Starting phenix.real_space_refine
on Sat Aug 23 17:43:37 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8pzu_18045/08_2025/8pzu_18045.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8pzu_18045/08_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 {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8pzu_18045/08_2025/8pzu_18045.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8pzu_18045/08_2025/8pzu_18045.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8pzu_18045/08_2025/8pzu_18045.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8pzu_18045/08_2025/8pzu_18045.map"
  }
  resolution = 3.5
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 3.13, per 1000 atoms: 0.23
  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: 1.00
  Conformation dependent library (CDL) restraints added in 510.5 milliseconds
  
  Enol-peptide restraints added in 1.2 microseconds
  

  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: 0.36
  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: 2.52

  Time building geometry restraints manager: 1.41 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:             2.420
  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:             0.020
  Extract box with map and model:          0.320
  Check model and map are aligned:         0.050
  Set scattering table:                    0.060
  Process input model:                     12.750
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.020
  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:1.150
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   16.830
-------------------------------------------------------------------------------
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 : 13.34
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  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
 ARG   0.010   0.000   ARG D  97 
 TYR   0.013   0.001   TYR A 522 
 PHE   0.024   0.001   PHE A 140 
 TRP   0.009   0.001   TRP B  93 
 HIS   0.003   0.001   HIS A 555 

Details of bonding type rmsd
  covalent geometry    : bond        0.00457 (14056)
  covalent geometry    : angle       0.63985 (19079)
  SS BOND              : bond        0.00234 (    1)
  SS BOND              : angle       0.85899 (    2)
  hydrogen bonds       : bond        0.12496 (  640)
  hydrogen bonds       : angle       6.06648 ( 1794)
  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  : 0.507 
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.
   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: 0.1015
  time to fit residues: 26.3604
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  : 0.331 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 173
   random chunks:
   chunk 98 optimal weight:    6.9990
   chunk 107 optimal weight:    0.9980
   chunk 10 optimal weight:    0.7980
   chunk 66 optimal weight:    0.8980
   chunk 130 optimal weight:    1.9990
   chunk 124 optimal weight:    4.9990
   chunk 103 optimal weight:    4.9990
   chunk 77 optimal weight:    5.9990
   chunk 122 optimal weight:    0.2980
   chunk 91 optimal weight:    1.9990
   chunk 149 optimal weight:    3.9990
   overall best weight:    0.9982

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

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

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3801 r_free = 0.3801 target = 0.119126 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3466 r_free = 0.3466 target = 0.097128 restraints weight = 28044.938|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3464 r_free = 0.3464 target = 0.097683 restraints weight = 19895.130|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3475 r_free = 0.3475 target = 0.098390 restraints weight = 14888.371|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3484 r_free = 0.3484 target = 0.098982 restraints weight = 12770.364|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3485 r_free = 0.3485 target = 0.099066 restraints weight = 11312.612|
|-----------------------------------------------------------------------------|
r_work (final): 0.3475
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7709
moved from start:          0.0985

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051  14060  Z= 0.155
  Angle     :  0.561   7.480  19081  Z= 0.298
  Chirality :  0.044   0.184   2097
  Planarity :  0.004   0.058   2514
  Dihedral  :  4.416  17.855   1922
  Min Nonbonded Distance : 1.935

Molprobity Statistics.
  All-atom Clashscore : 10.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.55 %
    Favored  : 95.45 %
  Rotamer:
    Outliers :  0.68 %
    Allowed  :  7.04 %
    Favored  : 92.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.31 (0.20), residues: 1737
  helix:  1.46 (0.24), residues: 455
  sheet: -0.77 (0.24), residues: 437
  loop : -0.76 (0.22), residues: 845

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG C  83 
 TYR   0.016   0.001   TYR D  62 
 PHE   0.015   0.001   PHE A 140 
 TRP   0.010   0.001   TRP B 143 
 HIS   0.002   0.001   HIS D 102 

