 1479 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 137
  time to evaluate  : 1.508 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 173
   random chunks:
   chunk 146 optimal weight:    1.9990
   chunk 131 optimal weight:    0.8980
   chunk 72 optimal weight:    4.9990
   chunk 44 optimal weight:    0.9990
   chunk 88 optimal weight:    3.9990
   chunk 70 optimal weight:    3.9990
   chunk 135 optimal weight:    0.5980
   chunk 52 optimal weight:    2.9990
   chunk 82 optimal weight:    0.6980
   chunk 100 optimal weight:    2.9990
   chunk 157 optimal weight:    0.6980
   overall best weight:    0.7782

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

Flipped N/Q/H residues before XYZ refinement:
** A 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  54 GLN
** F  59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 186 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3812 r_free = 0.3812 target = 0.119889 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3481 r_free = 0.3481 target = 0.098065 restraints weight = 27992.139|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3478 r_free = 0.3478 target = 0.098682 restraints weight = 18779.206|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3491 r_free = 0.3491 target = 0.099496 restraints weight = 15380.220|
|-----------------------------------------------------------------------------|
r_work (final): 0.3481
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7705
moved from start:          0.0940

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047  14060  Z= 0.140
  Angle     :  0.552   6.951  19081  Z= 0.294
  Chirality :  0.044   0.184   2097
  Planarity :  0.004   0.058   2514
  Dihedral  :  4.361  18.085   1922
  Min Nonbonded Distance : 1.962

Molprobity Statistics.
  All-atom Clashscore : 10.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.49 %
    Favored  : 95.51 %
  Rotamer:
    Outliers :  0.68 %
    Allowed  :  6.77 %
    Favored  : 92.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.27 (0.20), residues: 1737
  helix:  1.49 (0.24), residues: 455
  sheet: -0.77 (0.24), residues: 443
  loop : -0.72 (0.22), residues: 839

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 143 
 HIS   0.002   0.001   HIS F 178 
 PHE   0.015   0.001   PHE A 140 
 TYR   0.015   0.001   TYR D  62 
 ARG   0.005   0.000   ARG D  97 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03918 (  640)
  hydrogen bonds       : angle       5.26825 ( 1794)
  SS BOND              : bond        0.00081 (    1)
  SS BOND              : angle       0.79951 (    2)
  covalent geometry    : bond        0.00297 (14056)
  covalent geometry    : angle       0.55241 (19079)
  Misc. bond           : bond        0.00726 (    3)

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

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

  3474 Ramachandran restraints generated.
    1737 Oldfield, 0 Emsley, 1737 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3474 Ramachandran restraints generated.
    1737 Oldfield, 0 Emsley, 1737 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  170 residues out of total 1479 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 160
  time to evaluate  : 1.510 
Fit side-chains
TARDY: cannot create tardy model for: "LYS A 808 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "GLN B 234 " (corrupted residue). Skipping it.
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
TARDY: cannot create tardy model for: "SER F 427 " (corrupted residue). Skipping it.
REVERT: D  109 MET cc_start: 0.7539 (mtp) cc_final: 0.7269 (mtp)
REVERT: D  128 PHE cc_start: 0.3799 (t80) cc_final: 0.3506 (m-10)
REVERT: F  186 ASN cc_start: 0.7758 (m-40) cc_final: 0.7516 (m-40)
  outliers start: 10
  outliers final: 8
  residues processed: 163
  average time/residue: 0.2687
  time to fit residues: 64.0008
Evaluate side-chains
  149 residues out of total 1479 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 141
  time to evaluate  : 1.684 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   56 ILE
Chi-restraints excluded: chain B residue  178 ASP
Chi-restraints excluded: chain B residue  244 LEU
Chi-restraints excluded: chain B residue  316 LEU
Chi-restraints excluded: chain E residue   42 ASP
Chi-restraints excluded: chain E residue  102 THR
Chi-restraints excluded: chain F residue   31 VAL
Chi-restraints excluded: chain I residue    4 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 173
   random chunks:
   chunk 118 optimal weight:    0.0020
   chunk 71 optimal weight:    5.9990
   chunk 29 optimal weight:    5.9990
   chunk 20 optimal weight:    1.9990
   chunk 109 optimal weight:    0.9980
   chunk 9 optimal weight:    9.9990
   chunk 167 optimal weight:    6.9990
   chunk 107 optimal weight:    3.9990
   chunk 52 optimal weight:    4.9990
   chunk 101 optimal weight:    0.9980
   chunk 40 optimal weight:    0.9980
   overall best weight:    0.9990

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

Flipped N/Q/H residues before XYZ refinement:
** A 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 166 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3795 r_free = 0.3795 target = 0.118604 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3454 r_free = 0.3454 target = 0.096333 restraints weight = 28161.026|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3450 r_free = 0.3450 target = 0.096598 restraints weight = 19112.425|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3462 r_free = 0.3462 target = 0.097428 restraints weight = 14996.840|
|-----------------------------------------------------------------------------|
r_work (final): 0.3464
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7744
moved from start:          0.1251

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047  14060  Z= 0.151
  Angle     :  0.540   7.086  19081  Z= 0.285
  Chirality :  0.043   0.164   2097
  Planarity :  0.004   0.059   2514
  Dihedral  :  4.359  17.643   1922
  Min Nonbonded Distance : 1.938

