Starting phenix.real_space_refine
on Sat May 17 01:58:27 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8spr_40682/05_2025/8spr_40682.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8spr_40682/05_2025/8spr_40682.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.9
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8spr_40682/05_2025/8spr_40682.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8spr_40682/05_2025/8spr_40682.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8spr_40682/05_2025/8spr_40682.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8spr_40682/05_2025/8spr_40682.cif"
  }
  resolution = 3.9
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.004 sd=   0.064
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      40      5.16       5
     C    9458      2.51       5
     N    2575      2.21       5
     O    2959      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 69 residue(s): 0.08s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 15032
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 6226
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 787, 6226
          Classifications: {'peptide': 787}
          Link IDs: {'CIS': 1, 'PTRANS': 29, 'TRANS': 756}
    Chain: "B"
      Number of atoms: 2795
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 371, 2795
          Classifications: {'peptide': 371}
          Link IDs: {'CIS': 2, 'PTRANS': 11, 'TRANS': 357}
    Chain: "C"
      Number of atoms: 1231
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 161, 1231
          Classifications: {'peptide': 161}
          Link IDs: {'CIS': 1, 'PTRANS': 10, 'TRANS': 149}
    Chain: "D"
      Number of atoms: 1761
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 218, 1761
          Classifications: {'peptide': 218}
          Link IDs: {'PTRANS': 12, 'TRANS': 205}
    Chain: "E"
      Number of atoms: 721
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 93, 721
          Classifications: {'peptide': 93}
          Link IDs: {'PTRANS': 5, 'TRANS': 87}
    Chain: "F"
      Number of atoms: 2298
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 302, 2286
          Classifications: {'peptide': 302}
          Incomplete info: {'backbone_only': 3, 'truncation_to_alanine': 5}
          Link IDs: {'PTRANS': 2, 'TRANS': 299}
          Unresolved non-hydrogen bonds: 47
          Unresolved non-hydrogen angles: 55
          Unresolved non-hydrogen dihedrals: 39
          Unresolved non-hydrogen chiralities: 3
          Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 2, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 19
      Conformer: "B"
        Number of residues, atoms: 302, 2286
          Classifications: {'peptide': 302}
          Incomplete info: {'backbone_only': 3, 'truncation_to_alanine': 5}
          Link IDs: {'PTRANS': 2, 'TRANS': 299}
          Unresolved non-hydrogen bonds: 47
          Unresolved non-hydrogen angles: 55
          Unresolved non-hydrogen dihedrals: 39
          Unresolved non-hydrogen chiralities: 3
          Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 2, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 19
          bond proxies already assigned to first conformer: 2322
  Residues with excluded nonbonded symmetry interactions: 1
    residue:
      pdb=" N  ATYR F1150 " occ=0.50
      ... (22 atoms not shown)
      pdb=" OH BTYR F1150 " occ=0.50
  Time building chain proxies: 10.21, per 1000 atoms: 0.68
  Number of scatterers: 15032
  At special positions: 0
  Unit cell: (138.24, 140.4, 137.16, 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      40     16.00
     O    2959      8.00
     N    2575      7.00
     C    9458      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 806 " - pdb=" SG  CYS F1041 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 3.96
  Conformation dependent library (CDL) restraints added in 2.2 seconds
  

  3846 Ramachandran restraints generated.
    1923 Oldfield, 0 Emsley, 1923 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3508

  Finding SS restraints...
    Secondary structure from input PDB file:
      33 helices and 26 sheets defined
      20.5% alpha, 16.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.67
  Creating SS restraints...
    Processing helix  chain 'A' and resid 38 through 45
    Processing helix  chain 'A' and resid 55 through 70
    Processing helix  chain 'A' and resid 106 through 116
    Processing helix  chain 'A' and resid 126 through 128
      No H-bonds generated for 'chain 'A' and resid 126 through 128'
    Processing helix  chain 'A' and resid 129 through 144
    Processing helix  chain 'A' and resid 189 through 197
      removed outlier: 3.666A  pdb=" N   LEU A 193 " --> pdb=" O   THR A 189 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 215 through 232
    Processing helix  chain 'A' and resid 280 through 286
    Processing helix  chain 'A' and resid 297 through 313
    Processing helix  chain 'A' and resid 361 through 367
      removed outlier: 4.023A  pdb=" N   LEU A 365 " --> pdb=" O   LYS A 361 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 378 through 393
      removed outlier: 4.300A  pdb=" N   GLY A 393 " --> pdb=" O   LEU A 389 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 448 through 452
      removed outlier: 3.563A  pdb=" N   GLY A 451 " --> pdb=" O   ASN A 448 " (cutoff:3.500A)
      removed outlier: 3.740A  pdb=" N   THR A 452 " --> pdb=" O   TRP A 449 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 448 through 452'
    Processing helix  chain 'A' and resid 543 through 552
    Processing helix  chain 'A' and resid 647 through 651
    Processing helix  chain 'A' and resid 726 through 731
    Processing helix  chain 'B' and resid 22 through 27
      removed outlier: 3.989A  pdb=" N   GLU B  26 " --> pdb=" O   PHE B  23 " (cutoff:3.500A)
      removed outlier: 4.213A  pdb=" N   GLU B  27 " --> pdb=" O   ASN B  24 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 59 through 63
      removed outlier: 3.955A  pdb=" N   SER C  62 " --> pdb=" O   PRO C  59 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 76 through 80
    Processing helix  chain 'C' and resid 115 through 127
      removed outlier: 3.862A  pdb=" N   GLN C 119 " --> pdb=" O   THR C 115 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 31 through 45
    Processing helix  chain 'D' and resid 47 through 61
    Processing helix  chain 'D' and resid 67 through 82
    Processing helix  chain 'D' and resid 84 through 99
      removed outlier: 4.012A  pdb=" N   ALA D  88 " --> pdb=" O   ASP D  84 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 104 through 121
      removed outlier: 4.002A  pdb=" N   VAL D 108 " --> pdb=" O   ASN D 104 " (cutoff:3.500A)
      removed outlier: 4.090A  pdb=" N   ASP D 121 " --> pdb=" O   MET D 117 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 123 through 129
    Processing helix  chain 'D' and resid 138 through 154
    Processing helix  chain 'D' and resid 160 through 189
    Processing helix  chain 'D' and resid 190 through 202
      removed outlier: 3.599A  pdb=" N   VAL D 194 " --> pdb=" O   ALA D 190 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 208 through 224
      removed outlier: 4.164A  pdb=" N   ARG D 212 " --> pdb=" O   THR D 208 " (cutoff:3.500A)
      Proline residue:  D 216  - end of helix
    Processing helix  chain 'D' and resid 227 through 241
      removed outlier: 3.559A  pdb=" N   ALA D 231 " --> pdb=" O   MET D 227 " (cutoff:3.500A)
      removed outlier: 3.503A  pdb=" N   ASN D 241 " --> pdb=" O   ILE D 237 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 51 through 60
    Processing helix  chain 'F' and resid 1002 through 1021
    Processing helix  chain 'F' and resid 1111 through 1115
    Processing sheet with id=AA1, first strand: chain 'A' and resid 77 through 80
    Processing sheet with id=AA2, first strand: chain 'A' and resid 94 through 99
      removed outlier: 4.372A  pdb=" N   ILE A  94 " --> pdb=" O   VAL A 163 " (cutoff:3.500A)
      removed outlier: 6.754A  pdb=" N   LEU A 165 " --> pdb=" O   ILE A  94 " (cutoff:3.500A)
      removed outlier: 6.012A  pdb=" N   SER A  96 " --> pdb=" O   LEU A 165 " (cutoff:3.500A)
      removed outlier: 7.799A  pdb=" N   LEU A 167 " --> pdb=" O   SER A  96 " (cutoff:3.500A)
      removed outlier: 7.087A  pdb=" N   THR A  98 " --> pdb=" O   LEU A 167 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 149 through 150
    Processing sheet with id=AA4, first strand: chain 'A' and resid 176 through 180
      removed outlier: 7.688A  pdb=" N   VAL A 256 " --> pdb=" O   GLN A 178 " (cutoff:3.500A)
      removed outlier: 4.429A  pdb=" N   ILE A 180 " --> pdb=" O   VAL A 256 " (cutoff:3.500A)
      removed outlier: 7.053A  pdb=" N   VAL A 258 " --> pdb=" O   ILE A 180 " (cutoff:3.500A)
      removed outlier: 6.525A  pdb=" N   GLY A 253 " --> pdb=" O   LEU A 247 " (cutoff:3.500A)
      removed outlier: 4.621A  pdb=" N   LEU A 247 " --> pdb=" O   GLY A 253 " (cutoff:3.500A)
      removed outlier: 6.156A  pdb=" N   TYR A 255 " --> pdb=" O   VAL A 245 " (cutoff:3.500A)
      removed outlier: 4.206A  pdb=" N   VAL A 245 " --> pdb=" O   TYR A 255 " (cutoff:3.500A)
      removed outlier: 7.001A  pdb=" N   THR A 257 " --> pdb=" O   THR A 243 " (cutoff:3.500A)
      removed outlier: 4.918A  pdb=" N   THR A 243 " --> pdb=" O   THR A 257 " (cutoff:3.500A)
      removed outlier: 6.940A  pdb=" N   ASN A 259 " --> pdb=" O   ASP A 241 " (cutoff:3.500A)
      removed outlier: 3.661A  pdb=" N   THR A 261 " --> pdb=" O   ASN A 239 " (cutoff:3.500A)
      removed outlier: 3.917A  pdb=" N   ASN A 239 " --> pdb=" O   THR A 261 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 267 through 275
      removed outlier: 6.396A  pdb=" N   LYS A 267 " --> pdb=" O   VAL A 335 " (cutoff:3.500A)
      removed outlier: 8.147A  pdb=" N   LEU A 337 " --> pdb=" O   LYS A 267 " (cutoff:3.500A)
      removed outlier: 8.472A  pdb=" N   SER A 269 " --> pdb=" O   LEU A 337 " (cutoff:3.500A)
      removed outlier: 12.833A  pdb=" N   VAL A 339 " --> pdb=" O   SER A 269 " (cutoff:3.500A)
      removed outlier: 10.088A  pdb=" N   VAL A 271 " --> pdb=" O   VAL A 339 " (cutoff:3.500A)
      removed outlier: 12.679A  pdb=" N   VAL A 341 " --> pdb=" O   VAL A 271 " (cutoff:3.500A)
      removed outlier: 10.481A  pdb=" N   VAL A 273 " --> pdb=" O   VAL A 341 " (cutoff:3.500A)
      removed outlier: 3.531A  pdb=" N   ARG A 338 " --> pdb=" O   MET A 325 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 353 through 355
  WARNING: can't find start of bonding for strands!
    previous: chain 'A' and resid 353 through 355
    current: chain 'A' and resid 412 through 420
  No H-bonds generated for sheet with id=AA6
    Processing sheet with id=AA7, first strand: chain 'A' and resid 442 through 445
      removed outlier: 3.724A  pdb=" N   GLY A 457 " --> pdb=" O   SER A 472 " (cutoff:3.500A)
      removed outlier: 3.910A  pdb=" N   LEU A 489 " --> pdb=" O   LEU A 471 " (cutoff:3.500A)
      removed outlier: 4.022A  pdb=" N   VAL A 473 " --> pdb=" O   GLY A 487 " (cutoff:3.500A)
      removed outlier: 4.093A  pdb=" N   ARG A 488 " --> pdb=" O   ASP A 512 " (cutoff:3.500A)
      removed outlier: 3.901A  pdb=" N   ASP A 512 " --> pdb=" O   ARG A 488 " (cutoff:3.500A)
      removed outlier: 3.653A  pdb=" N   TYR A 531 " --> pdb=" O   THR A 511 " (cutoff:3.500A)
  WARNING: can't find start of bonding for strands!
    previous: chain 'A' and resid 530 through 531
    current: chain 'A' and resid 564 through 567
    Processing sheet with id=AA8, first strand: chain 'A' and resid 523 through 524
      removed outlier: 3.923A  pdb=" N   SER A 524 " --> pdb=" O   THR A 577 " (cutoff:3.500A)
      removed outlier: 3.890A  pdb=" N   LYS A 580 " --> pdb=" O   SER A 591 " (cutoff:3.500A)
      removed outlier: 3.888A  pdb=" N   GLY A 590 " --> pdb=" O   TYR A 618 " (cutoff:3.500A)
      removed outlier: 3.568A  pdb=" N   TYR A 618 " --> pdb=" O   GLY A 590 " (cutoff:3.500A)
      removed outlier: 4.112A  pdb=" N   ARG A 592 " --> pdb=" O   ALA A 616 " (cutoff:3.500A)
      removed outlier: 4.129A  pdb=" N   ASN A 594 " --> pdb=" O   ASP A 614 " (cutoff:3.500A)
      removed outlier: 3.596A  pdb=" N   ASP A 614 " --> pdb=" O   ASN A 594 " (cutoff:3.500A)
      removed outlier: 3.515A  pdb=" N   THR A 596 " --> pdb=" O   THR A 612 " (cutoff:3.500A)
  WARNING: can't find start of bonding for strands!
    previous: chain 'A' and resid 628 through 629
    current: chain 'A' and resid 714 through 720
      removed outlier: 3.690A  pdb=" N   THR A 735 " --> pdb=" O   THR A 720 " (cutoff:3.500A)
      removed outlier: 3.947A  pdb=" N   GLY A 771 " --> pdb=" O   PHE A 738 " (cutoff:3.500A)
      removed outlier: 3.820A  pdb=" N   TRP A 776 " --> pdb=" O   LEU A 783 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'A' and resid 673 through 674
      removed outlier: 3.777A  pdb=" N   CYS A 700 " --> pdb=" O   TYR A 674 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'B' and resid 45 through 46
    Processing sheet with id=AB2, first strand: chain 'B' and resid 66 through 68
      removed outlier: 3.954A  pdb=" N   ALA B  66 " --> pdb=" O   TYR B  73 " (cutoff:3.500A)
      removed outlier: 3.580A  pdb=" N   TYR B  73 " --> pdb=" O   ALA B  66 " (cutoff:3.500A)
      removed outlier: 6.082A  pdb=" N   VAL B  81 " --> pdb=" O   SER B  94 " (cutoff:3.500A)
      removed outlier: 4.786A  pdb=" N   SER B  94 " --> pdb=" O   VAL B  81 " (cutoff:3.500A)
      removed outlier: 6.706A  pdb=" N   ALA B  83 " --> pdb=" O   ILE B  92 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'B' and resid 123 through 125
      removed outlier: 3.879A  pdb=" N   ILE B 124 " --> pdb=" O   TYR B 132 " (cutoff:3.500A)
      removed outlier: 3.521A  pdb=" N   TYR B 132 " --> pdb=" O   ILE B 124 " (cutoff:3.500A)
      removed outlier: 3.521A  pdb=" N   VAL B 131 " --> pdb=" O   THR B 145 " (cutoff:3.500A)
      removed outlier: 3.730A  pdb=" N   THR B 145 " --> pdb=" O   VAL B 131 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB3
    Processing sheet with id=AB4, first strand: chain 'B' and resid 156 through 158
    Processing sheet with id=AB5, first strand: chain 'B' and resid 200 through 203
      removed outlier: 3.673A  pdb=" N   VAL B 209 " --> pdb=" O   SER B 217 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'B' and resid 252 through 253
      removed outlier: 4.294A  pdb=" N   LEU B 267 " --> pdb=" O   ARG B 281 " (cutoff:3.500A)
      removed outlier: 3.891A  pdb=" N   ALA B 269 " --> pdb=" O   TRP B 279 " (cutoff:3.500A)
      removed outlier: 4.148A  pdb=" N   TRP B 279 " --> pdb=" O   ALA B 269 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'B' and resid 290 through 292
      removed outlier: 3.606A  pdb=" N   TYR B 297 " --> pdb=" O   ILE B 290 " (cutoff:3.500A)
      removed outlier: 3.608A  pdb=" N   ASP B 292 " --> pdb=" O   ARG B 295 " (cutoff:3.500A)
      removed outlier: 3.540A  pdb=" N   LEU B 308 " --> pdb=" O   ILE B 296 " (cutoff:3.500A)
      removed outlier: 3.776A  pdb=" N   LEU B 298 " --> pdb=" O   MET B 306 " (cutoff:3.500A)
      removed outlier: 3.561A  pdb=" N   MET B 306 " --> pdb=" O   LEU B 298 " (cutoff:3.500A)
      removed outlier: 4.557A  pdb=" N   VAL B 314 " --> pdb=" O   THR B 309 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'B' and resid 331 through 333
    Processing sheet with id=AB9, first strand: chain 'B' and resid 372 through 374
      removed outlier: 3.914A  pdb=" N   LEU B 379 " --> pdb=" O   VAL B 372 " (cutoff:3.500A)
    Processing sheet with id=AC1, first strand: chain 'C' and resid 95 through 96
      removed outlier: 4.098A  pdb=" N   LEU C 107 " --> pdb=" O   ARG C  96 " (cutoff:3.500A)
    Processing sheet with id=AC2, first strand: chain 'C' and resid 133 through 134
      removed outlier: 3.639A  pdb=" N   GLN C 133 " --> pdb=" O   THR C 142 " (cutoff:3.500A)
      removed outlier: 3.586A  pdb=" N   THR C 142 " --> pdb=" O   GLN C 133 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AC2
    Processing sheet with id=AC3, first strand: chain 'C' and resid 145 through 148
      removed outlier: 3.703A  pdb=" N   TYR C 157 " --> pdb=" O   TRP C 148 " (cutoff:3.500A)
    Processing sheet with id=AC4, first strand: chain 'C' and resid 182 through 183
    Processing sheet with id=AC5, first strand: chain 'E' and resid 32 through 34
      removed outlier: 3.587A  pdb=" N   ARG E  78 " --> pdb=" O   GLN E  34 " (cutoff:3.500A)
      removed outlier: 3.584A  pdb=" N   ASN E 103 " --> pdb=" O   THR E  94 " (cutoff:3.500A)
    Processing sheet with id=AC6, first strand: chain 'F' and resid 1044 through 1046
  WARNING: can't find start of bonding for strands!
    previous: chain 'F' and resid 1044 through 1046
    current: chain 'F' and resid 1208 through 1213
  WARNING: can't find start of bonding for strands!
    previous: chain 'F' and resid 1221 through 1223
    current: chain 'F' and resid 1259 through 1261
  WARNING: can't find start of bonding for strands!
    previous: chain 'F' and resid 1259 through 1261
    current: chain 'F' and resid 1288 through 1295
    Processing sheet with id=AC7, first strand: chain 'F' and resid 1062 through 1065
      removed outlier: 3.809A  pdb=" N   VAL F1063 " --> pdb=" O   HIS F1086 " (cutoff:3.500A)
  WARNING: can't find start of bonding for strands!
    previous: chain 'F' and resid 1084 through 1087
    current: chain 'F' and resid 1097 through 1105
      removed outlier: 4.301A  pdb=" N   LYS F1101 " --> pdb=" O   ASP F1129 " (cutoff:3.500A)
      removed outlier: 3.823A  pdb=" N   ASP F1129 " --> pdb=" O   LYS F1101 " (cutoff:3.500A)
      removed outlier: 4.069A  pdb=" N   VAL F1103 " --> pdb=" O   HIS F1127 " (cutoff:3.500A)
      removed outlier: 3.602A  pdb=" N   HIS F1127 " --> pdb=" O   VAL F1103 " (cutoff:3.500A)
    Processing sheet with id=AC8, first strand: chain 'F' and resid 1182 through 1185