Details of bonding type rmsd
  covalent geometry    : bond        0.00335 (14056)
  covalent geometry    : angle       0.56064 (19079)
  SS BOND              : bond        0.00100 (    1)
  SS BOND              : angle       0.84206 (    2)
  hydrogen bonds       : bond        0.03869 (  640)
  hydrogen bonds       : angle       5.28685 ( 1794)
  Misc. bond           : bond        0.00766 (    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
  171 residues out of total 1479 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 161
  time to evaluate  : 0.351 
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: A  289 LYS cc_start: 0.8022 (mptt) cc_final: 0.7793 (mmmt)
REVERT: D  128 PHE cc_start: 0.3820 (t80) cc_final: 0.3545 (m-10)
REVERT: D  201 MET cc_start: 0.8005 (mmm) cc_final: 0.7743 (mtp)
REVERT: F  186 ASN cc_start: 0.7825 (m-40) cc_final: 0.7604 (m-40)
  outliers start: 10
  outliers final: 8
  residues processed: 164
  average time/residue: 0.0993
  time to fit residues: 23.8934
Evaluate side-chains
  147 residues out of total 1479 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 139
  time to evaluate  : 0.496 
-------------------------------------------------------------------------------
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 70 optimal weight:    7.9990
   chunk 83 optimal weight:    6.9990
   chunk 9 optimal weight:    9.9990
   chunk 5 optimal weight:    2.9990
   chunk 122 optimal weight:    1.9990
   chunk 100 optimal weight:    0.6980
   chunk 165 optimal weight:   10.0000
   chunk 102 optimal weight:    3.9990
   chunk 56 optimal weight:    1.9990
   chunk 104 optimal weight:    2.9990
   chunk 156 optimal weight:    9.9990
   overall best weight:    2.1388

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

Flipped N/Q/H residues before XYZ refinement:
A 179 GLN
A 441 GLN
** A 693 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 125 GLN
D 158 GLN
** F  59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 166 ASN
F 417 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3747 r_free = 0.3747 target = 0.115421 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3394 r_free = 0.3394 target = 0.092658 restraints weight = 28217.410|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3395 r_free = 0.3395 target = 0.093528 restraints weight = 18548.843|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3408 r_free = 0.3408 target = 0.094306 restraints weight = 13753.203|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3412 r_free = 0.3412 target = 0.094595 restraints weight = 12079.813|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3415 r_free = 0.3415 target = 0.094763 restraints weight = 10703.676|
|-----------------------------------------------------------------------------|
r_work (final): 0.3408
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7825
moved from start:          0.1669

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.055  14060  Z= 0.251
  Angle     :  0.616   8.208  19081  Z= 0.327
  Chirality :  0.046   0.197   2097
  Planarity :  0.005   0.059   2514
  Dihedral  :  4.767  17.592   1922
  Min Nonbonded Distance : 1.871

Molprobity Statistics.
  All-atom Clashscore : 13.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.58 %
    Favored  : 94.42 %
  Rotamer:
    Outliers :  1.42 %
    Allowed  : 10.09 %
    Favored  : 88.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.58 (0.20), residues: 1737
  helix:  1.25 (0.23), residues: 451
  sheet: -1.03 (0.23), residues: 459
  loop : -0.84 (0.22), residues: 827

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG C  83 
 TYR   0.015   0.002   TYR A 618 
 PHE   0.014   0.002   PHE A 802 
 TRP   0.011   0.002   TRP F 233 
 HIS   0.003   0.001   HIS B 121 

Details of bonding type rmsd
  covalent geometry    : bond        0.00554 (14056)
  covalent geometry    : angle       0.61629 (19079)
  SS BOND              : bond        0.00284 (    1)
  SS BOND              : angle       1.09040 (    2)
  hydrogen bonds       : bond        0.04054 (  640)
  hydrogen bonds       : angle       5.43790 ( 1794)
  Misc. bond           : bond        0.00817 (    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
  167 residues out of total 1479 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 146
  time to evaluate  : 0.462 
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  289 LYS cc_start: 0.8270 (mptt) cc_final: 0.7931 (mmmt)
REVERT: D  128 PHE cc_start: 0.3791 (t80) cc_final: 0.3484 (m-10)
REVERT: F  413 TRP cc_start: 0.8493 (t60) cc_final: 0.8199 (t60)
  outliers start: 21
  outliers final: 17
  residues processed: 161
  average time/residue: 0.0913
  time to fit residues: 21.9314
Evaluate side-chains
  154 residues out of total 1479 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 137
  time to evaluate  : 0.533 
-------------------------------------------------------------------------------
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 A residue  772 ILE
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   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=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 173
   random chunks:
   chunk 94 optimal weight:    0.0670
   chunk 105 optimal weight:    3.9990
   chunk 114 optimal weight:    0.7980
   chunk 16 optimal weight:    1.9990
   chunk 108 optimal weight:    0.8980
   chunk 135 optimal weight:    0.8980
   chunk 7 optimal weight:   20.0000
   chunk 104 optimal weight:    0.8980
   chunk 25 optimal weight:    0.9990
   chunk 95 optimal weight:    1.9990
   chunk 36 optimal weight:    0.9980
   overall best weight:    0.7118