Molprobity Statistics.
  All-atom Clashscore : 11.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.78 %
    Favored  : 95.22 %
  Rotamer:
    Outliers :  1.02 %
    Allowed  :  9.21 %
    Favored  : 89.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.27 (0.20), residues: 1737
  helix:  1.60 (0.24), residues: 452
  sheet: -0.83 (0.23), residues: 449
  loop : -0.74 (0.22), residues: 836

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 143 
 HIS   0.002   0.001   HIS F 178 
 PHE   0.016   0.001   PHE A  99 
 TYR   0.013   0.001   TYR A 522 
 ARG   0.006   0.000   ARG C  83 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03620 (  640)
  hydrogen bonds       : angle       5.09432 ( 1794)
  SS BOND              : bond        0.00171 (    1)
  SS BOND              : angle       0.81350 (    2)
  covalent geometry    : bond        0.00327 (14056)
  covalent geometry    : angle       0.53952 (19079)
  Misc. bond           : bond        0.00719 (    3)

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

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

  3474 Ramachandran restraints generated.
    1737 Oldfield, 0 Emsley, 1737 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3474 Ramachandran restraints generated.
    1737 Oldfield, 0 Emsley, 1737 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  165 residues out of total 1479 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 150
  time to evaluate  : 1.507 
Fit side-chains
TARDY: cannot create tardy model for: "LYS A 808 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "GLN B 234 " (corrupted residue). Skipping it.
   revert: symmetry clash
TARDY: cannot create tardy model for: "SER F 427 " (corrupted residue). Skipping it.
REVERT: B  221 MET cc_start: 0.8504 (tpt) cc_final: 0.8171 (tpt)
REVERT: D  128 PHE cc_start: 0.3962 (t80) cc_final: 0.3604 (m-10)
REVERT: F  413 TRP cc_start: 0.8360 (t60) cc_final: 0.8078 (t60)
  outliers start: 15
  outliers final: 14
  residues processed: 158
  average time/residue: 0.2576
  time to fit residues: 59.9217
Evaluate side-chains
  153 residues out of total 1479 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 139
  time to evaluate  : 1.512 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  189 THR
Chi-restraints excluded: chain B residue   40 ASN
Chi-restraints excluded: chain B residue   56 ILE
Chi-restraints excluded: chain B residue  178 ASP
Chi-restraints excluded: chain B residue  244 LEU
Chi-restraints excluded: chain B residue  316 LEU
Chi-restraints excluded: chain E residue   42 ASP
Chi-restraints excluded: chain E residue   43 VAL
Chi-restraints excluded: chain E residue  102 THR
Chi-restraints excluded: chain F residue   31 VAL
Chi-restraints excluded: chain F residue   66 LEU
Chi-restraints excluded: chain F residue  271 ASN
Chi-restraints excluded: chain F residue  272 ASP
Chi-restraints excluded: chain I residue    4 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 173
   random chunks:
   chunk 118 optimal weight:    0.0670
   chunk 50 optimal weight:    4.9990
   chunk 75 optimal weight:    0.9980
   chunk 2 optimal weight:    0.0000
   chunk 126 optimal weight:    5.9990
   chunk 167 optimal weight:    0.0670
   chunk 106 optimal weight:    4.9990
   chunk 102 optimal weight:    1.9990
   chunk 97 optimal weight:    0.4980
   chunk 47 optimal weight:    2.9990
   chunk 144 optimal weight:    0.7980
   overall best weight:    0.2860

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

Flipped N/Q/H residues before XYZ refinement:
A 113 ASN
A 555 HIS
B  85 ASN
** F  59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 198 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3830 r_free = 0.3830 target = 0.121052 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3490 r_free = 0.3490 target = 0.098813 restraints weight = 27975.758|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3500 r_free = 0.3500 target = 0.099743 restraints weight = 17799.179|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3507 r_free = 0.3507 target = 0.100259 restraints weight = 13849.537|
|-----------------------------------------------------------------------------|
r_work (final): 0.3498
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7688
moved from start:          0.1523

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.044  14060  Z= 0.105
  Angle     :  0.510   7.136  19081  Z= 0.270
  Chirality :  0.042   0.172   2097
  Planarity :  0.004   0.057   2514
  Dihedral  :  4.199  17.697   1922
  Min Nonbonded Distance : 2.046

Molprobity Statistics.
  All-atom Clashscore : 10.29
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  4.49 %
    Favored  : 95.45 %
  Rotamer:
    Outliers :  1.22 %
    Allowed  : 10.97 %
    Favored  : 87.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.13 (0.20), residues: 1737
  helix:  1.81 (0.24), residues: 449
  sheet: -0.75 (0.24), residues: 442
  loop : -0.70 (0.22), residues: 846

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 143 
 HIS   0.003   0.000   HIS F 178 
 PHE   0.015   0.001   PHE A 426 
 TYR   0.012   0.001   TYR D 184 
 ARG   0.006   0.000   ARG C  83 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03280 (  640)
  hydrogen bonds       : angle       4.83413 ( 1794)
  SS BOND              : bond        0.00186 (    1)
  SS BOND              : angle       0.99865 (    2)
  covalent geometry    : bond        0.00222 (14056)
  covalent geometry    : angle       0.50959 (19079)
  Misc. bond           : bond        0.00665 (    3)

