Starting phenix.real_space_refine
on Tue Apr 29 06:37:07 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8j9n_36111/04_2025/8j9n_36111.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8j9n_36111/04_2025/8j9n_36111.map

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

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

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8j9n_36111/04_2025/8j9n_36111.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8j9n_36111/04_2025/8j9n_36111.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8j9n_36111/04_2025/8j9n_36111.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8j9n_36111/04_2025/8j9n_36111.cif"
  }
  resolution = 3.5
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.024
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      55      5.16       5
     C    5396      2.51       5
     N    1461      2.21       5
     O    1571      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 12 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib"
  Total number of atoms: 8483
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "B"
      Number of atoms: 2775
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 356, 2761
          Classifications: {'peptide': 356}
          Incomplete info: {'truncation_to_alanine': 22}
          Link IDs: {'PTRANS': 16, 'TRANS': 339}
          Chain breaks: 1
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 93
          Unresolved non-hydrogen angles: 116
          Unresolved non-hydrogen dihedrals: 82
          Unresolved non-hydrogen chiralities: 3
          Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 1, 'TRP:plan': 1, 'ASP:plan': 2, 'PHE:plan': 2, 'GLU:plan': 2, 'ARG:plan': 4}
          Unresolved non-hydrogen planarities: 62
      Conformer: "B"
        Number of residues, atoms: 356, 2761
          Classifications: {'peptide': 356}
          Incomplete info: {'truncation_to_alanine': 22}
          Link IDs: {'PTRANS': 16, 'TRANS': 339}
          Chain breaks: 1
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 93
          Unresolved non-hydrogen angles: 116
          Unresolved non-hydrogen dihedrals: 82
          Unresolved non-hydrogen chiralities: 3
          Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 1, 'TRP:plan': 1, 'ASP:plan': 2, 'PHE:plan': 2, 'GLU:plan': 2, 'ARG:plan': 4}
          Unresolved non-hydrogen planarities: 62
          bond proxies already assigned to first conformer: 2827
    Chain: "C"
      Number of atoms: 1884
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 231, 1884
          Classifications: {'peptide': 231}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 8}
          Link IDs: {'PTRANS': 6, 'TRANS': 224}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 32
          Unresolved non-hydrogen angles: 36
          Unresolved non-hydrogen dihedrals: 28
          Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 2}
          Unresolved non-hydrogen planarities: 18
    Chain: "D"
      Number of atoms: 2500
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 337, 2500
          Classifications: {'peptide': 337}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 21}
          Link IDs: {'PTRANS': 5, 'TRANS': 331}
          Unresolved non-hydrogen bonds: 92
          Unresolved non-hydrogen angles: 110
          Unresolved non-hydrogen dihedrals: 74
          Unresolved non-hydrogen chiralities: 3
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 4, 'ARG:plan': 7, 'ASN:plan1': 1, 'ASP:plan': 2}
          Unresolved non-hydrogen planarities: 64
    Chain: "E"
      Number of atoms: 380
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 57, 380
          Classifications: {'peptide': 57}
          Incomplete info: {'truncation_to_alanine': 15}
          Link IDs: {'PTRANS': 4, 'TRANS': 52}
          Unresolved non-hydrogen bonds: 56
          Unresolved non-hydrogen angles: 67
          Unresolved non-hydrogen dihedrals: 45
          Unresolved non-hydrogen chiralities: 4
          Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 4, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 29
    Chain: "N"
      Number of atoms: 944
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 126, 944
          Classifications: {'peptide': 126}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 4}
          Link IDs: {'PTRANS': 5, 'TRANS': 120}
          Unresolved non-hydrogen bonds: 19
          Unresolved non-hydrogen angles: 24
          Unresolved non-hydrogen dihedrals: 17
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1}
          Unresolved non-hydrogen planarities: 11
  Residues with excluded nonbonded symmetry interactions: 1
    residue:
      pdb=" N  ATRP B 322 " occ=0.50
      ... (26 atoms not shown)
      pdb=" CH2BTRP B 322 " occ=0.50
  Time building chain proxies: 6.89, per 1000 atoms: 0.81
  Number of scatterers: 8483
  At special positions: 0
  Unit cell: (76.32, 98.58, 150.52, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      55     16.00
     O    1571      8.00
     N    1461      7.00
     C    5396      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=5, symmetry=0
    Simple disulfide: pdb=" SG  CYS B 276 " - pdb=" SG  CYS B 296 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 300 " - pdb=" SG  CYS B 381 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 402 " - pdb=" SG  CYS B 477 " distance=2.03
    Simple disulfide: pdb=" SG  CYS N  45 " - pdb=" SG  CYS N 119 " distance=2.04
    Simple disulfide: pdb=" SG  CYS N 122 " - pdb=" SG  CYS N 130 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.07
  Conformation dependent library (CDL) restraints added in 1.3 seconds
  

  2192 Ramachandran restraints generated.
    1096 Oldfield, 0 Emsley, 1096 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2070

