Starting phenix.real_space_refine
on Thu Jun 12 10:41:38 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8bnz_16137/06_2025/8bnz_16137.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8bnz_16137/06_2025/8bnz_16137.map

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

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

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8bnz_16137/06_2025/8bnz_16137.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8bnz_16137/06_2025/8bnz_16137.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8bnz_16137/06_2025/8bnz_16137.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8bnz_16137/06_2025/8bnz_16137.cif"
  }
  resolution = 3.5
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.031
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: 4
    Type Number    sf(0)   Gaussians
     S      41      5.16       5
     C    8855      2.51       5
     N    2409      2.21       5
     O    2768      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 26 residue(s): 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib"
  Total number of atoms: 14073
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 6209
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 785, 6209
          Classifications: {'peptide': 785}
          Link IDs: {'PTRANS': 29, 'TRANS': 755}
    Chain: "B"
      Number of atoms: 2750
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 367, 2750
          Classifications: {'peptide': 367}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 4}
          Link IDs: {'PTRANS': 11, 'TRANS': 355}
          Unresolved non-hydrogen bonds: 13
          Unresolved non-hydrogen angles: 16
          Unresolved non-hydrogen dihedrals: 10
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 8
    Chain: "C"
      Number of atoms: 414
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 57, 414
          Classifications: {'peptide': 57}
          Link IDs: {'PTRANS': 6, 'TRANS': 50}
    Chain: "D"
      Number of atoms: 1722
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 213, 1722
          Classifications: {'peptide': 213}
          Link IDs: {'PTRANS': 10, 'TRANS': 202}
    Chain: "E"
      Number of atoms: 645
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 83, 645
          Classifications: {'peptide': 83}
          Link IDs: {'PTRANS': 5, 'TRANS': 77}
    Chain: "P"
      Number of atoms: 2333
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 299}
  Time building chain proxies: 7.97, per 1000 atoms: 0.57
  Number of scatterers: 14073
  At special positions: 0
  Unit cell: (127.41, 131.13, 139.5, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      41     16.00
     O    2768      8.00
     N    2409      7.00
     C    8855      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 431 " - pdb=" SG  CYS P1293 " distance=2.03
    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=0, symmetry=0
  Time building additional restraints: 3.13
  Conformation dependent library (CDL) restraints added in 1.6 seconds
  

  3590 Ramachandran restraints generated.
    1795 Oldfield, 0 Emsley, 1795 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3286

