Starting phenix.real_space_refine
on Thu Jun 12 02:55:58 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7xoh_33348/06_2025/7xoh_33348_trim.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7xoh_33348/06_2025/7xoh_33348.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.6
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7xoh_33348/06_2025/7xoh_33348.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7xoh_33348/06_2025/7xoh_33348.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7xoh_33348/06_2025/7xoh_33348_trim.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7xoh_33348/06_2025/7xoh_33348_trim.cif"
  }
  resolution = 3.6
  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=   0.011
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P       4      5.49       5
     S      60      5.16       5
     C    8484      2.51       5
     N    2336      2.21       5
     O    2640      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 2 residue(s): 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib"
  Total number of atoms: 13524
  Number of models: 1
  Model: ""
    Number of chains: 8
    Chain: "B"
      Number of atoms: 3366
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 458, 3366
          Classifications: {'peptide': 458}
          Link IDs: {'PTRANS': 29, 'TRANS': 428}
    Chain: "A"
      Number of atoms: 3366
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 458, 3366
          Classifications: {'peptide': 458}
          Link IDs: {'PTRANS': 29, 'TRANS': 428}
    Chain: "C"
      Number of atoms: 3366
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 458, 3366
          Classifications: {'peptide': 458}
          Link IDs: {'PTRANS': 29, 'TRANS': 428}
    Chain: "D"
      Number of atoms: 3366
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 458, 3366
          Classifications: {'peptide': 458}
          Link IDs: {'PTRANS': 29, 'TRANS': 428}
    Chain: "B"
      Number of atoms: 15
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 15
          Unusual residues: {'PLP': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 1
          Unresolved non-hydrogen dihedrals: 1
    Chain: "A"
      Number of atoms: 15
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 15
          Unusual residues: {'PLP': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 1
          Unresolved non-hydrogen dihedrals: 1
    Chain: "C"
      Number of atoms: 15
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 15
          Unusual residues: {'PLP': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 1
          Unresolved non-hydrogen dihedrals: 1
    Chain: "D"
      Number of atoms: 15
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 15
          Unusual residues: {'PLP': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 1
          Unresolved non-hydrogen dihedrals: 1
  Time building chain proxies: 7.88, per 1000 atoms: 0.58
  Number of scatterers: 13524
  At special positions: 0
  Unit cell: (84.53, 146.59, 84.53, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      60     16.00
     P       4     15.00
     O    2640      8.00
     N    2336      7.00
     C    8484      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=4, symmetry=0
  Number of additional bonds: simple=4, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 3.24
  Conformation dependent library (CDL) restraints added in 1.7 seconds
  