    403 hydrogen bonds defined for protein.
    1080 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: 4.53

  Time building geometry restraints manager: 4.59 seconds

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

  Histogram of bond lengths:
        1.21 -     1.34: 5042
        1.34 -     1.46: 3743
        1.46 -     1.59: 6499
        1.59 -     1.71: 0
        1.71 -     1.84: 76
  Bond restraints: 15360
  Sorted by residual:
  bond pdb=" CA  ILE B 380 "
       pdb=" CB  ILE B 380 "
    ideal  model  delta    sigma   weight residual
    1.553  1.533  0.020 7.40e-03 1.83e+04 7.19e+00
  bond pdb=" CB  PHE A 347 "
       pdb=" CG  PHE A 347 "
    ideal  model  delta    sigma   weight residual
    1.502  1.444  0.058 2.30e-02 1.89e+03 6.42e+00
  bond pdb=" C   PRO D 206 "
       pdb=" N   ASP D 207 "
    ideal  model  delta    sigma   weight residual
    1.332  1.298  0.035 1.40e-02 5.10e+03 6.18e+00
  bond pdb=" CA  SER C  62 "
       pdb=" C   SER C  62 "
    ideal  model  delta    sigma   weight residual
    1.524  1.476  0.048 2.25e-02 1.98e+03 4.49e+00
  bond pdb=" CA  THR A 747 "
       pdb=" C   THR A 747 "
    ideal  model  delta    sigma   weight residual
    1.522  1.487  0.035 1.72e-02 3.38e+03 4.12e+00
  ... (remaining 15355 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.01: 20049
        2.01 -     4.01: 700
        4.01 -     6.02: 96
        6.02 -     8.02: 17
        8.02 -    10.03: 4
  Bond angle restraints: 20866
  Sorted by residual:
  angle pdb=" C   PRO A 159 "
        pdb=" N   ARG A 160 "
        pdb=" CA  ARG A 160 "
      ideal   model   delta    sigma   weight residual
     121.54  129.63   -8.09 1.91e+00 2.74e-01 1.79e+01
  angle pdb=" N   HIS D 102 "
        pdb=" CA  HIS D 102 "
        pdb=" C   HIS D 102 "
      ideal   model   delta    sigma   weight residual
     108.13  111.71   -3.58 9.00e-01 1.23e+00 1.58e+01
  angle pdb=" C   THR C  61 "
        pdb=" N   SER C  62 "
        pdb=" CA  SER C  62 "
      ideal   model   delta    sigma   weight residual
     122.55  114.86    7.69 2.03e+00 2.43e-01 1.43e+01
  angle pdb=" C   TYR D 185 "
        pdb=" N   THR D 186 "
        pdb=" CA  THR D 186 "
      ideal   model   delta    sigma   weight residual
     120.72  114.54    6.18 1.67e+00 3.59e-01 1.37e+01
  angle pdb=" N   ALA A 730 "
        pdb=" CA  ALA A 730 "
        pdb=" C   ALA A 730 "
      ideal   model   delta    sigma   weight residual
     113.19  108.84    4.35 1.19e+00 7.06e-01 1.33e+01
  ... (remaining 20861 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.91: 7983
       17.91 -    35.83: 867
       35.83 -    53.74: 131
       53.74 -    71.66: 27
       71.66 -    89.57: 17
  Dihedral angle restraints: 9025
    sinusoidal: 3491
      harmonic: 5534
  Sorted by residual:
  dihedral pdb=" CB  CYS A 806 "
           pdb=" SG  CYS A 806 "
           pdb=" SG  CYS F1041 "
           pdb=" CB  CYS F1041 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -154.03   68.03     1      1.00e+01 1.00e-02 6.01e+01
  dihedral pdb=" CA  ARG A  91 "
           pdb=" C   ARG A  91 "
           pdb=" N   PRO A  92 "
           pdb=" CA  PRO A  92 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  141.65   38.35     0      5.00e+00 4.00e-02 5.88e+01
  dihedral pdb=" CA  THR A 434 "
           pdb=" C   THR A 434 "
           pdb=" N   GLU A 435 "
           pdb=" CA  GLU A 435 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  143.20   36.80     0      5.00e+00 4.00e-02 5.42e+01
  ... (remaining 9022 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.037: 1322
       0.037 -    0.073: 612
       0.073 -    0.110: 244
       0.110 -    0.146: 68
       0.146 -    0.183: 15
  Chirality restraints: 2261
  Sorted by residual:
  chirality pdb=" CA  VAL A 593 "
            pdb=" N   VAL A 593 "
            pdb=" C   VAL A 593 "
            pdb=" CB  VAL A 593 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.62   -0.18 2.00e-01 2.50e+01 8.34e-01
  chirality pdb=" CA  VAL A 744 "
            pdb=" N   VAL A 744 "
            pdb=" C   VAL A 744 "
            pdb=" CB  VAL A 744 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.62   -0.18 2.00e-01 2.50e+01 8.20e-01
  chirality pdb=" CA  ILE F1045 "
            pdb=" N   ILE F1045 "
            pdb=" C   ILE F1045 "
            pdb=" CB  ILE F1045 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.60   -0.17 2.00e-01 2.50e+01 7.27e-01
  ... (remaining 2258 not shown)

