Starting phenix.real_space_refine
on Thu Jul 31 16:31:41 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8eyr_28693/07_2025/8eyr_28693.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8eyr_28693/07_2025/8eyr_28693.map

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

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

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8eyr_28693/07_2025/8eyr_28693.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8eyr_28693/07_2025/8eyr_28693.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8eyr_28693/07_2025/8eyr_28693.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8eyr_28693/07_2025/8eyr_28693.cif"
  }
  resolution = 4.0
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.001
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S     106      5.16       5
     C    8625      2.51       5
     N    2367      2.21       5
     O    2537      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 16 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 13635
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "B"
      Number of atoms: 6382
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 794, 6382
          Classifications: {'peptide': 794}
          Incomplete info: {'truncation_to_alanine': 8}
          Link IDs: {'PCIS': 1, 'PTRANS': 43, 'TRANS': 749}
          Chain breaks: 7
          Unresolved non-hydrogen bonds: 24
          Unresolved non-hydrogen angles: 29
          Unresolved non-hydrogen dihedrals: 19
          Planarities with less than four sites: {'GLU:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 18
    Chain: "A"
      Number of atoms: 6387
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 795, 6387
          Classifications: {'peptide': 795}
          Incomplete info: {'truncation_to_alanine': 9}
          Link IDs: {'PCIS': 1, 'PTRANS': 43, 'TRANS': 750}
          Chain breaks: 7
          Unresolved non-hydrogen bonds: 28
          Unresolved non-hydrogen angles: 33
          Unresolved non-hydrogen dihedrals: 23
          Planarities with less than four sites: {'GLU:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 18
    Chain: "C"
      Number of atoms: 433
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 58, 433
          Classifications: {'peptide': 58}
          Incomplete info: {'truncation_to_alanine': 7}
          Link IDs: {'PTRANS': 2, 'TRANS': 55}
          Chain breaks: 1
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 15
          Unresolved non-hydrogen angles: 18
          Unresolved non-hydrogen dihedrals: 13
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'ASN:plan1': 1}
          Unresolved non-hydrogen planarities: 3
    Chain: "D"
      Number of atoms: 433
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 58, 433
          Classifications: {'peptide': 58}
          Incomplete info: {'truncation_to_alanine': 7}
          Link IDs: {'PTRANS': 2, 'TRANS': 55}
          Chain breaks: 1
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 15
          Unresolved non-hydrogen angles: 18
          Unresolved non-hydrogen dihedrals: 13
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'ASN:plan1': 1}
          Unresolved non-hydrogen planarities: 3
  Time building chain proxies: 8.70, per 1000 atoms: 0.64
  Number of scatterers: 13635
  At special positions: 0
  Unit cell: (126.99, 122.01, 166, 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     106     16.00
     O    2537      8.00
     N    2367      7.00
     C    8625      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=32, symmetry=0
    Simple disulfide: pdb=" SG  CYS B   3 " - pdb=" SG  CYS B  22 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 120 " - pdb=" SG  CYS B 148 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 152 " - pdb=" SG  CYS B 175 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 162 " - pdb=" SG  CYS B 181 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 185 " - pdb=" SG  CYS B 194 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 189 " - pdb=" SG  CYS B 200 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 201 " - pdb=" SG  CYS B 209 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 205 " - pdb=" SG  CYS B 218 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 221 " - pdb=" SG  CYS B 230 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 234 " - pdb=" SG  CYS B 246 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 252 " - pdb=" SG  CYS B 273 " distance=2.04
    Simple disulfide: pdb=" SG  CYS B 302 " - pdb=" SG  CYS B 324 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 781 " - pdb=" SG  CYS B 790 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A   3 " - pdb=" SG  CYS A  22 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 120 " - pdb=" SG  CYS A 148 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 152 " - pdb=" SG  CYS A 175 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 162 " - pdb=" SG  CYS A 181 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 185 " - pdb=" SG  CYS A 194 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 189 " - pdb=" SG  CYS A 200 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 201 " - pdb=" SG  CYS A 209 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 205 " - pdb=" SG  CYS A 218 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 221 " - pdb=" SG  CYS A 230 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 234 " - pdb=" SG  CYS A 246 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 252 " - pdb=" SG  CYS A 273 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A 302 " - pdb=" SG  CYS A 324 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 781 " - pdb=" SG  CYS A 790 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C   6 " - pdb=" SG  CYS C  48 " distance=2.02
    Simple disulfide: pdb=" SG  CYS C  18 " - pdb=" SG  CYS C  61 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C  47 " - pdb=" SG  CYS C  52 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D   6 " - pdb=" SG  CYS D  48 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D  18 " - pdb=" SG  CYS D  61 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D  47 " - pdb=" SG  CYS D  52 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 3.18
  Conformation dependent library (CDL) restraints added in 1.8 seconds
  

  3330 Ramachandran restraints generated.
    1665 Oldfield, 0 Emsley, 1665 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3202

  Finding SS restraints...
    Secondary structure from input PDB file:
      30 helices and 32 sheets defined
      15.2% alpha, 19.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 2.05
  Creating SS restraints...
    Processing helix  chain 'B' and resid 12 through 20
    Processing helix  chain 'B' and resid 133 through 137
      removed outlier: 3.915A  pdb=" N   ASN B 136 " --> pdb=" O   ALA B 133 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 144 through 149
    Processing helix  chain 'B' and resid 248 through 254
      removed outlier: 3.519A  pdb=" N   CYS B 252 " --> pdb=" O   ASP B 248 " (cutoff:3.500A)
      removed outlier: 4.164A  pdb=" N   ASN B 254 " --> pdb=" O   ASP B 250 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 314 through 320
    Processing helix  chain 'B' and resid 341 through 350
    Processing helix  chain 'B' and resid 426 through 438
    Processing helix  chain 'B' and resid 439 through 443
      removed outlier: 3.627A  pdb=" N   GLN B 443 " --> pdb=" O   LYS B 440 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 625 through 631
    Processing helix  chain 'B' and resid 680 through 706
    Processing helix  chain 'B' and resid 856 through 863
    Processing helix  chain 'A' and resid 12 through 20
    Processing helix  chain 'A' and resid 133 through 137
    Processing helix  chain 'A' and resid 144 through 149
    Processing helix  chain 'A' and resid 314 through 320
      removed outlier: 3.974A  pdb=" N   MET A 320 " --> pdb=" O   THR A 316 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 341 through 350
      removed outlier: 3.871A  pdb=" N   ASN A 347 " --> pdb=" O   SER A 343 " (cutoff:3.500A)
      removed outlier: 3.579A  pdb=" N   PHE A 348 " --> pdb=" O   GLU A 344 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 426 through 438
    Processing helix  chain 'A' and resid 439 through 443
      removed outlier: 3.689A  pdb=" N   GLN A 443 " --> pdb=" O   LYS A 440 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 625 through 631
    Processing helix  chain 'A' and resid 680 through 706
      removed outlier: 3.673A  pdb=" N   PHE A 706 " --> pdb=" O   HIS A 702 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 856 through 863
    Processing helix  chain 'C' and resid 7 through 19
      removed outlier: 3.908A  pdb=" N   VAL C  11 " --> pdb=" O   GLY C   7 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 20 through 22
      No H-bonds generated for 'chain 'C' and resid 20 through 22'
    Processing helix  chain 'C' and resid 43 through 48
    Processing helix  chain 'C' and resid 53 through 58
    Processing helix  chain 'C' and resid 59 through 61
      No H-bonds generated for 'chain 'C' and resid 59 through 61'
    Processing helix  chain 'D' and resid 7 through 19
    Processing helix  chain 'D' and resid 43 through 48
    Processing helix  chain 'D' and resid 53 through 58
    Processing helix  chain 'D' and resid 59 through 61
      No H-bonds generated for 'chain 'D' and resid 59 through 61'
    Processing sheet with id=AA1, first strand: chain 'B' and resid 2 through 3
      removed outlier: 3.617A  pdb=" N   ILE B  25 " --> pdb=" O   VAL B  50 " (cutoff:3.500A)
      removed outlier: 3.633A  pdb=" N   ILE B  51 " --> pdb=" O   VAL B  75 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 7 through 10
      removed outlier: 6.479A  pdb=" N   ILE B   7 " --> pdb=" O   HIS B  30 " (cutoff:3.500A)
      removed outlier: 7.946A  pdb=" N   LEU B  32 " --> pdb=" O   ILE B   7 " (cutoff:3.500A)
      removed outlier: 5.946A  pdb=" N   ILE B   9 " --> pdb=" O   LEU B  32 " (cutoff:3.500A)
      removed outlier: 6.053A  pdb=" N   ILE B  34 " --> pdb=" O   ILE B   9 " (cutoff:3.500A)
      removed outlier: 6.739A  pdb=" N   VAL B  60 " --> pdb=" O   LEU B  33 " (cutoff:3.500A)
      removed outlier: 6.354A  pdb=" N   LEU B  55 " --> pdb=" O   VAL B  88 " (cutoff:3.500A)
      removed outlier: 7.756A  pdb=" N   PHE B  90 " --> pdb=" O   LEU B  55 " (cutoff:3.500A)
      removed outlier: 6.455A  pdb=" N   LEU B  57 " --> pdb=" O   PHE B  90 " (cutoff:3.500A)
      removed outlier: 5.628A  pdb=" N   ALA B 110 " --> pdb=" O   TYR B  85 " (cutoff:3.500A)
      removed outlier: 4.418A  pdb=" N   LEU B  87 " --> pdb=" O   ALA B 110 " (cutoff:3.500A)
      removed outlier: 3.708A  pdb=" N   VAL B 140 " --> pdb=" O   ILE B 113 " (cutoff:3.500A)
      removed outlier: 3.529A  pdb=" N   LYS B 115 " --> pdb=" O   VAL B 140 " (cutoff:3.500A)
      removed outlier: 6.745A  pdb=" N   ASN B 142 " --> pdb=" O   LYS B 115 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 164 through 166
    Processing sheet with id=AA4, first strand: chain 'B' and resid 239 through 241
    Processing sheet with id=AA5, first strand: chain 'B' and resid 267 through 269
    Processing sheet with id=AA6, first strand: chain 'B' and resid 281 through 284
      removed outlier: 5.901A  pdb=" N   TYR B 290 " --> pdb=" O   ASN B 284 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 310 through 312
      removed outlier: 3.873A  pdb=" N   LEU B 332 " --> pdb=" O   LYS B 310 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 326 through 327
      removed outlier: 9.131A  pdb=" N   LEU B 327 " --> pdb=" O   THR B 356 " (cutoff:3.500A)
      removed outlier: 10.590A  pdb=" N   VAL B 354 " --> pdb=" O   LEU B 380 " (cutoff:3.500A)
      removed outlier: 9.784A  pdb=" N   GLU B 382 " --> pdb=" O   VAL B 354 " (cutoff:3.500A)
      removed outlier: 9.103A  pdb=" N   THR B 356 " --> pdb=" O   GLU B 382 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 462 through 464
      removed outlier: 5.466A  pdb=" N   ASP B 462 " --> pdb=" O   LYS B 569 " (cutoff:3.500A)
      removed outlier: 3.908A  pdb=" N   ALA B 568 " --> pdb=" O   ALA B 554 " (cutoff:3.500A)
      removed outlier: 5.193A  pdb=" N   VAL B 552 " --> pdb=" O   SER B 570 " (cutoff:3.500A)
      removed outlier: 3.711A  pdb=" N   PHE B 494 " --> pdb=" O   VAL B 525 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'B' and resid 462 through 464
      removed outlier: 5.466A  pdb=" N   ASP B 462 " --> pdb=" O   LYS B 569 " (cutoff:3.500A)
      removed outlier: 3.908A  pdb=" N   ALA B 568 " --> pdb=" O   ALA B 554 " (cutoff:3.500A)
      removed outlier: 5.193A  pdb=" N   VAL B 552 " --> pdb=" O   SER B 570 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'B' and resid 466 through 471
    Processing sheet with id=AB3, first strand: chain 'B' and resid 589 through 594
      removed outlier: 3.782A  pdb=" N   ASN B 593 " --> pdb=" O   GLN B 597 " (cutoff:3.500A)
      removed outlier: 7.579A  pdb=" N   GLN B 597 " --> pdb=" O   ASN B 593 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'B' and resid 752 through 756
    Processing sheet with id=AB5, first strand: chain 'B' and resid 814 through 816
    Processing sheet with id=AB6, first strand: chain 'B' and resid 841 through 844
    Processing sheet with id=AB7, first strand: chain 'B' and resid 881 through 884
      removed outlier: 6.173A  pdb=" N   SER B 884 " --> pdb=" O   ASN B 888 " (cutoff:3.500A)
      removed outlier: 5.020A  pdb=" N   ASN B 888 " --> pdb=" O   SER B 884 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'A' and resid 2 through 3
      removed outlier: 3.607A  pdb=" N   ILE A  51 " --> pdb=" O   VAL A  75 " (cutoff:3.500A)
    Processing sheet with id=AB9, first strand: chain 'A' and resid 6 through 10
      removed outlier: 6.491A  pdb=" N   ILE A   7 " --> pdb=" O   HIS A  30 " (cutoff:3.500A)
      removed outlier: 7.958A  pdb=" N   LEU A  32 " --> pdb=" O   ILE A   7 " (cutoff:3.500A)
      removed outlier: 5.917A  pdb=" N   ILE A   9 " --> pdb=" O   LEU A  32 " (cutoff:3.500A)
      removed outlier: 5.976A  pdb=" N   ILE A  34 " --> pdb=" O   ILE A   9 " (cutoff:3.500A)
      removed outlier: 6.849A  pdb=" N   VAL A  60 " --> pdb=" O   LEU A  33 " (cutoff:3.500A)
      removed outlier: 6.354A  pdb=" N   LEU A  55 " --> pdb=" O   VAL A  88 " (cutoff:3.500A)
      removed outlier: 7.790A  pdb=" N   PHE A  90 " --> pdb=" O   LEU A  55 " (cutoff:3.500A)
      removed outlier: 6.456A  pdb=" N   LEU A  57 " --> pdb=" O   PHE A  90 " (cutoff:3.500A)
      removed outlier: 5.667A  pdb=" N   ALA A 110 " --> pdb=" O   TYR A  85 " (cutoff:3.500A)
      removed outlier: 4.461A  pdb=" N   LEU A  87 " --> pdb=" O   ALA A 110 " (cutoff:3.500A)
      removed outlier: 3.502A  pdb=" N   ARG A 112 " --> pdb=" O   LEU A  87 " (cutoff:3.500A)
      removed outlier: 3.558A  pdb=" N   VAL A 140 " --> pdb=" O   ILE A 113 " (cutoff:3.500A)
      removed outlier: 3.506A  pdb=" N   LYS A 115 " --> pdb=" O   VAL A 140 " (cutoff:3.500A)
      removed outlier: 6.582A  pdb=" N   ASN A 142 " --> pdb=" O   LYS A 115 " (cutoff:3.500A)
    Processing sheet with id=AC1, first strand: chain 'A' and resid 239 through 241
    Processing sheet with id=AC2, first strand: chain 'A' and resid 267 through 269
    Processing sheet with id=AC3, first strand: chain 'A' and resid 281 through 284
      removed outlier: 5.817A  pdb=" N   TYR A 290 " --> pdb=" O   ASN A 284 " (cutoff:3.500A)
    Processing sheet with id=AC4, first strand: chain 'A' and resid 309 through 312
      removed outlier: 3.800A  pdb=" N   LEU A 332 " --> pdb=" O   LYS A 310 " (cutoff:3.500A)
      removed outlier: 6.224A  pdb=" N   VAL A 359 " --> pdb=" O   TYR A 392 " (cutoff:3.500A)
      removed outlier: 7.976A  pdb=" N   LEU A 394 " --> pdb=" O   VAL A 359 " (cutoff:3.500A)
      removed outlier: 6.389A  pdb=" N   ILE A 361 " --> pdb=" O   LEU A 394 " (cutoff:3.500A)
    Processing sheet with id=AC5, first strand: chain 'A' and resid 326 through 327
    Processing sheet with id=AC6, first strand: chain 'A' and resid 462 through 464
      removed outlier: 5.588A  pdb=" N   ASP A 462 " --> pdb=" O   LYS A 569 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AC6
    Processing sheet with id=AC7, first strand: chain 'A' and resid 466 through 471
    Processing sheet with id=AC8, first strand: chain 'A' and resid 522 through 525
      removed outlier: 3.743A  pdb=" N   PHE A 494 " --> pdb=" O   VAL A 525 " (cutoff:3.500A)
    Processing sheet with id=AC9, first strand: chain 'A' and resid 589 through 594
      removed outlier: 6.833A  pdb=" N   GLN A 597 " --> pdb=" O   ASN A 593 " (cutoff:3.500A)
    Processing sheet with id=AD1, first strand: chain 'A' and resid 752 through 756
      removed outlier: 7.121A  pdb=" N   CYS A 781 " --> pdb=" O   SER A 613 " (cutoff:3.500A)
    Processing sheet with id=AD2, first strand: chain 'A' and resid 776 through 777
    Processing sheet with id=AD3, first strand: chain 'A' and resid 814 through 816
    Processing sheet with id=AD4, first strand: chain 'A' and resid 841 through 844
      removed outlier: 3.891A  pdb=" N   ILE A 842 " --> pdb=" O   GLU A 853 " (cutoff:3.500A)
    Processing sheet with id=AD5, first strand: chain 'A' and resid 881 through 884
      removed outlier: 5.688A  pdb=" N   ALA A 882 " --> pdb=" O   GLY A 889 " (cutoff:3.500A)
      removed outlier: 3.733A  pdb=" N   GLY A 889 " --> pdb=" O   ALA A 882 " (cutoff:3.500A)