  Finding SS restraints...
    Secondary structure from input PDB file:
      27 helices and 19 sheets defined
      21.1% alpha, 47.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 2.01
  Creating SS restraints...
    Processing helix  chain 'A' and resid 38 through 46
      removed outlier: 3.641A  pdb=" N   LEU A  43 " --> pdb=" O   VAL A  39 " (cutoff:3.500A)
      removed outlier: 3.803A  pdb=" N   LEU A  44 " --> pdb=" O   GLY A  40 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 55 through 70
      removed outlier: 4.371A  pdb=" N   GLY A  70 " --> pdb=" O   LEU A  66 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 106 through 117
    Processing helix  chain 'A' and resid 128 through 144
      removed outlier: 3.618A  pdb=" N   ASP A 132 " --> pdb=" O   THR A 128 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 189 through 196
      removed outlier: 3.873A  pdb=" N   LEU A 193 " --> pdb=" O   THR A 189 " (cutoff:3.500A)
      removed outlier: 4.130A  pdb=" N   HIS A 196 " --> pdb=" O   GLU A 192 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 215 through 233
    Processing helix  chain 'A' and resid 280 through 285
    Processing helix  chain 'A' and resid 297 through 315
      removed outlier: 3.624A  pdb=" N   TYR A 315 " --> pdb=" O   LEU A 311 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 361 through 367
      removed outlier: 3.715A  pdb=" N   LEU A 365 " --> pdb=" O   LYS A 361 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 378 through 393
      removed outlier: 3.880A  pdb=" N   GLY A 393 " --> pdb=" O   LEU A 389 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 449 through 452
    Processing helix  chain 'A' and resid 542 through 552
    Processing helix  chain 'A' and resid 647 through 651
      removed outlier: 3.626A  pdb=" N   ASN A 651 " --> pdb=" O   PHE A 648 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 726 through 731
      removed outlier: 4.102A  pdb=" N   ASN A 731 " --> pdb=" O   ASP A 727 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 32 through 45
    Processing helix  chain 'D' and resid 47 through 62
      removed outlier: 3.955A  pdb=" N   THR D  53 " --> pdb=" O   ARG D  49 " (cutoff:3.500A)
      removed outlier: 4.055A  pdb=" N   GLN D  54 " --> pdb=" O   GLN D  50 " (cutoff:3.500A)
      removed outlier: 3.579A  pdb=" N   LEU D  58 " --> pdb=" O   GLN D  54 " (cutoff:3.500A)
      removed outlier: 3.957A  pdb=" N   ARG D  61 " --> pdb=" O   ALA D  57 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 68 through 82
    Processing helix  chain 'D' and resid 84 through 99
    Processing helix  chain 'D' and resid 104 through 120
    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
      removed outlier: 3.739A  pdb=" N   ARG D 212 " --> pdb=" O   THR D 208 " (cutoff:3.500A)
      Proline residue:  D 216  - end of helix
    Processing helix  chain 'D' and resid 228 through 241
    Processing helix  chain 'E' and resid 42 through 46
    Processing helix  chain 'E' and resid 51 through 60
    Processing helix  chain 'P' and resid 1000 through 1036
      removed outlier: 4.289A  pdb=" N   ASP P1014 " --> pdb=" O   LEU P1010 " (cutoff:3.500A)
      removed outlier: 4.197A  pdb=" N   TYR P1015 " --> pdb=" O   PHE P1011 " (cutoff:3.500A)
      removed outlier: 3.820A  pdb=" N   LYS P1027 " --> pdb=" O   ASN P1023 " (cutoff:3.500A)
      removed outlier: 4.069A  pdb=" N   ARG P1028 " --> pdb=" O   ASN P1024 " (cutoff:3.500A)
      removed outlier: 3.930A  pdb=" N   MET P1029 " --> pdb=" O   LEU P1025 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 31
    Processing sheet with id=AA2, first strand: chain 'A' and resid 93 through 98
      removed outlier: 5.736A  pdb=" N   VAL A 163 " --> pdb=" O   ILE A  94 " (cutoff:3.500A)
      removed outlier: 3.610A  pdb=" N   SER A  96 " --> pdb=" O   VAL A 163 " (cutoff:3.500A)
      removed outlier: 3.906A  pdb=" N   LEU A 167 " --> pdb=" O   THR A  98 " (cutoff:3.500A)
      removed outlier: 4.010A  pdb=" N   ARG A 162 " --> pdb=" O   LEU A 158 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 176 through 183
      removed outlier: 4.573A  pdb=" N   ILE A 177 " --> pdb=" O   ILE A 254 " (cutoff:3.500A)
      removed outlier: 8.180A  pdb=" N   VAL A 256 " --> pdb=" O   ILE A 177 " (cutoff:3.500A)
      removed outlier: 6.289A  pdb=" N   GLN A 179 " --> pdb=" O   VAL A 256 " (cutoff:3.500A)
      removed outlier: 7.892A  pdb=" N   VAL A 258 " --> pdb=" O   GLN A 179 " (cutoff:3.500A)
      removed outlier: 6.835A  pdb=" N   ASN A 181 " --> pdb=" O   VAL A 258 " (cutoff:3.500A)
      removed outlier: 7.294A  pdb=" N   ILE A 260 " --> pdb=" O   ASN A 181 " (cutoff:3.500A)
      removed outlier: 5.903A  pdb=" N   VAL A 183 " --> pdb=" O   ILE A 260 " (cutoff:3.500A)
      removed outlier: 6.831A  pdb=" N   THR A 261 " --> pdb=" O   ILE A 240 " (cutoff:3.500A)
      removed outlier: 5.650A  pdb=" N   ILE A 240 " --> pdb=" O   THR A 261 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 267 through 276
      removed outlier: 4.236A  pdb=" N   LEU A 268 " --> pdb=" O   VAL A 335 " (cutoff:3.500A)
      removed outlier: 8.533A  pdb=" N   LEU A 337 " --> pdb=" O   LEU A 268 " (cutoff:3.500A)
      removed outlier: 7.057A  pdb=" N   GLY A 270 " --> pdb=" O   LEU A 337 " (cutoff:3.500A)
      removed outlier: 8.268A  pdb=" N   VAL A 339 " --> pdb=" O   GLY A 270 " (cutoff:3.500A)
      removed outlier: 6.913A  pdb=" N   GLU A 272 " --> pdb=" O   VAL A 339 " (cutoff:3.500A)
      removed outlier: 7.502A  pdb=" N   VAL A 341 " --> pdb=" O   GLU A 272 " (cutoff:3.500A)
      removed outlier: 6.258A  pdb=" N   SER A 274 " --> pdb=" O   VAL A 341 " (cutoff:3.500A)
      removed outlier: 7.876A  pdb=" N   ALA A 343 " --> pdb=" O   SER A 274 " (cutoff:3.500A)
      removed outlier: 6.508A  pdb=" N   ASN A 276 " --> pdb=" O   ALA A 343 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 348 through 355
      removed outlier: 4.255A  pdb=" N   VAL A 349 " --> pdb=" O   VAL A 412 " (cutoff:3.500A)
      removed outlier: 7.584A  pdb=" N   VAL A 414 " --> pdb=" O   VAL A 349 " (cutoff:3.500A)
      removed outlier: 6.800A  pdb=" N   LYS A 351 " --> pdb=" O   VAL A 414 " (cutoff:3.500A)
      removed outlier: 7.632A  pdb=" N   TYR A 416 " --> pdb=" O   LYS A 351 " (cutoff:3.500A)
      removed outlier: 6.762A  pdb=" N   ARG A 353 " --> pdb=" O   TYR A 416 " (cutoff:3.500A)
      removed outlier: 7.539A  pdb=" N   VAL A 418 " --> pdb=" O   ARG A 353 " (cutoff:3.500A)
      removed outlier: 6.415A  pdb=" N   GLU A 355 " --> pdb=" O   VAL A 418 " (cutoff:3.500A)
      removed outlier: 7.379A  pdb=" N   GLU A 420 " --> pdb=" O   GLU A 355 " (cutoff:3.500A)
      removed outlier: 6.683A  pdb=" N   LYS A 417 " --> pdb=" O   VAL A 398 " (cutoff:3.500A)
      removed outlier: 4.347A  pdb=" N   VAL A 398 " --> pdb=" O   LYS A 417 " (cutoff:3.500A)
      removed outlier: 6.651A  pdb=" N   LYS A 419 " --> pdb=" O   GLU A 396 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 348 through 355
      removed outlier: 4.255A  pdb=" N   VAL A 349 " --> pdb=" O   VAL A 412 " (cutoff:3.500A)
      removed outlier: 7.584A  pdb=" N   VAL A 414 " --> pdb=" O   VAL A 349 " (cutoff:3.500A)
      removed outlier: 6.800A  pdb=" N   LYS A 351 " --> pdb=" O   VAL A 414 " (cutoff:3.500A)
      removed outlier: 7.632A  pdb=" N   TYR A 416 " --> pdb=" O   LYS A 351 " (cutoff:3.500A)
      removed outlier: 6.762A  pdb=" N   ARG A 353 " --> pdb=" O   TYR A 416 " (cutoff:3.500A)
      removed outlier: 7.539A  pdb=" N   VAL A 418 " --> pdb=" O   ARG A 353 " (cutoff:3.500A)
      removed outlier: 6.415A  pdb=" N   GLU A 355 " --> pdb=" O   VAL A 418 " (cutoff:3.500A)
      removed outlier: 7.379A  pdb=" N   GLU A 420 " --> pdb=" O   GLU A 355 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 802 through 806
      removed outlier: 6.438A  pdb=" N   MET A 768 " --> pdb=" O   PHE A 791 " (cutoff:3.500A)
      removed outlier: 4.235A  pdb=" N   THR A 735 " --> pdb=" O   THR A 720 " (cutoff:3.500A)
      removed outlier: 3.823A  pdb=" N   VAL A 628 " --> pdb=" O   ILE A 719 " (cutoff:3.500A)
      removed outlier: 4.809A  pdb=" N   TYR A 608 " --> pdb=" O   THR A 600 " (cutoff:3.500A)
      removed outlier: 4.207A  pdb=" N   VAL P1292 " --> pdb=" O   TYR A 432 " (cutoff:3.500A)
      removed outlier: 6.950A  pdb=" N   VAL P1272 " --> pdb=" O   ILE P1268 " (cutoff:3.500A)
      removed outlier: 3.581A  pdb=" N   LEU P1227 " --> pdb=" O   VAL P1208 " (cutoff:3.500A)
      removed outlier: 6.301A  pdb=" N   LEU P1202 " --> pdb=" O   LEU P1233 " (cutoff:3.500A)
      removed outlier: 6.372A  pdb=" N   ALA P1165 " --> pdb=" O   VAL P1161 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 802 through 806
      removed outlier: 6.438A  pdb=" N   MET A 768 " --> pdb=" O   PHE A 791 " (cutoff:3.500A)
      removed outlier: 4.235A  pdb=" N   THR A 735 " --> pdb=" O   THR A 720 " (cutoff:3.500A)
      removed outlier: 3.823A  pdb=" N   VAL A 628 " --> pdb=" O   ILE A 719 " (cutoff:3.500A)
      removed outlier: 4.809A  pdb=" N   TYR A 608 " --> pdb=" O   THR A 600 " (cutoff:3.500A)
      removed outlier: 4.207A  pdb=" N   VAL P1292 " --> pdb=" O   TYR A 432 " (cutoff:3.500A)
      removed outlier: 6.950A  pdb=" N   VAL P1272 " --> pdb=" O   ILE P1268 " (cutoff:3.500A)
      removed outlier: 3.581A  pdb=" N   LEU P1227 " --> pdb=" O   VAL P1208 " (cutoff:3.500A)
      removed outlier: 6.301A  pdb=" N   LEU P1202 " --> pdb=" O   LEU P1233 " (cutoff:3.500A)
      removed outlier: 3.660A  pdb=" N   ALA P1117 " --> pdb=" O   PHE P1113 " (cutoff:3.500A)
      removed outlier: 3.596A  pdb=" N   SER P1097 " --> pdb=" O   THR P1133 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'A' and resid 671 through 674
      removed outlier: 5.152A  pdb=" N   ALA A 672 " --> pdb=" O   SER A 702 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'B' and resid 45 through 51
      removed outlier: 6.154A  pdb=" N   THR B  46 " --> pdb=" O   THR B 391 " (cutoff:3.500A)
      removed outlier: 7.507A  pdb=" N   THR B 391 " --> pdb=" O   THR B  46 " (cutoff:3.500A)
      removed outlier: 5.051A  pdb=" N   TRP B  48 " --> pdb=" O   SER B 389 " (cutoff:3.500A)
      removed outlier: 4.626A  pdb=" N   SER B 389 " --> pdb=" O   TRP B  48 " (cutoff:3.500A)
      removed outlier: 3.724A  pdb=" N   LEU B 378 " --> pdb=" O   ILE B 390 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'B' and resid 66 through 68
    Processing sheet with id=AB3, first strand: chain 'B' and resid 116 through 118
      removed outlier: 3.548A  pdb=" N   TRP B 143 " --> pdb=" O   ALA B 133 " (cutoff:3.500A)
      removed outlier: 6.490A  pdb=" N   ASN B 135 " --> pdb=" O   VAL B 141 " (cutoff:3.500A)
      removed outlier: 6.628A  pdb=" N   VAL B 141 " --> pdb=" O   ASN B 135 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'B' and resid 156 through 158
      removed outlier: 3.501A  pdb=" N   VAL B 156 " --> pdb=" O   LEU B 163 " (cutoff:3.500A)
      removed outlier: 3.553A  pdb=" N   GLN B 170 " --> pdb=" O   THR B 166 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'B' and resid 252 through 254
      removed outlier: 3.693A  pdb=" N   TRP B 279 " --> pdb=" O   ALA B 269 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'B' and resid 290 through 292
      removed outlier: 3.543A  pdb=" N   ARG B 295 " --> pdb=" O   ASP B 292 " (cutoff:3.500A)
      removed outlier: 3.895A  pdb=" N   LEU B 308 " --> pdb=" O   ILE B 296 " (cutoff:3.500A)
      removed outlier: 3.709A  pdb=" N   ARG B 304 " --> pdb=" O   ASP B 300 " (cutoff:3.500A)
      removed outlier: 3.536A  pdb=" N   TRP B 317 " --> pdb=" O   ALA B 307 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'B' and resid 331 through 333
      removed outlier: 5.473A  pdb=" N   ASN B 350 " --> pdb=" O   PHE B 356 " (cutoff:3.500A)
      removed outlier: 6.158A  pdb=" N   PHE B 356 " --> pdb=" O   ASN B 350 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'E' and resid 32 through 35
      removed outlier: 3.985A  pdb=" N   MET E  64 " --> pdb=" O   PHE E  74 " (cutoff:3.500A)
    Processing sheet with id=AB9, first strand: chain 'E' and resid 32 through 35
      removed outlier: 6.697A  pdb=" N   THR E  90 " --> pdb=" O   ASN E 106 " (cutoff:3.500A)
      removed outlier: 4.379A  pdb=" N   ASN E 106 " --> pdb=" O   THR E  90 " (cutoff:3.500A)
      removed outlier: 6.690A  pdb=" N   THR E  92 " --> pdb=" O   ILE E 104 " (cutoff:3.500A)
      removed outlier: 4.424A  pdb=" N   ILE E 104 " --> pdb=" O   THR E  92 " (cutoff:3.500A)
      removed outlier: 6.625A  pdb=" N   THR E  94 " --> pdb=" O   THR E 102 " (cutoff:3.500A)
    Processing sheet with id=AC1, first strand: chain 'P' and resid 1181 through 1184
      removed outlier: 4.688A  pdb=" N   LYS P1181 " --> pdb=" O   ASP P1196 " (cutoff:3.500A)
      removed outlier: 3.913A  pdb=" N   ASP P1196 " --> pdb=" O   LYS P1181 " (cutoff:3.500A)

    905 hydrogen bonds defined for protein.
    2553 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: 6.19