  Planarity restraints: 2753
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ARG A  91 "    0.058 5.00e-02 4.00e+02   8.87e-02 1.26e+01
        pdb=" N   PRO A  92 "   -0.153 5.00e-02 4.00e+02
        pdb=" CA  PRO A  92 "    0.046 5.00e-02 4.00e+02
        pdb=" CD  PRO A  92 "    0.049 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLU F1168 "   -0.043 5.00e-02 4.00e+02   6.58e-02 6.92e+00
        pdb=" N   PRO F1169 "    0.114 5.00e-02 4.00e+02
        pdb=" CA  PRO F1169 "   -0.034 5.00e-02 4.00e+02
        pdb=" CD  PRO F1169 "   -0.036 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLN A 789 "    0.038 5.00e-02 4.00e+02   5.79e-02 5.37e+00
        pdb=" N   PRO A 790 "   -0.100 5.00e-02 4.00e+02
        pdb=" CA  PRO A 790 "    0.030 5.00e-02 4.00e+02
        pdb=" CD  PRO A 790 "    0.032 5.00e-02 4.00e+02
  ... (remaining 2750 not shown)

  Histogram of nonbonded interaction distances:
        2.03 -     2.61: 328
        2.61 -     3.18: 14620
        3.18 -     3.75: 22171
        3.75 -     4.33: 30110
        4.33 -     4.90: 48518
  Nonbonded interactions: 115747
  Sorted by model distance:
  nonbonded pdb=" OE2 GLU A 521 "
            pdb=" OH  TYR E  28 "
     model   vdw
     2.032 3.040
  nonbonded pdb=" O   ASN E  33 "
            pdb=" NE2 GLN E  34 "
     model   vdw
     2.105 3.120
  nonbonded pdb=" OG  SER F1051 "
            pdb=" O   ASN F1287 "
     model   vdw
     2.125 3.040
  nonbonded pdb=" O   VAL F1095 "
            pdb=" OG1 THR F1135 "
     model   vdw
     2.134 3.040
  nonbonded pdb=" OH  TYR A 674 "
            pdb=" OD2 ASP A 704 "
     model   vdw
     2.145 3.040
  ... (remaining 115742 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:             1.840
  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:             0.050
  Extract box with map and model:          1.010
  Check model and map are aligned:         0.170
  Set scattering table:                    0.220
  Process input model:                     37.660
  Find NCS groups from input model:        0.140
  Set up NCS constraints:                  0.060
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:2.730
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   43.890
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8108
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.062  15361  Z= 0.347
  Angle     :  0.876  10.030  20868  Z= 0.493
  Chirality :  0.050   0.183   2261
  Planarity :  0.005   0.089   2753
  Dihedral  : 15.123  89.569   5514
  Min Nonbonded Distance : 2.032

Molprobity Statistics.
  All-atom Clashscore : 21.51
  Ramachandran Plot:
    Outliers :  0.21 %
    Allowed  : 17.60 %
    Favored  : 82.19 %
  Rotamer:
    Outliers :  0.32 %
    Allowed  : 10.53 %
    Favored  : 89.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.22 %
    Twisted Proline : 1.45 %
    Twisted General : 0.16 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -5.91 (0.14), residues: 1923
  helix: -2.12 (0.22), residues: 364
  sheet: -4.02 (0.17), residues: 565
  loop : -4.68 (0.13), residues: 994

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP A 449 
 HIS   0.007   0.001   HIS B  64 
 PHE   0.026   0.002   PHE B 289 
 TYR   0.035   0.002   TYR A 432 
 ARG   0.012   0.001   ARG E  78 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.21329 (  403)
  hydrogen bonds       : angle       8.58147 ( 1080)
  SS BOND              : bond        0.00033 (    1)
  SS BOND              : angle       4.39441 (    2)
  covalent geometry    : bond        0.00745 (15360)
  covalent geometry    : angle       0.87515 (20866)

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

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

  3846 Ramachandran restraints generated.
    1923 Oldfield, 0 Emsley, 1923 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3846 Ramachandran restraints generated.
    1923 Oldfield, 0 Emsley, 1923 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  214 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 209
  time to evaluate  : 1.614 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  465 TYR cc_start: 0.7448 (m-10) cc_final: 0.7215 (m-10)
REVERT: A  545 MET cc_start: 0.8532 (mtt) cc_final: 0.8031 (mtt)
REVERT: A  677 HIS cc_start: 0.6398 (t-170) cc_final: 0.5945 (t70)
REVERT: A  768 MET cc_start: 0.8504 (mtm) cc_final: 0.8292 (mtp)
REVERT: B  278 MET cc_start: 0.7788 (mmt) cc_final: 0.7474 (mmt)
REVERT: B  306 MET cc_start: 0.8158 (ppp) cc_final: 0.7334 (ppp)
REVERT: C   56 MET cc_start: 0.8076 (mpp) cc_final: 0.7627 (mpp)
REVERT: C   81 ASP cc_start: 0.8571 (p0) cc_final: 0.8319 (p0)
REVERT: D  205 TYR cc_start: 0.9087 (OUTLIER) cc_final: 0.8538 (m-80)
REVERT: E   53 GLN cc_start: 0.8663 (tp40) cc_final: 0.8399 (tp40)
REVERT: F 1124 LYS cc_start: 0.8944 (ttmm) cc_final: 0.8715 (ttmm)
REVERT: F 1127 HIS cc_start: 0.8773 (p90) cc_final: 0.8268 (p90)
REVERT: F 1166 TRP cc_start: 0.8752 (m-10) cc_final: 0.8465 (m100)
REVERT: F 1230 GLN cc_start: 0.8616 (tt0) cc_final: 0.8362 (tt0)
REVERT: F 1256 SER cc_start: 0.7853 (p) cc_final: 0.7427 (p)
  outliers start: 5
  outliers final: 1
  residues processed: 212
  average time/residue: 0.2815
  time to fit residues: 87.6681
Evaluate side-chains
  167 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 165
  time to evaluate  : 1.713 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  452 THR
Chi-restraints excluded: chain D residue  205 TYR
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 191
   random chunks:
   chunk 161 optimal weight:   20.0000
   chunk 144 optimal weight:    1.9990
   chunk 80 optimal weight:    4.9990
   chunk 49 optimal weight:    1.9990
   chunk 97 optimal weight:   10.0000
   chunk 77 optimal weight:    1.9990
   chunk 149 optimal weight:    0.8980
   chunk 57 optimal weight:    0.6980
   chunk 91 optimal weight:    2.9990
   chunk 111 optimal weight:    2.9990
   chunk 173 optimal weight:    8.9990
   overall best weight:    1.5186

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

Flipped N/Q/H residues before XYZ refinement:
** A 677 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 287 ASN
** B 347 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  72 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4166 r_free = 0.4166 target = 0.154244 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3671 r_free = 0.3671 target = 0.117486 restraints weight = 31278.766|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3590 r_free = 0.3590 target = 0.114468 restraints weight = 24569.275|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3604 r_free = 0.3604 target = 0.115726 restraints weight = 20433.437|
|-----------------------------------------------------------------------------|
r_work (final): 0.3584
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3584
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3584 r_free = 0.3584    target_work(ls_wunit_k1) = 0.116         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3584 r_free = 0.3584    target_work(ls_wunit_k1) = 0.116         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3584
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7845
moved from start:          0.1534

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045  15361  Z= 0.164
  Angle     :  0.720   9.610  20868  Z= 0.381
  Chirality :  0.047   0.169   2261
  Planarity :  0.005   0.088   2753
  Dihedral  :  6.325  36.304   2122
  Min Nonbonded Distance : 2.498

Molprobity Statistics.
  All-atom Clashscore : 12.95
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  : 12.19 %
    Favored  : 87.66 %
  Rotamer:
    Outliers :  1.89 %
    Allowed  : 15.26 %
    Favored  : 82.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.22 %
    Twisted Proline : 1.45 %
    Twisted General : 0.11 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.75 (0.16), residues: 1923
  helix: -0.41 (0.25), residues: 367
  sheet: -3.47 (0.19), residues: 559
  loop : -4.17 (0.15), residues: 997

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.001   TRP A 546 
 HIS   0.004   0.001   HIS B 347 
 PHE   0.031   0.002   PHE F1082 
 TYR   0.037   0.002   TYR A 432 
 ARG   0.007   0.001   ARG F1205 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04996 (  403)
  hydrogen bonds       : angle       6.15237 ( 1080)
  SS BOND              : bond        0.00057 (    1)
  SS BOND              : angle       6.00371 (    2)
  covalent geometry    : bond        0.00352 (15360)
  covalent geometry    : angle       0.71808 (20866)

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

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

  3846 Ramachandran restraints generated.
    1923 Oldfield, 0 Emsley, 1923 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3846 Ramachandran restraints generated.
    1923 Oldfield, 0 Emsley, 1923 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  227 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 197
  time to evaluate  : 1.734 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  465 TYR cc_start: 0.7332 (m-10) cc_final: 0.7081 (m-10)
REVERT: A  545 MET cc_start: 0.8174 (mtt) cc_final: 0.7744 (mtt)
REVERT: A  677 HIS cc_start: 0.6343 (t-170) cc_final: 0.6092 (t70)
REVERT: A  738 PHE cc_start: 0.9125 (p90) cc_final: 0.8774 (p90)
REVERT: B  174 LEU cc_start: 0.9243 (mm) cc_final: 0.9028 (mp)
REVERT: B  221 MET cc_start: 0.7607 (ttm) cc_final: 0.7354 (mtp)
REVERT: B  263 TYR cc_start: 0.5666 (t80) cc_final: 0.5106 (t80)
REVERT: C   49 GLU cc_start: 0.8454 (tm-30) cc_final: 0.8252 (tm-30)
REVERT: C   56 MET cc_start: 0.7920 (mpp) cc_final: 0.7530 (mpp)
REVERT: C   83 ARG cc_start: 0.7523 (ptt-90) cc_final: 0.7094 (ttp-110)
REVERT: D   56 GLU cc_start: 0.8554 (tp30) cc_final: 0.8343 (tp30)
REVERT: D  205 TYR cc_start: 0.8801 (OUTLIER) cc_final: 0.8312 (m-80)
REVERT: D  222 TYR cc_start: 0.8966 (OUTLIER) cc_final: 0.8734 (m-80)
REVERT: E   53 GLN cc_start: 0.8512 (tp40) cc_final: 0.8219 (tp40)
REVERT: F 1034 ASP cc_start: 0.7377 (t0) cc_final: 0.7124 (t0)
REVERT: F 1046 MET cc_start: 0.7618 (OUTLIER) cc_final: 0.7178 (ttp)
REVERT: F 1112 MET cc_start: 0.7597 (ptp) cc_final: 0.7306 (ptp)
REVERT: F 1212 LYS cc_start: 0.7144 (mttm) cc_final: 0.6900 (ptmm)
  outliers start: 30
  outliers final: 13
  residues processed: 216
  average time/residue: 0.2617
  time to fit residues: 85.3417
Evaluate side-chains
  192 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 176
  time to evaluate  : 1.673 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  139 ASP
Chi-restraints excluded: chain A residue  163 VAL
Chi-restraints excluded: chain A residue  245 VAL
Chi-restraints excluded: chain A residue  452 THR
Chi-restraints excluded: chain B residue  249 THR
Chi-restraints excluded: chain B residue  298 LEU
Chi-restraints excluded: chain B residue  300 ASP
Chi-restraints excluded: chain D residue   49 ARG
Chi-restraints excluded: chain D residue   72 GLN
Chi-restraints excluded: chain D residue  205 TYR
Chi-restraints excluded: chain D residue  222 TYR
Chi-restraints excluded: chain E residue   43 VAL
Chi-restraints excluded: chain E residue  111 SER
Chi-restraints excluded: chain F residue 1046 MET
Chi-restraints excluded: chain F residue 1107 LEU
Chi-restraints excluded: chain F residue 1268 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 191
   random chunks:
   chunk 86 optimal weight:    9.9990
   chunk 97 optimal weight:   10.0000
   chunk 146 optimal weight:    0.7980
   chunk 17 optimal weight:    0.3980
   chunk 22 optimal weight:    3.9990
   chunk 20 optimal weight:    3.9990
   chunk 134 optimal weight:    9.9990
   chunk 77 optimal weight:    0.0570
   chunk 154 optimal weight:    4.9990
   chunk 23 optimal weight:    2.9990
   chunk 157 optimal weight:    0.7980
   overall best weight:    1.0100

