Starting phenix.real_space_refine
on Sat Oct 11 10:39:03 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8qpv_18563/10_2025/8qpv_18563.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8qpv_18563/10_2025/8qpv_18563.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.0
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8qpv_18563/10_2025/8qpv_18563.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8qpv_18563/10_2025/8qpv_18563.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8qpv_18563/10_2025/8qpv_18563.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8qpv_18563/10_2025/8qpv_18563.map"
  }
  resolution = 4.0
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.001
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      49      5.16       5
     C    8844      2.51       5
     N    2438      2.21       5
     O    2757      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 14088
  Number of models: 1
  Model: ""
    Number of chains: 7
    Chain: "A"
      Number of atoms: 6038
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 769, 6038
          Classifications: {'peptide': 769}
          Incomplete info: {'truncation_to_alanine': 13}
          Link IDs: {'PTRANS': 29, 'TRANS': 739}
          Chain breaks: 2
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 63
          Unresolved non-hydrogen angles: 84
          Unresolved non-hydrogen dihedrals: 57
          Unresolved non-hydrogen chiralities: 3
          Planarities with less than four sites: {'TRP:plan': 1, 'TYR:plan': 3, 'GLU:plan': 1, 'ASP:plan': 1, 'GLN:plan1': 2}
          Unresolved non-hydrogen planarities: 45
    Chain: "B"
      Number of atoms: 2715
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 363, 2715
          Classifications: {'peptide': 363}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 11, 'TRANS': 351}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 6
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 5
    Chain: "C"
      Number of atoms: 1322
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 178, 1319
          Classifications: {'peptide': 178}
          Incomplete info: {'backbone_only': 2, 'truncation_to_alanine': 8}
          Link IDs: {'PTRANS': 10, 'TRANS': 167}
          Chain breaks: 1
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 43
          Unresolved non-hydrogen angles: 54
          Unresolved non-hydrogen dihedrals: 34
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'ARG:plan': 2, 'GLU:plan': 1, 'GLN:plan1': 3, 'TYR:plan': 1}
          Unresolved non-hydrogen planarities: 33
      Conformer: "B"
        Number of residues, atoms: 178, 1319
          Classifications: {'peptide': 178}
          Incomplete info: {'backbone_only': 2, 'truncation_to_alanine': 8}
          Link IDs: {'PTRANS': 10, 'TRANS': 167}
          Chain breaks: 1
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 43
          Unresolved non-hydrogen angles: 54
          Unresolved non-hydrogen dihedrals: 34
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'ARG:plan': 2, 'GLU:plan': 1, 'GLN:plan1': 3, 'TYR:plan': 1}
          Unresolved non-hydrogen planarities: 33
          bond proxies already assigned to first conformer: 1338
    Chain: "D"
      Number of atoms: 1760
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 218, 1760
          Classifications: {'peptide': 218}
          Link IDs: {'PTRANS': 12, 'TRANS': 205}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 1
    Chain: "E"
      Number of atoms: 693
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 89, 693
          Classifications: {'peptide': 89}
          Link IDs: {'PTRANS': 5, 'TRANS': 83}
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 1
    Chain: "F"
      Number of atoms: 1385
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 176, 1385
          Classifications: {'peptide': 176}
          Incomplete info: {'truncation_to_alanine': 6}
          Link IDs: {'PTRANS': 2, 'TRANS': 173}
          Chain breaks: 1
          Unresolved chain link angles: 3
          Unresolved non-hydrogen bonds: 27
          Unresolved non-hydrogen angles: 33
          Unresolved non-hydrogen dihedrals: 18
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLN:plan1': 3, 'ARG:plan': 1, 'ASN:plan1': 1}
          Unresolved non-hydrogen planarities: 20
    Chain: "F"
      Number of atoms: 175
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 32, 175
          Classifications: {'peptide': 32}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 25}
          Link IDs: {'TRANS': 31}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 60
          Unresolved non-hydrogen angles: 89
          Unresolved non-hydrogen dihedrals: 38
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'UNK:plan-1': 23, 'TRP:plan': 1}
          Unresolved non-hydrogen planarities: 32
  Time building chain proxies: 3.56, per 1000 atoms: 0.25
  Number of scatterers: 14088
  At special positions: 0
  Unit cell: (134.68, 125.06, 140.6, 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      49     16.00
     O    2757      8.00
     N    2438      7.00
     C    8844      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  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: 1.16
  Conformation dependent library (CDL) restraints added in 557.7 milliseconds
  
  Enol-peptide restraints added in 953.7 nanoseconds
  

  3558 Ramachandran restraints generated.
    1779 Oldfield, 0 Emsley, 1779 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3360