  3648 Ramachandran restraints generated.
    1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3208

  Finding SS restraints...
    Secondary structure from input PDB file:
      66 helices and 20 sheets defined
      37.4% alpha, 10.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.42
  Creating SS restraints...
    Processing helix  chain 'B' and resid 6 through 10
    Processing helix  chain 'B' and resid 45 through 58
    Processing helix  chain 'B' and resid 73 through 87
      removed outlier: 3.869A  pdb=" N   VAL B  77 " --> pdb=" O   GLY B  73 " (cutoff:3.500A)
      removed outlier: 3.751A  pdb=" N   GLY B  78 " --> pdb=" O   ASN B  74 " (cutoff:3.500A)
      removed outlier: 4.127A  pdb=" N   ARG B  86 " --> pdb=" O   VAL B  82 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 99 through 109
      removed outlier: 3.929A  pdb=" N   ARG B 103 " --> pdb=" O   SER B  99 " (cutoff:3.500A)
      removed outlier: 3.506A  pdb=" N   TYR B 109 " --> pdb=" O   VAL B 105 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 127 through 139
      removed outlier: 3.506A  pdb=" N   VAL B 131 " --> pdb=" O   SER B 127 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 151 through 160
    Processing helix  chain 'B' and resid 161 through 168
      removed outlier: 3.768A  pdb=" N   ILE B 165 " --> pdb=" O   THR B 161 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 187 through 196
      removed outlier: 3.512A  pdb=" N   ARG B 191 " --> pdb=" O   THR B 187 " (cutoff:3.500A)
      removed outlier: 3.545A  pdb=" N   TYR B 192 " --> pdb=" O   GLY B 188 " (cutoff:3.500A)
      removed outlier: 3.631A  pdb=" N   LEU B 193 " --> pdb=" O   ALA B 189 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 247 through 262
      removed outlier: 3.519A  pdb=" N   SER B 251 " --> pdb=" O   SER B 247 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 267 through 281
      removed outlier: 3.924A  pdb=" N   GLY B 271 " --> pdb=" O   GLY B 267 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 299 through 304
      removed outlier: 3.655A  pdb=" N   MET B 302 " --> pdb=" O   ARG B 299 " (cutoff:3.500A)
      removed outlier: 4.342A  pdb=" N   SER B 303 " --> pdb=" O   GLY B 300 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 329 through 334
    Processing helix  chain 'B' and resid 352 through 363
    Processing helix  chain 'B' and resid 390 through 395
    Processing helix  chain 'B' and resid 405 through 409
    Processing helix  chain 'B' and resid 422 through 431
    Processing helix  chain 'B' and resid 450 through 458
    Processing helix  chain 'A' and resid 6 through 10
      removed outlier: 3.753A  pdb=" N   LEU A  10 " --> pdb=" O   ILE A   7 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 44 through 58
    Processing helix  chain 'A' and resid 74 through 87
      removed outlier: 4.127A  pdb=" N   GLY A  78 " --> pdb=" O   ASN A  74 " (cutoff:3.500A)
      removed outlier: 4.158A  pdb=" N   ARG A  86 " --> pdb=" O   VAL A  82 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 99 through 109
      removed outlier: 3.653A  pdb=" N   ARG A 103 " --> pdb=" O   SER A  99 " (cutoff:3.500A)
      removed outlier: 3.557A  pdb=" N   TYR A 109 " --> pdb=" O   VAL A 105 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 127 through 139
      removed outlier: 3.580A  pdb=" N   VAL A 131 " --> pdb=" O   SER A 127 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 151 through 160
    Processing helix  chain 'A' and resid 161 through 170
      removed outlier: 3.680A  pdb=" N   THR A 169 " --> pdb=" O   ILE A 165 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 183 through 196
      removed outlier: 3.792A  pdb=" N   GLY A 188 " --> pdb=" O   GLY A 184 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 247 through 262
    Processing helix  chain 'A' and resid 267 through 281
      removed outlier: 3.827A  pdb=" N   GLY A 271 " --> pdb=" O   GLY A 267 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 309 through 314
      removed outlier: 3.883A  pdb=" N   TYR A 314 " --> pdb=" O   TRP A 310 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 329 through 334
    Processing helix  chain 'A' and resid 352 through 364
    Processing helix  chain 'A' and resid 392 through 397
      removed outlier: 3.874A  pdb=" N   PHE A 396 " --> pdb=" O   LEU A 392 " (cutoff:3.500A)
      removed outlier: 3.804A  pdb=" N   GLU A 397 " --> pdb=" O   SER A 393 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 392 through 397'
    Processing helix  chain 'A' and resid 405 through 409
    Processing helix  chain 'A' and resid 422 through 431
      removed outlier: 3.695A  pdb=" N   ALA A 426 " --> pdb=" O   LEU A 422 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 450 through 458
    Processing helix  chain 'C' and resid 6 through 10
    Processing helix  chain 'C' and resid 44 through 58
      removed outlier: 3.697A  pdb=" N   LYS C  50 " --> pdb=" O   ARG C  46 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 73 through 87
      removed outlier: 3.855A  pdb=" N   VAL C  77 " --> pdb=" O   GLY C  73 " (cutoff:3.500A)
      removed outlier: 3.676A  pdb=" N   GLY C  78 " --> pdb=" O   ASN C  74 " (cutoff:3.500A)
      removed outlier: 4.128A  pdb=" N   ARG C  86 " --> pdb=" O   VAL C  82 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 99 through 109
      removed outlier: 3.893A  pdb=" N   ARG C 103 " --> pdb=" O   SER C  99 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 127 through 139
      removed outlier: 3.506A  pdb=" N   VAL C 131 " --> pdb=" O   SER C 127 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 151 through 160
    Processing helix  chain 'C' and resid 161 through 168
      removed outlier: 3.646A  pdb=" N   ILE C 165 " --> pdb=" O   THR C 161 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 184 through 196
    Processing helix  chain 'C' and resid 247 through 262
      removed outlier: 3.561A  pdb=" N   SER C 251 " --> pdb=" O   SER C 247 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 267 through 281
      removed outlier: 3.902A  pdb=" N   GLY C 271 " --> pdb=" O   GLY C 267 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 299 through 303
      removed outlier: 3.671A  pdb=" N   MET C 302 " --> pdb=" O   ARG C 299 " (cutoff:3.500A)
      removed outlier: 4.340A  pdb=" N   SER C 303 " --> pdb=" O   GLY C 300 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 299 through 303'
    Processing helix  chain 'C' and resid 329 through 334
    Processing helix  chain 'C' and resid 352 through 362
    Processing helix  chain 'C' and resid 390 through 395
    Processing helix  chain 'C' and resid 405 through 409
    Processing helix  chain 'C' and resid 422 through 430
    Processing helix  chain 'C' and resid 450 through 458
      removed outlier: 3.511A  pdb=" N   GLY C 455 " --> pdb=" O   TYR C 451 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 6 through 10
      removed outlier: 3.749A  pdb=" N   LEU D  10 " --> pdb=" O   ILE D   7 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 44 through 58
      removed outlier: 3.802A  pdb=" N   LYS D  50 " --> pdb=" O   ARG D  46 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 74 through 87
      removed outlier: 4.422A  pdb=" N   GLY D  78 " --> pdb=" O   ASN D  74 " (cutoff:3.500A)
      removed outlier: 4.141A  pdb=" N   ARG D  86 " --> pdb=" O   VAL D  82 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 99 through 109
      removed outlier: 3.647A  pdb=" N   ARG D 103 " --> pdb=" O   SER D  99 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 127 through 139
      removed outlier: 3.577A  pdb=" N   VAL D 131 " --> pdb=" O   SER D 127 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 151 through 160
    Processing helix  chain 'D' and resid 161 through 170
      removed outlier: 3.704A  pdb=" N   THR D 169 " --> pdb=" O   ILE D 165 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 184 through 196
    Processing helix  chain 'D' and resid 247 through 262
    Processing helix  chain 'D' and resid 267 through 281
      removed outlier: 3.756A  pdb=" N   GLY D 271 " --> pdb=" O   GLY D 267 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 329 through 334
    Processing helix  chain 'D' and resid 352 through 364
      removed outlier: 3.685A  pdb=" N   TYR D 363 " --> pdb=" O   ILE D 359 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 405 through 409
    Processing helix  chain 'D' and resid 422 through 430
      removed outlier: 3.918A  pdb=" N   ALA D 426 " --> pdb=" O   LEU D 422 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 450 through 458
      removed outlier: 3.591A  pdb=" N   GLY D 455 " --> pdb=" O   TYR D 451 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'B' and resid 16 through 19
      removed outlier: 4.778A  pdb=" N   VAL B  30 " --> pdb=" O   LEU B  19 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 112 through 116
      removed outlier: 6.536A  pdb=" N   CYS B  90 " --> pdb=" O   GLU B 112 " (cutoff:3.500A)
      removed outlier: 7.657A  pdb=" N   VAL B 114 " --> pdb=" O   CYS B  90 " (cutoff:3.500A)
      removed outlier: 6.416A  pdb=" N   PHE B  92 " --> pdb=" O   VAL B 114 " (cutoff:3.500A)
      removed outlier: 7.708A  pdb=" N   CYS B 116 " --> pdb=" O   PHE B  92 " (cutoff:3.500A)
      removed outlier: 6.288A  pdb=" N   CYS B  94 " --> pdb=" O   CYS B 116 " (cutoff:3.500A)
      removed outlier: 6.725A  pdb=" N   ILE B  67 " --> pdb=" O   VAL B  91 " (cutoff:3.500A)
      removed outlier: 7.843A  pdb=" N   VAL B  93 " --> pdb=" O   ILE B  67 " (cutoff:3.500A)
      removed outlier: 6.744A  pdb=" N   GLU B  69 " --> pdb=" O   VAL B  93 " (cutoff:3.500A)
      removed outlier: 3.691A  pdb=" N   TRP B 143 " --> pdb=" O   THR B  66 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 204 through 205
    Processing sheet with id=AA4, first strand: chain 'B' and resid 367 through 370
      removed outlier: 3.506A  pdb=" N   GLY B 384 " --> pdb=" O   VAL B 370 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 416 through 418
      removed outlier: 6.318A  pdb=" N   ILE B 417 " --> pdb=" O   VAL B 439 " (cutoff:3.500A)
      removed outlier: 3.941A  pdb=" N   GLY B 446 " --> pdb=" O   VAL B 438 " (cutoff:3.500A)
      removed outlier: 5.896A  pdb=" N   GLU B 440 " --> pdb=" O   PRO B 444 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 16 through 18
    Processing sheet with id=AA7, first strand: chain 'A' and resid 111 through 116
      removed outlier: 3.531A  pdb=" N   VAL A 114 " --> pdb=" O   PHE A  92 " (cutoff:3.500A)
      removed outlier: 6.000A  pdb=" N   ILE A  67 " --> pdb=" O   VAL A  91 " (cutoff:3.500A)
      removed outlier: 7.821A  pdb=" N   VAL A  93 " --> pdb=" O   ILE A  67 " (cutoff:3.500A)
      removed outlier: 6.748A  pdb=" N   GLU A  69 " --> pdb=" O   VAL A  93 " (cutoff:3.500A)
      removed outlier: 3.579A  pdb=" N   TRP A 143 " --> pdb=" O   THR A  66 " (cutoff:3.500A)
      removed outlier: 3.604A  pdb=" N   VAL A  68 " --> pdb=" O   TRP A 143 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 178 through 179
      removed outlier: 6.580A  pdb=" N   ALA A 178 " --> pdb=" O   ALA A 206 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'A' and resid 367 through 370
      removed outlier: 3.619A  pdb=" N   GLY A 384 " --> pdb=" O   VAL A 370 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'A' and resid 416 through 418
      removed outlier: 4.134A  pdb=" N   GLY A 446 " --> pdb=" O   VAL A 438 " (cutoff:3.500A)
      removed outlier: 5.866A  pdb=" N   GLU A 440 " --> pdb=" O   PRO A 444 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'C' and resid 17 through 19
      removed outlier: 4.806A  pdb=" N   VAL C  30 " --> pdb=" O   LEU C  19 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'C' and resid 112 through 116
      removed outlier: 6.537A  pdb=" N   CYS C  90 " --> pdb=" O   GLU C 112 " (cutoff:3.500A)
      removed outlier: 7.661A  pdb=" N   VAL C 114 " --> pdb=" O   CYS C  90 " (cutoff:3.500A)
      removed outlier: 6.422A  pdb=" N   PHE C  92 " --> pdb=" O   VAL C 114 " (cutoff:3.500A)
      removed outlier: 7.697A  pdb=" N   CYS C 116 " --> pdb=" O   PHE C  92 " (cutoff:3.500A)
      removed outlier: 6.270A  pdb=" N   CYS C  94 " --> pdb=" O   CYS C 116 " (cutoff:3.500A)
      removed outlier: 6.746A  pdb=" N   ILE C  67 " --> pdb=" O   VAL C  91 " (cutoff:3.500A)
      removed outlier: 7.860A  pdb=" N   VAL C  93 " --> pdb=" O   ILE C  67 " (cutoff:3.500A)
      removed outlier: 6.757A  pdb=" N   GLU C  69 " --> pdb=" O   VAL C  93 " (cutoff:3.500A)
      removed outlier: 3.716A  pdb=" N   TRP C 143 " --> pdb=" O   THR C  66 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'C' and resid 175 through 177
      removed outlier: 3.679A  pdb=" N   PHE C 176 " --> pdb=" O   ARG C 202 " (cutoff:3.500A)
      removed outlier: 3.871A  pdb=" N   GLU C 242 " --> pdb=" O   ILE C 203 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'C' and resid 367 through 368
    Processing sheet with id=AB6, first strand: chain 'C' and resid 416 through 418
      removed outlier: 6.363A  pdb=" N   ILE C 417 " --> pdb=" O   VAL C 439 " (cutoff:3.500A)
      removed outlier: 4.015A  pdb=" N   GLY C 446 " --> pdb=" O   VAL C 438 " (cutoff:3.500A)
      removed outlier: 5.980A  pdb=" N   GLU C 440 " --> pdb=" O   PRO C 444 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'D' and resid 16 through 18
    Processing sheet with id=AB8, first strand: chain 'D' and resid 111 through 116
      removed outlier: 3.535A  pdb=" N   VAL D 114 " --> pdb=" O   PHE D  92 " (cutoff:3.500A)
      removed outlier: 5.994A  pdb=" N   ILE D  67 " --> pdb=" O   VAL D  91 " (cutoff:3.500A)
      removed outlier: 7.804A  pdb=" N   VAL D  93 " --> pdb=" O   ILE D  67 " (cutoff:3.500A)
      removed outlier: 6.721A  pdb=" N   GLU D  69 " --> pdb=" O   VAL D  93 " (cutoff:3.500A)
      removed outlier: 3.593A  pdb=" N   TRP D 143 " --> pdb=" O   THR D  66 " (cutoff:3.500A)
      removed outlier: 3.621A  pdb=" N   VAL D  68 " --> pdb=" O   TRP D 143 " (cutoff:3.500A)
    Processing sheet with id=AB9, first strand: chain 'D' and resid 178 through 179
      removed outlier: 3.705A  pdb=" N   ALA D 178 " --> pdb=" O   VAL D 204 " (cutoff:3.500A)
    Processing sheet with id=AC1, first strand: chain 'D' and resid 367 through 370
      removed outlier: 3.521A  pdb=" N   GLY D 384 " --> pdb=" O   VAL D 370 " (cutoff:3.500A)
    Processing sheet with id=AC2, first strand: chain 'D' and resid 416 through 418
      removed outlier: 4.146A  pdb=" N   GLY D 446 " --> pdb=" O   VAL D 438 " (cutoff:3.500A)
      removed outlier: 5.881A  pdb=" N   GLU D 440 " --> pdb=" O   PRO D 444 " (cutoff:3.500A)