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

Flipped N/Q/H residues before XYZ refinement:
** A 244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 677 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 347 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 139 GLN
** C 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F1295 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4173 r_free = 0.4173 target = 0.155115 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3672 r_free = 0.3672 target = 0.117447 restraints weight = 31016.142|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3603 r_free = 0.3603 target = 0.114780 restraints weight = 20927.031|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3615 r_free = 0.3615 target = 0.116126 restraints weight = 18738.663|
|-----------------------------------------------------------------------------|
r_work (final): 0.3627
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3627
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3627 r_free = 0.3627    target_work(ls_wunit_k1) = 0.115         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3627 r_free = 0.3627    target_work(ls_wunit_k1) = 0.115         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3627
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7851
moved from start:          0.2062

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  15361  Z= 0.132
  Angle     :  0.662   9.283  20868  Z= 0.348
  Chirality :  0.045   0.166   2261
  Planarity :  0.004   0.084   2753
  Dihedral  :  5.865  36.561   2122
  Min Nonbonded Distance : 2.511

Molprobity Statistics.
  All-atom Clashscore : 11.32
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  : 11.15 %
    Favored  : 88.70 %
  Rotamer:
    Outliers :  2.84 %
    Allowed  : 17.78 %
    Favored  : 79.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.22 %
    Twisted Proline : 1.45 %
    Twisted General : 0.11 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.10 (0.17), residues: 1923
  helix:  0.36 (0.26), residues: 366
  sheet: -3.08 (0.20), residues: 550
  loop : -3.83 (0.15), residues: 1007

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP A 546 
 HIS   0.004   0.001   HIS D 102 
 PHE   0.012   0.001   PHE D 144 
 TYR   0.037   0.001   TYR A 432 
 ARG   0.006   0.000   ARG A 233 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04532 (  403)
  hydrogen bonds       : angle       5.62937 ( 1080)
  SS BOND              : bond        0.00076 (    1)
  SS BOND              : angle       5.05354 (    2)
  covalent geometry    : bond        0.00284 (15360)
  covalent geometry    : angle       0.65997 (20866)

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

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

  3846 Ramachandran restraints generated.
    1923 Oldfield, 0 Emsley, 1923 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3846 Ramachandran restraints generated.
    1923 Oldfield, 0 Emsley, 1923 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  237 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 192
  time to evaluate  : 2.417 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  465 TYR cc_start: 0.7358 (m-10) cc_final: 0.7106 (m-10)
REVERT: A  614 ASP cc_start: 0.8427 (t70) cc_final: 0.8184 (t0)
REVERT: A  677 HIS cc_start: 0.6205 (t-170) cc_final: 0.5971 (t70)
REVERT: A  769 SER cc_start: 0.9416 (t) cc_final: 0.8878 (m)
REVERT: B  174 LEU cc_start: 0.9178 (mm) cc_final: 0.8973 (mp)
REVERT: B  263 TYR cc_start: 0.5708 (t80) cc_final: 0.5275 (t80)
REVERT: B  278 MET cc_start: 0.8680 (mtp) cc_final: 0.8370 (mtm)
REVERT: B  306 MET cc_start: 0.8518 (ppp) cc_final: 0.7534 (ppp)
REVERT: C   49 GLU cc_start: 0.8372 (tm-30) cc_final: 0.8135 (tm-30)
REVERT: C   56 MET cc_start: 0.7982 (mpp) cc_final: 0.7673 (mpp)
REVERT: C   81 ASP cc_start: 0.8142 (p0) cc_final: 0.7919 (p0)
REVERT: C   83 ARG cc_start: 0.7507 (ptt-90) cc_final: 0.7069 (ttp-110)
REVERT: D   56 GLU cc_start: 0.8476 (tp30) cc_final: 0.8225 (tp30)
REVERT: E   53 GLN cc_start: 0.8417 (tp40) cc_final: 0.8169 (tp40)
REVERT: F 1034 ASP cc_start: 0.7238 (t0) cc_final: 0.6988 (t0)
REVERT: F 1112 MET cc_start: 0.7600 (ptp) cc_final: 0.7335 (ptp)
  outliers start: 45
  outliers final: 29
  residues processed: 221
  average time/residue: 0.2486
  time to fit residues: 86.7224
Evaluate side-chains
  204 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 175
  time to evaluate  : 1.467 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  109 MET
Chi-restraints excluded: chain A residue  139 ASP
Chi-restraints excluded: chain A residue  163 VAL
Chi-restraints excluded: chain A residue  230 TYR
Chi-restraints excluded: chain A residue  245 VAL
Chi-restraints excluded: chain A residue  405 VAL
Chi-restraints excluded: chain A residue  452 THR
Chi-restraints excluded: chain A residue  458 ILE
Chi-restraints excluded: chain A residue  629 VAL
Chi-restraints excluded: chain A residue  720 THR
Chi-restraints excluded: chain B residue  157 VAL
Chi-restraints excluded: chain B residue  239 THR
Chi-restraints excluded: chain B residue  249 THR
Chi-restraints excluded: chain B residue  270 LEU
Chi-restraints excluded: chain B residue  298 LEU
Chi-restraints excluded: chain B residue  300 ASP
Chi-restraints excluded: chain B residue  387 VAL
Chi-restraints excluded: chain C residue  165 VAL
Chi-restraints excluded: chain D residue  181 VAL
Chi-restraints excluded: chain D residue  186 THR
Chi-restraints excluded: chain E residue   31 ASP
Chi-restraints excluded: chain E residue   51 THR
Chi-restraints excluded: chain E residue   94 THR
Chi-restraints excluded: chain E residue  111 SER
Chi-restraints excluded: chain F residue 1107 LEU
Chi-restraints excluded: chain F residue 1174 VAL
Chi-restraints excluded: chain F residue 1256 SER
Chi-restraints excluded: chain F residue 1262 VAL
Chi-restraints excluded: chain F residue 1268 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 191
   random chunks:
   chunk 149 optimal weight:    1.9990
   chunk 100 optimal weight:    9.9990
   chunk 182 optimal weight:    8.9990
   chunk 86 optimal weight:    8.9990
   chunk 144 optimal weight:    5.9990
   chunk 87 optimal weight:   10.0000
   chunk 101 optimal weight:    2.9990
   chunk 52 optimal weight:    0.8980
   chunk 65 optimal weight:    0.6980
   chunk 46 optimal weight:    6.9990
   chunk 139 optimal weight:    0.7980
   overall best weight:    1.4784

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

Flipped N/Q/H residues before XYZ refinement:
** A 677 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 347 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  87 GLN
** C 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  54 GLN
** E  34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4158 r_free = 0.4158 target = 0.154261 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3649 r_free = 0.3649 target = 0.116068 restraints weight = 30849.204|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3569 r_free = 0.3569 target = 0.112927 restraints weight = 20477.166|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3581 r_free = 0.3581 target = 0.114129 restraints weight = 18998.059|
|-----------------------------------------------------------------------------|
r_work (final): 0.3607
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3608
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3608 r_free = 0.3608    target_work(ls_wunit_k1) = 0.114         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3608 r_free = 0.3608    target_work(ls_wunit_k1) = 0.114         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3608
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7882
moved from start:          0.2385

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045  15361  Z= 0.145
  Angle     :  0.646   8.979  20868  Z= 0.339
  Chirality :  0.045   0.242   2261
  Planarity :  0.004   0.083   2753
  Dihedral  :  5.630  36.797   2120
  Min Nonbonded Distance : 2.553

Molprobity Statistics.
  All-atom Clashscore : 11.08
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  : 11.20 %
    Favored  : 88.65 %
  Rotamer:
    Outliers :  3.34 %
    Allowed  : 18.41 %
    Favored  : 78.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.22 %
    Twisted Proline : 1.45 %
    Twisted General : 0.11 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.66 (0.17), residues: 1923
  helix:  0.67 (0.27), residues: 368
  sheet: -2.79 (0.21), residues: 520
  loop : -3.55 (0.16), residues: 1035

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP A 546 
 HIS   0.003   0.001   HIS A 533 
 PHE   0.012   0.001   PHE C  99 
 TYR   0.037   0.001   TYR A 432 
 ARG   0.005   0.000   ARG A 233 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04347 (  403)
  hydrogen bonds       : angle       5.32505 ( 1080)
  SS BOND              : bond        0.00130 (    1)
  SS BOND              : angle       4.48563 (    2)
  covalent geometry    : bond        0.00319 (15360)
  covalent geometry    : angle       0.64417 (20866)