  Finding SS restraints...
    Secondary structure from input PDB file:
      38 helices and 22 sheets defined
      29.0% alpha, 27.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.47
  Creating SS restraints...
    Processing helix  chain 'A' and resid 58 through 69
      removed outlier: 3.739A  pdb=" N   THR A  69 " --> pdb=" O   ALA A  65 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 106 through 117
    Processing helix  chain 'A' and resid 126 through 145
      removed outlier: 3.751A  pdb=" N   ILE A 130 " --> pdb=" O   ASP A 126 " (cutoff:3.500A)
      removed outlier: 3.558A  pdb=" N   ALA A 131 " --> pdb=" O   ARG A 127 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 189 through 196
      removed outlier: 4.007A  pdb=" N   HIS A 196 " --> pdb=" O   GLU A 192 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 215 through 232
      removed outlier: 3.666A  pdb=" N   LEU A 219 " --> pdb=" O   GLN A 215 " (cutoff:3.500A)
      removed outlier: 3.762A  pdb=" N   ALA A 220 " --> pdb=" O   LYS A 216 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 280 through 288
    Processing helix  chain 'A' and resid 297 through 315
      removed outlier: 3.686A  pdb=" N   TYR A 315 " --> pdb=" O   LEU A 311 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 362 through 367
    Processing helix  chain 'A' and resid 378 through 391
      removed outlier: 3.918A  pdb=" N   ASP A 383 " --> pdb=" O   SER A 379 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 448 through 452
      removed outlier: 3.663A  pdb=" N   GLY A 451 " --> pdb=" O   ASN A 448 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 542 through 553
    Processing helix  chain 'A' and resid 647 through 651
      removed outlier: 3.776A  pdb=" N   GLU A 650 " --> pdb=" O   PRO A 647 " (cutoff:3.500A)
      removed outlier: 3.843A  pdb=" N   ASN A 651 " --> pdb=" O   PHE A 648 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 647 through 651'
    Processing helix  chain 'B' and resid 136 through 139
    Processing helix  chain 'B' and resid 237 through 242
    Processing helix  chain 'C' and resid 39 through 43
      removed outlier: 3.641A  pdb=" N   GLU C  43 " --> pdb=" O   ALA C  40 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 76 through 80
      removed outlier: 3.547A  pdb=" N   LEU C  80 " --> pdb=" O   GLY C  77 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 116 through 127
    Processing helix  chain 'C' and resid 190 through 211
      removed outlier: 3.898A  pdb=" N   MET C 201 " --> pdb=" O   TYR C 197 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 31 through 46
      removed outlier: 3.829A  pdb=" N   ILE D  35 " --> pdb=" O   PRO D  31 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 47 through 62
      removed outlier: 3.949A  pdb=" N   THR D  53 " --> pdb=" O   ARG D  49 " (cutoff:3.500A)
      removed outlier: 3.559A  pdb=" N   GLN D  54 " --> pdb=" O   GLN D  50 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 67 through 82
    Processing helix  chain 'D' and resid 84 through 99
    Processing helix  chain 'D' and resid 104 through 121
      removed outlier: 4.027A  pdb=" N   VAL D 108 " --> pdb=" O   ASN D 104 " (cutoff:3.500A)
      removed outlier: 3.799A  pdb=" N   ASP D 121 " --> pdb=" O   MET D 117 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 124 through 129
      removed outlier: 4.205A  pdb=" N   PHE D 128 " --> pdb=" O   LEU D 124 " (cutoff:3.500A)
    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 209 through 225
      Proline residue:  D 216  - end of helix
    Processing helix  chain 'D' and resid 227 through 241
      removed outlier: 4.144A  pdb=" N   LYS D 233 " --> pdb=" O   ALA D 229 " (cutoff:3.500A)
      removed outlier: 3.726A  pdb=" N   VAL D 234 " --> pdb=" O   GLN D 230 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 39 through 44
    Processing helix  chain 'E' and resid 51 through 60
    Processing helix  chain 'F' and resid 39 through 47
    Processing helix  chain 'F' and resid 62 through 88
      removed outlier: 3.854A  pdb=" N   HIS F  68 " --> pdb=" O   ALA F  64 " (cutoff:3.500A)
      removed outlier: 4.216A  pdb=" N   GLN F  69 " --> pdb=" O   THR F  65 " (cutoff:3.500A)
      removed outlier: 3.699A  pdb=" N   MET F  87 " --> pdb=" O   MET F  83 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 92 through 107
    Processing helix  chain 'F' and resid 110 through 122
    Processing helix  chain 'F' and resid 124 through 149
      removed outlier: 4.004A  pdb=" N   ARG F 149 " --> pdb=" O   GLU F 145 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 155 through 164
      removed outlier: 3.819A  pdb=" N   SER F 159 " --> pdb=" O   GLN F 155 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 395 through 420
      removed outlier: 3.905A  pdb=" N   ARG F 399 " --> pdb=" O   ASP F 395 " (cutoff:3.500A)
      removed outlier: 4.418A  pdb=" N   MET F 400 " --> pdb=" O   ARG F 396 " (cutoff:3.500A)
      removed outlier: 3.528A  pdb=" N   ALA F 411 " --> pdb=" O   SER F 407 " (cutoff:3.500A)
      removed outlier: 3.644A  pdb=" N   SER F 420 " --> pdb=" O   GLU F 416 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 30
      removed outlier: 6.551A  pdb=" N   HIS A  30 " --> pdb=" O   VAL A  86 " (cutoff:3.500A)
      removed outlier: 7.174A  pdb=" N   VAL A  88 " --> pdb=" O   HIS A  30 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 93 through 100
      removed outlier: 7.433A  pdb=" N   LEU A 165 " --> pdb=" O   ALA A  95 " (cutoff:3.500A)
      removed outlier: 4.692A  pdb=" N   ILE A  97 " --> pdb=" O   LEU A 165 " (cutoff:3.500A)
      removed outlier: 7.844A  pdb=" N   LEU A 167 " --> pdb=" O   ILE A  97 " (cutoff:3.500A)
      removed outlier: 4.625A  pdb=" N   PHE A  99 " --> pdb=" O   LEU A 167 " (cutoff:3.500A)
      removed outlier: 7.581A  pdb=" N   PHE A 169 " --> pdb=" O   PHE A  99 " (cutoff:3.500A)
      removed outlier: 3.665A  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 181
      removed outlier: 7.500A  pdb=" N   VAL A 256 " --> pdb=" O   GLN A 178 " (cutoff:3.500A)
      removed outlier: 4.444A  pdb=" N   ILE A 180 " --> pdb=" O   VAL A 256 " (cutoff:3.500A)
      removed outlier: 7.449A  pdb=" N   VAL A 258 " --> pdb=" O   ILE A 180 " (cutoff:3.500A)
      removed outlier: 3.641A  pdb=" N   SER A 242 " --> pdb=" O   ASN A 259 " (cutoff:3.500A)
      removed outlier: 6.855A  pdb=" N   THR A 261 " --> pdb=" O   ILE A 240 " (cutoff:3.500A)
      removed outlier: 6.460A  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: 4.724A  pdb=" N   LEU A 268 " --> pdb=" O   VAL A 335 " (cutoff:3.500A)
      removed outlier: 7.845A  pdb=" N   LEU A 337 " --> pdb=" O   LEU A 268 " (cutoff:3.500A)
      removed outlier: 6.662A  pdb=" N   GLY A 270 " --> pdb=" O   LEU A 337 " (cutoff:3.500A)
      removed outlier: 7.804A  pdb=" N   VAL A 339 " --> pdb=" O   GLY A 270 " (cutoff:3.500A)
      removed outlier: 6.457A  pdb=" N   GLU A 272 " --> pdb=" O   VAL A 339 " (cutoff:3.500A)
      removed outlier: 7.528A  pdb=" N   VAL A 341 " --> pdb=" O   GLU A 272 " (cutoff:3.500A)
      removed outlier: 6.339A  pdb=" N   SER A 274 " --> pdb=" O   VAL A 341 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 348 through 355
      removed outlier: 6.118A  pdb=" N   VAL A 412 " --> pdb=" O   VAL A 349 " (cutoff:3.500A)
      removed outlier: 4.196A  pdb=" N   LYS A 351 " --> pdb=" O   VAL A 412 " (cutoff:3.500A)
      removed outlier: 4.217A  pdb=" N   THR A 397 " --> pdb=" O   LYS A 419 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 802 through 805
      removed outlier: 3.972A  pdb=" N   ALA A 770 " --> pdb=" O   GLN A 789 " (cutoff:3.500A)
      removed outlier: 6.529A  pdb=" N   MET A 768 " --> pdb=" O   PHE A 791 " (cutoff:3.500A)
      removed outlier: 3.585A  pdb=" N   THR A 735 " --> pdb=" O   THR A 720 " (cutoff:3.500A)
      removed outlier: 3.785A  pdb=" N   VAL A 628 " --> pdb=" O   ILE A 719 " (cutoff:3.500A)
      removed outlier: 5.781A  pdb=" N   TYR A 608 " --> pdb=" O   THR A 600 " (cutoff:3.500A)
      removed outlier: 3.559A  pdb=" N   ASP A 493 " --> pdb=" O   THR A 467 " (cutoff:3.500A)
      removed outlier: 3.574A  pdb=" N   THR A 467 " --> pdb=" O   ASP A 493 " (cutoff:3.500A)
      removed outlier: 3.592A  pdb=" N   CYS A 425 " --> pdb=" O   GLN A 445 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 671 through 674
      removed outlier: 5.335A  pdb=" N   ASP A 704 " --> pdb=" O   ALA A 672 " (cutoff:3.500A)
      removed outlier: 7.533A  pdb=" N   TYR A 674 " --> pdb=" O   SER A 702 " (cutoff:3.500A)
      removed outlier: 7.614A  pdb=" N   SER A 702 " --> pdb=" O   TYR A 674 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 46 through 49
      removed outlier: 6.889A  pdb=" N   SER B 389 " --> pdb=" O   ALA B  47 " (cutoff:3.500A)
      removed outlier: 5.047A  pdb=" N   SER B  49 " --> pdb=" O   VAL B 387 " (cutoff:3.500A)
      removed outlier: 7.638A  pdb=" N   VAL B 387 " --> pdb=" O   SER B  49 " (cutoff:3.500A)
      removed outlier: 3.778A  pdb=" N   ILE B 390 " --> pdb=" O   LEU B 378 " (cutoff:3.500A)
      removed outlier: 4.569A  pdb=" N   LEU B 378 " --> pdb=" O   ILE B 390 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 66 through 67
      removed outlier: 3.640A  pdb=" N   ALA B  66 " --> pdb=" O   TYR B  73 " (cutoff:3.500A)
      removed outlier: 4.160A  pdb=" N   TRP B  93 " --> pdb=" O   ALA B  83 " (cutoff:3.500A)
      removed outlier: 5.874A  pdb=" N   ASN B  85 " --> pdb=" O   GLU B  91 " (cutoff:3.500A)
      removed outlier: 6.570A  pdb=" N   GLU B  91 " --> pdb=" O   ASN B  85 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'B' and resid 116 through 118
    Processing sheet with id=AB2, first strand: chain 'B' and resid 156 through 158
      removed outlier: 5.658A  pdb=" N   LEU B 171 " --> pdb=" O   THR B 184 " (cutoff:3.500A)
      removed outlier: 4.189A  pdb=" N   THR B 184 " --> pdb=" O   LEU B 171 " (cutoff:3.500A)
      removed outlier: 6.784A  pdb=" N   ALA B 173 " --> pdb=" O   LYS B 182 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'B' and resid 201 through 203
      removed outlier: 3.862A  pdb=" N   TRP B 228 " --> pdb=" O   ALA B 218 " (cutoff:3.500A)
      removed outlier: 5.396A  pdb=" N   LEU B 220 " --> pdb=" O   MET B 226 " (cutoff:3.500A)
      removed outlier: 6.060A  pdb=" N   MET B 226 " --> pdb=" O   LEU B 220 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'B' and resid 252 through 254
      removed outlier: 3.572A  pdb=" N   VAL B 252 " --> pdb=" O   PHE B 259 " (cutoff:3.500A)
      removed outlier: 6.258A  pdb=" N   ASP B 271 " --> pdb=" O   ILE B 277 " (cutoff:3.500A)
      removed outlier: 6.747A  pdb=" N   ILE B 277 " --> pdb=" O   ASP B 271 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'B' and resid 286 through 292
      removed outlier: 5.198A  pdb=" N   ASP B 288 " --> pdb=" O   VAL B 299 " (cutoff:3.500A)
      removed outlier: 3.873A  pdb=" N   VAL B 299 " --> pdb=" O   ASP B 288 " (cutoff:3.500A)
      removed outlier: 3.748A  pdb=" N   VAL B 305 " --> pdb=" O   GLN B 319 " (cutoff:3.500A)
      removed outlier: 3.755A  pdb=" N   TRP B 317 " --> pdb=" O   ALA B 307 " (cutoff:3.500A)
      removed outlier: 6.536A  pdb=" N   THR B 309 " --> pdb=" O   THR B 315 " (cutoff:3.500A)
      removed outlier: 6.381A  pdb=" N   THR B 315 " --> pdb=" O   THR B 309 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'B' and resid 331 through 333
      removed outlier: 4.102A  pdb=" N   ALA B 358 " --> pdb=" O   TRP B 348 " (cutoff:3.500A)
      removed outlier: 6.963A  pdb=" N   ASN B 350 " --> pdb=" O   PHE B 356 " (cutoff:3.500A)
      removed outlier: 7.152A  pdb=" N   PHE B 356 " --> pdb=" O   ASN B 350 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'C' and resid 97 through 99
      removed outlier: 6.418A  pdb=" N   ARG C 160 " --> pdb=" O   LEU C 179 " (cutoff:3.500A)
      removed outlier: 4.560A  pdb=" N   LEU C 181 " --> pdb=" O   ARG C 158 " (cutoff:3.500A)
      removed outlier: 6.772A  pdb=" N   ARG C 158 " --> pdb=" O   LEU C 181 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'C' and resid 97 through 99
    Processing sheet with id=AB9, first strand: chain 'C' and resid 131 through 135
    Processing sheet with id=AC1, first strand: chain 'E' and resid 32 through 33
      removed outlier: 3.942A  pdb=" N   MET E  64 " --> pdb=" O   PHE E  74 " (cutoff:3.500A)
    Processing sheet with id=AC2, first strand: chain 'E' and resid 32 through 33
    Processing sheet with id=AC3, first strand: chain 'F' and resid 36 through 38
    Processing sheet with id=AC4, first strand: chain 'F' and resid 445 through 446

    672 hydrogen bonds defined for protein.
    1901 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.67

  Time building geometry restraints manager: 1.57 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 4751
        1.34 -     1.46: 2786
        1.46 -     1.58: 6726
        1.58 -     1.70: 0
        1.70 -     1.82: 93
  Bond restraints: 14356
  Sorted by residual:
  bond pdb=" N   VAL A  54 "
       pdb=" CA  VAL A  54 "
    ideal  model  delta    sigma   weight residual
    1.459  1.499 -0.040 1.25e-02 6.40e+03 1.03e+01
  bond pdb=" N   GLU B 107 "
       pdb=" CA  GLU B 107 "
    ideal  model  delta    sigma   weight residual
    1.456  1.487 -0.031 9.80e-03 1.04e+04 1.02e+01
  bond pdb=" N   ASP A  56 "
       pdb=" CA  ASP A  56 "
    ideal  model  delta    sigma   weight residual
    1.457  1.497 -0.040 1.29e-02 6.01e+03 9.55e+00
  bond pdb=" N   THR A  53 "
       pdb=" CA  THR A  53 "
    ideal  model  delta    sigma   weight residual
    1.455  1.492 -0.037 1.27e-02 6.20e+03 8.48e+00
  bond pdb=" N   VAL F 599 "
       pdb=" CA  VAL F 599 "
    ideal  model  delta    sigma   weight residual
    1.457  1.494 -0.037 1.32e-02 5.74e+03 8.07e+00
  ... (remaining 14351 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.74: 18922
        1.74 -     3.48: 498
        3.48 -     5.22: 60
        5.22 -     6.96: 11
        6.96 -     8.70: 3
  Bond angle restraints: 19494
  Sorted by residual:
  angle pdb=" C   ILE C  57 "
        pdb=" N   LEU C  58 "
        pdb=" CA  LEU C  58 "
      ideal   model   delta    sigma   weight residual
     121.03  127.45   -6.42 1.60e+00 3.91e-01 1.61e+01
  angle pdb=" CA  THR A  53 "
        pdb=" C   THR A  53 "
        pdb=" O   THR A  53 "
      ideal   model   delta    sigma   weight residual
     121.56  117.68    3.88 1.09e+00 8.42e-01 1.27e+01
  angle pdb=" CA  VAL F 599 "
        pdb=" C   VAL F 599 "
        pdb=" O   VAL F 599 "
      ideal   model   delta    sigma   weight residual
     121.59  118.11    3.48 1.03e+00 9.43e-01 1.14e+01
  angle pdb=" N   GLU B 107 "
        pdb=" CA  GLU B 107 "
        pdb=" C   GLU B 107 "
      ideal   model   delta    sigma   weight residual
     108.13  111.16   -3.03 9.00e-01 1.23e+00 1.13e+01
  angle pdb=" C   SER F  48 "
        pdb=" N   VAL F  49 "
        pdb=" CA  VAL F  49 "
      ideal   model   delta    sigma   weight residual
     122.96  119.78    3.18 9.50e-01 1.11e+00 1.12e+01
  ... (remaining 19489 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.94: 7783
       17.94 -    35.88: 634
       35.88 -    53.82: 107
       53.82 -    71.76: 20
       71.76 -    89.70: 14
  Dihedral angle restraints: 8558
    sinusoidal: 3301
      harmonic: 5257
  Sorted by residual:
  dihedral pdb=" CA  SER B 191 "
           pdb=" C   SER B 191 "
           pdb=" N   LEU B 192 "
           pdb=" CA  LEU B 192 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.09   20.91     0      5.00e+00 4.00e-02 1.75e+01
  dihedral pdb=" CA  VAL A 480 "
           pdb=" C   VAL A 480 "
           pdb=" N   ASP A 481 "
           pdb=" CA  ASP A 481 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.28   20.72     0      5.00e+00 4.00e-02 1.72e+01
  dihedral pdb=" CA  TYR C 197 "
           pdb=" C   TYR C 197 "
           pdb=" N   SER C 198 "
           pdb=" CA  SER C 198 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.05   19.95     0      5.00e+00 4.00e-02 1.59e+01
  ... (remaining 8555 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.039: 1469
       0.039 -    0.077: 491
       0.077 -    0.116: 169
       0.116 -    0.155: 31
       0.155 -    0.194: 7
  Chirality restraints: 2167
  Sorted by residual:
  chirality pdb=" CA  ASP A  56 "
            pdb=" N   ASP A  56 "
            pdb=" C   ASP A  56 "
            pdb=" CB  ASP A  56 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.32    0.19 2.00e-01 2.50e+01 9.36e-01
  chirality pdb=" CB  THR B  43 "
            pdb=" CA  THR B  43 "
            pdb=" OG1 THR B  43 "
            pdb=" CG2 THR B  43 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.36    0.19 2.00e-01 2.50e+01 8.94e-01
  chirality pdb=" CA  VAL A  54 "
            pdb=" N   VAL A  54 "
            pdb=" C   VAL A  54 "
            pdb=" CB  VAL A  54 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.62   -0.18 2.00e-01 2.50e+01 8.40e-01
  ... (remaining 2164 not shown)