    308 hydrogen bonds defined for protein.
    795 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 4.96

  Time building geometry restraints manager: 3.84 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: 4487
        1.34 -     1.46: 3219
        1.46 -     1.58: 6113
        1.58 -     1.70: 2
        1.70 -     1.82: 132
  Bond restraints: 13953
  Sorted by residual:
  bond pdb=" CB  PRO B 894 "
       pdb=" CG  PRO B 894 "
    ideal  model  delta    sigma   weight residual
    1.492  1.666 -0.174 5.00e-02 4.00e+02 1.20e+01
  bond pdb=" CB  PRO A 894 "
       pdb=" CG  PRO A 894 "
    ideal  model  delta    sigma   weight residual
    1.492  1.606 -0.114 5.00e-02 4.00e+02 5.17e+00
  bond pdb=" N   PRO B 894 "
       pdb=" CA  PRO B 894 "
    ideal  model  delta    sigma   weight residual
    1.469  1.444  0.025 1.28e-02 6.10e+03 3.79e+00
  bond pdb=" CG  GLU B 386 "
       pdb=" CD  GLU B 386 "
    ideal  model  delta    sigma   weight residual
    1.516  1.474  0.042 2.50e-02 1.60e+03 2.79e+00
  bond pdb=" CB  ARG D  55 "
       pdb=" CG  ARG D  55 "
    ideal  model  delta    sigma   weight residual
    1.520  1.562 -0.042 3.00e-02 1.11e+03 1.94e+00
  ... (remaining 13948 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.69: 18704
        2.69 -     5.37: 182
        5.37 -     8.06: 28
        8.06 -    10.75: 6
       10.75 -    13.44: 3
  Bond angle restraints: 18923
  Sorted by residual:
  angle pdb=" CA  PRO B 894 "
        pdb=" N   PRO B 894 "
        pdb=" CD  PRO B 894 "
      ideal   model   delta    sigma   weight residual
     112.00   98.56   13.44 1.40e+00 5.10e-01 9.21e+01
  angle pdb=" C   HIS A 564 "
        pdb=" CA  HIS A 564 "
        pdb=" CB  HIS A 564 "
      ideal   model   delta    sigma   weight residual
     115.79  109.61    6.18 1.19e+00 7.06e-01 2.70e+01
  angle pdb=" CA  PRO A 894 "
        pdb=" N   PRO A 894 "
        pdb=" CD  PRO A 894 "
      ideal   model   delta    sigma   weight residual
     112.00  105.51    6.49 1.40e+00 5.10e-01 2.15e+01
  angle pdb=" N   PRO B 894 "
        pdb=" CD  PRO B 894 "
        pdb=" CG  PRO B 894 "
      ideal   model   delta    sigma   weight residual
     103.20   96.33    6.87 1.50e+00 4.44e-01 2.10e+01
  angle pdb=" CA  ARG D  55 "
        pdb=" CB  ARG D  55 "
        pdb=" CG  ARG D  55 "
      ideal   model   delta    sigma   weight residual
     114.10  123.04   -8.94 2.00e+00 2.50e-01 2.00e+01
  ... (remaining 18918 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.84: 7027
       16.84 -    33.68: 1019
       33.68 -    50.52: 314
       50.52 -    67.36: 64
       67.36 -    84.20: 25
  Dihedral angle restraints: 8449
    sinusoidal: 3470
      harmonic: 4979
  Sorted by residual:
  dihedral pdb=" CB  CYS D  18 "
           pdb=" SG  CYS D  18 "
           pdb=" SG  CYS D  61 "
           pdb=" CB  CYS D  61 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  175.61  -82.61     1      1.00e+01 1.00e-02 8.37e+01
  dihedral pdb=" CB  CYS C  18 "
           pdb=" SG  CYS C  18 "
           pdb=" SG  CYS C  61 "
           pdb=" CB  CYS C  61 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  173.15  -80.15     1      1.00e+01 1.00e-02 7.96e+01
  dihedral pdb=" CB  CYS B 162 "
           pdb=" SG  CYS B 162 "
           pdb=" SG  CYS B 181 "
           pdb=" CB  CYS B 181 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   16.25   76.75     1      1.00e+01 1.00e-02 7.40e+01
  ... (remaining 8446 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.038: 1299
       0.038 -    0.075: 507
       0.075 -    0.113: 190
       0.113 -    0.151: 40
       0.151 -    0.188: 5
  Chirality restraints: 2041
  Sorted by residual:
  chirality pdb=" CG  LEU A  32 "
            pdb=" CB  LEU A  32 "
            pdb=" CD1 LEU A  32 "
            pdb=" CD2 LEU A  32 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.40   -0.19 2.00e-01 2.50e+01 8.85e-01
  chirality pdb=" CB  ILE A 448 "
            pdb=" CA  ILE A 448 "
            pdb=" CG1 ILE A 448 "
            pdb=" CG2 ILE A 448 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.48    0.17 2.00e-01 2.50e+01 6.99e-01
  chirality pdb=" CA  VAL A 899 "
            pdb=" N   VAL A 899 "
            pdb=" C   VAL A 899 "
            pdb=" CB  VAL A 899 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.60   -0.16 2.00e-01 2.50e+01 6.41e-01
  ... (remaining 2038 not shown)

  Planarity restraints: 2459
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP B 893 "    0.098 5.00e-02 4.00e+02   1.38e-01 3.05e+01
        pdb=" N   PRO B 894 "   -0.238 5.00e-02 4.00e+02
        pdb=" CA  PRO B 894 "    0.069 5.00e-02 4.00e+02
        pdb=" CD  PRO B 894 "    0.071 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP A 893 "   -0.068 5.00e-02 4.00e+02   9.94e-02 1.58e+01
        pdb=" N   PRO A 894 "    0.172 5.00e-02 4.00e+02
        pdb=" CA  PRO A 894 "   -0.050 5.00e-02 4.00e+02
        pdb=" CD  PRO A 894 "   -0.054 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A 403 "    0.000 2.00e-02 2.50e+03   1.39e-02 4.85e+00
        pdb=" CG  TRP A 403 "   -0.032 2.00e-02 2.50e+03
        pdb=" CD1 TRP A 403 "    0.026 2.00e-02 2.50e+03
        pdb=" CD2 TRP A 403 "    0.001 2.00e-02 2.50e+03
        pdb=" NE1 TRP A 403 "   -0.002 2.00e-02 2.50e+03
        pdb=" CE2 TRP A 403 "   -0.003 2.00e-02 2.50e+03
        pdb=" CE3 TRP A 403 "    0.014 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A 403 "   -0.005 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A 403 "    0.002 2.00e-02 2.50e+03
        pdb=" CH2 TRP A 403 "   -0.003 2.00e-02 2.50e+03
  ... (remaining 2456 not shown)