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

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

  3474 Ramachandran restraints generated.
    1737 Oldfield, 0 Emsley, 1737 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3474 Ramachandran restraints generated.
    1737 Oldfield, 0 Emsley, 1737 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  175 residues out of total 1479 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 157
  time to evaluate  : 1.581 
Fit side-chains
TARDY: cannot create tardy model for: "LYS A 808 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "GLN B 234 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "SER F 427 " (corrupted residue). Skipping it.
REVERT: A  289 LYS cc_start: 0.7973 (mmtp) cc_final: 0.7744 (mmmt)
REVERT: B  221 MET cc_start: 0.8535 (tpt) cc_final: 0.7752 (tpt)
REVERT: D  128 PHE cc_start: 0.3928 (t80) cc_final: 0.3476 (m-10)
REVERT: F  413 TRP cc_start: 0.8352 (t60) cc_final: 0.7969 (t60)
  outliers start: 18
  outliers final: 13
  residues processed: 172
  average time/residue: 0.2549
  time to fit residues: 65.7618
Evaluate side-chains
  147 residues out of total 1479 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 134
  time to evaluate  : 1.665 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  473 VAL
Chi-restraints excluded: chain B residue   56 ILE
Chi-restraints excluded: chain B residue   84 LEU
Chi-restraints excluded: chain B residue  178 ASP
Chi-restraints excluded: chain B residue  316 LEU
Chi-restraints excluded: chain E residue   39 THR
Chi-restraints excluded: chain E residue   86 VAL
Chi-restraints excluded: chain E residue  102 THR
Chi-restraints excluded: chain F residue   31 VAL
Chi-restraints excluded: chain F residue   66 LEU
Chi-restraints excluded: chain F residue  271 ASN
Chi-restraints excluded: chain F residue  272 ASP
Chi-restraints excluded: chain I residue    4 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 173
   random chunks:
   chunk 161 optimal weight:    3.9990
   chunk 13 optimal weight:    5.9990
   chunk 132 optimal weight:    0.9990
   chunk 108 optimal weight:    5.9990
   chunk 32 optimal weight:    0.9990
   chunk 158 optimal weight:    0.0980
   chunk 90 optimal weight:    4.9990
   chunk 92 optimal weight:    2.9990
   chunk 79 optimal weight:    3.9990
   chunk 152 optimal weight:    2.9990
   chunk 14 optimal weight:   10.0000
   overall best weight:    1.6188

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

Flipped N/Q/H residues before XYZ refinement:
** A 693 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D 125 GLN
D 158 GLN
** F  59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3776 r_free = 0.3776 target = 0.117396 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3429 r_free = 0.3429 target = 0.095113 restraints weight = 28069.179|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3428 r_free = 0.3428 target = 0.095554 restraints weight = 17599.645|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3438 r_free = 0.3438 target = 0.096190 restraints weight = 14300.002|
|-----------------------------------------------------------------------------|
r_work (final): 0.3427
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7808
moved from start:          0.1775

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.056  14060  Z= 0.207
  Angle     :  0.583  10.477  19081  Z= 0.306
  Chirality :  0.044   0.168   2097
  Planarity :  0.004   0.057   2514
  Dihedral  :  4.502  19.032   1922
  Min Nonbonded Distance : 1.901

Molprobity Statistics.
  All-atom Clashscore : 11.91
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  5.01 %
    Favored  : 94.93 %
  Rotamer:
    Outliers :  1.69 %
    Allowed  : 11.44 %
    Favored  : 86.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.35 (0.20), residues: 1737
  helix:  1.51 (0.24), residues: 452
  sheet: -0.90 (0.23), residues: 465
  loop : -0.76 (0.22), residues: 820

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B  93 
 HIS   0.003   0.001   HIS D 102 
 PHE   0.013   0.002   PHE I   7 
 TYR   0.014   0.001   TYR B 388 
 ARG   0.007   0.000   ARG D  97 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03618 (  640)
  hydrogen bonds       : angle       5.06009 ( 1794)
  SS BOND              : bond        0.00379 (    1)
  SS BOND              : angle       1.22957 (    2)
  covalent geometry    : bond        0.00455 (14056)
  covalent geometry    : angle       0.58249 (19079)
  Misc. bond           : bond        0.00763 (    3)

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

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

  3474 Ramachandran restraints generated.
    1737 Oldfield, 0 Emsley, 1737 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3474 Ramachandran restraints generated.
    1737 Oldfield, 0 Emsley, 1737 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  175 residues out of total 1479 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 150
  time to evaluate  : 1.507 
Fit side-chains
   revert: symmetry clash
TARDY: cannot create tardy model for: "LYS A 808 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "GLN B 234 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "SER F 427 " (corrupted residue). Skipping it.
REVERT: B  123 TYR cc_start: 0.8135 (m-80) cc_final: 0.7823 (m-80)
REVERT: D  128 PHE cc_start: 0.3733 (t80) cc_final: 0.3435 (m-10)
REVERT: F  413 TRP cc_start: 0.8460 (t60) cc_final: 0.8100 (t60)
  outliers start: 25
  outliers final: 20
  residues processed: 170
  average time/residue: 0.2596
  time to fit residues: 65.3694
Evaluate side-chains
  158 residues out of total 1479 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 138
  time to evaluate  : 1.522 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  189 THR
Chi-restraints excluded: chain A residue  225 THR
Chi-restraints excluded: chain A residue  473 VAL
Chi-restraints excluded: chain A residue  735 THR
Chi-restraints excluded: chain B residue   29 VAL
Chi-restraints excluded: chain B residue   40 ASN
Chi-restraints excluded: chain B residue   56 ILE
Chi-restraints excluded: chain B residue  178 ASP
Chi-restraints excluded: chain B residue  244 LEU
Chi-restraints excluded: chain B residue  316 LEU
Chi-restraints excluded: chain C residue   51 HIS
Chi-restraints excluded: chain E residue   39 THR
Chi-restraints excluded: chain E residue   42 ASP
Chi-restraints excluded: chain E residue   43 VAL
Chi-restraints excluded: chain E residue   86 VAL
Chi-restraints excluded: chain F residue   31 VAL
Chi-restraints excluded: chain F residue   66 LEU
Chi-restraints excluded: chain F residue  271 ASN
Chi-restraints excluded: chain F residue  272 ASP
Chi-restraints excluded: chain I residue    4 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 173
   random chunks:
   chunk 160 optimal weight:    9.9990
   chunk 36 optimal weight:    1.9990
   chunk 152 optimal weight:    4.9990
   chunk 18 optimal weight:    0.6980
   chunk 118 optimal weight:    0.0870
   chunk 134 optimal weight:    0.7980
   chunk 0 optimal weight:    9.9990
   chunk 69 optimal weight:    0.2980
   chunk 77 optimal weight:    4.9990
   chunk 159 optimal weight:    6.9990
   chunk 137 optimal weight:    1.9990
   overall best weight:    0.7760