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

Flipped N/Q/H residues before XYZ refinement:
A 179 GLN
A 427 ASN
A 441 GLN
A 555 HIS
** 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: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3789 r_free = 0.3789 target = 0.118331 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3448 r_free = 0.3448 target = 0.095935 restraints weight = 28057.380|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3452 r_free = 0.3452 target = 0.097020 restraints weight = 18502.118|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3465 r_free = 0.3465 target = 0.097850 restraints weight = 13302.437|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3468 r_free = 0.3468 target = 0.098010 restraints weight = 11705.194|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3469 r_free = 0.3469 target = 0.098107 restraints weight = 10355.783|
|-----------------------------------------------------------------------------|
r_work (final): 0.3462
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7755
moved from start:          0.1682

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= 0.134
  Angle     :  0.541   6.996  19081  Z= 0.286
  Chirality :  0.043   0.174   2097
  Planarity :  0.004   0.060   2514
  Dihedral  :  4.507  18.596   1922
  Min Nonbonded Distance : 1.979

Molprobity Statistics.
  All-atom Clashscore : 11.43
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  5.12 %
    Favored  : 94.82 %
  Rotamer:
    Outliers :  1.62 %
    Allowed  : 11.44 %
    Favored  : 86.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.41 (0.20), residues: 1737
  helix:  1.48 (0.24), residues: 451
  sheet: -1.01 (0.23), residues: 458
  loop : -0.75 (0.22), residues: 828

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG C  83 
 TYR   0.014   0.001   TYR D 184 
 PHE   0.014   0.001   PHE A 426 
 TRP   0.011   0.001   TRP B 143 
 HIS   0.003   0.001   HIS F 178 

Details of bonding type rmsd
  covalent geometry    : bond        0.00288 (14056)
  covalent geometry    : angle       0.54064 (19079)
  SS BOND              : bond        0.00110 (    1)
  SS BOND              : angle       0.63944 (    2)
  hydrogen bonds       : bond        0.03530 (  640)
  hydrogen bonds       : angle       5.17075 ( 1794)
  Misc. bond           : bond        0.00702 (    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
  181 residues out of total 1479 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 157
  time to evaluate  : 0.465 
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  739 TRP cc_start: 0.7865 (t60) cc_final: 0.7505 (t60)
REVERT: D  128 PHE cc_start: 0.3778 (t80) cc_final: 0.3411 (m-10)
REVERT: F  413 TRP cc_start: 0.8398 (t60) cc_final: 0.8044 (t60)
  outliers start: 24
  outliers final: 18
  residues processed: 173
  average time/residue: 0.1017
  time to fit residues: 26.0548
Evaluate side-chains
  156 residues out of total 1479 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 138
  time to evaluate  : 0.449 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  382 VAL
Chi-restraints excluded: chain A residue  428 PHE
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 E residue   39 THR
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 F residue   66 LEU
Chi-restraints excluded: chain F residue  271 ASN
Chi-restraints excluded: chain F residue  272 ASP
Chi-restraints excluded: chain F residue  414 MET
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 113 optimal weight:    4.9990
   chunk 69 optimal weight:    1.9990
   chunk 161 optimal weight:    3.9990
   chunk 5 optimal weight:    0.0370
   chunk 156 optimal weight:    3.9990
   chunk 80 optimal weight:    0.5980
   chunk 31 optimal weight:    4.9990
   chunk 125 optimal weight:    0.5980
   chunk 67 optimal weight:    7.9990
   chunk 79 optimal weight:    0.9980
   chunk 33 optimal weight:    2.9990
   overall best weight:    0.8460

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

Flipped N/Q/H residues before XYZ refinement:
A 286 GLN
D  47 ASN
E  34 GLN
** F  59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3788 r_free = 0.3788 target = 0.118148 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3451 r_free = 0.3451 target = 0.096214 restraints weight = 28244.878|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3451 r_free = 0.3451 target = 0.096824 restraints weight = 17329.561|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3461 r_free = 0.3461 target = 0.097479 restraints weight = 13721.875|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3466 r_free = 0.3466 target = 0.097854 restraints weight = 12108.045|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3470 r_free = 0.3470 target = 0.098087 restraints weight = 10448.330|
|-----------------------------------------------------------------------------|
r_work (final): 0.3463
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7752
moved from start:          0.1807

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= 0.140
  Angle     :  0.541   7.296  19081  Z= 0.286
  Chirality :  0.043   0.177   2097
  Planarity :  0.004   0.059   2514
  Dihedral  :  4.448  19.918   1922
  Min Nonbonded Distance : 1.953