  Planarity restraints: 2566
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL A 203 "    0.064 5.00e-02 4.00e+02   9.64e-02 1.49e+01
        pdb=" N   PRO A 204 "   -0.167 5.00e-02 4.00e+02
        pdb=" CA  PRO A 204 "    0.051 5.00e-02 4.00e+02
        pdb=" CD  PRO A 204 "    0.052 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE A 517 "    0.037 5.00e-02 4.00e+02   5.56e-02 4.95e+00
        pdb=" N   PRO A 518 "   -0.096 5.00e-02 4.00e+02
        pdb=" CA  PRO A 518 "    0.029 5.00e-02 4.00e+02
        pdb=" CD  PRO A 518 "    0.031 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP A 762 "   -0.034 5.00e-02 4.00e+02   5.23e-02 4.38e+00
        pdb=" N   PRO A 763 "    0.090 5.00e-02 4.00e+02
        pdb=" CA  PRO A 763 "   -0.027 5.00e-02 4.00e+02
        pdb=" CD  PRO A 763 "   -0.029 5.00e-02 4.00e+02
  ... (remaining 2563 not shown)

  Histogram of nonbonded interaction distances:
        2.14 -     2.69: 319
        2.69 -     3.24: 14153
        3.24 -     3.80: 21290
        3.80 -     4.35: 27092
        4.35 -     4.90: 45837
  Nonbonded interactions: 108691
  Sorted by model distance:
  nonbonded pdb=" O   THR C 143 "
            pdb=" NH2 ARG C 160 "
     model   vdw
     2.138 3.120
  nonbonded pdb=" OD2 ASP F  26 "
            pdb=" OG  SER F  40 "
     model   vdw
     2.190 3.040
  nonbonded pdb=" OH  TYR C  41 "
            pdb=" OD1 ASP D 162 "
     model   vdw
     2.212 3.040
  nonbonded pdb=" OE2 GLU A 521 "
            pdb=" OH  TYR E  28 "
     model   vdw
     2.228 3.040
  nonbonded pdb=" O   GLY A 655 "
            pdb=" OG1 THR A 659 "
     model   vdw
     2.231 3.040
  ... (remaining 108686 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.50 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as 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:             1.560
  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:          0.330
  Check model and map are aligned:         0.040
  Set scattering table:                    0.040
  Process input model:                     14.190
  Find NCS groups from input model:        0.180
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.290
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   17.670
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8069
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      :  0.003   0.047  14356  Z= 0.182
  Angle     :  0.654   8.700  19494  Z= 0.364
  Chirality :  0.044   0.194   2167
  Planarity :  0.004   0.096   2566
  Dihedral  : 13.777  89.701   5198
  Min Nonbonded Distance : 2.138

Molprobity Statistics.
  All-atom Clashscore : 10.75
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  6.30 %
    Favored  : 93.59 %
  Rotamer:
    Outliers :  0.34 %
    Allowed  :  0.47 %
    Favored  : 99.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.37 (0.20), residues: 1779
  helix:  1.93 (0.24), residues: 474
  sheet: -0.27 (0.25), residues: 448
  loop : -1.53 (0.21), residues: 857

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG C  83 
 TYR   0.025   0.002   TYR C 197 
 PHE   0.033   0.002   PHE A 586 
 TRP   0.019   0.001   TRP C 117 
 HIS   0.007   0.001   HIS A 555 

Details of bonding type rmsd
  covalent geometry    : bond        0.00348 (14356)
  covalent geometry    : angle       0.65434 (19494)
  hydrogen bonds       : bond        0.13252 (  664)
  hydrogen bonds       : angle       6.10744 ( 1901)

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

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

  3558 Ramachandran restraints generated.
    1779 Oldfield, 0 Emsley, 1779 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3558 Ramachandran restraints generated.
    1779 Oldfield, 0 Emsley, 1779 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  235 residues out of total 1517 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 230
  time to evaluate  : 0.492 
Fit side-chains
   revert: symmetry clash
TARDY: cannot create tardy model for: "ILE A 806 " (corrupted residue). Skipping it.
   revert: symmetry clash
   revert: symmetry clash
TARDY: cannot create tardy model for: "ARG B 392 " (corrupted residue). Skipping it.
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
TARDY: cannot create tardy model for: "SER D 243 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "LEU E 110 " (corrupted residue). Skipping it.
   revert: symmetry clash
TARDY: cannot create tardy model for: "ASN F 107 " (corrupted residue). Skipping it.
REVERT: A   54 VAL cc_start: 0.2886 (OUTLIER) cc_final: 0.2661 (p)
REVERT: A  413 ASP cc_start: 0.8243 (m-30) cc_final: 0.7964 (m-30)
REVERT: A  777 MET cc_start: 0.8225 (mmm) cc_final: 0.7785 (mmp)
REVERT: B   32 MET cc_start: 0.5848 (mpp) cc_final: 0.5048 (mpp)
REVERT: B   93 TRP cc_start: 0.8366 (p-90) cc_final: 0.7794 (p-90)
REVERT: C   39 GLU cc_start: 0.7467 (mt-10) cc_final: 0.6709 (tm-30)
REVERT: D  111 MET cc_start: 0.8709 (tpp) cc_final: 0.8253 (tpp)
REVERT: F   83 MET cc_start: 0.7539 (tpt) cc_final: 0.7308 (tpt)
  outliers start: 5
  outliers final: 0
  residues processed: 234
  average time/residue: 0.1103
  time to fit residues: 39.5864
Evaluate side-chains
  176 residues out of total 1517 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 175
  time to evaluate  : 0.590 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   54 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 175
   random chunks:
   chunk 98 optimal weight:    4.9990
   chunk 107 optimal weight:    1.9990
   chunk 10 optimal weight:    9.9990
   chunk 66 optimal weight:   20.0000
   chunk 130 optimal weight:    0.9990
   chunk 124 optimal weight:    3.9990
   chunk 103 optimal weight:    0.9980
   chunk 77 optimal weight:    9.9990
   chunk 122 optimal weight:    8.9990
   chunk 91 optimal weight:    2.9990
   chunk 149 optimal weight:    0.9990
   overall best weight:    1.5988

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

Flipped N/Q/H residues before XYZ refinement:
A 215 GLN
** A 371 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 107 ASN
F 163 GLN
F 428 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3518 r_free = 0.3518 target = 0.112761 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3131 r_free = 0.3131 target = 0.088962 restraints weight = 39480.039|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3100 r_free = 0.3100 target = 0.087804 restraints weight = 35795.026|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3120 r_free = 0.3120 target = 0.089022 restraints weight = 33945.552|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3130 r_free = 0.3130 target = 0.089680 restraints weight = 20554.831|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3143 r_free = 0.3143 target = 0.090453 restraints weight = 18004.901|
|-----------------------------------------------------------------------------|
r_work (final): 0.3117
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3117
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3117 r_free = 0.3117    target_work(ls_wunit_k1) = 0.088         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3117 r_free = 0.3117    target_work(ls_wunit_k1) = 0.088         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.3117
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8093
moved from start:          0.1034

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  14356  Z= 0.131
  Angle     :  0.588   7.676  19494  Z= 0.308
  Chirality :  0.043   0.209   2167
  Planarity :  0.004   0.070   2566
  Dihedral  :  4.464  31.151   1991
  Min Nonbonded Distance : 2.468

Molprobity Statistics.
  All-atom Clashscore : 8.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.69 %
    Favored  : 93.31 %
  Rotamer:
    Outliers :  1.61 %
    Allowed  :  8.60 %
    Favored  : 89.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.33 (0.20), residues: 1779
  helix:  1.97 (0.24), residues: 470
  sheet: -0.29 (0.25), residues: 451
  loop : -1.46 (0.21), residues: 858

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG D 132 
 TYR   0.029   0.001   TYR C 197 
 PHE   0.028   0.001   PHE A 586 
 TRP   0.013   0.001   TRP C 117 
 HIS   0.002   0.001   HIS B 324 

Details of bonding type rmsd
  covalent geometry    : bond        0.00292 (14356)
  covalent geometry    : angle       0.58767 (19494)
  hydrogen bonds       : bond        0.03812 (  664)
  hydrogen bonds       : angle       4.99364 ( 1901)

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

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

  3558 Ramachandran restraints generated.
    1779 Oldfield, 0 Emsley, 1779 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3558 Ramachandran restraints generated.
    1779 Oldfield, 0 Emsley, 1779 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  216 residues out of total 1517 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 192
  time to evaluate  : 0.450 
Fit side-chains
   revert: symmetry clash
TARDY: cannot create tardy model for: "ILE A 806 " (corrupted residue). Skipping it.
   revert: symmetry clash
   revert: symmetry clash
TARDY: cannot create tardy model for: "ARG B 392 " (corrupted residue). Skipping it.
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
TARDY: cannot create tardy model for: "SER D 243 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "LEU E 110 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "ASN F 107 " (corrupted residue). Skipping it.
REVERT: A  383 ASP cc_start: 0.7820 (m-30) cc_final: 0.7558 (m-30)
REVERT: A  413 ASP cc_start: 0.8570 (m-30) cc_final: 0.8244 (m-30)
REVERT: A  550 TYR cc_start: 0.7936 (m-10) cc_final: 0.7652 (m-10)
REVERT: A  777 MET cc_start: 0.8344 (mmm) cc_final: 0.8011 (mmt)
REVERT: A  804 PHE cc_start: 0.8244 (t80) cc_final: 0.7868 (t80)
REVERT: A  805 ASN cc_start: 0.8017 (t0) cc_final: 0.7750 (t0)
REVERT: C   39 GLU cc_start: 0.7537 (mt-10) cc_final: 0.7008 (tm-30)
REVERT: C  162 GLN cc_start: 0.7711 (tt0) cc_final: 0.7414 (tm-30)
REVERT: C  201 MET cc_start: 0.7729 (tpp) cc_final: 0.7437 (tpp)
REVERT: F  403 ASN cc_start: 0.7962 (m-40) cc_final: 0.7569 (t0)
  outliers start: 24
  outliers final: 16
  residues processed: 204
  average time/residue: 0.1012
  time to fit residues: 31.5545
Evaluate side-chains
  188 residues out of total 1517 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 172
  time to evaluate  : 0.553 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   97 ILE
Chi-restraints excluded: chain A residue  130 ILE
Chi-restraints excluded: chain A residue  161 ASN
Chi-restraints excluded: chain A residue  531 TYR
Chi-restraints excluded: chain A residue  555 HIS
Chi-restraints excluded: chain A residue  743 THR
Chi-restraints excluded: chain B residue   37 THR
Chi-restraints excluded: chain B residue   80 LEU
Chi-restraints excluded: chain B residue  283 LEU
Chi-restraints excluded: chain B residue  314 VAL
Chi-restraints excluded: chain C residue   89 LEU
Chi-restraints excluded: chain C residue  166 LYS
Chi-restraints excluded: chain D residue   33 ASN
Chi-restraints excluded: chain D residue  186 THR
Chi-restraints excluded: chain E residue   38 LEU
Chi-restraints excluded: chain F residue   31 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 175
   random chunks:
   chunk 2 optimal weight:    6.9990
   chunk 13 optimal weight:    4.9990
   chunk 58 optimal weight:    6.9990
   chunk 73 optimal weight:    6.9990
   chunk 161 optimal weight:   20.0000
   chunk 54 optimal weight:    5.9990
   chunk 4 optimal weight:    1.9990
   chunk 79 optimal weight:    1.9990
   chunk 28 optimal weight:    6.9990
   chunk 57 optimal weight:    7.9990
   chunk 108 optimal weight:    0.9990
   overall best weight:    3.1990