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

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

  3846 Ramachandran restraints generated.
    1923 Oldfield, 0 Emsley, 1923 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3846 Ramachandran restraints generated.
    1923 Oldfield, 0 Emsley, 1923 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  232 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 53
    poor density    : 179
  time to evaluate  : 1.750 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  369 MET cc_start: 0.8769 (mmp) cc_final: 0.8231 (mmm)
REVERT: A  432 TYR cc_start: 0.5009 (t80) cc_final: 0.4693 (t80)
REVERT: A  465 TYR cc_start: 0.7232 (m-10) cc_final: 0.6923 (m-10)
REVERT: A  769 SER cc_start: 0.9430 (t) cc_final: 0.8872 (m)
REVERT: B  263 TYR cc_start: 0.5779 (t80) cc_final: 0.5402 (t80)
REVERT: B  278 MET cc_start: 0.8769 (mtp) cc_final: 0.8493 (mtm)
REVERT: C   49 GLU cc_start: 0.8434 (tm-30) cc_final: 0.8212 (tm-30)
REVERT: C   56 MET cc_start: 0.8088 (mpp) cc_final: 0.7746 (mpp)
REVERT: C   80 LEU cc_start: 0.8922 (tp) cc_final: 0.8537 (tt)
REVERT: C   83 ARG cc_start: 0.7485 (ptt-90) cc_final: 0.7125 (ttp-110)
REVERT: D   26 GLU cc_start: 0.7184 (tp30) cc_final: 0.6594 (tt0)
REVERT: D   54 GLN cc_start: 0.8179 (mm-40) cc_final: 0.7945 (tp40)
REVERT: D   56 GLU cc_start: 0.8574 (tp30) cc_final: 0.8147 (tp30)
REVERT: E   53 GLN cc_start: 0.8456 (tp40) cc_final: 0.8229 (tp40)
REVERT: F 1034 ASP cc_start: 0.7284 (t0) cc_final: 0.7066 (t0)
REVERT: F 1112 MET cc_start: 0.7617 (ptp) cc_final: 0.7394 (ptp)
  outliers start: 53
  outliers final: 36
  residues processed: 218
  average time/residue: 0.2331
  time to fit residues: 79.2497
Evaluate side-chains
  206 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 170
  time to evaluate  : 1.605 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  109 MET
Chi-restraints excluded: chain A residue  139 ASP
Chi-restraints excluded: chain A residue  163 VAL
Chi-restraints excluded: chain A residue  230 TYR
Chi-restraints excluded: chain A residue  245 VAL
Chi-restraints excluded: chain A residue  405 VAL
Chi-restraints excluded: chain A residue  438 VAL
Chi-restraints excluded: chain A residue  444 VAL
Chi-restraints excluded: chain A residue  452 THR
Chi-restraints excluded: chain A residue  458 ILE
Chi-restraints excluded: chain A residue  473 VAL
Chi-restraints excluded: chain A residue  629 VAL
Chi-restraints excluded: chain A residue  633 THR
Chi-restraints excluded: chain A residue  720 THR
Chi-restraints excluded: chain A residue  778 SER
Chi-restraints excluded: chain B residue  157 VAL
Chi-restraints excluded: chain B residue  209 VAL
Chi-restraints excluded: chain B residue  239 THR
Chi-restraints excluded: chain B residue  249 THR
Chi-restraints excluded: chain B residue  270 LEU
Chi-restraints excluded: chain B residue  300 ASP
Chi-restraints excluded: chain C residue  108 VAL
Chi-restraints excluded: chain C residue  165 VAL
Chi-restraints excluded: chain D residue   67 TYR
Chi-restraints excluded: chain D residue  181 VAL
Chi-restraints excluded: chain D residue  186 THR
Chi-restraints excluded: chain E residue   31 ASP
Chi-restraints excluded: chain E residue   46 ILE
Chi-restraints excluded: chain E residue   51 THR
Chi-restraints excluded: chain E residue   94 THR
Chi-restraints excluded: chain E residue  111 SER
Chi-restraints excluded: chain F residue 1107 LEU
Chi-restraints excluded: chain F residue 1146 THR
Chi-restraints excluded: chain F residue 1174 VAL
Chi-restraints excluded: chain F residue 1262 VAL
Chi-restraints excluded: chain F residue 1268 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 191
   random chunks:
   chunk 55 optimal weight:    1.9990
   chunk 95 optimal weight:    0.9980
   chunk 116 optimal weight:    0.0040
   chunk 115 optimal weight:    0.0070
   chunk 185 optimal weight:   10.0000
   chunk 178 optimal weight:   10.0000
   chunk 68 optimal weight:    0.0170
   chunk 96 optimal weight:    0.9980
   chunk 177 optimal weight:    8.9990
   chunk 49 optimal weight:    0.7980
   chunk 8 optimal weight:    7.9990
   overall best weight:    0.3648

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

Flipped N/Q/H residues before XYZ refinement:
** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 538 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 693 GLN
B 347 HIS
** B 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  34 GLN
E 113 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4181 r_free = 0.4181 target = 0.158796 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3547 r_free = 0.3547 target = 0.111552 restraints weight = 31270.306|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3583 r_free = 0.3583 target = 0.112870 restraints weight = 19924.032|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3585 r_free = 0.3585 target = 0.113746 restraints weight = 13823.106|
|-----------------------------------------------------------------------------|
r_work (final): 0.3616
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3615
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3615 r_free = 0.3615    target_work(ls_wunit_k1) = 0.113         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3615 r_free = 0.3615    target_work(ls_wunit_k1) = 0.113         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3615
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7857
moved from start:          0.2951

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.044  15361  Z= 0.108
  Angle     :  0.614   9.010  20868  Z= 0.320
  Chirality :  0.044   0.241   2261
  Planarity :  0.004   0.081   2753
  Dihedral  :  5.269  36.894   2120
  Min Nonbonded Distance : 2.494

Molprobity Statistics.
  All-atom Clashscore : 9.62
  Ramachandran Plot:
    Outliers :  0.05 %
    Allowed  :  8.96 %
    Favored  : 90.99 %
  Rotamer:
    Outliers :  2.90 %
    Allowed  : 20.05 %
    Favored  : 77.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.22 %
    Twisted Proline : 1.45 %
    Twisted General : 0.11 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.26 (0.18), residues: 1923
  helix:  0.96 (0.27), residues: 362
  sheet: -2.45 (0.21), residues: 523
  loop : -3.30 (0.16), residues: 1038

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP A 546 
 HIS   0.004   0.001   HIS B 347 
 PHE   0.016   0.001   PHE A 738 
 TYR   0.037   0.001   TYR A 432 
 ARG   0.003   0.000   ARG F1205 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03790 (  403)
  hydrogen bonds       : angle       4.98252 ( 1080)
  SS BOND              : bond        0.01056 (    1)
  SS BOND              : angle       3.92610 (    2)
  covalent geometry    : bond        0.00226 (15360)
  covalent geometry    : angle       0.61263 (20866)

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

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

  3846 Ramachandran restraints generated.
    1923 Oldfield, 0 Emsley, 1923 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3846 Ramachandran restraints generated.
    1923 Oldfield, 0 Emsley, 1923 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  245 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 199
  time to evaluate  : 1.625 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  369 MET cc_start: 0.8843 (mmp) cc_final: 0.8263 (mmm)
REVERT: A  422 ASN cc_start: 0.8479 (t0) cc_final: 0.8194 (t0)
REVERT: A  449 TRP cc_start: 0.8640 (t60) cc_final: 0.8419 (t60)
REVERT: A  465 TYR cc_start: 0.7212 (m-10) cc_final: 0.6902 (m-10)
REVERT: A  524 SER cc_start: 0.9186 (OUTLIER) cc_final: 0.8727 (p)
REVERT: A  545 MET cc_start: 0.8134 (mtm) cc_final: 0.5959 (mtm)
REVERT: A  619 VAL cc_start: 0.9333 (t) cc_final: 0.8906 (m)
REVERT: A  769 SER cc_start: 0.9291 (t) cc_final: 0.8892 (m)
REVERT: B   80 LEU cc_start: 0.8486 (OUTLIER) cc_final: 0.8102 (pt)
REVERT: B  263 TYR cc_start: 0.5813 (t80) cc_final: 0.5373 (t80)
REVERT: B  278 MET cc_start: 0.8833 (mtp) cc_final: 0.8389 (mtm)
REVERT: B  298 LEU cc_start: 0.7330 (OUTLIER) cc_final: 0.7040 (pp)
REVERT: B  306 MET cc_start: 0.8195 (ppp) cc_final: 0.7925 (ppp)
REVERT: B  356 PHE cc_start: 0.8645 (m-10) cc_final: 0.8283 (m-10)
REVERT: C   49 GLU cc_start: 0.8362 (tm-30) cc_final: 0.8120 (tm-30)
REVERT: C   56 MET cc_start: 0.8195 (mpp) cc_final: 0.7697 (mpp)
REVERT: C   80 LEU cc_start: 0.9104 (tp) cc_final: 0.8786 (tt)
REVERT: C   83 ARG cc_start: 0.7435 (ptt-90) cc_final: 0.7088 (ttp-110)
REVERT: D   54 GLN cc_start: 0.8489 (mm-40) cc_final: 0.8168 (tp40)
REVERT: D   56 GLU cc_start: 0.8721 (tp30) cc_final: 0.8484 (tp30)
REVERT: E   53 GLN cc_start: 0.8590 (tp40) cc_final: 0.8319 (tp40)
REVERT: F 1034 ASP cc_start: 0.7402 (t0) cc_final: 0.7169 (t0)
REVERT: F 1112 MET cc_start: 0.7747 (ptp) cc_final: 0.7508 (ptp)
  outliers start: 46
  outliers final: 30
  residues processed: 235
  average time/residue: 0.2215
  time to fit residues: 81.8025
Evaluate side-chains
  206 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 173
  time to evaluate  : 1.601 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  109 MET
Chi-restraints excluded: chain A residue  139 ASP
Chi-restraints excluded: chain A residue  163 VAL
Chi-restraints excluded: chain A residue  230 TYR
Chi-restraints excluded: chain A residue  245 VAL
Chi-restraints excluded: chain A residue  405 VAL
Chi-restraints excluded: chain A residue  438 VAL
Chi-restraints excluded: chain A residue  452 THR
Chi-restraints excluded: chain A residue  524 SER
Chi-restraints excluded: chain A residue  720 THR
Chi-restraints excluded: chain A residue  778 SER
Chi-restraints excluded: chain B residue   63 LEU
Chi-restraints excluded: chain B residue   80 LEU
Chi-restraints excluded: chain B residue  157 VAL
Chi-restraints excluded: chain B residue  239 THR
Chi-restraints excluded: chain B residue  249 THR
Chi-restraints excluded: chain B residue  270 LEU
Chi-restraints excluded: chain B residue  298 LEU
Chi-restraints excluded: chain B residue  387 VAL
Chi-restraints excluded: chain C residue  108 VAL
Chi-restraints excluded: chain C residue  165 VAL
Chi-restraints excluded: chain D residue   67 TYR
Chi-restraints excluded: chain D residue   76 ILE
Chi-restraints excluded: chain D residue  186 THR
Chi-restraints excluded: chain E residue   31 ASP
Chi-restraints excluded: chain E residue   94 THR
Chi-restraints excluded: chain E residue  111 SER
Chi-restraints excluded: chain F residue 1107 LEU
Chi-restraints excluded: chain F residue 1146 THR
Chi-restraints excluded: chain F residue 1174 VAL
Chi-restraints excluded: chain F residue 1256 SER
Chi-restraints excluded: chain F residue 1262 VAL
Chi-restraints excluded: chain F residue 1268 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 191
   random chunks:
   chunk 20 optimal weight:    2.9990
   chunk 135 optimal weight:    1.9990
   chunk 52 optimal weight:    2.9990
   chunk 38 optimal weight:    0.2980
   chunk 163 optimal weight:    2.9990
   chunk 141 optimal weight:    0.9980
   chunk 18 optimal weight:    4.9990
   chunk 67 optimal weight:    6.9990
   chunk 24 optimal weight:   10.0000
   chunk 45 optimal weight:    0.0370
   chunk 76 optimal weight:    4.9990
   overall best weight:    1.2662

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

Flipped N/Q/H residues before XYZ refinement:
** B 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 350 ASN
** B 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
F1026 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4193 r_free = 0.4193 target = 0.159556 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3673 r_free = 0.3673 target = 0.119862 restraints weight = 31028.642|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3604 r_free = 0.3604 target = 0.117194 restraints weight = 18936.355|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3607 r_free = 0.3607 target = 0.118039 restraints weight = 22362.280|
|-----------------------------------------------------------------------------|
r_work (final): 0.3633
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3631
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3631 r_free = 0.3631    target_work(ls_wunit_k1) = 0.115         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3631 r_free = 0.3631    target_work(ls_wunit_k1) = 0.115         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3631
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7802
moved from start:          0.3003

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046  15361  Z= 0.129
  Angle     :  0.628  14.138  20868  Z= 0.323
  Chirality :  0.044   0.175   2261
  Planarity :  0.004   0.082   2753
  Dihedral  :  5.246  36.309   2120
  Min Nonbonded Distance : 2.439

Molprobity Statistics.
  All-atom Clashscore : 10.77
  Ramachandran Plot:
    Outliers :  0.05 %
    Allowed  : 10.26 %
    Favored  : 89.69 %
  Rotamer:
    Outliers :  3.09 %
    Allowed  : 20.49 %
    Favored  : 76.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.22 %
    Twisted Proline : 1.45 %
    Twisted General : 0.11 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.07 (0.18), residues: 1923
  helix:  1.06 (0.27), residues: 363
  sheet: -2.33 (0.21), residues: 541
  loop : -3.15 (0.17), residues: 1019

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.001   TRP A 546 
 HIS   0.003   0.001   HIS A 533 
 PHE   0.014   0.001   PHE B  42 
 TYR   0.037   0.001   TYR A 432 
 ARG   0.004   0.000   ARG A 233 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03971 (  403)
  hydrogen bonds       : angle       4.94070 ( 1080)
  SS BOND              : bond        0.00054 (    1)
  SS BOND              : angle       4.02843 (    2)
  covalent geometry    : bond        0.00283 (15360)
  covalent geometry    : angle       0.62661 (20866)