    454 hydrogen bonds defined for protein.
    1311 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: 3.57

  Time building geometry restraints manager: 3.79 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 4589
        1.34 -     1.46: 2670
        1.46 -     1.58: 6429
        1.58 -     1.69: 4
        1.69 -     1.81: 104
  Bond restraints: 13796
  Sorted by residual:
  bond pdb=" CA  GLY A 297 "
       pdb=" C   GLY A 297 "
    ideal  model  delta    sigma   weight residual
    1.520  1.486  0.034 7.30e-03 1.88e+04 2.23e+01
  bond pdb=" N   ILE A 180 "
       pdb=" CA  ILE A 180 "
    ideal  model  delta    sigma   weight residual
    1.457  1.492 -0.036 1.15e-02 7.56e+03 9.63e+00
  bond pdb=" N   ILE C  47 "
       pdb=" CA  ILE C  47 "
    ideal  model  delta    sigma   weight residual
    1.460  1.495 -0.036 1.21e-02 6.83e+03 8.69e+00
  bond pdb=" N   ASP C  45 "
       pdb=" CA  ASP C  45 "
    ideal  model  delta    sigma   weight residual
    1.459  1.492 -0.033 1.23e-02 6.61e+03 7.04e+00
  bond pdb=" N   THR C 182 "
       pdb=" CA  THR C 182 "
    ideal  model  delta    sigma   weight residual
    1.456  1.490 -0.034 1.32e-02 5.74e+03 6.72e+00
  ... (remaining 13791 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.40: 18131
        1.40 -     2.80: 509
        2.80 -     4.21: 111
        4.21 -     5.61: 15
        5.61 -     7.01: 2
  Bond angle restraints: 18768
  Sorted by residual:
  angle pdb=" N   SER D 313 "
        pdb=" CA  SER D 313 "
        pdb=" C   SER D 313 "
      ideal   model   delta    sigma   weight residual
     112.54  105.53    7.01 1.22e+00 6.72e-01 3.30e+01
  angle pdb=" N   GLY C 183 "
        pdb=" CA  GLY C 183 "
        pdb=" C   GLY C 183 "
      ideal   model   delta    sigma   weight residual
     114.46  108.38    6.08 1.81e+00 3.05e-01 1.13e+01
  angle pdb=" C   LYS C  44 "
        pdb=" N   ASP C  45 "
        pdb=" CA  ASP C  45 "
      ideal   model   delta    sigma   weight residual
     120.38  116.06    4.32 1.37e+00 5.33e-01 9.94e+00
  angle pdb=" N   SER C  43 "
        pdb=" CA  SER C  43 "
        pdb=" C   SER C  43 "
      ideal   model   delta    sigma   weight residual
     113.23  109.44    3.79 1.24e+00 6.50e-01 9.34e+00
  angle pdb=" C   GLN B 367 "
        pdb=" N   MET B 368 "
        pdb=" CA  MET B 368 "
      ideal   model   delta    sigma   weight residual
     122.08  116.81    5.27 1.83e+00 2.99e-01 8.28e+00
  ... (remaining 18763 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    22.33: 7832
       22.33 -    44.65: 324
       44.65 -    66.98: 51
       66.98 -    89.30: 11
       89.30 -   111.63: 2
  Dihedral angle restraints: 8220
    sinusoidal: 3124
      harmonic: 5096
  Sorted by residual:
  dihedral pdb=" C5A PLP D 501 "
           pdb=" O4P PLP D 501 "
           pdb=" P   PLP D 501 "
           pdb=" O1P PLP D 501 "
      ideal   model   delta sinusoidal    sigma   weight residual
      76.43 -171.94 -111.63     1      2.00e+01 2.50e-03 3.28e+01
  dihedral pdb=" C5A PLP C 501 "
           pdb=" O4P PLP C 501 "
           pdb=" P   PLP C 501 "
           pdb=" O1P PLP C 501 "
      ideal   model   delta sinusoidal    sigma   weight residual
      76.43  177.79 -101.36     1      2.00e+01 2.50e-03 2.87e+01
  dihedral pdb=" C5  PLP B 501 "
           pdb=" C5A PLP B 501 "
           pdb=" O4P PLP B 501 "
           pdb=" P   PLP B 501 "
      ideal   model   delta sinusoidal    sigma   weight residual
     188.31  117.64   70.66     1      2.00e+01 2.50e-03 1.61e+01
  ... (remaining 8217 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.035: 1325
       0.035 -    0.070: 524
       0.070 -    0.105: 205
       0.105 -    0.140: 48
       0.140 -    0.175: 2
  Chirality restraints: 2104
  Sorted by residual:
  chirality pdb=" CA  ILE A 180 "
            pdb=" N   ILE A 180 "
            pdb=" C   ILE A 180 "
            pdb=" CB  ILE A 180 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.61   -0.18 2.00e-01 2.50e+01 7.69e-01
  chirality pdb=" CA  VAL C  49 "
            pdb=" N   VAL C  49 "
            pdb=" C   VAL C  49 "
            pdb=" CB  VAL C  49 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.60   -0.16 2.00e-01 2.50e+01 6.33e-01
  chirality pdb=" CA  ILE C  47 "
            pdb=" N   ILE C  47 "
            pdb=" C   ILE C  47 "
            pdb=" CB  ILE C  47 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 4.67e-01
  ... (remaining 2101 not shown)

  Planarity restraints: 2472
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE C 180 "   -0.013 2.00e-02 2.50e+03   2.59e-02 6.70e+00
        pdb=" C   ILE C 180 "    0.045 2.00e-02 2.50e+03
        pdb=" O   ILE C 180 "   -0.017 2.00e-02 2.50e+03
        pdb=" N   GLY C 181 "   -0.015 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU B 294 "   -0.027 5.00e-02 4.00e+02   4.01e-02 2.57e+00
        pdb=" N   PRO B 295 "    0.069 5.00e-02 4.00e+02
        pdb=" CA  PRO B 295 "   -0.021 5.00e-02 4.00e+02
        pdb=" CD  PRO B 295 "   -0.022 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  SER C 313 "   -0.008 2.00e-02 2.50e+03   1.58e-02 2.51e+00
        pdb=" C   SER C 313 "    0.027 2.00e-02 2.50e+03
        pdb=" O   SER C 313 "   -0.010 2.00e-02 2.50e+03
        pdb=" N   TYR C 314 "   -0.009 2.00e-02 2.50e+03
  ... (remaining 2469 not shown)

  Histogram of nonbonded interaction distances:
        2.01 -     2.58: 143
        2.58 -     3.16: 12621
        3.16 -     3.74: 19431
        3.74 -     4.32: 28236
        4.32 -     4.90: 46895
  Nonbonded interactions: 107326
  Sorted by model distance:
  nonbonded pdb=" OH  TYR D 158 "
            pdb=" OE1 GLU D 195 "
     model   vdw
     2.005 3.040
  nonbonded pdb=" O   LEU D 193 "
            pdb=" OG  SER D 197 "
     model   vdw
     2.013 3.040
  nonbonded pdb=" OG1 THR D  14 "
            pdb=" O   VAL D  34 "
     model   vdw
     2.068 3.040
  nonbonded pdb=" OH  TYR A 158 "
            pdb=" OE1 GLU A 195 "
     model   vdw
     2.081 3.040
  nonbonded pdb=" O   LEU A 193 "
            pdb=" OG  SER A 197 "
     model   vdw
     2.096 3.040
  ... (remaining 107321 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: 0.03
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = 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:             0.570
  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:          0.500
  Check model and map are aligned:         0.090
  Set scattering table:                    0.100
  Process input model:                     30.280
  Find NCS groups from input model:        0.470
  Set up NCS constraints:                  0.060
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.660
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   34.740
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8043
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.265  13800  Z= 0.296
  Angle     :  0.581   7.009  18768  Z= 0.319
  Chirality :  0.044   0.175   2104
  Planarity :  0.004   0.040   2472
  Dihedral  : 12.554 111.630   5012
  Min Nonbonded Distance : 2.005

Molprobity Statistics.
  All-atom Clashscore : 32.89
  Ramachandran Plot:
    Outliers :  0.05 %
    Allowed  : 10.64 %
    Favored  : 89.31 %
  Rotamer:
    Outliers :  4.34 %
    Allowed  :  3.06 %
    Favored  : 92.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.16 (0.18), residues: 1824
  helix: -1.69 (0.19), residues: 648
  sheet: -4.45 (0.25), residues: 200
  loop : -3.22 (0.18), residues: 976

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 310 
 HIS   0.002   0.001   HIS A 409 
 PHE   0.007   0.001   PHE D 230 
 TYR   0.015   0.001   TYR D  36 
 ARG   0.003   0.000   ARG A  86 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.17269 (  454)
  hydrogen bonds       : angle       6.94894 ( 1311)
  covalent geometry    : bond        0.00366 (13796)
  covalent geometry    : angle       0.58097 (18768)
  Misc. bond           : bond        0.13428 (    4)