  Finding SS restraints...
    Secondary structure from input PDB file:
      27 helices and 11 sheets defined
      37.8% alpha, 15.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.86
  Creating SS restraints...
    Processing helix  chain 'B' and resid 277 through 281
      removed outlier: 3.603A  pdb=" N   LYS B 281 " --> pdb=" O   ARG B 278 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 312 through 344
      removed outlier: 3.594A  pdb=" N   LEU B 316 " --> pdb=" O   GLY B 312 " (cutoff:3.500A)
      removed outlier: 3.831A  pdb=" N   PHE B 318 " --> pdb=" O   GLU B 314 " (cutoff:3.500A)
      removed outlier: 4.313A  pdb=" N   THR B 321 " --> pdb=" O   ARG B 317 " (cutoff:3.500A)
      removed outlier: 3.901A  pdb=" N   TRP B 326 " --> pdb=" O  ATRP B 322 " (cutoff:3.500A)
      removed outlier: 3.708A  pdb=" N   ASP B 344 " --> pdb=" O   THR B 340 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 352 through 376
      removed outlier: 4.368A  pdb=" N   ILE B 356 " --> pdb=" O   GLU B 352 " (cutoff:3.500A)
      removed outlier: 3.616A  pdb=" N   PHE B 357 " --> pdb=" O   ARG B 353 " (cutoff:3.500A)
      removed outlier: 3.772A  pdb=" N   ALA B 364 " --> pdb=" O   GLY B 360 " (cutoff:3.500A)
      removed outlier: 3.520A  pdb=" N   VAL B 365 " --> pdb=" O   CYS B 361 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 399 through 432
      removed outlier: 3.838A  pdb=" N   ALA B 415 " --> pdb=" O   PHE B 411 " (cutoff:3.500A)
      removed outlier: 4.265A  pdb=" N   SER B 416 " --> pdb=" O   PHE B 412 " (cutoff:3.500A)
      removed outlier: 3.539A  pdb=" N   SER B 417 " --> pdb=" O   SER B 413 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 443 through 466
      removed outlier: 4.330A  pdb=" N   VAL B 454 " --> pdb=" O   ALA B 450 " (cutoff:3.500A)
      Proline residue:  B 455  - end of helix
    Processing helix  chain 'B' and resid 484 through 489
    Processing helix  chain 'B' and resid 491 through 524
    Processing helix  chain 'B' and resid 527 through 573
      removed outlier: 3.540A  pdb=" N   TYR B 544 " --> pdb=" O   PHE B 540 " (cutoff:3.500A)
      removed outlier: 3.728A  pdb=" N   VAL B 546 " --> pdb=" O   VAL B 542 " (cutoff:3.500A)
      Proline residue:  B 547  - end of helix
      removed outlier: 3.509A  pdb=" N   ILE B 550 " --> pdb=" O   VAL B 546 " (cutoff:3.500A)
      removed outlier: 3.942A  pdb=" N   VAL B 551 " --> pdb=" O   PRO B 547 " (cutoff:3.500A)
      removed outlier: 3.908A  pdb=" N   ILE B 552 " --> pdb=" O   ALA B 548 " (cutoff:3.500A)
      removed outlier: 3.686A  pdb=" N   ALA B 553 " --> pdb=" O   THR B 549 " (cutoff:3.500A)
      removed outlier: 4.947A  pdb=" N   ASP B 563 " --> pdb=" O   GLN B 559 " (cutoff:3.500A)
      removed outlier: 4.821A  pdb=" N   GLN B 564 " --> pdb=" O   ALA B 560 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 599 through 609
      removed outlier: 3.891A  pdb=" N   PHE B 603 " --> pdb=" O   ASP B 599 " (cutoff:3.500A)
      removed outlier: 3.598A  pdb=" N   ILE B 605 " --> pdb=" O   THR B 601 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 611 through 616
      removed outlier: 3.972A  pdb=" N   ILE B 615 " --> pdb=" O   LEU B 611 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 617 through 621
      removed outlier: 3.931A  pdb=" N   TRP B 620 " --> pdb=" O   SER B 617 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 623 through 636
      removed outlier: 3.631A  pdb=" N   LEU B 627 " --> pdb=" O   SER B 623 " (cutoff:3.500A)
      removed outlier: 3.920A  pdb=" N   THR B 635 " --> pdb=" O   ARG B 631 " (cutoff:3.500A)
      removed outlier: 3.514A  pdb=" N   ARG B 636 " --> pdb=" O   LYS B 632 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 17 through 36
      removed outlier: 3.673A  pdb=" N   ALA C  36 " --> pdb=" O   ASP C  32 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 234 through 238
      removed outlier: 3.552A  pdb=" N   CYS C 237 " --> pdb=" O   TRP C 234 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 253 through 265
      No H-bonds generated for 'chain 'C' and resid 253 through 265'
    Processing helix  chain 'C' and resid 266 through 279
    Processing helix  chain 'C' and resid 280 through 283
      removed outlier: 3.828A  pdb=" N   ARG C 283 " --> pdb=" O   ARG C 280 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 280 through 283'
    Processing helix  chain 'C' and resid 293 through 303
      removed outlier: 3.752A  pdb=" N   GLU C 299 " --> pdb=" O   ASP C 295 " (cutoff:3.500A)
      removed outlier: 3.859A  pdb=" N   LYS C 300 " --> pdb=" O   LEU C 296 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 307 through 312
      removed outlier: 4.220A  pdb=" N   TYR C 311 " --> pdb=" O   LYS C 307 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 313 through 316
      removed outlier: 3.987A  pdb=" N   ALA C 316 " --> pdb=" O   PRO C 313 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 313 through 316'
    Processing helix  chain 'C' and resid 331 through 353
      removed outlier: 3.537A  pdb=" N   THR C 335 " --> pdb=" O   ASP C 331 " (cutoff:3.500A)
      removed outlier: 3.618A  pdb=" N   ALA C 337 " --> pdb=" O   ARG C 333 " (cutoff:3.500A)
      removed outlier: 4.375A  pdb=" N   ILE C 348 " --> pdb=" O   GLU C 344 " (cutoff:3.500A)
      removed outlier: 3.957A  pdb=" N   SER C 349 " --> pdb=" O   PHE C 345 " (cutoff:3.500A)
      removed outlier: 3.588A  pdb=" N   GLY C 353 " --> pdb=" O   SER C 349 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 371 through 391
      removed outlier: 3.640A  pdb=" N   TYR C 391 " --> pdb=" O   ASN C 387 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 5 through 26
    Processing helix  chain 'D' and resid 29 through 35
      removed outlier: 3.883A  pdb=" N   ILE D  33 " --> pdb=" O   THR D  29 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 35 through 47
      removed outlier: 3.950A  pdb=" N   ALA E  47 " --> pdb=" O   LEU E  43 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 53 through 68
    Processing helix  chain 'N' and resid 110 through 114
      removed outlier: 3.829A  pdb=" N   THR N 114 " --> pdb=" O   PRO N 111 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'B' and resid 468 through 470
    Processing sheet with id=AA2, first strand: chain 'C' and resid 207 through 214
      removed outlier: 3.585A  pdb=" N   LEU C  43 " --> pdb=" O   HIS C 220 " (cutoff:3.500A)
      removed outlier: 4.689A  pdb=" N   VAL C 224 " --> pdb=" O   LEU C  45 " (cutoff:3.500A)
      removed outlier: 6.288A  pdb=" N   LEU C  44 " --> pdb=" O   ILE C 245 " (cutoff:3.500A)
      removed outlier: 7.699A  pdb=" N   VAL C 247 " --> pdb=" O   LEU C  44 " (cutoff:3.500A)
      removed outlier: 6.495A  pdb=" N   ILE C 244 " --> pdb=" O   ILE C 288 " (cutoff:3.500A)
      removed outlier: 7.467A  pdb=" N   PHE C 290 " --> pdb=" O   ILE C 244 " (cutoff:3.500A)
      removed outlier: 6.596A  pdb=" N   PHE C 246 " --> pdb=" O   PHE C 290 " (cutoff:3.500A)
      removed outlier: 7.125A  pdb=" N   ASN C 292 " --> pdb=" O   PHE C 246 " (cutoff:3.500A)
      removed outlier: 6.383A  pdb=" N   VAL C 248 " --> pdb=" O   ASN C 292 " (cutoff:3.500A)
      removed outlier: 6.967A  pdb=" N   VAL C 287 " --> pdb=" O   TYR C 360 " (cutoff:3.500A)
      removed outlier: 7.831A  pdb=" N   HIS C 362 " --> pdb=" O   VAL C 287 " (cutoff:3.500A)
      removed outlier: 6.633A  pdb=" N   LEU C 289 " --> pdb=" O   HIS C 362 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'D' and resid 47 through 52
      removed outlier: 7.108A  pdb=" N   ILE D 338 " --> pdb=" O   ARG D  48 " (cutoff:3.500A)
      removed outlier: 5.015A  pdb=" N   THR D  50 " --> pdb=" O   LEU D 336 " (cutoff:3.500A)
      removed outlier: 7.094A  pdb=" N   LEU D 336 " --> pdb=" O   THR D  50 " (cutoff:3.500A)
      removed outlier: 4.244A  pdb=" N   PHE D 335 " --> pdb=" O   SER D 331 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'D' and resid 58 through 63
      removed outlier: 4.051A  pdb=" N   ALA D  60 " --> pdb=" O   ALA D  73 " (cutoff:3.500A)
      removed outlier: 3.620A  pdb=" N   LEU D  70 " --> pdb=" O   TRP D  82 " (cutoff:3.500A)
      removed outlier: 3.535A  pdb=" N   LYS D  78 " --> pdb=" O   SER D  74 " (cutoff:3.500A)
      removed outlier: 3.674A  pdb=" N   HIS D  91 " --> pdb=" O   ILE D  81 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'D' and resid 100 through 105
      removed outlier: 7.010A  pdb=" N   GLY D 115 " --> pdb=" O   MET D 101 " (cutoff:3.500A)
      removed outlier: 4.473A  pdb=" N   CYS D 103 " --> pdb=" O   ALA D 113 " (cutoff:3.500A)
      removed outlier: 6.514A  pdb=" N   ALA D 113 " --> pdb=" O   CYS D 103 " (cutoff:3.500A)
      removed outlier: 5.076A  pdb=" N   TYR D 105 " --> pdb=" O   TYR D 111 " (cutoff:3.500A)
      removed outlier: 7.106A  pdb=" N   TYR D 111 " --> pdb=" O   TYR D 105 " (cutoff:3.500A)
      removed outlier: 4.281A  pdb=" N   GLY D 116 " --> pdb=" O   ILE D 120 " (cutoff:3.500A)
      removed outlier: 4.834A  pdb=" N   ILE D 120 " --> pdb=" O   GLY D 116 " (cutoff:3.500A)
      removed outlier: 5.946A  pdb=" N   CYS D 121 " --> pdb=" O   GLU D 138 " (cutoff:3.500A)
      removed outlier: 4.412A  pdb=" N   GLU D 138 " --> pdb=" O   CYS D 121 " (cutoff:3.500A)
      removed outlier: 6.626A  pdb=" N   ILE D 123 " --> pdb=" O   SER D 136 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'D' and resid 146 through 153
      removed outlier: 6.783A  pdb=" N   SER D 160 " --> pdb=" O   SER D 147 " (cutoff:3.500A)
      removed outlier: 4.577A  pdb=" N   CYS D 149 " --> pdb=" O   VAL D 158 " (cutoff:3.500A)
      removed outlier: 6.890A  pdb=" N   VAL D 158 " --> pdb=" O   CYS D 149 " (cutoff:3.500A)
      removed outlier: 5.259A  pdb=" N   PHE D 151 " --> pdb=" O   GLN D 156 " (cutoff:3.500A)
      removed outlier: 7.691A  pdb=" N   GLN D 156 " --> pdb=" O   PHE D 151 " (cutoff:3.500A)
      removed outlier: 4.648A  pdb=" N   THR D 165 " --> pdb=" O   SER D 161 " (cutoff:3.500A)
      removed outlier: 4.479A  pdb=" N   THR D 178 " --> pdb=" O   LEU D 168 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'D' and resid 187 through 192
      removed outlier: 3.845A  pdb=" N   PHE D 199 " --> pdb=" O   TRP D 211 " (cutoff:3.500A)
      removed outlier: 3.570A  pdb=" N   ALA D 203 " --> pdb=" O   SER D 207 " (cutoff:3.500A)
      removed outlier: 4.610A  pdb=" N   SER D 207 " --> pdb=" O   ALA D 203 " (cutoff:3.500A)
      removed outlier: 7.112A  pdb=" N   ASP D 212 " --> pdb=" O   CYS D 218 " (cutoff:3.500A)
      removed outlier: 6.704A  pdb=" N   CYS D 218 " --> pdb=" O   ASP D 212 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'D' and resid 229 through 233
      removed outlier: 3.658A  pdb=" N   MET D 262 " --> pdb=" O   LEU D 252 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'D' and resid 273 through 277
      removed outlier: 6.686A  pdb=" N   GLY D 288 " --> pdb=" O   THR D 274 " (cutoff:3.500A)
      removed outlier: 4.621A  pdb=" N   VAL D 276 " --> pdb=" O   LEU D 286 " (cutoff:3.500A)
      removed outlier: 6.889A  pdb=" N   LEU D 286 " --> pdb=" O   VAL D 276 " (cutoff:3.500A)
      removed outlier: 4.170A  pdb=" N   CYS D 294 " --> pdb=" O   LEU D 308 " (cutoff:3.500A)
      removed outlier: 3.637A  pdb=" N   LEU D 308 " --> pdb=" O   CYS D 294 " (cutoff:3.500A)
      removed outlier: 3.706A  pdb=" N   GLY D 306 " --> pdb=" O   VAL D 296 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'N' and resid 26 through 29
      removed outlier: 3.552A  pdb=" N   ASP N  96 " --> pdb=" O   THR N 101 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'N' and resid 68 through 69

    357 hydrogen bonds defined for protein.
    1030 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.30

  Time building geometry restraints manager: 2.48 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2768
        1.34 -     1.46: 2069
        1.46 -     1.58: 3763
        1.58 -     1.70: 0
        1.70 -     1.82: 76
  Bond restraints: 8676
  Sorted by residual:
  bond pdb=" N   PRO B 598 "
       pdb=" CD  PRO B 598 "
    ideal  model  delta    sigma   weight residual
    1.473  1.537 -0.064 1.40e-02 5.10e+03 2.08e+01
  bond pdb=" C   ALA B 493 "
       pdb=" N   PRO B 494 "
    ideal  model  delta    sigma   weight residual
    1.334  1.373 -0.039 2.34e-02 1.83e+03 2.77e+00
  bond pdb=" N   THR D 196 "
       pdb=" CA  THR D 196 "
    ideal  model  delta    sigma   weight residual
    1.457  1.478 -0.020 1.29e-02 6.01e+03 2.47e+00
  bond pdb=" CB  GLU B 301 "
       pdb=" CG  GLU B 301 "
    ideal  model  delta    sigma   weight residual
    1.520  1.567 -0.047 3.00e-02 1.11e+03 2.41e+00
  bond pdb=" CB  GLN D  17 "
       pdb=" CG  GLN D  17 "
    ideal  model  delta    sigma   weight residual
    1.520  1.566 -0.046 3.00e-02 1.11e+03 2.40e+00
  ... (remaining 8671 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     4.84: 11748
        4.84 -     9.68: 44
        9.68 -    14.52: 3
       14.52 -    19.37: 1
       19.37 -    24.21: 1
  Bond angle restraints: 11797
  Sorted by residual:
  angle pdb=" CA  LEU B 608 "
        pdb=" CB  LEU B 608 "
        pdb=" CG  LEU B 608 "
      ideal   model   delta    sigma   weight residual
     116.30  140.51  -24.21 3.50e+00 8.16e-02 4.78e+01
  angle pdb=" CB  MET B 609 "
        pdb=" CG  MET B 609 "
        pdb=" SD  MET B 609 "
      ideal   model   delta    sigma   weight residual
     112.70  130.78  -18.08 3.00e+00 1.11e-01 3.63e+01
  angle pdb=" N   PRO B 598 "
        pdb=" CA  PRO B 598 "
        pdb=" C   PRO B 598 "
      ideal   model   delta    sigma   weight residual
     111.77  102.54    9.23 1.67e+00 3.59e-01 3.06e+01
  angle pdb=" CA  LEU B 291 "
        pdb=" CB  LEU B 291 "
        pdb=" CG  LEU B 291 "
      ideal   model   delta    sigma   weight residual
     116.30  130.42  -14.12 3.50e+00 8.16e-02 1.63e+01
  angle pdb=" C   LYS B 294 "
        pdb=" N   ASP B 295 "
        pdb=" CA  ASP B 295 "
      ideal   model   delta    sigma   weight residual
     121.54  128.85   -7.31 1.91e+00 2.74e-01 1.47e+01
  ... (remaining 11792 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.61: 4581
       16.61 -    33.22: 394
       33.22 -    49.82: 99
       49.82 -    66.43: 19
       66.43 -    83.04: 7
  Dihedral angle restraints: 5100
    sinusoidal: 1889
      harmonic: 3211
  Sorted by residual:
  dihedral pdb=" CA  LEU B 608 "
           pdb=" C   LEU B 608 "
           pdb=" N   MET B 609 "
           pdb=" CA  MET B 609 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -144.88  -35.12     0      5.00e+00 4.00e-02 4.93e+01
  dihedral pdb=" CB  CYS B 402 "
           pdb=" SG  CYS B 402 "
           pdb=" SG  CYS B 477 "
           pdb=" CB  CYS B 477 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -140.88   54.88     1      1.00e+01 1.00e-02 4.08e+01
  dihedral pdb=" CB  CYS B 276 "
           pdb=" SG  CYS B 276 "
           pdb=" SG  CYS B 296 "
           pdb=" CB  CYS B 296 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -139.85   53.85     1      1.00e+01 1.00e-02 3.94e+01
  ... (remaining 5097 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.049: 958
       0.049 -    0.098: 286
       0.098 -    0.147: 74
       0.147 -    0.197: 9
       0.197 -    0.246: 3
  Chirality restraints: 1330
  Sorted by residual:
  chirality pdb=" CB  ILE D  43 "
            pdb=" CA  ILE D  43 "
            pdb=" CG1 ILE D  43 "
            pdb=" CG2 ILE D  43 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.89   -0.25 2.00e-01 2.50e+01 1.51e+00
  chirality pdb=" CB  ILE B 579 "
            pdb=" CA  ILE B 579 "
            pdb=" CG1 ILE B 579 "
            pdb=" CG2 ILE B 579 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.41    0.23 2.00e-01 2.50e+01 1.33e+00
  chirality pdb=" CB  ILE B 440 "
            pdb=" CA  ILE B 440 "
            pdb=" CG1 ILE B 440 "
            pdb=" CG2 ILE B 440 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.86   -0.21 2.00e-01 2.50e+01 1.13e+00
  ... (remaining 1327 not shown)