  Histogram of nonbonded interaction distances:
        2.10 -     2.66: 407
        2.66 -     3.22: 14008
        3.22 -     3.78: 22603
        3.78 -     4.34: 29630
        4.34 -     4.90: 46281
  Nonbonded interactions: 112929
  Sorted by model distance:
  nonbonded pdb=" OD1 ASP A 313 "
            pdb=" OG  SER A 317 "
     model   vdw
     2.099 3.040
  nonbonded pdb=" OD1 ASP B 313 "
            pdb=" OG  SER B 317 "
     model   vdw
     2.101 3.040
  nonbonded pdb=" OE2 GLU B 690 "
            pdb=" OH  TYR A 138 "
     model   vdw
     2.151 3.040
  nonbonded pdb=" O   ARG B  77 "
            pdb=" OG1 THR B 107 "
     model   vdw
     2.153 3.040
  nonbonded pdb=" OG  SER A 461 "
            pdb=" O   ARG A 566 "
     model   vdw
     2.194 3.040
  ... (remaining 112924 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
Found NCS groups:
ncs_group {
  reference = (chain 'A' and (resid 1 through 294 or resid 301 through 901))
  selection = chain 'B'
}
ncs_group {
  reference = chain 'C'
  selection = chain 'D'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.640
  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:          0.560
  Check model and map are aligned:         0.080
  Set scattering table:                    0.120
  Process input model:                     34.200
  Find NCS groups from input model:        0.650
  Set up NCS constraints:                  0.090
  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:2.840
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   41.200
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8131
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      :  0.005   0.174  13985  Z= 0.227
  Angle     :  0.756  13.437  18987  Z= 0.398
  Chirality :  0.046   0.188   2041
  Planarity :  0.006   0.138   2459
  Dihedral  : 17.459  84.202   5151
  Min Nonbonded Distance : 2.099

Molprobity Statistics.
  All-atom Clashscore : 23.63
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  : 11.47 %
    Favored  : 88.35 %
  Rotamer:
    Outliers :  0.27 %
    Allowed  : 33.20 %
    Favored  : 66.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.17 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.25 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.62 (0.20), residues: 1665
  helix: -1.38 (0.36), residues: 190
  sheet: -1.70 (0.29), residues: 333
  loop : -1.91 (0.18), residues: 1142

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.032   0.002   TRP A 403 
 HIS   0.006   0.001   HIS B 269 
 PHE   0.020   0.001   PHE A 752 
 TYR   0.017   0.002   TYR B 488 
 ARG   0.007   0.001   ARG A 762 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.18840 (  306)
  hydrogen bonds       : angle       8.96608 (  795)
  SS BOND              : bond        0.00361 (   32)
  SS BOND              : angle       1.08219 (   64)
  covalent geometry    : bond        0.00526 (13953)
  covalent geometry    : angle       0.75459 (18923)

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

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

  3330 Ramachandran restraints generated.
    1665 Oldfield, 0 Emsley, 1665 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3330 Ramachandran restraints generated.
    1665 Oldfield, 0 Emsley, 1665 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  94 residues out of total 1525 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 90
  time to evaluate  : 1.599 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  558 THR cc_start: 0.9215 (p) cc_final: 0.8948 (t)
REVERT: A  320 MET cc_start: 0.8508 (ptm) cc_final: 0.8182 (ptt)
  outliers start: 4
  outliers final: 2
  residues processed: 93
  average time/residue: 0.2498
  time to fit residues: 35.8059
Evaluate side-chains
  86 residues out of total 1525 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 84
  time to evaluate  : 1.477 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   57 LEU
Chi-restraints excluded: chain A residue  522 MET
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 168
   random chunks:
   chunk 141 optimal weight:    0.9980
   chunk 127 optimal weight:    2.9990
   chunk 70 optimal weight:    7.9990
   chunk 43 optimal weight:    0.1980
   chunk 85 optimal weight:    0.9980
   chunk 68 optimal weight:    8.9990
   chunk 131 optimal weight:    7.9990
   chunk 50 optimal weight:    0.9990
   chunk 80 optimal weight:    2.9990
   chunk 98 optimal weight:    7.9990
   chunk 152 optimal weight:   50.0000
   overall best weight:    1.2384

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

Flipped N/Q/H residues before XYZ refinement:
** B 481 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A  14 GLN
** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 443 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 453 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 481 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 779 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3964 r_free = 0.3964 target = 0.100768 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3301 r_free = 0.3301 target = 0.068099 restraints weight = 45183.953|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3240 r_free = 0.3240 target = 0.066185 restraints weight = 39224.777|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3252 r_free = 0.3252 target = 0.066676 restraints weight = 32709.144|
|-----------------------------------------------------------------------------|
r_work (final): 0.3209
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8138
moved from start:          0.0986

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.056  13985  Z= 0.141
  Angle     :  0.634  10.590  18987  Z= 0.324
  Chirality :  0.045   0.154   2041
  Planarity :  0.005   0.066   2459
  Dihedral  :  5.332  35.903   1892
  Min Nonbonded Distance : 2.542

Molprobity Statistics.
  All-atom Clashscore : 14.06
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  9.55 %
    Favored  : 90.27 %
  Rotamer:
    Outliers :  4.28 %
    Allowed  : 29.59 %
    Favored  : 66.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.17 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.38 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.43 (0.20), residues: 1665
  helix: -0.90 (0.38), residues: 195
  sheet: -1.58 (0.30), residues: 323
  loop : -1.85 (0.18), residues: 1147

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 815 
 HIS   0.007   0.001   HIS B 269 
 PHE   0.017   0.001   PHE B 697 
 TYR   0.010   0.001   TYR B  13 
 ARG   0.004   0.000   ARG A 762 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04246 (  306)
  hydrogen bonds       : angle       6.87143 (  795)
  SS BOND              : bond        0.00300 (   32)
  SS BOND              : angle       0.81249 (   64)
  covalent geometry    : bond        0.00328 (13953)
  covalent geometry    : angle       0.63304 (18923)

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

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

  3330 Ramachandran restraints generated.
    1665 Oldfield, 0 Emsley, 1665 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3330 Ramachandran restraints generated.
    1665 Oldfield, 0 Emsley, 1665 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  168 residues out of total 1525 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 64
    poor density    : 104
  time to evaluate  : 1.660 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  274 MET cc_start: 0.8291 (pmm) cc_final: 0.7332 (pmm)
REVERT: B  599 ILE cc_start: 0.9340 (OUTLIER) cc_final: 0.8988 (tp)
REVERT: B  628 LEU cc_start: 0.8833 (OUTLIER) cc_final: 0.8454 (mt)
REVERT: B  690 GLU cc_start: 0.8477 (OUTLIER) cc_final: 0.7921 (tp30)
REVERT: A  180 ARG cc_start: 0.8582 (OUTLIER) cc_final: 0.8074 (ttm110)
REVERT: A  752 PHE cc_start: 0.9441 (OUTLIER) cc_final: 0.9205 (t80)
REVERT: C   46 GLU cc_start: 0.8918 (OUTLIER) cc_final: 0.8407 (tm-30)
  outliers start: 64
  outliers final: 27
  residues processed: 158
  average time/residue: 0.2301
  time to fit residues: 55.5713
Evaluate side-chains
  126 residues out of total 1525 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 93
  time to evaluate  : 1.610 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   51 ILE
Chi-restraints excluded: chain B residue  131 LEU
Chi-restraints excluded: chain B residue  139 ILE
Chi-restraints excluded: chain B residue  175 CYS
Chi-restraints excluded: chain B residue  231 VAL
Chi-restraints excluded: chain B residue  270 ASP
Chi-restraints excluded: chain B residue  393 VAL
Chi-restraints excluded: chain B residue  417 MET
Chi-restraints excluded: chain B residue  434 GLU
Chi-restraints excluded: chain B residue  444 SER
Chi-restraints excluded: chain B residue  448 ILE
Chi-restraints excluded: chain B residue  491 LEU
Chi-restraints excluded: chain B residue  599 ILE
Chi-restraints excluded: chain B residue  628 LEU
Chi-restraints excluded: chain B residue  690 GLU
Chi-restraints excluded: chain B residue  813 VAL
Chi-restraints excluded: chain A residue    2 ILE
Chi-restraints excluded: chain A residue   51 ILE
Chi-restraints excluded: chain A residue   60 VAL
Chi-restraints excluded: chain A residue   91 GLU
Chi-restraints excluded: chain A residue  124 THR
Chi-restraints excluded: chain A residue  180 ARG
Chi-restraints excluded: chain A residue  277 CYS
Chi-restraints excluded: chain A residue  320 MET
Chi-restraints excluded: chain A residue  369 SER
Chi-restraints excluded: chain A residue  448 ILE
Chi-restraints excluded: chain A residue  488 TYR
Chi-restraints excluded: chain A residue  522 MET
Chi-restraints excluded: chain A residue  752 PHE
Chi-restraints excluded: chain C residue   43 ILE
Chi-restraints excluded: chain C residue   44 VAL
Chi-restraints excluded: chain C residue   46 GLU
Chi-restraints excluded: chain D residue   10 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 168
   random chunks:
   chunk 152 optimal weight:   40.0000
   chunk 112 optimal weight:    4.9990
   chunk 51 optimal weight:    6.9990
   chunk 83 optimal weight:    0.2980
   chunk 124 optimal weight:    0.9980
   chunk 122 optimal weight:    5.9990
   chunk 13 optimal weight:    0.9980
   chunk 7 optimal weight:    1.9990
   chunk 35 optimal weight:    0.9980
   chunk 33 optimal weight:    4.9990
   chunk 70 optimal weight:    6.9990
   overall best weight:    1.0582

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

Flipped N/Q/H residues before XYZ refinement:
** B 481 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 443 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 453 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 481 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 609 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 779 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3976 r_free = 0.3976 target = 0.101256 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3319 r_free = 0.3319 target = 0.068906 restraints weight = 45248.836|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3288 r_free = 0.3288 target = 0.068037 restraints weight = 33540.868|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3282 r_free = 0.3282 target = 0.067850 restraints weight = 31204.022|
|-----------------------------------------------------------------------------|
r_work (final): 0.3238
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8091
moved from start:          0.1440

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  13985  Z= 0.127
  Angle     :  0.613   9.349  18987  Z= 0.309
  Chirality :  0.045   0.167   2041
  Planarity :  0.004   0.056   2459
  Dihedral  :  5.110  38.799   1890
  Min Nonbonded Distance : 2.549

Molprobity Statistics.
  All-atom Clashscore : 12.60
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  9.07 %
    Favored  : 90.75 %
  Rotamer:
    Outliers :  5.89 %
    Allowed  : 28.38 %
    Favored  : 65.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.17 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.31 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.32 (0.20), residues: 1665
  helix: -0.82 (0.37), residues: 195
  sheet: -1.61 (0.29), residues: 340
  loop : -1.73 (0.18), residues: 1130

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 815 
 HIS   0.006   0.001   HIS B 269 
 PHE   0.017   0.001   PHE B 697 
 TYR   0.009   0.001   TYR B  13 
 ARG   0.003   0.000   ARG A 762 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03880 (  306)
  hydrogen bonds       : angle       6.36474 (  795)
  SS BOND              : bond        0.00252 (   32)
  SS BOND              : angle       0.67857 (   64)
  covalent geometry    : bond        0.00294 (13953)
  covalent geometry    : angle       0.61289 (18923)