  Time building geometry restraints manager: 3.69 seconds

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

  Histogram of bond lengths:
        1.11 -     1.25: 2115
        1.25 -     1.40: 3237
        1.40 -     1.54: 7250
        1.54 -     1.69: 1696
        1.69 -     1.83: 80
  Bond restraints: 14378
  Sorted by residual:
  bond pdb=" CA  VAL A 173 "
       pdb=" CB  VAL A 173 "
    ideal  model  delta    sigma   weight residual
    1.548  1.399  0.150 1.49e-02 4.50e+03 1.01e+02
  bond pdb=" CA  GLU B  26 "
       pdb=" CB  GLU B  26 "
    ideal  model  delta    sigma   weight residual
    1.530  1.706 -0.176 2.00e-02 2.50e+03 7.76e+01
  bond pdb=" CA  LYS A 103 "
       pdb=" C   LYS A 103 "
    ideal  model  delta    sigma   weight residual
    1.524  1.395  0.129 1.57e-02 4.06e+03 6.79e+01
  bond pdb=" C   LYS A 103 "
       pdb=" O   LYS A 103 "
    ideal  model  delta    sigma   weight residual
    1.235  1.110  0.125 1.62e-02 3.81e+03 5.97e+01
  bond pdb=" CB  LYS A 103 "
       pdb=" CG  LYS A 103 "
    ideal  model  delta    sigma   weight residual
    1.520  1.750 -0.230 3.00e-02 1.11e+03 5.88e+01
  ... (remaining 14373 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     6.27: 19393
        6.27 -    12.54: 110
       12.54 -    18.81: 7
       18.81 -    25.07: 5
       25.07 -    31.34: 1
  Bond angle restraints: 19516
  Sorted by residual:
  angle pdb=" O   GLU B  27 "
        pdb=" C   GLU B  27 "
        pdb=" N   ASP B  28 "
      ideal   model   delta    sigma   weight residual
     123.27  103.23   20.04 1.22e+00 6.72e-01 2.70e+02
  angle pdb=" CB  LYS A 103 "
        pdb=" CG  LYS A 103 "
        pdb=" CD  LYS A 103 "
      ideal   model   delta    sigma   weight residual
     111.30  142.64  -31.34 2.30e+00 1.89e-01 1.86e+02
  angle pdb=" CA  LYS A 103 "
        pdb=" C   LYS A 103 "
        pdb=" O   LYS A 103 "
      ideal   model   delta    sigma   weight residual
     120.32  105.83   14.49 1.18e+00 7.18e-01 1.51e+02
  angle pdb=" C   GLU B  26 "
        pdb=" CA  GLU B  26 "
        pdb=" CB  GLU B  26 "
      ideal   model   delta    sigma   weight residual
     110.10  132.96  -22.86 1.90e+00 2.77e-01 1.45e+02
  angle pdb=" C   GLU B  26 "
        pdb=" N   GLU B  27 "
        pdb=" CA  GLU B  27 "
      ideal   model   delta    sigma   weight residual
     122.73  142.21  -19.48 1.62e+00 3.81e-01 1.45e+02
  ... (remaining 19511 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.87: 7813
       17.87 -    35.74: 498
       35.74 -    53.60: 79
       53.60 -    71.47: 49
       71.47 -    89.34: 30
  Dihedral angle restraints: 8469
    sinusoidal: 3290
      harmonic: 5179
  Sorted by residual:
  dihedral pdb=" C   SER A 104 "
           pdb=" N   SER A 104 "
           pdb=" CA  SER A 104 "
           pdb=" CB  SER A 104 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -159.60   37.00     0      2.50e+00 1.60e-01 2.19e+02
  dihedral pdb=" N   SER A 104 "
           pdb=" C   SER A 104 "
           pdb=" CA  SER A 104 "
           pdb=" CB  SER A 104 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80  158.82  -36.02     0      2.50e+00 1.60e-01 2.08e+02
  dihedral pdb=" N   GLU B  26 "
           pdb=" C   GLU B  26 "
           pdb=" CA  GLU B  26 "
           pdb=" CB  GLU B  26 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80  104.54   18.26     0      2.50e+00 1.60e-01 5.33e+01
  ... (remaining 8466 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.303: 2070
       0.303 -    0.606: 41
       0.606 -    0.908: 0
       0.908 -    1.211: 0
       1.211 -    1.514: 1
  Chirality restraints: 2112
  Sorted by residual:
  chirality pdb=" CA  SER A 104 "
            pdb=" N   SER A 104 "
            pdb=" C   SER A 104 "
            pdb=" CB  SER A 104 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.00    1.51 2.00e-01 2.50e+01 5.73e+01
  chirality pdb=" CB  VAL A 173 "
            pdb=" CA  VAL A 173 "
            pdb=" CG1 VAL A 173 "
            pdb=" CG2 VAL A 173 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.03   -0.60 2.00e-01 2.50e+01 8.97e+00
  chirality pdb=" CA  THR B 239 "
            pdb=" N   THR B 239 "
            pdb=" C   THR B 239 "
            pdb=" CB  THR B 239 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    1.99    0.54 2.00e-01 2.50e+01 7.17e+00
  ... (remaining 2109 not shown)

  Planarity restraints: 2571
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR D 184 "    0.167 2.00e-02 2.50e+03   9.35e-02 1.75e+02
        pdb=" CG  TYR D 184 "   -0.049 2.00e-02 2.50e+03
        pdb=" CD1 TYR D 184 "   -0.071 2.00e-02 2.50e+03
        pdb=" CD2 TYR D 184 "   -0.069 2.00e-02 2.50e+03
        pdb=" CE1 TYR D 184 "   -0.057 2.00e-02 2.50e+03
        pdb=" CE2 TYR D 184 "   -0.055 2.00e-02 2.50e+03
        pdb=" CZ  TYR D 184 "   -0.018 2.00e-02 2.50e+03
        pdb=" OH  TYR D 184 "    0.152 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR A 229 "   -0.078 2.00e-02 2.50e+03   8.10e-02 1.31e+02
        pdb=" CG  TYR A 229 "   -0.039 2.00e-02 2.50e+03
        pdb=" CD1 TYR A 229 "    0.024 2.00e-02 2.50e+03
        pdb=" CD2 TYR A 229 "    0.030 2.00e-02 2.50e+03
        pdb=" CE1 TYR A 229 "    0.076 2.00e-02 2.50e+03
        pdb=" CE2 TYR A 229 "    0.079 2.00e-02 2.50e+03
        pdb=" CZ  TYR A 229 "    0.071 2.00e-02 2.50e+03
        pdb=" OH  TYR A 229 "   -0.163 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP B  93 "    0.035 2.00e-02 2.50e+03   6.06e-02 9.19e+01
        pdb=" CG  TRP B  93 "   -0.123 2.00e-02 2.50e+03
        pdb=" CD1 TRP B  93 "   -0.009 2.00e-02 2.50e+03
        pdb=" CD2 TRP B  93 "   -0.022 2.00e-02 2.50e+03
        pdb=" NE1 TRP B  93 "    0.103 2.00e-02 2.50e+03
        pdb=" CE2 TRP B  93 "    0.027 2.00e-02 2.50e+03
        pdb=" CE3 TRP B  93 "    0.039 2.00e-02 2.50e+03
        pdb=" CZ2 TRP B  93 "   -0.066 2.00e-02 2.50e+03
        pdb=" CZ3 TRP B  93 "    0.044 2.00e-02 2.50e+03
        pdb=" CH2 TRP B  93 "   -0.027 2.00e-02 2.50e+03
  ... (remaining 2568 not shown)

  Histogram of nonbonded interaction distances:
        2.18 -     2.72: 774
        2.72 -     3.27: 12872
        3.27 -     3.81: 22518
        3.81 -     4.36: 29491
        4.36 -     4.90: 49812
  Nonbonded interactions: 115467
  Sorted by model distance:
  nonbonded pdb=" O   LYS A 103 "
            pdb=" CB  LYS A 103 "
     model   vdw
     2.180 2.752
  nonbonded pdb=" O   GLU B  27 "
            pdb=" CA  ASP B  28 "
     model   vdw
     2.292 2.776
  nonbonded pdb=" O   LYS A 103 "
            pdb=" CA  GLU B  26 "
     model   vdw
     2.335 3.470
  nonbonded pdb=" CB  LYS A 103 "
            pdb=" O   GLU B  27 "
     model   vdw
     2.346 3.440
  nonbonded pdb=" N   VAL A 105 "
            pdb=" OE2 GLU B  26 "
     model   vdw
     2.353 3.120
  ... (remaining 115462 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.310
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.550
  Check model and map are aligned:         0.090
  Set scattering table:                    0.130
  Process input model:                     34.730
  Find NCS groups from input model:        0.130
  Set up NCS constraints:                  0.060
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:2.880
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   39.900
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5602
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      :  0.018   0.230  14380  Z= 1.091
  Angle     :  2.270  31.343  19520  Z= 1.605
  Chirality :  0.122   1.514   2112
  Planarity :  0.017   0.149   2571
  Dihedral  : 14.407  89.338   5177
  Min Nonbonded Distance : 2.180

Molprobity Statistics.
  All-atom Clashscore : 3.88
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  5.01 %
    Favored  : 94.93 %
  Rotamer:
    Outliers :  0.67 %
    Allowed  :  6.10 %
    Favored  : 93.23 %
  Cbeta Deviations :  0.91 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.42 (0.19), residues: 1795
  helix:  1.93 (0.27), residues: 352
  sheet:  0.37 (0.21), residues: 602
  loop : -1.81 (0.18), residues: 841

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.123   0.018   TRP B  93 
 HIS   0.018   0.005   HIS A 677 
 PHE   0.068   0.012   PHE B 356 
 TYR   0.167   0.022   TYR D 184 
 ARG   0.032   0.004   ARG A 212 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.15430 (  693)
  hydrogen bonds       : angle       7.07216 ( 2553)
  SS BOND              : bond        0.00182 (    2)
  SS BOND              : angle       1.00743 (    4)
  covalent geometry    : bond        0.01752 (14378)
  covalent geometry    : angle       2.26970 (19516)

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

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

  3590 Ramachandran restraints generated.
    1795 Oldfield, 0 Emsley, 1795 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3590 Ramachandran restraints generated.
    1795 Oldfield, 0 Emsley, 1795 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  460 residues out of total 1496 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 450
  time to evaluate  : 1.502 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  345 TYR cc_start: 0.5421 (m-80) cc_final: 0.5161 (m-10)
REVERT: C   58 LEU cc_start: 0.8255 (mt) cc_final: 0.8052 (mp)
REVERT: E   32 ILE cc_start: 0.8533 (mm) cc_final: 0.8268 (mt)
REVERT: P 1285 LYS cc_start: 0.3243 (tttp) cc_final: 0.2608 (tmtt)
  outliers start: 10
  outliers final: 3
  residues processed: 460
  average time/residue: 0.2852
  time to fit residues: 186.7327
Evaluate side-chains
  266 residues out of total 1496 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 263
  time to evaluate  : 1.555 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  105 VAL
Chi-restraints excluded: chain B residue  326 LEU
Chi-restraints excluded: chain P residue 1053 SER
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 178
   random chunks:
   chunk 150 optimal weight:    5.9990
   chunk 134 optimal weight:    0.7980
   chunk 74 optimal weight:    1.9990
   chunk 46 optimal weight:    2.9990
   chunk 91 optimal weight:    2.9990
   chunk 72 optimal weight:    0.4980
   chunk 139 optimal weight:    0.9980
   chunk 53 optimal weight:    5.9990
   chunk 84 optimal weight:    7.9990
   chunk 103 optimal weight:    7.9990
   chunk 161 optimal weight:    5.9990
   overall best weight:    1.4584