Molprobity Statistics.
  All-atom Clashscore : 11.09
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  5.24 %
    Favored  : 94.70 %
  Rotamer:
    Outliers :  1.69 %
    Allowed  : 12.59 %
    Favored  : 85.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.36 (0.20), residues: 1737
  helix:  1.52 (0.24), residues: 451
  sheet: -0.94 (0.23), residues: 464
  loop : -0.73 (0.23), residues: 822

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG C  83 
 TYR   0.014   0.001   TYR D 184 
 PHE   0.014   0.001   PHE A 426 
 TRP   0.010   0.001   TRP B 143 
 HIS   0.002   0.001   HIS F 178 

Details of bonding type rmsd
  covalent geometry    : bond        0.00304 (14056)
  covalent geometry    : angle       0.54140 (19079)
  SS BOND              : bond        0.00274 (    1)
  SS BOND              : angle       0.86280 (    2)
  hydrogen bonds       : bond        0.03410 (  640)
  hydrogen bonds       : angle       5.06907 ( 1794)
  Misc. bond           : bond        0.00712 (    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
  176 residues out of total 1479 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 151
  time to evaluate  : 0.423 
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: 0.7862 (t60) cc_final: 0.7517 (t60)
REVERT: B  123 TYR cc_start: 0.8123 (m-80) cc_final: 0.7819 (m-80)
REVERT: D  128 PHE cc_start: 0.3810 (t80) cc_final: 0.3427 (m-10)
REVERT: F  400 MET cc_start: 0.6339 (mtt) cc_final: 0.5978 (mtm)
REVERT: F  413 TRP cc_start: 0.8454 (t60) cc_final: 0.8093 (t60)
  outliers start: 25
  outliers final: 22
  residues processed: 170
  average time/residue: 0.0985
  time to fit residues: 25.0889
Evaluate side-chains
  160 residues out of total 1479 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 138
  time to evaluate  : 0.474 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  382 VAL
Chi-restraints excluded: chain A residue  473 VAL
Chi-restraints excluded: chain A residue  623 ASP
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  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  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 F residue  414 MET
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 138 optimal weight:    0.9990
   chunk 26 optimal weight:    0.4980
   chunk 56 optimal weight:    2.9990
   chunk 169 optimal weight:   10.0000
   chunk 48 optimal weight:    3.9990
   chunk 19 optimal weight:    2.9990
   chunk 132 optimal weight:    1.9990
   chunk 13 optimal weight:    0.0170
   chunk 11 optimal weight:    0.9980
   chunk 21 optimal weight:    0.9980
   chunk 154 optimal weight:    7.9990
   overall best weight:    0.7020

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

Flipped N/Q/H residues before XYZ refinement:
A 286 GLN
E  54 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: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3788 r_free = 0.3788 target = 0.118060 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3454 r_free = 0.3454 target = 0.096373 restraints weight = 28001.864|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3464 r_free = 0.3464 target = 0.097772 restraints weight = 19577.768|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3476 r_free = 0.3476 target = 0.098499 restraints weight = 14494.886|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3477 r_free = 0.3477 target = 0.098565 restraints weight = 12538.039|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3482 r_free = 0.3482 target = 0.098877 restraints weight = 10788.645|
|-----------------------------------------------------------------------------|
r_work (final): 0.3475
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7713
moved from start:          0.1934

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= 0.128
  Angle     :  0.526   7.511  19081  Z= 0.279
  Chirality :  0.043   0.175   2097
  Planarity :  0.004   0.058   2514
  Dihedral  :  4.393  18.617   1922
  Min Nonbonded Distance : 1.977

Molprobity Statistics.
  All-atom Clashscore : 11.28
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  5.12 %
    Favored  : 94.82 %
  Rotamer:
    Outliers :  2.03 %
    Allowed  : 12.39 %
    Favored  : 85.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.31 (0.20), residues: 1737
  helix:  1.58 (0.24), residues: 452
  sheet: -0.89 (0.23), residues: 470
  loop : -0.73 (0.23), residues: 815

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.000   ARG D  97 
 TYR   0.014   0.001   TYR D 184 
 PHE   0.015   0.001   PHE A 426 
 TRP   0.010   0.001   TRP B 143 
 HIS   0.002   0.001   HIS F 178 