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

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

  3846 Ramachandran restraints generated.
    1923 Oldfield, 0 Emsley, 1923 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3846 Ramachandran restraints generated.
    1923 Oldfield, 0 Emsley, 1923 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  236 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 187
  time to evaluate  : 1.596 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  251 LYS cc_start: 0.8195 (mtpt) cc_final: 0.7976 (mmtm)
REVERT: A  422 ASN cc_start: 0.8499 (t0) cc_final: 0.8202 (t0)
REVERT: A  449 TRP cc_start: 0.8703 (t60) cc_final: 0.8469 (t60)
REVERT: A  465 TYR cc_start: 0.7233 (m-10) cc_final: 0.6958 (m-10)
REVERT: A  769 SER cc_start: 0.9315 (t) cc_final: 0.8850 (m)
REVERT: B  221 MET cc_start: 0.8184 (mpp) cc_final: 0.7881 (mpp)
REVERT: B  263 TYR cc_start: 0.5916 (t80) cc_final: 0.5444 (t80)
REVERT: B  278 MET cc_start: 0.8840 (mtp) cc_final: 0.8429 (mtm)
REVERT: B  306 MET cc_start: 0.8391 (ppp) cc_final: 0.7163 (ppp)
REVERT: B  356 PHE cc_start: 0.8636 (m-10) cc_final: 0.8312 (m-10)
REVERT: C   56 MET cc_start: 0.8250 (mpp) cc_final: 0.7726 (mpp)
REVERT: C   83 ARG cc_start: 0.7469 (ptt-90) cc_final: 0.7210 (ttp-110)
REVERT: D   79 TYR cc_start: 0.8428 (m-80) cc_final: 0.8089 (m-10)
REVERT: E   53 GLN cc_start: 0.8539 (tp40) cc_final: 0.8316 (tp40)
REVERT: F 1021 GLU cc_start: 0.6915 (tp30) cc_final: 0.5910 (pt0)
REVERT: F 1034 ASP cc_start: 0.7448 (t0) cc_final: 0.7201 (t0)
REVERT: F 1112 MET cc_start: 0.7677 (ptp) cc_final: 0.7449 (ptp)
  outliers start: 49
  outliers final: 41
  residues processed: 223
  average time/residue: 0.2338
  time to fit residues: 81.0354
Evaluate side-chains
  223 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 182
  time to evaluate  : 1.822 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  139 ASP
Chi-restraints excluded: chain A residue  163 VAL
Chi-restraints excluded: chain A residue  230 TYR
Chi-restraints excluded: chain A residue  245 VAL
Chi-restraints excluded: chain A residue  405 VAL
Chi-restraints excluded: chain A residue  438 VAL
Chi-restraints excluded: chain A residue  444 VAL
Chi-restraints excluded: chain A residue  452 THR
Chi-restraints excluded: chain A residue  458 ILE
Chi-restraints excluded: chain A residue  511 THR
Chi-restraints excluded: chain A residue  524 SER
Chi-restraints excluded: chain A residue  629 VAL
Chi-restraints excluded: chain A residue  633 THR
Chi-restraints excluded: chain A residue  720 THR
Chi-restraints excluded: chain A residue  778 SER
Chi-restraints excluded: chain B residue   63 LEU
Chi-restraints excluded: chain B residue  157 VAL
Chi-restraints excluded: chain B residue  209 VAL
Chi-restraints excluded: chain B residue  239 THR
Chi-restraints excluded: chain B residue  249 THR
Chi-restraints excluded: chain B residue  270 LEU
Chi-restraints excluded: chain B residue  387 VAL
Chi-restraints excluded: chain C residue  108 VAL
Chi-restraints excluded: chain C residue  165 VAL
Chi-restraints excluded: chain D residue   67 TYR
Chi-restraints excluded: chain D residue   75 LEU
Chi-restraints excluded: chain D residue  181 VAL
Chi-restraints excluded: chain D residue  185 TYR
Chi-restraints excluded: chain D residue  186 THR
Chi-restraints excluded: chain E residue   31 ASP
Chi-restraints excluded: chain E residue   51 THR
Chi-restraints excluded: chain E residue   70 THR
Chi-restraints excluded: chain E residue   86 VAL
Chi-restraints excluded: chain E residue   94 THR
Chi-restraints excluded: chain E residue  111 SER
Chi-restraints excluded: chain F residue 1107 LEU
Chi-restraints excluded: chain F residue 1146 THR
Chi-restraints excluded: chain F residue 1174 VAL
Chi-restraints excluded: chain F residue 1256 SER
Chi-restraints excluded: chain F residue 1262 VAL
Chi-restraints excluded: chain F residue 1268 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 191
   random chunks:
   chunk 71 optimal weight:    4.9990
   chunk 121 optimal weight:    2.9990
   chunk 68 optimal weight:    4.9990
   chunk 0 optimal weight:   40.0000
   chunk 87 optimal weight:    6.9990
   chunk 33 optimal weight:    0.8980
   chunk 69 optimal weight:    2.9990
   chunk 177 optimal weight:    7.9990
   chunk 173 optimal weight:    5.9990
   chunk 14 optimal weight:   20.0000
   chunk 162 optimal weight:   10.0000
   overall best weight:    3.3788

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

Flipped N/Q/H residues before XYZ refinement:
** A 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4135 r_free = 0.4135 target = 0.157485 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3440 r_free = 0.3440 target = 0.107064 restraints weight = 31636.036|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3483 r_free = 0.3483 target = 0.109201 restraints weight = 20254.763|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3471 r_free = 0.3471 target = 0.108946 restraints weight = 13479.800|
|-----------------------------------------------------------------------------|
r_work (final): 0.3429
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3429
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3429 r_free = 0.3429    target_work(ls_wunit_k1) = 0.102         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3429 r_free = 0.3429    target_work(ls_wunit_k1) = 0.102         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3429
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8030
moved from start:          0.2811

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.062  15361  Z= 0.252
  Angle     :  0.730  12.209  20868  Z= 0.378
  Chirality :  0.047   0.186   2261
  Planarity :  0.005   0.081   2753
  Dihedral  :  5.693  36.083   2120
  Min Nonbonded Distance : 2.314

Molprobity Statistics.
  All-atom Clashscore : 13.32
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  : 13.39 %
    Favored  : 86.46 %
  Rotamer:
    Outliers :  3.72 %
    Allowed  : 20.37 %
    Favored  : 75.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.22 %
    Twisted Proline : 1.45 %
    Twisted General : 0.11 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.23 (0.18), residues: 1923
  helix:  0.83 (0.27), residues: 364
  sheet: -2.47 (0.21), residues: 570
  loop : -3.18 (0.17), residues: 989

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP D 191 
 HIS   0.005   0.001   HIS B  64 
 PHE   0.027   0.002   PHE B 289 
 TYR   0.055   0.002   TYR A 432 
 ARG   0.006   0.000   ARG F1044 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04783 (  403)
  hydrogen bonds       : angle       5.32009 ( 1080)
  SS BOND              : bond        0.00314 (    1)
  SS BOND              : angle       4.52548 (    2)
  covalent geometry    : bond        0.00564 (15360)
  covalent geometry    : angle       0.72910 (20866)

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

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

  3846 Ramachandran restraints generated.
    1923 Oldfield, 0 Emsley, 1923 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3846 Ramachandran restraints generated.
    1923 Oldfield, 0 Emsley, 1923 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  231 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 59
    poor density    : 172
  time to evaluate  : 1.670 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  465 TYR cc_start: 0.7298 (m-10) cc_final: 0.7001 (m-10)
REVERT: A  738 PHE cc_start: 0.9092 (p90) cc_final: 0.8824 (p90)
REVERT: B  221 MET cc_start: 0.8265 (OUTLIER) cc_final: 0.7854 (mpp)
REVERT: B  263 TYR cc_start: 0.6092 (t80) cc_final: 0.5657 (t80)
REVERT: B  278 MET cc_start: 0.8857 (mtp) cc_final: 0.8488 (mtm)
REVERT: C   56 MET cc_start: 0.8354 (mpp) cc_final: 0.7761 (mpp)
REVERT: C   80 LEU cc_start: 0.9154 (tp) cc_final: 0.8767 (tt)
REVERT: D   79 TYR cc_start: 0.8643 (m-80) cc_final: 0.8279 (m-10)
REVERT: E   53 GLN cc_start: 0.8735 (tp40) cc_final: 0.8464 (tp40)
REVERT: F 1021 GLU cc_start: 0.7039 (tp30) cc_final: 0.5999 (pt0)
REVERT: F 1034 ASP cc_start: 0.7418 (t0) cc_final: 0.7111 (t0)
REVERT: F 1112 MET cc_start: 0.7942 (ptp) cc_final: 0.7691 (ptp)
  outliers start: 59
  outliers final: 48
  residues processed: 217
  average time/residue: 0.2348
  time to fit residues: 79.1449
Evaluate side-chains
  217 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 168
  time to evaluate  : 1.656 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  139 ASP
Chi-restraints excluded: chain A residue  163 VAL
Chi-restraints excluded: chain A residue  230 TYR
Chi-restraints excluded: chain A residue  245 VAL
Chi-restraints excluded: chain A residue  273 VAL
Chi-restraints excluded: chain A residue  325 MET
Chi-restraints excluded: chain A residue  405 VAL
Chi-restraints excluded: chain A residue  438 VAL
Chi-restraints excluded: chain A residue  444 VAL
Chi-restraints excluded: chain A residue  452 THR
Chi-restraints excluded: chain A residue  458 ILE
Chi-restraints excluded: chain A residue  473 VAL
Chi-restraints excluded: chain A residue  511 THR
Chi-restraints excluded: chain A residue  524 SER
Chi-restraints excluded: chain A residue  629 VAL
Chi-restraints excluded: chain A residue  633 THR
Chi-restraints excluded: chain A residue  719 ILE
Chi-restraints excluded: chain A residue  720 THR
Chi-restraints excluded: chain B residue   63 LEU
Chi-restraints excluded: chain B residue  157 VAL
Chi-restraints excluded: chain B residue  209 VAL
Chi-restraints excluded: chain B residue  221 MET
Chi-restraints excluded: chain B residue  239 THR
Chi-restraints excluded: chain B residue  249 THR
Chi-restraints excluded: chain B residue  270 LEU
Chi-restraints excluded: chain B residue  300 ASP
Chi-restraints excluded: chain B residue  303 ASP
Chi-restraints excluded: chain B residue  322 LEU
Chi-restraints excluded: chain C residue   61 THR
Chi-restraints excluded: chain C residue  108 VAL
Chi-restraints excluded: chain C residue  165 VAL
Chi-restraints excluded: chain D residue   67 TYR
Chi-restraints excluded: chain D residue   75 LEU
Chi-restraints excluded: chain D residue  181 VAL
Chi-restraints excluded: chain D residue  185 TYR
Chi-restraints excluded: chain E residue   31 ASP
Chi-restraints excluded: chain E residue   43 VAL
Chi-restraints excluded: chain E residue   46 ILE
Chi-restraints excluded: chain E residue   51 THR
Chi-restraints excluded: chain E residue   86 VAL
Chi-restraints excluded: chain E residue   94 THR
Chi-restraints excluded: chain E residue  111 SER
Chi-restraints excluded: chain F residue 1087 THR
Chi-restraints excluded: chain F residue 1107 LEU
Chi-restraints excluded: chain F residue 1146 THR
Chi-restraints excluded: chain F residue 1174 VAL
Chi-restraints excluded: chain F residue 1256 SER
Chi-restraints excluded: chain F residue 1262 VAL
Chi-restraints excluded: chain F residue 1268 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 191
   random chunks:
   chunk 43 optimal weight:    0.9980
   chunk 4 optimal weight:    7.9990
   chunk 149 optimal weight:    0.0970
   chunk 120 optimal weight:    4.9990
   chunk 135 optimal weight:    3.9990
   chunk 30 optimal weight:   10.0000
   chunk 20 optimal weight:    1.9990
   chunk 123 optimal weight:    0.0570
   chunk 32 optimal weight:    0.8980
   chunk 59 optimal weight:    1.9990
   chunk 107 optimal weight:    8.9990
   overall best weight:    0.8098