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

Flipped N/Q/H residues before XYZ refinement:
A 113 ASN
A 215 GLN
A 280 HIS
A 448 ASN
** A 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 561 GLN
A 563 ASN
A 664 GLN
A 731 ASN
A 748 ASN
B 121 HIS
B 170 GLN
B 172 GLN
** B 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 294 ASN
B 359 GLN
** B 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  70 GLN
D  82 ASN
D 104 ASN
D 138 GLN
** D 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
P1064 GLN
P1170 GLN

Total number of N/Q/H flips: 20

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4604 r_free = 0.4604 target = 0.228782 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 93)----------------|
| r_work = 0.4149 r_free = 0.4149 target = 0.176188 restraints weight = 17183.751|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.4129 r_free = 0.4129 target = 0.176116 restraints weight = 14212.951|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.4139 r_free = 0.4139 target = 0.178998 restraints weight = 10105.577|
|-----------------------------------------------------------------------------|
r_work (final): 0.4121
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6976
moved from start:          0.3203

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.065  14380  Z= 0.181
  Angle     :  0.673  14.649  19520  Z= 0.363
  Chirality :  0.046   0.292   2112
  Planarity :  0.005   0.073   2571
  Dihedral  :  5.739  67.162   1985
  Min Nonbonded Distance : 2.330

Molprobity Statistics.
  All-atom Clashscore : 8.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.06 %
    Favored  : 96.94 %
  Rotamer:
    Outliers :  2.88 %
    Allowed  : 11.73 %
    Favored  : 85.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.12 (0.19), residues: 1795
  helix:  2.55 (0.27), residues: 366
  sheet:  0.43 (0.21), residues: 617
  loop : -1.42 (0.20), residues: 812

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.032   0.002   TRP B  48 
 HIS   0.007   0.001   HIS A 677 
 PHE   0.017   0.002   PHE A 804 
 TYR   0.025   0.002   TYR P1015 
 ARG   0.004   0.001   ARG P1257 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04094 (  693)
  hydrogen bonds       : angle       5.14663 ( 2553)
  SS BOND              : bond        0.00220 (    2)
  SS BOND              : angle       0.48415 (    4)
  covalent geometry    : bond        0.00397 (14378)
  covalent geometry    : angle       0.67255 (19516)

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

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

  3590 Ramachandran restraints generated.
    1795 Oldfield, 0 Emsley, 1795 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3590 Ramachandran restraints generated.
    1795 Oldfield, 0 Emsley, 1795 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  310 residues out of total 1496 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 267
  time to evaluate  : 1.527 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  340 ASN cc_start: 0.7900 (t0) cc_final: 0.7306 (p0)
REVERT: A  391 ARG cc_start: 0.7155 (OUTLIER) cc_final: 0.6877 (ttp80)
REVERT: B   69 ASP cc_start: 0.7015 (t0) cc_final: 0.6774 (t0)
REVERT: B   80 LEU cc_start: 0.7274 (tt) cc_final: 0.6518 (tp)
REVERT: B  359 GLN cc_start: 0.5794 (OUTLIER) cc_final: 0.5335 (tt0)
REVERT: B  368 GLN cc_start: 0.7703 (pp30) cc_final: 0.7455 (pp30)
REVERT: C   58 LEU cc_start: 0.8793 (mt) cc_final: 0.8487 (mp)
REVERT: P 1170 GLN cc_start: 0.4237 (pt0) cc_final: 0.4026 (pt0)
  outliers start: 43
  outliers final: 21
  residues processed: 290
  average time/residue: 0.2595
  time to fit residues: 110.4594
Evaluate side-chains
  243 residues out of total 1496 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 220
  time to evaluate  : 1.387 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  264 ASP
Chi-restraints excluded: chain A residue  294 GLU
Chi-restraints excluded: chain A residue  304 MET
Chi-restraints excluded: chain A residue  345 ASN
Chi-restraints excluded: chain A residue  359 THR
Chi-restraints excluded: chain A residue  391 ARG
Chi-restraints excluded: chain A residue  396 GLU
Chi-restraints excluded: chain A residue  400 THR
Chi-restraints excluded: chain A residue  483 VAL
Chi-restraints excluded: chain A residue  551 SER
Chi-restraints excluded: chain A residue  611 VAL
Chi-restraints excluded: chain A residue  768 MET
Chi-restraints excluded: chain A residue  786 SER
Chi-restraints excluded: chain B residue  157 VAL
Chi-restraints excluded: chain B residue  201 THR
Chi-restraints excluded: chain B residue  339 VAL
Chi-restraints excluded: chain B residue  359 GLN
Chi-restraints excluded: chain C residue   70 THR
Chi-restraints excluded: chain E residue   46 ILE
Chi-restraints excluded: chain E residue   51 THR
Chi-restraints excluded: chain E residue   98 SER
Chi-restraints excluded: chain P residue 1080 THR
Chi-restraints excluded: chain P residue 1292 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 178
   random chunks:
   chunk 110 optimal weight:   10.0000
   chunk 55 optimal weight:    4.9990
   chunk 131 optimal weight:    1.9990
   chunk 37 optimal weight:    2.9990
   chunk 87 optimal weight:    0.9990
   chunk 157 optimal weight:   50.0000
   chunk 46 optimal weight:    2.9990
   chunk 51 optimal weight:    1.9990
   chunk 172 optimal weight:    6.9990
   chunk 151 optimal weight:    6.9990
   chunk 10 optimal weight:   10.0000
   overall best weight:    2.1990

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

Flipped N/Q/H residues before XYZ refinement:
A 179 GLN
A 403 GLN
** B 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  70 GLN
** D 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
P1064 GLN
P1160 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4566 r_free = 0.4566 target = 0.224477 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 116)---------------|
| r_work = 0.3968 r_free = 0.3968 target = 0.163800 restraints weight = 17369.787|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3979 r_free = 0.3979 target = 0.165443 restraints weight = 10437.705|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3962 r_free = 0.3962 target = 0.164328 restraints weight = 8516.216|
|-----------------------------------------------------------------------------|
r_work (final): 0.3926
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7321
moved from start:          0.3881

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.043  14380  Z= 0.214
  Angle     :  0.654  12.178  19520  Z= 0.348
  Chirality :  0.045   0.172   2112
  Planarity :  0.005   0.058   2571
  Dihedral  :  5.543  63.678   1981
  Min Nonbonded Distance : 2.359

Molprobity Statistics.
  All-atom Clashscore : 10.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.18 %
    Favored  : 95.82 %
  Rotamer:
    Outliers :  3.22 %
    Allowed  : 13.94 %
    Favored  : 82.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.01 (0.19), residues: 1795
  helix:  2.12 (0.27), residues: 356
  sheet:  0.34 (0.20), residues: 636
  loop : -1.26 (0.20), residues: 803

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.035   0.002   TRP B  48 
 HIS   0.008   0.001   HIS A 677 
 PHE   0.024   0.002   PHE A 804 
 TYR   0.025   0.002   TYR B 388 
 ARG   0.005   0.001   ARG P1257 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03960 (  693)
  hydrogen bonds       : angle       4.93789 ( 2553)
  SS BOND              : bond        0.00299 (    2)
  SS BOND              : angle       0.70525 (    4)
  covalent geometry    : bond        0.00465 (14378)
  covalent geometry    : angle       0.65362 (19516)

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

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

  3590 Ramachandran restraints generated.
    1795 Oldfield, 0 Emsley, 1795 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3590 Ramachandran restraints generated.
    1795 Oldfield, 0 Emsley, 1795 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  280 residues out of total 1496 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 232
  time to evaluate  : 1.409 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  222 ASP cc_start: 0.7635 (m-30) cc_final: 0.7419 (t0)
REVERT: A  340 ASN cc_start: 0.7995 (t0) cc_final: 0.7232 (p0)
REVERT: A  391 ARG cc_start: 0.7334 (OUTLIER) cc_final: 0.7020 (ttp80)
REVERT: B   69 ASP cc_start: 0.7303 (t0) cc_final: 0.6924 (t0)
REVERT: B   90 LYS cc_start: 0.7629 (mttt) cc_final: 0.7393 (mttt)
REVERT: B  228 TRP cc_start: 0.8057 (p-90) cc_final: 0.7851 (p90)
REVERT: B  246 ASP cc_start: 0.6483 (OUTLIER) cc_final: 0.6085 (m-30)
REVERT: B  323 LEU cc_start: 0.7257 (mt) cc_final: 0.7051 (tp)
REVERT: B  368 GLN cc_start: 0.7875 (pp30) cc_final: 0.7642 (pp30)
REVERT: B  388 TYR cc_start: 0.6628 (m-80) cc_final: 0.6247 (m-80)
REVERT: C   58 LEU cc_start: 0.8868 (mt) cc_final: 0.8477 (mp)
REVERT: D   81 LYS cc_start: 0.7649 (mmtm) cc_final: 0.7285 (mmtt)
REVERT: E   45 LYS cc_start: 0.8529 (ttpp) cc_final: 0.8316 (tttt)
  outliers start: 48
  outliers final: 27
  residues processed: 269
  average time/residue: 0.2461
  time to fit residues: 98.4308
Evaluate side-chains
  242 residues out of total 1496 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 213
  time to evaluate  : 1.549 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  264 ASP
Chi-restraints excluded: chain A residue  302 THR
Chi-restraints excluded: chain A residue  304 MET
Chi-restraints excluded: chain A residue  345 ASN
Chi-restraints excluded: chain A residue  359 THR
Chi-restraints excluded: chain A residue  391 ARG
Chi-restraints excluded: chain A residue  400 THR
Chi-restraints excluded: chain A residue  483 VAL
Chi-restraints excluded: chain A residue  508 SER
Chi-restraints excluded: chain A residue  511 THR
Chi-restraints excluded: chain A residue  539 MET
Chi-restraints excluded: chain A residue  551 SER
Chi-restraints excluded: chain A residue  611 VAL
Chi-restraints excluded: chain A residue  711 MET
Chi-restraints excluded: chain A residue  786 SER
Chi-restraints excluded: chain B residue  138 ASP
Chi-restraints excluded: chain B residue  157 VAL
Chi-restraints excluded: chain B residue  198 SER
Chi-restraints excluded: chain B residue  201 THR
Chi-restraints excluded: chain B residue  246 ASP
Chi-restraints excluded: chain B residue  257 VAL
Chi-restraints excluded: chain B residue  329 SER
Chi-restraints excluded: chain C residue   70 THR
Chi-restraints excluded: chain D residue   53 THR
Chi-restraints excluded: chain E residue   51 THR
Chi-restraints excluded: chain E residue   97 SER
Chi-restraints excluded: chain E residue   98 SER
Chi-restraints excluded: chain P residue 1080 THR
Chi-restraints excluded: chain P residue 1292 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 178
   random chunks:
   chunk 86 optimal weight:    0.9980
   chunk 131 optimal weight:    0.1980
   chunk 36 optimal weight:    4.9990
   chunk 82 optimal weight:    4.9990
   chunk 141 optimal weight:    0.9990
   chunk 88 optimal weight:    0.8980
   chunk 12 optimal weight:   20.0000
   chunk 101 optimal weight:    8.9990
   chunk 95 optimal weight:    3.9990
   chunk 33 optimal weight:    0.6980
   chunk 107 optimal weight:    3.9990
   overall best weight:    0.7582