Details of bonding type rmsd
  covalent geometry    : bond        0.00278 (14056)
  covalent geometry    : angle       0.52617 (19079)
  SS BOND              : bond        0.00132 (    1)
  SS BOND              : angle       0.60545 (    2)
  hydrogen bonds       : bond        0.03310 (  640)
  hydrogen bonds       : angle       4.95718 ( 1794)
  Misc. bond           : bond        0.00693 (    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
  183 residues out of total 1479 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 153
  time to evaluate  : 0.454 
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
   revert: symmetry clash
TARDY: cannot create tardy model for: "SER F 427 " (corrupted residue). Skipping it.
REVERT: A  739 TRP cc_start: 0.7826 (t60) cc_final: 0.7516 (t60)
REVERT: B  123 TYR cc_start: 0.8110 (m-80) cc_final: 0.7785 (m-80)
REVERT: D  128 PHE cc_start: 0.3806 (t80) cc_final: 0.3427 (m-10)
REVERT: F  413 TRP cc_start: 0.8436 (t60) cc_final: 0.8122 (t60)
  outliers start: 30
  outliers final: 21
  residues processed: 176
  average time/residue: 0.0989
  time to fit residues: 25.9465
Evaluate side-chains
  162 residues out of total 1479 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 141
  time to evaluate  : 0.332 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  382 VAL
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  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 E residue   39 THR
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   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 128 optimal weight:    0.8980
   chunk 67 optimal weight:    0.0770
   chunk 148 optimal weight:    5.9990
   chunk 118 optimal weight:    5.9990
   chunk 141 optimal weight:    1.9990
   chunk 3 optimal weight:    0.9990
   chunk 77 optimal weight:    5.9990
   chunk 123 optimal weight:    2.9990
   chunk 97 optimal weight:    0.9980
   chunk 172 optimal weight:    0.6980
   chunk 15 optimal weight:    4.9990
   overall best weight:    0.7340

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

Flipped N/Q/H residues before XYZ refinement:
** 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 = 0.3790 r_free = 0.3790 target = 0.118179 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3456 r_free = 0.3456 target = 0.096450 restraints weight = 28032.282|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3455 r_free = 0.3455 target = 0.097028 restraints weight = 19144.156|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3465 r_free = 0.3465 target = 0.097677 restraints weight = 15909.583|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3472 r_free = 0.3472 target = 0.098133 restraints weight = 13049.127|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3474 r_free = 0.3474 target = 0.098231 restraints weight = 11380.881|
|-----------------------------------------------------------------------------|
r_work (final): 0.3474
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7731
moved from start:          0.1999

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= 0.129
  Angle     :  0.528   8.811  19081  Z= 0.279
  Chirality :  0.043   0.177   2097
  Planarity :  0.004   0.058   2514
  Dihedral  :  4.340  18.428   1922
  Min Nonbonded Distance : 1.967

Molprobity Statistics.
  All-atom Clashscore : 10.98
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  5.07 %
    Favored  : 94.88 %
  Rotamer:
    Outliers :  1.83 %
    Allowed  : 12.73 %
    Favored  : 85.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.26 (0.21), residues: 1737
  helix:  1.58 (0.24), residues: 455
  sheet: -0.82 (0.23), residues: 470
  loop : -0.71 (0.23), residues: 812

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG D  97 
 TYR   0.013   0.001   TYR D 184 
 PHE   0.014   0.001   PHE A 426 
 TRP   0.010   0.001   TRP B 143 
 HIS   0.002   0.000   HIS F 178 

Details of bonding type rmsd
  covalent geometry    : bond        0.00281 (14056)
  covalent geometry    : angle       0.52797 (19079)
  SS BOND              : bond        0.00137 (    1)
  SS BOND              : angle       0.59730 (    2)
  hydrogen bonds       : bond        0.03267 (  640)
  hydrogen bonds       : angle       4.90211 ( 1794)
  Misc. bond           : bond        0.00701 (    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
  173 residues out of total 1479 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 146
  time to evaluate  : 0.400 
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: 0.4038 (tm-30) cc_final: 0.2718 (mt0)
REVERT: A  739 TRP cc_start: 0.7824 (t60) cc_final: 0.7516 (t60)
REVERT: D  128 PHE cc_start: 0.3778 (t80) cc_final: 0.3382 (m-10)
REVERT: F  413 TRP cc_start: 0.8445 (t60) cc_final: 0.8104 (t60)
  outliers start: 27
  outliers final: 24
  residues processed: 166
  average time/residue: 0.1074
  time to fit residues: 26.3260
Evaluate side-chains
  162 residues out of total 1479 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 138
  time to evaluate  : 0.503 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  382 VAL
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 A residue  623 ASP
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  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 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 F residue  414 MET
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 153 optimal weight:    4.9990
   chunk 34 optimal weight:    2.9990
   chunk 15 optimal weight:    3.9990
   chunk 33 optimal weight:    0.5980
   chunk 143 optimal weight:    4.9990
   chunk 20 optimal weight:    1.9990
   chunk 144 optimal weight:    0.0770
   chunk 94 optimal weight:    0.5980
   chunk 5 optimal weight:    4.9990
   chunk 119 optimal weight:    3.9990
   chunk 156 optimal weight:    5.9990
   overall best weight:    1.2542