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

Flipped N/Q/H residues before XYZ refinement:
** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 538 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  47 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4184 r_free = 0.4184 target = 0.164242 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3511 r_free = 0.3511 target = 0.110457 restraints weight = 31875.335|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3557 r_free = 0.3557 target = 0.114331 restraints weight = 18456.757|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3571 r_free = 0.3571 target = 0.115124 restraints weight = 11715.498|
|-----------------------------------------------------------------------------|
r_work (final): 0.3539
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3539
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3539 r_free = 0.3539    target_work(ls_wunit_k1) = 0.109         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3539 r_free = 0.3539    target_work(ls_wunit_k1) = 0.109         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3539
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7895
moved from start:          0.3193

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.080  15361  Z= 0.120
  Angle     :  0.653  11.768  20868  Z= 0.334
  Chirality :  0.044   0.203   2261
  Planarity :  0.004   0.080   2753
  Dihedral  :  5.333  35.648   2120
  Min Nonbonded Distance : 2.304

Molprobity Statistics.
  All-atom Clashscore : 10.54
  Ramachandran Plot:
    Outliers :  0.05 %
    Allowed  :  9.84 %
    Favored  : 90.10 %
  Rotamer:
    Outliers :  2.96 %
    Allowed  : 21.31 %
    Favored  : 75.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.22 %
    Twisted Proline : 1.45 %
    Twisted General : 0.11 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.94 (0.18), residues: 1923
  helix:  1.05 (0.27), residues: 363
  sheet: -2.20 (0.22), residues: 539
  loop : -3.05 (0.17), residues: 1021

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A 449 
 HIS   0.003   0.000   HIS F1086 
 PHE   0.012   0.001   PHE B  42 
 TYR   0.045   0.001   TYR A 432 
 ARG   0.004   0.000   ARG B 325 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03984 (  403)
  hydrogen bonds       : angle       4.89645 ( 1080)
  SS BOND              : bond        0.00234 (    1)
  SS BOND              : angle       3.88408 (    2)
  covalent geometry    : bond        0.00264 (15360)
  covalent geometry    : angle       0.65214 (20866)

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

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

  3846 Ramachandran restraints generated.
    1923 Oldfield, 0 Emsley, 1923 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3846 Ramachandran restraints generated.
    1923 Oldfield, 0 Emsley, 1923 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  232 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 185
  time to evaluate  : 1.626 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  422 ASN cc_start: 0.8543 (t0) cc_final: 0.8222 (t0)
REVERT: A  449 TRP cc_start: 0.8695 (t60) cc_final: 0.8357 (t-100)
REVERT: A  465 TYR cc_start: 0.7273 (m-10) cc_final: 0.6987 (m-10)
REVERT: A  741 MET cc_start: 0.7860 (ttm) cc_final: 0.7596 (ttt)
REVERT: A  769 SER cc_start: 0.9431 (t) cc_final: 0.8913 (m)
REVERT: B  192 LEU cc_start: 0.9401 (mt) cc_final: 0.9019 (tt)
REVERT: B  221 MET cc_start: 0.8242 (OUTLIER) cc_final: 0.7903 (mpp)
REVERT: B  263 TYR cc_start: 0.5825 (t80) cc_final: 0.5300 (t80)
REVERT: B  278 MET cc_start: 0.8877 (mtp) cc_final: 0.8438 (mtm)
REVERT: B  356 PHE cc_start: 0.8680 (m-10) cc_final: 0.8323 (m-10)
REVERT: C   56 MET cc_start: 0.8196 (mpp) cc_final: 0.7640 (mpp)
REVERT: C   80 LEU cc_start: 0.9150 (tp) cc_final: 0.8826 (tt)
REVERT: C   83 ARG cc_start: 0.7409 (ptp-110) cc_final: 0.7121 (mtm180)
REVERT: E   53 GLN cc_start: 0.8666 (tp40) cc_final: 0.8402 (tp40)
REVERT: F 1021 GLU cc_start: 0.6861 (tp30) cc_final: 0.6120 (pt0)
REVERT: F 1034 ASP cc_start: 0.7412 (t0) cc_final: 0.7125 (t0)
REVERT: F 1112 MET cc_start: 0.7865 (ptp) cc_final: 0.7614 (ptp)
  outliers start: 47
  outliers final: 38
  residues processed: 220
  average time/residue: 0.2412
  time to fit residues: 81.7161
Evaluate side-chains
  216 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 177
  time to evaluate  : 1.624 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  129 THR
Chi-restraints excluded: chain A residue  139 ASP
Chi-restraints excluded: chain A residue  163 VAL
Chi-restraints excluded: chain A residue  230 TYR
Chi-restraints excluded: chain A residue  245 VAL
Chi-restraints excluded: chain A residue  325 MET
Chi-restraints excluded: chain A residue  405 VAL
Chi-restraints excluded: chain A residue  444 VAL
Chi-restraints excluded: chain A residue  452 THR
Chi-restraints excluded: chain A residue  458 ILE
Chi-restraints excluded: chain A residue  511 THR
Chi-restraints excluded: chain A residue  524 SER
Chi-restraints excluded: chain A residue  629 VAL
Chi-restraints excluded: chain A residue  633 THR
Chi-restraints excluded: chain A residue  660 VAL
Chi-restraints excluded: chain A residue  720 THR
Chi-restraints excluded: chain B residue   63 LEU
Chi-restraints excluded: chain B residue  157 VAL
Chi-restraints excluded: chain B residue  209 VAL
Chi-restraints excluded: chain B residue  221 MET
Chi-restraints excluded: chain B residue  239 THR
Chi-restraints excluded: chain B residue  249 THR
Chi-restraints excluded: chain B residue  300 ASP
Chi-restraints excluded: chain C residue  108 VAL
Chi-restraints excluded: chain C residue  165 VAL
Chi-restraints excluded: chain D residue   67 TYR
Chi-restraints excluded: chain D residue   75 LEU
Chi-restraints excluded: chain D residue  181 VAL
Chi-restraints excluded: chain D residue  185 TYR
Chi-restraints excluded: chain E residue   31 ASP
Chi-restraints excluded: chain E residue   46 ILE
Chi-restraints excluded: chain E residue   94 THR
Chi-restraints excluded: chain E residue  111 SER
Chi-restraints excluded: chain F residue 1107 LEU
Chi-restraints excluded: chain F residue 1146 THR
Chi-restraints excluded: chain F residue 1174 VAL
Chi-restraints excluded: chain F residue 1256 SER
Chi-restraints excluded: chain F residue 1262 VAL
Chi-restraints excluded: chain F residue 1268 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 191
   random chunks:
   chunk 180 optimal weight:   20.0000
   chunk 52 optimal weight:    0.9990
   chunk 161 optimal weight:   20.0000
   chunk 132 optimal weight:    2.9990
   chunk 2 optimal weight:    9.9990
   chunk 116 optimal weight:    0.8980
   chunk 58 optimal weight:    1.9990
   chunk 139 optimal weight:    0.9990
   chunk 65 optimal weight:    0.9990
   chunk 150 optimal weight:    0.8980
   chunk 122 optimal weight:    8.9990
   overall best weight:    0.9586

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

Flipped N/Q/H residues before XYZ refinement:
** A 538 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4190 r_free = 0.4190 target = 0.157183 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3690 r_free = 0.3690 target = 0.118816 restraints weight = 30605.025|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3615 r_free = 0.3615 target = 0.115490 restraints weight = 22266.653|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3627 r_free = 0.3627 target = 0.116899 restraints weight = 19928.514|
|-----------------------------------------------------------------------------|
r_work (final): 0.3627
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3627
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3627 r_free = 0.3627    target_work(ls_wunit_k1) = 0.115         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3627 r_free = 0.3627    target_work(ls_wunit_k1) = 0.115         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3627
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7846
moved from start:          0.3362

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.081  15361  Z= 0.123
  Angle     :  0.643  11.174  20868  Z= 0.331
  Chirality :  0.044   0.260   2261
  Planarity :  0.004   0.080   2753
  Dihedral  :  5.241  37.220   2120
  Min Nonbonded Distance : 2.380

Molprobity Statistics.
  All-atom Clashscore : 10.77
  Ramachandran Plot:
    Outliers :  0.05 %
    Allowed  : 10.05 %
    Favored  : 89.90 %
  Rotamer:
    Outliers :  2.90 %
    Allowed  : 21.63 %
    Favored  : 75.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.22 %
    Twisted Proline : 1.45 %
    Twisted General : 0.11 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.78 (0.18), residues: 1923
  helix:  1.07 (0.28), residues: 364
  sheet: -1.97 (0.22), residues: 523
  loop : -2.98 (0.17), residues: 1036

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 449 
 HIS   0.003   0.000   HIS F1086 
 PHE   0.015   0.001   PHE F1018 
 TYR   0.064   0.001   TYR A 432 
 ARG   0.004   0.000   ARG D  49 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04048 (  403)
  hydrogen bonds       : angle       4.84745 ( 1080)
  SS BOND              : bond        0.00172 (    1)
  SS BOND              : angle       3.69838 (    2)
  covalent geometry    : bond        0.00273 (15360)
  covalent geometry    : angle       0.64189 (20866)

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

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

  3846 Ramachandran restraints generated.
    1923 Oldfield, 0 Emsley, 1923 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3846 Ramachandran restraints generated.
    1923 Oldfield, 0 Emsley, 1923 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  229 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 183
  time to evaluate  : 1.649 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  422 ASN cc_start: 0.8424 (t0) cc_final: 0.8080 (t0)
REVERT: A  449 TRP cc_start: 0.8631 (t60) cc_final: 0.8355 (t-100)
REVERT: A  465 TYR cc_start: 0.7257 (m-10) cc_final: 0.7015 (m-10)
REVERT: A  769 SER cc_start: 0.9283 (t) cc_final: 0.8814 (m)
REVERT: B  192 LEU cc_start: 0.9286 (mt) cc_final: 0.8968 (tt)
REVERT: B  221 MET cc_start: 0.8210 (OUTLIER) cc_final: 0.7851 (mpp)
REVERT: B  263 TYR cc_start: 0.6001 (t80) cc_final: 0.5435 (t80)
REVERT: B  278 MET cc_start: 0.8731 (mtp) cc_final: 0.8392 (mtm)
REVERT: B  356 PHE cc_start: 0.8513 (m-10) cc_final: 0.8297 (m-10)
REVERT: C   56 MET cc_start: 0.8105 (mpp) cc_final: 0.7720 (mpp)
REVERT: C   83 ARG cc_start: 0.7395 (ptp-170) cc_final: 0.7184 (mtm180)
REVERT: D   64 PHE cc_start: 0.8237 (t80) cc_final: 0.7805 (t80)
REVERT: D   79 TYR cc_start: 0.8407 (m-10) cc_final: 0.8065 (m-10)
REVERT: E   53 GLN cc_start: 0.8383 (tp40) cc_final: 0.8151 (tp40)
REVERT: F 1021 GLU cc_start: 0.6416 (tp30) cc_final: 0.6057 (pt0)
REVERT: F 1034 ASP cc_start: 0.7222 (t0) cc_final: 0.6993 (t0)
REVERT: F 1112 MET cc_start: 0.7550 (ptp) cc_final: 0.7298 (ptp)
REVERT: F 1166 TRP cc_start: 0.7997 (m-10) cc_final: 0.7622 (m100)
  outliers start: 46
  outliers final: 41
  residues processed: 217
  average time/residue: 0.2440
  time to fit residues: 81.7472
Evaluate side-chains
  218 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 176
  time to evaluate  : 1.695 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  129 THR
Chi-restraints excluded: chain A residue  139 ASP
Chi-restraints excluded: chain A residue  163 VAL
Chi-restraints excluded: chain A residue  230 TYR
Chi-restraints excluded: chain A residue  245 VAL
Chi-restraints excluded: chain A residue  325 MET
Chi-restraints excluded: chain A residue  369 MET
Chi-restraints excluded: chain A residue  405 VAL
Chi-restraints excluded: chain A residue  438 VAL
Chi-restraints excluded: chain A residue  444 VAL
Chi-restraints excluded: chain A residue  452 THR
Chi-restraints excluded: chain A residue  458 ILE
Chi-restraints excluded: chain A residue  473 VAL
Chi-restraints excluded: chain A residue  511 THR
Chi-restraints excluded: chain A residue  524 SER
Chi-restraints excluded: chain A residue  629 VAL
Chi-restraints excluded: chain A residue  633 THR
Chi-restraints excluded: chain A residue  660 VAL
Chi-restraints excluded: chain A residue  720 THR
Chi-restraints excluded: chain A residue  778 SER
Chi-restraints excluded: chain B residue   63 LEU
Chi-restraints excluded: chain B residue  157 VAL
Chi-restraints excluded: chain B residue  221 MET
Chi-restraints excluded: chain B residue  239 THR
Chi-restraints excluded: chain B residue  249 THR
Chi-restraints excluded: chain C residue  108 VAL
Chi-restraints excluded: chain C residue  165 VAL
Chi-restraints excluded: chain D residue   67 TYR
Chi-restraints excluded: chain D residue   75 LEU
Chi-restraints excluded: chain D residue  181 VAL
Chi-restraints excluded: chain D residue  185 TYR
Chi-restraints excluded: chain E residue   31 ASP
Chi-restraints excluded: chain E residue   70 THR
Chi-restraints excluded: chain E residue   94 THR
Chi-restraints excluded: chain E residue  111 SER
Chi-restraints excluded: chain F residue 1107 LEU
Chi-restraints excluded: chain F residue 1146 THR
Chi-restraints excluded: chain F residue 1154 GLU
Chi-restraints excluded: chain F residue 1174 VAL
Chi-restraints excluded: chain F residue 1256 SER
Chi-restraints excluded: chain F residue 1262 VAL
Chi-restraints excluded: chain F residue 1268 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 191
   random chunks:
   chunk 187 optimal weight:    9.9990
   chunk 102 optimal weight:    3.9990
   chunk 125 optimal weight:    0.2980
   chunk 161 optimal weight:   20.0000
   chunk 184 optimal weight:    3.9990
   chunk 168 optimal weight:    0.6980
   chunk 68 optimal weight:    6.9990
   chunk 51 optimal weight:    0.4980
   chunk 9 optimal weight:    9.9990
   chunk 54 optimal weight:    4.9990
   chunk 112 optimal weight:    5.9990
   overall best weight:    1.8984