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

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

  3330 Ramachandran restraints generated.
    1665 Oldfield, 0 Emsley, 1665 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3330 Ramachandran restraints generated.
    1665 Oldfield, 0 Emsley, 1665 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  190 residues out of total 1525 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 88
    poor density    : 102
  time to evaluate  : 1.701 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  272 GLU cc_start: 0.6048 (OUTLIER) cc_final: 0.4886 (mm-30)
REVERT: B  274 MET cc_start: 0.8336 (pmm) cc_final: 0.7486 (pmm)
REVERT: B  488 TYR cc_start: 0.8854 (OUTLIER) cc_final: 0.8618 (p90)
REVERT: B  599 ILE cc_start: 0.9300 (OUTLIER) cc_final: 0.8934 (tp)
REVERT: B  628 LEU cc_start: 0.8771 (OUTLIER) cc_final: 0.8314 (mt)
REVERT: B  690 GLU cc_start: 0.8375 (OUTLIER) cc_final: 0.7754 (tm-30)
REVERT: B  771 PHE cc_start: 0.8918 (OUTLIER) cc_final: 0.8653 (t80)
REVERT: A  180 ARG cc_start: 0.8511 (OUTLIER) cc_final: 0.7877 (ptp-170)
REVERT: A  274 MET cc_start: 0.8259 (pmm) cc_final: 0.7444 (pmm)
REVERT: A  618 ARG cc_start: 0.9375 (OUTLIER) cc_final: 0.8508 (ptp90)
REVERT: A  752 PHE cc_start: 0.9445 (OUTLIER) cc_final: 0.9093 (t80)
REVERT: C   46 GLU cc_start: 0.8919 (OUTLIER) cc_final: 0.8387 (tm-30)
  outliers start: 88
  outliers final: 42
  residues processed: 176
  average time/residue: 0.2323
  time to fit residues: 63.0079
Evaluate side-chains
  142 residues out of total 1525 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 52
    poor density    : 90
  time to evaluate  : 1.592 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   50 VAL
Chi-restraints excluded: chain B residue   51 ILE
Chi-restraints excluded: chain B residue   60 VAL
Chi-restraints excluded: chain B residue   91 GLU
Chi-restraints excluded: chain B residue   98 ILE
Chi-restraints excluded: chain B residue  106 ILE
Chi-restraints excluded: chain B residue  139 ILE
Chi-restraints excluded: chain B residue  175 CYS
Chi-restraints excluded: chain B residue  185 CYS
Chi-restraints excluded: chain B residue  272 GLU
Chi-restraints excluded: chain B residue  309 THR
Chi-restraints excluded: chain B residue  354 VAL
Chi-restraints excluded: chain B residue  430 ILE
Chi-restraints excluded: chain B residue  444 SER
Chi-restraints excluded: chain B residue  448 ILE
Chi-restraints excluded: chain B residue  488 TYR
Chi-restraints excluded: chain B residue  491 LEU
Chi-restraints excluded: chain B residue  577 THR
Chi-restraints excluded: chain B residue  599 ILE
Chi-restraints excluded: chain B residue  628 LEU
Chi-restraints excluded: chain B residue  690 GLU
Chi-restraints excluded: chain B residue  771 PHE
Chi-restraints excluded: chain B residue  788 LEU
Chi-restraints excluded: chain B residue  795 PHE
Chi-restraints excluded: chain B residue  813 VAL
Chi-restraints excluded: chain A residue   60 VAL
Chi-restraints excluded: chain A residue   98 ILE
Chi-restraints excluded: chain A residue  106 ILE
Chi-restraints excluded: chain A residue  124 THR
Chi-restraints excluded: chain A residue  167 ILE
Chi-restraints excluded: chain A residue  175 CYS
Chi-restraints excluded: chain A residue  180 ARG
Chi-restraints excluded: chain A residue  188 VAL
Chi-restraints excluded: chain A residue  244 TRP
Chi-restraints excluded: chain A residue  277 CYS
Chi-restraints excluded: chain A residue  320 MET
Chi-restraints excluded: chain A residue  354 VAL
Chi-restraints excluded: chain A residue  369 SER
Chi-restraints excluded: chain A residue  448 ILE
Chi-restraints excluded: chain A residue  488 TYR
Chi-restraints excluded: chain A residue  577 THR
Chi-restraints excluded: chain A residue  618 ARG
Chi-restraints excluded: chain A residue  752 PHE
Chi-restraints excluded: chain A residue  763 THR
Chi-restraints excluded: chain A residue  796 VAL
Chi-restraints excluded: chain A residue  842 ILE
Chi-restraints excluded: chain C residue   10 LEU
Chi-restraints excluded: chain C residue   44 VAL
Chi-restraints excluded: chain C residue   46 GLU
Chi-restraints excluded: chain D residue   10 LEU
Chi-restraints excluded: chain D residue   54 LEU
Chi-restraints excluded: chain D residue   58 GLU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 168
   random chunks:
   chunk 144 optimal weight:    6.9990
   chunk 33 optimal weight:    4.9990
   chunk 37 optimal weight:    1.9990
   chunk 100 optimal weight:    7.9990
   chunk 90 optimal weight:    3.9990
   chunk 80 optimal weight:    4.9990
   chunk 167 optimal weight:    4.9990
   chunk 53 optimal weight:    0.6980
   chunk 50 optimal weight:    7.9990
   chunk 60 optimal weight:   30.0000
   chunk 150 optimal weight:   30.0000
   overall best weight:    3.3388

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

Flipped N/Q/H residues before XYZ refinement:
** B 481 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 334 ASN
** A 443 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 453 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 481 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 609 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 779 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3908 r_free = 0.3908 target = 0.097770 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3210 r_free = 0.3210 target = 0.064935 restraints weight = 45266.338|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3169 r_free = 0.3169 target = 0.063324 restraints weight = 32829.556|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3155 r_free = 0.3155 target = 0.062881 restraints weight = 35528.289|
|-----------------------------------------------------------------------------|
r_work (final): 0.3104
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8267
moved from start:          0.1634

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.059  13985  Z= 0.280
  Angle     :  0.721   9.654  18987  Z= 0.364
  Chirality :  0.048   0.181   2041
  Planarity :  0.005   0.055   2459
  Dihedral  :  5.488  36.234   1887
  Min Nonbonded Distance : 2.528

Molprobity Statistics.
  All-atom Clashscore : 18.84
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  : 10.87 %
    Favored  : 88.95 %
  Rotamer:
    Outliers :  6.63 %
    Allowed  : 28.65 %
    Favored  : 64.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.17 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.31 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.44 (0.20), residues: 1665
  helix: -0.97 (0.37), residues: 195
  sheet: -1.67 (0.28), residues: 348
  loop : -1.80 (0.18), residues: 1122

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP A 403 
 HIS   0.007   0.001   HIS B 269 
 PHE   0.028   0.002   PHE B 241 
 TYR   0.016   0.002   TYR A 551 
 ARG   0.005   0.001   ARG A 857 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04356 (  306)
  hydrogen bonds       : angle       6.80992 (  795)
  SS BOND              : bond        0.00420 (   32)
  SS BOND              : angle       1.37649 (   64)
  covalent geometry    : bond        0.00634 (13953)
  covalent geometry    : angle       0.71761 (18923)

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

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

  3330 Ramachandran restraints generated.
    1665 Oldfield, 0 Emsley, 1665 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3330 Ramachandran restraints generated.
    1665 Oldfield, 0 Emsley, 1665 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  185 residues out of total 1525 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 99
    poor density    : 86
  time to evaluate  : 1.503 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  272 GLU cc_start: 0.6001 (OUTLIER) cc_final: 0.4734 (mm-30)
REVERT: B  274 MET cc_start: 0.8341 (pmm) cc_final: 0.7495 (pmm)
REVERT: B  628 LEU cc_start: 0.8863 (OUTLIER) cc_final: 0.8431 (mt)
REVERT: B  690 GLU cc_start: 0.8387 (OUTLIER) cc_final: 0.7843 (tm-30)
REVERT: A  180 ARG cc_start: 0.8688 (OUTLIER) cc_final: 0.8246 (ttm110)
REVERT: A  274 MET cc_start: 0.8309 (pmm) cc_final: 0.7562 (pmm)
REVERT: A  314 SER cc_start: 0.9375 (OUTLIER) cc_final: 0.9145 (t)
REVERT: A  752 PHE cc_start: 0.9501 (OUTLIER) cc_final: 0.9186 (t80)
REVERT: C   46 GLU cc_start: 0.8845 (OUTLIER) cc_final: 0.8300 (tm-30)
  outliers start: 99
  outliers final: 63
  residues processed: 176
  average time/residue: 0.2172
  time to fit residues: 59.4009
Evaluate side-chains
  153 residues out of total 1525 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 70
    poor density    : 83
  time to evaluate  : 1.509 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   51 ILE
Chi-restraints excluded: chain B residue   60 VAL
Chi-restraints excluded: chain B residue   69 LEU
Chi-restraints excluded: chain B residue   91 GLU
Chi-restraints excluded: chain B residue   98 ILE
Chi-restraints excluded: chain B residue  106 ILE
Chi-restraints excluded: chain B residue  107 THR
Chi-restraints excluded: chain B residue  131 LEU
Chi-restraints excluded: chain B residue  139 ILE
Chi-restraints excluded: chain B residue  167 ILE
Chi-restraints excluded: chain B residue  175 CYS
Chi-restraints excluded: chain B residue  185 CYS
Chi-restraints excluded: chain B residue  272 GLU
Chi-restraints excluded: chain B residue  309 THR
Chi-restraints excluded: chain B residue  314 SER
Chi-restraints excluded: chain B residue  348 PHE
Chi-restraints excluded: chain B residue  354 VAL
Chi-restraints excluded: chain B residue  355 VAL
Chi-restraints excluded: chain B residue  368 VAL
Chi-restraints excluded: chain B residue  427 VAL
Chi-restraints excluded: chain B residue  430 ILE
Chi-restraints excluded: chain B residue  444 SER
Chi-restraints excluded: chain B residue  448 ILE
Chi-restraints excluded: chain B residue  469 THR
Chi-restraints excluded: chain B residue  491 LEU
Chi-restraints excluded: chain B residue  546 THR
Chi-restraints excluded: chain B residue  577 THR
Chi-restraints excluded: chain B residue  628 LEU
Chi-restraints excluded: chain B residue  690 GLU
Chi-restraints excluded: chain B residue  788 LEU
Chi-restraints excluded: chain B residue  795 PHE
Chi-restraints excluded: chain B residue  813 VAL
Chi-restraints excluded: chain A residue   51 ILE
Chi-restraints excluded: chain A residue   60 VAL
Chi-restraints excluded: chain A residue   63 LEU
Chi-restraints excluded: chain A residue   91 GLU
Chi-restraints excluded: chain A residue   98 ILE
Chi-restraints excluded: chain A residue  107 THR
Chi-restraints excluded: chain A residue  124 THR
Chi-restraints excluded: chain A residue  167 ILE
Chi-restraints excluded: chain A residue  175 CYS
Chi-restraints excluded: chain A residue  180 ARG
Chi-restraints excluded: chain A residue  188 VAL
Chi-restraints excluded: chain A residue  277 CYS
Chi-restraints excluded: chain A residue  314 SER
Chi-restraints excluded: chain A residue  320 MET
Chi-restraints excluded: chain A residue  334 ASN
Chi-restraints excluded: chain A residue  354 VAL
Chi-restraints excluded: chain A residue  368 VAL
Chi-restraints excluded: chain A residue  369 SER
Chi-restraints excluded: chain A residue  393 VAL
Chi-restraints excluded: chain A residue  417 MET
Chi-restraints excluded: chain A residue  422 ASN
Chi-restraints excluded: chain A residue  426 CYS
Chi-restraints excluded: chain A residue  430 ILE
Chi-restraints excluded: chain A residue  448 ILE
Chi-restraints excluded: chain A residue  517 SER
Chi-restraints excluded: chain A residue  540 HIS
Chi-restraints excluded: chain A residue  542 LEU
Chi-restraints excluded: chain A residue  577 THR
Chi-restraints excluded: chain A residue  752 PHE
Chi-restraints excluded: chain A residue  796 VAL
Chi-restraints excluded: chain A residue  842 ILE
Chi-restraints excluded: chain C residue   10 LEU
Chi-restraints excluded: chain C residue   43 ILE
Chi-restraints excluded: chain C residue   44 VAL
Chi-restraints excluded: chain C residue   46 GLU
Chi-restraints excluded: chain D residue   10 LEU
Chi-restraints excluded: chain D residue   43 ILE
Chi-restraints excluded: chain D residue   54 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 168
   random chunks:
   chunk 34 optimal weight:    0.9980
   chunk 57 optimal weight:    8.9990
   chunk 144 optimal weight:   20.0000
   chunk 53 optimal weight:    3.9990
   chunk 118 optimal weight:    0.6980
   chunk 154 optimal weight:    9.9990
   chunk 17 optimal weight:    5.9990
   chunk 68 optimal weight:    9.9990
   chunk 98 optimal weight:    0.9990
   chunk 102 optimal weight:    0.9980
   chunk 61 optimal weight:    1.9990
   overall best weight:    1.1384

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

Flipped N/Q/H residues before XYZ refinement:
B 347 ASN
** B 481 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 334 ASN
** A 443 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 481 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 609 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 779 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3953 r_free = 0.3953 target = 0.100102 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3240 r_free = 0.3240 target = 0.066056 restraints weight = 44910.577|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3212 r_free = 0.3212 target = 0.064835 restraints weight = 35068.996|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3229 r_free = 0.3229 target = 0.065753 restraints weight = 30716.629|
|-----------------------------------------------------------------------------|
r_work (final): 0.3181
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8179
moved from start:          0.1891

