Starting phenix.real_space_refine
on Sat May 17 06:04:49 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8wui_37855/05_2025/8wui_37855_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8wui_37855/05_2025/8wui_37855.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.4
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8wui_37855/05_2025/8wui_37855.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8wui_37855/05_2025/8wui_37855.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8wui_37855/05_2025/8wui_37855_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8wui_37855/05_2025/8wui_37855_neut.cif"
  }
  resolution = 3.4
  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=   0.002 sd=   0.032
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P       2      5.49       5
     S      92      5.16       5
     C   10130      2.51       5
     N    2498      2.21       5
     O    2618      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 17 residue(s): 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 15340
  Number of models: 1
  Model: ""
    Number of chains: 8
    Chain: "B"
      Number of atoms: 3706
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 449, 3706
          Classifications: {'peptide': 449}
          Link IDs: {'PTRANS': 13, 'TRANS': 435}
          Chain breaks: 1
    Chain: "A"
      Number of atoms: 3832
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 464, 3832
          Classifications: {'peptide': 464}
          Link IDs: {'PTRANS': 13, 'TRANS': 450}
          Chain breaks: 1
    Chain: "D"
      Number of atoms: 3706
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 449, 3706
          Classifications: {'peptide': 449}
          Link IDs: {'PTRANS': 13, 'TRANS': 435}
          Chain breaks: 1
    Chain: "C"
      Number of atoms: 3832
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 464, 3832
          Classifications: {'peptide': 464}
          Link IDs: {'PTRANS': 13, 'TRANS': 450}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 51
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 51
          Unusual residues: {'PC1': 3}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 111
          Unresolved non-hydrogen angles: 138
          Unresolved non-hydrogen dihedrals: 102
          Unresolved non-hydrogen chiralities: 3
          Planarities with less than four sites: {'PC1:plan-2': 3, 'PC1:plan-1': 3}
          Unresolved non-hydrogen planarities: 18
    Chain: "A"
      Number of atoms: 81
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 81
          Unusual residues: {'PC1': 4}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}
          Unresolved non-hydrogen bonds: 135
          Unresolved non-hydrogen angles: 165
          Unresolved non-hydrogen dihedrals: 124
          Unresolved non-hydrogen chiralities: 3
          Planarities with less than four sites: {'PC1:plan-2': 3, 'PC1:plan-1': 3}
          Unresolved non-hydrogen planarities: 18
    Chain: "D"
      Number of atoms: 51
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 51
          Unusual residues: {'PC1': 3}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 111
          Unresolved non-hydrogen angles: 138
          Unresolved non-hydrogen dihedrals: 102
          Unresolved non-hydrogen chiralities: 3
          Planarities with less than four sites: {'PC1:plan-2': 3, 'PC1:plan-1': 3}
          Unresolved non-hydrogen planarities: 18
    Chain: "C"
      Number of atoms: 81
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 81
          Unusual residues: {'PC1': 4}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}
          Unresolved non-hydrogen bonds: 135
          Unresolved non-hydrogen angles: 165
          Unresolved non-hydrogen dihedrals: 124
          Unresolved non-hydrogen chiralities: 3
          Planarities with less than four sites: {'PC1:plan-2': 3, 'PC1:plan-1': 3}
          Unresolved non-hydrogen planarities: 18
  Time building chain proxies: 9.20, per 1000 atoms: 0.60
  Number of scatterers: 15340
  At special positions: 0
  Unit cell: (117.52, 115.44, 125.84, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      92     16.00
     P       2     15.00
     O    2618      8.00
     N    2498      7.00
     C   10130      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=8, symmetry=0
  Number of additional bonds: simple=8, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 4.33
  Conformation dependent library (CDL) restraints added in 2.1 seconds
  

  3620 Ramachandran restraints generated.
    1810 Oldfield, 0 Emsley, 1810 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3468

  Finding SS restraints...
    Secondary structure from input PDB file:
      91 helices and 10 sheets defined
      67.4% alpha, 5.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.77
  Creating SS restraints...
    Processing helix  chain 'B' and resid 79 through 97
    Processing helix  chain 'B' and resid 99 through 105
    Processing helix  chain 'B' and resid 114 through 132
      removed outlier: 3.582A  pdb=" N   PHE B 125 " --> pdb=" O   GLY B 121 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 152 through 158
      removed outlier: 3.895A  pdb=" N   TYR B 156 " --> pdb=" O   ILE B 152 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 161 through 167
    Processing helix  chain 'B' and resid 170 through 178
    Processing helix  chain 'B' and resid 181 through 193
      removed outlier: 3.514A  pdb=" N   VAL B 184 " --> pdb=" O   LYS B 181 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 194 through 208
      removed outlier: 4.240A  pdb=" N   VAL B 198 " --> pdb=" O   ARG B 194 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 212 through 243
      removed outlier: 3.670A  pdb=" N   ILE B 218 " --> pdb=" O   LEU B 214 " (cutoff:3.500A)
      removed outlier: 3.976A  pdb=" N   LEU B 226 " --> pdb=" O   ILE B 222 " (cutoff:3.500A)
      removed outlier: 4.008A  pdb=" N   ALA B 233 " --> pdb=" O   THR B 229 " (cutoff:3.500A)
      removed outlier: 3.553A  pdb=" N   PHE B 236 " --> pdb=" O   ALA B 232 " (cutoff:3.500A)
      removed outlier: 3.528A  pdb=" N   ALA B 240 " --> pdb=" O   PHE B 236 " (cutoff:3.500A)
      removed outlier: 4.188A  pdb=" N   LEU B 243 " --> pdb=" O   LEU B 239 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 244 through 248
    Processing helix  chain 'B' and resid 265 through 269
    Processing helix  chain 'B' and resid 270 through 287
    Processing helix  chain 'B' and resid 299 through 330
      removed outlier: 3.508A  pdb=" N   ALA B 317 " --> pdb=" O   MET B 313 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 332 through 351
      removed outlier: 4.130A  pdb=" N   PHE B 336 " --> pdb=" O   LYS B 332 " (cutoff:3.500A)
      removed outlier: 3.553A  pdb=" N   ARG B 337 " --> pdb=" O   THR B 333 " (cutoff:3.500A)
      removed outlier: 4.160A  pdb=" N   ASP B 338 " --> pdb=" O   GLU B 334 " (cutoff:3.500A)
      removed outlier: 3.539A  pdb=" N   LYS B 339 " --> pdb=" O   ARG B 335 " (cutoff:3.500A)
      removed outlier: 3.654A  pdb=" N   ILE B 343 " --> pdb=" O   LYS B 339 " (cutoff:3.500A)
      removed outlier: 3.754A  pdb=" N   ARG B 345 " --> pdb=" O   ALA B 341 " (cutoff:3.500A)
      removed outlier: 3.829A  pdb=" N   ASN B 348 " --> pdb=" O   MET B 344 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 353 through 369
    Processing helix  chain 'B' and resid 382 through 394
      removed outlier: 5.277A  pdb=" N   LYS B 388 " --> pdb=" O   SER B 384 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 394 through 400
      removed outlier: 4.038A  pdb=" N   LYS B 400 " --> pdb=" O   PRO B 396 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 401 through 405
    Processing helix  chain 'B' and resid 408 through 418
      removed outlier: 3.575A  pdb=" N   ARG B 418 " --> pdb=" O   GLN B 414 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 472 through 479
      removed outlier: 3.837A  pdb=" N   ILE B 476 " --> pdb=" O   GLY B 472 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 499 through 509
    Processing helix  chain 'B' and resid 509 through 524
    Processing helix  chain 'A' and resid 79 through 98
      removed outlier: 3.720A  pdb=" N   SER A  96 " --> pdb=" O   TRP A  92 " (cutoff:3.500A)
      removed outlier: 3.568A  pdb=" N   PHE A  98 " --> pdb=" O   LEU A  94 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 99 through 105
    Processing helix  chain 'A' and resid 113 through 131
      removed outlier: 4.018A  pdb=" N   LEU A 117 " --> pdb=" O   ASN A 113 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 148 through 160
      removed outlier: 4.131A  pdb=" N   ALA A 153 " --> pdb=" O   ARG A 149 " (cutoff:3.500A)
      removed outlier: 4.435A  pdb=" N   LEU A 154 " --> pdb=" O   SER A 150 " (cutoff:3.500A)
      removed outlier: 4.818A  pdb=" N   ARG A 155 " --> pdb=" O   SER A 151 " (cutoff:3.500A)
      removed outlier: 3.993A  pdb=" N   TYR A 156 " --> pdb=" O   ILE A 152 " (cutoff:3.500A)
      removed outlier: 4.113A  pdb=" N   LYS A 158 " --> pdb=" O   LEU A 154 " (cutoff:3.500A)
      removed outlier: 3.514A  pdb=" N   THR A 160 " --> pdb=" O   TYR A 156 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 160 through 167
      removed outlier: 3.603A  pdb=" N   LEU A 166 " --> pdb=" O   ILE A 162 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 170 through 178
    Processing helix  chain 'A' and resid 181 through 187
      removed outlier: 4.441A  pdb=" N   ARG A 185 " --> pdb=" O   LYS A 181 " (cutoff:3.500A)
      removed outlier: 3.767A  pdb=" N   TYR A 186 " --> pdb=" O   GLU A 182 " (cutoff:3.500A)
      removed outlier: 3.990A  pdb=" N   LEU A 187 " --> pdb=" O   GLU A 183 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 181 through 187'
    Processing helix  chain 'A' and resid 188 through 193
    Processing helix  chain 'A' and resid 194 through 208
      removed outlier: 4.187A  pdb=" N   VAL A 198 " --> pdb=" O   ARG A 194 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 212 through 242
      removed outlier: 3.847A  pdb=" N   CYS A 228 " --> pdb=" O   VAL A 224 " (cutoff:3.500A)
      removed outlier: 3.581A  pdb=" N   ILE A 235 " --> pdb=" O   THR A 231 " (cutoff:3.500A)
      removed outlier: 3.664A  pdb=" N   TYR A 238 " --> pdb=" O   CYS A 234 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 247 through 251
      removed outlier: 3.557A  pdb=" N   THR A 251 " --> pdb=" O   GLU A 248 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 265 through 269
    Processing helix  chain 'A' and resid 270 through 287
      removed outlier: 3.591A  pdb=" N   SER A 278 " --> pdb=" O   ARG A 274 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 298 through 330
    Processing helix  chain 'A' and resid 331 through 351
    Processing helix  chain 'A' and resid 353 through 380
      removed outlier: 3.988A  pdb=" N   ARG A 357 " --> pdb=" O   GLY A 353 " (cutoff:3.500A)
      removed outlier: 3.684A  pdb=" N   ASP A 380 " --> pdb=" O   ALA A 376 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 382 through 394
    Processing helix  chain 'A' and resid 394 through 400
      removed outlier: 4.102A  pdb=" N   LYS A 400 " --> pdb=" O   PRO A 396 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 408 through 418
      removed outlier: 3.768A  pdb=" N   ILE A 417 " --> pdb=" O   ASN A 413 " (cutoff:3.500A)
      removed outlier: 4.056A  pdb=" N   ARG A 418 " --> pdb=" O   GLN A 414 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 473 through 478
    Processing helix  chain 'A' and resid 499 through 509
      removed outlier: 3.561A  pdb=" N   ILE A 508 " --> pdb=" O   ASN A 504 " (cutoff:3.500A)
      removed outlier: 3.562A  pdb=" N   PHE A 509 " --> pdb=" O   ILE A 505 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 509 through 521
      removed outlier: 3.516A  pdb=" N   ARG A 515 " --> pdb=" O   HIS A 511 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 532 through 545
      removed outlier: 4.208A  pdb=" N   PHE A 539 " --> pdb=" O   SER A 535 " (cutoff:3.500A)
      removed outlier: 4.162A  pdb=" N   HIS A 540 " --> pdb=" O   ASP A 536 " (cutoff:3.500A)
      removed outlier: 3.506A  pdb=" N   ILE A 541 " --> pdb=" O   ILE A 537 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 79 through 97
    Processing helix  chain 'D' and resid 99 through 105
    Processing helix  chain 'D' and resid 114 through 132
      removed outlier: 3.582A  pdb=" N   PHE D 125 " --> pdb=" O   GLY D 121 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 152 through 158
      removed outlier: 3.894A  pdb=" N   TYR D 156 " --> pdb=" O   ILE D 152 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 161 through 167
    Processing helix  chain 'D' and resid 170 through 178
    Processing helix  chain 'D' and resid 181 through 193
      removed outlier: 3.515A  pdb=" N   VAL D 184 " --> pdb=" O   LYS D 181 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 194 through 208
      removed outlier: 4.241A  pdb=" N   VAL D 198 " --> pdb=" O   ARG D 194 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 212 through 221
      removed outlier: 3.670A  pdb=" N   ILE D 218 " --> pdb=" O   LEU D 214 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 223 through 243
      removed outlier: 4.217A  pdb=" N   THR D 229 " --> pdb=" O   GLU D 225 " (cutoff:3.500A)
      removed outlier: 4.050A  pdb=" N   HIS D 230 " --> pdb=" O   LEU D 226 " (cutoff:3.500A)
      removed outlier: 3.553A  pdb=" N   PHE D 236 " --> pdb=" O   ALA D 232 " (cutoff:3.500A)
      removed outlier: 3.528A  pdb=" N   ALA D 240 " --> pdb=" O   PHE D 236 " (cutoff:3.500A)
      removed outlier: 4.189A  pdb=" N   LEU D 243 " --> pdb=" O   LEU D 239 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 244 through 248
    Processing helix  chain 'D' and resid 265 through 269
    Processing helix  chain 'D' and resid 270 through 287
    Processing helix  chain 'D' and resid 299 through 330
      removed outlier: 3.508A  pdb=" N   ALA D 317 " --> pdb=" O   MET D 313 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 332 through 351
      removed outlier: 4.130A  pdb=" N   PHE D 336 " --> pdb=" O   LYS D 332 " (cutoff:3.500A)
      removed outlier: 3.553A  pdb=" N   ARG D 337 " --> pdb=" O   THR D 333 " (cutoff:3.500A)
      removed outlier: 4.160A  pdb=" N   ASP D 338 " --> pdb=" O   GLU D 334 " (cutoff:3.500A)
      removed outlier: 3.539A  pdb=" N   LYS D 339 " --> pdb=" O   ARG D 335 " (cutoff:3.500A)
      removed outlier: 3.653A  pdb=" N   ILE D 343 " --> pdb=" O   LYS D 339 " (cutoff:3.500A)
      removed outlier: 3.754A  pdb=" N   ARG D 345 " --> pdb=" O   ALA D 341 " (cutoff:3.500A)
      removed outlier: 3.829A  pdb=" N   ASN D 348 " --> pdb=" O   MET D 344 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 353 through 369
    Processing helix  chain 'D' and resid 382 through 394
      removed outlier: 5.277A  pdb=" N   LYS D 388 " --> pdb=" O   SER D 384 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 394 through 400
      removed outlier: 4.038A  pdb=" N   LYS D 400 " --> pdb=" O   PRO D 396 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 401 through 405
    Processing helix  chain 'D' and resid 408 through 418
      removed outlier: 3.576A  pdb=" N   ARG D 418 " --> pdb=" O   GLN D 414 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 472 through 479
      removed outlier: 3.838A  pdb=" N   ILE D 476 " --> pdb=" O   GLY D 472 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 499 through 509
    Processing helix  chain 'D' and resid 509 through 524
    Processing helix  chain 'C' and resid 79 through 98
      removed outlier: 3.719A  pdb=" N   SER C  96 " --> pdb=" O   TRP C  92 " (cutoff:3.500A)
      removed outlier: 3.568A  pdb=" N   PHE C  98 " --> pdb=" O   LEU C  94 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 99 through 105
    Processing helix  chain 'C' and resid 113 through 131
      removed outlier: 4.018A  pdb=" N   LEU C 117 " --> pdb=" O   ASN C 113 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 148 through 160
      removed outlier: 4.131A  pdb=" N   ALA C 153 " --> pdb=" O   ARG C 149 " (cutoff:3.500A)
      removed outlier: 4.435A  pdb=" N   LEU C 154 " --> pdb=" O   SER C 150 " (cutoff:3.500A)
      removed outlier: 4.818A  pdb=" N   ARG C 155 " --> pdb=" O   SER C 151 " (cutoff:3.500A)
      removed outlier: 3.994A  pdb=" N   TYR C 156 " --> pdb=" O   ILE C 152 " (cutoff:3.500A)
      removed outlier: 4.113A  pdb=" N   LYS C 158 " --> pdb=" O   LEU C 154 " (cutoff:3.500A)
      removed outlier: 3.514A  pdb=" N   THR C 160 " --> pdb=" O   TYR C 156 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 160 through 167
      removed outlier: 3.603A  pdb=" N   LEU C 166 " --> pdb=" O   ILE C 162 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 170 through 178
    Processing helix  chain 'C' and resid 181 through 187
      removed outlier: 4.441A  pdb=" N   ARG C 185 " --> pdb=" O   LYS C 181 " (cutoff:3.500A)
      removed outlier: 3.767A  pdb=" N   TYR C 186 " --> pdb=" O   GLU C 182 " (cutoff:3.500A)
      removed outlier: 3.990A  pdb=" N   LEU C 187 " --> pdb=" O   GLU C 183 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 181 through 187'
    Processing helix  chain 'C' and resid 188 through 193
    Processing helix  chain 'C' and resid 194 through 208
      removed outlier: 4.188A  pdb=" N   VAL C 198 " --> pdb=" O   ARG C 194 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 212 through 242
      removed outlier: 3.961A  pdb=" N   CYS C 228 " --> pdb=" O   VAL C 224 " (cutoff:3.500A)
      removed outlier: 3.581A  pdb=" N   ILE C 235 " --> pdb=" O   THR C 231 " (cutoff:3.500A)
      removed outlier: 3.664A  pdb=" N   TYR C 238 " --> pdb=" O   CYS C 234 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 247 through 251
      removed outlier: 3.557A  pdb=" N   THR C 251 " --> pdb=" O   GLU C 248 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 265 through 269
    Processing helix  chain 'C' and resid 270 through 287
      removed outlier: 3.591A  pdb=" N   SER C 278 " --> pdb=" O   ARG C 274 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 298 through 330
    Processing helix  chain 'C' and resid 331 through 351
    Processing helix  chain 'C' and resid 353 through 380
      removed outlier: 3.988A  pdb=" N   ARG C 357 " --> pdb=" O   GLY C 353 " (cutoff:3.500A)
      removed outlier: 3.684A  pdb=" N   ASP C 380 " --> pdb=" O   ALA C 376 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 382 through 394
    Processing helix  chain 'C' and resid 394 through 400
      removed outlier: 4.102A  pdb=" N   LYS C 400 " --> pdb=" O   PRO C 396 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 408 through 418
      removed outlier: 3.768A  pdb=" N   ILE C 417 " --> pdb=" O   ASN C 413 " (cutoff:3.500A)
      removed outlier: 4.055A  pdb=" N   ARG C 418 " --> pdb=" O   GLN C 414 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 473 through 478
    Processing helix  chain 'C' and resid 499 through 509
      removed outlier: 3.561A  pdb=" N   ILE C 508 " --> pdb=" O   ASN C 504 " (cutoff:3.500A)
      removed outlier: 3.563A  pdb=" N   PHE C 509 " --> pdb=" O   ILE C 505 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 509 through 521
      removed outlier: 3.516A  pdb=" N   ARG C 515 " --> pdb=" O   HIS C 511 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 532 through 545
      removed outlier: 4.208A  pdb=" N   PHE C 539 " --> pdb=" O   SER C 535 " (cutoff:3.500A)
      removed outlier: 4.162A  pdb=" N   HIS C 540 " --> pdb=" O   ASP C 536 " (cutoff:3.500A)
      removed outlier: 3.506A  pdb=" N   ILE C 541 " --> pdb=" O   ILE C 537 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'B' and resid 137 through 139
      removed outlier: 3.758A  pdb=" N   TYR B 137 " --> pdb=" O   ILE B 146 " (cutoff:3.500A)
      removed outlier: 3.698A  pdb=" N   ASP B 139 " --> pdb=" O   ARG B 144 " (cutoff:3.500A)
      removed outlier: 3.711A  pdb=" N   ARG B 144 " --> pdb=" O   ASP B 139 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 420 through 424
      removed outlier: 3.563A  pdb=" N   GLU B 422 " --> pdb=" O   ILE B 494 " (cutoff:3.500A)
      removed outlier: 3.589A  pdb=" N   ILE B 494 " --> pdb=" O   GLU B 422 " (cutoff:3.500A)
      removed outlier: 3.948A  pdb=" N   PHE B 424 " --> pdb=" O   CYS B 492 " (cutoff:3.500A)
      removed outlier: 3.926A  pdb=" N   CYS B 492 " --> pdb=" O   PHE B 424 " (cutoff:3.500A)
      removed outlier: 6.856A  pdb=" N   ARG B 493 " --> pdb=" O   CYS B 444 " (cutoff:3.500A)
      removed outlier: 3.692A  pdb=" N   TYR B 441 " --> pdb=" O   PHE B 471 " (cutoff:3.500A)
      removed outlier: 3.529A  pdb=" N   PHE B 471 " --> pdb=" O   TYR B 441 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 460 through 465
      removed outlier: 6.620A  pdb=" N   GLU B 450 " --> pdb=" O   VAL B 462 " (cutoff:3.500A)
      removed outlier: 4.686A  pdb=" N   VAL B 464 " --> pdb=" O   LEU B 448 " (cutoff:3.500A)
      removed outlier: 6.370A  pdb=" N   LEU B 448 " --> pdb=" O   VAL B 464 " (cutoff:3.500A)
      removed outlier: 3.599A  pdb=" N   GLU B 449 " --> pdb=" O   ARG B 487 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 420 through 421
    Processing sheet with id=AA5, first strand: chain 'A' and resid 463 through 465
      removed outlier: 3.502A  pdb=" N   ALA A 463 " --> pdb=" O   GLU A 450 " (cutoff:3.500A)
      removed outlier: 6.719A  pdb=" N   VAL A 447 " --> pdb=" O   ALA A 489 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'D' and resid 137 through 139
      removed outlier: 3.759A  pdb=" N   TYR D 137 " --> pdb=" O   ILE D 146 " (cutoff:3.500A)
      removed outlier: 3.698A  pdb=" N   ASP D 139 " --> pdb=" O   ARG D 144 " (cutoff:3.500A)
      removed outlier: 3.712A  pdb=" N   ARG D 144 " --> pdb=" O   ASP D 139 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'D' and resid 420 through 424
      removed outlier: 3.563A  pdb=" N   GLU D 422 " --> pdb=" O   ILE D 494 " (cutoff:3.500A)
      removed outlier: 3.588A  pdb=" N   ILE D 494 " --> pdb=" O   GLU D 422 " (cutoff:3.500A)
      removed outlier: 3.948A  pdb=" N   PHE D 424 " --> pdb=" O   CYS D 492 " (cutoff:3.500A)
      removed outlier: 3.926A  pdb=" N   CYS D 492 " --> pdb=" O   PHE D 424 " (cutoff:3.500A)
      removed outlier: 6.856A  pdb=" N   ARG D 493 " --> pdb=" O   CYS D 444 " (cutoff:3.500A)
      removed outlier: 3.692A  pdb=" N   TYR D 441 " --> pdb=" O   PHE D 471 " (cutoff:3.500A)
      removed outlier: 3.529A  pdb=" N   PHE D 471 " --> pdb=" O   TYR D 441 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'D' and resid 460 through 465
      removed outlier: 6.621A  pdb=" N   GLU D 450 " --> pdb=" O   VAL D 462 " (cutoff:3.500A)
      removed outlier: 4.687A  pdb=" N   VAL D 464 " --> pdb=" O   LEU D 448 " (cutoff:3.500A)
      removed outlier: 6.369A  pdb=" N   LEU D 448 " --> pdb=" O   VAL D 464 " (cutoff:3.500A)
      removed outlier: 3.600A  pdb=" N   GLU D 449 " --> pdb=" O   ARG D 487 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'C' and resid 420 through 421
    Processing sheet with id=AB1, first strand: chain 'C' and resid 463 through 465
      removed outlier: 3.502A  pdb=" N   ALA C 463 " --> pdb=" O   GLU C 450 " (cutoff:3.500A)
      removed outlier: 6.719A  pdb=" N   VAL C 447 " --> pdb=" O   ALA C 489 " (cutoff:3.500A)