-------------------------------------------------------------------------------
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**
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 = 0.3769 r_free = 0.3769 target = 0.116711 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3429 r_free = 0.3429 target = 0.094822 restraints weight = 28061.848|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3429 r_free = 0.3429 target = 0.095567 restraints weight = 19341.667|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3441 r_free = 0.3441 target = 0.096259 restraints weight = 14965.714|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3446 r_free = 0.3446 target = 0.096552 restraints weight = 12597.639|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3448 r_free = 0.3448 target = 0.096684 restraints weight = 11142.164|
|-----------------------------------------------------------------------------|
r_work (final): 0.3436
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7771
moved from start:          0.2154

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.049  14060  Z= 0.171
  Angle     :  0.556   7.589  19081  Z= 0.294
  Chirality :  0.044   0.179   2097
  Planarity :  0.004   0.057   2514
  Dihedral  :  4.460  18.469   1922
  Min Nonbonded Distance : 1.918

Molprobity Statistics.
  All-atom Clashscore : 12.13
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  5.18 %
    Favored  : 94.76 %
  Rotamer:
    Outliers :  1.96 %
    Allowed  : 13.00 %
    Favored  : 85.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.36 (0.20), residues: 1737
  helix:  1.52 (0.24), residues: 452
  sheet: -0.90 (0.23), residues: 473
  loop : -0.76 (0.23), residues: 812

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.000   ARG D  97 
 TYR   0.016   0.001   TYR A 608 
 PHE   0.013   0.001   PHE A 426 
 TRP   0.010   0.001   TRP B  93 
 HIS   0.002   0.001   HIS A 677 

Details of bonding type rmsd
  covalent geometry    : bond        0.00375 (14056)
  covalent geometry    : angle       0.55567 (19079)
  SS BOND              : bond        0.00230 (    1)
  SS BOND              : angle       0.81153 (    2)
  hydrogen bonds       : bond        0.03447 (  640)
  hydrogen bonds       : angle       5.01591 ( 1794)
  Misc. bond           : bond        0.00727 (    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
  177 residues out of total 1479 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 148
  time to evaluate  : 0.520 
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.
   revert: symmetry clash
TARDY: cannot create tardy model for: "SER F 427 " (corrupted residue). Skipping it.
REVERT: D  128 PHE cc_start: 0.3797 (t80) cc_final: 0.3384 (m-10)
REVERT: F  197 SER cc_start: 0.8338 (m) cc_final: 0.8080 (p)
REVERT: F  413 TRP cc_start: 0.8499 (t60) cc_final: 0.8155 (t60)
  outliers start: 29
  outliers final: 27
  residues processed: 170
  average time/residue: 0.1054
  time to fit residues: 26.5730
Evaluate side-chains
  168 residues out of total 1479 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 141
  time to evaluate  : 0.375 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  189 THR
Chi-restraints excluded: chain A residue  382 VAL
Chi-restraints excluded: chain A residue  423 THR
Chi-restraints excluded: chain A residue  428 PHE
Chi-restraints excluded: chain A residue  444 VAL
Chi-restraints excluded: chain A residue  473 VAL
Chi-restraints excluded: chain A residue  623 ASP
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  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 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  271 ASN
Chi-restraints excluded: chain F residue  272 ASP
Chi-restraints excluded: chain F residue  414 MET
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 134 optimal weight:    0.6980
   chunk 71 optimal weight:    0.8980
   chunk 170 optimal weight:    3.9990
   chunk 50 optimal weight:    4.9990
   chunk 162 optimal weight:    0.9990
   chunk 5 optimal weight:    7.9990
   chunk 150 optimal weight:    1.9990
   chunk 18 optimal weight:    5.9990
   chunk 136 optimal weight:    0.6980
   chunk 70 optimal weight:    1.9990
   chunk 103 optimal weight:    2.9990
   overall best weight:    1.0584

-------------------------------------------------------------------------------
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
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 = 0.3774 r_free = 0.3774 target = 0.117102 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3424 r_free = 0.3424 target = 0.094568 restraints weight = 28177.815|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3432 r_free = 0.3432 target = 0.095579 restraints weight = 17393.872|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3439 r_free = 0.3439 target = 0.096043 restraints weight = 13668.218|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3441 r_free = 0.3441 target = 0.096160 restraints weight = 11948.730|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3458 r_free = 0.3458 target = 0.097226 restraints weight = 10972.772|
|-----------------------------------------------------------------------------|
r_work (final): 0.3460
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7767
moved from start:          0.2175