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.056  13985  Z= 0.134
  Angle     :  0.652  11.698  18987  Z= 0.324
  Chirality :  0.046   0.262   2041
  Planarity :  0.004   0.053   2459
  Dihedral  :  5.293  40.990   1887
  Min Nonbonded Distance : 2.547

Molprobity Statistics.
  All-atom Clashscore : 14.13
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  8.83 %
    Favored  : 90.99 %
  Rotamer:
    Outliers :  6.43 %
    Allowed  : 28.38 %
    Favored  : 65.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.17 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.31 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.31 (0.20), residues: 1665
  helix: -0.85 (0.37), residues: 196
  sheet: -1.52 (0.29), residues: 332
  loop : -1.74 (0.18), residues: 1137

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 520 
 HIS   0.005   0.001   HIS B 269 
 PHE   0.023   0.001   PHE B 348 
 TYR   0.011   0.001   TYR B 418 
 ARG   0.003   0.000   ARG B 756 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03792 (  306)
  hydrogen bonds       : angle       6.34796 (  795)
  SS BOND              : bond        0.00438 (   32)
  SS BOND              : angle       1.73792 (   64)
  covalent geometry    : bond        0.00310 (13953)
  covalent geometry    : angle       0.64512 (18923)

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

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

  3330 Ramachandran restraints generated.
    1665 Oldfield, 0 Emsley, 1665 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3330 Ramachandran restraints generated.
    1665 Oldfield, 0 Emsley, 1665 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  195 residues out of total 1525 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 96
    poor density    : 99
  time to evaluate  : 1.589 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  272 GLU cc_start: 0.6007 (OUTLIER) cc_final: 0.4885 (mm-30)
REVERT: B  274 MET cc_start: 0.8439 (pmm) cc_final: 0.7565 (pmm)
REVERT: B  599 ILE cc_start: 0.9327 (OUTLIER) cc_final: 0.8989 (tp)
REVERT: B  628 LEU cc_start: 0.8896 (OUTLIER) cc_final: 0.8465 (mt)
REVERT: B  690 GLU cc_start: 0.8403 (OUTLIER) cc_final: 0.7766 (tp30)
REVERT: B  771 PHE cc_start: 0.8940 (OUTLIER) cc_final: 0.8681 (t80)
REVERT: A  180 ARG cc_start: 0.8593 (OUTLIER) cc_final: 0.8139 (ttm110)
REVERT: A  274 MET cc_start: 0.8278 (pmm) cc_final: 0.7539 (pmm)
REVERT: A  314 SER cc_start: 0.9452 (OUTLIER) cc_final: 0.9081 (t)
REVERT: A  752 PHE cc_start: 0.9470 (OUTLIER) cc_final: 0.9247 (t80)
REVERT: C   46 GLU cc_start: 0.8826 (OUTLIER) cc_final: 0.8251 (tm-30)
  outliers start: 96
  outliers final: 59
  residues processed: 185
  average time/residue: 0.2198
  time to fit residues: 65.1713
Evaluate side-chains
  159 residues out of total 1525 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 68
    poor density    : 91
  time to evaluate  : 1.487 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   17 LYS
Chi-restraints excluded: chain B residue   51 ILE
Chi-restraints excluded: chain B residue   57 LEU
Chi-restraints excluded: chain B residue   60 VAL
Chi-restraints excluded: chain B residue   69 LEU
Chi-restraints excluded: chain B residue   91 GLU
Chi-restraints excluded: chain B residue  106 ILE
Chi-restraints excluded: chain B residue  131 LEU
Chi-restraints excluded: chain B residue  139 ILE
Chi-restraints excluded: chain B residue  167 ILE
Chi-restraints excluded: chain B residue  175 CYS
Chi-restraints excluded: chain B residue  185 CYS
Chi-restraints excluded: chain B residue  272 GLU
Chi-restraints excluded: chain B residue  273 CYS
Chi-restraints excluded: chain B residue  309 THR
Chi-restraints excluded: chain B residue  368 VAL
Chi-restraints excluded: chain B residue  427 VAL
Chi-restraints excluded: chain B residue  430 ILE
Chi-restraints excluded: chain B residue  444 SER
Chi-restraints excluded: chain B residue  448 ILE
Chi-restraints excluded: chain B residue  469 THR
Chi-restraints excluded: chain B residue  491 LEU
Chi-restraints excluded: chain B residue  540 HIS
Chi-restraints excluded: chain B residue  546 THR
Chi-restraints excluded: chain B residue  577 THR
Chi-restraints excluded: chain B residue  599 ILE
Chi-restraints excluded: chain B residue  628 LEU
Chi-restraints excluded: chain B residue  690 GLU
Chi-restraints excluded: chain B residue  771 PHE
Chi-restraints excluded: chain B residue  788 LEU
Chi-restraints excluded: chain B residue  795 PHE
Chi-restraints excluded: chain B residue  813 VAL
Chi-restraints excluded: chain A residue    2 ILE
Chi-restraints excluded: chain A residue   51 ILE
Chi-restraints excluded: chain A residue   60 VAL
Chi-restraints excluded: chain A residue   63 LEU
Chi-restraints excluded: chain A residue  106 ILE
Chi-restraints excluded: chain A residue  107 THR
Chi-restraints excluded: chain A residue  124 THR
Chi-restraints excluded: chain A residue  167 ILE
Chi-restraints excluded: chain A residue  175 CYS
Chi-restraints excluded: chain A residue  180 ARG
Chi-restraints excluded: chain A residue  244 TRP
Chi-restraints excluded: chain A residue  269 HIS
Chi-restraints excluded: chain A residue  277 CYS
Chi-restraints excluded: chain A residue  314 SER
Chi-restraints excluded: chain A residue  320 MET
Chi-restraints excluded: chain A residue  354 VAL
Chi-restraints excluded: chain A residue  369 SER
Chi-restraints excluded: chain A residue  370 LEU
Chi-restraints excluded: chain A residue  426 CYS
Chi-restraints excluded: chain A residue  427 VAL
Chi-restraints excluded: chain A residue  430 ILE
Chi-restraints excluded: chain A residue  448 ILE
Chi-restraints excluded: chain A residue  488 TYR
Chi-restraints excluded: chain A residue  517 SER
Chi-restraints excluded: chain A residue  540 HIS
Chi-restraints excluded: chain A residue  559 MET
Chi-restraints excluded: chain A residue  577 THR
Chi-restraints excluded: chain A residue  752 PHE
Chi-restraints excluded: chain A residue  763 THR
Chi-restraints excluded: chain A residue  796 VAL
Chi-restraints excluded: chain A residue  842 ILE
Chi-restraints excluded: chain C residue   10 LEU
Chi-restraints excluded: chain C residue   43 ILE
Chi-restraints excluded: chain C residue   46 GLU
Chi-restraints excluded: chain D residue   10 LEU
Chi-restraints excluded: chain D residue   58 GLU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 168
   random chunks:
   chunk 141 optimal weight:    0.7980
   chunk 62 optimal weight:    0.9980
   chunk 109 optimal weight:    0.8980
   chunk 155 optimal weight:   30.0000
   chunk 13 optimal weight:    0.0060
   chunk 78 optimal weight:    8.9990
   chunk 58 optimal weight:    5.9990
   chunk 73 optimal weight:    9.9990
   chunk 138 optimal weight:    1.9990
   chunk 162 optimal weight:    3.9990
   chunk 86 optimal weight:    0.2980
   overall best weight:    0.5996

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

Flipped N/Q/H residues before XYZ refinement:
B 347 ASN
** B 481 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 794 ASN
** B 834 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 481 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 609 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3986 r_free = 0.3986 target = 0.101724 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3296 r_free = 0.3296 target = 0.067975 restraints weight = 45537.169|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3259 r_free = 0.3259 target = 0.066804 restraints weight = 38268.007|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3266 r_free = 0.3266 target = 0.067165 restraints weight = 31381.329|
|-----------------------------------------------------------------------------|
r_work (final): 0.3219
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8130
moved from start:          0.2242

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.050  13985  Z= 0.108
  Angle     :  0.633  12.243  18987  Z= 0.311
  Chirality :  0.046   0.195   2041
  Planarity :  0.004   0.053   2459
  Dihedral  :  5.012  36.190   1887
  Min Nonbonded Distance : 2.550

Molprobity Statistics.
  All-atom Clashscore : 12.15
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  8.47 %
    Favored  : 91.35 %
  Rotamer:
    Outliers :  5.49 %
    Allowed  : 28.65 %
    Favored  : 65.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.17 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.25 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.23 (0.20), residues: 1665
  helix: -0.70 (0.37), residues: 190
  sheet: -1.35 (0.30), residues: 322
  loop : -1.74 (0.18), residues: 1153

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 827 
 HIS   0.004   0.001   HIS B 269 
 PHE   0.025   0.001   PHE B 348 
 TYR   0.012   0.001   TYR B  13 
 ARG   0.005   0.000   ARG B 337 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03537 (  306)
  hydrogen bonds       : angle       6.02314 (  795)
  SS BOND              : bond        0.00321 (   32)
  SS BOND              : angle       1.28837 (   64)
  covalent geometry    : bond        0.00249 (13953)
  covalent geometry    : angle       0.63008 (18923)

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

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

  3330 Ramachandran restraints generated.
    1665 Oldfield, 0 Emsley, 1665 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3330 Ramachandran restraints generated.
    1665 Oldfield, 0 Emsley, 1665 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  193 residues out of total 1525 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 82
    poor density    : 111
  time to evaluate  : 1.447 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   32 LEU cc_start: 0.9149 (OUTLIER) cc_final: 0.8781 (pp)
REVERT: B  272 GLU cc_start: 0.5944 (OUTLIER) cc_final: 0.4894 (mm-30)
REVERT: B  274 MET cc_start: 0.8425 (pmm) cc_final: 0.7642 (pmm)
REVERT: B  559 MET cc_start: 0.8187 (tpp) cc_final: 0.7979 (tpp)
REVERT: B  599 ILE cc_start: 0.9297 (OUTLIER) cc_final: 0.8962 (tp)
REVERT: B  628 LEU cc_start: 0.8880 (OUTLIER) cc_final: 0.8449 (mt)
REVERT: B  690 GLU cc_start: 0.8371 (OUTLIER) cc_final: 0.7726 (tm-30)
REVERT: B  771 PHE cc_start: 0.8892 (OUTLIER) cc_final: 0.8568 (t80)
REVERT: A  180 ARG cc_start: 0.8493 (OUTLIER) cc_final: 0.7803 (ptp-170)
REVERT: A  274 MET cc_start: 0.8349 (pmm) cc_final: 0.7759 (pmm)
REVERT: A  314 SER cc_start: 0.9544 (OUTLIER) cc_final: 0.9244 (t)
REVERT: A  370 LEU cc_start: 0.8984 (OUTLIER) cc_final: 0.7711 (tt)
REVERT: A  403 TRP cc_start: 0.8618 (OUTLIER) cc_final: 0.8079 (p90)
REVERT: A  752 PHE cc_start: 0.9504 (OUTLIER) cc_final: 0.9233 (t80)
REVERT: C   46 GLU cc_start: 0.8735 (OUTLIER) cc_final: 0.8418 (tm-30)
REVERT: D   55 ARG cc_start: 0.8544 (tpm170) cc_final: 0.8326 (tpm170)
  outliers start: 82
  outliers final: 51
  residues processed: 184
  average time/residue: 0.2082
  time to fit residues: 60.8220
Evaluate side-chains
  157 residues out of total 1525 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 63
    poor density    : 94
  time to evaluate  : 1.594 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   17 LYS
Chi-restraints excluded: chain B residue   32 LEU
Chi-restraints excluded: chain B residue   51 ILE
Chi-restraints excluded: chain B residue   57 LEU
Chi-restraints excluded: chain B residue   60 VAL
Chi-restraints excluded: chain B residue   69 LEU
Chi-restraints excluded: chain B residue  106 ILE
Chi-restraints excluded: chain B residue  139 ILE
Chi-restraints excluded: chain B residue  167 ILE
Chi-restraints excluded: chain B residue  175 CYS
Chi-restraints excluded: chain B residue  185 CYS
Chi-restraints excluded: chain B residue  209 CYS
Chi-restraints excluded: chain B residue  272 GLU
Chi-restraints excluded: chain B residue  273 CYS
Chi-restraints excluded: chain B residue  309 THR
Chi-restraints excluded: chain B residue  354 VAL
Chi-restraints excluded: chain B residue  430 ILE
Chi-restraints excluded: chain B residue  444 SER
Chi-restraints excluded: chain B residue  448 ILE
Chi-restraints excluded: chain B residue  469 THR
Chi-restraints excluded: chain B residue  540 HIS
Chi-restraints excluded: chain B residue  577 THR
Chi-restraints excluded: chain B residue  599 ILE
Chi-restraints excluded: chain B residue  628 LEU
Chi-restraints excluded: chain B residue  690 GLU
Chi-restraints excluded: chain B residue  771 PHE
Chi-restraints excluded: chain B residue  795 PHE
Chi-restraints excluded: chain B residue  813 VAL
Chi-restraints excluded: chain A residue    2 ILE
Chi-restraints excluded: chain A residue   60 VAL
Chi-restraints excluded: chain A residue   63 LEU
Chi-restraints excluded: chain A residue  106 ILE
Chi-restraints excluded: chain A residue  124 THR
Chi-restraints excluded: chain A residue  167 ILE
Chi-restraints excluded: chain A residue  175 CYS
Chi-restraints excluded: chain A residue  180 ARG
Chi-restraints excluded: chain A residue  188 VAL
Chi-restraints excluded: chain A residue  244 TRP
Chi-restraints excluded: chain A residue  269 HIS
Chi-restraints excluded: chain A residue  277 CYS
Chi-restraints excluded: chain A residue  314 SER
Chi-restraints excluded: chain A residue  320 MET
Chi-restraints excluded: chain A residue  354 VAL
Chi-restraints excluded: chain A residue  369 SER
Chi-restraints excluded: chain A residue  370 LEU
Chi-restraints excluded: chain A residue  403 TRP
Chi-restraints excluded: chain A residue  430 ILE
Chi-restraints excluded: chain A residue  448 ILE
Chi-restraints excluded: chain A residue  469 THR
Chi-restraints excluded: chain A residue  488 TYR
Chi-restraints excluded: chain A residue  517 SER
Chi-restraints excluded: chain A residue  540 HIS
Chi-restraints excluded: chain A residue  577 THR
Chi-restraints excluded: chain A residue  752 PHE
Chi-restraints excluded: chain A residue  763 THR
Chi-restraints excluded: chain A residue  796 VAL
Chi-restraints excluded: chain A residue  842 ILE
Chi-restraints excluded: chain C residue   10 LEU
Chi-restraints excluded: chain C residue   46 GLU
Chi-restraints excluded: chain C residue   58 GLU
Chi-restraints excluded: chain D residue   10 LEU
Chi-restraints excluded: chain D residue   54 LEU
Chi-restraints excluded: chain D residue   58 GLU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 168
   random chunks:
   chunk 56 optimal weight:   30.0000
   chunk 78 optimal weight:    8.9990
   chunk 57 optimal weight:    7.9990
   chunk 85 optimal weight:    9.9990
   chunk 12 optimal weight:    0.9990
   chunk 60 optimal weight:   30.0000
   chunk 7 optimal weight:    2.9990
   chunk 127 optimal weight:    9.9990
   chunk 141 optimal weight:    3.9990
   chunk 38 optimal weight:    0.0060
   chunk 43 optimal weight:    0.8980
   overall best weight:    1.7802