    837 hydrogen bonds defined for protein.
    2355 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: 4.64

  Time building geometry restraints manager: 4.90 seconds

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

  Histogram of bond lengths:
        1.17 -     1.30: 2302
        1.30 -     1.43: 4363
        1.43 -     1.56: 8865
        1.56 -     1.69: 8
        1.69 -     1.82: 156
  Bond restraints: 15694
  Sorted by residual:
  bond pdb=" C   ASN A 355 "
       pdb=" O   ASN A 355 "
    ideal  model  delta    sigma   weight residual
    1.235  1.310 -0.075 1.26e-02 6.30e+03 3.52e+01
  bond pdb=" C   ASN C 355 "
       pdb=" O   ASN C 355 "
    ideal  model  delta    sigma   weight residual
    1.235  1.309 -0.074 1.26e-02 6.30e+03 3.45e+01
  bond pdb=" C   SER A 331 "
       pdb=" O   SER A 331 "
    ideal  model  delta    sigma   weight residual
    1.235  1.170  0.065 1.32e-02 5.74e+03 2.40e+01
  bond pdb=" C   SER C 331 "
       pdb=" O   SER C 331 "
    ideal  model  delta    sigma   weight residual
    1.235  1.171  0.064 1.32e-02 5.74e+03 2.35e+01
  bond pdb=" C   GLN A 359 "
       pdb=" O   GLN A 359 "
    ideal  model  delta    sigma   weight residual
    1.236  1.290 -0.053 1.15e-02 7.56e+03 2.15e+01
  ... (remaining 15689 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.58: 20930
        3.58 -     7.16: 177
        7.16 -    10.75: 25
       10.75 -    14.33: 0
       14.33 -    17.91: 2
  Bond angle restraints: 21134
  Sorted by residual:
  angle pdb=" N   ASN A 348 "
        pdb=" CA  ASN A 348 "
        pdb=" C   ASN A 348 "
      ideal   model   delta    sigma   weight residual
     112.23  101.94   10.29 1.26e+00 6.30e-01 6.67e+01
  angle pdb=" N   ASN C 348 "
        pdb=" CA  ASN C 348 "
        pdb=" C   ASN C 348 "
      ideal   model   delta    sigma   weight residual
     112.23  101.96   10.27 1.26e+00 6.30e-01 6.65e+01
  angle pdb=" N   LEU D 226 "
        pdb=" CA  LEU D 226 "
        pdb=" C   LEU D 226 "
      ideal   model   delta    sigma   weight residual
     113.72  104.00    9.72 1.30e+00 5.92e-01 5.60e+01
  angle pdb=" N   LYS C 332 "
        pdb=" CA  LYS C 332 "
        pdb=" C   LYS C 332 "
      ideal   model   delta    sigma   weight residual
     111.14  103.08    8.06 1.08e+00 8.57e-01 5.58e+01
  angle pdb=" N   LYS A 332 "
        pdb=" CA  LYS A 332 "
        pdb=" C   LYS A 332 "
      ideal   model   delta    sigma   weight residual
     111.14  103.10    8.04 1.08e+00 8.57e-01 5.54e+01
  ... (remaining 21129 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.75: 7694
       17.75 -    35.50: 1141
       35.50 -    53.25: 408
       53.25 -    71.00: 91
       71.00 -    88.75: 22
  Dihedral angle restraints: 9356
    sinusoidal: 3958
      harmonic: 5398
  Sorted by residual:
  dihedral pdb=" CA  GLU D 112 "
           pdb=" C   GLU D 112 "
           pdb=" N   ASN D 113 "
           pdb=" CA  ASN D 113 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -159.59  -20.41     0      5.00e+00 4.00e-02 1.67e+01
  dihedral pdb=" CA  GLU B 112 "
           pdb=" C   GLU B 112 "
           pdb=" N   ASN B 113 "
           pdb=" CA  ASN B 113 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -159.61  -20.39     0      5.00e+00 4.00e-02 1.66e+01
  dihedral pdb=" C   CYS D 228 "
           pdb=" N   CYS D 228 "
           pdb=" CA  CYS D 228 "
           pdb=" CB  CYS D 228 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -131.35    8.75     0      2.50e+00 1.60e-01 1.23e+01
  ... (remaining 9353 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.061: 1916
       0.061 -    0.121: 331
       0.121 -    0.182: 52
       0.182 -    0.243: 22
       0.243 -    0.304: 7
  Chirality restraints: 2328
  Sorted by residual:
  chirality pdb=" CA  CYS D 228 "
            pdb=" N   CYS D 228 "
            pdb=" C   CYS D 228 "
            pdb=" CB  CYS D 228 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.21    0.30 2.00e-01 2.50e+01 2.30e+00
  chirality pdb=" CA  ASN C 350 "
            pdb=" N   ASN C 350 "
            pdb=" C   ASN C 350 "
            pdb=" CB  ASN C 350 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.22    0.29 2.00e-01 2.50e+01 2.08e+00
  chirality pdb=" CA  ASN A 350 "
            pdb=" N   ASN A 350 "
            pdb=" C   ASN A 350 "
            pdb=" CB  ASN A 350 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.22    0.29 2.00e-01 2.50e+01 2.06e+00
  ... (remaining 2325 not shown)