-------------------------------------------------------------------------------
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 506 ASN
** A 677 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
P1024 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4562 r_free = 0.4562 target = 0.225290 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 103)---------------|
| r_work = 0.3978 r_free = 0.3978 target = 0.164758 restraints weight = 17176.368|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3961 r_free = 0.3961 target = 0.163874 restraints weight = 10061.252|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3975 r_free = 0.3975 target = 0.166104 restraints weight = 9171.040|
|-----------------------------------------------------------------------------|
r_work (final): 0.3983
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7209
moved from start:          0.4306

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  14380  Z= 0.126
  Angle     :  0.583  11.836  19520  Z= 0.308
  Chirality :  0.043   0.186   2112
  Planarity :  0.004   0.052   2571
  Dihedral  :  5.160  59.958   1981
  Min Nonbonded Distance : 2.407

Molprobity Statistics.
  All-atom Clashscore : 8.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.45 %
    Favored  : 96.55 %
  Rotamer:
    Outliers :  2.35 %
    Allowed  : 14.54 %
    Favored  : 83.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.13 (0.20), residues: 1795
  helix:  2.23 (0.27), residues: 350
  sheet:  0.37 (0.20), residues: 639
  loop : -1.12 (0.21), residues: 806

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.031   0.002   TRP B  48 
 HIS   0.008   0.001   HIS A 677 
 PHE   0.022   0.001   PHE A 804 
 TYR   0.022   0.001   TYR D 184 
 ARG   0.006   0.000   ARG B 355 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03454 (  693)
  hydrogen bonds       : angle       4.58921 ( 2553)
  SS BOND              : bond        0.00134 (    2)
  SS BOND              : angle       0.48444 (    4)
  covalent geometry    : bond        0.00258 (14378)
  covalent geometry    : angle       0.58254 (19516)

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

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

  3590 Ramachandran restraints generated.
    1795 Oldfield, 0 Emsley, 1795 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3590 Ramachandran restraints generated.
    1795 Oldfield, 0 Emsley, 1795 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  280 residues out of total 1496 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 245
  time to evaluate  : 1.438 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  222 ASP cc_start: 0.7649 (m-30) cc_final: 0.7442 (t0)
REVERT: A  229 TYR cc_start: 0.8589 (t80) cc_final: 0.7994 (t80)
REVERT: A  340 ASN cc_start: 0.7964 (t0) cc_final: 0.7227 (p0)
REVERT: A  432 TYR cc_start: 0.6522 (t80) cc_final: 0.6181 (t80)
REVERT: B   69 ASP cc_start: 0.7245 (t0) cc_final: 0.6955 (t0)
REVERT: B  246 ASP cc_start: 0.6167 (OUTLIER) cc_final: 0.5730 (m-30)
REVERT: C   58 LEU cc_start: 0.8870 (mt) cc_final: 0.8459 (mp)
REVERT: D   81 LYS cc_start: 0.7550 (mmtm) cc_final: 0.7311 (mmtt)
REVERT: P 1112 MET cc_start: 0.6131 (mmm) cc_final: 0.5765 (ppp)
REVERT: P 1144 TYR cc_start: 0.5977 (t80) cc_final: 0.5301 (t80)
  outliers start: 35
  outliers final: 24
  residues processed: 273
  average time/residue: 0.2530
  time to fit residues: 103.2857
Evaluate side-chains
  234 residues out of total 1496 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 209
  time to evaluate  : 1.396 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   37 VAL
Chi-restraints excluded: chain A residue  264 ASP
Chi-restraints excluded: chain A residue  345 ASN
Chi-restraints excluded: chain A residue  483 VAL
Chi-restraints excluded: chain A residue  508 SER
Chi-restraints excluded: chain A residue  539 MET
Chi-restraints excluded: chain A residue  551 SER
Chi-restraints excluded: chain A residue  596 THR
Chi-restraints excluded: chain A residue  711 MET
Chi-restraints excluded: chain A residue  786 SER
Chi-restraints excluded: chain B residue  138 ASP
Chi-restraints excluded: chain B residue  157 VAL
Chi-restraints excluded: chain B residue  198 SER
Chi-restraints excluded: chain B residue  201 THR
Chi-restraints excluded: chain B residue  246 ASP
Chi-restraints excluded: chain B residue  329 SER
Chi-restraints excluded: chain C residue   70 THR
Chi-restraints excluded: chain D residue   53 THR
Chi-restraints excluded: chain D residue   96 ILE
Chi-restraints excluded: chain D residue  205 TYR
Chi-restraints excluded: chain E residue   51 THR
Chi-restraints excluded: chain E residue   98 SER
Chi-restraints excluded: chain E residue  101 LEU
Chi-restraints excluded: chain P residue 1080 THR
Chi-restraints excluded: chain P residue 1292 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 178
   random chunks:
   chunk 82 optimal weight:    0.6980
   chunk 111 optimal weight:    5.9990
   chunk 65 optimal weight:    6.9990
   chunk 30 optimal weight:    0.9980
   chunk 46 optimal weight:    3.9990
   chunk 88 optimal weight:    3.9990
   chunk 49 optimal weight:    0.3980
   chunk 58 optimal weight:    0.9990
   chunk 121 optimal weight:    0.7980
   chunk 126 optimal weight:    0.9990
   chunk 118 optimal weight:    0.7980
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
A 323 GLN
A 403 GLN
A 677 HIS
B 168 ASN
** B 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
P1020 ASN
P1059 ASN
** P1128 HIS ** 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 = 0.4566 r_free = 0.4566 target = 0.225395 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 118)---------------|
| r_work = 0.3983 r_free = 0.3983 target = 0.165020 restraints weight = 17284.723|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3972 r_free = 0.3972 target = 0.165185 restraints weight = 10337.068|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3975 r_free = 0.3975 target = 0.166024 restraints weight = 9024.253|
|-----------------------------------------------------------------------------|
r_work (final): 0.3980
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7229
moved from start:          0.4552

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  14380  Z= 0.122
  Angle     :  0.582   9.821  19520  Z= 0.307
  Chirality :  0.043   0.186   2112
  Planarity :  0.004   0.046   2571
  Dihedral  :  5.009  58.382   1981
  Min Nonbonded Distance : 2.427

Molprobity Statistics.
  All-atom Clashscore : 9.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.96 %
    Favored  : 96.04 %
  Rotamer:
    Outliers :  2.41 %
    Allowed  : 16.09 %
    Favored  : 81.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.09 (0.20), residues: 1795
  helix:  2.08 (0.27), residues: 359
  sheet:  0.34 (0.20), residues: 635
  loop : -1.12 (0.21), residues: 801

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.036   0.002   TRP B  93 
 HIS   0.005   0.001   HIS P1062 
 PHE   0.024   0.001   PHE A 804 
 TYR   0.025   0.001   TYR P1150 
 ARG   0.006   0.000   ARG B 355 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03399 (  693)
  hydrogen bonds       : angle       4.46063 ( 2553)
  SS BOND              : bond        0.00119 (    2)
  SS BOND              : angle       0.42111 (    4)
  covalent geometry    : bond        0.00258 (14378)
  covalent geometry    : angle       0.58197 (19516)

