Starting phenix.real_space_refine
on Wed May 14 11:36:23 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8go9_34174/05_2025/8go9_34174.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8go9_34174/05_2025/8go9_34174.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.35
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8go9_34174/05_2025/8go9_34174.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8go9_34174/05_2025/8go9_34174.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8go9_34174/05_2025/8go9_34174.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8go9_34174/05_2025/8go9_34174.cif"
  }
  resolution = 3.35
  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=   0.039
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      12      5.49       5
     S      26      5.16       5
     C    7376      2.51       5
     N    1988      2.21       5
     O    2260      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 4 residue(s): 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 11662
  Number of models: 1
  Model: ""
    Number of chains: 8
    Chain: "A"
      Number of atoms: 2888
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 363, 2888
          Classifications: {'peptide': 363}
          Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 24, 'TRANS': 335}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 1479
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 202, 1479
          Classifications: {'peptide': 202}
          Incomplete info: {'truncation_to_alanine': 16}
          Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 9, 'TRANS': 189}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 46
          Unresolved non-hydrogen angles: 54
          Unresolved non-hydrogen dihedrals: 38
          Unresolved non-hydrogen chiralities: 6
          Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 1}
          Unresolved non-hydrogen planarities: 7
    Chain: "C"
      Number of atoms: 1359
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 185, 1359
          Classifications: {'peptide': 185}
          Incomplete info: {'truncation_to_alanine': 20}
          Link IDs: {'PCIS': 3, 'PTRANS': 7, 'TRANS': 174}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 60
          Unresolved non-hydrogen angles: 72
          Unresolved non-hydrogen dihedrals: 50
          Unresolved non-hydrogen chiralities: 4
          Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 1, 'ASP:plan': 3}
          Unresolved non-hydrogen planarities: 26
    Chain: "D"
      Number of atoms: 1479
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 202, 1479
          Classifications: {'peptide': 202}
          Incomplete info: {'truncation_to_alanine': 16}
          Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 9, 'TRANS': 189}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 46
          Unresolved non-hydrogen angles: 54
          Unresolved non-hydrogen dihedrals: 38
          Unresolved non-hydrogen chiralities: 6
          Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 1}
          Unresolved non-hydrogen planarities: 7
    Chain: "E"
      Number of atoms: 1359
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 185, 1359
          Classifications: {'peptide': 185}
          Incomplete info: {'truncation_to_alanine': 20}
          Link IDs: {'PCIS': 3, 'PTRANS': 7, 'TRANS': 174}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 60
          Unresolved non-hydrogen angles: 72
          Unresolved non-hydrogen dihedrals: 50
          Unresolved non-hydrogen chiralities: 4
          Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 1, 'ASP:plan': 3}
          Unresolved non-hydrogen planarities: 26
    Chain: "F"
      Number of atoms: 2888
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 363, 2888
          Classifications: {'peptide': 363}
          Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 24, 'TRANS': 335}
          Chain breaks: 1
    Chain: "G"
      Number of atoms: 105
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 12, 105
          Classifications: {'peptide': 12}
          Link IDs: {'TRANS': 11}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Planarities with less than four sites: {'TPO:plan-1': 1}
          Unresolved non-hydrogen planarities: 1
    Chain: "H"
      Number of atoms: 105
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 12, 105
          Classifications: {'peptide': 12}
          Link IDs: {'TRANS': 11}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Planarities with less than four sites: {'TPO:plan-1': 1}
          Unresolved non-hydrogen planarities: 1
  Time building chain proxies: 7.04, per 1000 atoms: 0.60
  Number of scatterers: 11662
  At special positions: 0
  Unit cell: (186.038, 87.6375, 121.463, 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      26     16.00
     P      12     15.00
     O    2260      8.00
     N    1988      7.00
     C    7376      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=6, symmetry=0
    Simple disulfide: pdb=" SG  CYS B  25 " - pdb=" SG  CYS B  99 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 150 " - pdb=" SG  CYS B 206 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C  24 " - pdb=" SG  CYS C  89 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D  25 " - pdb=" SG  CYS D  99 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D 150 " - pdb=" SG  CYS D 206 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E  24 " - pdb=" SG  CYS E  89 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.82
  Conformation dependent library (CDL) restraints added in 1.5 seconds
  

  2944 Ramachandran restraints generated.
    1472 Oldfield, 0 Emsley, 1472 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2868

  Finding SS restraints...