  Planarity restraints: 2592
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASP C 380 "   -0.027 2.00e-02 2.50e+03   5.40e-02 2.92e+01
        pdb=" C   ASP C 380 "    0.094 2.00e-02 2.50e+03
        pdb=" O   ASP C 380 "   -0.034 2.00e-02 2.50e+03
        pdb=" N   ILE C 381 "   -0.032 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASP A 380 "    0.027 2.00e-02 2.50e+03   5.39e-02 2.91e+01
        pdb=" C   ASP A 380 "   -0.093 2.00e-02 2.50e+03
        pdb=" O   ASP A 380 "    0.034 2.00e-02 2.50e+03
        pdb=" N   ILE A 381 "    0.032 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP A 270 "    0.070 5.00e-02 4.00e+02   1.00e-01 1.61e+01
        pdb=" N   PRO A 271 "   -0.173 5.00e-02 4.00e+02
        pdb=" CA  PRO A 271 "    0.049 5.00e-02 4.00e+02
        pdb=" CD  PRO A 271 "    0.054 5.00e-02 4.00e+02
  ... (remaining 2589 not shown)

  Histogram of nonbonded interaction distances:
        1.05 -     1.82: 11
        1.82 -     2.59: 198
        2.59 -     3.36: 20841
        3.36 -     4.13: 37714
        4.13 -     4.90: 68846
  Nonbonded interactions: 127610
  Sorted by model distance:
  nonbonded pdb=" CG1 ILE A 360 "
            pdb=" CD1 ILE D 385 "
     model   vdw
     1.049 3.860
  nonbonded pdb=" CG1 ILE A 360 "
            pdb=" CG1 ILE D 385 "
     model   vdw
     1.127 3.840
  nonbonded pdb=" NH2 ARG A 345 "
            pdb=" OE1 GLU D 374 "
     model   vdw
     1.261 3.120
  nonbonded pdb=" CD1 ILE B 385 "
            pdb=" CG1 ILE C 360 "
     model   vdw
     1.395 3.860
  nonbonded pdb=" CD1 ILE A 360 "
            pdb=" CG1 ILE D 385 "
     model   vdw
     1.405 3.860
  ... (remaining 127605 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: 0.04
Found NCS groups:
ncs_group {
  reference = (chain 'A' and (resid 73 through 525 or resid 902 or (resid 903 and (name C21 or \ 
 name C22 or name C23 or name C24 or name C25 or name C26 or name C27 or name C2 \ 
8 or name C29 or name C2A)) or resid 904))
  selection = (chain 'B' and (resid 73 through 452 or resid 462 through 525 or resid 901 or (r \ 
esid 902 and (name C21 or name C22 or name C23 or name C24 or name C25 or name C \ 
26 or name C27 or name C28 or name C29 or name C2A)) or resid 903))
  selection = (chain 'C' and (resid 73 through 525 or resid 902 or (resid 903 and (name C21 or \ 
 name C22 or name C23 or name C24 or name C25 or name C26 or name C27 or name C2 \ 
8 or name C29 or name C2A)) or resid 904))
  selection = (chain 'D' and (resid 73 through 452 or resid 462 through 525 or resid 901 or (r \ 
esid 902 and (name C21 or name C22 or name C23 or name C24 or name C25 or name C \ 
26 or name C27 or name C28 or name C29 or name C2A)) or resid 903))
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
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:             1.180
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.020
  Extract box with map and model:          0.520
  Check model and map are aligned:         0.110
  Set scattering table:                    0.130
  Process input model:                     35.780
  Find NCS groups from input model:        1.080
  Set up NCS constraints:                  0.060
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:3.040
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   41.920
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6584
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      :  0.012   0.884  15702  Z= 1.124
  Angle     :  0.838  17.910  21134  Z= 0.532
  Chirality :  0.053   0.304   2328
  Planarity :  0.006   0.100   2592
  Dihedral  : 19.522  88.748   5888
  Min Nonbonded Distance : 1.049

Molprobity Statistics.
  All-atom Clashscore : 21.56
  Ramachandran Plot:
    Outliers :  0.72 %
    Allowed  :  6.24 %
    Favored  : 93.04 %
  Rotamer:
    Outliers :  5.09 %
    Allowed  : 27.30 %
    Favored  : 67.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.15 (0.20), residues: 1810
  helix: -0.98 (0.16), residues: 1040
  sheet: -0.97 (0.97), residues: 34
  loop : -0.12 (0.25), residues: 736

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP C 171 
 HIS   0.004   0.001   HIS C 295 
 PHE   0.030   0.002   PHE D 223 
 TYR   0.013   0.001   TYR B 237 
 ARG   0.004   0.000   ARG C 194 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.26261 (  837)
  hydrogen bonds       : angle       9.26269 ( 2355)
  covalent geometry    : bond        0.00576 (15694)
  covalent geometry    : angle       0.83753 (21134)
  Misc. bond           : bond        0.47052 (    8)

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

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

  3620 Ramachandran restraints generated.
    1810 Oldfield, 0 Emsley, 1810 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3620 Ramachandran restraints generated.
    1810 Oldfield, 0 Emsley, 1810 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  318 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 83
    poor density    : 235
  time to evaluate  : 1.502 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  152 ILE cc_start: 0.5216 (OUTLIER) cc_final: 0.4568 (tp)
REVERT: B  377 VAL cc_start: 0.6841 (OUTLIER) cc_final: 0.6438 (t)
REVERT: B  468 ASP cc_start: 0.5185 (t0) cc_final: 0.4528 (t0)
REVERT: A  145 MET cc_start: 0.6947 (tpp) cc_final: 0.6686 (tpp)
REVERT: A  351 LYS cc_start: 0.3960 (OUTLIER) cc_final: 0.3589 (mttp)
REVERT: A  365 ARG cc_start: 0.0571 (OUTLIER) cc_final: 0.0045 (ttp-170)
REVERT: D  128 ASP cc_start: 0.7860 (t0) cc_final: 0.7659 (t70)
REVERT: D  468 ASP cc_start: 0.5363 (t0) cc_final: 0.5022 (t0)
REVERT: C  183 GLU cc_start: 0.5865 (tm-30) cc_final: 0.5435 (tt0)
REVERT: C  365 ARG cc_start: 0.1331 (OUTLIER) cc_final: 0.0286 (ttp-170)
REVERT: C  369 GLU cc_start: 0.2964 (OUTLIER) cc_final: 0.2512 (pt0)
  outliers start: 83
  outliers final: 31
  residues processed: 306
  average time/residue: 0.2972
  time to fit residues: 129.9292
Evaluate side-chains
  227 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 190
  time to evaluate  : 1.562 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  152 ILE
Chi-restraints excluded: chain B residue  222 ILE
Chi-restraints excluded: chain B residue  224 VAL
Chi-restraints excluded: chain B residue  377 VAL
Chi-restraints excluded: chain B residue  385 ILE
Chi-restraints excluded: chain A residue  333 THR
Chi-restraints excluded: chain A residue  334 GLU
Chi-restraints excluded: chain A residue  336 PHE
Chi-restraints excluded: chain A residue  340 MET
Chi-restraints excluded: chain A residue  343 ILE
Chi-restraints excluded: chain A residue  351 LYS
Chi-restraints excluded: chain A residue  352 LEU
Chi-restraints excluded: chain A residue  354 ARG
Chi-restraints excluded: chain A residue  356 ILE
Chi-restraints excluded: chain A residue  360 ILE
Chi-restraints excluded: chain A residue  364 LEU
Chi-restraints excluded: chain A residue  365 ARG
Chi-restraints excluded: chain A residue  369 GLU
Chi-restraints excluded: chain A residue  377 VAL
Chi-restraints excluded: chain A residue  380 ASP
Chi-restraints excluded: chain D residue  224 VAL
Chi-restraints excluded: chain D residue  377 VAL
Chi-restraints excluded: chain D residue  385 ILE
Chi-restraints excluded: chain C residue  333 THR
Chi-restraints excluded: chain C residue  336 PHE
Chi-restraints excluded: chain C residue  340 MET
Chi-restraints excluded: chain C residue  344 MET
Chi-restraints excluded: chain C residue  351 LYS
Chi-restraints excluded: chain C residue  352 LEU
Chi-restraints excluded: chain C residue  360 ILE
Chi-restraints excluded: chain C residue  364 LEU
Chi-restraints excluded: chain C residue  365 ARG
Chi-restraints excluded: chain C residue  367 GLN
Chi-restraints excluded: chain C residue  369 GLU
Chi-restraints excluded: chain C residue  377 VAL
Chi-restraints excluded: chain C residue  379 GLN
Chi-restraints excluded: chain C residue  380 ASP
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 180
   random chunks:
   chunk 151 optimal weight:    1.9990
   chunk 136 optimal weight:    0.5980
   chunk 75 optimal weight:    9.9990
   chunk 46 optimal weight:    0.5980
   chunk 92 optimal weight:    0.6980
   chunk 72 optimal weight:    3.9990
   chunk 141 optimal weight:    2.9990
   chunk 54 optimal weight:    2.9990
   chunk 85 optimal weight:   10.0000
   chunk 105 optimal weight:    0.5980
   chunk 163 optimal weight:    7.9990
   overall best weight:    0.8982

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

Flipped N/Q/H residues before XYZ refinement:
B 439 GLN
A 359 GLN
D 295 HIS
D 312 ASN
D 439 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4835 r_free = 0.4835 target = 0.260546 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 69)----------------|
| r_work = 0.4312 r_free = 0.4312 target = 0.196125 restraints weight = 19494.340|
|-----------------------------------------------------------------------------|
r_work (start): 0.4222 rms_B_bonded: 2.31
r_work: 0.3740 rms_B_bonded: 2.82 restraints_weight: 0.5000
r_work: 0.3605 rms_B_bonded: 4.44 restraints_weight: 0.2500
r_work (final): 0.3605
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7389
moved from start:          0.2031

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045  15702  Z= 0.169
  Angle     :  0.658  11.054  21134  Z= 0.346
  Chirality :  0.044   0.172   2328
  Planarity :  0.005   0.064   2592
  Dihedral  : 11.799  94.086   2360
  Min Nonbonded Distance : 2.489

Molprobity Statistics.
  All-atom Clashscore : 13.57
  Ramachandran Plot:
    Outliers :  0.44 %
    Allowed  :  5.58 %
    Favored  : 93.98 %
  Rotamer:
    Outliers :  4.91 %
    Allowed  : 25.64 %
    Favored  : 69.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.37 (0.20), residues: 1810
  helix: -0.26 (0.16), residues: 1074
  sheet: -0.55 (1.21), residues: 20
  loop :  0.06 (0.25), residues: 716

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP D  92 
 HIS   0.004   0.001   HIS A 469 
 PHE   0.024   0.002   PHE D 281 
 TYR   0.020   0.001   TYR C 368 
 ARG   0.013   0.001   ARG C 365 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05557 (  837)
  hydrogen bonds       : angle       5.86682 ( 2355)
  covalent geometry    : bond        0.00363 (15694)
  covalent geometry    : angle       0.65761 (21134)
  Misc. bond           : bond        0.00310 (    8)

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

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

  3620 Ramachandran restraints generated.
    1810 Oldfield, 0 Emsley, 1810 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3620 Ramachandran restraints generated.
    1810 Oldfield, 0 Emsley, 1810 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  298 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 80
    poor density    : 218
  time to evaluate  : 1.532 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   87 MET cc_start: 0.7534 (mmp) cc_final: 0.6454 (mmm)
REVERT: B  152 ILE cc_start: 0.5870 (OUTLIER) cc_final: 0.5241 (tp)
REVERT: B  218 ILE cc_start: 0.6358 (OUTLIER) cc_final: 0.5387 (tt)
REVERT: B  367 GLN cc_start: 0.7872 (mt0) cc_final: 0.7496 (mp10)
REVERT: B  377 VAL cc_start: 0.7248 (OUTLIER) cc_final: 0.7044 (t)
REVERT: A   89 ILE cc_start: 0.8273 (OUTLIER) cc_final: 0.7995 (tp)
REVERT: A  145 MET cc_start: 0.8231 (tpp) cc_final: 0.7719 (tpp)
REVERT: A  260 ASP cc_start: 0.8137 (m-30) cc_final: 0.7801 (t70)
REVERT: A  339 LYS cc_start: 0.6523 (mmtt) cc_final: 0.6318 (pttm)
REVERT: A  355 ASN cc_start: 0.6425 (OUTLIER) cc_final: 0.5655 (p0)
REVERT: A  360 ILE cc_start: 0.4338 (OUTLIER) cc_final: 0.4025 (mm)
REVERT: A  369 GLU cc_start: 0.0300 (OUTLIER) cc_final: -0.0112 (pt0)
REVERT: A  404 PHE cc_start: 0.7513 (OUTLIER) cc_final: 0.7295 (t80)
REVERT: D  340 MET cc_start: 0.6553 (mpp) cc_final: 0.6350 (mpp)
REVERT: D  421 GLU cc_start: 0.6943 (mt-10) cc_final: 0.6505 (tm-30)
REVERT: C   89 ILE cc_start: 0.7861 (OUTLIER) cc_final: 0.7499 (tp)
REVERT: C   92 TRP cc_start: 0.7763 (m100) cc_final: 0.7520 (m100)
REVERT: C  171 TRP cc_start: 0.7764 (m100) cc_final: 0.7303 (m100)
REVERT: C  221 LEU cc_start: 0.7963 (mm) cc_final: 0.7577 (mt)
REVERT: C  359 GLN cc_start: 0.4510 (tm-30) cc_final: 0.4104 (mm110)
REVERT: C  369 GLU cc_start: 0.1040 (OUTLIER) cc_final: 0.0719 (pt0)
REVERT: C  404 PHE cc_start: 0.7528 (OUTLIER) cc_final: 0.7178 (t80)
  outliers start: 80
  outliers final: 37
  residues processed: 282
  average time/residue: 0.2393
  time to fit residues: 104.9782
Evaluate side-chains
  229 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 181
  time to evaluate  : 1.580 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  116 ILE
Chi-restraints excluded: chain B residue  130 VAL
Chi-restraints excluded: chain B residue  152 ILE
Chi-restraints excluded: chain B residue  154 LEU
Chi-restraints excluded: chain B residue  211 ILE
Chi-restraints excluded: chain B residue  218 ILE
Chi-restraints excluded: chain B residue  222 ILE
Chi-restraints excluded: chain B residue  301 GLU
Chi-restraints excluded: chain B residue  302 MET
Chi-restraints excluded: chain B residue  377 VAL
Chi-restraints excluded: chain B residue  445 HIS
Chi-restraints excluded: chain B residue  516 ILE
Chi-restraints excluded: chain A residue   89 ILE
Chi-restraints excluded: chain A residue  119 ILE
Chi-restraints excluded: chain A residue  192 LEU
Chi-restraints excluded: chain A residue  301 GLU
Chi-restraints excluded: chain A residue  310 SER
Chi-restraints excluded: chain A residue  336 PHE
Chi-restraints excluded: chain A residue  354 ARG
Chi-restraints excluded: chain A residue  355 ASN
Chi-restraints excluded: chain A residue  360 ILE
Chi-restraints excluded: chain A residue  369 GLU
Chi-restraints excluded: chain A residue  380 ASP
Chi-restraints excluded: chain A residue  404 PHE
Chi-restraints excluded: chain A residue  407 CYS
Chi-restraints excluded: chain A residue  537 ILE
Chi-restraints excluded: chain D residue   97 SER
Chi-restraints excluded: chain D residue  116 ILE
Chi-restraints excluded: chain D residue  211 ILE
Chi-restraints excluded: chain D residue  218 ILE
Chi-restraints excluded: chain D residue  301 GLU
Chi-restraints excluded: chain D residue  302 MET
Chi-restraints excluded: chain D residue  319 LEU
Chi-restraints excluded: chain D residue  338 ASP
Chi-restraints excluded: chain D residue  364 LEU
Chi-restraints excluded: chain D residue  377 VAL
Chi-restraints excluded: chain D residue  445 HIS
Chi-restraints excluded: chain D residue  516 ILE
Chi-restraints excluded: chain C residue   89 ILE
Chi-restraints excluded: chain C residue  301 GLU
Chi-restraints excluded: chain C residue  310 SER
Chi-restraints excluded: chain C residue  336 PHE
Chi-restraints excluded: chain C residue  344 MET
Chi-restraints excluded: chain C residue  360 ILE
Chi-restraints excluded: chain C residue  369 GLU
Chi-restraints excluded: chain C residue  380 ASP
Chi-restraints excluded: chain C residue  404 PHE
Chi-restraints excluded: chain C residue  407 CYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 180
   random chunks:
   chunk 57 optimal weight:    5.9990
   chunk 37 optimal weight:   20.0000
   chunk 20 optimal weight:    0.8980
   chunk 146 optimal weight:    0.6980
   chunk 35 optimal weight:    7.9990
   chunk 171 optimal weight:   20.0000
   chunk 156 optimal weight:    0.9980
   chunk 160 optimal weight:    5.9990
   chunk 13 optimal weight:    4.9990
   chunk 31 optimal weight:    2.9990
   chunk 36 optimal weight:    6.9990
   overall best weight:    2.1184