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

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

  3590 Ramachandran restraints generated.
    1795 Oldfield, 0 Emsley, 1795 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3590 Ramachandran restraints generated.
    1795 Oldfield, 0 Emsley, 1795 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  261 residues out of total 1496 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 225
  time to evaluate  : 1.658 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  229 TYR cc_start: 0.8589 (t80) cc_final: 0.7999 (t80)
REVERT: A  321 ARG cc_start: 0.7057 (mmm-85) cc_final: 0.6791 (mtp85)
REVERT: A  340 ASN cc_start: 0.7944 (t0) cc_final: 0.7207 (p0)
REVERT: A  432 TYR cc_start: 0.6515 (t80) cc_final: 0.6181 (t80)
REVERT: A  777 MET cc_start: 0.7402 (mmp) cc_final: 0.6986 (mmt)
REVERT: B   32 MET cc_start: 0.7198 (mmt) cc_final: 0.6979 (tpp)
REVERT: B   69 ASP cc_start: 0.7319 (t0) cc_final: 0.7027 (t0)
REVERT: B  246 ASP cc_start: 0.6096 (OUTLIER) cc_final: 0.5737 (m-30)
REVERT: C   58 LEU cc_start: 0.8871 (mt) cc_final: 0.8444 (mp)
REVERT: P 1144 TYR cc_start: 0.6151 (t80) cc_final: 0.5865 (t80)
  outliers start: 36
  outliers final: 24
  residues processed: 251
  average time/residue: 0.2547
  time to fit residues: 95.1788
Evaluate side-chains
  242 residues out of total 1496 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 217
  time to evaluate  : 1.653 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  264 ASP
Chi-restraints excluded: chain A residue  304 MET
Chi-restraints excluded: chain A residue  345 ASN
Chi-restraints excluded: chain A residue  481 ASP
Chi-restraints excluded: chain A residue  483 VAL
Chi-restraints excluded: chain A residue  517 PHE
Chi-restraints excluded: chain A residue  539 MET
Chi-restraints excluded: chain A residue  551 SER
Chi-restraints excluded: chain A residue  596 THR
Chi-restraints excluded: chain A residue  711 MET
Chi-restraints excluded: chain A residue  786 SER
Chi-restraints excluded: chain B residue  138 ASP
Chi-restraints excluded: chain B residue  157 VAL
Chi-restraints excluded: chain B residue  198 SER
Chi-restraints excluded: chain B residue  201 THR
Chi-restraints excluded: chain B residue  202 THR
Chi-restraints excluded: chain B residue  246 ASP
Chi-restraints excluded: chain C residue   70 THR
Chi-restraints excluded: chain D residue   53 THR
Chi-restraints excluded: chain D residue   96 ILE
Chi-restraints excluded: chain D residue  205 TYR
Chi-restraints excluded: chain E residue  101 LEU
Chi-restraints excluded: chain P residue 1015 TYR
Chi-restraints excluded: chain P residue 1080 THR
Chi-restraints excluded: chain P residue 1292 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 178
   random chunks:
   chunk 164 optimal weight:    3.9990
   chunk 140 optimal weight:    0.8980
   chunk 161 optimal weight:   30.0000
   chunk 62 optimal weight:    1.9990
   chunk 126 optimal weight:    1.9990
   chunk 143 optimal weight:    0.6980
   chunk 36 optimal weight:    4.9990
   chunk 44 optimal weight:   10.0000
   chunk 95 optimal weight:    0.9980
   chunk 18 optimal weight:    0.1980
   chunk 29 optimal weight:    3.9990
   overall best weight:    0.9582

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

Flipped N/Q/H residues before XYZ refinement:
** B 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 324 HIS
** D 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** P1023 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
P1128 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4567 r_free = 0.4567 target = 0.225236 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 97)----------------|
| r_work = 0.4089 r_free = 0.4089 target = 0.170451 restraints weight = 17428.123|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.4079 r_free = 0.4079 target = 0.172153 restraints weight = 13545.599|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.4100 r_free = 0.4100 target = 0.174617 restraints weight = 9123.629|
|-----------------------------------------------------------------------------|
r_work (final): 0.4108
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7020
moved from start:          0.4769

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030  14380  Z= 0.128
  Angle     :  0.562   7.992  19520  Z= 0.298
  Chirality :  0.043   0.198   2112
  Planarity :  0.004   0.047   2571
  Dihedral  :  4.930  57.254   1981
  Min Nonbonded Distance : 2.463

Molprobity Statistics.
  All-atom Clashscore : 9.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.79 %
    Favored  : 96.21 %
  Rotamer:
    Outliers :  2.41 %
    Allowed  : 16.29 %
    Favored  : 81.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.05 (0.20), residues: 1795
  helix:  2.07 (0.27), residues: 352
  sheet:  0.27 (0.20), residues: 639
  loop : -1.10 (0.21), residues: 804

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.038   0.002   TRP B  93 
 HIS   0.005   0.001   HIS P1062 
 PHE   0.016   0.001   PHE A 804 
 TYR   0.022   0.001   TYR D 184 
 ARG   0.005   0.000   ARG D 112 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03317 (  693)
  hydrogen bonds       : angle       4.41912 ( 2553)
  SS BOND              : bond        0.00150 (    2)
  SS BOND              : angle       0.50402 (    4)
  covalent geometry    : bond        0.00272 (14378)
  covalent geometry    : angle       0.56151 (19516)

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

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

  3590 Ramachandran restraints generated.
    1795 Oldfield, 0 Emsley, 1795 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3590 Ramachandran restraints generated.
    1795 Oldfield, 0 Emsley, 1795 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  253 residues out of total 1496 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 217
  time to evaluate  : 1.867 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  229 TYR cc_start: 0.8176 (t80) cc_final: 0.7703 (t80)
REVERT: A  272 GLU cc_start: 0.7218 (pp20) cc_final: 0.6995 (pp20)
REVERT: A  340 ASN cc_start: 0.7913 (t0) cc_final: 0.7331 (p0)
REVERT: B  246 ASP cc_start: 0.5690 (OUTLIER) cc_final: 0.5369 (m-30)
REVERT: C   58 LEU cc_start: 0.8891 (mt) cc_final: 0.8443 (mp)
REVERT: E   51 THR cc_start: 0.7879 (m) cc_final: 0.7591 (m)
  outliers start: 36
  outliers final: 30
  residues processed: 245
  average time/residue: 0.2959
  time to fit residues: 107.2654
Evaluate side-chains
  233 residues out of total 1496 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 202
  time to evaluate  : 2.379 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  264 ASP
Chi-restraints excluded: chain A residue  304 MET
Chi-restraints excluded: chain A residue  345 ASN
Chi-restraints excluded: chain A residue  359 THR
Chi-restraints excluded: chain A residue  481 ASP
Chi-restraints excluded: chain A residue  483 VAL
Chi-restraints excluded: chain A residue  508 SER
Chi-restraints excluded: chain A residue  517 PHE
Chi-restraints excluded: chain A residue  539 MET
Chi-restraints excluded: chain A residue  551 SER
Chi-restraints excluded: chain A residue  596 THR
Chi-restraints excluded: chain A residue  711 MET
Chi-restraints excluded: chain A residue  786 SER
Chi-restraints excluded: chain B residue   80 LEU
Chi-restraints excluded: chain B residue  138 ASP
Chi-restraints excluded: chain B residue  157 VAL
Chi-restraints excluded: chain B residue  198 SER
Chi-restraints excluded: chain B residue  201 THR
Chi-restraints excluded: chain B residue  202 THR
Chi-restraints excluded: chain B residue  246 ASP
Chi-restraints excluded: chain B residue  324 HIS
Chi-restraints excluded: chain B residue  339 VAL
Chi-restraints excluded: chain B residue  370 GLU
Chi-restraints excluded: chain C residue   70 THR
Chi-restraints excluded: chain D residue   53 THR
Chi-restraints excluded: chain D residue  205 TYR
Chi-restraints excluded: chain E residue  101 LEU
Chi-restraints excluded: chain P residue 1019 LEU
Chi-restraints excluded: chain P residue 1080 THR
Chi-restraints excluded: chain P residue 1285 LYS
Chi-restraints excluded: chain P residue 1292 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 178
   random chunks:
   chunk 170 optimal weight:    2.9990
   chunk 135 optimal weight:    1.9990
   chunk 42 optimal weight:    3.9990
   chunk 69 optimal weight:    5.9990
   chunk 129 optimal weight:    0.3980
   chunk 15 optimal weight:    9.9990
   chunk 101 optimal weight:    4.9990
   chunk 155 optimal weight:    0.8980
   chunk 165 optimal weight:    9.9990
   chunk 160 optimal weight:    6.9990
   chunk 10 optimal weight:   40.0000
   overall best weight:    2.0586

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

Flipped N/Q/H residues before XYZ refinement:
** B 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 276 GLN
** D 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  52 GLN
E  54 GLN
P1023 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4546 r_free = 0.4546 target = 0.221830 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 109)---------------|
| r_work = 0.3937 r_free = 0.3937 target = 0.160475 restraints weight = 17320.280|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3938 r_free = 0.3938 target = 0.161348 restraints weight = 9823.319|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3949 r_free = 0.3949 target = 0.162742 restraints weight = 8878.493|
|-----------------------------------------------------------------------------|
r_work (final): 0.3914
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7337
moved from start:          0.5023

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041  14380  Z= 0.202
  Angle     :  0.627   9.283  19520  Z= 0.331
  Chirality :  0.045   0.212   2112
  Planarity :  0.004   0.049   2571
  Dihedral  :  5.110  59.637   1981
  Min Nonbonded Distance : 2.427

Molprobity Statistics.
  All-atom Clashscore : 9.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.46 %
    Favored  : 95.54 %
  Rotamer:
    Outliers :  2.55 %
    Allowed  : 16.96 %
    Favored  : 80.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.17 (0.19), residues: 1795
  helix:  1.83 (0.27), residues: 351
  sheet:  0.13 (0.20), residues: 631
  loop : -1.16 (0.20), residues: 813

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.027   0.002   TRP P1219 
 HIS   0.015   0.001   HIS B 324 
 PHE   0.016   0.001   PHE A 440 
 TYR   0.026   0.002   TYR A 550 
 ARG   0.006   0.001   ARG B 325 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03633 (  693)
  hydrogen bonds       : angle       4.62956 ( 2553)
  SS BOND              : bond        0.00256 (    2)
  SS BOND              : angle       0.57011 (    4)
  covalent geometry    : bond        0.00440 (14378)
  covalent geometry    : angle       0.62652 (19516)