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048  14060  Z= 0.157
  Angle     :  0.558   9.963  19081  Z= 0.294
  Chirality :  0.044   0.177   2097
  Planarity :  0.004   0.057   2514
  Dihedral  :  4.437  18.779   1922
  Min Nonbonded Distance : 1.950

Molprobity Statistics.
  All-atom Clashscore : 11.98
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  5.30 %
    Favored  : 94.65 %
  Rotamer:
    Outliers :  1.90 %
    Allowed  : 13.34 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.35 (0.20), residues: 1737
  helix:  1.51 (0.24), residues: 455
  sheet: -0.90 (0.23), residues: 473
  loop : -0.75 (0.23), residues: 809

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG D  97 
 TYR   0.013   0.001   TYR D 184 
 PHE   0.014   0.001   PHE A 140 
 TRP   0.010   0.001   TRP B 143 
 HIS   0.002   0.001   HIS F 178 

Details of bonding type rmsd
  covalent geometry    : bond        0.00346 (14056)
  covalent geometry    : angle       0.55818 (19079)
  SS BOND              : bond        0.00157 (    1)
  SS BOND              : angle       0.63474 (    2)
  hydrogen bonds       : bond        0.03403 (  640)
  hydrogen bonds       : angle       4.99528 ( 1794)
  Misc. bond           : bond        0.00715 (    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
  171 residues out of total 1479 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 143
  time to evaluate  : 0.382 
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: 0.4202 (tm-30) cc_final: 0.2680 (mt0)
REVERT: D  128 PHE cc_start: 0.3796 (t80) cc_final: 0.3394 (m-10)
REVERT: F  197 SER cc_start: 0.8391 (m) cc_final: 0.8111 (p)
REVERT: F  413 TRP cc_start: 0.8505 (t60) cc_final: 0.8150 (t60)
  outliers start: 28
  outliers final: 28
  residues processed: 163
  average time/residue: 0.1049
  time to fit residues: 25.3639
Evaluate side-chains
  165 residues out of total 1479 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 137
  time to evaluate  : 0.404 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  189 THR
Chi-restraints excluded: chain A residue  382 VAL
Chi-restraints excluded: chain A residue  423 THR
Chi-restraints excluded: chain A residue  428 PHE
Chi-restraints excluded: chain A residue  444 VAL
Chi-restraints excluded: chain A residue  473 VAL
Chi-restraints excluded: chain A residue  623 ASP
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  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 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 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 F residue  414 MET
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 77 optimal weight:    4.9990
   chunk 158 optimal weight:    0.0270
   chunk 153 optimal weight:    0.0870
   chunk 78 optimal weight:    0.9990
   chunk 122 optimal weight:    3.9990
   chunk 44 optimal weight:    0.8980
   chunk 149 optimal weight:    1.9990
   chunk 36 optimal weight:    1.9990
   chunk 154 optimal weight:    1.9990
   chunk 33 optimal weight:    0.7980
   chunk 22 optimal weight:    0.7980
   overall best weight:    0.5216

-------------------------------------------------------------------------------
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  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 = 0.3809 r_free = 0.3809 target = 0.119410 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3454 r_free = 0.3454 target = 0.096658 restraints weight = 28068.744|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3468 r_free = 0.3468 target = 0.097727 restraints weight = 18551.674|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3477 r_free = 0.3477 target = 0.098290 restraints weight = 14250.287|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3492 r_free = 0.3492 target = 0.099268 restraints weight = 11709.714|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3493 r_free = 0.3493 target = 0.099308 restraints weight = 10888.822|
|-----------------------------------------------------------------------------|
r_work (final): 0.3482
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7722
moved from start:          0.2238

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045  14060  Z= 0.120
  Angle     :  0.541   7.995  19081  Z= 0.287
  Chirality :  0.043   0.194   2097
  Planarity :  0.004   0.056   2514
  Dihedral  :  4.347  18.050   1922
  Min Nonbonded Distance : 2.013

Molprobity Statistics.
  All-atom Clashscore : 11.57
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  4.78 %
    Favored  : 95.16 %
  Rotamer:
    Outliers :  1.62 %
    Allowed  : 13.74 %
    Favored  : 84.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.26 (0.20), residues: 1737
  helix:  1.61 (0.24), residues: 455
  sheet: -0.83 (0.23), residues: 484
  loop : -0.71 (0.23), residues: 798