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

Flipped N/Q/H residues before XYZ refinement:
B 230 HIS
D 230 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4800 r_free = 0.4800 target = 0.255560 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.4287 r_free = 0.4287 target = 0.194317 restraints weight = 18991.166|
|-----------------------------------------------------------------------------|
r_work (start): 0.4227 rms_B_bonded: 3.27
r_work: 0.3536 rms_B_bonded: 3.85 restraints_weight: 0.5000
r_work (final): 0.3536
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7300
moved from start:          0.2823

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.050  15702  Z= 0.236
  Angle     :  0.676  11.019  21134  Z= 0.353
  Chirality :  0.046   0.152   2328
  Planarity :  0.005   0.061   2592
  Dihedral  : 10.396  88.191   2307
  Min Nonbonded Distance : 2.451

Molprobity Statistics.
  All-atom Clashscore : 14.53
  Ramachandran Plot:
    Outliers :  0.44 %
    Allowed  :  5.97 %
    Favored  : 93.59 %
  Rotamer:
    Outliers :  5.28 %
    Allowed  : 25.21 %
    Favored  : 69.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.40 (0.20), residues: 1810
  helix: -0.16 (0.15), residues: 1088
  sheet: -0.81 (0.70), residues: 60
  loop : -0.08 (0.26), residues: 662

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP D  92 
 HIS   0.006   0.001   HIS A 295 
 PHE   0.020   0.002   PHE D 281 
 TYR   0.017   0.002   TYR C 238 
 ARG   0.009   0.001   ARG B 349 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04951 (  837)
  hydrogen bonds       : angle       5.53737 ( 2355)
  covalent geometry    : bond        0.00544 (15694)
  covalent geometry    : angle       0.67616 (21134)
  Misc. bond           : bond        0.00218 (    8)

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

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

  3620 Ramachandran restraints generated.
    1810 Oldfield, 0 Emsley, 1810 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3620 Ramachandran restraints generated.
    1810 Oldfield, 0 Emsley, 1810 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  272 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 86
    poor density    : 186
  time to evaluate  : 1.821 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  158 LYS cc_start: 0.7871 (OUTLIER) cc_final: 0.7364 (tppt)
REVERT: B  218 ILE cc_start: 0.5683 (OUTLIER) cc_final: 0.4897 (tt)
REVERT: B  421 GLU cc_start: 0.6849 (tp30) cc_final: 0.6638 (mt-10)
REVERT: A   89 ILE cc_start: 0.8077 (OUTLIER) cc_final: 0.7857 (tp)
REVERT: A  126 LEU cc_start: 0.7497 (mt) cc_final: 0.6899 (mt)
REVERT: A  306 MET cc_start: 0.8102 (mmt) cc_final: 0.7857 (mmp)
REVERT: A  339 LYS cc_start: 0.6709 (mmtt) cc_final: 0.6241 (pttm)
REVERT: A  340 MET cc_start: 0.4047 (mmt) cc_final: 0.3242 (ptp)
REVERT: A  344 MET cc_start: 0.5453 (mmm) cc_final: 0.4695 (pmm)
REVERT: A  368 TYR cc_start: 0.3787 (OUTLIER) cc_final: 0.3445 (p90)
REVERT: A  404 PHE cc_start: 0.7489 (OUTLIER) cc_final: 0.7112 (t80)
REVERT: A  431 MET cc_start: 0.3680 (mmm) cc_final: 0.3474 (mmm)
REVERT: D  218 ILE cc_start: 0.6225 (OUTLIER) cc_final: 0.5242 (tt)
REVERT: D  222 ILE cc_start: 0.8068 (tt) cc_final: 0.7755 (tt)
REVERT: D  334 GLU cc_start: 0.7001 (OUTLIER) cc_final: 0.6709 (pm20)
REVERT: D  421 GLU cc_start: 0.6834 (mt-10) cc_final: 0.6426 (tm-30)
REVERT: C   89 ILE cc_start: 0.7971 (OUTLIER) cc_final: 0.7673 (tp)
REVERT: C  306 MET cc_start: 0.8101 (OUTLIER) cc_final: 0.7895 (mmp)
REVERT: C  322 ASN cc_start: 0.7664 (OUTLIER) cc_final: 0.6998 (m-40)
REVERT: C  355 ASN cc_start: 0.4736 (OUTLIER) cc_final: 0.4211 (p0)
REVERT: C  359 GLN cc_start: 0.4497 (tm-30) cc_final: 0.3965 (mp10)
REVERT: C  369 GLU cc_start: 0.2728 (OUTLIER) cc_final: 0.2300 (pt0)
REVERT: C  404 PHE cc_start: 0.7553 (OUTLIER) cc_final: 0.7099 (t80)
  outliers start: 86
  outliers final: 42
  residues processed: 255
  average time/residue: 0.2449
  time to fit residues: 95.4465
Evaluate side-chains
  232 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 55
    poor density    : 177
  time to evaluate  : 1.508 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  116 ILE
Chi-restraints excluded: chain B residue  158 LYS
Chi-restraints excluded: chain B residue  218 ILE
Chi-restraints excluded: chain B residue  258 LEU
Chi-restraints excluded: chain B residue  299 MET
Chi-restraints excluded: chain B residue  302 MET
Chi-restraints excluded: chain B residue  310 SER
Chi-restraints excluded: chain B residue  319 LEU
Chi-restraints excluded: chain B residue  445 HIS
Chi-restraints excluded: chain A residue   89 ILE
Chi-restraints excluded: chain A residue  119 ILE
Chi-restraints excluded: chain A residue  129 ILE
Chi-restraints excluded: chain A residue  137 TYR
Chi-restraints excluded: chain A residue  221 LEU
Chi-restraints excluded: chain A residue  236 PHE
Chi-restraints excluded: chain A residue  310 SER
Chi-restraints excluded: chain A residue  322 ASN
Chi-restraints excluded: chain A residue  326 LEU
Chi-restraints excluded: chain A residue  336 PHE
Chi-restraints excluded: chain A residue  354 ARG
Chi-restraints excluded: chain A residue  368 TYR
Chi-restraints excluded: chain A residue  380 ASP
Chi-restraints excluded: chain A residue  404 PHE
Chi-restraints excluded: chain A residue  407 CYS
Chi-restraints excluded: chain D residue   97 SER
Chi-restraints excluded: chain D residue  116 ILE
Chi-restraints excluded: chain D residue  218 ILE
Chi-restraints excluded: chain D residue  258 LEU
Chi-restraints excluded: chain D residue  302 MET
Chi-restraints excluded: chain D residue  319 LEU
Chi-restraints excluded: chain D residue  334 GLU
Chi-restraints excluded: chain D residue  364 LEU
Chi-restraints excluded: chain D residue  377 VAL
Chi-restraints excluded: chain D residue  385 ILE
Chi-restraints excluded: chain D residue  445 HIS
Chi-restraints excluded: chain C residue   89 ILE
Chi-restraints excluded: chain C residue   91 ILE
Chi-restraints excluded: chain C residue  106 PHE
Chi-restraints excluded: chain C residue  137 TYR
Chi-restraints excluded: chain C residue  218 ILE
Chi-restraints excluded: chain C residue  301 GLU
Chi-restraints excluded: chain C residue  306 MET
Chi-restraints excluded: chain C residue  310 SER
Chi-restraints excluded: chain C residue  322 ASN
Chi-restraints excluded: chain C residue  336 PHE
Chi-restraints excluded: chain C residue  344 MET
Chi-restraints excluded: chain C residue  355 ASN
Chi-restraints excluded: chain C residue  356 ILE
Chi-restraints excluded: chain C residue  360 ILE
Chi-restraints excluded: chain C residue  369 GLU
Chi-restraints excluded: chain C residue  380 ASP
Chi-restraints excluded: chain C residue  393 LEU
Chi-restraints excluded: chain C residue  404 PHE
Chi-restraints excluded: chain C residue  407 CYS
Chi-restraints excluded: chain C residue  530 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 180
   random chunks:
   chunk 174 optimal weight:   20.0000
   chunk 90 optimal weight:   10.0000
   chunk 173 optimal weight:    5.9990
   chunk 22 optimal weight:    0.7980
   chunk 167 optimal weight:    0.9990
   chunk 43 optimal weight:    1.9990
   chunk 120 optimal weight:   10.0000
   chunk 70 optimal weight:    5.9990
   chunk 32 optimal weight:   20.0000
   chunk 3 optimal weight:    0.2980
   chunk 118 optimal weight:    0.7980
   overall best weight:    0.9784

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4827 r_free = 0.4827 target = 0.259489 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 75)----------------|
| r_work = 0.4226 r_free = 0.4226 target = 0.185799 restraints weight = 18781.867|
|-----------------------------------------------------------------------------|
r_work (start): 0.4110 rms_B_bonded: 2.16
r_work: 0.3694 rms_B_bonded: 2.91 restraints_weight: 0.5000
r_work: 0.3570 rms_B_bonded: 4.28 restraints_weight: 0.2500
r_work (final): 0.3570
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7440
moved from start:          0.3164

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  15702  Z= 0.151
  Angle     :  0.607  10.355  21134  Z= 0.314
  Chirality :  0.044   0.215   2328
  Planarity :  0.005   0.058   2592
  Dihedral  :  9.332  77.582   2297
  Min Nonbonded Distance : 2.563

Molprobity Statistics.
  All-atom Clashscore : 11.89
  Ramachandran Plot:
    Outliers :  0.44 %
    Allowed  :  5.64 %
    Favored  : 93.92 %
  Rotamer:
    Outliers :  4.91 %
    Allowed  : 26.20 %
    Favored  : 68.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.15 (0.20), residues: 1810
  helix:  0.12 (0.16), residues: 1080
  sheet: -0.84 (0.72), residues: 60
  loop : -0.15 (0.26), residues: 670

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B  92 
 HIS   0.003   0.001   HIS C 295 
 PHE   0.017   0.001   PHE D 281 
 TYR   0.014   0.001   TYR C 238 
 ARG   0.006   0.000   ARG B 349 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04437 (  837)
  hydrogen bonds       : angle       5.19772 ( 2355)
  covalent geometry    : bond        0.00336 (15694)
  covalent geometry    : angle       0.60684 (21134)
  Misc. bond           : bond        0.00138 (    8)