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

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

  3590 Ramachandran restraints generated.
    1795 Oldfield, 0 Emsley, 1795 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3590 Ramachandran restraints generated.
    1795 Oldfield, 0 Emsley, 1795 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  246 residues out of total 1496 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 208
  time to evaluate  : 1.833 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  229 TYR cc_start: 0.8645 (t80) cc_final: 0.8016 (t80)
REVERT: A  340 ASN cc_start: 0.8040 (t0) cc_final: 0.7258 (p0)
REVERT: A  777 MET cc_start: 0.7505 (mmp) cc_final: 0.7063 (mmt)
REVERT: B  246 ASP cc_start: 0.6091 (OUTLIER) cc_final: 0.5786 (m-30)
REVERT: P 1112 MET cc_start: 0.6484 (mmm) cc_final: 0.6069 (ppp)
  outliers start: 38
  outliers final: 27
  residues processed: 238
  average time/residue: 0.2959
  time to fit residues: 107.8589
Evaluate side-chains
  231 residues out of total 1496 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 203
  time to evaluate  : 1.459 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  264 ASP
Chi-restraints excluded: chain A residue  304 MET
Chi-restraints excluded: chain A residue  345 ASN
Chi-restraints excluded: chain A residue  359 THR
Chi-restraints excluded: chain A residue  481 ASP
Chi-restraints excluded: chain A residue  483 VAL
Chi-restraints excluded: chain A residue  508 SER
Chi-restraints excluded: chain A residue  517 PHE
Chi-restraints excluded: chain A residue  539 MET
Chi-restraints excluded: chain A residue  551 SER
Chi-restraints excluded: chain A residue  596 THR
Chi-restraints excluded: chain A residue  711 MET
Chi-restraints excluded: chain A residue  786 SER
Chi-restraints excluded: chain B residue   80 LEU
Chi-restraints excluded: chain B residue  138 ASP
Chi-restraints excluded: chain B residue  157 VAL
Chi-restraints excluded: chain B residue  198 SER
Chi-restraints excluded: chain B residue  201 THR
Chi-restraints excluded: chain B residue  246 ASP
Chi-restraints excluded: chain B residue  329 SER
Chi-restraints excluded: chain B residue  339 VAL
Chi-restraints excluded: chain B residue  370 GLU
Chi-restraints excluded: chain C residue   70 THR
Chi-restraints excluded: chain D residue   53 THR
Chi-restraints excluded: chain E residue  101 LEU
Chi-restraints excluded: chain P residue 1019 LEU
Chi-restraints excluded: chain P residue 1080 THR
Chi-restraints excluded: chain P residue 1292 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 178
   random chunks:
   chunk 114 optimal weight:    4.9990
   chunk 151 optimal weight:    0.7980
   chunk 62 optimal weight:    0.6980
   chunk 132 optimal weight:    0.7980
   chunk 83 optimal weight:    0.9990
   chunk 28 optimal weight:    0.7980
   chunk 167 optimal weight:    8.9990
   chunk 149 optimal weight:    5.9990
   chunk 177 optimal weight:    0.9980
   chunk 32 optimal weight:    0.4980
   chunk 52 optimal weight:    0.9980
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
A 323 GLN
** B 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4566 r_free = 0.4566 target = 0.224525 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 107)---------------|
| r_work = 0.3937 r_free = 0.3937 target = 0.162637 restraints weight = 17337.251|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3954 r_free = 0.3954 target = 0.163032 restraints weight = 10501.246|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3959 r_free = 0.3959 target = 0.164344 restraints weight = 9181.902|
|-----------------------------------------------------------------------------|
r_work (final): 0.3923
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7317
moved from start:          0.5123

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  14380  Z= 0.121
  Angle     :  0.574   8.697  19520  Z= 0.304
  Chirality :  0.043   0.218   2112
  Planarity :  0.004   0.048   2571
  Dihedral  :  4.875  57.787   1981
  Min Nonbonded Distance : 2.473

Molprobity Statistics.
  All-atom Clashscore : 9.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.79 %
    Favored  : 96.21 %
  Rotamer:
    Outliers :  2.01 %
    Allowed  : 17.90 %
    Favored  : 80.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.11 (0.19), residues: 1795
  helix:  1.93 (0.27), residues: 351
  sheet:  0.18 (0.21), residues: 628
  loop : -1.18 (0.20), residues: 816

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP B  93 
 HIS   0.013   0.001   HIS P1062 
 PHE   0.011   0.001   PHE A 440 
 TYR   0.028   0.001   TYR A 550 
 ARG   0.005   0.000   ARG A 321 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03310 (  693)
  hydrogen bonds       : angle       4.41845 ( 2553)
  SS BOND              : bond        0.00136 (    2)
  SS BOND              : angle       0.46236 (    4)
  covalent geometry    : bond        0.00254 (14378)
  covalent geometry    : angle       0.57436 (19516)

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

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

  3590 Ramachandran restraints generated.
    1795 Oldfield, 0 Emsley, 1795 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3590 Ramachandran restraints generated.
    1795 Oldfield, 0 Emsley, 1795 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  240 residues out of total 1496 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 210
  time to evaluate  : 1.697 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  227 ARG cc_start: 0.8622 (ttm110) cc_final: 0.8215 (ttm110)
REVERT: A  229 TYR cc_start: 0.8690 (t80) cc_final: 0.8051 (t80)
REVERT: A  340 ASN cc_start: 0.8009 (t0) cc_final: 0.7173 (p0)
REVERT: A  777 MET cc_start: 0.7655 (mmp) cc_final: 0.7244 (mmt)
REVERT: B  246 ASP cc_start: 0.6053 (OUTLIER) cc_final: 0.5691 (m-30)
REVERT: D   41 GLN cc_start: 0.7805 (mm-40) cc_final: 0.7525 (mm-40)
REVERT: P 1112 MET cc_start: 0.6524 (mmm) cc_final: 0.5951 (ppp)
REVERT: P 1257 ARG cc_start: 0.6829 (ptm160) cc_final: 0.6056 (mtm-85)
  outliers start: 30
  outliers final: 26
  residues processed: 232
  average time/residue: 0.3414
  time to fit residues: 118.9380
Evaluate side-chains
  228 residues out of total 1496 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 201
  time to evaluate  : 1.542 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  254 ILE
Chi-restraints excluded: chain A residue  264 ASP
Chi-restraints excluded: chain A residue  304 MET
Chi-restraints excluded: chain A residue  359 THR
Chi-restraints excluded: chain A residue  481 ASP
Chi-restraints excluded: chain A residue  483 VAL
Chi-restraints excluded: chain A residue  517 PHE
Chi-restraints excluded: chain A residue  539 MET
Chi-restraints excluded: chain A residue  551 SER
Chi-restraints excluded: chain A residue  596 THR
Chi-restraints excluded: chain A residue  711 MET
Chi-restraints excluded: chain A residue  786 SER
Chi-restraints excluded: chain B residue   80 LEU
Chi-restraints excluded: chain B residue  138 ASP
Chi-restraints excluded: chain B residue  157 VAL
Chi-restraints excluded: chain B residue  198 SER
Chi-restraints excluded: chain B residue  201 THR
Chi-restraints excluded: chain B residue  246 ASP
Chi-restraints excluded: chain B residue  323 LEU
Chi-restraints excluded: chain B residue  370 GLU
Chi-restraints excluded: chain C residue   70 THR
Chi-restraints excluded: chain D residue  205 TYR
Chi-restraints excluded: chain E residue  101 LEU
Chi-restraints excluded: chain E residue  103 ASN
Chi-restraints excluded: chain P residue 1080 THR
Chi-restraints excluded: chain P residue 1285 LYS
Chi-restraints excluded: chain P residue 1292 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 178
   random chunks:
   chunk 12 optimal weight:   20.0000
   chunk 13 optimal weight:    6.9990
   chunk 59 optimal weight:   10.0000
   chunk 24 optimal weight:    4.9990
   chunk 135 optimal weight:    1.9990
   chunk 34 optimal weight:    2.9990
   chunk 127 optimal weight:    0.5980
   chunk 45 optimal weight:    2.9990
   chunk 10 optimal weight:   10.0000
   chunk 121 optimal weight:    1.9990
   chunk 72 optimal weight:    0.7980
   overall best weight:    1.6786

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

Flipped N/Q/H residues before XYZ refinement:
** B 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4543 r_free = 0.4543 target = 0.221869 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 79)----------------|
| r_work = 0.4084 r_free = 0.4084 target = 0.169363 restraints weight = 17284.935|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.4074 r_free = 0.4074 target = 0.172503 restraints weight = 15373.656|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.4070 r_free = 0.4070 target = 0.171673 restraints weight = 8413.234|
|-----------------------------------------------------------------------------|
r_work (final): 0.4064
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7083
moved from start:          0.5272

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034  14380  Z= 0.173
  Angle     :  0.605   8.140  19520  Z= 0.319
  Chirality :  0.045   0.321   2112
  Planarity :  0.004   0.048   2571
  Dihedral  :  4.991  58.994   1981
  Min Nonbonded Distance : 2.476

Molprobity Statistics.
  All-atom Clashscore : 9.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.62 %
    Favored  : 95.38 %
  Rotamer:
    Outliers :  2.41 %
    Allowed  : 17.96 %
    Favored  : 79.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.25 (0.19), residues: 1795
  helix:  1.88 (0.27), residues: 353
  sheet: -0.01 (0.20), residues: 637
  loop : -1.21 (0.20), residues: 805

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.028   0.002   TRP P1219 
 HIS   0.009   0.001   HIS P1062 
 PHE   0.014   0.001   PHE P1056 
 TYR   0.020   0.001   TYR D 184 
 ARG   0.005   0.000   ARG A 321 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03469 (  693)
  hydrogen bonds       : angle       4.50720 ( 2553)
  SS BOND              : bond        0.00236 (    2)
  SS BOND              : angle       0.56053 (    4)
  covalent geometry    : bond        0.00376 (14378)
  covalent geometry    : angle       0.60511 (19516)