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

Flipped N/Q/H residues before XYZ refinement:
** A 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 538 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4168 r_free = 0.4168 target = 0.155312 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3689 r_free = 0.3689 target = 0.118327 restraints weight = 31005.765|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3592 r_free = 0.3592 target = 0.116266 restraints weight = 22792.560|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3599 r_free = 0.3599 target = 0.116728 restraints weight = 21480.631|
|-----------------------------------------------------------------------------|
r_work (final): 0.3582
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3583
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3583 r_free = 0.3583    target_work(ls_wunit_k1) = 0.115         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3583 r_free = 0.3583    target_work(ls_wunit_k1) = 0.115         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3583
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7836
moved from start:          0.3360

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.069  15361  Z= 0.164
  Angle     :  0.673  11.034  20868  Z= 0.345
  Chirality :  0.045   0.265   2261
  Planarity :  0.004   0.081   2753
  Dihedral  :  5.365  38.349   2120
  Min Nonbonded Distance : 2.434

Molprobity Statistics.
  All-atom Clashscore : 11.83
  Ramachandran Plot:
    Outliers :  0.05 %
    Allowed  : 11.20 %
    Favored  : 88.75 %
  Rotamer:
    Outliers :  3.09 %
    Allowed  : 21.75 %
    Favored  : 75.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.22 %
    Twisted Proline : 1.45 %
    Twisted General : 0.11 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.78 (0.19), residues: 1923
  helix:  1.00 (0.27), residues: 364
  sheet: -2.06 (0.22), residues: 540
  loop : -2.90 (0.17), residues: 1019

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP D 191 
 HIS   0.004   0.001   HIS F1128 
 PHE   0.018   0.001   PHE F1018 
 TYR   0.068   0.002   TYR A 432 
 ARG   0.004   0.000   ARG D  49 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04276 (  403)
  hydrogen bonds       : angle       4.96827 ( 1080)
  SS BOND              : bond        0.00208 (    1)
  SS BOND              : angle       3.82508 (    2)
  covalent geometry    : bond        0.00367 (15360)
  covalent geometry    : angle       0.67195 (20866)

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

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

  3846 Ramachandran restraints generated.
    1923 Oldfield, 0 Emsley, 1923 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3846 Ramachandran restraints generated.
    1923 Oldfield, 0 Emsley, 1923 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  231 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 182
  time to evaluate  : 1.633 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  449 TRP cc_start: 0.8694 (t60) cc_final: 0.8364 (t-100)
REVERT: A  465 TYR cc_start: 0.7244 (m-10) cc_final: 0.6995 (m-10)
REVERT: B  192 LEU cc_start: 0.9370 (mt) cc_final: 0.9093 (tt)
REVERT: B  221 MET cc_start: 0.8316 (OUTLIER) cc_final: 0.7913 (mpp)
REVERT: B  263 TYR cc_start: 0.5971 (t80) cc_final: 0.5410 (t80)
REVERT: B  278 MET cc_start: 0.8824 (mtp) cc_final: 0.8509 (mtm)
REVERT: B  306 MET cc_start: 0.8126 (ppp) cc_final: 0.7297 (ppp)
REVERT: B  356 PHE cc_start: 0.8571 (m-10) cc_final: 0.8338 (m-10)
REVERT: C   56 MET cc_start: 0.8184 (mpp) cc_final: 0.7725 (mpp)
REVERT: C   83 ARG cc_start: 0.7491 (ptp-170) cc_final: 0.7194 (mtm110)
REVERT: D   64 PHE cc_start: 0.8339 (t80) cc_final: 0.7897 (t80)
REVERT: E   53 GLN cc_start: 0.8515 (tp40) cc_final: 0.8272 (tp40)
REVERT: F 1021 GLU cc_start: 0.6637 (tp30) cc_final: 0.6069 (pt0)
REVERT: F 1034 ASP cc_start: 0.7253 (t0) cc_final: 0.7007 (t0)
REVERT: F 1112 MET cc_start: 0.7656 (ptp) cc_final: 0.7441 (ptp)
REVERT: F 1166 TRP cc_start: 0.8102 (m-10) cc_final: 0.7668 (m100)
REVERT: F 1298 TYR cc_start: 0.8328 (t80) cc_final: 0.8098 (t80)
  outliers start: 49
  outliers final: 43
  residues processed: 217
  average time/residue: 0.2462
  time to fit residues: 83.5434
Evaluate side-chains
  219 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 175
  time to evaluate  : 1.612 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  129 THR
Chi-restraints excluded: chain A residue  139 ASP
Chi-restraints excluded: chain A residue  163 VAL
Chi-restraints excluded: chain A residue  230 TYR
Chi-restraints excluded: chain A residue  245 VAL
Chi-restraints excluded: chain A residue  325 MET
Chi-restraints excluded: chain A residue  369 MET
Chi-restraints excluded: chain A residue  405 VAL
Chi-restraints excluded: chain A residue  438 VAL
Chi-restraints excluded: chain A residue  444 VAL
Chi-restraints excluded: chain A residue  452 THR
Chi-restraints excluded: chain A residue  458 ILE
Chi-restraints excluded: chain A residue  473 VAL
Chi-restraints excluded: chain A residue  511 THR
Chi-restraints excluded: chain A residue  524 SER
Chi-restraints excluded: chain A residue  629 VAL
Chi-restraints excluded: chain A residue  633 THR
Chi-restraints excluded: chain A residue  660 VAL
Chi-restraints excluded: chain A residue  720 THR
Chi-restraints excluded: chain A residue  778 SER
Chi-restraints excluded: chain B residue   63 LEU
Chi-restraints excluded: chain B residue  157 VAL
Chi-restraints excluded: chain B residue  209 VAL
Chi-restraints excluded: chain B residue  221 MET
Chi-restraints excluded: chain B residue  249 THR
Chi-restraints excluded: chain B residue  300 ASP
Chi-restraints excluded: chain C residue   61 THR
Chi-restraints excluded: chain C residue  108 VAL
Chi-restraints excluded: chain C residue  165 VAL
Chi-restraints excluded: chain D residue   67 TYR
Chi-restraints excluded: chain D residue   75 LEU
Chi-restraints excluded: chain D residue  181 VAL
Chi-restraints excluded: chain D residue  185 TYR
Chi-restraints excluded: chain E residue   31 ASP
Chi-restraints excluded: chain E residue   70 THR
Chi-restraints excluded: chain E residue   94 THR
Chi-restraints excluded: chain E residue  111 SER
Chi-restraints excluded: chain F residue 1107 LEU
Chi-restraints excluded: chain F residue 1146 THR
Chi-restraints excluded: chain F residue 1154 GLU
Chi-restraints excluded: chain F residue 1174 VAL
Chi-restraints excluded: chain F residue 1256 SER
Chi-restraints excluded: chain F residue 1262 VAL
Chi-restraints excluded: chain F residue 1268 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 191
   random chunks:
   chunk 49 optimal weight:    0.9990
   chunk 59 optimal weight:    0.2980
   chunk 92 optimal weight:    5.9990
   chunk 132 optimal weight:    3.9990
   chunk 13 optimal weight:    0.9980
   chunk 137 optimal weight:    2.9990
   chunk 88 optimal weight:    3.9990
   chunk 144 optimal weight:    0.0980
   chunk 45 optimal weight:    1.9990
   chunk 2 optimal weight:   20.0000
   chunk 80 optimal weight:    4.9990
   overall best weight:    0.8784

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

Flipped N/Q/H residues before XYZ refinement:
** A 538 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4200 r_free = 0.4200 target = 0.158024 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3738 r_free = 0.3738 target = 0.121545 restraints weight = 30907.117|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3649 r_free = 0.3649 target = 0.118025 restraints weight = 22717.192|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3668 r_free = 0.3668 target = 0.119736 restraints weight = 20002.487|
|-----------------------------------------------------------------------------|
r_work (final): 0.3669
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3668
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3668 r_free = 0.3668    target_work(ls_wunit_k1) = 0.118         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3668 r_free = 0.3668    target_work(ls_wunit_k1) = 0.118         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3668
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7771
moved from start:          0.3622

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.060  15361  Z= 0.119
  Angle     :  0.649  13.343  20868  Z= 0.331
  Chirality :  0.044   0.226   2261
  Planarity :  0.004   0.079   2753
  Dihedral  :  5.200  38.541   2120
  Min Nonbonded Distance : 2.434

Molprobity Statistics.
  All-atom Clashscore : 10.64
  Ramachandran Plot:
    Outliers :  0.05 %
    Allowed  :  9.74 %
    Favored  : 90.21 %
  Rotamer:
    Outliers :  2.77 %
    Allowed  : 22.01 %
    Favored  : 75.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.22 %
    Twisted Proline : 1.45 %
    Twisted General : 0.11 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.62 (0.19), residues: 1923
  helix:  1.08 (0.28), residues: 364
  sheet: -1.90 (0.23), residues: 515
  loop : -2.81 (0.17), residues: 1044

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 449 
 HIS   0.005   0.001   HIS F1086 
 PHE   0.016   0.001   PHE B 259 
 TYR   0.056   0.001   TYR A 432 
 ARG   0.004   0.000   ARG D  49 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04014 (  403)
  hydrogen bonds       : angle       4.81119 ( 1080)
  SS BOND              : bond        0.00150 (    1)
  SS BOND              : angle       3.52989 (    2)
  covalent geometry    : bond        0.00260 (15360)
  covalent geometry    : angle       0.64789 (20866)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5222.83 seconds
wall clock time: 91 minutes 59.64 seconds (5519.64 seconds total)