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

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

  3620 Ramachandran restraints generated.
    1810 Oldfield, 0 Emsley, 1810 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3620 Ramachandran restraints generated.
    1810 Oldfield, 0 Emsley, 1810 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  277 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 80
    poor density    : 197
  time to evaluate  : 1.525 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   86 THR cc_start: 0.7567 (OUTLIER) cc_final: 0.7238 (m)
REVERT: B   87 MET cc_start: 0.7587 (mmp) cc_final: 0.6318 (mmm)
REVERT: B   89 ILE cc_start: 0.7002 (OUTLIER) cc_final: 0.6136 (tp)
REVERT: B  202 PHE cc_start: 0.7155 (m-80) cc_final: 0.6886 (m-80)
REVERT: B  218 ILE cc_start: 0.6298 (OUTLIER) cc_final: 0.5451 (tt)
REVERT: B  236 PHE cc_start: 0.8002 (OUTLIER) cc_final: 0.7736 (t80)
REVERT: B  431 MET cc_start: 0.1541 (mtm) cc_final: 0.1313 (pmm)
REVERT: A   89 ILE cc_start: 0.8221 (OUTLIER) cc_final: 0.7984 (tp)
REVERT: A  115 PHE cc_start: 0.7736 (t80) cc_final: 0.7533 (t80)
REVERT: A  126 LEU cc_start: 0.7439 (mt) cc_final: 0.6772 (mt)
REVERT: A  145 MET cc_start: 0.7978 (tpp) cc_final: 0.7764 (tpp)
REVERT: A  260 ASP cc_start: 0.7820 (m-30) cc_final: 0.7447 (t70)
REVERT: A  322 ASN cc_start: 0.7595 (OUTLIER) cc_final: 0.6797 (m-40)
REVERT: A  339 LYS cc_start: 0.6835 (mmtt) cc_final: 0.6547 (pttp)
REVERT: A  344 MET cc_start: 0.5221 (mmm) cc_final: 0.4489 (pmm)
REVERT: A  368 TYR cc_start: 0.3945 (OUTLIER) cc_final: 0.3587 (p90)
REVERT: A  393 LEU cc_start: 0.7413 (tp) cc_final: 0.6806 (pp)
REVERT: A  404 PHE cc_start: 0.7509 (OUTLIER) cc_final: 0.7149 (t80)
REVERT: D   87 MET cc_start: 0.7567 (mmp) cc_final: 0.6057 (mmm)
REVERT: D   89 ILE cc_start: 0.7047 (OUTLIER) cc_final: 0.6341 (tp)
REVERT: D  218 ILE cc_start: 0.6627 (OUTLIER) cc_final: 0.5591 (tt)
REVERT: D  222 ILE cc_start: 0.8106 (tt) cc_final: 0.7796 (tt)
REVERT: D  347 MET cc_start: 0.5692 (OUTLIER) cc_final: 0.5463 (mmt)
REVERT: D  421 GLU cc_start: 0.6818 (mt-10) cc_final: 0.5938 (tm-30)
REVERT: C   89 ILE cc_start: 0.8204 (OUTLIER) cc_final: 0.7933 (tp)
REVERT: C  221 LEU cc_start: 0.7920 (OUTLIER) cc_final: 0.7422 (mt)
REVERT: C  322 ASN cc_start: 0.7698 (OUTLIER) cc_final: 0.7087 (m-40)
REVERT: C  365 ARG cc_start: 0.1994 (OUTLIER) cc_final: 0.1686 (ttp-170)
REVERT: C  404 PHE cc_start: 0.7525 (OUTLIER) cc_final: 0.7088 (t80)
REVERT: C  410 GLU cc_start: 0.8370 (pm20) cc_final: 0.7986 (mt-10)
  outliers start: 80
  outliers final: 37
  residues processed: 258
  average time/residue: 0.2348
  time to fit residues: 93.7073
Evaluate side-chains
  229 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 53
    poor density    : 176
  time to evaluate  : 1.586 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   86 THR
Chi-restraints excluded: chain B residue   89 ILE
Chi-restraints excluded: chain B residue  110 LEU
Chi-restraints excluded: chain B residue  116 ILE
Chi-restraints excluded: chain B residue  190 ILE
Chi-restraints excluded: chain B residue  218 ILE
Chi-restraints excluded: chain B residue  236 PHE
Chi-restraints excluded: chain B residue  273 THR
Chi-restraints excluded: chain B residue  302 MET
Chi-restraints excluded: chain B residue  310 SER
Chi-restraints excluded: chain B residue  377 VAL
Chi-restraints excluded: chain B residue  445 HIS
Chi-restraints excluded: chain A residue   89 ILE
Chi-restraints excluded: chain A residue  218 ILE
Chi-restraints excluded: chain A residue  221 LEU
Chi-restraints excluded: chain A residue  301 GLU
Chi-restraints excluded: chain A residue  310 SER
Chi-restraints excluded: chain A residue  319 LEU
Chi-restraints excluded: chain A residue  322 ASN
Chi-restraints excluded: chain A residue  368 TYR
Chi-restraints excluded: chain A residue  380 ASP
Chi-restraints excluded: chain A residue  404 PHE
Chi-restraints excluded: chain A residue  407 CYS
Chi-restraints excluded: chain A residue  530 ILE
Chi-restraints excluded: chain D residue   89 ILE
Chi-restraints excluded: chain D residue   97 SER
Chi-restraints excluded: chain D residue  116 ILE
Chi-restraints excluded: chain D residue  190 ILE
Chi-restraints excluded: chain D residue  218 ILE
Chi-restraints excluded: chain D residue  273 THR
Chi-restraints excluded: chain D residue  302 MET
Chi-restraints excluded: chain D residue  347 MET
Chi-restraints excluded: chain D residue  364 LEU
Chi-restraints excluded: chain D residue  377 VAL
Chi-restraints excluded: chain D residue  385 ILE
Chi-restraints excluded: chain D residue  445 HIS
Chi-restraints excluded: chain C residue   89 ILE
Chi-restraints excluded: chain C residue   91 ILE
Chi-restraints excluded: chain C residue  106 PHE
Chi-restraints excluded: chain C residue  137 TYR
Chi-restraints excluded: chain C residue  221 LEU
Chi-restraints excluded: chain C residue  301 GLU
Chi-restraints excluded: chain C residue  310 SER
Chi-restraints excluded: chain C residue  319 LEU
Chi-restraints excluded: chain C residue  322 ASN
Chi-restraints excluded: chain C residue  324 THR
Chi-restraints excluded: chain C residue  336 PHE
Chi-restraints excluded: chain C residue  365 ARG
Chi-restraints excluded: chain C residue  380 ASP
Chi-restraints excluded: chain C residue  404 PHE
Chi-restraints excluded: chain C residue  407 CYS
Chi-restraints excluded: chain C residue  474 ILE
Chi-restraints excluded: chain C residue  530 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 180
   random chunks:
   chunk 10 optimal weight:    1.9990
   chunk 165 optimal weight:    5.9990
   chunk 94 optimal weight:    3.9990
   chunk 97 optimal weight:    0.1980
   chunk 75 optimal weight:    9.9990
   chunk 49 optimal weight:    0.7980
   chunk 24 optimal weight:    0.6980
   chunk 127 optimal weight:    6.9990
   chunk 23 optimal weight:    0.8980
   chunk 82 optimal weight:   40.0000
   chunk 5 optimal weight:    1.9990
   overall best weight:    0.9182

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4821 r_free = 0.4821 target = 0.259440 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 72)----------------|
| r_work = 0.4269 r_free = 0.4269 target = 0.191003 restraints weight = 19604.709|
|-----------------------------------------------------------------------------|
r_work (start): 0.4163 rms_B_bonded: 2.36
r_work: 0.3724 rms_B_bonded: 2.81 restraints_weight: 0.5000
r_work: 0.3596 rms_B_bonded: 4.28 restraints_weight: 0.2500
r_work (final): 0.3596
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7421
moved from start:          0.3381

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051  15702  Z= 0.147
  Angle     :  0.593  12.346  21134  Z= 0.306
  Chirality :  0.044   0.223   2328
  Planarity :  0.004   0.056   2592
  Dihedral  :  8.515  63.032   2283
  Min Nonbonded Distance : 2.579

Molprobity Statistics.
  All-atom Clashscore : 11.63
  Ramachandran Plot:
    Outliers :  0.44 %
    Allowed  :  5.58 %
    Favored  : 93.98 %
  Rotamer:
    Outliers :  4.29 %
    Allowed  : 26.81 %
    Favored  : 68.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.03 (0.20), residues: 1810
  helix:  0.27 (0.16), residues: 1078
  sheet: -1.02 (0.70), residues: 60
  loop : -0.15 (0.26), residues: 672

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP B  92 
 HIS   0.003   0.001   HIS C 295 
 PHE   0.017   0.001   PHE D 281 
 TYR   0.013   0.001   TYR A 238 
 ARG   0.004   0.000   ARG B 349 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04324 (  837)
  hydrogen bonds       : angle       5.05676 ( 2355)
  covalent geometry    : bond        0.00326 (15694)
  covalent geometry    : angle       0.59261 (21134)
  Misc. bond           : bond        0.00081 (    8)

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

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

  3620 Ramachandran restraints generated.
    1810 Oldfield, 0 Emsley, 1810 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3620 Ramachandran restraints generated.
    1810 Oldfield, 0 Emsley, 1810 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  265 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 70
    poor density    : 195
  time to evaluate  : 1.628 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   89 ILE cc_start: 0.7091 (OUTLIER) cc_final: 0.6256 (tp)
REVERT: B  103 GLU cc_start: 0.8771 (tm-30) cc_final: 0.8570 (tm-30)
REVERT: B  202 PHE cc_start: 0.7172 (m-80) cc_final: 0.6920 (m-80)
REVERT: B  218 ILE cc_start: 0.6287 (OUTLIER) cc_final: 0.4854 (tt)
REVERT: B  236 PHE cc_start: 0.7923 (OUTLIER) cc_final: 0.7704 (t80)
REVERT: A   89 ILE cc_start: 0.8248 (OUTLIER) cc_final: 0.8042 (tp)
REVERT: A  115 PHE cc_start: 0.7770 (t80) cc_final: 0.7557 (t80)
REVERT: A  145 MET cc_start: 0.7981 (tpp) cc_final: 0.7777 (tpp)
REVERT: A  260 ASP cc_start: 0.7802 (m-30) cc_final: 0.7474 (t70)
REVERT: A  319 LEU cc_start: 0.8134 (OUTLIER) cc_final: 0.7823 (tt)
REVERT: A  322 ASN cc_start: 0.7659 (OUTLIER) cc_final: 0.6883 (m-40)
REVERT: A  339 LYS cc_start: 0.6798 (mmtt) cc_final: 0.6468 (pttm)
REVERT: A  340 MET cc_start: 0.4280 (mmm) cc_final: 0.3965 (mmm)
REVERT: A  344 MET cc_start: 0.4465 (mmm) cc_final: 0.4017 (pmm)
REVERT: A  368 TYR cc_start: 0.3826 (OUTLIER) cc_final: 0.3454 (p90)
REVERT: A  393 LEU cc_start: 0.7554 (tp) cc_final: 0.6928 (pp)
REVERT: A  404 PHE cc_start: 0.7420 (OUTLIER) cc_final: 0.7077 (t80)
REVERT: D   89 ILE cc_start: 0.7093 (OUTLIER) cc_final: 0.6406 (tp)
REVERT: D  218 ILE cc_start: 0.6574 (OUTLIER) cc_final: 0.5584 (tt)
REVERT: D  222 ILE cc_start: 0.8047 (tt) cc_final: 0.7731 (tt)
REVERT: D  347 MET cc_start: 0.5601 (OUTLIER) cc_final: 0.5279 (mmp)
REVERT: C   89 ILE cc_start: 0.8324 (OUTLIER) cc_final: 0.8046 (tp)
REVERT: C  126 LEU cc_start: 0.7487 (mt) cc_final: 0.7003 (mt)
REVERT: C  148 LYS cc_start: 0.5580 (tptp) cc_final: 0.5371 (mmmt)
REVERT: C  306 MET cc_start: 0.8258 (mmp) cc_final: 0.7999 (mmt)
REVERT: C  322 ASN cc_start: 0.7671 (OUTLIER) cc_final: 0.7059 (m-40)
REVERT: C  398 ILE cc_start: 0.6946 (OUTLIER) cc_final: 0.6542 (mt)
REVERT: C  404 PHE cc_start: 0.7462 (OUTLIER) cc_final: 0.7047 (t80)
  outliers start: 70
  outliers final: 41
  residues processed: 252
  average time/residue: 0.2424
  time to fit residues: 94.4076
Evaluate side-chains
  238 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 56
    poor density    : 182
  time to evaluate  : 1.622 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   89 ILE
Chi-restraints excluded: chain B residue   97 SER
Chi-restraints excluded: chain B residue  110 LEU
Chi-restraints excluded: chain B residue  116 ILE
Chi-restraints excluded: chain B residue  190 ILE
Chi-restraints excluded: chain B residue  218 ILE
Chi-restraints excluded: chain B residue  236 PHE
Chi-restraints excluded: chain B residue  256 LEU
Chi-restraints excluded: chain B residue  273 THR
Chi-restraints excluded: chain B residue  302 MET
Chi-restraints excluded: chain B residue  309 ILE
Chi-restraints excluded: chain B residue  366 LEU
Chi-restraints excluded: chain B residue  377 VAL
Chi-restraints excluded: chain B residue  445 HIS
Chi-restraints excluded: chain A residue   89 ILE
Chi-restraints excluded: chain A residue  218 ILE
Chi-restraints excluded: chain A residue  221 LEU
Chi-restraints excluded: chain A residue  236 PHE
Chi-restraints excluded: chain A residue  301 GLU
Chi-restraints excluded: chain A residue  310 SER
Chi-restraints excluded: chain A residue  319 LEU
Chi-restraints excluded: chain A residue  322 ASN
Chi-restraints excluded: chain A residue  324 THR
Chi-restraints excluded: chain A residue  326 LEU
Chi-restraints excluded: chain A residue  368 TYR
Chi-restraints excluded: chain A residue  380 ASP
Chi-restraints excluded: chain A residue  404 PHE
Chi-restraints excluded: chain A residue  407 CYS
Chi-restraints excluded: chain D residue   89 ILE
Chi-restraints excluded: chain D residue   97 SER
Chi-restraints excluded: chain D residue  116 ILE
Chi-restraints excluded: chain D residue  190 ILE
Chi-restraints excluded: chain D residue  218 ILE
Chi-restraints excluded: chain D residue  273 THR
Chi-restraints excluded: chain D residue  302 MET
Chi-restraints excluded: chain D residue  347 MET
Chi-restraints excluded: chain D residue  364 LEU
Chi-restraints excluded: chain D residue  366 LEU
Chi-restraints excluded: chain D residue  377 VAL
Chi-restraints excluded: chain D residue  385 ILE
Chi-restraints excluded: chain D residue  445 HIS
Chi-restraints excluded: chain C residue   89 ILE
Chi-restraints excluded: chain C residue   91 ILE
Chi-restraints excluded: chain C residue  106 PHE
Chi-restraints excluded: chain C residue  221 LEU
Chi-restraints excluded: chain C residue  301 GLU
Chi-restraints excluded: chain C residue  310 SER
Chi-restraints excluded: chain C residue  319 LEU
Chi-restraints excluded: chain C residue  322 ASN
Chi-restraints excluded: chain C residue  324 THR
Chi-restraints excluded: chain C residue  380 ASP
Chi-restraints excluded: chain C residue  398 ILE
Chi-restraints excluded: chain C residue  404 PHE
Chi-restraints excluded: chain C residue  407 CYS
Chi-restraints excluded: chain C residue  474 ILE
Chi-restraints excluded: chain C residue  530 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 180
   random chunks:
   chunk 155 optimal weight:    0.6980
   chunk 40 optimal weight:   20.0000
   chunk 164 optimal weight:   10.0000
   chunk 121 optimal weight:    1.9990
   chunk 157 optimal weight:    0.0870
   chunk 123 optimal weight:    7.9990
   chunk 87 optimal weight:   40.0000
   chunk 4 optimal weight:    1.9990
   chunk 159 optimal weight:    3.9990
   chunk 90 optimal weight:   10.0000
   chunk 81 optimal weight:    7.9990
   overall best weight:    1.7564

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4798 r_free = 0.4798 target = 0.256496 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 72)----------------|
| r_work = 0.4230 r_free = 0.4230 target = 0.187401 restraints weight = 19329.293|
|-----------------------------------------------------------------------------|
r_work (start): 0.4135 rms_B_bonded: 2.36
r_work: 0.3663 rms_B_bonded: 2.84 restraints_weight: 0.5000
r_work: 0.3538 rms_B_bonded: 4.25 restraints_weight: 0.2500
r_work (final): 0.3538
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7434
moved from start:          0.3560

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.049  15702  Z= 0.202
  Angle     :  0.630  11.231  21134  Z= 0.324
  Chirality :  0.045   0.214   2328
  Planarity :  0.004   0.055   2592
  Dihedral  :  8.606  59.091   2281
  Min Nonbonded Distance : 2.560

Molprobity Statistics.
  All-atom Clashscore : 12.28
  Ramachandran Plot:
    Outliers :  0.50 %
    Allowed  :  5.91 %
    Favored  : 93.59 %
  Rotamer:
    Outliers :  4.91 %
    Allowed  : 27.30 %
    Favored  : 67.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.13 (0.20), residues: 1810
  helix:  0.18 (0.16), residues: 1066
  sheet: -1.16 (0.71), residues: 60
  loop : -0.18 (0.26), residues: 684

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 171 
 HIS   0.003   0.001   HIS C 230 
 PHE   0.017   0.002   PHE D 304 
 TYR   0.015   0.002   TYR C 368 
 ARG   0.008   0.000   ARG A 418 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04382 (  837)
  hydrogen bonds       : angle       5.07588 ( 2355)
  covalent geometry    : bond        0.00471 (15694)
  covalent geometry    : angle       0.62963 (21134)
  Misc. bond           : bond        0.00101 (    8)