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

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

  3590 Ramachandran restraints generated.
    1795 Oldfield, 0 Emsley, 1795 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3590 Ramachandran restraints generated.
    1795 Oldfield, 0 Emsley, 1795 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  237 residues out of total 1496 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 201
  time to evaluate  : 1.443 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  229 TYR cc_start: 0.8127 (t80) cc_final: 0.7634 (t80)
REVERT: A  340 ASN cc_start: 0.8014 (t0) cc_final: 0.7325 (p0)
REVERT: A  430 ILE cc_start: 0.7881 (OUTLIER) cc_final: 0.7649 (tt)
REVERT: A  551 SER cc_start: 0.8363 (OUTLIER) cc_final: 0.8031 (p)
REVERT: A  646 MET cc_start: 0.8810 (ttt) cc_final: 0.8578 (ttt)
REVERT: A  777 MET cc_start: 0.7034 (mmp) cc_final: 0.6629 (mmt)
REVERT: B   48 TRP cc_start: 0.6393 (m-90) cc_final: 0.6059 (m-90)
REVERT: P 1257 ARG cc_start: 0.6352 (ptm160) cc_final: 0.5806 (mtm-85)
  outliers start: 36
  outliers final: 30
  residues processed: 226
  average time/residue: 0.2448
  time to fit residues: 83.4964
Evaluate side-chains
  230 residues out of total 1496 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 198
  time to evaluate  : 1.388 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  254 ILE
Chi-restraints excluded: chain A residue  264 ASP
Chi-restraints excluded: chain A residue  304 MET
Chi-restraints excluded: chain A residue  345 ASN
Chi-restraints excluded: chain A residue  359 THR
Chi-restraints excluded: chain A residue  430 ILE
Chi-restraints excluded: chain A residue  481 ASP
Chi-restraints excluded: chain A residue  483 VAL
Chi-restraints excluded: chain A residue  517 PHE
Chi-restraints excluded: chain A residue  539 MET
Chi-restraints excluded: chain A residue  551 SER
Chi-restraints excluded: chain A residue  596 THR
Chi-restraints excluded: chain A residue  611 VAL
Chi-restraints excluded: chain A residue  711 MET
Chi-restraints excluded: chain A residue  786 SER
Chi-restraints excluded: chain B residue   80 LEU
Chi-restraints excluded: chain B residue  138 ASP
Chi-restraints excluded: chain B residue  157 VAL
Chi-restraints excluded: chain B residue  198 SER
Chi-restraints excluded: chain B residue  201 THR
Chi-restraints excluded: chain B residue  370 GLU
Chi-restraints excluded: chain C residue   42 LEU
Chi-restraints excluded: chain C residue   70 THR
Chi-restraints excluded: chain D residue   53 THR
Chi-restraints excluded: chain E residue   76 VAL
Chi-restraints excluded: chain E residue  101 LEU
Chi-restraints excluded: chain E residue  103 ASN
Chi-restraints excluded: chain P residue 1019 LEU
Chi-restraints excluded: chain P residue 1080 THR
Chi-restraints excluded: chain P residue 1210 VAL
Chi-restraints excluded: chain P residue 1285 LYS
Chi-restraints excluded: chain P residue 1292 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 178
   random chunks:
   chunk 53 optimal weight:    3.9990
   chunk 44 optimal weight:    6.9990
   chunk 49 optimal weight:    0.2980
   chunk 152 optimal weight:    1.9990
   chunk 176 optimal weight:    6.9990
   chunk 138 optimal weight:    0.0270
   chunk 111 optimal weight:   10.0000
   chunk 166 optimal weight:    4.9990
   chunk 173 optimal weight:    3.9990
   chunk 77 optimal weight:    6.9990
   chunk 131 optimal weight:    1.9990
   overall best weight:    1.6644

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

Flipped N/Q/H residues before XYZ refinement:
A 561 GLN
** B 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  52 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4543 r_free = 0.4543 target = 0.221813 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 89)----------------|
| r_work = 0.4039 r_free = 0.4039 target = 0.166016 restraints weight = 17354.380|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.4017 r_free = 0.4017 target = 0.166336 restraints weight = 14146.241|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.4022 r_free = 0.4022 target = 0.168037 restraints weight = 9145.744|
|-----------------------------------------------------------------------------|
r_work (final): 0.4015
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7163
moved from start:          0.5386

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043  14380  Z= 0.171
  Angle     :  0.598   8.296  19520  Z= 0.315
  Chirality :  0.044   0.302   2112
  Planarity :  0.004   0.050   2571
  Dihedral  :  4.985  60.302   1981
  Min Nonbonded Distance : 2.472

Molprobity Statistics.
  All-atom Clashscore : 9.42
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  4.29 %
    Favored  : 95.65 %
  Rotamer:
    Outliers :  2.35 %
    Allowed  : 18.16 %
    Favored  : 79.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.25 (0.19), residues: 1795
  helix:  1.85 (0.27), residues: 355
  sheet: -0.01 (0.20), residues: 631
  loop : -1.21 (0.20), residues: 809

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.027   0.002   TRP P1219 
 HIS   0.008   0.001   HIS P1062 
 PHE   0.011   0.001   PHE A 347 
 TYR   0.027   0.002   TYR A 550 
 ARG   0.005   0.000   ARG A 321 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03416 (  693)
  hydrogen bonds       : angle       4.49220 ( 2553)
  SS BOND              : bond        0.00223 (    2)
  SS BOND              : angle       0.56763 (    4)
  covalent geometry    : bond        0.00373 (14378)
  covalent geometry    : angle       0.59816 (19516)

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

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

  3590 Ramachandran restraints generated.
    1795 Oldfield, 0 Emsley, 1795 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3590 Ramachandran restraints generated.
    1795 Oldfield, 0 Emsley, 1795 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  237 residues out of total 1496 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 202
  time to evaluate  : 1.594 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  227 ARG cc_start: 0.8598 (ttm110) cc_final: 0.8334 (ttm110)
REVERT: A  229 TYR cc_start: 0.8234 (t80) cc_final: 0.7703 (t80)
REVERT: A  340 ASN cc_start: 0.8025 (t0) cc_final: 0.7295 (p0)
REVERT: A  355 GLU cc_start: 0.7471 (mt-10) cc_final: 0.7252 (mt-10)
REVERT: A  430 ILE cc_start: 0.7899 (OUTLIER) cc_final: 0.7661 (tt)
REVERT: A  551 SER cc_start: 0.8356 (OUTLIER) cc_final: 0.8020 (p)
REVERT: A  646 MET cc_start: 0.8806 (ttt) cc_final: 0.8576 (ttt)
REVERT: B   48 TRP cc_start: 0.6381 (m-90) cc_final: 0.6066 (m-90)
REVERT: P 1257 ARG cc_start: 0.6455 (ptm160) cc_final: 0.5887 (mtm-85)
  outliers start: 35
  outliers final: 29
  residues processed: 227
  average time/residue: 0.2808
  time to fit residues: 97.1091
Evaluate side-chains
  230 residues out of total 1496 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 199
  time to evaluate  : 1.450 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  254 ILE
Chi-restraints excluded: chain A residue  264 ASP
Chi-restraints excluded: chain A residue  304 MET
Chi-restraints excluded: chain A residue  345 ASN
Chi-restraints excluded: chain A residue  359 THR
Chi-restraints excluded: chain A residue  430 ILE
Chi-restraints excluded: chain A residue  481 ASP
Chi-restraints excluded: chain A residue  483 VAL
Chi-restraints excluded: chain A residue  517 PHE
Chi-restraints excluded: chain A residue  539 MET
Chi-restraints excluded: chain A residue  551 SER
Chi-restraints excluded: chain A residue  596 THR
Chi-restraints excluded: chain A residue  611 VAL
Chi-restraints excluded: chain A residue  711 MET
Chi-restraints excluded: chain A residue  786 SER
Chi-restraints excluded: chain B residue   37 THR
Chi-restraints excluded: chain B residue   80 LEU
Chi-restraints excluded: chain B residue  138 ASP
Chi-restraints excluded: chain B residue  157 VAL
Chi-restraints excluded: chain B residue  198 SER
Chi-restraints excluded: chain B residue  201 THR
Chi-restraints excluded: chain B residue  370 GLU
Chi-restraints excluded: chain C residue   42 LEU
Chi-restraints excluded: chain C residue   70 THR
Chi-restraints excluded: chain D residue   53 THR
Chi-restraints excluded: chain E residue   76 VAL
Chi-restraints excluded: chain E residue   98 SER
Chi-restraints excluded: chain E residue  101 LEU
Chi-restraints excluded: chain P residue 1019 LEU
Chi-restraints excluded: chain P residue 1080 THR
Chi-restraints excluded: chain P residue 1292 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 178
   random chunks:
   chunk 176 optimal weight:    7.9990
   chunk 38 optimal weight:    0.9990
   chunk 125 optimal weight:    0.6980
   chunk 92 optimal weight:    1.9990
   chunk 28 optimal weight:    1.9990
   chunk 145 optimal weight:    2.9990
   chunk 166 optimal weight:   30.0000
   chunk 2 optimal weight:   30.0000
   chunk 175 optimal weight:    2.9990
   chunk 127 optimal weight:    0.9990
   chunk 86 optimal weight:    0.9990
   overall best weight:    1.1388

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

Flipped N/Q/H residues before XYZ refinement:
** B 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4549 r_free = 0.4549 target = 0.222499 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 109)---------------|
| r_work = 0.3920 r_free = 0.3920 target = 0.159897 restraints weight = 17431.284|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3948 r_free = 0.3948 target = 0.162570 restraints weight = 10333.933|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3941 r_free = 0.3941 target = 0.162144 restraints weight = 7913.513|
|-----------------------------------------------------------------------------|
r_work (final): 0.3919
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7325
moved from start:          0.5458

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  14380  Z= 0.141
  Angle     :  0.585   8.191  19520  Z= 0.308
  Chirality :  0.044   0.252   2112
  Planarity :  0.004   0.047   2571
  Dihedral  :  4.886  59.793   1981
  Min Nonbonded Distance : 2.479

Molprobity Statistics.
  All-atom Clashscore : 9.28
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  4.74 %
    Favored  : 95.21 %
  Rotamer:
    Outliers :  2.08 %
    Allowed  : 18.57 %
    Favored  : 79.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.23 (0.19), residues: 1795
  helix:  1.93 (0.27), residues: 355
  sheet:  0.03 (0.21), residues: 627
  loop : -1.24 (0.20), residues: 813

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.002   TRP P1219 
 HIS   0.007   0.001   HIS P1062 
 PHE   0.013   0.001   PHE P1113 
 TYR   0.022   0.001   TYR A 608 
 ARG   0.006   0.000   ARG A 321 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03305 (  693)
  hydrogen bonds       : angle       4.41181 ( 2553)
  SS BOND              : bond        0.00157 (    2)
  SS BOND              : angle       0.54241 (    4)
  covalent geometry    : bond        0.00305 (14378)
  covalent geometry    : angle       0.58508 (19516)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 6401.71 seconds
wall clock time: 115 minutes 47.38 seconds (6947.38 seconds total)