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

Flipped N/Q/H residues before XYZ refinement:
** A 803 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 170 GLN
** B 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 350 ASN
F 107 ASN
F 163 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3468 r_free = 0.3468 target = 0.109455 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3057 r_free = 0.3057 target = 0.084724 restraints weight = 36484.493|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3046 r_free = 0.3046 target = 0.084397 restraints weight = 29093.419|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3053 r_free = 0.3053 target = 0.084886 restraints weight = 32899.468|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3065 r_free = 0.3065 target = 0.085612 restraints weight = 20574.812|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3079 r_free = 0.3079 target = 0.086468 restraints weight = 17224.073|
|-----------------------------------------------------------------------------|
r_work (final): 0.3065
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3066
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3066 r_free = 0.3066    target_work(ls_wunit_k1) = 0.085         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3066 r_free = 0.3066    target_work(ls_wunit_k1) = 0.085         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.3066
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8159
moved from start:          0.1439

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.056  14356  Z= 0.200
  Angle     :  0.605   7.130  19494  Z= 0.321
  Chirality :  0.044   0.218   2167
  Planarity :  0.005   0.060   2566
  Dihedral  :  4.581  21.616   1990
  Min Nonbonded Distance : 2.496

Molprobity Statistics.
  All-atom Clashscore : 8.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.26 %
    Favored  : 92.74 %
  Rotamer:
    Outliers :  2.42 %
    Allowed  : 12.63 %
    Favored  : 84.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.53 (0.20), residues: 1779
  helix:  1.78 (0.23), residues: 475
  sheet: -0.46 (0.24), residues: 461
  loop : -1.58 (0.21), residues: 843

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG D 132 
 TYR   0.030   0.002   TYR C 197 
 PHE   0.043   0.002   PHE A 586 
 TRP   0.010   0.001   TRP B  93 
 HIS   0.005   0.001   HIS A 625 

Details of bonding type rmsd
  covalent geometry    : bond        0.00463 (14356)
  covalent geometry    : angle       0.60508 (19494)
  hydrogen bonds       : bond        0.04206 (  664)
  hydrogen bonds       : angle       4.91702 ( 1901)

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

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

  3558 Ramachandran restraints generated.
    1779 Oldfield, 0 Emsley, 1779 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3558 Ramachandran restraints generated.
    1779 Oldfield, 0 Emsley, 1779 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  221 residues out of total 1517 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 185
  time to evaluate  : 0.525 
Fit side-chains
   revert: symmetry clash
TARDY: cannot create tardy model for: "ILE A 806 " (corrupted residue). Skipping it.
   revert: symmetry clash
TARDY: cannot create tardy model for: "ARG B 392 " (corrupted residue). Skipping it.
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
TARDY: cannot create tardy model for: "SER D 243 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "LEU E 110 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "ASN F 107 " (corrupted residue). Skipping it.
REVERT: A  413 ASP cc_start: 0.8583 (m-30) cc_final: 0.8326 (m-30)
REVERT: A  550 TYR cc_start: 0.7943 (m-10) cc_final: 0.7577 (m-10)
REVERT: A  565 PHE cc_start: 0.7810 (t80) cc_final: 0.7120 (t80)
REVERT: A  805 ASN cc_start: 0.8106 (t0) cc_final: 0.7746 (t0)
REVERT: C   39 GLU cc_start: 0.7634 (mt-10) cc_final: 0.6966 (pp20)
REVERT: C   43 GLU cc_start: 0.7920 (mp0) cc_final: 0.7430 (mp0)
REVERT: C  162 GLN cc_start: 0.7782 (tt0) cc_final: 0.7537 (tm-30)
REVERT: F  140 GLU cc_start: 0.8450 (tp30) cc_final: 0.8171 (tp30)
REVERT: F  403 ASN cc_start: 0.7928 (m-40) cc_final: 0.7698 (t0)
  outliers start: 36
  outliers final: 28
  residues processed: 210
  average time/residue: 0.1030
  time to fit residues: 33.3093
Evaluate side-chains
  204 residues out of total 1517 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 176
  time to evaluate  : 0.557 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   54 VAL
Chi-restraints excluded: chain A residue   97 ILE
Chi-restraints excluded: chain A residue  130 ILE
Chi-restraints excluded: chain A residue  161 ASN
Chi-restraints excluded: chain A residue  209 VAL
Chi-restraints excluded: chain A residue  273 VAL
Chi-restraints excluded: chain A residue  444 VAL
Chi-restraints excluded: chain A residue  479 THR
Chi-restraints excluded: chain A residue  531 TYR
Chi-restraints excluded: chain A residue  555 HIS
Chi-restraints excluded: chain A residue  585 TYR
Chi-restraints excluded: chain A residue  743 THR
Chi-restraints excluded: chain A residue  784 VAL
Chi-restraints excluded: chain B residue   37 THR
Chi-restraints excluded: chain B residue   80 LEU
Chi-restraints excluded: chain B residue  270 LEU
Chi-restraints excluded: chain B residue  283 LEU
Chi-restraints excluded: chain B residue  314 VAL
Chi-restraints excluded: chain B residue  387 VAL
Chi-restraints excluded: chain C residue   89 LEU
Chi-restraints excluded: chain C residue  166 LYS
Chi-restraints excluded: chain D residue   33 ASN
Chi-restraints excluded: chain D residue  186 THR
Chi-restraints excluded: chain E residue   26 VAL
Chi-restraints excluded: chain E residue   38 LEU
Chi-restraints excluded: chain F residue   31 VAL
Chi-restraints excluded: chain F residue  163 GLN
Chi-restraints excluded: chain F residue  407 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 175
   random chunks:
   chunk 2 optimal weight:    0.0000
   chunk 129 optimal weight:    0.7980
   chunk 141 optimal weight:    1.9990
   chunk 116 optimal weight:    0.0570
   chunk 136 optimal weight:    3.9990
   chunk 45 optimal weight:    1.9990
   chunk 17 optimal weight:    8.9990
   chunk 106 optimal weight:    0.4980
   chunk 64 optimal weight:    8.9990
   chunk 96 optimal weight:    8.9990
   chunk 19 optimal weight:    1.9990
   overall best weight:    0.6704

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

Flipped N/Q/H residues before XYZ refinement:
A 371 GLN
** A 803 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 350 ASN
D 125 GLN
F 163 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3523 r_free = 0.3523 target = 0.113130 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3137 r_free = 0.3137 target = 0.089208 restraints weight = 40447.486|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3130 r_free = 0.3130 target = 0.089735 restraints weight = 40413.579|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3140 r_free = 0.3140 target = 0.090260 restraints weight = 34871.762|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3154 r_free = 0.3154 target = 0.091151 restraints weight = 20663.918|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3176 r_free = 0.3176 target = 0.092538 restraints weight = 17207.214|
|-----------------------------------------------------------------------------|
r_work (final): 0.3157
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3157
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3157 r_free = 0.3157    target_work(ls_wunit_k1) = 0.090         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3157 r_free = 0.3157    target_work(ls_wunit_k1) = 0.090         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.3157
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8055
moved from start:          0.1647

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.040  14356  Z= 0.101
  Angle     :  0.547   8.344  19494  Z= 0.284
  Chirality :  0.042   0.247   2167
  Planarity :  0.004   0.054   2566
  Dihedral  :  4.263  21.835   1990
  Min Nonbonded Distance : 2.520

Molprobity Statistics.
  All-atom Clashscore : 6.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.19 %
    Favored  : 93.81 %
  Rotamer:
    Outliers :  2.02 %
    Allowed  : 14.31 %
    Favored  : 83.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.29 (0.20), residues: 1779
  helix:  2.04 (0.24), residues: 472
  sheet: -0.25 (0.24), residues: 451
  loop : -1.49 (0.21), residues: 856

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG C  83 
 TYR   0.020   0.001   TYR D 184 
 PHE   0.020   0.001   PHE A 426 
 TRP   0.008   0.001   TRP A 376 
 HIS   0.003   0.001   HIS A 280 

Details of bonding type rmsd
  covalent geometry    : bond        0.00220 (14356)
  covalent geometry    : angle       0.54657 (19494)
  hydrogen bonds       : bond        0.03327 (  664)
  hydrogen bonds       : angle       4.57523 ( 1901)

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

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

  3558 Ramachandran restraints generated.
    1779 Oldfield, 0 Emsley, 1779 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3558 Ramachandran restraints generated.
    1779 Oldfield, 0 Emsley, 1779 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  224 residues out of total 1517 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 194
  time to evaluate  : 0.570 
Fit side-chains
TARDY: cannot create tardy model for: "ILE A 806 " (corrupted residue). Skipping it.
   revert: symmetry clash
TARDY: cannot create tardy model for: "ARG B 392 " (corrupted residue). Skipping it.
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
TARDY: cannot create tardy model for: "SER D 243 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "LEU E 110 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "ASN F 107 " (corrupted residue). Skipping it.
REVERT: A  383 ASP cc_start: 0.7819 (m-30) cc_final: 0.7492 (m-30)
REVERT: A  413 ASP cc_start: 0.8525 (m-30) cc_final: 0.8319 (m-30)
REVERT: A  550 TYR cc_start: 0.7960 (m-10) cc_final: 0.7659 (m-10)
REVERT: A  777 MET cc_start: 0.8177 (mmm) cc_final: 0.7790 (mmp)
REVERT: A  805 ASN cc_start: 0.8093 (t0) cc_final: 0.7689 (t0)
REVERT: B   32 MET cc_start: 0.5952 (mpp) cc_final: 0.5642 (mtm)
REVERT: C   39 GLU cc_start: 0.7550 (mt-10) cc_final: 0.6931 (pp20)
REVERT: C   43 GLU cc_start: 0.7863 (mp0) cc_final: 0.7426 (mp0)
REVERT: C  162 GLN cc_start: 0.7712 (tt0) cc_final: 0.7395 (tm-30)
REVERT: D  157 SER cc_start: 0.9061 (t) cc_final: 0.8430 (p)
REVERT: F  140 GLU cc_start: 0.8452 (tp30) cc_final: 0.8110 (tp30)
REVERT: F  400 MET cc_start: 0.7356 (tmm) cc_final: 0.7103 (tmm)
  outliers start: 30
  outliers final: 21
  residues processed: 212
  average time/residue: 0.0976
  time to fit residues: 32.2520
Evaluate side-chains
  191 residues out of total 1517 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 170
  time to evaluate  : 0.446 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   54 VAL
Chi-restraints excluded: chain A residue   97 ILE
Chi-restraints excluded: chain A residue  161 ASN
Chi-restraints excluded: chain A residue  398 VAL
Chi-restraints excluded: chain A residue  531 TYR
Chi-restraints excluded: chain A residue  555 HIS
Chi-restraints excluded: chain A residue  784 VAL
Chi-restraints excluded: chain B residue   80 LEU
Chi-restraints excluded: chain B residue  145 THR
Chi-restraints excluded: chain B residue  253 VAL
Chi-restraints excluded: chain B residue  283 LEU
Chi-restraints excluded: chain B residue  314 VAL
Chi-restraints excluded: chain B residue  372 VAL
Chi-restraints excluded: chain C residue   89 LEU
Chi-restraints excluded: chain C residue  124 LEU
Chi-restraints excluded: chain C residue  166 LYS
Chi-restraints excluded: chain D residue   33 ASN
Chi-restraints excluded: chain E residue   26 VAL
Chi-restraints excluded: chain E residue   31 ASP
Chi-restraints excluded: chain E residue   38 LEU
Chi-restraints excluded: chain F residue   31 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 175
   random chunks:
   chunk 126 optimal weight:    7.9990
   chunk 115 optimal weight:    0.0870
   chunk 27 optimal weight:    9.9990
   chunk 152 optimal weight:    0.0670
   chunk 78 optimal weight:    5.9990
   chunk 101 optimal weight:    5.9990
   chunk 137 optimal weight:    4.9990
   chunk 133 optimal weight:    4.9990
   chunk 59 optimal weight:    6.9990
   chunk 65 optimal weight:    0.0060
   chunk 45 optimal weight:    1.9990
   overall best weight:    1.4316