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

Flipped N/Q/H residues before XYZ refinement:
** A 693 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  34 GLN
E  54 GLN
** F  59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3793 r_free = 0.3793 target = 0.118346 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3457 r_free = 0.3457 target = 0.096578 restraints weight = 28258.768|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3453 r_free = 0.3453 target = 0.096916 restraints weight = 19054.746|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3463 r_free = 0.3463 target = 0.097574 restraints weight = 15246.652|
|-----------------------------------------------------------------------------|
r_work (final): 0.3449
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7742
moved from start:          0.1841

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046  14060  Z= 0.134
  Angle     :  0.530   7.639  19081  Z= 0.281
  Chirality :  0.043   0.180   2097
  Planarity :  0.004   0.057   2514
  Dihedral  :  4.350  17.700   1922
  Min Nonbonded Distance : 1.982

Molprobity Statistics.
  All-atom Clashscore : 11.10
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  5.12 %
    Favored  : 94.82 %
  Rotamer:
    Outliers :  1.62 %
    Allowed  : 12.46 %
    Favored  : 85.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.23 (0.20), residues: 1737
  helix:  1.65 (0.24), residues: 449
  sheet: -0.85 (0.23), residues: 465
  loop : -0.66 (0.23), residues: 823

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 546 
 HIS   0.002   0.001   HIS F 178 
 PHE   0.014   0.001   PHE A 426 
 TYR   0.013   0.001   TYR B 388 
 ARG   0.006   0.000   ARG C  83 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03306 (  640)
  hydrogen bonds       : angle       4.92144 ( 1794)
  SS BOND              : bond        0.00152 (    1)
  SS BOND              : angle       0.61032 (    2)
  covalent geometry    : bond        0.00293 (14056)
  covalent geometry    : angle       0.53040 (19079)
  Misc. bond           : bond        0.00692 (    3)

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

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

  3474 Ramachandran restraints generated.
    1737 Oldfield, 0 Emsley, 1737 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3474 Ramachandran restraints generated.
    1737 Oldfield, 0 Emsley, 1737 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  171 residues out of total 1479 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 147
  time to evaluate  : 1.519 
Fit side-chains
   revert: symmetry clash
TARDY: cannot create tardy model for: "LYS A 808 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "GLN B 234 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "GLN C  87 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "SER F 427 " (corrupted residue). Skipping it.
REVERT: A  739 TRP cc_start: 0.7848 (t60) cc_final: 0.7512 (t60)
REVERT: D  128 PHE cc_start: 0.3774 (t80) cc_final: 0.3389 (m-10)
REVERT: F  413 TRP cc_start: 0.8407 (t60) cc_final: 0.8073 (t60)
  outliers start: 24
  outliers final: 18
  residues processed: 165
  average time/residue: 0.2876
  time to fit residues: 69.6212
Evaluate side-chains
  150 residues out of total 1479 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 132
  time to evaluate  : 1.490 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  189 THR
Chi-restraints excluded: chain A residue  473 VAL
Chi-restraints excluded: chain B residue   56 ILE
Chi-restraints excluded: chain B residue   84 LEU
Chi-restraints excluded: chain B residue  107 GLU
Chi-restraints excluded: chain B residue  178 ASP
Chi-restraints excluded: chain B residue  244 LEU
Chi-restraints excluded: chain B residue  316 LEU
Chi-restraints excluded: chain C residue   87 GLN
Chi-restraints excluded: chain E residue   39 THR
Chi-restraints excluded: chain E residue   42 ASP
Chi-restraints excluded: chain E residue   86 VAL
Chi-restraints excluded: chain E residue   94 THR
Chi-restraints excluded: chain F residue   31 VAL
Chi-restraints excluded: chain F residue   66 LEU
Chi-restraints excluded: chain F residue  271 ASN
Chi-restraints excluded: chain F residue  272 ASP
Chi-restraints excluded: chain I residue    4 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 173
   random chunks:
   chunk 9 optimal weight:    0.0060
   chunk 49 optimal weight:    1.9990
   chunk 51 optimal weight:    2.9990
   chunk 14 optimal weight:   10.0000
   chunk 100 optimal weight:    0.9980
   chunk 139 optimal weight:    0.7980
   chunk 91 optimal weight:    0.6980
   chunk 147 optimal weight:    0.0770
   chunk 6 optimal weight:    0.2980
   chunk 165 optimal weight:    5.9990
   chunk 11 optimal weight:    0.9980
   overall best weight:    0.3754