  Planarity restraints: 1509
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER B 597 "   -0.082 5.00e-02 4.00e+02   1.22e-01 2.39e+01
        pdb=" N   PRO B 598 "    0.211 5.00e-02 4.00e+02
        pdb=" CA  PRO B 598 "   -0.066 5.00e-02 4.00e+02
        pdb=" CD  PRO B 598 "   -0.064 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  SER B 597 "    0.015 2.00e-02 2.50e+03   3.05e-02 9.33e+00
        pdb=" C   SER B 597 "   -0.053 2.00e-02 2.50e+03
        pdb=" O   SER B 597 "    0.020 2.00e-02 2.50e+03
        pdb=" N   PRO B 598 "    0.018 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP C 331 "    0.044 5.00e-02 4.00e+02   6.72e-02 7.22e+00
        pdb=" N   PRO C 332 "   -0.116 5.00e-02 4.00e+02
        pdb=" CA  PRO C 332 "    0.035 5.00e-02 4.00e+02
        pdb=" CD  PRO C 332 "    0.037 5.00e-02 4.00e+02
  ... (remaining 1506 not shown)

  Histogram of nonbonded interaction distances:
        2.24 -     2.78: 1733
        2.78 -     3.31: 7916
        3.31 -     3.84: 13951
        3.84 -     4.37: 15682
        4.37 -     4.90: 27304
  Nonbonded interactions: 66586
  Sorted by model distance:
  nonbonded pdb=" OH  TYR C 318 "
            pdb=" OD2 ASP C 343 "
     model   vdw
     2.245 3.040
  nonbonded pdb=" OG  SER B 327 "
            pdb=" O   ALA B 366 "
     model   vdw
     2.252 3.040
  nonbonded pdb=" OH  TYR B 410 "
            pdb=" NZ  LYS B 458 "
     model   vdw
     2.256 3.120
  nonbonded pdb=" OG  SER D 331 "
            pdb=" OD1 ASP D 333 "
     model   vdw
     2.273 3.040
  nonbonded pdb=" O   GLU B 441 "
            pdb=" OG  SER B 444 "
     model   vdw
     2.290 3.040
  ... (remaining 66581 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.50 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             6.100
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.380
  Check model and map are aligned:         0.070
  Set scattering table:                    0.090
  Process input model:                     24.170
  Find NCS groups from input model:        0.100
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:2.830
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   33.790
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6989
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      :  0.004   0.064   8681  Z= 0.177
  Angle     :  0.869  24.207  11807  Z= 0.431
  Chirality :  0.050   0.246   1330
  Planarity :  0.006   0.122   1509
  Dihedral  : 13.711  83.038   3015
  Min Nonbonded Distance : 2.245

Molprobity Statistics.
  All-atom Clashscore : 6.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.04 %
    Favored  : 93.96 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.34 %
    Favored  : 99.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

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: -1.50 (0.25), residues: 1096
  helix:  0.20 (0.26), residues: 387
  sheet: -0.79 (0.35), residues: 226
  loop : -2.10 (0.25), residues: 483

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP D  63 
 HIS   0.005   0.001   HIS C 220 
 PHE   0.035   0.002   PHE B 600 
 TYR   0.035   0.002   TYR B 498 
 ARG   0.012   0.001   ARG D 251 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.14053 (  357)
  hydrogen bonds       : angle       5.95799 ( 1030)
  SS BOND              : bond        0.00246 (    5)
  SS BOND              : angle       0.64360 (   10)
  covalent geometry    : bond        0.00384 ( 8676)
  covalent geometry    : angle       0.86874 (11797)

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

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

  2192 Ramachandran restraints generated.
    1096 Oldfield, 0 Emsley, 1096 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2192 Ramachandran restraints generated.
    1096 Oldfield, 0 Emsley, 1096 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  241 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 241
  time to evaluate  : 0.875 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  441 GLU cc_start: 0.6560 (mm-30) cc_final: 0.6338 (mm-30)
REVERT: B  500 PHE cc_start: 0.6938 (t80) cc_final: 0.6717 (t80)
REVERT: B  558 GLU cc_start: 0.6386 (mm-30) cc_final: 0.6002 (mm-30)
REVERT: C  274 LYS cc_start: 0.7902 (ttmt) cc_final: 0.7644 (ttpt)
REVERT: C  295 ASP cc_start: 0.7412 (m-30) cc_final: 0.7000 (m-30)
REVERT: C  300 LYS cc_start: 0.7912 (tttm) cc_final: 0.7569 (tttp)
REVERT: C  382 THR cc_start: 0.8087 (m) cc_final: 0.7876 (m)
REVERT: D  148 CYS cc_start: 0.7766 (t) cc_final: 0.7388 (t)
REVERT: D  163 ASP cc_start: 0.6613 (p0) cc_final: 0.6225 (p0)
REVERT: D  188 MET cc_start: 0.7132 (mmm) cc_final: 0.6564 (mmm)
REVERT: D  204 CYS cc_start: 0.7468 (m) cc_final: 0.7172 (m)
REVERT: D  280 LYS cc_start: 0.8090 (mtpp) cc_final: 0.7882 (mtpp)
  outliers start: 0
  outliers final: 0
  residues processed: 241
  average time/residue: 0.2564
  time to fit residues: 80.0077
Evaluate side-chains
  223 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 223
  time to evaluate  : 0.879 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 91 optimal weight:    2.9990
   chunk 81 optimal weight:    0.9990
   chunk 45 optimal weight:    1.9990
   chunk 27 optimal weight:    0.0980
   chunk 55 optimal weight:    0.7980
   chunk 43 optimal weight:    0.9990
   chunk 84 optimal weight:    3.9990
   chunk 32 optimal weight:    0.9980
   chunk 51 optimal weight:    1.9990
   chunk 63 optimal weight:    0.9980
   chunk 98 optimal weight:    0.8980
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
D  44 GLN
D  88 ASN
** D 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  68 HIS
N  54 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3877 r_free = 0.3877 target = 0.145510 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3597 r_free = 0.3597 target = 0.124521 restraints weight = 13048.637|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3653 r_free = 0.3653 target = 0.128535 restraints weight = 6453.285|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3688 r_free = 0.3688 target = 0.131203 restraints weight = 3918.928|
|-----------------------------------------------------------------------------|
r_work (final): 0.3687
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3686
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3686 r_free = 0.3686    target_work(ls_wunit_k1) = 0.131         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3686 r_free = 0.3686    target_work(ls_wunit_k1) = 0.131         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3686
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7029
moved from start:          0.1057

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   8681  Z= 0.165
  Angle     :  0.668  19.461  11807  Z= 0.341
  Chirality :  0.044   0.181   1330
  Planarity :  0.005   0.066   1509
  Dihedral  :  4.699  24.536   1201
  Min Nonbonded Distance : 2.510

Molprobity Statistics.
  All-atom Clashscore : 7.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.86 %
    Favored  : 94.14 %
  Rotamer:
    Outliers :  1.38 %
    Allowed  :  9.75 %
    Favored  : 88.88 %
  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: -1.11 (0.25), residues: 1096
  helix:  0.89 (0.28), residues: 385
  sheet: -0.90 (0.35), residues: 235
  loop : -2.03 (0.26), residues: 476

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP B 420 
 HIS   0.004   0.001   HIS C 220 
 PHE   0.033   0.002   PHE C 212 
 TYR   0.025   0.002   TYR B 498 
 ARG   0.005   0.000   ARG D  49 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04025 (  357)
  hydrogen bonds       : angle       4.64926 ( 1030)
  SS BOND              : bond        0.00347 (    5)
  SS BOND              : angle       0.50793 (   10)
  covalent geometry    : bond        0.00371 ( 8676)
  covalent geometry    : angle       0.66840 (11797)

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

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

  2192 Ramachandran restraints generated.
    1096 Oldfield, 0 Emsley, 1096 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2192 Ramachandran restraints generated.
    1096 Oldfield, 0 Emsley, 1096 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  250 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 238
  time to evaluate  : 0.870 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  408 MET cc_start: 0.7106 (ttt) cc_final: 0.6889 (ttt)
REVERT: B  500 PHE cc_start: 0.7112 (t80) cc_final: 0.6862 (t80)
REVERT: B  554 CYS cc_start: 0.7574 (t) cc_final: 0.7145 (t)
REVERT: B  558 GLU cc_start: 0.6575 (mm-30) cc_final: 0.6115 (mm-30)
REVERT: C  212 PHE cc_start: 0.6938 (p90) cc_final: 0.6653 (p90)
REVERT: C  221 MET cc_start: 0.7359 (ttm) cc_final: 0.7098 (ttm)
REVERT: C  274 LYS cc_start: 0.7754 (ttmt) cc_final: 0.7506 (ttpt)
REVERT: C  295 ASP cc_start: 0.7599 (m-30) cc_final: 0.7133 (m-30)
REVERT: C  381 ASP cc_start: 0.7835 (t70) cc_final: 0.7245 (t0)
REVERT: C  382 THR cc_start: 0.8104 (m) cc_final: 0.7901 (m)
REVERT: D   65 THR cc_start: 0.8372 (p) cc_final: 0.8149 (p)
REVERT: D  118 ASP cc_start: 0.7257 (p0) cc_final: 0.7022 (p0)
REVERT: D  121 CYS cc_start: 0.7706 (t) cc_final: 0.7315 (t)
REVERT: D  143 THR cc_start: 0.8056 (p) cc_final: 0.7777 (t)
REVERT: D  148 CYS cc_start: 0.7939 (t) cc_final: 0.7544 (t)
REVERT: D  177 THR cc_start: 0.8186 (m) cc_final: 0.7971 (t)
REVERT: D  188 MET cc_start: 0.7341 (mmm) cc_final: 0.6848 (mmm)
REVERT: D  204 CYS cc_start: 0.7625 (m) cc_final: 0.7235 (m)
REVERT: D  277 SER cc_start: 0.7704 (t) cc_final: 0.7474 (t)
REVERT: D  284 LEU cc_start: 0.7905 (tp) cc_final: 0.7543 (tp)
REVERT: D  298 ASP cc_start: 0.8043 (t70) cc_final: 0.7783 (t0)
  outliers start: 12
  outliers final: 6
  residues processed: 241
  average time/residue: 0.2556
  time to fit residues: 80.0772
Evaluate side-chains
  239 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 233
  time to evaluate  : 0.974 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  329 LEU
Chi-restraints excluded: chain C residue  314 GLU
Chi-restraints excluded: chain D residue  259 GLN
Chi-restraints excluded: chain N residue   54 ASN
Chi-restraints excluded: chain N residue   82 SER
Chi-restraints excluded: chain N residue   92 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 81 optimal weight:    0.9980
   chunk 10 optimal weight:    0.1980
   chunk 55 optimal weight:    2.9990
   chunk 20 optimal weight:    1.9990
   chunk 61 optimal weight:    0.0670
   chunk 96 optimal weight:    3.9990
   chunk 91 optimal weight:   10.0000
   chunk 99 optimal weight:    0.5980
   chunk 28 optimal weight:    0.5980
   chunk 80 optimal weight:    1.9990
   chunk 83 optimal weight:    0.9980
   overall best weight:    0.4918