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

Flipped N/Q/H residues before XYZ refinement:
B 350 ASN
** C 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 163 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3510 r_free = 0.3510 target = 0.112202 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3111 r_free = 0.3111 target = 0.087658 restraints weight = 39092.003|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3099 r_free = 0.3099 target = 0.087519 restraints weight = 30816.790|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3109 r_free = 0.3109 target = 0.088209 restraints weight = 31865.366|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3120 r_free = 0.3120 target = 0.088880 restraints weight = 20254.584|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3140 r_free = 0.3140 target = 0.090118 restraints weight = 17190.460|
|-----------------------------------------------------------------------------|
r_work (final): 0.3124
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3123
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3123 r_free = 0.3123    target_work(ls_wunit_k1) = 0.088         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3123 r_free = 0.3123    target_work(ls_wunit_k1) = 0.088         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.3123
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8099
moved from start:          0.1792

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.060  14356  Z= 0.119
  Angle     :  0.544   7.758  19494  Z= 0.285
  Chirality :  0.043   0.262   2167
  Planarity :  0.004   0.051   2566
  Dihedral  :  4.214  21.572   1990
  Min Nonbonded Distance : 2.539

Molprobity Statistics.
  All-atom Clashscore : 6.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.41 %
    Favored  : 93.59 %
  Rotamer:
    Outliers :  3.02 %
    Allowed  : 14.65 %
    Favored  : 82.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.27 (0.20), residues: 1779
  helix:  2.03 (0.24), residues: 472
  sheet: -0.27 (0.24), residues: 449
  loop : -1.44 (0.21), residues: 858

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C  83 
 TYR   0.019   0.001   TYR D 184 
 PHE   0.026   0.001   PHE A 586 
 TRP   0.006   0.001   TRP C 148 
 HIS   0.002   0.001   HIS A 625 

Details of bonding type rmsd
  covalent geometry    : bond        0.00270 (14356)
  covalent geometry    : angle       0.54424 (19494)
  hydrogen bonds       : bond        0.03394 (  664)
  hydrogen bonds       : angle       4.51364 ( 1901)

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

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

  3558 Ramachandran restraints generated.
    1779 Oldfield, 0 Emsley, 1779 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3558 Ramachandran restraints generated.
    1779 Oldfield, 0 Emsley, 1779 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  223 residues out of total 1517 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 178
  time to evaluate  : 0.845 
Fit side-chains
TARDY: cannot create tardy model for: "ILE A 806 " (corrupted residue). Skipping it.
   revert: symmetry clash
   revert: symmetry clash
TARDY: cannot create tardy model for: "ARG B 392 " (corrupted residue). Skipping it.
   revert: symmetry clash
   revert: symmetry clash
TARDY: cannot create tardy model for: "SER D 243 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "LEU E 110 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "ASN F 107 " (corrupted residue). Skipping it.
REVERT: A  189 THR cc_start: 0.7877 (m) cc_final: 0.7585 (m)
REVERT: A  383 ASP cc_start: 0.7835 (m-30) cc_final: 0.7530 (m-30)
REVERT: A  550 TYR cc_start: 0.7969 (m-10) cc_final: 0.7644 (m-10)
REVERT: A  777 MET cc_start: 0.8219 (mmm) cc_final: 0.7854 (mmt)
REVERT: A  804 PHE cc_start: 0.8147 (t80) cc_final: 0.7890 (t80)
REVERT: A  805 ASN cc_start: 0.8154 (t0) cc_final: 0.7770 (t0)
REVERT: B   32 MET cc_start: 0.6093 (mpp) cc_final: 0.5773 (mtm)
REVERT: C   39 GLU cc_start: 0.7575 (mt-10) cc_final: 0.6932 (pp20)
REVERT: C   43 GLU cc_start: 0.7836 (mp0) cc_final: 0.7362 (mp0)
REVERT: C  202 MET cc_start: 0.8187 (tpp) cc_final: 0.7950 (tpp)
REVERT: D  157 SER cc_start: 0.9079 (t) cc_final: 0.8455 (p)
  outliers start: 45
  outliers final: 36
  residues processed: 209
  average time/residue: 0.1056
  time to fit residues: 33.9611
Evaluate side-chains
  205 residues out of total 1517 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 169
  time to evaluate  : 0.556 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   54 VAL
Chi-restraints excluded: chain A residue   97 ILE
Chi-restraints excluded: chain A residue  130 ILE
Chi-restraints excluded: chain A residue  161 ASN
Chi-restraints excluded: chain A residue  209 VAL
Chi-restraints excluded: chain A residue  230 TYR
Chi-restraints excluded: chain A residue  273 VAL
Chi-restraints excluded: chain A residue  398 VAL
Chi-restraints excluded: chain A residue  444 VAL
Chi-restraints excluded: chain A residue  531 TYR
Chi-restraints excluded: chain A residue  555 HIS
Chi-restraints excluded: chain A residue  743 THR
Chi-restraints excluded: chain A residue  784 VAL
Chi-restraints excluded: chain B residue   37 THR
Chi-restraints excluded: chain B residue   72 VAL
Chi-restraints excluded: chain B residue   80 LEU
Chi-restraints excluded: chain B residue  145 THR
Chi-restraints excluded: chain B residue  244 LEU
Chi-restraints excluded: chain B residue  247 VAL
Chi-restraints excluded: chain B residue  253 VAL
Chi-restraints excluded: chain B residue  283 LEU
Chi-restraints excluded: chain B residue  305 VAL
Chi-restraints excluded: chain B residue  306 MET
Chi-restraints excluded: chain B residue  314 VAL
Chi-restraints excluded: chain B residue  372 VAL
Chi-restraints excluded: chain B residue  387 VAL
Chi-restraints excluded: chain C residue   89 LEU
Chi-restraints excluded: chain C residue  124 LEU
Chi-restraints excluded: chain C residue  166 LYS
Chi-restraints excluded: chain D residue   33 ASN
Chi-restraints excluded: chain D residue  186 THR
Chi-restraints excluded: chain E residue   26 VAL
Chi-restraints excluded: chain E residue   31 ASP
Chi-restraints excluded: chain E residue   38 LEU
Chi-restraints excluded: chain F residue   31 VAL
Chi-restraints excluded: chain F residue  163 GLN
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 175
   random chunks:
   chunk 131 optimal weight:    7.9990
   chunk 72 optimal weight:    4.9990
   chunk 42 optimal weight:    4.9990
   chunk 34 optimal weight:    0.9990
   chunk 81 optimal weight:   10.0000
   chunk 66 optimal weight:   20.0000
   chunk 112 optimal weight:    4.9990
   chunk 22 optimal weight:    4.9990
   chunk 140 optimal weight:    4.9990
   chunk 115 optimal weight:    0.0370
   chunk 65 optimal weight:    0.0370
   overall best weight:    2.2142

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

Flipped N/Q/H residues before XYZ refinement:
B 350 ASN
F 163 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3494 r_free = 0.3494 target = 0.111078 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3096 r_free = 0.3096 target = 0.086803 restraints weight = 39171.248|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3088 r_free = 0.3088 target = 0.086912 restraints weight = 32880.124|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3096 r_free = 0.3096 target = 0.087359 restraints weight = 33568.671|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3113 r_free = 0.3113 target = 0.088426 restraints weight = 20131.811|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3123 r_free = 0.3123 target = 0.089030 restraints weight = 16525.649|
|-----------------------------------------------------------------------------|
r_work (final): 0.3107
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3109
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3109 r_free = 0.3109    target_work(ls_wunit_k1) = 0.087         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3109 r_free = 0.3109    target_work(ls_wunit_k1) = 0.087         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.3109
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8115
moved from start:          0.1865

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.058  14356  Z= 0.149
  Angle     :  0.568   8.693  19494  Z= 0.299
  Chirality :  0.043   0.271   2167
  Planarity :  0.004   0.049   2566
  Dihedral  :  4.271  22.145   1990
  Min Nonbonded Distance : 2.548

Molprobity Statistics.
  All-atom Clashscore : 7.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.58 %
    Favored  : 93.42 %
  Rotamer:
    Outliers :  2.96 %
    Allowed  : 15.39 %
    Favored  : 81.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.28 (0.20), residues: 1779
  helix:  2.03 (0.24), residues: 472
  sheet: -0.28 (0.24), residues: 449
  loop : -1.44 (0.21), residues: 858

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C 160 
 TYR   0.028   0.002   TYR C 197 
 PHE   0.033   0.001   PHE A 586 
 TRP   0.006   0.001   TRP C 148 
 HIS   0.003   0.001   HIS A 625 

Details of bonding type rmsd
  covalent geometry    : bond        0.00344 (14356)
  covalent geometry    : angle       0.56762 (19494)
  hydrogen bonds       : bond        0.03592 (  664)
  hydrogen bonds       : angle       4.53547 ( 1901)