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

Flipped N/Q/H residues before XYZ refinement:
** B 481 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 564 HIS
** B 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 794 ASN
B 834 ASN
** A 443 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 453 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 481 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 609 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3952 r_free = 0.3952 target = 0.099985 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3265 r_free = 0.3265 target = 0.066826 restraints weight = 45704.654|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3209 r_free = 0.3209 target = 0.064933 restraints weight = 38313.832|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3215 r_free = 0.3215 target = 0.065228 restraints weight = 35019.614|
|-----------------------------------------------------------------------------|
r_work (final): 0.3163
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8201
moved from start:          0.2214

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048  13985  Z= 0.168
  Angle     :  0.648  11.323  18987  Z= 0.322
  Chirality :  0.046   0.165   2041
  Planarity :  0.004   0.052   2459
  Dihedral  :  5.103  37.022   1887
  Min Nonbonded Distance : 2.560

Molprobity Statistics.
  All-atom Clashscore : 14.06
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  9.31 %
    Favored  : 90.51 %
  Rotamer:
    Outliers :  5.89 %
    Allowed  : 28.92 %
    Favored  : 65.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.17 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.19 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.17 (0.20), residues: 1665
  helix: -0.54 (0.38), residues: 183
  sheet: -1.32 (0.30), residues: 324
  loop : -1.73 (0.18), residues: 1158

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.001   TRP B 403 
 HIS   0.008   0.001   HIS B 564 
 PHE   0.023   0.001   PHE B 348 
 TYR   0.020   0.001   TYR B  13 
 ARG   0.004   0.000   ARG D  50 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03765 (  306)
  hydrogen bonds       : angle       6.21539 (  795)
  SS BOND              : bond        0.00417 (   32)
  SS BOND              : angle       1.39750 (   64)
  covalent geometry    : bond        0.00389 (13953)
  covalent geometry    : angle       0.64381 (18923)

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

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

  3330 Ramachandran restraints generated.
    1665 Oldfield, 0 Emsley, 1665 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3330 Ramachandran restraints generated.
    1665 Oldfield, 0 Emsley, 1665 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  181 residues out of total 1525 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 88
    poor density    : 93
  time to evaluate  : 1.658 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   32 LEU cc_start: 0.9173 (OUTLIER) cc_final: 0.8818 (pp)
REVERT: B  272 GLU cc_start: 0.5887 (OUTLIER) cc_final: 0.4768 (mm-30)
REVERT: B  274 MET cc_start: 0.8417 (pmm) cc_final: 0.7621 (pmm)
REVERT: B  559 MET cc_start: 0.8338 (tpp) cc_final: 0.8109 (tpp)
REVERT: B  628 LEU cc_start: 0.8882 (OUTLIER) cc_final: 0.8442 (mt)
REVERT: B  690 GLU cc_start: 0.8430 (OUTLIER) cc_final: 0.7769 (tm-30)
REVERT: A  180 ARG cc_start: 0.8563 (OUTLIER) cc_final: 0.8114 (ttm110)
REVERT: A  274 MET cc_start: 0.8335 (pmm) cc_final: 0.7742 (pmm)
REVERT: A  752 PHE cc_start: 0.9526 (OUTLIER) cc_final: 0.9240 (t80)
REVERT: C   46 GLU cc_start: 0.8782 (OUTLIER) cc_final: 0.8407 (tm-30)
  outliers start: 88
  outliers final: 64
  residues processed: 174
  average time/residue: 0.2053
  time to fit residues: 57.1836
Evaluate side-chains
  158 residues out of total 1525 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 71
    poor density    : 87
  time to evaluate  : 1.514 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue    2 ILE
Chi-restraints excluded: chain B residue   32 LEU
Chi-restraints excluded: chain B residue   51 ILE
Chi-restraints excluded: chain B residue   57 LEU
Chi-restraints excluded: chain B residue   60 VAL
Chi-restraints excluded: chain B residue   69 LEU
Chi-restraints excluded: chain B residue   98 ILE
Chi-restraints excluded: chain B residue  106 ILE
Chi-restraints excluded: chain B residue  107 THR
Chi-restraints excluded: chain B residue  131 LEU
Chi-restraints excluded: chain B residue  139 ILE
Chi-restraints excluded: chain B residue  167 ILE
Chi-restraints excluded: chain B residue  175 CYS
Chi-restraints excluded: chain B residue  185 CYS
Chi-restraints excluded: chain B residue  209 CYS
Chi-restraints excluded: chain B residue  211 THR
Chi-restraints excluded: chain B residue  272 GLU
Chi-restraints excluded: chain B residue  273 CYS
Chi-restraints excluded: chain B residue  309 THR
Chi-restraints excluded: chain B residue  354 VAL
Chi-restraints excluded: chain B residue  422 ASN
Chi-restraints excluded: chain B residue  427 VAL
Chi-restraints excluded: chain B residue  430 ILE
Chi-restraints excluded: chain B residue  444 SER
Chi-restraints excluded: chain B residue  448 ILE
Chi-restraints excluded: chain B residue  469 THR
Chi-restraints excluded: chain B residue  540 HIS
Chi-restraints excluded: chain B residue  546 THR
Chi-restraints excluded: chain B residue  577 THR
Chi-restraints excluded: chain B residue  628 LEU
Chi-restraints excluded: chain B residue  690 GLU
Chi-restraints excluded: chain B residue  795 PHE
Chi-restraints excluded: chain B residue  813 VAL
Chi-restraints excluded: chain A residue    2 ILE
Chi-restraints excluded: chain A residue   51 ILE
Chi-restraints excluded: chain A residue   60 VAL
Chi-restraints excluded: chain A residue   63 LEU
Chi-restraints excluded: chain A residue   98 ILE
Chi-restraints excluded: chain A residue  106 ILE
Chi-restraints excluded: chain A residue  107 THR
Chi-restraints excluded: chain A residue  124 THR
Chi-restraints excluded: chain A residue  167 ILE
Chi-restraints excluded: chain A residue  175 CYS
Chi-restraints excluded: chain A residue  180 ARG
Chi-restraints excluded: chain A residue  188 VAL
Chi-restraints excluded: chain A residue  244 TRP
Chi-restraints excluded: chain A residue  269 HIS
Chi-restraints excluded: chain A residue  277 CYS
Chi-restraints excluded: chain A residue  320 MET
Chi-restraints excluded: chain A residue  354 VAL
Chi-restraints excluded: chain A residue  369 SER
Chi-restraints excluded: chain A residue  422 ASN
Chi-restraints excluded: chain A residue  427 VAL
Chi-restraints excluded: chain A residue  430 ILE
Chi-restraints excluded: chain A residue  448 ILE
Chi-restraints excluded: chain A residue  469 THR
Chi-restraints excluded: chain A residue  488 TYR
Chi-restraints excluded: chain A residue  517 SER
Chi-restraints excluded: chain A residue  540 HIS
Chi-restraints excluded: chain A residue  542 LEU
Chi-restraints excluded: chain A residue  559 MET
Chi-restraints excluded: chain A residue  577 THR
Chi-restraints excluded: chain A residue  752 PHE
Chi-restraints excluded: chain A residue  763 THR
Chi-restraints excluded: chain A residue  796 VAL
Chi-restraints excluded: chain A residue  842 ILE
Chi-restraints excluded: chain C residue   10 LEU
Chi-restraints excluded: chain C residue   43 ILE
Chi-restraints excluded: chain C residue   46 GLU
Chi-restraints excluded: chain D residue   10 LEU
Chi-restraints excluded: chain D residue   58 GLU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 168
   random chunks:
   chunk 43 optimal weight:    0.6980
   chunk 53 optimal weight:    4.9990
   chunk 157 optimal weight:   20.0000
   chunk 160 optimal weight:    1.9990
   chunk 74 optimal weight:   30.0000
   chunk 64 optimal weight:    6.9990
   chunk 167 optimal weight:    5.9990
   chunk 5 optimal weight:    0.7980
   chunk 109 optimal weight:    3.9990
   chunk 123 optimal weight:    3.9990
   chunk 137 optimal weight:    0.5980
   overall best weight:    1.6184

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

Flipped N/Q/H residues before XYZ refinement:
** B 481 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 443 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 453 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 481 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 609 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3951 r_free = 0.3951 target = 0.099945 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3278 r_free = 0.3278 target = 0.067065 restraints weight = 45619.899|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3256 r_free = 0.3256 target = 0.066607 restraints weight = 38537.036|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3256 r_free = 0.3256 target = 0.066690 restraints weight = 30487.258|
|-----------------------------------------------------------------------------|
r_work (final): 0.3218
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8112
moved from start:          0.2357

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042  13985  Z= 0.158
  Angle     :  0.668  12.805  18987  Z= 0.327
  Chirality :  0.046   0.202   2041
  Planarity :  0.004   0.051   2459
  Dihedral  :  5.088  36.901   1887
  Min Nonbonded Distance : 2.478

Molprobity Statistics.
  All-atom Clashscore : 14.47
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  9.01 %
    Favored  : 90.81 %
  Rotamer:
    Outliers :  6.16 %
    Allowed  : 28.98 %
    Favored  : 64.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.17 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.13 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.20 (0.20), residues: 1665
  helix: -0.64 (0.37), residues: 189
  sheet: -1.28 (0.30), residues: 324
  loop : -1.75 (0.18), residues: 1152