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

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

  3620 Ramachandran restraints generated.
    1810 Oldfield, 0 Emsley, 1810 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3620 Ramachandran restraints generated.
    1810 Oldfield, 0 Emsley, 1810 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  258 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 80
    poor density    : 178
  time to evaluate  : 1.715 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   87 MET cc_start: 0.7641 (mmp) cc_final: 0.6266 (mmm)
REVERT: B   89 ILE cc_start: 0.7096 (OUTLIER) cc_final: 0.6184 (tp)
REVERT: B  218 ILE cc_start: 0.6236 (OUTLIER) cc_final: 0.5396 (tt)
REVERT: B  236 PHE cc_start: 0.8213 (OUTLIER) cc_final: 0.7855 (t80)
REVERT: A   89 ILE cc_start: 0.8264 (OUTLIER) cc_final: 0.8061 (tp)
REVERT: A  131 LEU cc_start: 0.8301 (OUTLIER) cc_final: 0.7968 (tt)
REVERT: A  217 ARG cc_start: 0.7984 (OUTLIER) cc_final: 0.7046 (mmm-85)
REVERT: A  260 ASP cc_start: 0.8263 (m-30) cc_final: 0.7805 (t70)
REVERT: A  322 ASN cc_start: 0.7677 (OUTLIER) cc_final: 0.6751 (m-40)
REVERT: A  393 LEU cc_start: 0.7439 (tp) cc_final: 0.6826 (pp)
REVERT: A  398 ILE cc_start: 0.7272 (OUTLIER) cc_final: 0.6941 (mm)
REVERT: A  404 PHE cc_start: 0.7447 (OUTLIER) cc_final: 0.7107 (t80)
REVERT: D   87 MET cc_start: 0.7538 (mmp) cc_final: 0.6376 (mmm)
REVERT: D   89 ILE cc_start: 0.7077 (OUTLIER) cc_final: 0.6426 (tp)
REVERT: D  218 ILE cc_start: 0.6288 (OUTLIER) cc_final: 0.5104 (tt)
REVERT: D  222 ILE cc_start: 0.8054 (tt) cc_final: 0.7725 (tt)
REVERT: D  347 MET cc_start: 0.5518 (OUTLIER) cc_final: 0.5146 (mmp)
REVERT: D  432 GLU cc_start: 0.7629 (mt-10) cc_final: 0.7073 (tp30)
REVERT: C   89 ILE cc_start: 0.8333 (OUTLIER) cc_final: 0.8099 (tp)
REVERT: C  126 LEU cc_start: 0.7552 (mt) cc_final: 0.7049 (mt)
REVERT: C  260 ASP cc_start: 0.8074 (m-30) cc_final: 0.7666 (t70)
REVERT: C  306 MET cc_start: 0.8449 (mmp) cc_final: 0.8023 (mmt)
REVERT: C  322 ASN cc_start: 0.7720 (OUTLIER) cc_final: 0.7047 (m-40)
REVERT: C  398 ILE cc_start: 0.6965 (OUTLIER) cc_final: 0.6574 (mt)
REVERT: C  404 PHE cc_start: 0.7501 (OUTLIER) cc_final: 0.7074 (t80)
  outliers start: 80
  outliers final: 47
  residues processed: 245
  average time/residue: 0.2409
  time to fit residues: 91.0831
Evaluate side-chains
  236 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 63
    poor density    : 173
  time to evaluate  : 1.396 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   89 ILE
Chi-restraints excluded: chain B residue   97 SER
Chi-restraints excluded: chain B residue  110 LEU
Chi-restraints excluded: chain B residue  116 ILE
Chi-restraints excluded: chain B residue  190 ILE
Chi-restraints excluded: chain B residue  218 ILE
Chi-restraints excluded: chain B residue  236 PHE
Chi-restraints excluded: chain B residue  256 LEU
Chi-restraints excluded: chain B residue  273 THR
Chi-restraints excluded: chain B residue  302 MET
Chi-restraints excluded: chain B residue  309 ILE
Chi-restraints excluded: chain B residue  346 TYR
Chi-restraints excluded: chain B residue  377 VAL
Chi-restraints excluded: chain B residue  445 HIS
Chi-restraints excluded: chain A residue   89 ILE
Chi-restraints excluded: chain A residue  131 LEU
Chi-restraints excluded: chain A residue  217 ARG
Chi-restraints excluded: chain A residue  218 ILE
Chi-restraints excluded: chain A residue  221 LEU
Chi-restraints excluded: chain A residue  222 ILE
Chi-restraints excluded: chain A residue  301 GLU
Chi-restraints excluded: chain A residue  310 SER
Chi-restraints excluded: chain A residue  322 ASN
Chi-restraints excluded: chain A residue  324 THR
Chi-restraints excluded: chain A residue  326 LEU
Chi-restraints excluded: chain A residue  380 ASP
Chi-restraints excluded: chain A residue  398 ILE
Chi-restraints excluded: chain A residue  404 PHE
Chi-restraints excluded: chain A residue  407 CYS
Chi-restraints excluded: chain A residue  443 VAL
Chi-restraints excluded: chain D residue   89 ILE
Chi-restraints excluded: chain D residue   97 SER
Chi-restraints excluded: chain D residue  116 ILE
Chi-restraints excluded: chain D residue  135 VAL
Chi-restraints excluded: chain D residue  184 VAL
Chi-restraints excluded: chain D residue  190 ILE
Chi-restraints excluded: chain D residue  218 ILE
Chi-restraints excluded: chain D residue  229 THR
Chi-restraints excluded: chain D residue  273 THR
Chi-restraints excluded: chain D residue  302 MET
Chi-restraints excluded: chain D residue  309 ILE
Chi-restraints excluded: chain D residue  347 MET
Chi-restraints excluded: chain D residue  364 LEU
Chi-restraints excluded: chain D residue  377 VAL
Chi-restraints excluded: chain D residue  385 ILE
Chi-restraints excluded: chain D residue  445 HIS
Chi-restraints excluded: chain C residue   89 ILE
Chi-restraints excluded: chain C residue   91 ILE
Chi-restraints excluded: chain C residue  106 PHE
Chi-restraints excluded: chain C residue  132 THR
Chi-restraints excluded: chain C residue  137 TYR
Chi-restraints excluded: chain C residue  221 LEU
Chi-restraints excluded: chain C residue  301 GLU
Chi-restraints excluded: chain C residue  310 SER
Chi-restraints excluded: chain C residue  322 ASN
Chi-restraints excluded: chain C residue  324 THR
Chi-restraints excluded: chain C residue  336 PHE
Chi-restraints excluded: chain C residue  380 ASP
Chi-restraints excluded: chain C residue  398 ILE
Chi-restraints excluded: chain C residue  404 PHE
Chi-restraints excluded: chain C residue  407 CYS
Chi-restraints excluded: chain C residue  474 ILE
Chi-restraints excluded: chain C residue  530 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 180
   random chunks:
   chunk 57 optimal weight:    0.2980
   chunk 138 optimal weight:    8.9990
   chunk 42 optimal weight:   20.0000
   chunk 134 optimal weight:   10.0000
   chunk 49 optimal weight:    1.9990
   chunk 63 optimal weight:    2.9990
   chunk 36 optimal weight:   20.0000
   chunk 33 optimal weight:   10.0000
   chunk 27 optimal weight:    0.5980
   chunk 17 optimal weight:    0.9980
   chunk 47 optimal weight:    0.2980
   overall best weight:    0.8382

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

Flipped N/Q/H residues before XYZ refinement:
A 420 HIS
C 420 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4815 r_free = 0.4815 target = 0.259113 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 77)----------------|
| r_work = 0.4260 r_free = 0.4260 target = 0.190243 restraints weight = 19314.447|
|-----------------------------------------------------------------------------|
r_work (start): 0.4169 rms_B_bonded: 2.02
r_work: 0.3742 rms_B_bonded: 2.69 restraints_weight: 0.5000
r_work: 0.3621 rms_B_bonded: 4.00 restraints_weight: 0.2500
r_work (final): 0.3621
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7415
moved from start:          0.3713

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  15702  Z= 0.140
  Angle     :  0.610  11.421  21134  Z= 0.309
  Chirality :  0.044   0.187   2328
  Planarity :  0.004   0.054   2592
  Dihedral  :  8.342  59.812   2281
  Min Nonbonded Distance : 2.564

Molprobity Statistics.
  All-atom Clashscore : 11.44
  Ramachandran Plot:
    Outliers :  0.50 %
    Allowed  :  5.30 %
    Favored  : 94.20 %
  Rotamer:
    Outliers :  5.09 %
    Allowed  : 26.99 %
    Favored  : 67.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.04 (0.20), residues: 1810
  helix:  0.26 (0.16), residues: 1066
  sheet: -1.12 (0.71), residues: 60
  loop : -0.15 (0.26), residues: 684

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP B  92 
 HIS   0.003   0.001   HIS C 295 
 PHE   0.018   0.001   PHE D 281 
 TYR   0.023   0.001   TYR A 368 
 ARG   0.009   0.000   ARG B 496 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04265 (  837)
  hydrogen bonds       : angle       4.94063 ( 2355)
  covalent geometry    : bond        0.00309 (15694)
  covalent geometry    : angle       0.60955 (21134)
  Misc. bond           : bond        0.00069 (    8)

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

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

  3620 Ramachandran restraints generated.
    1810 Oldfield, 0 Emsley, 1810 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3620 Ramachandran restraints generated.
    1810 Oldfield, 0 Emsley, 1810 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  272 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 83
    poor density    : 189
  time to evaluate  : 1.707 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   87 MET cc_start: 0.7531 (mmp) cc_final: 0.6466 (mmm)
REVERT: B   89 ILE cc_start: 0.7118 (OUTLIER) cc_final: 0.6190 (tp)
REVERT: B   90 LEU cc_start: 0.7213 (tt) cc_final: 0.6988 (tp)
REVERT: B  202 PHE cc_start: 0.7191 (m-80) cc_final: 0.6893 (m-80)
REVERT: B  218 ILE cc_start: 0.6204 (OUTLIER) cc_final: 0.4839 (tt)
REVERT: B  236 PHE cc_start: 0.7828 (OUTLIER) cc_final: 0.7592 (t80)
REVERT: B  274 ARG cc_start: 0.7650 (OUTLIER) cc_final: 0.6768 (mtm-85)
REVERT: A  131 LEU cc_start: 0.8248 (OUTLIER) cc_final: 0.7939 (tt)
REVERT: A  260 ASP cc_start: 0.8001 (m-30) cc_final: 0.7704 (t70)
REVERT: A  322 ASN cc_start: 0.7602 (OUTLIER) cc_final: 0.6823 (m-40)
REVERT: A  344 MET cc_start: 0.7217 (pmm) cc_final: 0.6101 (mpp)
REVERT: A  393 LEU cc_start: 0.7449 (tp) cc_final: 0.6845 (pp)
REVERT: A  404 PHE cc_start: 0.7349 (OUTLIER) cc_final: 0.6964 (t80)
REVERT: A  445 HIS cc_start: 0.3958 (m90) cc_final: 0.3280 (t70)
REVERT: D   87 MET cc_start: 0.7497 (mmp) cc_final: 0.6315 (mmm)
REVERT: D   89 ILE cc_start: 0.7039 (OUTLIER) cc_final: 0.6364 (tp)
REVERT: D  218 ILE cc_start: 0.6333 (OUTLIER) cc_final: 0.5213 (tt)
REVERT: D  222 ILE cc_start: 0.8097 (tt) cc_final: 0.7771 (tt)
REVERT: D  347 MET cc_start: 0.5387 (OUTLIER) cc_final: 0.5076 (mmp)
REVERT: D  432 GLU cc_start: 0.7738 (mt-10) cc_final: 0.7170 (tp30)
REVERT: C   89 ILE cc_start: 0.8321 (OUTLIER) cc_final: 0.8099 (tp)
REVERT: C  217 ARG cc_start: 0.7966 (OUTLIER) cc_final: 0.6974 (mmm-85)
REVERT: C  260 ASP cc_start: 0.7795 (m-30) cc_final: 0.7555 (t70)
REVERT: C  322 ASN cc_start: 0.7714 (OUTLIER) cc_final: 0.7018 (m-40)
REVERT: C  329 LYS cc_start: 0.8051 (OUTLIER) cc_final: 0.7374 (tttm)
REVERT: C  344 MET cc_start: 0.4907 (mmt) cc_final: 0.4062 (pmm)
REVERT: C  398 ILE cc_start: 0.6971 (OUTLIER) cc_final: 0.6580 (mt)
REVERT: C  404 PHE cc_start: 0.7441 (OUTLIER) cc_final: 0.7033 (t80)
  outliers start: 83
  outliers final: 48
  residues processed: 257
  average time/residue: 0.2327
  time to fit residues: 92.9189
Evaluate side-chains
  244 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 64
    poor density    : 180
  time to evaluate  : 1.490 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   89 ILE
Chi-restraints excluded: chain B residue  110 LEU
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  173 ILE
Chi-restraints excluded: chain B residue  190 ILE
Chi-restraints excluded: chain B residue  218 ILE
Chi-restraints excluded: chain B residue  236 PHE
Chi-restraints excluded: chain B residue  256 LEU
Chi-restraints excluded: chain B residue  273 THR
Chi-restraints excluded: chain B residue  274 ARG
Chi-restraints excluded: chain B residue  302 MET
Chi-restraints excluded: chain B residue  309 ILE
Chi-restraints excluded: chain B residue  310 SER
Chi-restraints excluded: chain B residue  346 TYR
Chi-restraints excluded: chain B residue  377 VAL
Chi-restraints excluded: chain B residue  445 HIS
Chi-restraints excluded: chain A residue  131 LEU
Chi-restraints excluded: chain A residue  132 THR
Chi-restraints excluded: chain A residue  221 LEU
Chi-restraints excluded: chain A residue  301 GLU
Chi-restraints excluded: chain A residue  310 SER
Chi-restraints excluded: chain A residue  322 ASN
Chi-restraints excluded: chain A residue  324 THR
Chi-restraints excluded: chain A residue  336 PHE
Chi-restraints excluded: chain A residue  380 ASP
Chi-restraints excluded: chain A residue  404 PHE
Chi-restraints excluded: chain A residue  407 CYS
Chi-restraints excluded: chain A residue  443 VAL
Chi-restraints excluded: chain A residue  530 ILE
Chi-restraints excluded: chain D residue   89 ILE
Chi-restraints excluded: chain D residue   97 SER
Chi-restraints excluded: chain D residue  116 ILE
Chi-restraints excluded: chain D residue  135 VAL
Chi-restraints excluded: chain D residue  190 ILE
Chi-restraints excluded: chain D residue  218 ILE
Chi-restraints excluded: chain D residue  229 THR
Chi-restraints excluded: chain D residue  273 THR
Chi-restraints excluded: chain D residue  302 MET
Chi-restraints excluded: chain D residue  309 ILE
Chi-restraints excluded: chain D residue  347 MET
Chi-restraints excluded: chain D residue  364 LEU
Chi-restraints excluded: chain D residue  366 LEU
Chi-restraints excluded: chain D residue  377 VAL
Chi-restraints excluded: chain D residue  385 ILE
Chi-restraints excluded: chain D residue  445 HIS
Chi-restraints excluded: chain C residue   89 ILE
Chi-restraints excluded: chain C residue   91 ILE
Chi-restraints excluded: chain C residue  106 PHE
Chi-restraints excluded: chain C residue  132 THR
Chi-restraints excluded: chain C residue  137 TYR
Chi-restraints excluded: chain C residue  217 ARG
Chi-restraints excluded: chain C residue  221 LEU
Chi-restraints excluded: chain C residue  301 GLU
Chi-restraints excluded: chain C residue  310 SER
Chi-restraints excluded: chain C residue  322 ASN
Chi-restraints excluded: chain C residue  324 THR
Chi-restraints excluded: chain C residue  329 LYS
Chi-restraints excluded: chain C residue  380 ASP
Chi-restraints excluded: chain C residue  398 ILE
Chi-restraints excluded: chain C residue  404 PHE
Chi-restraints excluded: chain C residue  407 CYS
Chi-restraints excluded: chain C residue  474 ILE
Chi-restraints excluded: chain C residue  528 VAL
Chi-restraints excluded: chain C residue  530 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 180
   random chunks:
   chunk 177 optimal weight:    8.9990
   chunk 41 optimal weight:    4.9990
   chunk 31 optimal weight:    5.9990
   chunk 86 optimal weight:    1.9990
   chunk 58 optimal weight:    0.8980
   chunk 20 optimal weight:    0.9980
   chunk 112 optimal weight:    0.7980
   chunk 4 optimal weight:    3.9990
   chunk 51 optimal weight:    2.9990
   chunk 103 optimal weight:    6.9990
   chunk 61 optimal weight:    0.9990
   overall best weight:    1.1384