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

Flipped N/Q/H residues before XYZ refinement:
D 259 GLN
N  54 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3887 r_free = 0.3887 target = 0.146320 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3606 r_free = 0.3606 target = 0.125169 restraints weight = 13168.931|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3662 r_free = 0.3662 target = 0.129230 restraints weight = 6520.197|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3699 r_free = 0.3699 target = 0.131923 restraints weight = 3952.654|
|-----------------------------------------------------------------------------|
r_work (final): 0.3696
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3689
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3689 r_free = 0.3689    target_work(ls_wunit_k1) = 0.131         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3689 r_free = 0.3689    target_work(ls_wunit_k1) = 0.131         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3689
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7008
moved from start:          0.1345

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   8681  Z= 0.129
  Angle     :  0.615  18.976  11807  Z= 0.311
  Chirality :  0.043   0.187   1330
  Planarity :  0.004   0.058   1509
  Dihedral  :  4.491  21.358   1201
  Min Nonbonded Distance : 2.538

Molprobity Statistics.
  All-atom Clashscore : 7.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.58 %
    Favored  : 94.42 %
  Rotamer:
    Outliers :  2.06 %
    Allowed  : 14.56 %
    Favored  : 83.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -0.92 (0.26), residues: 1096
  helix:  1.17 (0.28), residues: 386
  sheet: -0.86 (0.35), residues: 233
  loop : -2.00 (0.26), residues: 477

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.032   0.002   TRP B 420 
 HIS   0.004   0.001   HIS C 220 
 PHE   0.025   0.002   PHE C 212 
 TYR   0.023   0.001   TYR B 498 
 ARG   0.004   0.000   ARG D 251 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03608 (  357)
  hydrogen bonds       : angle       4.40679 ( 1030)
  SS BOND              : bond        0.00246 (    5)
  SS BOND              : angle       0.42746 (   10)
  covalent geometry    : bond        0.00292 ( 8676)
  covalent geometry    : angle       0.61475 (11797)

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

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

  2192 Ramachandran restraints generated.
    1096 Oldfield, 0 Emsley, 1096 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2192 Ramachandran restraints generated.
    1096 Oldfield, 0 Emsley, 1096 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  253 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 235
  time to evaluate  : 0.941 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  407 MET cc_start: 0.6728 (mmt) cc_final: 0.6212 (mmt)
REVERT: B  408 MET cc_start: 0.7327 (ttt) cc_final: 0.7092 (ttt)
REVERT: B  500 PHE cc_start: 0.7116 (t80) cc_final: 0.6873 (t80)
REVERT: B  505 PHE cc_start: 0.7769 (m-10) cc_final: 0.7546 (m-10)
REVERT: B  554 CYS cc_start: 0.7550 (t) cc_final: 0.7090 (t)
REVERT: B  558 GLU cc_start: 0.6558 (mm-30) cc_final: 0.6073 (mm-30)
REVERT: C  212 PHE cc_start: 0.7015 (p90) cc_final: 0.6761 (p90)
REVERT: C  221 MET cc_start: 0.7404 (ttm) cc_final: 0.7032 (ttt)
REVERT: C  274 LYS cc_start: 0.7792 (ttmt) cc_final: 0.7536 (ttpt)
REVERT: C  295 ASP cc_start: 0.7641 (m-30) cc_final: 0.7153 (m-30)
REVERT: C  336 ARG cc_start: 0.6329 (ttp80) cc_final: 0.6077 (mtp85)
REVERT: C  381 ASP cc_start: 0.7845 (t70) cc_final: 0.7195 (t0)
REVERT: C  382 THR cc_start: 0.8073 (m) cc_final: 0.7869 (m)
REVERT: D   17 GLN cc_start: 0.8641 (tm-30) cc_final: 0.8338 (tm-30)
REVERT: D   65 THR cc_start: 0.8405 (p) cc_final: 0.8146 (p)
REVERT: D  111 TYR cc_start: 0.8182 (m-80) cc_final: 0.7835 (m-80)
REVERT: D  118 ASP cc_start: 0.7248 (p0) cc_final: 0.6966 (p0)
REVERT: D  121 CYS cc_start: 0.7711 (t) cc_final: 0.7326 (t)
REVERT: D  143 THR cc_start: 0.8091 (p) cc_final: 0.7749 (t)
REVERT: D  148 CYS cc_start: 0.7910 (t) cc_final: 0.7497 (t)
REVERT: D  188 MET cc_start: 0.7376 (mmm) cc_final: 0.6881 (mmm)
REVERT: D  204 CYS cc_start: 0.7685 (m) cc_final: 0.7252 (m)
REVERT: D  277 SER cc_start: 0.7759 (t) cc_final: 0.7493 (t)
REVERT: D  284 LEU cc_start: 0.7964 (tp) cc_final: 0.7538 (tp)
REVERT: D  298 ASP cc_start: 0.8067 (t70) cc_final: 0.7862 (t0)
REVERT: E   45 MET cc_start: 0.5263 (tmm) cc_final: 0.4989 (tmm)
  outliers start: 18
  outliers final: 14
  residues processed: 240
  average time/residue: 0.2742
  time to fit residues: 84.7603
Evaluate side-chains
  250 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 236
  time to evaluate  : 1.005 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  285 TYR
Chi-restraints excluded: chain B residue  329 LEU
Chi-restraints excluded: chain B residue  433 MET
Chi-restraints excluded: chain B residue  608 LEU
Chi-restraints excluded: chain C residue   29 LEU
Chi-restraints excluded: chain C residue   57 VAL
Chi-restraints excluded: chain C residue  209 GLU
Chi-restraints excluded: chain C residue  335 THR
Chi-restraints excluded: chain D residue  201 SER
Chi-restraints excluded: chain D residue  259 GLN
Chi-restraints excluded: chain N residue   54 ASN
Chi-restraints excluded: chain N residue   82 SER
Chi-restraints excluded: chain N residue   92 THR
Chi-restraints excluded: chain N residue   94 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 99 optimal weight:    1.9990
   chunk 19 optimal weight:    0.8980
   chunk 43 optimal weight:    0.7980
   chunk 81 optimal weight:    0.9990
   chunk 8 optimal weight:    0.7980
   chunk 34 optimal weight:    1.9990
   chunk 53 optimal weight:    0.6980
   chunk 62 optimal weight:    3.9990
   chunk 20 optimal weight:    0.4980
   chunk 101 optimal weight:    0.9980
   chunk 2 optimal weight:    0.9990
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
** D 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
N  54 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3868 r_free = 0.3868 target = 0.144698 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3586 r_free = 0.3586 target = 0.123802 restraints weight = 13191.497|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3640 r_free = 0.3640 target = 0.127666 restraints weight = 6681.433|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3677 r_free = 0.3677 target = 0.130292 restraints weight = 4134.390|
|-----------------------------------------------------------------------------|
r_work (final): 0.3670
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3676
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3676 r_free = 0.3676    target_work(ls_wunit_k1) = 0.130         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3676 r_free = 0.3676    target_work(ls_wunit_k1) = 0.130         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3676
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7043
moved from start:          0.1539

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   8681  Z= 0.155
  Angle     :  0.630  19.140  11807  Z= 0.317
  Chirality :  0.043   0.178   1330
  Planarity :  0.004   0.057   1509
  Dihedral  :  4.441  20.283   1201
  Min Nonbonded Distance : 2.536

Molprobity Statistics.
  All-atom Clashscore : 8.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.95 %
    Favored  : 94.05 %
  Rotamer:
    Outliers :  2.87 %
    Allowed  : 14.79 %
    Favored  : 82.34 %
  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: -0.84 (0.26), residues: 1096
  helix:  1.26 (0.28), residues: 386
  sheet: -0.87 (0.36), residues: 230
  loop : -1.95 (0.26), residues: 480

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.002   TRP B 420 
 HIS   0.004   0.001   HIS D 183 
 PHE   0.027   0.002   PHE B 540 
 TYR   0.023   0.002   TYR B 498 
 ARG   0.004   0.000   ARG D  49 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03715 (  357)
  hydrogen bonds       : angle       4.34153 ( 1030)
  SS BOND              : bond        0.00330 (    5)
  SS BOND              : angle       0.48242 (   10)
  covalent geometry    : bond        0.00352 ( 8676)
  covalent geometry    : angle       0.63045 (11797)