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

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

  3558 Ramachandran restraints generated.
    1779 Oldfield, 0 Emsley, 1779 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3558 Ramachandran restraints generated.
    1779 Oldfield, 0 Emsley, 1779 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  214 residues out of total 1517 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 170
  time to evaluate  : 0.557 
Fit side-chains
TARDY: cannot create tardy model for: "ILE A 806 " (corrupted residue). Skipping it.
   revert: symmetry clash
   revert: symmetry clash
TARDY: cannot create tardy model for: "ARG B 392 " (corrupted residue). Skipping it.
   revert: symmetry clash
   revert: symmetry clash
TARDY: cannot create tardy model for: "SER D 243 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "LEU E 110 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "ASN F 107 " (corrupted residue). Skipping it.
REVERT: A  165 LEU cc_start: 0.8294 (OUTLIER) cc_final: 0.7941 (tt)
REVERT: A  189 THR cc_start: 0.7932 (m) cc_final: 0.7663 (m)
REVERT: A  550 TYR cc_start: 0.7969 (m-10) cc_final: 0.7581 (m-10)
REVERT: A  777 MET cc_start: 0.8230 (mmm) cc_final: 0.7878 (mmt)
REVERT: A  805 ASN cc_start: 0.8193 (t0) cc_final: 0.7807 (t0)
REVERT: B   32 MET cc_start: 0.6121 (mpp) cc_final: 0.5780 (mtm)
REVERT: C   39 GLU cc_start: 0.7659 (mt-10) cc_final: 0.6964 (pp20)
REVERT: C   43 GLU cc_start: 0.7859 (mp0) cc_final: 0.7352 (mp0)
REVERT: C  194 MET cc_start: 0.8252 (OUTLIER) cc_final: 0.7308 (mtp)
REVERT: D  157 SER cc_start: 0.9089 (t) cc_final: 0.8472 (p)
REVERT: F  140 GLU cc_start: 0.8526 (tp30) cc_final: 0.8241 (tp30)
REVERT: F  403 ASN cc_start: 0.7875 (m-40) cc_final: 0.7518 (t0)
  outliers start: 44
  outliers final: 38
  residues processed: 198
  average time/residue: 0.1065
  time to fit residues: 32.7971
Evaluate side-chains
  206 residues out of total 1517 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 166
  time to evaluate  : 0.537 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   54 VAL
Chi-restraints excluded: chain A residue   97 ILE
Chi-restraints excluded: chain A residue  130 ILE
Chi-restraints excluded: chain A residue  161 ASN
Chi-restraints excluded: chain A residue  165 LEU
Chi-restraints excluded: chain A residue  183 VAL
Chi-restraints excluded: chain A residue  203 VAL
Chi-restraints excluded: chain A residue  209 VAL
Chi-restraints excluded: chain A residue  273 VAL
Chi-restraints excluded: chain A residue  398 VAL
Chi-restraints excluded: chain A residue  444 VAL
Chi-restraints excluded: chain A residue  531 TYR
Chi-restraints excluded: chain A residue  555 HIS
Chi-restraints excluded: chain A residue  743 THR
Chi-restraints excluded: chain A residue  784 VAL
Chi-restraints excluded: chain B residue   37 THR
Chi-restraints excluded: chain B residue   72 VAL
Chi-restraints excluded: chain B residue   76 ASP
Chi-restraints excluded: chain B residue   80 LEU
Chi-restraints excluded: chain B residue  145 THR
Chi-restraints excluded: chain B residue  244 LEU
Chi-restraints excluded: chain B residue  247 VAL
Chi-restraints excluded: chain B residue  253 VAL
Chi-restraints excluded: chain B residue  283 LEU
Chi-restraints excluded: chain B residue  305 VAL
Chi-restraints excluded: chain B residue  306 MET
Chi-restraints excluded: chain B residue  314 VAL
Chi-restraints excluded: chain B residue  372 VAL
Chi-restraints excluded: chain B residue  378 LEU
Chi-restraints excluded: chain B residue  387 VAL
Chi-restraints excluded: chain C residue   89 LEU
Chi-restraints excluded: chain C residue  124 LEU
Chi-restraints excluded: chain C residue  166 LYS
Chi-restraints excluded: chain C residue  194 MET
Chi-restraints excluded: chain D residue   33 ASN
Chi-restraints excluded: chain D residue  105 ILE
Chi-restraints excluded: chain D residue  186 THR
Chi-restraints excluded: chain E residue   26 VAL
Chi-restraints excluded: chain E residue   38 LEU
Chi-restraints excluded: chain F residue   31 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 175
   random chunks:
   chunk 145 optimal weight:    0.7980
   chunk 61 optimal weight:    3.9990
   chunk 103 optimal weight:    3.9990
   chunk 79 optimal weight:    5.9990
   chunk 150 optimal weight:    4.9990
   chunk 174 optimal weight:   10.0000
   chunk 107 optimal weight:    3.9990
   chunk 171 optimal weight:    4.9990
   chunk 130 optimal weight:    0.7980
   chunk 170 optimal weight:   30.0000
   chunk 111 optimal weight:    2.9990
   overall best weight:    2.5186

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

Flipped N/Q/H residues before XYZ refinement:
B 350 ASN
C 125 GLN
F 163 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3483 r_free = 0.3483 target = 0.110354 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3099 r_free = 0.3099 target = 0.087017 restraints weight = 48937.360|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3101 r_free = 0.3101 target = 0.088266 restraints weight = 46568.208|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3111 r_free = 0.3111 target = 0.088852 restraints weight = 30119.267|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3124 r_free = 0.3124 target = 0.089633 restraints weight = 18741.363|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3144 r_free = 0.3144 target = 0.090875 restraints weight = 15504.014|
|-----------------------------------------------------------------------------|
r_work (final): 0.3114
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3115
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3115 r_free = 0.3115    target_work(ls_wunit_k1) = 0.088         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3115 r_free = 0.3115    target_work(ls_wunit_k1) = 0.088         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.3115
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8114
moved from start:          0.1978

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.053  14356  Z= 0.163
  Angle     :  0.577   7.203  19494  Z= 0.304
  Chirality :  0.043   0.284   2167
  Planarity :  0.004   0.048   2566
  Dihedral  :  4.362  22.137   1990
  Min Nonbonded Distance : 2.537

Molprobity Statistics.
  All-atom Clashscore : 7.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.14 %
    Favored  : 92.86 %
  Rotamer:
    Outliers :  3.56 %
    Allowed  : 15.79 %
    Favored  : 80.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.30 (0.20), residues: 1779
  helix:  2.02 (0.24), residues: 470
  sheet: -0.30 (0.24), residues: 448
  loop : -1.44 (0.21), residues: 861

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 366 
 TYR   0.020   0.002   TYR F 128 
 PHE   0.036   0.002   PHE A 586 
 TRP   0.006   0.001   TRP A 749 
 HIS   0.003   0.001   HIS A 625 

Details of bonding type rmsd
  covalent geometry    : bond        0.00377 (14356)
  covalent geometry    : angle       0.57663 (19494)
  hydrogen bonds       : bond        0.03725 (  664)
  hydrogen bonds       : angle       4.55774 ( 1901)

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

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

  3558 Ramachandran restraints generated.
    1779 Oldfield, 0 Emsley, 1779 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3558 Ramachandran restraints generated.
    1779 Oldfield, 0 Emsley, 1779 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  227 residues out of total 1517 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 53
    poor density    : 174
  time to evaluate  : 0.571 
Fit side-chains
TARDY: cannot create tardy model for: "ILE A 806 " (corrupted residue). Skipping it.
   revert: symmetry clash
   revert: symmetry clash
TARDY: cannot create tardy model for: "ARG B 392 " (corrupted residue). Skipping it.
   revert: symmetry clash
   revert: symmetry clash
TARDY: cannot create tardy model for: "SER D 243 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "LEU E 110 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "ASN F 107 " (corrupted residue). Skipping it.
REVERT: A  165 LEU cc_start: 0.8265 (OUTLIER) cc_final: 0.7895 (tt)
REVERT: A  189 THR cc_start: 0.7929 (m) cc_final: 0.7658 (m)
REVERT: A  550 TYR cc_start: 0.7938 (m-10) cc_final: 0.7564 (m-10)
REVERT: A  777 MET cc_start: 0.8218 (mmm) cc_final: 0.7846 (mmp)
REVERT: A  805 ASN cc_start: 0.8219 (t0) cc_final: 0.7850 (t0)
REVERT: B   32 MET cc_start: 0.6130 (mpp) cc_final: 0.5745 (mtm)
REVERT: C   39 GLU cc_start: 0.7598 (mt-10) cc_final: 0.7012 (pp20)
REVERT: C   43 GLU cc_start: 0.7897 (mp0) cc_final: 0.7460 (mp0)
REVERT: C  194 MET cc_start: 0.8273 (OUTLIER) cc_final: 0.7422 (mtp)
REVERT: C  202 MET cc_start: 0.8097 (tpp) cc_final: 0.7885 (tpp)
REVERT: D  157 SER cc_start: 0.9093 (t) cc_final: 0.8467 (p)
REVERT: F   72 GLU cc_start: 0.8100 (mt-10) cc_final: 0.7817 (mt-10)
REVERT: F  140 GLU cc_start: 0.8506 (tp30) cc_final: 0.8200 (tp30)
REVERT: F  403 ASN cc_start: 0.7918 (m-40) cc_final: 0.7623 (t0)
  outliers start: 53
  outliers final: 43
  residues processed: 209
  average time/residue: 0.0964
  time to fit residues: 31.8525
Evaluate side-chains
  209 residues out of total 1517 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 164
  time to evaluate  : 0.572 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   54 VAL
Chi-restraints excluded: chain A residue   97 ILE
Chi-restraints excluded: chain A residue  130 ILE
Chi-restraints excluded: chain A residue  161 ASN
Chi-restraints excluded: chain A residue  165 LEU
Chi-restraints excluded: chain A residue  183 VAL
Chi-restraints excluded: chain A residue  203 VAL
Chi-restraints excluded: chain A residue  209 VAL
Chi-restraints excluded: chain A residue  273 VAL
Chi-restraints excluded: chain A residue  398 VAL
Chi-restraints excluded: chain A residue  444 VAL
Chi-restraints excluded: chain A residue  479 THR
Chi-restraints excluded: chain A residue  531 TYR
Chi-restraints excluded: chain A residue  555 HIS
Chi-restraints excluded: chain A residue  629 VAL
Chi-restraints excluded: chain A residue  743 THR
Chi-restraints excluded: chain A residue  784 VAL
Chi-restraints excluded: chain B residue   37 THR
Chi-restraints excluded: chain B residue   72 VAL
Chi-restraints excluded: chain B residue   76 ASP
Chi-restraints excluded: chain B residue   80 LEU
Chi-restraints excluded: chain B residue  145 THR
Chi-restraints excluded: chain B residue  244 LEU
Chi-restraints excluded: chain B residue  247 VAL
Chi-restraints excluded: chain B residue  253 VAL
Chi-restraints excluded: chain B residue  270 LEU
Chi-restraints excluded: chain B residue  283 LEU
Chi-restraints excluded: chain B residue  305 VAL
Chi-restraints excluded: chain B residue  306 MET
Chi-restraints excluded: chain B residue  314 VAL
Chi-restraints excluded: chain B residue  372 VAL
Chi-restraints excluded: chain B residue  378 LEU
Chi-restraints excluded: chain B residue  387 VAL
Chi-restraints excluded: chain C residue   89 LEU
Chi-restraints excluded: chain C residue  124 LEU
Chi-restraints excluded: chain C residue  166 LYS
Chi-restraints excluded: chain C residue  194 MET
Chi-restraints excluded: chain D residue   33 ASN
Chi-restraints excluded: chain D residue  105 ILE
Chi-restraints excluded: chain D residue  186 THR
Chi-restraints excluded: chain E residue   26 VAL
Chi-restraints excluded: chain E residue   38 LEU
Chi-restraints excluded: chain F residue   31 VAL
Chi-restraints excluded: chain F residue  407 SER
Chi-restraints excluded: chain F residue  412 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 175
   random chunks:
   chunk 138 optimal weight:    6.9990
   chunk 14 optimal weight:   10.0000
   chunk 47 optimal weight:   10.0000
   chunk 110 optimal weight:    0.4980
   chunk 75 optimal weight:    0.0980
   chunk 127 optimal weight:    9.9990
   chunk 88 optimal weight:    0.9990
   chunk 117 optimal weight:    0.7980
   chunk 87 optimal weight:    2.9990
   chunk 123 optimal weight:   10.0000
   chunk 153 optimal weight:    0.9990
   overall best weight:    0.6784