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

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

  3648 Ramachandran restraints generated.
    1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3648 Ramachandran restraints generated.
    1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  342 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 61
    poor density    : 281
  time to evaluate  : 1.354 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   60 GLN cc_start: 0.7381 (tt0) cc_final: 0.7157 (tt0)
REVERT: B  172 LYS cc_start: 0.7080 (ttpt) cc_final: 0.6662 (tptt)
REVERT: B  200 ARG cc_start: 0.7771 (mtp-110) cc_final: 0.7227 (ptm160)
REVERT: B  287 ASP cc_start: 0.7236 (t0) cc_final: 0.6862 (t0)
REVERT: B  401 LYS cc_start: 0.8474 (mttp) cc_final: 0.8211 (mtpt)
REVERT: A  260 ARG cc_start: 0.8162 (tpt-90) cc_final: 0.7484 (ttm110)
REVERT: A  363 TYR cc_start: 0.8061 (m-80) cc_final: 0.7700 (m-80)
REVERT: C   58 SER cc_start: 0.8274 (m) cc_final: 0.7957 (p)
REVERT: C   60 GLN cc_start: 0.7385 (tt0) cc_final: 0.7172 (tt0)
REVERT: C  200 ARG cc_start: 0.7823 (mtp-110) cc_final: 0.7233 (ptm160)
REVERT: C  287 ASP cc_start: 0.7246 (t0) cc_final: 0.6846 (t0)
REVERT: D  260 ARG cc_start: 0.8144 (tpt-90) cc_final: 0.7454 (ttm110)
REVERT: D  362 GLU cc_start: 0.8026 (tt0) cc_final: 0.7693 (tt0)
REVERT: D  431 ARG cc_start: 0.8496 (ttt-90) cc_final: 0.7751 (tmt-80)
  outliers start: 61
  outliers final: 23
  residues processed: 325
  average time/residue: 0.2713
  time to fit residues: 123.8361
Evaluate side-chains
  213 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 190
  time to evaluate  : 1.323 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   16 LEU
Chi-restraints excluded: chain B residue  177 VAL
Chi-restraints excluded: chain B residue  180 ILE
Chi-restraints excluded: chain B residue  182 THR
Chi-restraints excluded: chain B residue  265 LEU
Chi-restraints excluded: chain B residue  371 VAL
Chi-restraints excluded: chain B residue  436 LEU
Chi-restraints excluded: chain A residue   23 VAL
Chi-restraints excluded: chain A residue   44 LYS
Chi-restraints excluded: chain A residue  177 VAL
Chi-restraints excluded: chain A residue  278 LEU
Chi-restraints excluded: chain A residue  436 LEU
Chi-restraints excluded: chain C residue   16 LEU
Chi-restraints excluded: chain C residue   43 SER
Chi-restraints excluded: chain C residue   45 ASP
Chi-restraints excluded: chain C residue  165 ILE
Chi-restraints excluded: chain C residue  177 VAL
Chi-restraints excluded: chain C residue  265 LEU
Chi-restraints excluded: chain C residue  436 LEU
Chi-restraints excluded: chain D residue   23 VAL
Chi-restraints excluded: chain D residue  177 VAL
Chi-restraints excluded: chain D residue  278 LEU
Chi-restraints excluded: chain D residue  436 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 180
   random chunks:
   chunk 151 optimal weight:    1.9990
   chunk 136 optimal weight:    0.6980
   chunk 75 optimal weight:    4.9990
   chunk 46 optimal weight:    2.9990
   chunk 92 optimal weight:    4.9990
   chunk 72 optimal weight:    1.9990
   chunk 141 optimal weight:    0.9980
   chunk 54 optimal weight:    0.8980
   chunk 85 optimal weight:    1.9990
   chunk 105 optimal weight:    5.9990
   chunk 163 optimal weight:    1.9990
   overall best weight:    1.3184

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

Flipped N/Q/H residues before XYZ refinement:
** B   6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B  20 ASN
** A   6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A  84 GLN
C   5 GLN
C   6 HIS
C  20 ASN
** D   6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3414 r_free = 0.3414 target = 0.133955 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3131 r_free = 0.3131 target = 0.110777 restraints weight = 16950.734|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3164 r_free = 0.3164 target = 0.113353 restraints weight = 11462.231|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3187 r_free = 0.3187 target = 0.115122 restraints weight = 8836.849|
|-----------------------------------------------------------------------------|
r_work (final): 0.3188
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8087
moved from start:          0.2085

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.049  13800  Z= 0.157
  Angle     :  0.668   6.980  18768  Z= 0.337
  Chirality :  0.048   0.374   2104
  Planarity :  0.005   0.041   2472
  Dihedral  :  7.237  72.405   2043
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 9.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.50 %
    Favored  : 91.50 %
  Rotamer:
    Outliers :  2.42 %
    Allowed  :  9.76 %
    Favored  : 87.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.31 (0.18), residues: 1824
  helix: -1.24 (0.20), residues: 684
  sheet: -3.55 (0.29), residues: 200
  loop : -2.64 (0.19), residues: 940

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 310 
 HIS   0.007   0.002   HIS C 348 
 PHE   0.013   0.001   PHE B 230 
 TYR   0.018   0.002   TYR A  36 
 ARG   0.004   0.000   ARG C 260 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04046 (  454)
  hydrogen bonds       : angle       4.99300 ( 1311)
  covalent geometry    : bond        0.00385 (13796)
  covalent geometry    : angle       0.66824 (18768)
  Misc. bond           : bond        0.00052 (    4)

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

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

  3648 Ramachandran restraints generated.
    1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3648 Ramachandran restraints generated.
    1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  244 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 210
  time to evaluate  : 1.503 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  182 THR cc_start: 0.8392 (OUTLIER) cc_final: 0.8075 (t)
REVERT: B  200 ARG cc_start: 0.7442 (mtp-110) cc_final: 0.7135 (ptm160)
REVERT: B  401 LYS cc_start: 0.8455 (mttp) cc_final: 0.8151 (mtpt)
REVERT: A   84 GLN cc_start: 0.8785 (OUTLIER) cc_final: 0.8190 (pt0)
REVERT: A  228 GLU cc_start: 0.7880 (mm-30) cc_final: 0.7670 (mm-30)
REVERT: A  260 ARG cc_start: 0.7915 (tpt-90) cc_final: 0.7467 (ttm110)
REVERT: A  363 TYR cc_start: 0.8050 (m-80) cc_final: 0.7741 (m-80)
REVERT: C  200 ARG cc_start: 0.7505 (mtp-110) cc_final: 0.7199 (ptm160)
REVERT: C  272 MET cc_start: 0.8837 (ttm) cc_final: 0.8632 (ttp)
REVERT: D   18 ARG cc_start: 0.8278 (OUTLIER) cc_final: 0.7948 (ttt-90)
REVERT: D   35 GLU cc_start: 0.7925 (tt0) cc_final: 0.7606 (tt0)
REVERT: D  147 GLN cc_start: 0.8665 (OUTLIER) cc_final: 0.8142 (pm20)
REVERT: D  158 TYR cc_start: 0.8308 (t80) cc_final: 0.7970 (t80)
REVERT: D  185 THR cc_start: 0.8056 (OUTLIER) cc_final: 0.7771 (m)
REVERT: D  228 GLU cc_start: 0.7853 (mm-30) cc_final: 0.7645 (mm-30)
REVERT: D  260 ARG cc_start: 0.7892 (tpt-90) cc_final: 0.7342 (ttm110)
REVERT: D  359 ILE cc_start: 0.9098 (tt) cc_final: 0.8888 (tt)
REVERT: D  428 LYS cc_start: 0.8626 (tptm) cc_final: 0.8404 (tttt)
  outliers start: 34
  outliers final: 19
  residues processed: 232
  average time/residue: 0.2533
  time to fit residues: 86.4093
Evaluate side-chains
  204 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 180
  time to evaluate  : 1.385 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   16 LEU
Chi-restraints excluded: chain B residue   84 GLN
Chi-restraints excluded: chain B residue  115 VAL
Chi-restraints excluded: chain B residue  177 VAL
Chi-restraints excluded: chain B residue  180 ILE
Chi-restraints excluded: chain B residue  182 THR
Chi-restraints excluded: chain B residue  371 VAL
Chi-restraints excluded: chain B residue  436 LEU
Chi-restraints excluded: chain A residue   23 VAL
Chi-restraints excluded: chain A residue   84 GLN
Chi-restraints excluded: chain A residue  177 VAL
Chi-restraints excluded: chain A residue  368 MET
Chi-restraints excluded: chain A residue  436 LEU
Chi-restraints excluded: chain C residue   43 SER
Chi-restraints excluded: chain C residue   84 GLN
Chi-restraints excluded: chain C residue  177 VAL
Chi-restraints excluded: chain C residue  436 LEU
Chi-restraints excluded: chain D residue   18 ARG
Chi-restraints excluded: chain D residue   23 VAL
Chi-restraints excluded: chain D residue  147 GLN
Chi-restraints excluded: chain D residue  177 VAL
Chi-restraints excluded: chain D residue  185 THR
Chi-restraints excluded: chain D residue  264 MET
Chi-restraints excluded: chain D residue  436 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 180
   random chunks:
   chunk 27 optimal weight:    1.9990
   chunk 117 optimal weight:    3.9990
   chunk 75 optimal weight:    2.9990
   chunk 33 optimal weight:    5.9990
   chunk 79 optimal weight:    3.9990
   chunk 155 optimal weight:    3.9990
   chunk 173 optimal weight:    2.9990
   chunk 86 optimal weight:    5.9990
   chunk 126 optimal weight:    3.9990
   chunk 136 optimal weight:    1.9990
   chunk 37 optimal weight:    0.0770
   overall best weight:    2.0146