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

Flipped N/Q/H residues before XYZ refinement:
E  34 GLN
F  33 ASN
** F  59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F  78 GLN
F  82 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3819 r_free = 0.3819 target = 0.120139 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3483 r_free = 0.3483 target = 0.098415 restraints weight = 28036.737|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3484 r_free = 0.3484 target = 0.098749 restraints weight = 17517.949|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3491 r_free = 0.3491 target = 0.099250 restraints weight = 14189.907|
|-----------------------------------------------------------------------------|
r_work (final): 0.3481
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7707
moved from start:          0.1964

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.045  14060  Z= 0.113
  Angle     :  0.516   7.717  19081  Z= 0.275
  Chirality :  0.043   0.175   2097
  Planarity :  0.004   0.057   2514
  Dihedral  :  4.242  21.974   1922
  Min Nonbonded Distance : 2.027

Molprobity Statistics.
  All-atom Clashscore : 10.62
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  4.61 %
    Favored  : 95.34 %
  Rotamer:
    Outliers :  1.42 %
    Allowed  : 12.93 %
    Favored  : 85.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.14 (0.21), residues: 1737
  helix:  1.77 (0.24), residues: 449
  sheet: -0.76 (0.23), residues: 465
  loop : -0.67 (0.23), residues: 823

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 546 
 HIS   0.002   0.000   HIS F 178 
 PHE   0.015   0.001   PHE A 426 
 TYR   0.013   0.001   TYR D 184 
 ARG   0.011   0.000   ARG D  97 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03188 (  640)
  hydrogen bonds       : angle       4.76834 ( 1794)
  SS BOND              : bond        0.00071 (    1)
  SS BOND              : angle       0.46964 (    2)
  covalent geometry    : bond        0.00242 (14056)
  covalent geometry    : angle       0.51558 (19079)
  Misc. bond           : bond        0.00682 (    3)

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

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

  3474 Ramachandran restraints generated.
    1737 Oldfield, 0 Emsley, 1737 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3474 Ramachandran restraints generated.
    1737 Oldfield, 0 Emsley, 1737 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  166 residues out of total 1479 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 145
  time to evaluate  : 1.487 
Fit side-chains
TARDY: cannot create tardy model for: "LYS A 808 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "GLN B 234 " (corrupted residue). Skipping it.
   revert: symmetry clash
TARDY: cannot create tardy model for: "SER F 427 " (corrupted residue). Skipping it.
REVERT: A   87 GLN cc_start: 0.3865 (tm-30) cc_final: 0.2555 (mt0)
REVERT: A  739 TRP cc_start: 0.7771 (t60) cc_final: 0.7466 (t60)
REVERT: B  221 MET cc_start: 0.8629 (tpt) cc_final: 0.8322 (tpt)
REVERT: D  128 PHE cc_start: 0.3705 (t80) cc_final: 0.3379 (m-10)
REVERT: F  413 TRP cc_start: 0.8388 (t60) cc_final: 0.8051 (t60)
  outliers start: 21
  outliers final: 19
  residues processed: 161
  average time/residue: 0.2541
  time to fit residues: 60.6198
Evaluate side-chains
  152 residues out of total 1479 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 133
  time to evaluate  : 1.473 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  189 THR
Chi-restraints excluded: chain A residue  423 THR
Chi-restraints excluded: chain A residue  428 PHE
Chi-restraints excluded: chain A residue  473 VAL
Chi-restraints excluded: chain B residue   29 VAL
Chi-restraints excluded: chain B residue   40 ASN
Chi-restraints excluded: chain B residue   56 ILE
Chi-restraints excluded: chain B residue   84 LEU
Chi-restraints excluded: chain B residue  107 GLU
Chi-restraints excluded: chain B residue  178 ASP
Chi-restraints excluded: chain B residue  316 LEU
Chi-restraints excluded: chain D residue  205 TYR
Chi-restraints excluded: chain E residue   39 THR
Chi-restraints excluded: chain E residue   42 ASP
Chi-restraints excluded: chain E residue   86 VAL
Chi-restraints excluded: chain F residue   31 VAL
Chi-restraints excluded: chain F residue  271 ASN
Chi-restraints excluded: chain F residue  272 ASP
Chi-restraints excluded: chain I residue    4 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 173
   random chunks:
   chunk 113 optimal weight:    6.9990
   chunk 16 optimal weight:    3.9990
   chunk 33 optimal weight:    1.9990
   chunk 13 optimal weight:    0.6980
   chunk 114 optimal weight:    4.9990
   chunk 142 optimal weight:    0.0000
   chunk 65 optimal weight:    2.9990
   chunk 89 optimal weight:    2.9990
   chunk 99 optimal weight:    3.9990
   chunk 23 optimal weight:    1.9990
   chunk 118 optimal weight:    0.4980
   overall best weight:    1.0388

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

Flipped N/Q/H residues before XYZ refinement:
** A 693 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  54 GLN
** F  59 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 = 0.3793 r_free = 0.3793 target = 0.118314 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3447 r_free = 0.3447 target = 0.096027 restraints weight = 28152.641|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3451 r_free = 0.3451 target = 0.096738 restraints weight = 17365.242|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3464 r_free = 0.3464 target = 0.097647 restraints weight = 13658.811|
|-----------------------------------------------------------------------------|
r_work (final): 0.3465
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7749
moved from start:          0.2042