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

Flipped N/Q/H residues before XYZ refinement:
A 420 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4785 r_free = 0.4785 target = 0.255396 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 126)---------------|
| r_work = 0.3992 r_free = 0.3992 target = 0.165972 restraints weight = 19078.511|
|-----------------------------------------------------------------------------|
r_work (start): 0.3974 rms_B_bonded: 5.43
r_work: 0.3607 rms_B_bonded: 3.52 restraints_weight: 0.5000
r_work (final): 0.3607
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7198
moved from start:          0.3909

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041  15702  Z= 0.159
  Angle     :  0.613  10.479  21134  Z= 0.312
  Chirality :  0.044   0.160   2328
  Planarity :  0.004   0.055   2592
  Dihedral  :  8.323  59.888   2281
  Min Nonbonded Distance : 2.575

Molprobity Statistics.
  All-atom Clashscore : 11.47
  Ramachandran Plot:
    Outliers :  0.44 %
    Allowed  :  5.19 %
    Favored  : 94.36 %
  Rotamer:
    Outliers :  4.72 %
    Allowed  : 26.87 %
    Favored  : 68.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.04 (0.20), residues: 1810
  helix:  0.25 (0.16), residues: 1066
  sheet: -1.15 (0.72), residues: 60
  loop : -0.12 (0.26), residues: 684

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B  92 
 HIS   0.003   0.001   HIS B 363 
 PHE   0.024   0.002   PHE D 411 
 TYR   0.031   0.001   TYR C 368 
 ARG   0.009   0.000   ARG D 349 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04238 (  837)
  hydrogen bonds       : angle       4.91815 ( 2355)
  covalent geometry    : bond        0.00362 (15694)
  covalent geometry    : angle       0.61330 (21134)
  Misc. bond           : bond        0.00081 (    8)

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

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

  3620 Ramachandran restraints generated.
    1810 Oldfield, 0 Emsley, 1810 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3620 Ramachandran restraints generated.
    1810 Oldfield, 0 Emsley, 1810 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  261 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 77
    poor density    : 184
  time to evaluate  : 1.671 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   87 MET cc_start: 0.7557 (mmp) cc_final: 0.6463 (mmm)
REVERT: B   89 ILE cc_start: 0.6543 (OUTLIER) cc_final: 0.5879 (tp)
REVERT: B  202 PHE cc_start: 0.6754 (m-80) cc_final: 0.6543 (m-80)
REVERT: B  218 ILE cc_start: 0.5295 (OUTLIER) cc_final: 0.4264 (tt)
REVERT: B  236 PHE cc_start: 0.7937 (OUTLIER) cc_final: 0.7590 (t80)
REVERT: B  274 ARG cc_start: 0.7705 (OUTLIER) cc_final: 0.6628 (mtm-85)
REVERT: B  431 MET cc_start: 0.2542 (mtt) cc_final: 0.2158 (pmm)
REVERT: A  131 LEU cc_start: 0.7825 (OUTLIER) cc_final: 0.7514 (tt)
REVERT: A  217 ARG cc_start: 0.7853 (OUTLIER) cc_final: 0.6823 (mmm-85)
REVERT: A  260 ASP cc_start: 0.8078 (m-30) cc_final: 0.7717 (t70)
REVERT: A  322 ASN cc_start: 0.7297 (OUTLIER) cc_final: 0.6376 (m-40)
REVERT: A  344 MET cc_start: 0.7111 (pmm) cc_final: 0.6379 (mpp)
REVERT: A  393 LEU cc_start: 0.7239 (tp) cc_final: 0.6757 (pp)
REVERT: A  404 PHE cc_start: 0.7490 (OUTLIER) cc_final: 0.7062 (t80)
REVERT: A  445 HIS cc_start: 0.4226 (m90) cc_final: 0.3635 (t70)
REVERT: D   87 MET cc_start: 0.7536 (mmp) cc_final: 0.6348 (mmm)
REVERT: D   89 ILE cc_start: 0.6592 (OUTLIER) cc_final: 0.5930 (tp)
REVERT: D  218 ILE cc_start: 0.5518 (OUTLIER) cc_final: 0.4666 (tt)
REVERT: D  222 ILE cc_start: 0.7839 (tt) cc_final: 0.7472 (tt)
REVERT: D  347 MET cc_start: 0.5333 (OUTLIER) cc_final: 0.5089 (mmp)
REVERT: D  432 GLU cc_start: 0.7546 (mt-10) cc_final: 0.7189 (tp30)
REVERT: C  217 ARG cc_start: 0.7825 (OUTLIER) cc_final: 0.6818 (mmm-85)
REVERT: C  260 ASP cc_start: 0.7992 (m-30) cc_final: 0.7629 (t70)
REVERT: C  322 ASN cc_start: 0.7461 (OUTLIER) cc_final: 0.6662 (m-40)
REVERT: C  329 LYS cc_start: 0.7734 (OUTLIER) cc_final: 0.7157 (tttm)
REVERT: C  344 MET cc_start: 0.4789 (mmt) cc_final: 0.4242 (pmm)
REVERT: C  398 ILE cc_start: 0.7081 (OUTLIER) cc_final: 0.6743 (mt)
REVERT: C  404 PHE cc_start: 0.7538 (OUTLIER) cc_final: 0.7126 (t80)
REVERT: C  445 HIS cc_start: 0.4023 (m90) cc_final: 0.3500 (t70)
  outliers start: 77
  outliers final: 51
  residues processed: 247
  average time/residue: 0.2419
  time to fit residues: 91.7061
Evaluate side-chains
  245 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 67
    poor density    : 178
  time to evaluate  : 1.530 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   89 ILE
Chi-restraints excluded: chain B residue   97 SER
Chi-restraints excluded: chain B residue  110 LEU
Chi-restraints excluded: chain B residue  116 ILE
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  173 ILE
Chi-restraints excluded: chain B residue  190 ILE
Chi-restraints excluded: chain B residue  218 ILE
Chi-restraints excluded: chain B residue  236 PHE
Chi-restraints excluded: chain B residue  256 LEU
Chi-restraints excluded: chain B residue  273 THR
Chi-restraints excluded: chain B residue  274 ARG
Chi-restraints excluded: chain B residue  302 MET
Chi-restraints excluded: chain B residue  309 ILE
Chi-restraints excluded: chain B residue  346 TYR
Chi-restraints excluded: chain B residue  377 VAL
Chi-restraints excluded: chain B residue  445 HIS
Chi-restraints excluded: chain A residue  131 LEU
Chi-restraints excluded: chain A residue  132 THR
Chi-restraints excluded: chain A residue  137 TYR
Chi-restraints excluded: chain A residue  217 ARG
Chi-restraints excluded: chain A residue  221 LEU
Chi-restraints excluded: chain A residue  236 PHE
Chi-restraints excluded: chain A residue  301 GLU
Chi-restraints excluded: chain A residue  310 SER
Chi-restraints excluded: chain A residue  322 ASN
Chi-restraints excluded: chain A residue  324 THR
Chi-restraints excluded: chain A residue  336 PHE
Chi-restraints excluded: chain A residue  380 ASP
Chi-restraints excluded: chain A residue  398 ILE
Chi-restraints excluded: chain A residue  404 PHE
Chi-restraints excluded: chain A residue  407 CYS
Chi-restraints excluded: chain A residue  443 VAL
Chi-restraints excluded: chain D residue   89 ILE
Chi-restraints excluded: chain D residue   97 SER
Chi-restraints excluded: chain D residue  116 ILE
Chi-restraints excluded: chain D residue  135 VAL
Chi-restraints excluded: chain D residue  190 ILE
Chi-restraints excluded: chain D residue  218 ILE
Chi-restraints excluded: chain D residue  229 THR
Chi-restraints excluded: chain D residue  273 THR
Chi-restraints excluded: chain D residue  302 MET
Chi-restraints excluded: chain D residue  309 ILE
Chi-restraints excluded: chain D residue  347 MET
Chi-restraints excluded: chain D residue  364 LEU
Chi-restraints excluded: chain D residue  377 VAL
Chi-restraints excluded: chain D residue  385 ILE
Chi-restraints excluded: chain D residue  445 HIS
Chi-restraints excluded: chain C residue   91 ILE
Chi-restraints excluded: chain C residue  106 PHE
Chi-restraints excluded: chain C residue  132 THR
Chi-restraints excluded: chain C residue  137 TYR
Chi-restraints excluded: chain C residue  217 ARG
Chi-restraints excluded: chain C residue  221 LEU
Chi-restraints excluded: chain C residue  301 GLU
Chi-restraints excluded: chain C residue  310 SER
Chi-restraints excluded: chain C residue  322 ASN
Chi-restraints excluded: chain C residue  324 THR
Chi-restraints excluded: chain C residue  329 LYS
Chi-restraints excluded: chain C residue  336 PHE
Chi-restraints excluded: chain C residue  380 ASP
Chi-restraints excluded: chain C residue  398 ILE
Chi-restraints excluded: chain C residue  404 PHE
Chi-restraints excluded: chain C residue  407 CYS
Chi-restraints excluded: chain C residue  474 ILE
Chi-restraints excluded: chain C residue  528 VAL
Chi-restraints excluded: chain C residue  530 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 180
   random chunks:
   chunk 37 optimal weight:    5.9990
   chunk 1 optimal weight:    0.5980
   chunk 176 optimal weight:    5.9990
   chunk 132 optimal weight:   20.0000
   chunk 127 optimal weight:   30.0000
   chunk 96 optimal weight:   10.0000
   chunk 100 optimal weight:    5.9990
   chunk 143 optimal weight:    3.9990
   chunk 46 optimal weight:    0.0070
   chunk 50 optimal weight:    6.9990
   chunk 7 optimal weight:    5.9990
   overall best weight:    3.3204

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

Flipped N/Q/H residues before XYZ refinement:
** B  79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 295 HIS
** A 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 420 HIS
** D  79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 295 HIS ** 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 = 0.4731 r_free = 0.4731 target = 0.248575 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 102)---------------|
| r_work = 0.3943 r_free = 0.3943 target = 0.158479 restraints weight = 19071.475|
|-----------------------------------------------------------------------------|
r_work (start): 0.3868 rms_B_bonded: 4.59
r_work: 0.3521 rms_B_bonded: 3.18 restraints_weight: 0.5000
r_work: 0.3386 rms_B_bonded: 4.68 restraints_weight: 0.2500
r_work (final): 0.3386
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7608
moved from start:          0.4104

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.069  15702  Z= 0.331
  Angle     :  0.756  11.968  21134  Z= 0.389
  Chirality :  0.050   0.176   2328
  Planarity :  0.005   0.055   2592
  Dihedral  :  9.131  59.821   2281
  Min Nonbonded Distance : 2.513

Molprobity Statistics.
  All-atom Clashscore : 15.34
  Ramachandran Plot:
    Outliers :  0.44 %
    Allowed  :  5.97 %
    Favored  : 93.59 %
  Rotamer:
    Outliers :  4.48 %
    Allowed  : 27.55 %
    Favored  : 67.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.54 (0.20), residues: 1810
  helix: -0.18 (0.16), residues: 1064
  sheet: -1.04 (0.59), residues: 80
  loop : -0.29 (0.26), residues: 666

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.002   TRP C 171 
 HIS   0.007   0.001   HIS A 230 
 PHE   0.025   0.003   PHE D 411 
 TYR   0.043   0.002   TYR A  82 
 ARG   0.008   0.001   ARG B 337 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04692 (  837)
  hydrogen bonds       : angle       5.26277 ( 2355)
  covalent geometry    : bond        0.00784 (15694)
  covalent geometry    : angle       0.75631 (21134)
  Misc. bond           : bond        0.00144 (    8)