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

Flipped N/Q/H residues before XYZ refinement:
** B   6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B  84 GLN
** A   6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A  84 GLN
** C  84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D   6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D  84 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3384 r_free = 0.3384 target = 0.131504 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3092 r_free = 0.3092 target = 0.108010 restraints weight = 17271.823|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3125 r_free = 0.3125 target = 0.110536 restraints weight = 11807.748|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3148 r_free = 0.3148 target = 0.112291 restraints weight = 9114.565|
|-----------------------------------------------------------------------------|
r_work (final): 0.3148
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8115
moved from start:          0.2361

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.042  13800  Z= 0.192
  Angle     :  0.671   7.225  18768  Z= 0.333
  Chirality :  0.047   0.147   2104
  Planarity :  0.005   0.044   2472
  Dihedral  :  6.384  64.214   2025
  Min Nonbonded Distance : 2.528

Molprobity Statistics.
  All-atom Clashscore : 8.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.22 %
    Favored  : 91.78 %
  Rotamer:
    Outliers :  3.21 %
    Allowed  : 13.68 %
    Favored  : 83.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.93 (0.19), residues: 1824
  helix: -1.07 (0.20), residues: 696
  sheet: -2.90 (0.31), residues: 204
  loop : -2.41 (0.19), residues: 924

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 310 
 HIS   0.008   0.002   HIS C 348 
 PHE   0.016   0.001   PHE C 230 
 TYR   0.019   0.002   TYR D  36 
 ARG   0.004   0.000   ARG C 336 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04285 (  454)
  hydrogen bonds       : angle       4.84055 ( 1311)
  covalent geometry    : bond        0.00476 (13796)
  covalent geometry    : angle       0.67053 (18768)
  Misc. bond           : bond        0.00073 (    4)

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

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

  3648 Ramachandran restraints generated.
    1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3648 Ramachandran restraints generated.
    1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  233 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 188
  time to evaluate  : 1.394 
Fit side-chains
   revert: symmetry clash
REVERT: B  182 THR cc_start: 0.8853 (OUTLIER) cc_final: 0.8627 (t)
REVERT: B  200 ARG cc_start: 0.7481 (mtp-110) cc_final: 0.7119 (ptm160)
REVERT: B  401 LYS cc_start: 0.8485 (mttp) cc_final: 0.8137 (mtpt)
REVERT: A  260 ARG cc_start: 0.7935 (tpt-90) cc_final: 0.7494 (ttm110)
REVERT: A  363 TYR cc_start: 0.8096 (m-80) cc_final: 0.7777 (m-80)
REVERT: A  404 ASP cc_start: 0.7808 (m-30) cc_final: 0.7398 (m-30)
REVERT: A  452 ASP cc_start: 0.7540 (t0) cc_final: 0.7227 (t0)
REVERT: C  200 ARG cc_start: 0.7611 (mtp-110) cc_final: 0.7233 (ptm160)
REVERT: D   18 ARG cc_start: 0.8401 (OUTLIER) cc_final: 0.7932 (ttt-90)
REVERT: D   35 GLU cc_start: 0.7974 (tt0) cc_final: 0.7660 (tt0)
REVERT: D  147 GLN cc_start: 0.8631 (OUTLIER) cc_final: 0.8084 (pm20)
REVERT: D  185 THR cc_start: 0.8071 (OUTLIER) cc_final: 0.7823 (m)
REVERT: D  228 GLU cc_start: 0.8011 (mm-30) cc_final: 0.7758 (mm-30)
REVERT: D  260 ARG cc_start: 0.7940 (tpt-90) cc_final: 0.7277 (ttm110)
REVERT: D  404 ASP cc_start: 0.7790 (m-30) cc_final: 0.7381 (m-30)
  outliers start: 45
  outliers final: 26
  residues processed: 216
  average time/residue: 0.2320
  time to fit residues: 75.4526
Evaluate side-chains
  202 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 172
  time to evaluate  : 1.385 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   16 LEU
Chi-restraints excluded: chain B residue   84 GLN
Chi-restraints excluded: chain B residue  115 VAL
Chi-restraints excluded: chain B residue  177 VAL
Chi-restraints excluded: chain B residue  182 THR
Chi-restraints excluded: chain B residue  436 LEU
Chi-restraints excluded: chain A residue   23 VAL
Chi-restraints excluded: chain A residue   84 GLN
Chi-restraints excluded: chain A residue  177 VAL
Chi-restraints excluded: chain A residue  196 VAL
Chi-restraints excluded: chain A residue  264 MET
Chi-restraints excluded: chain A residue  292 VAL
Chi-restraints excluded: chain A residue  385 SER
Chi-restraints excluded: chain A residue  436 LEU
Chi-restraints excluded: chain C residue   43 SER
Chi-restraints excluded: chain C residue   84 GLN
Chi-restraints excluded: chain C residue  177 VAL
Chi-restraints excluded: chain C residue  404 ASP
Chi-restraints excluded: chain C residue  436 LEU
Chi-restraints excluded: chain D residue   18 ARG
Chi-restraints excluded: chain D residue   23 VAL
Chi-restraints excluded: chain D residue  147 GLN
Chi-restraints excluded: chain D residue  177 VAL
Chi-restraints excluded: chain D residue  185 THR
Chi-restraints excluded: chain D residue  196 VAL
Chi-restraints excluded: chain D residue  223 VAL
Chi-restraints excluded: chain D residue  264 MET
Chi-restraints excluded: chain D residue  292 VAL
Chi-restraints excluded: chain D residue  385 SER
Chi-restraints excluded: chain D residue  436 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 180
   random chunks:
   chunk 9 optimal weight:    7.9990
   chunk 12 optimal weight:    6.9990
   chunk 145 optimal weight:    3.9990
   chunk 70 optimal weight:    2.9990
   chunk 67 optimal weight:    0.0020
   chunk 53 optimal weight:    4.9990
   chunk 110 optimal weight:    6.9990
   chunk 136 optimal weight:    3.9990
   chunk 127 optimal weight:    0.7980
   chunk 34 optimal weight:    3.9990
   chunk 72 optimal weight:    1.9990
   overall best weight:    1.9594

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

Flipped N/Q/H residues before XYZ refinement:
** B   6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B  84 GLN
** A   6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D   6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D 123 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3383 r_free = 0.3383 target = 0.131526 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3090 r_free = 0.3090 target = 0.107965 restraints weight = 17092.656|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3123 r_free = 0.3123 target = 0.110462 restraints weight = 11709.287|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3146 r_free = 0.3146 target = 0.112222 restraints weight = 9104.911|
|-----------------------------------------------------------------------------|
r_work (final): 0.3154
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8124
moved from start:          0.2586

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.043  13800  Z= 0.185
  Angle     :  0.653   7.153  18768  Z= 0.325
  Chirality :  0.046   0.141   2104
  Planarity :  0.005   0.042   2472
  Dihedral  :  6.079  58.742   2022
  Min Nonbonded Distance : 2.540

Molprobity Statistics.
  All-atom Clashscore : 8.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.33 %
    Favored  : 91.67 %
  Rotamer:
    Outliers :  3.42 %
    Allowed  : 15.53 %
    Favored  : 81.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.64 (0.19), residues: 1824
  helix: -0.96 (0.20), residues: 696
  sheet: -2.51 (0.34), residues: 204
  loop : -2.20 (0.20), residues: 924

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 310 
 HIS   0.008   0.002   HIS C 348 
 PHE   0.016   0.001   PHE C 230 
 TYR   0.019   0.002   TYR D  36 
 ARG   0.003   0.000   ARG C 260 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04171 (  454)
  hydrogen bonds       : angle       4.78230 ( 1311)
  covalent geometry    : bond        0.00455 (13796)
  covalent geometry    : angle       0.65321 (18768)
  Misc. bond           : bond        0.00064 (    4)