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048  14060  Z= 0.154
  Angle     :  0.552   8.995  19081  Z= 0.290
  Chirality :  0.043   0.174   2097
  Planarity :  0.004   0.056   2514
  Dihedral  :  4.321  21.628   1922
  Min Nonbonded Distance : 1.928

Molprobity Statistics.
  All-atom Clashscore : 11.02
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  4.89 %
    Favored  : 95.05 %
  Rotamer:
    Outliers :  1.69 %
    Allowed  : 13.07 %
    Favored  : 85.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.20 (0.20), residues: 1737
  helix:  1.64 (0.24), residues: 455
  sheet: -0.75 (0.23), residues: 474
  loop : -0.70 (0.23), residues: 808

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B  93 
 HIS   0.004   0.001   HIS A 280 
 PHE   0.013   0.001   PHE A 426 
 TYR   0.017   0.001   TYR A 608 
 ARG   0.008   0.000   ARG D  97 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03329 (  640)
  hydrogen bonds       : angle       4.84419 ( 1794)
  SS BOND              : bond        0.00156 (    1)
  SS BOND              : angle       0.65468 (    2)
  covalent geometry    : bond        0.00340 (14056)
  covalent geometry    : angle       0.55166 (19079)
  Misc. bond           : bond        0.00714 (    3)

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

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

  3474 Ramachandran restraints generated.
    1737 Oldfield, 0 Emsley, 1737 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3474 Ramachandran restraints generated.
    1737 Oldfield, 0 Emsley, 1737 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  172 residues out of total 1479 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 147
  time to evaluate  : 1.529 
Fit side-chains
TARDY: cannot create tardy model for: "LYS A 808 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "GLN B 234 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "GLN C  87 " (corrupted residue). Skipping it.
   revert: symmetry clash
TARDY: cannot create tardy model for: "SER F 427 " (corrupted residue). Skipping it.
REVERT: A  739 TRP cc_start: 0.7820 (t60) cc_final: 0.7514 (t60)
REVERT: B  123 TYR cc_start: 0.8152 (m-80) cc_final: 0.7807 (m-80)
REVERT: D  128 PHE cc_start: 0.3712 (t80) cc_final: 0.3370 (m-10)
REVERT: F  413 TRP cc_start: 0.8454 (t60) cc_final: 0.8105 (t60)
  outliers start: 25
  outliers final: 21
  residues processed: 168
  average time/residue: 0.3212
  time to fit residues: 79.6092
Evaluate side-chains
  157 residues out of total 1479 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 136
  time to evaluate  : 1.694 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  189 THR
Chi-restraints excluded: chain A residue  423 THR
Chi-restraints excluded: chain A residue  473 VAL
Chi-restraints excluded: chain B residue   29 VAL
Chi-restraints excluded: chain B residue   40 ASN
Chi-restraints excluded: chain B residue   56 ILE
Chi-restraints excluded: chain B residue   84 LEU
Chi-restraints excluded: chain B residue  107 GLU
Chi-restraints excluded: chain B residue  178 ASP
Chi-restraints excluded: chain B residue  316 LEU
Chi-restraints excluded: chain C residue   51 HIS
Chi-restraints excluded: chain C residue   87 GLN
Chi-restraints excluded: chain D residue  205 TYR
Chi-restraints excluded: chain E residue   39 THR
Chi-restraints excluded: chain E residue   42 ASP
Chi-restraints excluded: chain E residue   86 VAL
Chi-restraints excluded: chain E residue  102 THR
Chi-restraints excluded: chain F residue   31 VAL
Chi-restraints excluded: chain F residue  271 ASN
Chi-restraints excluded: chain F residue  272 ASP
Chi-restraints excluded: chain I residue    4 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 173
   random chunks:
   chunk 10 optimal weight:    0.9980
   chunk 7 optimal weight:   20.0000
   chunk 48 optimal weight:    6.9990
   chunk 0 optimal weight:   10.0000
   chunk 88 optimal weight:    0.9980
   chunk 11 optimal weight:    1.9990
   chunk 146 optimal weight:    5.9990
   chunk 96 optimal weight:    3.9990
   chunk 164 optimal weight:    3.9990
   chunk 125 optimal weight:    0.6980
   chunk 167 optimal weight:    4.9990
   overall best weight:    1.7384

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

Flipped N/Q/H residues before XYZ refinement:
** A 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 693 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
E  34 GLN
E  54 GLN
** F  59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3771 r_free = 0.3771 target = 0.116949 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3428 r_free = 0.3428 target = 0.094908 restraints weight = 27929.822|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3429 r_free = 0.3429 target = 0.095717 restraints weight = 18072.457|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3439 r_free = 0.3439 target = 0.096335 restraints weight = 14325.594|
|-----------------------------------------------------------------------------|
r_work (final): 0.3429
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7799
moved from start:          0.2197

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.058  14060  Z= 0.214
  Angle     :  0.593   8.879  19081  Z= 0.313
  Chirality :  0.045   0.196   2097
  Planarity :  0.004   0.057   2514
  Dihedral  :  4.561  21.295   1922
  Min Nonbonded Distance : 1.905