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

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

  2192 Ramachandran restraints generated.
    1096 Oldfield, 0 Emsley, 1096 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2192 Ramachandran restraints generated.
    1096 Oldfield, 0 Emsley, 1096 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  254 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 229
  time to evaluate  : 0.974 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  407 MET cc_start: 0.6739 (mmt) cc_final: 0.6240 (mmt)
REVERT: B  496 PHE cc_start: 0.7541 (t80) cc_final: 0.7254 (t80)
REVERT: B  500 PHE cc_start: 0.7119 (t80) cc_final: 0.6895 (t80)
REVERT: B  558 GLU cc_start: 0.6580 (mm-30) cc_final: 0.6076 (mm-30)
REVERT: C  212 PHE cc_start: 0.6986 (p90) cc_final: 0.6712 (p90)
REVERT: C  221 MET cc_start: 0.7402 (ttm) cc_final: 0.7040 (ttm)
REVERT: C  274 LYS cc_start: 0.7796 (ttmt) cc_final: 0.7567 (ttpt)
REVERT: C  295 ASP cc_start: 0.7566 (m-30) cc_final: 0.7084 (m-30)
REVERT: C  336 ARG cc_start: 0.6373 (ttp80) cc_final: 0.6129 (mtp85)
REVERT: C  381 ASP cc_start: 0.7865 (t70) cc_final: 0.7195 (t0)
REVERT: C  382 THR cc_start: 0.8122 (m) cc_final: 0.7918 (m)
REVERT: D   17 GLN cc_start: 0.8629 (tm-30) cc_final: 0.8386 (tm-30)
REVERT: D   59 TYR cc_start: 0.7922 (OUTLIER) cc_final: 0.7614 (m-80)
REVERT: D   65 THR cc_start: 0.8422 (p) cc_final: 0.8163 (p)
REVERT: D  118 ASP cc_start: 0.7229 (p0) cc_final: 0.6941 (p0)
REVERT: D  121 CYS cc_start: 0.7693 (t) cc_final: 0.7364 (t)
REVERT: D  137 ARG cc_start: 0.7120 (tpp-160) cc_final: 0.6674 (tpp-160)
REVERT: D  143 THR cc_start: 0.8098 (p) cc_final: 0.7774 (t)
REVERT: D  148 CYS cc_start: 0.7904 (t) cc_final: 0.7518 (t)
REVERT: D  188 MET cc_start: 0.7325 (mmm) cc_final: 0.6810 (mmm)
REVERT: D  204 CYS cc_start: 0.7682 (m) cc_final: 0.7231 (m)
REVERT: D  277 SER cc_start: 0.7731 (t) cc_final: 0.7471 (t)
REVERT: D  284 LEU cc_start: 0.7958 (tp) cc_final: 0.7522 (tp)
REVERT: E   45 MET cc_start: 0.5112 (tmm) cc_final: 0.4903 (tmm)
REVERT: N  106 MET cc_start: 0.6613 (mmm) cc_final: 0.6219 (tpp)
  outliers start: 25
  outliers final: 19
  residues processed: 235
  average time/residue: 0.2798
  time to fit residues: 86.2398
Evaluate side-chains
  251 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 231
  time to evaluate  : 0.893 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  285 TYR
Chi-restraints excluded: chain B residue  387 GLU
Chi-restraints excluded: chain B residue  418 ILE
Chi-restraints excluded: chain B residue  433 MET
Chi-restraints excluded: chain B residue  608 LEU
Chi-restraints excluded: chain C residue   29 LEU
Chi-restraints excluded: chain C residue   57 VAL
Chi-restraints excluded: chain C residue  209 GLU
Chi-restraints excluded: chain C residue  218 ASN
Chi-restraints excluded: chain C residue  268 GLU
Chi-restraints excluded: chain C residue  320 THR
Chi-restraints excluded: chain C residue  335 THR
Chi-restraints excluded: chain D residue   59 TYR
Chi-restraints excluded: chain D residue  259 GLN
Chi-restraints excluded: chain E residue   49 ILE
Chi-restraints excluded: chain N residue   54 ASN
Chi-restraints excluded: chain N residue   60 VAL
Chi-restraints excluded: chain N residue   82 SER
Chi-restraints excluded: chain N residue   92 THR
Chi-restraints excluded: chain N residue   94 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 41 optimal weight:    1.9990
   chunk 12 optimal weight:    0.0030
   chunk 64 optimal weight:    1.9990
   chunk 11 optimal weight:    0.9980
   chunk 27 optimal weight:    0.2980
   chunk 87 optimal weight:    0.9990
   chunk 92 optimal weight:    2.9990
   chunk 34 optimal weight:    0.6980
   chunk 21 optimal weight:    0.7980
   chunk 3 optimal weight:    3.9990
   chunk 4 optimal weight:    0.0170
   overall best weight:    0.3628

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

Flipped N/Q/H residues before XYZ refinement:
D 259 GLN
N  54 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3893 r_free = 0.3893 target = 0.146924 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3616 r_free = 0.3616 target = 0.126099 restraints weight = 13002.934|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3669 r_free = 0.3669 target = 0.129947 restraints weight = 6609.866|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3704 r_free = 0.3704 target = 0.132537 restraints weight = 4094.921|
|-----------------------------------------------------------------------------|
r_work (final): 0.3699
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3699
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3699 r_free = 0.3699    target_work(ls_wunit_k1) = 0.132         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3699 r_free = 0.3699    target_work(ls_wunit_k1) = 0.132         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3699
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7027
moved from start:          0.1676

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   8681  Z= 0.115
  Angle     :  0.604  18.762  11807  Z= 0.301
  Chirality :  0.042   0.168   1330
  Planarity :  0.004   0.057   1509
  Dihedral  :  4.299  20.950   1201
  Min Nonbonded Distance : 2.537

Molprobity Statistics.
  All-atom Clashscore : 7.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.12 %
    Favored  : 94.88 %
  Rotamer:
    Outliers :  2.75 %
    Allowed  : 14.33 %
    Favored  : 82.91 %
  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: -0.76 (0.26), residues: 1096
  helix:  1.32 (0.28), residues: 383
  sheet: -0.86 (0.35), residues: 233
  loop : -1.86 (0.26), residues: 480

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.042   0.002   TRP B 420 
 HIS   0.003   0.001   HIS C 220 
 PHE   0.038   0.001   PHE B 540 
 TYR   0.025   0.001   TYR B 607 
 ARG   0.005   0.000   ARG D  49 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03373 (  357)
  hydrogen bonds       : angle       4.17020 ( 1030)
  SS BOND              : bond        0.00200 (    5)
  SS BOND              : angle       0.39316 (   10)
  covalent geometry    : bond        0.00261 ( 8676)
  covalent geometry    : angle       0.60458 (11797)

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

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

  2192 Ramachandran restraints generated.
    1096 Oldfield, 0 Emsley, 1096 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2192 Ramachandran restraints generated.
    1096 Oldfield, 0 Emsley, 1096 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  263 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 239
  time to evaluate  : 0.864 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  407 MET cc_start: 0.6586 (mmt) cc_final: 0.6152 (mmt)
REVERT: B  496 PHE cc_start: 0.7513 (t80) cc_final: 0.7195 (t80)
REVERT: B  540 PHE cc_start: 0.7505 (t80) cc_final: 0.7296 (t80)
REVERT: B  544 TYR cc_start: 0.7055 (t80) cc_final: 0.6806 (t80)
REVERT: C  274 LYS cc_start: 0.7813 (ttmt) cc_final: 0.7589 (ttpt)
REVERT: C  295 ASP cc_start: 0.7404 (m-30) cc_final: 0.6943 (m-30)
REVERT: C  381 ASP cc_start: 0.7824 (t70) cc_final: 0.7099 (t0)
REVERT: C  382 THR cc_start: 0.8149 (m) cc_final: 0.7909 (m)
REVERT: C  385 GLN cc_start: 0.8126 (tp40) cc_final: 0.7803 (mm-40)
REVERT: D   59 TYR cc_start: 0.7994 (OUTLIER) cc_final: 0.7627 (m-80)
REVERT: D   65 THR cc_start: 0.8415 (p) cc_final: 0.8145 (p)
REVERT: D  111 TYR cc_start: 0.8144 (m-80) cc_final: 0.7814 (m-80)
REVERT: D  118 ASP cc_start: 0.7149 (p0) cc_final: 0.6863 (p0)
REVERT: D  121 CYS cc_start: 0.7596 (t) cc_final: 0.7282 (t)
REVERT: D  137 ARG cc_start: 0.7052 (tpp-160) cc_final: 0.6649 (tpp-160)
REVERT: D  143 THR cc_start: 0.8081 (p) cc_final: 0.7559 (t)
REVERT: D  148 CYS cc_start: 0.7859 (t) cc_final: 0.7466 (t)
REVERT: D  188 MET cc_start: 0.7218 (mmm) cc_final: 0.6635 (mmm)
REVERT: D  204 CYS cc_start: 0.7566 (m) cc_final: 0.7180 (m)
REVERT: D  277 SER cc_start: 0.7671 (t) cc_final: 0.7422 (t)
REVERT: D  284 LEU cc_start: 0.7925 (tp) cc_final: 0.7515 (tp)
REVERT: D  291 ASP cc_start: 0.7223 (p0) cc_final: 0.7011 (p0)
REVERT: N  106 MET cc_start: 0.6670 (mmm) cc_final: 0.6399 (tpp)
  outliers start: 24
  outliers final: 18
  residues processed: 245
  average time/residue: 0.2598
  time to fit residues: 81.9046
Evaluate side-chains
  253 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 234
  time to evaluate  : 0.901 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  285 TYR
Chi-restraints excluded: chain B residue  329 LEU
Chi-restraints excluded: chain B residue  387 GLU
Chi-restraints excluded: chain B residue  418 ILE
Chi-restraints excluded: chain B residue  433 MET
Chi-restraints excluded: chain B residue  608 LEU
Chi-restraints excluded: chain C residue   57 VAL
Chi-restraints excluded: chain C residue  209 GLU
Chi-restraints excluded: chain C residue  310 ASP
Chi-restraints excluded: chain C residue  320 THR
Chi-restraints excluded: chain C residue  335 THR
Chi-restraints excluded: chain D residue   59 TYR
Chi-restraints excluded: chain D residue  201 SER
Chi-restraints excluded: chain D residue  259 GLN
Chi-restraints excluded: chain E residue   49 ILE
Chi-restraints excluded: chain N residue   54 ASN
Chi-restraints excluded: chain N residue   82 SER
Chi-restraints excluded: chain N residue   92 THR
Chi-restraints excluded: chain N residue   94 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 17 optimal weight:    2.9990
   chunk 75 optimal weight:    0.9990
   chunk 94 optimal weight:    0.6980
   chunk 107 optimal weight:    2.9990
   chunk 12 optimal weight:    0.5980
   chunk 26 optimal weight:    0.7980
   chunk 6 optimal weight:    0.6980
   chunk 35 optimal weight:    1.9990
   chunk 82 optimal weight:    1.9990
   chunk 95 optimal weight:    3.9990
   chunk 54 optimal weight:    0.0470
   overall best weight:    0.5678

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

Flipped N/Q/H residues before XYZ refinement:
B 448 HIS
D  75 GLN
** D 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
N  54 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3884 r_free = 0.3884 target = 0.146270 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3604 r_free = 0.3604 target = 0.125305 restraints weight = 13012.136|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3659 r_free = 0.3659 target = 0.129248 restraints weight = 6639.640|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3693 r_free = 0.3693 target = 0.131819 restraints weight = 4101.678|
|-----------------------------------------------------------------------------|
r_work (final): 0.3689
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3689
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3689 r_free = 0.3689    target_work(ls_wunit_k1) = 0.131         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3689 r_free = 0.3689    target_work(ls_wunit_k1) = 0.131         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3689
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7043
moved from start:          0.1809

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   8681  Z= 0.136
  Angle     :  0.627  19.763  11807  Z= 0.314
  Chirality :  0.042   0.157   1330
  Planarity :  0.004   0.057   1509
  Dihedral  :  4.332  24.912   1201
  Min Nonbonded Distance : 2.534

Molprobity Statistics.
  All-atom Clashscore : 8.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.40 %
    Favored  : 94.60 %
  Rotamer:
    Outliers :  2.75 %
    Allowed  : 15.94 %
    Favored  : 81.31 %
  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: -0.68 (0.26), residues: 1096
  helix:  1.42 (0.28), residues: 384
  sheet: -0.81 (0.36), residues: 234
  loop : -1.87 (0.26), residues: 478