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

Flipped N/Q/H residues before XYZ refinement:
B  70 ASN
F 163 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3526 r_free = 0.3526 target = 0.113120 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3133 r_free = 0.3133 target = 0.088971 restraints weight = 36319.819|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3110 r_free = 0.3110 target = 0.088317 restraints weight = 27334.221|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3119 r_free = 0.3119 target = 0.088880 restraints weight = 31652.015|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3135 r_free = 0.3135 target = 0.089809 restraints weight = 18834.453|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3140 r_free = 0.3140 target = 0.090161 restraints weight = 15757.450|
|-----------------------------------------------------------------------------|
r_work (final): 0.3122
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3123
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3123 r_free = 0.3123    target_work(ls_wunit_k1) = 0.088         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3123 r_free = 0.3123    target_work(ls_wunit_k1) = 0.088         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.3123
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8100
moved from start:          0.2105

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.046  14356  Z= 0.100
  Angle     :  0.562  14.651  19494  Z= 0.288
  Chirality :  0.042   0.305   2167
  Planarity :  0.004   0.047   2566
  Dihedral  :  4.127  21.578   1990
  Min Nonbonded Distance : 2.411

Molprobity Statistics.
  All-atom Clashscore : 7.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.02 %
    Favored  : 93.98 %
  Rotamer:
    Outliers :  2.62 %
    Allowed  : 16.94 %
    Favored  : 80.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.14 (0.20), residues: 1779
  helix:  2.31 (0.24), residues: 460
  sheet: -0.17 (0.24), residues: 448
  loop : -1.43 (0.21), residues: 871

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C  83 
 TYR   0.026   0.001   TYR F 128 
 PHE   0.022   0.001   PHE A 426 
 TRP   0.008   0.001   TRP A 376 
 HIS   0.002   0.000   HIS A 280 

Details of bonding type rmsd
  covalent geometry    : bond        0.00223 (14356)
  covalent geometry    : angle       0.56228 (19494)
  hydrogen bonds       : bond        0.03199 (  664)
  hydrogen bonds       : angle       4.36643 ( 1901)

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

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

  3558 Ramachandran restraints generated.
    1779 Oldfield, 0 Emsley, 1779 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3558 Ramachandran restraints generated.
    1779 Oldfield, 0 Emsley, 1779 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  214 residues out of total 1517 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 175
  time to evaluate  : 0.526 
Fit side-chains
TARDY: cannot create tardy model for: "ILE A 806 " (corrupted residue). Skipping it.
   revert: symmetry clash
   revert: symmetry clash
TARDY: cannot create tardy model for: "ARG B 392 " (corrupted residue). Skipping it.
   revert: symmetry clash
TARDY: cannot create tardy model for: "SER D 243 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "LEU E 110 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "ASN F 107 " (corrupted residue). Skipping it.
REVERT: A  165 LEU cc_start: 0.8231 (OUTLIER) cc_final: 0.7913 (tt)
REVERT: A  383 ASP cc_start: 0.7873 (m-30) cc_final: 0.7628 (m-30)
REVERT: A  550 TYR cc_start: 0.8045 (m-10) cc_final: 0.7727 (m-10)
REVERT: A  777 MET cc_start: 0.8243 (mmm) cc_final: 0.7892 (mmt)
REVERT: A  805 ASN cc_start: 0.8170 (t0) cc_final: 0.7778 (t0)
REVERT: B   32 MET cc_start: 0.6144 (mpp) cc_final: 0.5764 (mtm)
REVERT: C   39 GLU cc_start: 0.7684 (mt-10) cc_final: 0.6953 (pp20)
REVERT: C   43 GLU cc_start: 0.7852 (mp0) cc_final: 0.7385 (mp0)
REVERT: C  194 MET cc_start: 0.8232 (OUTLIER) cc_final: 0.7426 (mtp)
REVERT: D   41 GLN cc_start: 0.8281 (tm-30) cc_final: 0.8017 (tp40)
REVERT: D  157 SER cc_start: 0.9088 (t) cc_final: 0.8487 (p)
REVERT: F   72 GLU cc_start: 0.8064 (mt-10) cc_final: 0.7798 (mt-10)
REVERT: F  109 MET cc_start: 0.1194 (mmm) cc_final: 0.0991 (tpt)
  outliers start: 39
  outliers final: 32
  residues processed: 203
  average time/residue: 0.0982
  time to fit residues: 31.3375
Evaluate side-chains
  196 residues out of total 1517 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 162
  time to evaluate  : 0.553 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   54 VAL
Chi-restraints excluded: chain A residue   97 ILE
Chi-restraints excluded: chain A residue  161 ASN
Chi-restraints excluded: chain A residue  165 LEU
Chi-restraints excluded: chain A residue  183 VAL
Chi-restraints excluded: chain A residue  209 VAL
Chi-restraints excluded: chain A residue  230 TYR
Chi-restraints excluded: chain A residue  273 VAL
Chi-restraints excluded: chain A residue  398 VAL
Chi-restraints excluded: chain A residue  444 VAL
Chi-restraints excluded: chain A residue  531 TYR
Chi-restraints excluded: chain A residue  555 HIS
Chi-restraints excluded: chain A residue  629 VAL
Chi-restraints excluded: chain A residue  743 THR
Chi-restraints excluded: chain A residue  784 VAL
Chi-restraints excluded: chain B residue   37 THR
Chi-restraints excluded: chain B residue   70 ASN
Chi-restraints excluded: chain B residue   76 ASP
Chi-restraints excluded: chain B residue   80 LEU
Chi-restraints excluded: chain B residue  145 THR
Chi-restraints excluded: chain B residue  247 VAL
Chi-restraints excluded: chain B residue  253 VAL
Chi-restraints excluded: chain B residue  283 LEU
Chi-restraints excluded: chain B residue  305 VAL
Chi-restraints excluded: chain B residue  372 VAL
Chi-restraints excluded: chain B residue  378 LEU
Chi-restraints excluded: chain C residue   89 LEU
Chi-restraints excluded: chain C residue  124 LEU
Chi-restraints excluded: chain C residue  194 MET
Chi-restraints excluded: chain D residue   33 ASN
Chi-restraints excluded: chain D residue  186 THR
Chi-restraints excluded: chain E residue   26 VAL
Chi-restraints excluded: chain F residue   31 VAL
Chi-restraints excluded: chain F residue  163 GLN
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 175
   random chunks:
   chunk 121 optimal weight:   20.0000
   chunk 60 optimal weight:    5.9990
   chunk 77 optimal weight:    9.9990
   chunk 104 optimal weight:    0.8980
   chunk 101 optimal weight:    6.9990
   chunk 94 optimal weight:    0.3980
   chunk 139 optimal weight:    5.9990
   chunk 93 optimal weight:    0.9990
   chunk 37 optimal weight:    5.9990
   chunk 29 optimal weight:    0.7980
   chunk 87 optimal weight:    7.9990
   overall best weight:    1.8184

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

Flipped N/Q/H residues before XYZ refinement:
F 163 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3504 r_free = 0.3504 target = 0.111688 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3111 r_free = 0.3111 target = 0.087691 restraints weight = 49089.900|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3117 r_free = 0.3117 target = 0.089122 restraints weight = 47685.485|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3126 r_free = 0.3126 target = 0.089632 restraints weight = 32882.895|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3145 r_free = 0.3145 target = 0.090793 restraints weight = 19723.876|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3157 r_free = 0.3157 target = 0.091527 restraints weight = 15966.872|
|-----------------------------------------------------------------------------|
r_work (final): 0.3131
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3132
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3132 r_free = 0.3132    target_work(ls_wunit_k1) = 0.089         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3132 r_free = 0.3132    target_work(ls_wunit_k1) = 0.089         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.3132
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8087
moved from start:          0.2125

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047  14356  Z= 0.135
  Angle     :  0.581  13.229  19494  Z= 0.301
  Chirality :  0.043   0.312   2167
  Planarity :  0.004   0.046   2566
  Dihedral  :  4.200  21.860   1990
  Min Nonbonded Distance : 2.514

Molprobity Statistics.
  All-atom Clashscore : 7.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.97 %
    Favored  : 93.03 %
  Rotamer:
    Outliers :  2.82 %
    Allowed  : 17.20 %
    Favored  : 79.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.17 (0.20), residues: 1779
  helix:  2.31 (0.24), residues: 458
  sheet: -0.24 (0.24), residues: 448
  loop : -1.42 (0.21), residues: 873

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.000   ARG C 160 
 TYR   0.024   0.001   TYR F 128 
 PHE   0.027   0.001   PHE A 586 
 TRP   0.014   0.001   TRP C 145 
 HIS   0.004   0.001   HIS C  51 

Details of bonding type rmsd
  covalent geometry    : bond        0.00311 (14356)
  covalent geometry    : angle       0.58074 (19494)
  hydrogen bonds       : bond        0.03400 (  664)
  hydrogen bonds       : angle       4.37632 ( 1901)

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

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

  3558 Ramachandran restraints generated.
    1779 Oldfield, 0 Emsley, 1779 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3558 Ramachandran restraints generated.
    1779 Oldfield, 0 Emsley, 1779 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  207 residues out of total 1517 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 165
  time to evaluate  : 0.568 
Fit side-chains
TARDY: cannot create tardy model for: "ILE A 806 " (corrupted residue). Skipping it.
   revert: symmetry clash
   revert: symmetry clash
TARDY: cannot create tardy model for: "ARG B 392 " (corrupted residue). Skipping it.
   revert: symmetry clash
TARDY: cannot create tardy model for: "SER D 243 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "LEU E 110 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "ASN F 107 " (corrupted residue). Skipping it.
REVERT: A  165 LEU cc_start: 0.8217 (OUTLIER) cc_final: 0.7868 (tt)
REVERT: A  383 ASP cc_start: 0.7921 (m-30) cc_final: 0.7656 (m-30)
REVERT: A  550 TYR cc_start: 0.8025 (m-10) cc_final: 0.7715 (m-10)
REVERT: A  777 MET cc_start: 0.8280 (mmm) cc_final: 0.7926 (mmt)
REVERT: A  805 ASN cc_start: 0.8180 (t0) cc_final: 0.7790 (t0)
REVERT: B   32 MET cc_start: 0.6156 (mpp) cc_final: 0.5724 (mtm)
REVERT: C   39 GLU cc_start: 0.7684 (mt-10) cc_final: 0.6982 (pp20)
REVERT: C   43 GLU cc_start: 0.7856 (mp0) cc_final: 0.7351 (mp0)
REVERT: C  194 MET cc_start: 0.8253 (OUTLIER) cc_final: 0.7467 (mtp)
REVERT: C  202 MET cc_start: 0.8068 (tpp) cc_final: 0.7850 (tpp)
REVERT: D   41 GLN cc_start: 0.8263 (tm-30) cc_final: 0.8011 (tp40)
REVERT: D   67 TYR cc_start: 0.6932 (OUTLIER) cc_final: 0.5479 (p90)
REVERT: D  157 SER cc_start: 0.9094 (t) cc_final: 0.8487 (p)
REVERT: F  140 GLU cc_start: 0.8666 (tp30) cc_final: 0.8379 (tp30)
  outliers start: 42
  outliers final: 37
  residues processed: 194
  average time/residue: 0.0990
  time to fit residues: 30.4971
Evaluate side-chains
  203 residues out of total 1517 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 163
  time to evaluate  : 0.567 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   54 VAL
Chi-restraints excluded: chain A residue   97 ILE
Chi-restraints excluded: chain A residue  161 ASN
Chi-restraints excluded: chain A residue  165 LEU
Chi-restraints excluded: chain A residue  183 VAL
Chi-restraints excluded: chain A residue  203 VAL
Chi-restraints excluded: chain A residue  209 VAL
Chi-restraints excluded: chain A residue  230 TYR
Chi-restraints excluded: chain A residue  273 VAL
Chi-restraints excluded: chain A residue  398 VAL
Chi-restraints excluded: chain A residue  444 VAL
Chi-restraints excluded: chain A residue  531 TYR
Chi-restraints excluded: chain A residue  532 VAL
Chi-restraints excluded: chain A residue  555 HIS
Chi-restraints excluded: chain A residue  629 VAL
Chi-restraints excluded: chain A residue  743 THR
Chi-restraints excluded: chain A residue  784 VAL
Chi-restraints excluded: chain B residue   37 THR
Chi-restraints excluded: chain B residue   72 VAL
Chi-restraints excluded: chain B residue   76 ASP
Chi-restraints excluded: chain B residue   80 LEU
Chi-restraints excluded: chain B residue  145 THR
Chi-restraints excluded: chain B residue  247 VAL
Chi-restraints excluded: chain B residue  253 VAL
Chi-restraints excluded: chain B residue  283 LEU
Chi-restraints excluded: chain B residue  305 VAL
Chi-restraints excluded: chain B residue  314 VAL
Chi-restraints excluded: chain B residue  372 VAL
Chi-restraints excluded: chain B residue  378 LEU
Chi-restraints excluded: chain B residue  387 VAL
Chi-restraints excluded: chain C residue   89 LEU
Chi-restraints excluded: chain C residue  124 LEU
Chi-restraints excluded: chain C residue  194 MET
Chi-restraints excluded: chain D residue   33 ASN
Chi-restraints excluded: chain D residue   67 TYR
Chi-restraints excluded: chain D residue   84 ASP
Chi-restraints excluded: chain D residue  105 ILE
Chi-restraints excluded: chain D residue  186 THR
Chi-restraints excluded: chain E residue   26 VAL
Chi-restraints excluded: chain F residue   31 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 175
   random chunks:
   chunk 44 optimal weight:    7.9990
   chunk 10 optimal weight:    7.9990
   chunk 116 optimal weight:    9.9990
   chunk 58 optimal weight:    2.9990
   chunk 42 optimal weight:    1.9990
   chunk 170 optimal weight:   20.0000
   chunk 11 optimal weight:    4.9990
   chunk 158 optimal weight:    0.9980
   chunk 98 optimal weight:    0.6980
   chunk 31 optimal weight:    7.9990
   chunk 133 optimal weight:    1.9990
   overall best weight:    1.7386