Molprobity Statistics.
  All-atom Clashscore : 12.72
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  5.24 %
    Favored  : 94.70 %
  Rotamer:
    Outliers :  1.69 %
    Allowed  : 13.13 %
    Favored  : 85.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.34 (0.20), residues: 1737
  helix:  1.53 (0.24), residues: 448
  sheet: -0.84 (0.23), residues: 477
  loop : -0.76 (0.23), residues: 812

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B  93 
 HIS   0.004   0.001   HIS A 280 
 PHE   0.013   0.002   PHE A 140 
 TYR   0.015   0.002   TYR A 608 
 ARG   0.019   0.001   ARG D  97 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03590 (  640)
  hydrogen bonds       : angle       5.06047 ( 1794)
  SS BOND              : bond        0.00226 (    1)
  SS BOND              : angle       0.88215 (    2)
  covalent geometry    : bond        0.00476 (14056)
  covalent geometry    : angle       0.59251 (19079)
  Misc. bond           : bond        0.00754 (    3)

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

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

  3474 Ramachandran restraints generated.
    1737 Oldfield, 0 Emsley, 1737 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3474 Ramachandran restraints generated.
    1737 Oldfield, 0 Emsley, 1737 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  165 residues out of total 1479 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 140
  time to evaluate  : 1.638 
Fit side-chains
TARDY: cannot create tardy model for: "LYS A 808 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "GLN B 234 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "GLN C  87 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "SER F 427 " (corrupted residue). Skipping it.
REVERT: A   87 GLN cc_start: 0.4279 (tm-30) cc_final: 0.2736 (mt0)
REVERT: A  739 TRP cc_start: 0.7921 (t60) cc_final: 0.7573 (t60)
REVERT: D  128 PHE cc_start: 0.3793 (t80) cc_final: 0.3402 (m-10)
REVERT: F  197 SER cc_start: 0.8446 (m) cc_final: 0.8157 (p)
REVERT: F  413 TRP cc_start: 0.8515 (t60) cc_final: 0.8156 (t60)
  outliers start: 25
  outliers final: 24
  residues processed: 158
  average time/residue: 0.2621
  time to fit residues: 61.8714
Evaluate side-chains
  161 residues out of total 1479 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 137
  time to evaluate  : 1.632 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  189 THR
Chi-restraints excluded: chain A residue  423 THR
Chi-restraints excluded: chain A residue  473 VAL
Chi-restraints excluded: chain B residue   29 VAL
Chi-restraints excluded: chain B residue   40 ASN
Chi-restraints excluded: chain B residue   56 ILE
Chi-restraints excluded: chain B residue   84 LEU
Chi-restraints excluded: chain B residue  178 ASP
Chi-restraints excluded: chain B residue  220 LEU
Chi-restraints excluded: chain B residue  244 LEU
Chi-restraints excluded: chain B residue  316 LEU
Chi-restraints excluded: chain C residue   87 GLN
Chi-restraints excluded: chain D residue  205 TYR
Chi-restraints excluded: chain E residue   39 THR
Chi-restraints excluded: chain E residue   42 ASP
Chi-restraints excluded: chain E residue   43 VAL
Chi-restraints excluded: chain E residue   57 TYR
Chi-restraints excluded: chain E residue   86 VAL
Chi-restraints excluded: chain E residue   94 THR
Chi-restraints excluded: chain E residue  102 THR
Chi-restraints excluded: chain F residue   31 VAL
Chi-restraints excluded: chain F residue  271 ASN
Chi-restraints excluded: chain F residue  272 ASP
Chi-restraints excluded: chain I residue    4 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 173
   random chunks:
   chunk 93 optimal weight:    4.9990
   chunk 137 optimal weight:    0.9980
   chunk 92 optimal weight:    0.9990
   chunk 66 optimal weight:   10.0000
   chunk 120 optimal weight:    0.9980
   chunk 112 optimal weight:    0.5980
   chunk 135 optimal weight:    0.7980
   chunk 99 optimal weight:    0.0050
   chunk 127 optimal weight:    0.7980
   chunk 147 optimal weight:    4.9990
   chunk 40 optimal weight:    0.9990
   overall best weight:    0.6394

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

Flipped N/Q/H residues before XYZ refinement:
A 286 GLN
** A 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 693 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  59 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 = 0.3794 r_free = 0.3794 target = 0.118493 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3447 r_free = 0.3447 target = 0.096228 restraints weight = 28031.160|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3451 r_free = 0.3451 target = 0.096795 restraints weight = 17259.507|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3465 r_free = 0.3465 target = 0.097670 restraints weight = 13651.522|
|-----------------------------------------------------------------------------|
r_work (final): 0.3465
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7759
moved from start:          0.2207

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046  14060  Z= 0.131
  Angle     :  0.559  10.025  19081  Z= 0.294
  Chirality :  0.043   0.175   2097
  Planarity :  0.004   0.057   2514
  Dihedral  :  4.424  20.812   1922
  Min Nonbonded Distance : 2.004

Molprobity Statistics.
  All-atom Clashscore : 11.54
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  4.78 %
    Favored  : 95.16 %
  Rotamer:
    Outliers :  1.56 %
    Allowed  : 13.27 %
    Favored  : 85.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.31 (0.20), residues: 1737
  helix:  1.49 (0.24), residues: 455
  sheet: -0.83 (0.23), residues: 468
  loop : -0.72 (0.23), residues: 814