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP B 427 
 HIS   0.004   0.001   HIS C 220 
 PHE   0.026   0.001   PHE B 540 
 TYR   0.019   0.001   TYR B 498 
 ARG   0.007   0.000   ARG B 567 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03456 (  357)
  hydrogen bonds       : angle       4.15288 ( 1030)
  SS BOND              : bond        0.00261 (    5)
  SS BOND              : angle       0.44249 (   10)
  covalent geometry    : bond        0.00308 ( 8676)
  covalent geometry    : angle       0.62695 (11797)

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

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

  2192 Ramachandran restraints generated.
    1096 Oldfield, 0 Emsley, 1096 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2192 Ramachandran restraints generated.
    1096 Oldfield, 0 Emsley, 1096 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  258 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 234
  time to evaluate  : 0.963 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  352 GLU cc_start: 0.7080 (mm-30) cc_final: 0.6776 (mm-30)
REVERT: B  407 MET cc_start: 0.6479 (mmt) cc_final: 0.5999 (mmt)
REVERT: B  496 PHE cc_start: 0.7507 (t80) cc_final: 0.7258 (t80)
REVERT: B  544 TYR cc_start: 0.7420 (t80) cc_final: 0.6956 (t80)
REVERT: C   15 GLU cc_start: 0.6762 (tp30) cc_final: 0.6427 (tp30)
REVERT: C  221 MET cc_start: 0.7298 (ttm) cc_final: 0.7013 (ttp)
REVERT: C  274 LYS cc_start: 0.7828 (ttmt) cc_final: 0.7600 (ttpt)
REVERT: C  295 ASP cc_start: 0.7406 (m-30) cc_final: 0.6945 (m-30)
REVERT: C  338 LYS cc_start: 0.8311 (tttm) cc_final: 0.8081 (tttm)
REVERT: C  381 ASP cc_start: 0.7827 (t70) cc_final: 0.7124 (t0)
REVERT: C  382 THR cc_start: 0.8159 (m) cc_final: 0.7936 (m)
REVERT: C  385 GLN cc_start: 0.8127 (tp40) cc_final: 0.7834 (mm-40)
REVERT: D   65 THR cc_start: 0.8431 (p) cc_final: 0.8160 (p)
REVERT: D  111 TYR cc_start: 0.8149 (m-80) cc_final: 0.7836 (m-80)
REVERT: D  118 ASP cc_start: 0.7149 (p0) cc_final: 0.6889 (p0)
REVERT: D  121 CYS cc_start: 0.7608 (t) cc_final: 0.7387 (t)
REVERT: D  137 ARG cc_start: 0.7094 (tpp-160) cc_final: 0.6811 (tpp-160)
REVERT: D  143 THR cc_start: 0.7960 (p) cc_final: 0.7722 (t)
REVERT: D  148 CYS cc_start: 0.7885 (t) cc_final: 0.7517 (t)
REVERT: D  163 ASP cc_start: 0.7329 (p0) cc_final: 0.6688 (p0)
REVERT: D  188 MET cc_start: 0.7229 (mmm) cc_final: 0.6649 (mmm)
REVERT: D  204 CYS cc_start: 0.7579 (m) cc_final: 0.7188 (m)
REVERT: D  277 SER cc_start: 0.7660 (t) cc_final: 0.7403 (t)
REVERT: D  284 LEU cc_start: 0.7948 (tp) cc_final: 0.7529 (tp)
REVERT: D  291 ASP cc_start: 0.7237 (p0) cc_final: 0.7036 (p0)
REVERT: N  106 MET cc_start: 0.6633 (mmm) cc_final: 0.6411 (tpp)
  outliers start: 24
  outliers final: 22
  residues processed: 240
  average time/residue: 0.2999
  time to fit residues: 92.1662
Evaluate side-chains
  251 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 229
  time to evaluate  : 0.889 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  285 TYR
Chi-restraints excluded: chain B residue  329 LEU
Chi-restraints excluded: chain B residue  387 GLU
Chi-restraints excluded: chain B residue  418 ILE
Chi-restraints excluded: chain B residue  433 MET
Chi-restraints excluded: chain B residue  520 MET
Chi-restraints excluded: chain B residue  534 MET
Chi-restraints excluded: chain B residue  608 LEU
Chi-restraints excluded: chain C residue   29 LEU
Chi-restraints excluded: chain C residue   57 VAL
Chi-restraints excluded: chain C residue  209 GLU
Chi-restraints excluded: chain C residue  268 GLU
Chi-restraints excluded: chain C residue  310 ASP
Chi-restraints excluded: chain C residue  320 THR
Chi-restraints excluded: chain C residue  335 THR
Chi-restraints excluded: chain D residue  201 SER
Chi-restraints excluded: chain E residue   49 ILE
Chi-restraints excluded: chain N residue   54 ASN
Chi-restraints excluded: chain N residue   60 VAL
Chi-restraints excluded: chain N residue   82 SER
Chi-restraints excluded: chain N residue   92 THR
Chi-restraints excluded: chain N residue   94 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 61 optimal weight:    5.9990
   chunk 107 optimal weight:    1.9990
   chunk 79 optimal weight:    0.7980
   chunk 6 optimal weight:    0.9990
   chunk 33 optimal weight:    0.7980
   chunk 27 optimal weight:    0.0270
   chunk 51 optimal weight:    0.2980
   chunk 8 optimal weight:    0.7980
   chunk 1 optimal weight:    2.9990
   chunk 81 optimal weight:    0.9990
   chunk 32 optimal weight:    0.9990
   overall best weight:    0.5438

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

Flipped N/Q/H residues before XYZ refinement:
B 448 HIS
D  75 GLN
D 259 GLN
N  54 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3885 r_free = 0.3885 target = 0.146236 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3605 r_free = 0.3605 target = 0.125276 restraints weight = 13051.889|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3659 r_free = 0.3659 target = 0.129189 restraints weight = 6634.824|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3695 r_free = 0.3695 target = 0.131823 restraints weight = 4091.535|
|-----------------------------------------------------------------------------|
r_work (final): 0.3692
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3692
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3692 r_free = 0.3692    target_work(ls_wunit_k1) = 0.132         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3692 r_free = 0.3692    target_work(ls_wunit_k1) = 0.132         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3692
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7040
moved from start:          0.1933

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   8681  Z= 0.132
  Angle     :  0.633  19.561  11807  Z= 0.315
  Chirality :  0.042   0.157   1330
  Planarity :  0.004   0.057   1509
  Dihedral  :  4.315  24.107   1201
  Min Nonbonded Distance : 2.536

Molprobity Statistics.
  All-atom Clashscore : 8.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.22 %
    Favored  : 94.78 %
  Rotamer:
    Outliers :  2.87 %
    Allowed  : 16.74 %
    Favored  : 80.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.62 (0.26), residues: 1096
  helix:  1.51 (0.28), residues: 384
  sheet: -0.81 (0.36), residues: 234
  loop : -1.84 (0.26), residues: 478

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.058   0.002   TRP B 420 
 HIS   0.003   0.001   HIS C 220 
 PHE   0.016   0.001   PHE B 600 
 TYR   0.022   0.001   TYR B 498 
 ARG   0.005   0.000   ARG D  49 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03425 (  357)
  hydrogen bonds       : angle       4.12225 ( 1030)
  SS BOND              : bond        0.00255 (    5)
  SS BOND              : angle       0.41807 (   10)
  covalent geometry    : bond        0.00302 ( 8676)
  covalent geometry    : angle       0.63364 (11797)

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

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

  2192 Ramachandran restraints generated.
    1096 Oldfield, 0 Emsley, 1096 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2192 Ramachandran restraints generated.
    1096 Oldfield, 0 Emsley, 1096 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  255 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 230
  time to evaluate  : 0.936 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  407 MET cc_start: 0.6548 (mmt) cc_final: 0.6079 (mmt)
REVERT: B  496 PHE cc_start: 0.7498 (t80) cc_final: 0.7239 (t80)
REVERT: C  221 MET cc_start: 0.7297 (ttm) cc_final: 0.7030 (ttm)
REVERT: C  274 LYS cc_start: 0.7836 (ttmt) cc_final: 0.7606 (ttpt)
REVERT: C  295 ASP cc_start: 0.7386 (m-30) cc_final: 0.7132 (m-30)
REVERT: C  338 LYS cc_start: 0.8316 (tttm) cc_final: 0.8083 (tttm)
REVERT: C  381 ASP cc_start: 0.7834 (t70) cc_final: 0.7142 (t0)
REVERT: C  382 THR cc_start: 0.8145 (m) cc_final: 0.7910 (m)
REVERT: D   65 THR cc_start: 0.8445 (p) cc_final: 0.8175 (p)
REVERT: D  111 TYR cc_start: 0.8144 (m-80) cc_final: 0.7841 (m-80)
REVERT: D  118 ASP cc_start: 0.7128 (p0) cc_final: 0.6884 (p0)
REVERT: D  137 ARG cc_start: 0.7092 (tpp-160) cc_final: 0.6815 (tpp-160)
REVERT: D  143 THR cc_start: 0.7985 (p) cc_final: 0.7703 (t)
REVERT: D  148 CYS cc_start: 0.7894 (t) cc_final: 0.7511 (t)
REVERT: D  163 ASP cc_start: 0.7251 (p0) cc_final: 0.6996 (p0)
REVERT: D  177 THR cc_start: 0.8050 (p) cc_final: 0.7831 (t)
REVERT: D  188 MET cc_start: 0.7179 (mmm) cc_final: 0.6644 (mmm)
REVERT: D  198 LEU cc_start: 0.7931 (OUTLIER) cc_final: 0.7691 (mt)
REVERT: D  204 CYS cc_start: 0.7558 (m) cc_final: 0.7188 (m)
REVERT: D  277 SER cc_start: 0.7643 (t) cc_final: 0.7379 (t)
REVERT: D  284 LEU cc_start: 0.7936 (tp) cc_final: 0.7523 (tp)
  outliers start: 25
  outliers final: 21
  residues processed: 236
  average time/residue: 0.2652
  time to fit residues: 80.8652
Evaluate side-chains
  248 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 226
  time to evaluate  : 0.881 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  285 TYR
Chi-restraints excluded: chain B residue  329 LEU
Chi-restraints excluded: chain B residue  387 GLU
Chi-restraints excluded: chain B residue  418 ILE
Chi-restraints excluded: chain B residue  433 MET
Chi-restraints excluded: chain B residue  520 MET
Chi-restraints excluded: chain B residue  608 LEU
Chi-restraints excluded: chain C residue   29 LEU
Chi-restraints excluded: chain C residue   57 VAL
Chi-restraints excluded: chain C residue  209 GLU
Chi-restraints excluded: chain C residue  252 ASP
Chi-restraints excluded: chain C residue  320 THR
Chi-restraints excluded: chain C residue  335 THR
Chi-restraints excluded: chain D residue  198 LEU
Chi-restraints excluded: chain D residue  259 GLN
Chi-restraints excluded: chain D residue  329 THR
Chi-restraints excluded: chain E residue   49 ILE
Chi-restraints excluded: chain N residue   54 ASN
Chi-restraints excluded: chain N residue   60 VAL
Chi-restraints excluded: chain N residue   82 SER
Chi-restraints excluded: chain N residue   92 THR
Chi-restraints excluded: chain N residue   94 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 62 optimal weight:    4.9990
   chunk 59 optimal weight:    6.9990
   chunk 83 optimal weight:    0.5980
   chunk 69 optimal weight:    0.6980
   chunk 5 optimal weight:    5.9990
   chunk 3 optimal weight:    0.9990
   chunk 34 optimal weight:    0.6980
   chunk 37 optimal weight:    0.5980
   chunk 72 optimal weight:    0.7980
   chunk 66 optimal weight:    2.9990
   chunk 21 optimal weight:    1.9990
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
B 448 HIS
D  75 GLN
D 259 GLN
N  54 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3873 r_free = 0.3873 target = 0.145237 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3590 r_free = 0.3590 target = 0.124034 restraints weight = 13238.215|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3645 r_free = 0.3645 target = 0.128020 restraints weight = 6733.256|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3681 r_free = 0.3681 target = 0.130685 restraints weight = 4150.096|
|-----------------------------------------------------------------------------|
r_work (final): 0.3683
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3683
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3683 r_free = 0.3683    target_work(ls_wunit_k1) = 0.131         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3683 r_free = 0.3683    target_work(ls_wunit_k1) = 0.131         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3683
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7055
moved from start:          0.1983