    Secondary structure from input PDB file:
      12 helices and 30 sheets defined
      7.0% alpha, 42.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.52
  Creating SS restraints...
    Processing helix  chain 'A' and resid 45 through 50
      removed outlier: 3.920A  pdb=" N   LEU A  49 " --> pdb=" O   ASP A  45 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 99 through 110
    Processing helix  chain 'A' and resid 393 through 408
    Processing helix  chain 'B' and resid 90 through 94
      removed outlier: 4.022A  pdb=" N   THR B  94 " --> pdb=" O   ALA B  91 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 122 through 128
    Processing helix  chain 'C' and resid 184 through 190
      removed outlier: 4.003A  pdb=" N   HIS C 190 " --> pdb=" O   ASP C 186 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 90 through 94
      removed outlier: 4.022A  pdb=" N   THR D  94 " --> pdb=" O   ALA D  91 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 122 through 128
    Processing helix  chain 'E' and resid 184 through 190
      removed outlier: 4.002A  pdb=" N   HIS E 190 " --> pdb=" O   ASP E 186 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 45 through 50
      removed outlier: 3.920A  pdb=" N   LEU F  49 " --> pdb=" O   ASP F  45 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 99 through 110
    Processing helix  chain 'F' and resid 393 through 408
    Processing sheet with id=AA1, first strand: chain 'A' and resid 113 through 118
    Processing sheet with id=AA2, first strand: chain 'A' and resid 27 through 30
      removed outlier: 3.605A  pdb=" N   ILE A 169 " --> pdb=" O   PHE A 145 " (cutoff:3.500A)
      removed outlier: 4.097A  pdb=" N   PHE A 145 " --> pdb=" O   ILE A 169 " (cutoff:3.500A)
      removed outlier: 8.206A  pdb=" N   LYS A 171 " --> pdb=" O   VAL A 143 " (cutoff:3.500A)
      removed outlier: 10.267A  pdb=" N   VAL A 143 " --> pdb=" O   LYS A 171 " (cutoff:3.500A)
      removed outlier: 3.734A  pdb=" N   ARG A  63 " --> pdb=" O   GLY A 142 " (cutoff:3.500A)
      removed outlier: 7.106A  pdb=" N   VAL A  54 " --> pdb=" O   GLN A  86 " (cutoff:3.500A)
      removed outlier: 4.479A  pdb=" N   GLN A  86 " --> pdb=" O   VAL A  54 " (cutoff:3.500A)
      removed outlier: 6.748A  pdb=" N   VAL A  56 " --> pdb=" O   ASN A  84 " (cutoff:3.500A)
      removed outlier: 4.571A  pdb=" N   ASN A  84 " --> pdb=" O   VAL A  56 " (cutoff:3.500A)
      removed outlier: 6.695A  pdb=" N   LEU A  58 " --> pdb=" O   ILE A  82 " (cutoff:3.500A)
      removed outlier: 4.316A  pdb=" N   ILE A  82 " --> pdb=" O   LEU A  58 " (cutoff:3.500A)
      removed outlier: 6.728A  pdb=" N   VAL A  60 " --> pdb=" O   LEU A  80 " (cutoff:3.500A)
      removed outlier: 4.065A  pdb=" N   LYS A  78 " --> pdb=" O   PHE A  62 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 128 through 130