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

Flipped N/Q/H residues before XYZ refinement:
F 163 GLN
F 428 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3503 r_free = 0.3503 target = 0.111622 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3125 r_free = 0.3125 target = 0.088581 restraints weight = 57249.205|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3065 r_free = 0.3065 target = 0.085910 restraints weight = 37176.946|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3095 r_free = 0.3095 target = 0.087631 restraints weight = 33290.535|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3101 r_free = 0.3101 target = 0.088076 restraints weight = 20670.552|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3123 r_free = 0.3123 target = 0.089363 restraints weight = 18067.133|
|-----------------------------------------------------------------------------|
r_work (final): 0.3097
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3098
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3098 r_free = 0.3098    target_work(ls_wunit_k1) = 0.087         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3098 r_free = 0.3098    target_work(ls_wunit_k1) = 0.087         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.3098
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8135
moved from start:          0.2158

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046  14356  Z= 0.131
  Angle     :  0.585  13.040  19494  Z= 0.302
  Chirality :  0.043   0.317   2167
  Planarity :  0.004   0.046   2566
  Dihedral  :  4.200  21.454   1990
  Min Nonbonded Distance : 2.519

Molprobity Statistics.
  All-atom Clashscore : 7.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.52 %
    Favored  : 93.48 %
  Rotamer:
    Outliers :  2.96 %
    Allowed  : 17.00 %
    Favored  : 80.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.19 (0.20), residues: 1779
  helix:  2.29 (0.24), residues: 458
  sheet: -0.26 (0.24), residues: 449
  loop : -1.43 (0.21), residues: 872

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C 160 
 TYR   0.029   0.001   TYR F 128 
 PHE   0.027   0.001   PHE A 586 
 TRP   0.008   0.001   TRP C 145 
 HIS   0.002   0.001   HIS A 625 

Details of bonding type rmsd
  covalent geometry    : bond        0.00302 (14356)
  covalent geometry    : angle       0.58522 (19494)
  hydrogen bonds       : bond        0.03436 (  664)
  hydrogen bonds       : angle       4.37483 ( 1901)

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

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

  3558 Ramachandran restraints generated.
    1779 Oldfield, 0 Emsley, 1779 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3558 Ramachandran restraints generated.
    1779 Oldfield, 0 Emsley, 1779 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  217 residues out of total 1517 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 173
  time to evaluate  : 0.571 
Fit side-chains
TARDY: cannot create tardy model for: "ILE A 806 " (corrupted residue). Skipping it.
   revert: symmetry clash
   revert: symmetry clash
TARDY: cannot create tardy model for: "ARG B 392 " (corrupted residue). Skipping it.
   revert: symmetry clash
TARDY: cannot create tardy model for: "SER D 243 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "LEU E 110 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "ASN F 107 " (corrupted residue). Skipping it.
REVERT: A  165 LEU cc_start: 0.8249 (OUTLIER) cc_final: 0.7881 (tt)
REVERT: A  550 TYR cc_start: 0.8068 (m-10) cc_final: 0.7757 (m-10)
REVERT: A  777 MET cc_start: 0.8270 (mmm) cc_final: 0.7909 (mmt)
REVERT: A  805 ASN cc_start: 0.8178 (t0) cc_final: 0.7795 (t0)
REVERT: B   32 MET cc_start: 0.6091 (mpp) cc_final: 0.5652 (mtm)
REVERT: C   39 GLU cc_start: 0.7662 (mt-10) cc_final: 0.6970 (pp20)
REVERT: C   43 GLU cc_start: 0.7883 (mp0) cc_final: 0.7382 (mp0)
REVERT: C  194 MET cc_start: 0.8287 (OUTLIER) cc_final: 0.7544 (mtp)
REVERT: D   67 TYR cc_start: 0.6956 (OUTLIER) cc_final: 0.5498 (p90)
REVERT: D  111 MET cc_start: 0.8692 (tpp) cc_final: 0.8274 (tpp)
REVERT: D  157 SER cc_start: 0.9117 (t) cc_final: 0.8437 (p)
REVERT: F   72 GLU cc_start: 0.8077 (mt-10) cc_final: 0.7791 (mt-10)
REVERT: F  140 GLU cc_start: 0.8678 (tp30) cc_final: 0.8376 (tp30)
  outliers start: 44
  outliers final: 39
  residues processed: 204
  average time/residue: 0.1013
  time to fit residues: 32.7443
Evaluate side-chains
  207 residues out of total 1517 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 165
  time to evaluate  : 0.546 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   54 VAL
Chi-restraints excluded: chain A residue   97 ILE
Chi-restraints excluded: chain A residue  161 ASN
Chi-restraints excluded: chain A residue  165 LEU
Chi-restraints excluded: chain A residue  183 VAL
Chi-restraints excluded: chain A residue  203 VAL
Chi-restraints excluded: chain A residue  209 VAL
Chi-restraints excluded: chain A residue  230 TYR
Chi-restraints excluded: chain A residue  273 VAL
Chi-restraints excluded: chain A residue  398 VAL
Chi-restraints excluded: chain A residue  444 VAL
Chi-restraints excluded: chain A residue  531 TYR
Chi-restraints excluded: chain A residue  532 VAL
Chi-restraints excluded: chain A residue  555 HIS
Chi-restraints excluded: chain A residue  629 VAL
Chi-restraints excluded: chain A residue  743 THR
Chi-restraints excluded: chain A residue  784 VAL
Chi-restraints excluded: chain B residue   37 THR
Chi-restraints excluded: chain B residue   76 ASP
Chi-restraints excluded: chain B residue   80 LEU
Chi-restraints excluded: chain B residue  145 THR
Chi-restraints excluded: chain B residue  247 VAL
Chi-restraints excluded: chain B residue  253 VAL
Chi-restraints excluded: chain B residue  283 LEU
Chi-restraints excluded: chain B residue  305 VAL
Chi-restraints excluded: chain B residue  314 VAL
Chi-restraints excluded: chain B residue  372 VAL
Chi-restraints excluded: chain B residue  378 LEU
Chi-restraints excluded: chain B residue  387 VAL
Chi-restraints excluded: chain C residue   89 LEU
Chi-restraints excluded: chain C residue  124 LEU
Chi-restraints excluded: chain C residue  194 MET
Chi-restraints excluded: chain D residue   33 ASN
Chi-restraints excluded: chain D residue   67 TYR
Chi-restraints excluded: chain D residue   84 ASP
Chi-restraints excluded: chain D residue  105 ILE
Chi-restraints excluded: chain D residue  186 THR
Chi-restraints excluded: chain E residue   26 VAL
Chi-restraints excluded: chain E residue   38 LEU
Chi-restraints excluded: chain F residue   31 VAL
Chi-restraints excluded: chain F residue  407 SER
Chi-restraints excluded: chain F residue  423 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 175
   random chunks:
   chunk 66 optimal weight:   20.0000
   chunk 168 optimal weight:    7.9990
   chunk 136 optimal weight:    1.9990
   chunk 102 optimal weight:    3.9990
   chunk 16 optimal weight:    0.7980
   chunk 30 optimal weight:    9.9990
   chunk 10 optimal weight:    6.9990
   chunk 127 optimal weight:    4.9990
   chunk 110 optimal weight:    8.9990
   chunk 6 optimal weight:    5.9990
   chunk 171 optimal weight:   30.0000
   overall best weight:    3.5588

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

Flipped N/Q/H residues before XYZ refinement:
B 350 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3464 r_free = 0.3464 target = 0.109077 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3088 r_free = 0.3088 target = 0.086183 restraints weight = 40514.735|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3071 r_free = 0.3071 target = 0.085835 restraints weight = 50183.519|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3087 r_free = 0.3087 target = 0.086791 restraints weight = 39498.253|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3118 r_free = 0.3118 target = 0.088680 restraints weight = 23358.749|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3121 r_free = 0.3121 target = 0.088899 restraints weight = 17156.616|
|-----------------------------------------------------------------------------|
r_work (final): 0.3105
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3106
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3106 r_free = 0.3106    target_work(ls_wunit_k1) = 0.087         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3106 r_free = 0.3106    target_work(ls_wunit_k1) = 0.087         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.3106
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8128
moved from start:          0.2242

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.052  14356  Z= 0.216
  Angle     :  0.650  12.872  19494  Z= 0.339
  Chirality :  0.045   0.304   2167
  Planarity :  0.004   0.046   2566
  Dihedral  :  4.580  22.211   1990
  Min Nonbonded Distance : 2.508

Molprobity Statistics.
  All-atom Clashscore : 9.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.16 %
    Favored  : 91.84 %
  Rotamer:
    Outliers :  3.49 %
    Allowed  : 17.14 %
    Favored  : 79.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.53 (0.20), residues: 1779
  helix:  1.84 (0.24), residues: 473
  sheet: -0.46 (0.24), residues: 459
  loop : -1.60 (0.21), residues: 847

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 366 
 TYR   0.029   0.002   TYR F 128 
 PHE   0.046   0.002   PHE A 586 
 TRP   0.014   0.001   TRP C 145 
 HIS   0.005   0.001   HIS A 625 

Details of bonding type rmsd
  covalent geometry    : bond        0.00500 (14356)
  covalent geometry    : angle       0.65018 (19494)
  hydrogen bonds       : bond        0.04109 (  664)
  hydrogen bonds       : angle       4.66327 ( 1901)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2289.22 seconds
wall clock time: 40 minutes 22.90 seconds (2422.90 seconds total)