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

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

  3648 Ramachandran restraints generated.
    1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3648 Ramachandran restraints generated.
    1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  223 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 175
  time to evaluate  : 1.458 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  152 GLU cc_start: 0.7965 (mm-30) cc_final: 0.7472 (mt-10)
REVERT: B  200 ARG cc_start: 0.7467 (mtp-110) cc_final: 0.7078 (ptm160)
REVERT: B  401 LYS cc_start: 0.8506 (mttp) cc_final: 0.8141 (mtpt)
REVERT: B  404 ASP cc_start: 0.8116 (t0) cc_final: 0.7901 (t0)
REVERT: A   84 GLN cc_start: 0.8713 (OUTLIER) cc_final: 0.8133 (pt0)
REVERT: A  260 ARG cc_start: 0.7951 (tpt-90) cc_final: 0.7502 (ttm110)
REVERT: A  302 MET cc_start: 0.8913 (tpp) cc_final: 0.8703 (mmp)
REVERT: A  363 TYR cc_start: 0.8045 (m-80) cc_final: 0.7761 (m-80)
REVERT: A  404 ASP cc_start: 0.7855 (m-30) cc_final: 0.7484 (m-30)
REVERT: A  452 ASP cc_start: 0.7568 (t0) cc_final: 0.7266 (t0)
REVERT: C  152 GLU cc_start: 0.7947 (mm-30) cc_final: 0.7501 (mt-10)
REVERT: C  200 ARG cc_start: 0.7607 (mtp-110) cc_final: 0.7216 (ptm160)
REVERT: C  424 SER cc_start: 0.9031 (t) cc_final: 0.8732 (p)
REVERT: D   35 GLU cc_start: 0.7975 (tt0) cc_final: 0.7708 (tt0)
REVERT: D   69 GLU cc_start: 0.8509 (OUTLIER) cc_final: 0.8271 (tp30)
REVERT: D  147 GLN cc_start: 0.8652 (OUTLIER) cc_final: 0.8065 (pm20)
REVERT: D  185 THR cc_start: 0.7985 (OUTLIER) cc_final: 0.7756 (m)
REVERT: D  228 GLU cc_start: 0.7944 (mm-30) cc_final: 0.7727 (mm-30)
REVERT: D  260 ARG cc_start: 0.8028 (tpt-90) cc_final: 0.7348 (ttm110)
REVERT: D  404 ASP cc_start: 0.7822 (m-30) cc_final: 0.7434 (m-30)
  outliers start: 48
  outliers final: 32
  residues processed: 209
  average time/residue: 0.2295
  time to fit residues: 72.9696
Evaluate side-chains
  198 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 162
  time to evaluate  : 1.599 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   16 LEU
Chi-restraints excluded: chain B residue   84 GLN
Chi-restraints excluded: chain B residue  113 VAL
Chi-restraints excluded: chain B residue  115 VAL
Chi-restraints excluded: chain B residue  177 VAL
Chi-restraints excluded: chain B residue  436 LEU
Chi-restraints excluded: chain A residue   23 VAL
Chi-restraints excluded: chain A residue   84 GLN
Chi-restraints excluded: chain A residue  159 VAL
Chi-restraints excluded: chain A residue  177 VAL
Chi-restraints excluded: chain A residue  196 VAL
Chi-restraints excluded: chain A residue  264 MET
Chi-restraints excluded: chain A residue  352 THR
Chi-restraints excluded: chain A residue  385 SER
Chi-restraints excluded: chain A residue  436 LEU
Chi-restraints excluded: chain C residue   43 SER
Chi-restraints excluded: chain C residue   58 SER
Chi-restraints excluded: chain C residue   84 GLN
Chi-restraints excluded: chain C residue  177 VAL
Chi-restraints excluded: chain C residue  305 ILE
Chi-restraints excluded: chain C residue  436 LEU
Chi-restraints excluded: chain D residue   17 VAL
Chi-restraints excluded: chain D residue   18 ARG
Chi-restraints excluded: chain D residue   23 VAL
Chi-restraints excluded: chain D residue   69 GLU
Chi-restraints excluded: chain D residue   98 VAL
Chi-restraints excluded: chain D residue  147 GLN
Chi-restraints excluded: chain D residue  159 VAL
Chi-restraints excluded: chain D residue  177 VAL
Chi-restraints excluded: chain D residue  185 THR
Chi-restraints excluded: chain D residue  196 VAL
Chi-restraints excluded: chain D residue  223 VAL
Chi-restraints excluded: chain D residue  292 VAL
Chi-restraints excluded: chain D residue  352 THR
Chi-restraints excluded: chain D residue  385 SER
Chi-restraints excluded: chain D residue  436 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 180
   random chunks:
   chunk 127 optimal weight:    5.9990
   chunk 122 optimal weight:    2.9990
   chunk 165 optimal weight:    4.9990
   chunk 111 optimal weight:    3.9990
   chunk 159 optimal weight:    3.9990
   chunk 29 optimal weight:    1.9990
   chunk 25 optimal weight:    0.7980
   chunk 146 optimal weight:    0.5980
   chunk 94 optimal weight:    7.9990
   chunk 166 optimal weight:    3.9990
   chunk 33 optimal weight:    4.9990
   overall best weight:    2.0786

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

Flipped N/Q/H residues before XYZ refinement:
B  84 GLN
** A   6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A  84 GLN
A 123 HIS
** C  84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D   6 HIS ** 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 = 0.3381 r_free = 0.3381 target = 0.131275 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3095 r_free = 0.3095 target = 0.108110 restraints weight = 17062.411|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 47)----------------|
| r_work = 0.3128 r_free = 0.3128 target = 0.110625 restraints weight = 11630.017|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3150 r_free = 0.3150 target = 0.112329 restraints weight = 8981.563|
|-----------------------------------------------------------------------------|
r_work (final): 0.3147
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8122
moved from start:          0.2716

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.044  13800  Z= 0.192
  Angle     :  0.656   6.952  18768  Z= 0.326
  Chirality :  0.047   0.169   2104
  Planarity :  0.005   0.041   2472
  Dihedral  :  5.888  53.019   2021
  Min Nonbonded Distance : 2.557

Molprobity Statistics.
  All-atom Clashscore : 7.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.61 %
    Favored  : 91.39 %
  Rotamer:
    Outliers :  3.70 %
    Allowed  : 17.31 %
    Favored  : 78.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.45 (0.19), residues: 1824
  helix: -0.89 (0.20), residues: 700
  sheet: -2.13 (0.35), residues: 204
  loop : -2.08 (0.20), residues: 920

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 310 
 HIS   0.007   0.002   HIS C 348 
 PHE   0.017   0.001   PHE C 230 
 TYR   0.019   0.002   TYR D  36 
 ARG   0.005   0.000   ARG B  85 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04182 (  454)
  hydrogen bonds       : angle       4.73562 ( 1311)
  covalent geometry    : bond        0.00473 (13796)
  covalent geometry    : angle       0.65616 (18768)
  Misc. bond           : bond        0.00064 (    4)

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

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

  3648 Ramachandran restraints generated.
    1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3648 Ramachandran restraints generated.
    1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  218 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 52
    poor density    : 166
  time to evaluate  : 1.449 
Fit side-chains
   revert: symmetry clash
REVERT: B  152 GLU cc_start: 0.7980 (mm-30) cc_final: 0.7513 (mt-10)
REVERT: B  401 LYS cc_start: 0.8521 (mttp) cc_final: 0.8139 (mtpt)
REVERT: B  404 ASP cc_start: 0.8153 (t0) cc_final: 0.7950 (t0)
REVERT: B  430 LEU cc_start: 0.8589 (mp) cc_final: 0.8384 (mp)
REVERT: A   84 GLN cc_start: 0.8674 (OUTLIER) cc_final: 0.8105 (pt0)
REVERT: A  260 ARG cc_start: 0.7968 (tpt-90) cc_final: 0.7433 (ttm110)
REVERT: A  332 ASP cc_start: 0.8421 (t0) cc_final: 0.8118 (m-30)
REVERT: A  363 TYR cc_start: 0.8117 (m-80) cc_final: 0.7813 (m-80)
REVERT: A  404 ASP cc_start: 0.7899 (m-30) cc_final: 0.7530 (m-30)
REVERT: A  452 ASP cc_start: 0.7591 (t0) cc_final: 0.7234 (t0)
REVERT: C  152 GLU cc_start: 0.7966 (mm-30) cc_final: 0.7550 (mt-10)
REVERT: C  378 MET cc_start: 0.7985 (pmm) cc_final: 0.6919 (mmm)
REVERT: C  424 SER cc_start: 0.9031 (t) cc_final: 0.8744 (p)
REVERT: D   35 GLU cc_start: 0.7982 (tt0) cc_final: 0.7743 (tt0)
REVERT: D  147 GLN cc_start: 0.8647 (OUTLIER) cc_final: 0.8126 (pm20)
REVERT: D  185 THR cc_start: 0.8033 (OUTLIER) cc_final: 0.7811 (m)
REVERT: D  228 GLU cc_start: 0.7948 (mm-30) cc_final: 0.7719 (mm-30)
REVERT: D  260 ARG cc_start: 0.8087 (tpt-90) cc_final: 0.7317 (ttm110)
REVERT: D  404 ASP cc_start: 0.7865 (m-30) cc_final: 0.7484 (m-30)
  outliers start: 52
  outliers final: 37
  residues processed: 207
  average time/residue: 0.2186
  time to fit residues: 69.5861
Evaluate side-chains
  198 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 158
  time to evaluate  : 1.529 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   16 LEU
Chi-restraints excluded: chain B residue   29 THR
Chi-restraints excluded: chain B residue   58 SER
Chi-restraints excluded: chain B residue   84 GLN
Chi-restraints excluded: chain B residue  113 VAL
Chi-restraints excluded: chain B residue  115 VAL
Chi-restraints excluded: chain B residue  177 VAL
Chi-restraints excluded: chain B residue  436 LEU
Chi-restraints excluded: chain A residue   23 VAL
Chi-restraints excluded: chain A residue   84 GLN
Chi-restraints excluded: chain A residue  159 VAL
Chi-restraints excluded: chain A residue  177 VAL
Chi-restraints excluded: chain A residue  196 VAL
Chi-restraints excluded: chain A residue  264 MET
Chi-restraints excluded: chain A residue  292 VAL
Chi-restraints excluded: chain A residue  352 THR
Chi-restraints excluded: chain A residue  385 SER
Chi-restraints excluded: chain A residue  436 LEU
Chi-restraints excluded: chain C residue   43 SER
Chi-restraints excluded: chain C residue   58 SER
Chi-restraints excluded: chain C residue   84 GLN
Chi-restraints excluded: chain C residue  177 VAL
Chi-restraints excluded: chain C residue  305 ILE
Chi-restraints excluded: chain C residue  345 VAL
Chi-restraints excluded: chain C residue  377 VAL
Chi-restraints excluded: chain C residue  404 ASP
Chi-restraints excluded: chain C residue  436 LEU
Chi-restraints excluded: chain D residue   17 VAL
Chi-restraints excluded: chain D residue   18 ARG
Chi-restraints excluded: chain D residue   23 VAL
Chi-restraints excluded: chain D residue   98 VAL
Chi-restraints excluded: chain D residue  147 GLN
Chi-restraints excluded: chain D residue  159 VAL
Chi-restraints excluded: chain D residue  177 VAL
Chi-restraints excluded: chain D residue  185 THR
Chi-restraints excluded: chain D residue  196 VAL
Chi-restraints excluded: chain D residue  223 VAL
Chi-restraints excluded: chain D residue  292 VAL
Chi-restraints excluded: chain D residue  352 THR
Chi-restraints excluded: chain D residue  436 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 180
   random chunks:
   chunk 62 optimal weight:    5.9990
   chunk 87 optimal weight:    2.9990
   chunk 134 optimal weight:    3.9990
   chunk 179 optimal weight:    0.9980
   chunk 105 optimal weight:    5.9990
   chunk 53 optimal weight:    0.9990
   chunk 157 optimal weight:    5.9990
   chunk 110 optimal weight:    7.9990
   chunk 137 optimal weight:    4.9990
   chunk 72 optimal weight:    0.8980
   chunk 35 optimal weight:    3.9990
   overall best weight:    1.9786