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.015   0.000   ARG D  97 
 TYR   0.014   0.001   TYR D 184 
 PHE   0.015   0.001   PHE A 140 
 TRP   0.016   0.001   TRP A 739 
 HIS   0.002   0.000   HIS F 178 

Details of bonding type rmsd
  covalent geometry    : bond        0.00262 (14056)
  covalent geometry    : angle       0.54096 (19079)
  SS BOND              : bond        0.00059 (    1)
  SS BOND              : angle       0.43004 (    2)
  hydrogen bonds       : bond        0.03281 (  640)
  hydrogen bonds       : angle       4.87486 ( 1794)
  Misc. bond           : bond        0.00684 (    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
  172 residues out of total 1479 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 148
  time to evaluate  : 0.476 
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.
   revert: symmetry clash
   revert: symmetry clash
TARDY: cannot create tardy model for: "SER F 427 " (corrupted residue). Skipping it.
REVERT: A   87 GLN cc_start: 0.4069 (tm-30) cc_final: 0.2736 (mt0)
REVERT: D  128 PHE cc_start: 0.3793 (t80) cc_final: 0.3399 (m-10)
REVERT: F  186 ASN cc_start: 0.7424 (m110) cc_final: 0.7107 (m-40)
REVERT: F  413 TRP cc_start: 0.8464 (t60) cc_final: 0.8121 (t60)
  outliers start: 24
  outliers final: 21
  residues processed: 167
  average time/residue: 0.0947
  time to fit residues: 23.8662
Evaluate side-chains
  161 residues out of total 1479 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 140
  time to evaluate  : 0.337 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  382 VAL
Chi-restraints excluded: chain A residue  423 THR
Chi-restraints excluded: chain A residue  428 PHE
Chi-restraints excluded: chain A residue  444 VAL
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   84 LEU
Chi-restraints excluded: chain B residue  220 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 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 F residue  414 MET
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 162 optimal weight:    1.9990
   chunk 153 optimal weight:    0.9980
   chunk 147 optimal weight:    0.3980
   chunk 48 optimal weight:    6.9990
   chunk 57 optimal weight:    0.7980
   chunk 38 optimal weight:    2.9990
   chunk 34 optimal weight:    3.9990
   chunk 121 optimal weight:    5.9990
   chunk 92 optimal weight:    5.9990
   chunk 46 optimal weight:    5.9990
   chunk 1 optimal weight:    6.9990
   overall best weight:    1.4384

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

Flipped N/Q/H residues before XYZ refinement:
A 179 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  47 ASN ** 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 = 0.3771 r_free = 0.3771 target = 0.116820 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3423 r_free = 0.3423 target = 0.094306 restraints weight = 28312.111|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3420 r_free = 0.3420 target = 0.094845 restraints weight = 18215.939|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3434 r_free = 0.3434 target = 0.095711 restraints weight = 14083.825|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3438 r_free = 0.3438 target = 0.096008 restraints weight = 12658.976|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3440 r_free = 0.3440 target = 0.096075 restraints weight = 11614.306|
|-----------------------------------------------------------------------------|
r_work (final): 0.3439
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7794
moved from start:          0.2315

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.049  14060  Z= 0.188
  Angle     :  0.585   9.660  19081  Z= 0.310
  Chirality :  0.044   0.245   2097
  Planarity :  0.004   0.056   2514
  Dihedral  :  4.547  25.313   1922
  Min Nonbonded Distance : 1.907

Molprobity Statistics.
  All-atom Clashscore : 12.02
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  5.07 %
    Favored  : 94.88 %
  Rotamer:
    Outliers :  1.62 %
    Allowed  : 14.08 %
    Favored  : 84.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.39 (0.20), residues: 1737
  helix:  1.45 (0.24), residues: 455
  sheet: -0.83 (0.23), residues: 478
  loop : -0.81 (0.23), residues: 804

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.000   ARG D  97 
 TYR   0.013   0.001   TYR D 184 
 PHE   0.015   0.001   PHE A 140 
 TRP   0.023   0.001   TRP A 739 
 HIS   0.002   0.001   HIS A 196 

Details of bonding type rmsd
  covalent geometry    : bond        0.00415 (14056)
  covalent geometry    : angle       0.58531 (19079)
  SS BOND              : bond        0.00168 (    1)
  SS BOND              : angle       0.74759 (    2)
  hydrogen bonds       : bond        0.03517 (  640)
  hydrogen bonds       : angle       5.03746 ( 1794)
  Misc. bond           : bond        0.00730 (    3)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1867.66 seconds
wall clock time: 33 minutes 14.53 seconds (1994.53 seconds total)