    Processing sheet with id=AA4, first strand: chain 'A' and resid 184 through 189
      removed outlier: 3.530A  pdb=" N   THR A 187 " --> pdb=" O   LEU A 200 " (cutoff:3.500A)
      removed outlier: 3.545A  pdb=" N   LYS A 271 " --> pdb=" O   VAL A 219 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 208 through 209
      removed outlier: 3.845A  pdb=" N   VAL A 336 " --> pdb=" O   LEU A 328 " (cutoff:3.500A)
      removed outlier: 4.079A  pdb=" N   TYR A 322 " --> pdb=" O   PHE A 342 " (cutoff:3.500A)
      removed outlier: 7.649A  pdb=" N   LEU A 344 " --> pdb=" O   VAL A 320 " (cutoff:3.500A)
      removed outlier: 9.520A  pdb=" N   VAL A 320 " --> pdb=" O   LEU A 344 " (cutoff:3.500A)
      removed outlier: 4.348A  pdb=" N   LYS A 231 " --> pdb=" O   VAL A 329 " (cutoff:3.500A)
      removed outlier: 3.547A  pdb=" N   ILE A 232 " --> pdb=" O   GLN A 259 " (cutoff:3.500A)
      removed outlier: 3.699A  pdb=" N   ALA A 255 " --> pdb=" O   VAL A 236 " (cutoff:3.500A)
      removed outlier: 6.114A  pdb=" N   GLN A 238 " --> pdb=" O   PRO A 253 " (cutoff:3.500A)
      removed outlier: 7.164A  pdb=" N   ALA A 240 " --> pdb=" O   LYS A 251 " (cutoff:3.500A)
      removed outlier: 5.787A  pdb=" N   LYS A 251 " --> pdb=" O   ALA A 240 " (cutoff:3.500A)
      removed outlier: 7.113A  pdb=" N   ILE A 242 " --> pdb=" O   GLN A 249 " (cutoff:3.500A)
      removed outlier: 5.433A  pdb=" N   GLN A 249 " --> pdb=" O   ILE A 242 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 6 through 10
      removed outlier: 3.668A  pdb=" N   VAL B   8 " --> pdb=" O   ALA B  26 " (cutoff:3.500A)
      removed outlier: 3.515A  pdb=" N   SER B  24 " --> pdb=" O   SER B  10 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 13 through 15
      removed outlier: 3.729A  pdb=" N   ALA B  52 " --> pdb=" O   TRP B  39 " (cutoff:3.500A)
      removed outlier: 6.392A  pdb=" N   ARG B  41 " --> pdb=" O   TRP B  50 " (cutoff:3.500A)
      removed outlier: 5.142A  pdb=" N   TRP B  50 " --> pdb=" O   ARG B  41 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 13 through 15
    Processing sheet with id=AA9, first strand: chain 'B' and resid 130 through 134
      removed outlier: 3.735A  pdb=" N   GLY B 149 " --> pdb=" O   LEU B 134 " (cutoff:3.500A)
      removed outlier: 6.353A  pdb=" N   TYR B 186 " --> pdb=" O   ASP B 154 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'B' and resid 130 through 134
      removed outlier: 3.735A  pdb=" N   GLY B 149 " --> pdb=" O   LEU B 134 " (cutoff:3.500A)
      removed outlier: 6.353A  pdb=" N   TYR B 186 " --> pdb=" O   ASP B 154 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'B' and resid 161 through 163
    Processing sheet with id=AB3, first strand: chain 'C' and resid 5 through 8
    Processing sheet with id=AB4, first strand: chain 'C' and resid 11 through 14