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   8681  Z= 0.150
  Angle     :  0.657  20.001  11807  Z= 0.327
  Chirality :  0.043   0.173   1330
  Planarity :  0.004   0.057   1509
  Dihedral  :  4.365  25.383   1201
  Min Nonbonded Distance : 2.534

Molprobity Statistics.
  All-atom Clashscore : 8.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.95 %
    Favored  : 94.05 %
  Rotamer:
    Outliers :  3.10 %
    Allowed  : 17.43 %
    Favored  : 79.47 %
  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: -0.60 (0.26), residues: 1096
  helix:  1.53 (0.28), residues: 385
  sheet: -0.78 (0.36), residues: 230
  loop : -1.84 (0.26), residues: 481

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP B 427 
 HIS   0.004   0.001   HIS D 183 
 PHE   0.020   0.001   PHE B 600 
 TYR   0.024   0.002   TYR B 498 
 ARG   0.009   0.000   ARG D  49 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03556 (  357)
  hydrogen bonds       : angle       4.15675 ( 1030)
  SS BOND              : bond        0.00295 (    5)
  SS BOND              : angle       0.44841 (   10)
  covalent geometry    : bond        0.00340 ( 8676)
  covalent geometry    : angle       0.65724 (11797)

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

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

  2192 Ramachandran restraints generated.
    1096 Oldfield, 0 Emsley, 1096 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2192 Ramachandran restraints generated.
    1096 Oldfield, 0 Emsley, 1096 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  259 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 232
  time to evaluate  : 0.925 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  407 MET cc_start: 0.6563 (mmt) cc_final: 0.6102 (mmt)
REVERT: B  496 PHE cc_start: 0.7499 (t80) cc_final: 0.7271 (t80)
REVERT: C  221 MET cc_start: 0.7290 (ttm) cc_final: 0.7027 (ttp)
REVERT: C  274 LYS cc_start: 0.7842 (ttmt) cc_final: 0.7605 (ttpt)
REVERT: C  295 ASP cc_start: 0.7396 (m-30) cc_final: 0.6777 (m-30)
REVERT: C  338 LYS cc_start: 0.8330 (tttm) cc_final: 0.8083 (tttm)
REVERT: C  381 ASP cc_start: 0.7842 (t70) cc_final: 0.7162 (t0)
REVERT: C  382 THR cc_start: 0.8145 (m) cc_final: 0.7911 (m)
REVERT: D   65 THR cc_start: 0.8474 (p) cc_final: 0.8211 (p)
REVERT: D   75 GLN cc_start: 0.8452 (mm-40) cc_final: 0.8115 (tp40)
REVERT: D  118 ASP cc_start: 0.7078 (p0) cc_final: 0.6840 (p0)
REVERT: D  143 THR cc_start: 0.8008 (p) cc_final: 0.7711 (t)
REVERT: D  148 CYS cc_start: 0.7870 (t) cc_final: 0.7487 (t)
REVERT: D  163 ASP cc_start: 0.7228 (p0) cc_final: 0.6976 (p0)
REVERT: D  188 MET cc_start: 0.7197 (mmm) cc_final: 0.6666 (mmm)
REVERT: D  198 LEU cc_start: 0.7956 (OUTLIER) cc_final: 0.7718 (mt)
REVERT: D  204 CYS cc_start: 0.7588 (m) cc_final: 0.7193 (m)
REVERT: D  277 SER cc_start: 0.7633 (t) cc_final: 0.7397 (t)
REVERT: D  284 LEU cc_start: 0.7950 (tp) cc_final: 0.7529 (tp)
  outliers start: 27
  outliers final: 23
  residues processed: 240
  average time/residue: 0.2589
  time to fit residues: 80.3940
Evaluate side-chains
  253 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 229
  time to evaluate  : 0.940 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  285 TYR
Chi-restraints excluded: chain B residue  387 GLU
Chi-restraints excluded: chain B residue  418 ILE
Chi-restraints excluded: chain B residue  433 MET
Chi-restraints excluded: chain B residue  520 MET
Chi-restraints excluded: chain B residue  608 LEU
Chi-restraints excluded: chain C residue   29 LEU
Chi-restraints excluded: chain C residue   57 VAL
Chi-restraints excluded: chain C residue  209 GLU
Chi-restraints excluded: chain C residue  252 ASP
Chi-restraints excluded: chain C residue  310 ASP
Chi-restraints excluded: chain C residue  320 THR
Chi-restraints excluded: chain C residue  335 THR
Chi-restraints excluded: chain C residue  385 GLN
Chi-restraints excluded: chain D residue  198 LEU
Chi-restraints excluded: chain D residue  201 SER
Chi-restraints excluded: chain D residue  329 THR
Chi-restraints excluded: chain E residue   45 MET
Chi-restraints excluded: chain E residue   49 ILE
Chi-restraints excluded: chain N residue   54 ASN
Chi-restraints excluded: chain N residue   60 VAL
Chi-restraints excluded: chain N residue   82 SER
Chi-restraints excluded: chain N residue   92 THR
Chi-restraints excluded: chain N residue   94 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 6 optimal weight:    0.8980
   chunk 69 optimal weight:    0.0870
   chunk 104 optimal weight:    2.9990
   chunk 79 optimal weight:    0.0020
   chunk 86 optimal weight:    0.9980
   chunk 72 optimal weight:    0.7980
   chunk 33 optimal weight:    0.6980
   chunk 15 optimal weight:    2.9990
   chunk 8 optimal weight:    0.5980
   chunk 63 optimal weight:    3.9990
   chunk 93 optimal weight:    0.1980
   overall best weight:    0.3166

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

Flipped N/Q/H residues before XYZ refinement:
B 448 HIS
D 237 ASN
D 259 GLN
N  54 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3901 r_free = 0.3901 target = 0.147294 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3620 r_free = 0.3620 target = 0.126176 restraints weight = 13154.877|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3674 r_free = 0.3674 target = 0.130095 restraints weight = 6655.655|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3711 r_free = 0.3711 target = 0.132761 restraints weight = 4118.522|
|-----------------------------------------------------------------------------|
r_work (final): 0.3707
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3707
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3707 r_free = 0.3707    target_work(ls_wunit_k1) = 0.132         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3707 r_free = 0.3707    target_work(ls_wunit_k1) = 0.132         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3707
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7024
moved from start:          0.2055

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   8681  Z= 0.116
  Angle     :  0.646  20.293  11807  Z= 0.319
  Chirality :  0.042   0.160   1330
  Planarity :  0.004   0.057   1509
  Dihedral  :  4.277  27.592   1201
  Min Nonbonded Distance : 2.493

Molprobity Statistics.
  All-atom Clashscore : 8.44
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  5.03 %
    Favored  : 94.88 %
  Rotamer:
    Outliers :  3.10 %
    Allowed  : 17.32 %
    Favored  : 79.59 %
  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 (0.26), residues: 1096
  helix:  1.55 (0.28), residues: 385
  sheet: -0.81 (0.36), residues: 235
  loop : -1.75 (0.27), residues: 476

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.050   0.002   TRP B 420 
 HIS   0.003   0.001   HIS C 220 
 PHE   0.013   0.001   PHE D 199 
 TYR   0.025   0.001   TYR B 498 
 ARG   0.008   0.000   ARG D  49 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03299 (  357)
  hydrogen bonds       : angle       4.09171 ( 1030)
  SS BOND              : bond        0.00194 (    5)
  SS BOND              : angle       0.37374 (   10)
  covalent geometry    : bond        0.00262 ( 8676)
  covalent geometry    : angle       0.64618 (11797)