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

Flipped N/Q/H residues before XYZ refinement:
** B   6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B  84 GLN
** A   6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A  84 GLN
C   5 GLN
** C  84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D   6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  84 GLN ** 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 = 0.3383 r_free = 0.3383 target = 0.131347 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3090 r_free = 0.3090 target = 0.107776 restraints weight = 17330.183|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3122 r_free = 0.3122 target = 0.110252 restraints weight = 11814.518|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3145 r_free = 0.3145 target = 0.112033 restraints weight = 9140.840|
|-----------------------------------------------------------------------------|
r_work (final): 0.3144
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8124
moved from start:          0.2865

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.042  13800  Z= 0.185
  Angle     :  0.650   6.842  18768  Z= 0.323
  Chirality :  0.047   0.180   2104
  Planarity :  0.005   0.041   2472
  Dihedral  :  5.749  48.354   2021
  Min Nonbonded Distance : 2.567

Molprobity Statistics.
  All-atom Clashscore : 7.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.77 %
    Favored  : 91.23 %
  Rotamer:
    Outliers :  3.70 %
    Allowed  : 17.95 %
    Favored  : 78.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.29 (0.19), residues: 1824
  helix: -0.84 (0.20), residues: 700
  sheet: -1.87 (0.36), residues: 204
  loop : -1.97 (0.20), residues: 920

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 310 
 HIS   0.007   0.001   HIS C 348 
 PHE   0.017   0.001   PHE C 230 
 TYR   0.019   0.002   TYR D  36 
 ARG   0.004   0.000   ARG B 260 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04131 (  454)
  hydrogen bonds       : angle       4.71025 ( 1311)
  covalent geometry    : bond        0.00453 (13796)
  covalent geometry    : angle       0.65002 (18768)
  Misc. bond           : bond        0.00059 (    4)

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

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

  3648 Ramachandran restraints generated.
    1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3648 Ramachandran restraints generated.
    1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  213 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 52
    poor density    : 161
  time to evaluate  : 1.531 
Fit side-chains
   revert: symmetry clash
REVERT: B  152 GLU cc_start: 0.7984 (mm-30) cc_final: 0.7559 (mt-10)
REVERT: B  401 LYS cc_start: 0.8524 (mttp) cc_final: 0.8139 (mtpt)
REVERT: B  404 ASP cc_start: 0.8162 (t0) cc_final: 0.7949 (t0)
REVERT: B  430 LEU cc_start: 0.8567 (mp) cc_final: 0.8364 (mp)
REVERT: A  135 LEU cc_start: 0.7984 (tp) cc_final: 0.7554 (mp)
REVERT: A  158 TYR cc_start: 0.8359 (t80) cc_final: 0.7971 (t80)
REVERT: A  260 ARG cc_start: 0.7963 (tpt-90) cc_final: 0.7376 (ttm110)
REVERT: A  332 ASP cc_start: 0.8406 (t0) cc_final: 0.8103 (m-30)
REVERT: A  363 TYR cc_start: 0.8193 (m-80) cc_final: 0.7939 (m-80)
REVERT: A  404 ASP cc_start: 0.7914 (m-30) cc_final: 0.7542 (m-30)
REVERT: A  452 ASP cc_start: 0.7588 (t0) cc_final: 0.7208 (t0)
REVERT: C  152 GLU cc_start: 0.7963 (mm-30) cc_final: 0.7582 (mt-10)
REVERT: C  378 MET cc_start: 0.8004 (pmm) cc_final: 0.7128 (mmm)
REVERT: C  424 SER cc_start: 0.9068 (t) cc_final: 0.8760 (p)
REVERT: D   35 GLU cc_start: 0.8018 (tt0) cc_final: 0.7792 (tt0)
REVERT: D  147 GLN cc_start: 0.8675 (OUTLIER) cc_final: 0.8157 (pm20)
REVERT: D  185 THR cc_start: 0.8010 (OUTLIER) cc_final: 0.7808 (m)
REVERT: D  228 GLU cc_start: 0.7941 (mm-30) cc_final: 0.7711 (mm-30)
REVERT: D  260 ARG cc_start: 0.8113 (tpt-90) cc_final: 0.7379 (ttm110)
REVERT: D  332 ASP cc_start: 0.8429 (t0) cc_final: 0.8131 (m-30)
REVERT: D  404 ASP cc_start: 0.7870 (m-30) cc_final: 0.7510 (m-30)
  outliers start: 52
  outliers final: 42
  residues processed: 203
  average time/residue: 0.2066
  time to fit residues: 65.7547
Evaluate side-chains
  202 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 158
  time to evaluate  : 1.344 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   16 LEU
Chi-restraints excluded: chain B residue   29 THR
Chi-restraints excluded: chain B residue   58 SER
Chi-restraints excluded: chain B residue   84 GLN
Chi-restraints excluded: chain B residue  113 VAL
Chi-restraints excluded: chain B residue  115 VAL
Chi-restraints excluded: chain B residue  177 VAL
Chi-restraints excluded: chain B residue  345 VAL
Chi-restraints excluded: chain B residue  377 VAL
Chi-restraints excluded: chain B residue  436 LEU
Chi-restraints excluded: chain A residue   23 VAL
Chi-restraints excluded: chain A residue   84 GLN
Chi-restraints excluded: chain A residue  159 VAL
Chi-restraints excluded: chain A residue  177 VAL
Chi-restraints excluded: chain A residue  196 VAL
Chi-restraints excluded: chain A residue  264 MET
Chi-restraints excluded: chain A residue  278 LEU
Chi-restraints excluded: chain A residue  292 VAL
Chi-restraints excluded: chain A residue  352 THR
Chi-restraints excluded: chain A residue  385 SER
Chi-restraints excluded: chain A residue  436 LEU
Chi-restraints excluded: chain C residue   34 VAL
Chi-restraints excluded: chain C residue   43 SER
Chi-restraints excluded: chain C residue   58 SER
Chi-restraints excluded: chain C residue   84 GLN
Chi-restraints excluded: chain C residue  177 VAL
Chi-restraints excluded: chain C residue  305 ILE
Chi-restraints excluded: chain C residue  345 VAL
Chi-restraints excluded: chain C residue  347 THR
Chi-restraints excluded: chain C residue  377 VAL
Chi-restraints excluded: chain C residue  404 ASP
Chi-restraints excluded: chain C residue  436 LEU
Chi-restraints excluded: chain D residue   17 VAL
Chi-restraints excluded: chain D residue   23 VAL
Chi-restraints excluded: chain D residue   98 VAL
Chi-restraints excluded: chain D residue  147 GLN
Chi-restraints excluded: chain D residue  159 VAL
Chi-restraints excluded: chain D residue  177 VAL
Chi-restraints excluded: chain D residue  185 THR
Chi-restraints excluded: chain D residue  196 VAL
Chi-restraints excluded: chain D residue  223 VAL
Chi-restraints excluded: chain D residue  352 THR
Chi-restraints excluded: chain D residue  385 SER
Chi-restraints excluded: chain D residue  436 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 180
   random chunks:
   chunk 20 optimal weight:    4.9990
   chunk 65 optimal weight:    4.9990
   chunk 83 optimal weight:    3.9990
   chunk 145 optimal weight:    3.9990
   chunk 84 optimal weight:    0.0770
   chunk 152 optimal weight:    2.9990
   chunk 48 optimal weight:    1.9990
   chunk 122 optimal weight:    0.6980
   chunk 33 optimal weight:    3.9990
   chunk 27 optimal weight:    0.6980
   chunk 52 optimal weight:    1.9990
   overall best weight:    1.0942