      removed outlier: 3.581A  pdb=" N   GLU C 106 " --> pdb=" O   LEU C  12 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'C' and resid 54 through 55
      removed outlier: 6.485A  pdb=" N   TRP C  36 " --> pdb=" O   LEU C  48 " (cutoff:3.500A)
      removed outlier: 4.633A  pdb=" N   TYR C  50 " --> pdb=" O   VAL C  34 " (cutoff:3.500A)
      removed outlier: 6.779A  pdb=" N   VAL C  34 " --> pdb=" O   TYR C  50 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'C' and resid 117 through 119
      removed outlier: 6.331A  pdb=" N   TYR C 174 " --> pdb=" O   ASN C 139 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'D' and resid 6 through 10
      removed outlier: 3.668A  pdb=" N   VAL D   8 " --> pdb=" O   ALA D  26 " (cutoff:3.500A)
      removed outlier: 3.516A  pdb=" N   SER D  24 " --> pdb=" O   SER D  10 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'D' and resid 13 through 15
      removed outlier: 3.730A  pdb=" N   ALA D  52 " --> pdb=" O   TRP D  39 " (cutoff:3.500A)
      removed outlier: 6.392A  pdb=" N   ARG D  41 " --> pdb=" O   TRP D  50 " (cutoff:3.500A)
      removed outlier: 5.143A  pdb=" N   TRP D  50 " --> pdb=" O   ARG D  41 " (cutoff:3.500A)
    Processing sheet with id=AB9, first strand: chain 'D' and resid 13 through 15
    Processing sheet with id=AC1, first strand: chain 'D' and resid 130 through 134
      removed outlier: 3.735A  pdb=" N   GLY D 149 " --> pdb=" O   LEU D 134 " (cutoff:3.500A)
      removed outlier: 6.353A  pdb=" N   TYR D 186 " --> pdb=" O   ASP D 154 " (cutoff:3.500A)
    Processing sheet with id=AC2, first strand: chain 'D' and resid 130 through 134
      removed outlier: 3.735A  pdb=" N   GLY D 149 " --> pdb=" O   LEU D 134 " (cutoff:3.500A)
      removed outlier: 6.353A  pdb=" N   TYR D 186 " --> pdb=" O   ASP D 154 " (cutoff:3.500A)
    Processing sheet with id=AC3, first strand: chain 'D' and resid 161 through 163
    Processing sheet with id=AC4, first strand: chain 'E' and resid 5 through 8
    Processing sheet with id=AC5, first strand: chain 'E' and resid 11 through 14
      removed outlier: 3.581A  pdb=" N   GLU E 106 " --> pdb=" O   LEU E  12 " (cutoff:3.500A)
    Processing sheet with id=AC6, first strand: chain 'E' and resid 54 through 55
      removed outlier: 6.484A  pdb=" N   TRP E  36 " --> pdb=" O   LEU E  48 " (cutoff:3.500A)
      removed outlier: 4.633A  pdb=" N   TYR E  50 " --> pdb=" O   VAL E  34 " (cutoff:3.500A)
      removed outlier: 6.778A  pdb=" N   VAL E  34 " --> pdb=" O   TYR E  50 " (cutoff:3.500A)
    Processing sheet with id=AC7, first strand: chain 'E' and resid 117 through 119
      removed outlier: 6.331A  pdb=" N   TYR E 174 " --> pdb=" O   ASN E 139 " (cutoff:3.500A)
    Processing sheet with id=AC8, first strand: chain 'F' and resid 113 through 118
    Processing sheet with id=AC9, first strand: chain 'F' and resid 27 through 30