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.032   0.001   TRP B 403 
 HIS   0.004   0.001   HIS B 269 
 PHE   0.027   0.001   PHE B 348 
 TYR   0.010   0.001   TYR A 551 
 ARG   0.003   0.000   ARG B 337 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03787 (  306)
  hydrogen bonds       : angle       6.17312 (  795)
  SS BOND              : bond        0.00325 (   32)
  SS BOND              : angle       1.29690 (   64)
  covalent geometry    : bond        0.00365 (13953)
  covalent geometry    : angle       0.66453 (18923)

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

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

  3330 Ramachandran restraints generated.
    1665 Oldfield, 0 Emsley, 1665 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3330 Ramachandran restraints generated.
    1665 Oldfield, 0 Emsley, 1665 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  181 residues out of total 1525 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 92
    poor density    : 89
  time to evaluate  : 1.453 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   32 LEU cc_start: 0.9163 (OUTLIER) cc_final: 0.8806 (pp)
REVERT: B   91 GLU cc_start: 0.7284 (mt-10) cc_final: 0.7053 (tt0)
REVERT: B  272 GLU cc_start: 0.5910 (OUTLIER) cc_final: 0.4768 (mm-30)
REVERT: B  274 MET cc_start: 0.8403 (pmm) cc_final: 0.7642 (pmm)
REVERT: B  559 MET cc_start: 0.8315 (tpp) cc_final: 0.8083 (tpp)
REVERT: B  599 ILE cc_start: 0.9222 (OUTLIER) cc_final: 0.8872 (tp)
REVERT: B  628 LEU cc_start: 0.8704 (OUTLIER) cc_final: 0.8250 (mt)
REVERT: B  690 GLU cc_start: 0.8352 (OUTLIER) cc_final: 0.7710 (tm-30)
REVERT: B  771 PHE cc_start: 0.8699 (OUTLIER) cc_final: 0.8331 (t80)
REVERT: A  180 ARG cc_start: 0.8580 (OUTLIER) cc_final: 0.8135 (ttm110)
REVERT: A  274 MET cc_start: 0.8264 (pmm) cc_final: 0.7696 (pmm)
REVERT: A  752 PHE cc_start: 0.9409 (OUTLIER) cc_final: 0.9001 (t80)
REVERT: C   46 GLU cc_start: 0.8759 (OUTLIER) cc_final: 0.8373 (tm-30)
  outliers start: 92
  outliers final: 67
  residues processed: 175
  average time/residue: 0.1932
  time to fit residues: 54.6514
Evaluate side-chains
  162 residues out of total 1525 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 76
    poor density    : 86
  time to evaluate  : 1.452 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue    2 ILE
Chi-restraints excluded: chain B residue   32 LEU
Chi-restraints excluded: chain B residue   51 ILE
Chi-restraints excluded: chain B residue   57 LEU
Chi-restraints excluded: chain B residue   60 VAL
Chi-restraints excluded: chain B residue   69 LEU
Chi-restraints excluded: chain B residue   98 ILE
Chi-restraints excluded: chain B residue  106 ILE
Chi-restraints excluded: chain B residue  131 LEU
Chi-restraints excluded: chain B residue  139 ILE
Chi-restraints excluded: chain B residue  167 ILE
Chi-restraints excluded: chain B residue  175 CYS
Chi-restraints excluded: chain B residue  185 CYS
Chi-restraints excluded: chain B residue  188 VAL
Chi-restraints excluded: chain B residue  209 CYS
Chi-restraints excluded: chain B residue  211 THR
Chi-restraints excluded: chain B residue  272 GLU
Chi-restraints excluded: chain B residue  273 CYS
Chi-restraints excluded: chain B residue  309 THR
Chi-restraints excluded: chain B residue  354 VAL
Chi-restraints excluded: chain B residue  422 ASN
Chi-restraints excluded: chain B residue  426 CYS
Chi-restraints excluded: chain B residue  427 VAL
Chi-restraints excluded: chain B residue  430 ILE
Chi-restraints excluded: chain B residue  444 SER
Chi-restraints excluded: chain B residue  448 ILE
Chi-restraints excluded: chain B residue  469 THR
Chi-restraints excluded: chain B residue  540 HIS
Chi-restraints excluded: chain B residue  546 THR
Chi-restraints excluded: chain B residue  577 THR
Chi-restraints excluded: chain B residue  599 ILE
Chi-restraints excluded: chain B residue  628 LEU
Chi-restraints excluded: chain B residue  690 GLU
Chi-restraints excluded: chain B residue  771 PHE
Chi-restraints excluded: chain B residue  788 LEU
Chi-restraints excluded: chain B residue  795 PHE
Chi-restraints excluded: chain B residue  813 VAL
Chi-restraints excluded: chain A residue    2 ILE
Chi-restraints excluded: chain A residue   51 ILE
Chi-restraints excluded: chain A residue   60 VAL
Chi-restraints excluded: chain A residue   63 LEU
Chi-restraints excluded: chain A residue   75 VAL
Chi-restraints excluded: chain A residue   98 ILE
Chi-restraints excluded: chain A residue  106 ILE
Chi-restraints excluded: chain A residue  107 THR
Chi-restraints excluded: chain A residue  124 THR
Chi-restraints excluded: chain A residue  167 ILE
Chi-restraints excluded: chain A residue  175 CYS
Chi-restraints excluded: chain A residue  180 ARG
Chi-restraints excluded: chain A residue  185 CYS
Chi-restraints excluded: chain A residue  188 VAL
Chi-restraints excluded: chain A residue  244 TRP
Chi-restraints excluded: chain A residue  269 HIS
Chi-restraints excluded: chain A residue  277 CYS
Chi-restraints excluded: chain A residue  320 MET
Chi-restraints excluded: chain A residue  354 VAL
Chi-restraints excluded: chain A residue  369 SER
Chi-restraints excluded: chain A residue  426 CYS
Chi-restraints excluded: chain A residue  427 VAL
Chi-restraints excluded: chain A residue  430 ILE
Chi-restraints excluded: chain A residue  448 ILE
Chi-restraints excluded: chain A residue  469 THR
Chi-restraints excluded: chain A residue  488 TYR
Chi-restraints excluded: chain A residue  517 SER
Chi-restraints excluded: chain A residue  540 HIS
Chi-restraints excluded: chain A residue  542 LEU
Chi-restraints excluded: chain A residue  577 THR
Chi-restraints excluded: chain A residue  752 PHE
Chi-restraints excluded: chain A residue  763 THR
Chi-restraints excluded: chain A residue  796 VAL
Chi-restraints excluded: chain A residue  842 ILE
Chi-restraints excluded: chain C residue   10 LEU
Chi-restraints excluded: chain C residue   43 ILE
Chi-restraints excluded: chain C residue   46 GLU
Chi-restraints excluded: chain D residue   10 LEU
Chi-restraints excluded: chain D residue   52 CYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 168
   random chunks:
   chunk 85 optimal weight:    9.9990
   chunk 20 optimal weight:    0.3980
   chunk 76 optimal weight:    4.9990
   chunk 65 optimal weight:   20.0000
   chunk 120 optimal weight:    1.9990
   chunk 70 optimal weight:    0.4980
   chunk 140 optimal weight:    6.9990
   chunk 111 optimal weight:    2.9990
   chunk 142 optimal weight:    0.7980
   chunk 35 optimal weight:    0.0470
   chunk 94 optimal weight:    6.9990
   overall best weight:    0.7480

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

Flipped N/Q/H residues before XYZ refinement:
** B 481 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 453 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 481 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 609 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 881 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3980 r_free = 0.3980 target = 0.101527 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3318 r_free = 0.3318 target = 0.068713 restraints weight = 45007.383|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3294 r_free = 0.3294 target = 0.068122 restraints weight = 34369.269|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3292 r_free = 0.3292 target = 0.068131 restraints weight = 29676.957|
|-----------------------------------------------------------------------------|
r_work (final): 0.3254
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8070
moved from start:          0.2581

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  13985  Z= 0.112
  Angle     :  0.650  13.299  18987  Z= 0.314
  Chirality :  0.046   0.196   2041
  Planarity :  0.004   0.051   2459
  Dihedral  :  4.921  37.202   1887
  Min Nonbonded Distance : 2.571

Molprobity Statistics.
  All-atom Clashscore : 12.00
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  7.99 %
    Favored  : 91.83 %
  Rotamer:
    Outliers :  4.75 %
    Allowed  : 30.12 %
    Favored  : 65.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.17 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.13 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.15 (0.20), residues: 1665
  helix: -0.61 (0.37), residues: 190
  sheet: -1.21 (0.30), residues: 324
  loop : -1.73 (0.18), residues: 1151

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP B 403 
 HIS   0.004   0.001   HIS A 702 
 PHE   0.020   0.001   PHE B 348 
 TYR   0.010   0.001   TYR B 418 
 ARG   0.003   0.000   ARG B 337 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03579 (  306)
  hydrogen bonds       : angle       5.96260 (  795)
  SS BOND              : bond        0.00283 (   32)
  SS BOND              : angle       1.15329 (   64)
  covalent geometry    : bond        0.00260 (13953)
  covalent geometry    : angle       0.64755 (18923)

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

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

  3330 Ramachandran restraints generated.
    1665 Oldfield, 0 Emsley, 1665 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3330 Ramachandran restraints generated.
    1665 Oldfield, 0 Emsley, 1665 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  168 residues out of total 1525 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 71
    poor density    : 97
  time to evaluate  : 1.573 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   32 LEU cc_start: 0.9086 (OUTLIER) cc_final: 0.8756 (pp)
REVERT: B  272 GLU cc_start: 0.5882 (OUTLIER) cc_final: 0.4722 (mm-30)
REVERT: B  274 MET cc_start: 0.8416 (pmm) cc_final: 0.7721 (pmm)
REVERT: B  599 ILE cc_start: 0.9205 (OUTLIER) cc_final: 0.8854 (tp)
REVERT: B  628 LEU cc_start: 0.8714 (OUTLIER) cc_final: 0.8243 (mt)
REVERT: B  690 GLU cc_start: 0.8306 (OUTLIER) cc_final: 0.7668 (tm-30)
REVERT: B  771 PHE cc_start: 0.8741 (OUTLIER) cc_final: 0.8363 (t80)
REVERT: A  274 MET cc_start: 0.8279 (pmm) cc_final: 0.7779 (pmm)
REVERT: A  752 PHE cc_start: 0.9425 (OUTLIER) cc_final: 0.9010 (t80)
REVERT: C   46 GLU cc_start: 0.8701 (OUTLIER) cc_final: 0.8361 (tm-30)
  outliers start: 71
  outliers final: 54
  residues processed: 161
  average time/residue: 0.2000
  time to fit residues: 51.9264
Evaluate side-chains
  152 residues out of total 1525 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 62
    poor density    : 90
  time to evaluate  : 1.579 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue    2 ILE
Chi-restraints excluded: chain B residue   32 LEU
Chi-restraints excluded: chain B residue   51 ILE
Chi-restraints excluded: chain B residue   69 LEU
Chi-restraints excluded: chain B residue  106 ILE
Chi-restraints excluded: chain B residue  139 ILE
Chi-restraints excluded: chain B residue  167 ILE
Chi-restraints excluded: chain B residue  175 CYS
Chi-restraints excluded: chain B residue  185 CYS
Chi-restraints excluded: chain B residue  188 VAL
Chi-restraints excluded: chain B residue  209 CYS
Chi-restraints excluded: chain B residue  272 GLU
Chi-restraints excluded: chain B residue  273 CYS
Chi-restraints excluded: chain B residue  309 THR
Chi-restraints excluded: chain B residue  354 VAL
Chi-restraints excluded: chain B residue  427 VAL
Chi-restraints excluded: chain B residue  430 ILE
Chi-restraints excluded: chain B residue  444 SER
Chi-restraints excluded: chain B residue  448 ILE
Chi-restraints excluded: chain B residue  469 THR
Chi-restraints excluded: chain B residue  488 TYR
Chi-restraints excluded: chain B residue  540 HIS
Chi-restraints excluded: chain B residue  577 THR
Chi-restraints excluded: chain B residue  599 ILE
Chi-restraints excluded: chain B residue  628 LEU
Chi-restraints excluded: chain B residue  690 GLU
Chi-restraints excluded: chain B residue  771 PHE
Chi-restraints excluded: chain B residue  795 PHE
Chi-restraints excluded: chain B residue  813 VAL
Chi-restraints excluded: chain A residue   60 VAL
Chi-restraints excluded: chain A residue   63 LEU
Chi-restraints excluded: chain A residue   75 VAL
Chi-restraints excluded: chain A residue   98 ILE
Chi-restraints excluded: chain A residue  106 ILE
Chi-restraints excluded: chain A residue  124 THR
Chi-restraints excluded: chain A residue  167 ILE
Chi-restraints excluded: chain A residue  175 CYS
Chi-restraints excluded: chain A residue  185 CYS
Chi-restraints excluded: chain A residue  188 VAL
Chi-restraints excluded: chain A residue  244 TRP
Chi-restraints excluded: chain A residue  269 HIS
Chi-restraints excluded: chain A residue  277 CYS
Chi-restraints excluded: chain A residue  320 MET
Chi-restraints excluded: chain A residue  354 VAL
Chi-restraints excluded: chain A residue  369 SER
Chi-restraints excluded: chain A residue  427 VAL
Chi-restraints excluded: chain A residue  430 ILE
Chi-restraints excluded: chain A residue  448 ILE
Chi-restraints excluded: chain A residue  469 THR
Chi-restraints excluded: chain A residue  488 TYR
Chi-restraints excluded: chain A residue  517 SER
Chi-restraints excluded: chain A residue  540 HIS
Chi-restraints excluded: chain A residue  577 THR
Chi-restraints excluded: chain A residue  752 PHE
Chi-restraints excluded: chain A residue  763 THR
Chi-restraints excluded: chain A residue  796 VAL
Chi-restraints excluded: chain A residue  842 ILE
Chi-restraints excluded: chain C residue   10 LEU
Chi-restraints excluded: chain C residue   46 GLU
Chi-restraints excluded: chain D residue   10 LEU
Chi-restraints excluded: chain D residue   52 CYS
Chi-restraints excluded: chain D residue   58 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 168
   random chunks:
   chunk 79 optimal weight:    8.9990
   chunk 85 optimal weight:    0.9990
   chunk 108 optimal weight:    0.7980
   chunk 36 optimal weight:    3.9990
   chunk 107 optimal weight:    8.9990
   chunk 71 optimal weight:    2.9990
   chunk 123 optimal weight:    4.9990
   chunk 33 optimal weight:    2.9990
   chunk 92 optimal weight:    0.9990
   chunk 37 optimal weight:    1.9990
   chunk 90 optimal weight:    0.9980
   overall best weight:    1.1586