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 143 
 HIS   0.003   0.001   HIS F 178 
 PHE   0.014   0.001   PHE A 426 
 TYR   0.015   0.001   TYR D 107 
 ARG   0.010   0.000   ARG D  97 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03302 (  640)
  hydrogen bonds       : angle       4.92883 ( 1794)
  SS BOND              : bond        0.00084 (    1)
  SS BOND              : angle       0.45948 (    2)
  covalent geometry    : bond        0.00289 (14056)
  covalent geometry    : angle       0.55857 (19079)
  Misc. bond           : bond        0.00696 (    3)

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

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

  3474 Ramachandran restraints generated.
    1737 Oldfield, 0 Emsley, 1737 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3474 Ramachandran restraints generated.
    1737 Oldfield, 0 Emsley, 1737 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  165 residues out of total 1479 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 142
  time to evaluate  : 1.579 
Fit side-chains
TARDY: cannot create tardy model for: "LYS A 808 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "GLN B 234 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "GLN C  87 " (corrupted residue). Skipping it.
   revert: symmetry clash
TARDY: cannot create tardy model for: "SER F 427 " (corrupted residue). Skipping it.
REVERT: A   87 GLN cc_start: 0.4044 (tm-30) cc_final: 0.2597 (mt0)
REVERT: A  739 TRP cc_start: 0.7796 (t60) cc_final: 0.7484 (t60)
REVERT: D  128 PHE cc_start: 0.3746 (t80) cc_final: 0.3332 (m-10)
REVERT: D  225 MET cc_start: 0.8594 (mtm) cc_final: 0.8282 (mtm)
REVERT: F  413 TRP cc_start: 0.8453 (t60) cc_final: 0.8097 (t60)
  outliers start: 23
  outliers final: 22
  residues processed: 160
  average time/residue: 0.2490
  time to fit residues: 59.8501
Evaluate side-chains
  156 residues out of total 1479 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 134
  time to evaluate  : 1.458 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  189 THR
Chi-restraints excluded: chain A residue  423 THR
Chi-restraints excluded: chain A residue  473 VAL
Chi-restraints excluded: chain B residue   29 VAL
Chi-restraints excluded: chain B residue   40 ASN
Chi-restraints excluded: chain B residue   56 ILE
Chi-restraints excluded: chain B residue   84 LEU
Chi-restraints excluded: chain B residue  178 ASP
Chi-restraints excluded: chain B residue  244 LEU
Chi-restraints excluded: chain B residue  316 LEU
Chi-restraints excluded: chain C residue   87 GLN
Chi-restraints excluded: chain D residue  205 TYR
Chi-restraints excluded: chain E residue   39 THR
Chi-restraints excluded: chain E residue   42 ASP
Chi-restraints excluded: chain E residue   86 VAL
Chi-restraints excluded: chain E residue   94 THR
Chi-restraints excluded: chain E residue  102 THR
Chi-restraints excluded: chain F residue   31 VAL
Chi-restraints excluded: chain F residue   80 ILE
Chi-restraints excluded: chain F residue  271 ASN
Chi-restraints excluded: chain F residue  272 ASP
Chi-restraints excluded: chain I residue    4 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 173
   random chunks:
   chunk 153 optimal weight:    0.4980
   chunk 154 optimal weight:    0.0970
   chunk 141 optimal weight:    2.9990
   chunk 56 optimal weight:    0.9980
   chunk 7 optimal weight:   20.0000
   chunk 111 optimal weight:    0.9990
   chunk 143 optimal weight:    3.9990
   chunk 38 optimal weight:    0.9980
   chunk 147 optimal weight:    2.9990
   chunk 118 optimal weight:    0.0070
   chunk 35 optimal weight:    0.5980
   overall best weight:    0.4396

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

Flipped N/Q/H residues before XYZ refinement:
** A 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
E  34 GLN
** F  59 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 = 0.3816 r_free = 0.3816 target = 0.119835 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3483 r_free = 0.3483 target = 0.098465 restraints weight = 28190.102|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3481 r_free = 0.3481 target = 0.098491 restraints weight = 18051.889|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3490 r_free = 0.3490 target = 0.099067 restraints weight = 14277.418|
|-----------------------------------------------------------------------------|
r_work (final): 0.3480
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7726
moved from start:          0.2267

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046  14060  Z= 0.117
  Angle     :  0.538   8.083  19081  Z= 0.285
  Chirality :  0.043   0.176   2097
  Planarity :  0.004   0.056   2514
  Dihedral  :  4.309  20.355   1922
  Min Nonbonded Distance : 2.016

Molprobity Statistics.
  All-atom Clashscore : 11.36
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  4.84 %
    Favored  : 95.11 %
  Rotamer:
    Outliers :  1.62 %
    Allowed  : 13.61 %
    Favored  : 84.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.24 (0.21), residues: 1737
  helix:  1.52 (0.24), residues: 455
  sheet: -0.70 (0.23), residues: 466
  loop : -0.71 (0.23), residues: 816

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 143 
 HIS   0.003   0.000   HIS F 178 
 PHE   0.015   0.001   PHE A 426 
 TYR   0.013   0.001   TYR D 184 
 ARG   0.015   0.000   ARG D  97 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03185 (  640)
  hydrogen bonds       : angle       4.80572 ( 1794)
  SS BOND              : bond        0.00056 (    1)
  SS BOND              : angle       0.43271 (    2)
  covalent geometry    : bond        0.00258 (14056)
  covalent geometry    : angle       0.53825 (19079)
  Misc. bond           : bond        0.00687 (    3)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4111.69 seconds
wall clock time: 72 minutes 33.95 seconds (4353.95 seconds total)