      removed outlier: 3.605A  pdb=" N   ILE F 169 " --> pdb=" O   PHE F 145 " (cutoff:3.500A)
      removed outlier: 4.097A  pdb=" N   PHE F 145 " --> pdb=" O   ILE F 169 " (cutoff:3.500A)
      removed outlier: 8.206A  pdb=" N   LYS F 171 " --> pdb=" O   VAL F 143 " (cutoff:3.500A)
      removed outlier: 10.268A  pdb=" N   VAL F 143 " --> pdb=" O   LYS F 171 " (cutoff:3.500A)
      removed outlier: 3.735A  pdb=" N   ARG F  63 " --> pdb=" O   GLY F 142 " (cutoff:3.500A)
      removed outlier: 7.107A  pdb=" N   VAL F  54 " --> pdb=" O   GLN F  86 " (cutoff:3.500A)
      removed outlier: 4.478A  pdb=" N   GLN F  86 " --> pdb=" O   VAL F  54 " (cutoff:3.500A)
      removed outlier: 6.749A  pdb=" N   VAL F  56 " --> pdb=" O   ASN F  84 " (cutoff:3.500A)
      removed outlier: 4.571A  pdb=" N   ASN F  84 " --> pdb=" O   VAL F  56 " (cutoff:3.500A)
      removed outlier: 6.695A  pdb=" N   LEU F  58 " --> pdb=" O   ILE F  82 " (cutoff:3.500A)
      removed outlier: 4.315A  pdb=" N   ILE F  82 " --> pdb=" O   LEU F  58 " (cutoff:3.500A)
      removed outlier: 6.728A  pdb=" N   VAL F  60 " --> pdb=" O   LEU F  80 " (cutoff:3.500A)
      removed outlier: 4.065A  pdb=" N   LYS F  78 " --> pdb=" O   PHE F  62 " (cutoff:3.500A)
    Processing sheet with id=AD1, first strand: chain 'F' and resid 128 through 130
    Processing sheet with id=AD2, first strand: chain 'F' and resid 184 through 189
      removed outlier: 3.529A  pdb=" N   THR F 187 " --> pdb=" O   LEU F 200 " (cutoff:3.500A)
      removed outlier: 3.546A  pdb=" N   LYS F 271 " --> pdb=" O   VAL F 219 " (cutoff:3.500A)
    Processing sheet with id=AD3, first strand: chain 'F' and resid 208 through 209
      removed outlier: 3.844A  pdb=" N   VAL F 336 " --> pdb=" O   LEU F 328 " (cutoff:3.500A)
      removed outlier: 4.079A  pdb=" N   TYR F 322 " --> pdb=" O   PHE F 342 " (cutoff:3.500A)
      removed outlier: 7.650A  pdb=" N   LEU F 344 " --> pdb=" O   VAL F 320 " (cutoff:3.500A)
      removed outlier: 9.521A  pdb=" N   VAL F 320 " --> pdb=" O   LEU F 344 " (cutoff:3.500A)
      removed outlier: 4.348A  pdb=" N   LYS F 231 " --> pdb=" O   VAL F 329 " (cutoff:3.500A)
      removed outlier: 3.547A  pdb=" N   ILE F 232 " --> pdb=" O   GLN F 259 " (cutoff:3.500A)
      removed outlier: 3.699A  pdb=" N   ALA F 255 " --> pdb=" O   VAL F 236 " (cutoff:3.500A)
      removed outlier: 6.114A  pdb=" N   GLN F 238 " --> pdb=" O   PRO F 253 " (cutoff:3.500A)
      removed outlier: 7.164A  pdb=" N   ALA F 240 " --> pdb=" O   LYS F 251 " (cutoff:3.500A)
      removed outlier: 5.787A  pdb=" N   LYS F 251 " --> pdb=" O   ALA F 240 " (cutoff:3.500A)
      removed outlier: 7.112A  pdb=" N   ILE F 242 " --> pdb=" O   GLN F 249 " (cutoff:3.500A)
      removed outlier: 5.432A  pdb=" N   GLN F 249 " --> pdb=" O   ILE F 242 " (cutoff:3.500A)

    480 hydrogen bonds defined for protein.