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

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

  2192 Ramachandran restraints generated.
    1096 Oldfield, 0 Emsley, 1096 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2192 Ramachandran restraints generated.
    1096 Oldfield, 0 Emsley, 1096 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  258 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 231
  time to evaluate  : 0.947 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  407 MET cc_start: 0.6528 (mmt) cc_final: 0.6082 (mmt)
REVERT: B  600 PHE cc_start: 0.6627 (t80) cc_final: 0.6426 (t80)
REVERT: B  608 LEU cc_start: 0.7134 (OUTLIER) cc_final: 0.6932 (mt)
REVERT: C  212 PHE cc_start: 0.6991 (p90) cc_final: 0.6729 (p90)
REVERT: C  221 MET cc_start: 0.7283 (ttm) cc_final: 0.7015 (ttm)
REVERT: C  274 LYS cc_start: 0.7839 (ttmt) cc_final: 0.7597 (ttpt)
REVERT: C  338 LYS cc_start: 0.8290 (tttm) cc_final: 0.8023 (tttm)
REVERT: C  381 ASP cc_start: 0.7842 (t70) cc_final: 0.7142 (t0)
REVERT: C  382 THR cc_start: 0.8132 (m) cc_final: 0.7908 (m)
REVERT: D   65 THR cc_start: 0.8495 (p) cc_final: 0.8202 (p)
REVERT: D  111 TYR cc_start: 0.8138 (m-80) cc_final: 0.7833 (m-80)
REVERT: D  118 ASP cc_start: 0.7041 (p0) cc_final: 0.6802 (p0)
REVERT: D  143 THR cc_start: 0.7993 (p) cc_final: 0.7555 (t)
REVERT: D  148 CYS cc_start: 0.7883 (t) cc_final: 0.7505 (t)
REVERT: D  188 MET cc_start: 0.7145 (mmm) cc_final: 0.6688 (mmm)
REVERT: D  198 LEU cc_start: 0.7902 (OUTLIER) cc_final: 0.7657 (mt)
REVERT: D  204 CYS cc_start: 0.7522 (m) cc_final: 0.7127 (m)
REVERT: D  234 PHE cc_start: 0.7884 (OUTLIER) cc_final: 0.6932 (t80)
REVERT: D  277 SER cc_start: 0.7629 (t) cc_final: 0.7376 (t)
REVERT: D  284 LEU cc_start: 0.7907 (tp) cc_final: 0.7499 (tp)
  outliers start: 27
  outliers final: 22
  residues processed: 238
  average time/residue: 0.2688
  time to fit residues: 82.3456
Evaluate side-chains
  252 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 227
  time to evaluate  : 0.890 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  285 TYR
Chi-restraints excluded: chain B residue  329 LEU
Chi-restraints excluded: chain B residue  387 GLU
Chi-restraints excluded: chain B residue  418 ILE
Chi-restraints excluded: chain B residue  433 MET
Chi-restraints excluded: chain B residue  520 MET
Chi-restraints excluded: chain B residue  608 LEU
Chi-restraints excluded: chain C residue   57 VAL
Chi-restraints excluded: chain C residue  209 GLU
Chi-restraints excluded: chain C residue  252 ASP
Chi-restraints excluded: chain C residue  320 THR
Chi-restraints excluded: chain C residue  335 THR
Chi-restraints excluded: chain C residue  385 GLN
Chi-restraints excluded: chain D residue  198 LEU
Chi-restraints excluded: chain D residue  201 SER
Chi-restraints excluded: chain D residue  234 PHE
Chi-restraints excluded: chain D residue  261 LEU
Chi-restraints excluded: chain D residue  329 THR
Chi-restraints excluded: chain E residue   45 MET
Chi-restraints excluded: chain E residue   49 ILE
Chi-restraints excluded: chain N residue   54 ASN
Chi-restraints excluded: chain N residue   60 VAL
Chi-restraints excluded: chain N residue   82 SER
Chi-restraints excluded: chain N residue   92 THR
Chi-restraints excluded: chain N residue   94 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 97 optimal weight:    1.9990
   chunk 36 optimal weight:    0.5980
   chunk 9 optimal weight:    0.3980
   chunk 7 optimal weight:    0.8980
   chunk 63 optimal weight:    3.9990
   chunk 73 optimal weight:    2.9990
   chunk 66 optimal weight:    1.9990
   chunk 60 optimal weight:    0.9990
   chunk 17 optimal weight:    0.9990
   chunk 91 optimal weight:    7.9990
   chunk 53 optimal weight:    0.5980
   overall best weight:    0.6982

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

Flipped N/Q/H residues before XYZ refinement:
B 448 HIS
** C 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 387 ASN
D 259 GLN
N  54 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3872 r_free = 0.3872 target = 0.144873 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3582 r_free = 0.3582 target = 0.123282 restraints weight = 13076.377|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 47)----------------|
| r_work = 0.3640 r_free = 0.3640 target = 0.127412 restraints weight = 6456.073|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3677 r_free = 0.3677 target = 0.130147 restraints weight = 3921.760|
|-----------------------------------------------------------------------------|
r_work (final): 0.3677
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3673
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3673 r_free = 0.3673    target_work(ls_wunit_k1) = 0.130         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3673 r_free = 0.3673    target_work(ls_wunit_k1) = 0.130         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3673
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7042
moved from start:          0.2102

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   8681  Z= 0.154
  Angle     :  0.664  21.258  11807  Z= 0.331
  Chirality :  0.043   0.161   1330
  Planarity :  0.004   0.056   1509
  Dihedral  :  4.372  30.886   1201
  Min Nonbonded Distance : 2.504

Molprobity Statistics.
  All-atom Clashscore : 8.86
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  5.95 %
    Favored  : 93.96 %
  Rotamer:
    Outliers :  3.44 %
    Allowed  : 17.43 %
    Favored  : 79.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

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 (0.26), residues: 1096
  helix:  1.54 (0.28), residues: 384
  sheet: -0.75 (0.36), residues: 235
  loop : -1.76 (0.26), residues: 477

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP B 427 
 HIS   0.004   0.001   HIS D 183 
 PHE   0.014   0.001   PHE D 199 
 TYR   0.028   0.002   TYR B 498 
 ARG   0.009   0.000   ARG D  49 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03568 (  357)
  hydrogen bonds       : angle       4.16391 ( 1030)
  SS BOND              : bond        0.00302 (    5)
  SS BOND              : angle       0.45705 (   10)
  covalent geometry    : bond        0.00348 ( 8676)
  covalent geometry    : angle       0.66453 (11797)

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

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

  2192 Ramachandran restraints generated.
    1096 Oldfield, 0 Emsley, 1096 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2192 Ramachandran restraints generated.
    1096 Oldfield, 0 Emsley, 1096 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  260 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 230
  time to evaluate  : 0.932 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  407 MET cc_start: 0.6606 (mmt) cc_final: 0.6115 (mmt)
REVERT: B  496 PHE cc_start: 0.7482 (t80) cc_final: 0.7242 (t80)
REVERT: B  608 LEU cc_start: 0.7033 (OUTLIER) cc_final: 0.6826 (mt)
REVERT: C  212 PHE cc_start: 0.7022 (p90) cc_final: 0.6789 (p90)
REVERT: C  221 MET cc_start: 0.7363 (ttm) cc_final: 0.7031 (ttp)
REVERT: C  274 LYS cc_start: 0.7831 (ttmt) cc_final: 0.7594 (ttpt)
REVERT: C  295 ASP cc_start: 0.7828 (m-30) cc_final: 0.7134 (m-30)
REVERT: C  338 LYS cc_start: 0.8304 (tttm) cc_final: 0.8040 (tttm)
REVERT: C  381 ASP cc_start: 0.7857 (t70) cc_final: 0.7157 (t0)
REVERT: D   61 MET cc_start: 0.7501 (ppp) cc_final: 0.7172 (ppp)
REVERT: D   65 THR cc_start: 0.8484 (p) cc_final: 0.8226 (p)
REVERT: D  111 TYR cc_start: 0.8170 (m-80) cc_final: 0.7870 (m-80)
REVERT: D  118 ASP cc_start: 0.7116 (p0) cc_final: 0.6882 (p0)
REVERT: D  143 THR cc_start: 0.7980 (p) cc_final: 0.7708 (t)
REVERT: D  148 CYS cc_start: 0.7932 (t) cc_final: 0.7585 (t)
REVERT: D  163 ASP cc_start: 0.7162 (p0) cc_final: 0.6798 (p0)
REVERT: D  188 MET cc_start: 0.7282 (mmm) cc_final: 0.6840 (mmm)
REVERT: D  198 LEU cc_start: 0.7942 (OUTLIER) cc_final: 0.7691 (mt)
REVERT: D  204 CYS cc_start: 0.7671 (m) cc_final: 0.7240 (m)
REVERT: D  234 PHE cc_start: 0.7926 (OUTLIER) cc_final: 0.7043 (t80)
REVERT: D  277 SER cc_start: 0.7690 (t) cc_final: 0.7411 (t)
REVERT: D  284 LEU cc_start: 0.7947 (tp) cc_final: 0.7543 (tp)
  outliers start: 30
  outliers final: 23
  residues processed: 238
  average time/residue: 0.2865
  time to fit residues: 88.1748
Evaluate side-chains
  255 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 229
  time to evaluate  : 0.916 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  329 LEU
Chi-restraints excluded: chain B residue  387 GLU
Chi-restraints excluded: chain B residue  418 ILE
Chi-restraints excluded: chain B residue  433 MET
Chi-restraints excluded: chain B residue  520 MET
Chi-restraints excluded: chain B residue  608 LEU
Chi-restraints excluded: chain C residue   57 VAL
Chi-restraints excluded: chain C residue  209 GLU
Chi-restraints excluded: chain C residue  252 ASP
Chi-restraints excluded: chain C residue  314 GLU
Chi-restraints excluded: chain C residue  320 THR
Chi-restraints excluded: chain C residue  335 THR
Chi-restraints excluded: chain C residue  385 GLN
Chi-restraints excluded: chain D residue  198 LEU
Chi-restraints excluded: chain D residue  201 SER
Chi-restraints excluded: chain D residue  234 PHE
Chi-restraints excluded: chain D residue  255 LEU
Chi-restraints excluded: chain D residue  259 GLN
Chi-restraints excluded: chain D residue  329 THR
Chi-restraints excluded: chain E residue   45 MET
Chi-restraints excluded: chain E residue   49 ILE
Chi-restraints excluded: chain N residue   54 ASN
Chi-restraints excluded: chain N residue   60 VAL
Chi-restraints excluded: chain N residue   82 SER
Chi-restraints excluded: chain N residue   92 THR
Chi-restraints excluded: chain N residue   94 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 13 optimal weight:    0.8980
   chunk 84 optimal weight:    0.8980
   chunk 39 optimal weight:    3.9990
   chunk 27 optimal weight:    0.0050
   chunk 96 optimal weight:    3.9990
   chunk 43 optimal weight:    0.5980
   chunk 97 optimal weight:    5.9990
   chunk 20 optimal weight:    2.9990
   chunk 22 optimal weight:    0.9990
   chunk 67 optimal weight:    0.0870
   chunk 40 optimal weight:    0.9990
   overall best weight:    0.4972

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

Flipped N/Q/H residues before XYZ refinement:
B 448 HIS
** C 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 387 ASN
D 259 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3889 r_free = 0.3889 target = 0.146619 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3607 r_free = 0.3607 target = 0.125368 restraints weight = 13237.161|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3662 r_free = 0.3662 target = 0.129380 restraints weight = 6694.056|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3699 r_free = 0.3699 target = 0.132068 restraints weight = 4122.316|
|-----------------------------------------------------------------------------|
r_work (final): 0.3699
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3700
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3700 r_free = 0.3700    target_work(ls_wunit_k1) = 0.132         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3700 r_free = 0.3700    target_work(ls_wunit_k1) = 0.132         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3700
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7036
moved from start:          0.2174

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   8681  Z= 0.134
  Angle     :  0.662  24.804  11807  Z= 0.330
  Chirality :  0.043   0.176   1330
  Planarity :  0.004   0.057   1509
  Dihedral  :  4.397  33.486   1201
  Min Nonbonded Distance : 2.526

Molprobity Statistics.
  All-atom Clashscore : 8.98
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  5.31 %
    Favored  : 94.60 %
  Rotamer:
    Outliers :  2.98 %
    Allowed  : 18.12 %
    Favored  : 78.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

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: -0.52 (0.26), residues: 1096
  helix:  1.54 (0.28), residues: 384
  sheet: -0.74 (0.36), residues: 235
  loop : -1.75 (0.26), residues: 477

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.056   0.002   TRP B 420 
 HIS   0.003   0.001   HIS C 220 
 PHE   0.023   0.001   PHE B 600 
 TYR   0.032   0.001   TYR B 498 
 ARG   0.008   0.000   ARG D  49 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03453 (  357)
  hydrogen bonds       : angle       4.16326 ( 1030)
  SS BOND              : bond        0.00239 (    5)
  SS BOND              : angle       0.42980 (   10)
  covalent geometry    : bond        0.00303 ( 8676)
  covalent geometry    : angle       0.66234 (11797)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3825.43 seconds
wall clock time: 68 minutes 20.42 seconds (4100.42 seconds total)