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

Flipped N/Q/H residues before XYZ refinement:
** B 481 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 564 HIS
** B 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 443 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 453 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 481 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 609 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3972 r_free = 0.3972 target = 0.100977 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3268 r_free = 0.3268 target = 0.066991 restraints weight = 45251.853|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3246 r_free = 0.3246 target = 0.066058 restraints weight = 36219.252|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3254 r_free = 0.3254 target = 0.066569 restraints weight = 30167.128|
|-----------------------------------------------------------------------------|
r_work (final): 0.3206
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8149
moved from start:          0.2635

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  13985  Z= 0.131
  Angle     :  0.656  12.727  18987  Z= 0.319
  Chirality :  0.046   0.205   2041
  Planarity :  0.004   0.051   2459
  Dihedral  :  4.922  36.981   1887
  Min Nonbonded Distance : 2.549

Molprobity Statistics.
  All-atom Clashscore : 13.38
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  8.53 %
    Favored  : 91.29 %
  Rotamer:
    Outliers :  4.82 %
    Allowed  : 29.92 %
    Favored  : 65.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.17 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.13 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.14 (0.20), residues: 1665
  helix: -0.53 (0.38), residues: 184
  sheet: -1.23 (0.30), residues: 326
  loop : -1.72 (0.18), residues: 1155

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP B 403 
 HIS   0.012   0.001   HIS B 564 
 PHE   0.020   0.001   PHE B 348 
 TYR   0.009   0.001   TYR B 418 
 ARG   0.003   0.000   ARG B 174 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03613 (  306)
  hydrogen bonds       : angle       5.95067 (  795)
  SS BOND              : bond        0.00294 (   32)
  SS BOND              : angle       1.18145 (   64)
  covalent geometry    : bond        0.00304 (13953)
  covalent geometry    : angle       0.65341 (18923)

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

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

  3330 Ramachandran restraints generated.
    1665 Oldfield, 0 Emsley, 1665 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3330 Ramachandran restraints generated.
    1665 Oldfield, 0 Emsley, 1665 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  163 residues out of total 1525 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 72
    poor density    : 91
  time to evaluate  : 1.685 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   32 LEU cc_start: 0.9025 (OUTLIER) cc_final: 0.8678 (pp)
REVERT: B   91 GLU cc_start: 0.7292 (mt-10) cc_final: 0.7045 (mt-10)
REVERT: B  272 GLU cc_start: 0.5811 (OUTLIER) cc_final: 0.4720 (mm-30)
REVERT: B  274 MET cc_start: 0.8456 (pmm) cc_final: 0.7739 (pmm)
REVERT: B  599 ILE cc_start: 0.9297 (OUTLIER) cc_final: 0.8942 (tp)
REVERT: B  628 LEU cc_start: 0.8797 (OUTLIER) cc_final: 0.8330 (mt)
REVERT: B  690 GLU cc_start: 0.8326 (OUTLIER) cc_final: 0.7769 (tp30)
REVERT: B  771 PHE cc_start: 0.8912 (OUTLIER) cc_final: 0.8519 (t80)
REVERT: A  180 ARG cc_start: 0.8565 (OUTLIER) cc_final: 0.8142 (ttm110)
REVERT: A  274 MET cc_start: 0.8304 (pmm) cc_final: 0.7751 (pmm)
REVERT: A  403 TRP cc_start: 0.8673 (OUTLIER) cc_final: 0.8383 (p90)
REVERT: A  752 PHE cc_start: 0.9508 (OUTLIER) cc_final: 0.9176 (t80)
REVERT: C   46 GLU cc_start: 0.8736 (OUTLIER) cc_final: 0.8342 (tm-30)
  outliers start: 72
  outliers final: 59
  residues processed: 157
  average time/residue: 0.2043
  time to fit residues: 51.7198
Evaluate side-chains
  156 residues out of total 1525 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 69
    poor density    : 87
  time to evaluate  : 1.472 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue    2 ILE
Chi-restraints excluded: chain B residue   32 LEU
Chi-restraints excluded: chain B residue   51 ILE
Chi-restraints excluded: chain B residue   60 VAL
Chi-restraints excluded: chain B residue   69 LEU
Chi-restraints excluded: chain B residue  106 ILE
Chi-restraints excluded: chain B residue  139 ILE
Chi-restraints excluded: chain B residue  167 ILE
Chi-restraints excluded: chain B residue  175 CYS
Chi-restraints excluded: chain B residue  185 CYS
Chi-restraints excluded: chain B residue  188 VAL
Chi-restraints excluded: chain B residue  209 CYS
Chi-restraints excluded: chain B residue  272 GLU
Chi-restraints excluded: chain B residue  273 CYS
Chi-restraints excluded: chain B residue  309 THR
Chi-restraints excluded: chain B residue  354 VAL
Chi-restraints excluded: chain B residue  422 ASN
Chi-restraints excluded: chain B residue  426 CYS
Chi-restraints excluded: chain B residue  427 VAL
Chi-restraints excluded: chain B residue  430 ILE
Chi-restraints excluded: chain B residue  444 SER
Chi-restraints excluded: chain B residue  448 ILE
Chi-restraints excluded: chain B residue  469 THR
Chi-restraints excluded: chain B residue  488 TYR
Chi-restraints excluded: chain B residue  540 HIS
Chi-restraints excluded: chain B residue  577 THR
Chi-restraints excluded: chain B residue  599 ILE
Chi-restraints excluded: chain B residue  628 LEU
Chi-restraints excluded: chain B residue  690 GLU
Chi-restraints excluded: chain B residue  771 PHE
Chi-restraints excluded: chain B residue  788 LEU
Chi-restraints excluded: chain B residue  795 PHE
Chi-restraints excluded: chain B residue  813 VAL
Chi-restraints excluded: chain A residue   60 VAL
Chi-restraints excluded: chain A residue   63 LEU
Chi-restraints excluded: chain A residue   75 VAL
Chi-restraints excluded: chain A residue   98 ILE
Chi-restraints excluded: chain A residue  106 ILE
Chi-restraints excluded: chain A residue  124 THR
Chi-restraints excluded: chain A residue  167 ILE
Chi-restraints excluded: chain A residue  175 CYS
Chi-restraints excluded: chain A residue  180 ARG
Chi-restraints excluded: chain A residue  185 CYS
Chi-restraints excluded: chain A residue  188 VAL
Chi-restraints excluded: chain A residue  244 TRP
Chi-restraints excluded: chain A residue  269 HIS
Chi-restraints excluded: chain A residue  277 CYS
Chi-restraints excluded: chain A residue  320 MET
Chi-restraints excluded: chain A residue  354 VAL
Chi-restraints excluded: chain A residue  369 SER
Chi-restraints excluded: chain A residue  403 TRP
Chi-restraints excluded: chain A residue  427 VAL
Chi-restraints excluded: chain A residue  430 ILE
Chi-restraints excluded: chain A residue  448 ILE
Chi-restraints excluded: chain A residue  469 THR
Chi-restraints excluded: chain A residue  488 TYR
Chi-restraints excluded: chain A residue  517 SER
Chi-restraints excluded: chain A residue  540 HIS
Chi-restraints excluded: chain A residue  577 THR
Chi-restraints excluded: chain A residue  752 PHE
Chi-restraints excluded: chain A residue  763 THR
Chi-restraints excluded: chain A residue  796 VAL
Chi-restraints excluded: chain A residue  842 ILE
Chi-restraints excluded: chain C residue   10 LEU
Chi-restraints excluded: chain C residue   43 ILE
Chi-restraints excluded: chain C residue   46 GLU
Chi-restraints excluded: chain D residue   10 LEU
Chi-restraints excluded: chain D residue   52 CYS
Chi-restraints excluded: chain D residue   58 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 168
   random chunks:
   chunk 31 optimal weight:    4.9990
   chunk 39 optimal weight:    4.9990
   chunk 92 optimal weight:    0.0020
   chunk 131 optimal weight:    6.9990
   chunk 64 optimal weight:    9.9990
   chunk 95 optimal weight:    0.7980
   chunk 166 optimal weight:    7.9990
   chunk 62 optimal weight:    3.9990
   chunk 71 optimal weight:    3.9990
   chunk 114 optimal weight:    0.0870
   chunk 30 optimal weight:    3.9990
   overall best weight:    1.7770

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

Flipped N/Q/H residues before XYZ refinement:
** B 481 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 443 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 453 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 481 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 609 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3952 r_free = 0.3952 target = 0.099821 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3250 r_free = 0.3250 target = 0.066159 restraints weight = 45537.897|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3209 r_free = 0.3209 target = 0.064782 restraints weight = 37079.190|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3215 r_free = 0.3215 target = 0.065208 restraints weight = 33221.535|
|-----------------------------------------------------------------------------|
r_work (final): 0.3164
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8198
moved from start:          0.2628

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042  13985  Z= 0.167
  Angle     :  0.674  12.412  18987  Z= 0.331
  Chirality :  0.046   0.202   2041
  Planarity :  0.004   0.050   2459
  Dihedral  :  5.018  37.524   1887
  Min Nonbonded Distance : 2.540

Molprobity Statistics.
  All-atom Clashscore : 14.69
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  9.07 %
    Favored  : 90.75 %
  Rotamer:
    Outliers :  5.09 %
    Allowed  : 29.92 %
    Favored  : 64.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.17 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.13 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.15 (0.20), residues: 1665
  helix: -0.56 (0.38), residues: 184
  sheet: -1.24 (0.30), residues: 326
  loop : -1.73 (0.18), residues: 1155

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP B 403 
 HIS   0.004   0.001   HIS B 269 
 PHE   0.020   0.001   PHE B 348 
 TYR   0.011   0.001   TYR B 392 
 ARG   0.004   0.000   ARG B 756 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03705 (  306)
  hydrogen bonds       : angle       6.03852 (  795)
  SS BOND              : bond        0.00318 (   32)
  SS BOND              : angle       1.25565 (   64)
  covalent geometry    : bond        0.00387 (13953)
  covalent geometry    : angle       0.67153 (18923)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4228.58 seconds
wall clock time: 74 minutes 14.96 seconds (4454.96 seconds total)