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

Flipped N/Q/H residues before XYZ refinement:
B  84 GLN
A   6 HIS
A 348 HIS
** C  84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D   6 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3412 r_free = 0.3412 target = 0.133891 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3122 r_free = 0.3122 target = 0.110298 restraints weight = 17054.396|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3156 r_free = 0.3156 target = 0.112914 restraints weight = 11631.671|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3179 r_free = 0.3179 target = 0.114694 restraints weight = 8967.140|
|-----------------------------------------------------------------------------|
r_work (final): 0.3180
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8081
moved from start:          0.3017

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  13800  Z= 0.129
  Angle     :  0.605   7.591  18768  Z= 0.300
  Chirality :  0.045   0.141   2104
  Planarity :  0.004   0.041   2472
  Dihedral  :  5.406  43.214   2021
  Min Nonbonded Distance : 2.570

Molprobity Statistics.
  All-atom Clashscore : 7.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.24 %
    Favored  : 92.76 %
  Rotamer:
    Outliers :  2.99 %
    Allowed  : 19.37 %
    Favored  : 77.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.03 (0.20), residues: 1824
  helix: -0.64 (0.20), residues: 700
  sheet: -1.65 (0.37), residues: 204
  loop : -1.82 (0.20), residues: 920

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 310 
 HIS   0.005   0.001   HIS C 348 
 PHE   0.015   0.001   PHE C 230 
 TYR   0.015   0.001   TYR D  36 
 ARG   0.003   0.000   ARG B 260 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03611 (  454)
  hydrogen bonds       : angle       4.54918 ( 1311)
  covalent geometry    : bond        0.00314 (13796)
  covalent geometry    : angle       0.60478 (18768)
  Misc. bond           : bond        0.00034 (    4)

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

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

  3648 Ramachandran restraints generated.
    1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3648 Ramachandran restraints generated.
    1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  220 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 178
  time to evaluate  : 1.482 
Fit side-chains
   revert: symmetry clash
REVERT: B  152 GLU cc_start: 0.7842 (mm-30) cc_final: 0.7496 (mt-10)
REVERT: B  401 LYS cc_start: 0.8505 (mttp) cc_final: 0.8108 (mtpt)
REVERT: B  404 ASP cc_start: 0.8160 (t0) cc_final: 0.7857 (t0)
REVERT: A   84 GLN cc_start: 0.8665 (OUTLIER) cc_final: 0.8195 (pt0)
REVERT: A  135 LEU cc_start: 0.7849 (tp) cc_final: 0.7502 (mp)
REVERT: A  158 TYR cc_start: 0.8220 (t80) cc_final: 0.7894 (t80)
REVERT: A  260 ARG cc_start: 0.7881 (tpt-90) cc_final: 0.7293 (ttm110)
REVERT: A  332 ASP cc_start: 0.8401 (t0) cc_final: 0.8119 (m-30)
REVERT: A  363 TYR cc_start: 0.8155 (m-80) cc_final: 0.7890 (m-80)
REVERT: A  404 ASP cc_start: 0.7920 (m-30) cc_final: 0.7560 (m-30)
REVERT: A  452 ASP cc_start: 0.7314 (t0) cc_final: 0.6977 (t0)
REVERT: C  152 GLU cc_start: 0.7916 (mm-30) cc_final: 0.7579 (mt-10)
REVERT: C  424 SER cc_start: 0.9085 (t) cc_final: 0.8769 (p)
REVERT: D   35 GLU cc_start: 0.8012 (tt0) cc_final: 0.7769 (tt0)
REVERT: D  147 GLN cc_start: 0.8660 (OUTLIER) cc_final: 0.8130 (pm20)
REVERT: D  158 TYR cc_start: 0.8282 (t80) cc_final: 0.7941 (t80)
REVERT: D  228 GLU cc_start: 0.7871 (mm-30) cc_final: 0.7650 (mm-30)
REVERT: D  260 ARG cc_start: 0.8057 (tpt-90) cc_final: 0.7295 (ttm110)
REVERT: D  332 ASP cc_start: 0.8392 (t0) cc_final: 0.8119 (m-30)
REVERT: D  404 ASP cc_start: 0.7876 (m-30) cc_final: 0.7533 (m-30)
  outliers start: 42
  outliers final: 34
  residues processed: 210
  average time/residue: 0.2389
  time to fit residues: 77.1173
Evaluate side-chains
  200 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 164
  time to evaluate  : 1.621 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   16 LEU
Chi-restraints excluded: chain B residue   29 THR
Chi-restraints excluded: chain B residue   84 GLN
Chi-restraints excluded: chain B residue  113 VAL
Chi-restraints excluded: chain B residue  115 VAL
Chi-restraints excluded: chain B residue  177 VAL
Chi-restraints excluded: chain B residue  345 VAL
Chi-restraints excluded: chain B residue  377 VAL
Chi-restraints excluded: chain B residue  436 LEU
Chi-restraints excluded: chain A residue   23 VAL
Chi-restraints excluded: chain A residue   84 GLN
Chi-restraints excluded: chain A residue  159 VAL
Chi-restraints excluded: chain A residue  177 VAL
Chi-restraints excluded: chain A residue  196 VAL
Chi-restraints excluded: chain A residue  292 VAL
Chi-restraints excluded: chain A residue  352 THR
Chi-restraints excluded: chain A residue  436 LEU
Chi-restraints excluded: chain C residue   34 VAL
Chi-restraints excluded: chain C residue   84 GLN
Chi-restraints excluded: chain C residue  177 VAL
Chi-restraints excluded: chain C residue  345 VAL
Chi-restraints excluded: chain C residue  347 THR
Chi-restraints excluded: chain C residue  377 VAL
Chi-restraints excluded: chain C residue  404 ASP
Chi-restraints excluded: chain C residue  436 LEU
Chi-restraints excluded: chain D residue   17 VAL
Chi-restraints excluded: chain D residue   23 VAL
Chi-restraints excluded: chain D residue  147 GLN
Chi-restraints excluded: chain D residue  159 VAL
Chi-restraints excluded: chain D residue  177 VAL
Chi-restraints excluded: chain D residue  196 VAL
Chi-restraints excluded: chain D residue  223 VAL
Chi-restraints excluded: chain D residue  292 VAL
Chi-restraints excluded: chain D residue  352 THR
Chi-restraints excluded: chain D residue  385 SER
Chi-restraints excluded: chain D residue  436 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Traceback (most recent call last):
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in <module>
    run_program(real_space_refine.Program)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program
    task.run()
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run
    log         = self.logger)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__
    log                   = log)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__
    self.caller(self.refine_xyz)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller
    func()
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz
    self.minimization_no_ncs()
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs
    log                         = self.log)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__
    gradients_method            = gradients_method)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__
    rms_angles_limit = rms_angles_limit)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine
    rms_angles_limit = rms_angles_limit)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__
    weight     = weight)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine
    states_collector                = self.states_accumulator)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__
    exception_handling_params=lbfgs_exception_handling_params)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run
    line_search)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus
    f, g = target_evaluator.compute_functional_and_gradients()
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients
    compute_gradients=True)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites
    flags=flags, sites_cart=sites_cart, site_labels=site_labels)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies
    check_bonded_distance_cutoff(sites_frac=sites_frac)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff
    raise RuntimeError(msg)
RuntimeError: Bond distance > max_reasonable_bond_distance: 64.2239 > 50:
  distance: 20 - 25:  29.876
  distance: 25 - 26:  18.840
  distance: 26 - 27:  25.561
  distance: 27 - 28:  20.496
  distance: 27 - 29:  41.052
  distance: 29 - 30:  59.678
  distance: 30 - 31:  41.887
  distance: 30 - 33:  49.612
  distance: 31 - 32:  28.242
  distance: 31 - 34:  30.302
  distance: 34 - 35:  23.897
  distance: 35 - 36:  40.232
  distance: 35 - 38:   8.084
  distance: 36 - 37:   3.058
  distance: 36 - 43:  30.861
  distance: 38 - 39:  28.562
  distance: 39 - 40:  25.307
  distance: 40 - 41:  34.859
  distance: 40 - 42:  26.361
  distance: 43 - 44:  42.627
  distance: 43 - 49:  25.805
  distance: 44 - 45:  30.098
  distance: 44 - 47:  19.784
  distance: 45 - 46:  11.565
  distance: 45 - 50:  46.101
  distance: 47 - 48:  53.314
  distance: 48 - 49:   5.690
  distance: 50 - 51:  18.584
  distance: 50 - 56:  34.135
  distance: 51 - 52:  18.457
  distance: 51 - 54:  31.558
  distance: 52 - 53:  21.358
  distance: 52 - 57:   7.815
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  distance: 58 - 59:  15.443
  distance: 58 - 61:  15.397
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  distance: 59 - 64:  22.181
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