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

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

  3620 Ramachandran restraints generated.
    1810 Oldfield, 0 Emsley, 1810 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3620 Ramachandran restraints generated.
    1810 Oldfield, 0 Emsley, 1810 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  242 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 73
    poor density    : 169
  time to evaluate  : 1.516 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   87 MET cc_start: 0.7778 (mmp) cc_final: 0.6614 (mmm)
REVERT: B   89 ILE cc_start: 0.7296 (OUTLIER) cc_final: 0.6578 (tp)
REVERT: B  218 ILE cc_start: 0.6432 (OUTLIER) cc_final: 0.5552 (tt)
REVERT: B  236 PHE cc_start: 0.8396 (OUTLIER) cc_final: 0.7880 (t80)
REVERT: B  431 MET cc_start: 0.2696 (mtt) cc_final: 0.2187 (pmm)
REVERT: A  131 LEU cc_start: 0.8028 (OUTLIER) cc_final: 0.7780 (tt)
REVERT: A  217 ARG cc_start: 0.8048 (OUTLIER) cc_final: 0.7198 (mmm-85)
REVERT: A  260 ASP cc_start: 0.8498 (m-30) cc_final: 0.7991 (t0)
REVERT: A  306 MET cc_start: 0.8459 (mmt) cc_final: 0.8054 (mmt)
REVERT: A  344 MET cc_start: 0.7095 (pmm) cc_final: 0.5601 (mmt)
REVERT: A  393 LEU cc_start: 0.7230 (tp) cc_final: 0.6721 (pp)
REVERT: A  404 PHE cc_start: 0.7434 (OUTLIER) cc_final: 0.6973 (t80)
REVERT: A  445 HIS cc_start: 0.4474 (m90) cc_final: 0.3711 (t70)
REVERT: D   87 MET cc_start: 0.7741 (mmp) cc_final: 0.6443 (mmm)
REVERT: D   89 ILE cc_start: 0.7140 (OUTLIER) cc_final: 0.6473 (tp)
REVERT: D  218 ILE cc_start: 0.6579 (OUTLIER) cc_final: 0.5470 (tt)
REVERT: D  222 ILE cc_start: 0.8121 (tt) cc_final: 0.7818 (tt)
REVERT: D  279 MET cc_start: 0.8160 (ttt) cc_final: 0.7921 (ttt)
REVERT: C  115 PHE cc_start: 0.7837 (t80) cc_final: 0.7573 (t80)
REVERT: C  217 ARG cc_start: 0.8056 (OUTLIER) cc_final: 0.7240 (mmm-85)
REVERT: C  260 ASP cc_start: 0.8494 (m-30) cc_final: 0.7955 (t0)
REVERT: C  306 MET cc_start: 0.8515 (mmt) cc_final: 0.7974 (mmt)
REVERT: C  329 LYS cc_start: 0.8115 (OUTLIER) cc_final: 0.7858 (tttm)
REVERT: C  340 MET cc_start: 0.4033 (mmt) cc_final: 0.3638 (ptp)
REVERT: C  398 ILE cc_start: 0.7060 (OUTLIER) cc_final: 0.6794 (mm)
REVERT: C  404 PHE cc_start: 0.7525 (OUTLIER) cc_final: 0.7089 (t80)
REVERT: C  445 HIS cc_start: 0.4329 (m90) cc_final: 0.3774 (t70)
  outliers start: 73
  outliers final: 53
  residues processed: 230
  average time/residue: 0.2362
  time to fit residues: 83.9853
Evaluate side-chains
  226 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 65
    poor density    : 161
  time to evaluate  : 1.679 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   89 ILE
Chi-restraints excluded: chain B residue   97 SER
Chi-restraints excluded: chain B residue  110 LEU
Chi-restraints excluded: chain B residue  116 ILE
Chi-restraints excluded: chain B residue  130 VAL
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  173 ILE
Chi-restraints excluded: chain B residue  190 ILE
Chi-restraints excluded: chain B residue  218 ILE
Chi-restraints excluded: chain B residue  236 PHE
Chi-restraints excluded: chain B residue  256 LEU
Chi-restraints excluded: chain B residue  258 LEU
Chi-restraints excluded: chain B residue  273 THR
Chi-restraints excluded: chain B residue  302 MET
Chi-restraints excluded: chain B residue  310 SER
Chi-restraints excluded: chain B residue  319 LEU
Chi-restraints excluded: chain B residue  346 TYR
Chi-restraints excluded: chain B residue  377 VAL
Chi-restraints excluded: chain B residue  445 HIS
Chi-restraints excluded: chain A residue  131 LEU
Chi-restraints excluded: chain A residue  137 TYR
Chi-restraints excluded: chain A residue  217 ARG
Chi-restraints excluded: chain A residue  218 ILE
Chi-restraints excluded: chain A residue  221 LEU
Chi-restraints excluded: chain A residue  301 GLU
Chi-restraints excluded: chain A residue  310 SER
Chi-restraints excluded: chain A residue  322 ASN
Chi-restraints excluded: chain A residue  324 THR
Chi-restraints excluded: chain A residue  336 PHE
Chi-restraints excluded: chain A residue  380 ASP
Chi-restraints excluded: chain A residue  398 ILE
Chi-restraints excluded: chain A residue  404 PHE
Chi-restraints excluded: chain A residue  407 CYS
Chi-restraints excluded: chain A residue  443 VAL
Chi-restraints excluded: chain A residue  492 CYS
Chi-restraints excluded: chain A residue  530 ILE
Chi-restraints excluded: chain D residue   89 ILE
Chi-restraints excluded: chain D residue   97 SER
Chi-restraints excluded: chain D residue  116 ILE
Chi-restraints excluded: chain D residue  135 VAL
Chi-restraints excluded: chain D residue  190 ILE
Chi-restraints excluded: chain D residue  218 ILE
Chi-restraints excluded: chain D residue  229 THR
Chi-restraints excluded: chain D residue  273 THR
Chi-restraints excluded: chain D residue  302 MET
Chi-restraints excluded: chain D residue  364 LEU
Chi-restraints excluded: chain D residue  385 ILE
Chi-restraints excluded: chain D residue  445 HIS
Chi-restraints excluded: chain C residue   91 ILE
Chi-restraints excluded: chain C residue  106 PHE
Chi-restraints excluded: chain C residue  137 TYR
Chi-restraints excluded: chain C residue  217 ARG
Chi-restraints excluded: chain C residue  221 LEU
Chi-restraints excluded: chain C residue  301 GLU
Chi-restraints excluded: chain C residue  310 SER
Chi-restraints excluded: chain C residue  322 ASN
Chi-restraints excluded: chain C residue  324 THR
Chi-restraints excluded: chain C residue  329 LYS
Chi-restraints excluded: chain C residue  336 PHE
Chi-restraints excluded: chain C residue  380 ASP
Chi-restraints excluded: chain C residue  398 ILE
Chi-restraints excluded: chain C residue  404 PHE
Chi-restraints excluded: chain C residue  407 CYS
Chi-restraints excluded: chain C residue  528 VAL
Chi-restraints excluded: chain C residue  530 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 180
   random chunks:
   chunk 132 optimal weight:    0.5980
   chunk 54 optimal weight:    4.9990
   chunk 125 optimal weight:    0.0370
   chunk 23 optimal weight:    0.5980
   chunk 111 optimal weight:    0.6980
   chunk 53 optimal weight:    0.7980
   chunk 78 optimal weight:    1.9990
   chunk 33 optimal weight:   20.0000
   chunk 42 optimal weight:    2.9990
   chunk 99 optimal weight:    0.7980
   chunk 140 optimal weight:    3.9990
   overall best weight:    0.5458

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

Flipped N/Q/H residues before XYZ refinement:
A 420 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4816 r_free = 0.4816 target = 0.259396 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 79)----------------|
| r_work = 0.4260 r_free = 0.4260 target = 0.189939 restraints weight = 19481.647|
|-----------------------------------------------------------------------------|
r_work (start): 0.4145 rms_B_bonded: 2.06
r_work: 0.3733 rms_B_bonded: 2.73 restraints_weight: 0.5000
r_work: 0.3612 rms_B_bonded: 4.07 restraints_weight: 0.2500
r_work (final): 0.3612
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7405
moved from start:          0.4199

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.057  15702  Z= 0.134
  Angle     :  0.637  10.913  21134  Z= 0.321
  Chirality :  0.044   0.160   2328
  Planarity :  0.004   0.064   2592
  Dihedral  :  8.307  57.806   2280
  Min Nonbonded Distance : 2.516

Molprobity Statistics.
  All-atom Clashscore : 11.95
  Ramachandran Plot:
    Outliers :  0.44 %
    Allowed  :  5.14 %
    Favored  : 94.42 %
  Rotamer:
    Outliers :  3.50 %
    Allowed  : 28.34 %
    Favored  : 68.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.18 (0.20), residues: 1810
  helix:  0.17 (0.16), residues: 1070
  sheet: -1.08 (0.58), residues: 80
  loop : -0.22 (0.27), residues: 660

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP B  92 
 HIS   0.003   0.001   HIS B 363 
 PHE   0.024   0.001   PHE D 411 
 TYR   0.034   0.001   TYR C 368 
 ARG   0.013   0.001   ARG B 274 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04200 (  837)
  hydrogen bonds       : angle       4.95324 ( 2355)
  covalent geometry    : bond        0.00290 (15694)
  covalent geometry    : angle       0.63737 (21134)
  Misc. bond           : bond        0.00068 (    8)

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

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

  3620 Ramachandran restraints generated.
    1810 Oldfield, 0 Emsley, 1810 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3620 Ramachandran restraints generated.
    1810 Oldfield, 0 Emsley, 1810 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  238 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 57
    poor density    : 181
  time to evaluate  : 1.725 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   87 MET cc_start: 0.7594 (mmp) cc_final: 0.6516 (mmm)
REVERT: B   89 ILE cc_start: 0.7090 (OUTLIER) cc_final: 0.6204 (tp)
REVERT: B   90 LEU cc_start: 0.7387 (tp) cc_final: 0.6693 (tt)
REVERT: B  123 ILE cc_start: 0.8021 (pp) cc_final: 0.7820 (pp)
REVERT: B  236 PHE cc_start: 0.7845 (OUTLIER) cc_final: 0.7620 (t80)
REVERT: A  306 MET cc_start: 0.7847 (mmt) cc_final: 0.7452 (mmp)
REVERT: A  322 ASN cc_start: 0.7552 (OUTLIER) cc_final: 0.6797 (m-40)
REVERT: A  344 MET cc_start: 0.7181 (pmm) cc_final: 0.5539 (mmt)
REVERT: A  393 LEU cc_start: 0.7314 (tp) cc_final: 0.6744 (pp)
REVERT: A  404 PHE cc_start: 0.7364 (OUTLIER) cc_final: 0.6913 (t80)
REVERT: A  445 HIS cc_start: 0.4392 (m90) cc_final: 0.3625 (t70)
REVERT: D   87 MET cc_start: 0.7589 (mmp) cc_final: 0.6483 (mmm)
REVERT: D  218 ILE cc_start: 0.6463 (OUTLIER) cc_final: 0.4904 (tt)
REVERT: D  222 ILE cc_start: 0.8192 (tt) cc_final: 0.7872 (tt)
REVERT: C  126 LEU cc_start: 0.7481 (mt) cc_final: 0.6885 (mt)
REVERT: C  217 ARG cc_start: 0.7984 (OUTLIER) cc_final: 0.6902 (mmm-85)
REVERT: C  322 ASN cc_start: 0.7666 (OUTLIER) cc_final: 0.6833 (m-40)
REVERT: C  344 MET cc_start: 0.4889 (mmt) cc_final: 0.4117 (pmm)
REVERT: C  445 HIS cc_start: 0.4094 (m90) cc_final: 0.3476 (t70)
  outliers start: 57
  outliers final: 42
  residues processed: 229
  average time/residue: 0.2432
  time to fit residues: 86.2145
Evaluate side-chains
  226 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 177
  time to evaluate  : 1.548 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   89 ILE
Chi-restraints excluded: chain B residue   94 LEU
Chi-restraints excluded: chain B residue   97 SER
Chi-restraints excluded: chain B residue  116 ILE
Chi-restraints excluded: chain B residue  173 ILE
Chi-restraints excluded: chain B residue  190 ILE
Chi-restraints excluded: chain B residue  236 PHE
Chi-restraints excluded: chain B residue  273 THR
Chi-restraints excluded: chain B residue  302 MET
Chi-restraints excluded: chain B residue  310 SER
Chi-restraints excluded: chain B residue  346 TYR
Chi-restraints excluded: chain B residue  377 VAL
Chi-restraints excluded: chain B residue  445 HIS
Chi-restraints excluded: chain A residue  221 LEU
Chi-restraints excluded: chain A residue  301 GLU
Chi-restraints excluded: chain A residue  310 SER
Chi-restraints excluded: chain A residue  322 ASN
Chi-restraints excluded: chain A residue  324 THR
Chi-restraints excluded: chain A residue  336 PHE
Chi-restraints excluded: chain A residue  380 ASP
Chi-restraints excluded: chain A residue  398 ILE
Chi-restraints excluded: chain A residue  404 PHE
Chi-restraints excluded: chain A residue  407 CYS
Chi-restraints excluded: chain A residue  443 VAL
Chi-restraints excluded: chain A residue  492 CYS
Chi-restraints excluded: chain A residue  530 ILE
Chi-restraints excluded: chain D residue  135 VAL
Chi-restraints excluded: chain D residue  190 ILE
Chi-restraints excluded: chain D residue  218 ILE
Chi-restraints excluded: chain D residue  273 THR
Chi-restraints excluded: chain D residue  302 MET
Chi-restraints excluded: chain D residue  364 LEU
Chi-restraints excluded: chain D residue  366 LEU
Chi-restraints excluded: chain D residue  385 ILE
Chi-restraints excluded: chain D residue  445 HIS
Chi-restraints excluded: chain C residue   91 ILE
Chi-restraints excluded: chain C residue  106 PHE
Chi-restraints excluded: chain C residue  137 TYR
Chi-restraints excluded: chain C residue  217 ARG
Chi-restraints excluded: chain C residue  221 LEU
Chi-restraints excluded: chain C residue  301 GLU
Chi-restraints excluded: chain C residue  310 SER
Chi-restraints excluded: chain C residue  322 ASN
Chi-restraints excluded: chain C residue  324 THR
Chi-restraints excluded: chain C residue  336 PHE
Chi-restraints excluded: chain C residue  380 ASP
Chi-restraints excluded: chain C residue  407 CYS
Chi-restraints excluded: chain C residue  528 VAL
Chi-restraints excluded: chain C residue  530 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 180
   random chunks:
   chunk 152 optimal weight:    0.0980
   chunk 24 optimal weight:    0.5980
   chunk 61 optimal weight:   10.0000
   chunk 53 optimal weight:    0.8980
   chunk 107 optimal weight:    0.3980
   chunk 52 optimal weight:   10.0000
   chunk 3 optimal weight:    1.9990
   chunk 172 optimal weight:    3.9990
   chunk 141 optimal weight:    7.9990
   chunk 178 optimal weight:    0.9990
   chunk 166 optimal weight:    9.9990
   overall best weight:    0.5982

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

Flipped N/Q/H residues before XYZ refinement:
A 420 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4794 r_free = 0.4794 target = 0.256924 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 114)---------------|
| r_work = 0.4090 r_free = 0.4090 target = 0.172442 restraints weight = 19008.225|
|-----------------------------------------------------------------------------|
r_work (start): 0.4013 rms_B_bonded: 4.36
r_work: 0.3649 rms_B_bonded: 3.29 restraints_weight: 0.5000
r_work: 0.3507 rms_B_bonded: 4.90 restraints_weight: 0.2500
r_work (final): 0.3507
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7306
moved from start:          0.4328

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  15702  Z= 0.136
  Angle     :  0.636  12.117  21134  Z= 0.318
  Chirality :  0.044   0.189   2328
  Planarity :  0.004   0.055   2592
  Dihedral  :  7.996  58.832   2280
  Min Nonbonded Distance : 2.532

Molprobity Statistics.
  All-atom Clashscore : 11.37
  Ramachandran Plot:
    Outliers :  0.44 %
    Allowed  :  5.36 %
    Favored  : 94.20 %
  Rotamer:
    Outliers :  3.37 %
    Allowed  : 28.53 %
    Favored  : 68.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.02 (0.20), residues: 1810
  helix:  0.31 (0.16), residues: 1062
  sheet: -1.29 (0.70), residues: 60
  loop : -0.20 (0.26), residues: 688

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B  92 
 HIS   0.004   0.000   HIS B 363 
 PHE   0.024   0.001   PHE D 411 
 TYR   0.033   0.001   TYR C 368 
 ARG   0.016   0.001   ARG A 210 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04108 (  837)
  hydrogen bonds       : angle       4.87830 ( 2355)
  covalent geometry    : bond        0.00294 (15694)
  covalent geometry    : angle       0.63607 (21134)
  Misc. bond           : bond        0.00067 (    8)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 10784.54 seconds
wall clock time: 186 minutes 32.74 seconds (11192.74 seconds total)