    1242 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: 3.58

  Time building geometry restraints manager: 3.29 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: 3752
        1.34 -     1.46: 2723
        1.46 -     1.58: 5375
        1.58 -     1.69: 46
        1.69 -     1.81: 34
  Bond restraints: 11930
  Sorted by residual:
  bond pdb=" OG1 TPO G 354 "
       pdb=" P   TPO G 354 "
    ideal  model  delta    sigma   weight residual
    1.717  1.609  0.108 2.00e-02 2.50e+03 2.91e+01
  bond pdb=" OG1 TPO H 354 "
       pdb=" P   TPO H 354 "
    ideal  model  delta    sigma   weight residual
    1.717  1.609  0.108 2.00e-02 2.50e+03 2.91e+01
  bond pdb=" O3P TPO G 354 "
       pdb=" P   TPO G 354 "
    ideal  model  delta    sigma   weight residual
    1.528  1.610 -0.082 2.00e-02 2.50e+03 1.70e+01
  bond pdb=" O2P TPO G 354 "
       pdb=" P   TPO G 354 "
    ideal  model  delta    sigma   weight residual
    1.528  1.610 -0.082 2.00e-02 2.50e+03 1.67e+01
  bond pdb=" O2P TPO H 354 "
       pdb=" P   TPO H 354 "
    ideal  model  delta    sigma   weight residual
    1.528  1.610 -0.082 2.00e-02 2.50e+03 1.66e+01
  ... (remaining 11925 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.42: 16096
        2.42 -     4.84: 134
        4.84 -     7.25: 14
        7.25 -     9.67: 4
        9.67 -    12.09: 2
  Bond angle restraints: 16250
  Sorted by residual:
  angle pdb=" CB  TPO H 354 "
        pdb=" OG1 TPO H 354 "
        pdb=" P   TPO H 354 "
      ideal   model   delta    sigma   weight residual
     119.31  107.22   12.09 3.00e+00 1.11e-01 1.62e+01
  angle pdb=" CB  TPO G 354 "
        pdb=" OG1 TPO G 354 "
        pdb=" P   TPO G 354 "
      ideal   model   delta    sigma   weight residual
     119.31  107.27   12.04 3.00e+00 1.11e-01 1.61e+01
  angle pdb=" OG1 TPO G 354 "
        pdb=" P   TPO G 354 "
        pdb=" O1P TPO G 354 "
      ideal   model   delta    sigma   weight residual
     100.43  109.46   -9.03 3.00e+00 1.11e-01 9.06e+00
  angle pdb=" OG1 TPO H 354 "
        pdb=" P   TPO H 354 "
        pdb=" O1P TPO H 354 "
      ideal   model   delta    sigma   weight residual
     100.43  109.43   -9.00 3.00e+00 1.11e-01 8.99e+00
  angle pdb=" C   LEU F  49 "
        pdb=" N   LYS F  50 "
        pdb=" CA  LYS F  50 "
      ideal   model   delta    sigma   weight residual
     121.54  127.26   -5.72 1.91e+00 2.74e-01 8.97e+00
  ... (remaining 16245 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.99: 6599
       17.99 -    35.99: 463
       35.99 -    53.98: 86
       53.98 -    71.97: 16
       71.97 -    89.96: 8
  Dihedral angle restraints: 7172
    sinusoidal: 2730
      harmonic: 4442
  Sorted by residual:
  dihedral pdb=" CA  ARG A  96 "
           pdb=" C   ARG A  96 "
           pdb=" N   PRO A  97 "
           pdb=" CA  PRO A  97 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  147.99   32.01     0      5.00e+00 4.00e-02 4.10e+01
  dihedral pdb=" CA  ARG F  96 "
           pdb=" C   ARG F  96 "
           pdb=" N   PRO F  97 "
           pdb=" CA  PRO F  97 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  148.06   31.94     0      5.00e+00 4.00e-02 4.08e+01
  dihedral pdb=" CA  PRO F  95 "
           pdb=" C   PRO F  95 "
           pdb=" N   ARG F  96 "
           pdb=" CA  ARG F  96 "
      ideal   model   delta  harmonic     sigma   weight residual
       0.00  -30.10   30.10     0      5.00e+00 4.00e-02 3.62e+01
  ... (remaining 7169 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.035: 1290
       0.035 -    0.071: 337
       0.071 -    0.106: 157
       0.106 -    0.141: 56
       0.141 -    0.177: 4
  Chirality restraints: 1844
  Sorted by residual:
  chirality pdb=" CA  LYS A 295 "
            pdb=" N   LYS A 295 "
            pdb=" C   LYS A 295 "
            pdb=" CB  LYS A 295 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.69   -0.18 2.00e-01 2.50e+01 7.80e-01
  chirality pdb=" CA  LYS A 108 "
            pdb=" N   LYS A 108 "
            pdb=" C   LYS A 108 "
            pdb=" CB  LYS A 108 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.67   -0.15 2.00e-01 2.50e+01 5.98e-01
  chirality pdb=" CA  LYS F 108 "
            pdb=" N   LYS F 108 "
            pdb=" C   LYS F 108 "
            pdb=" CB  LYS F 108 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.66   -0.15 2.00e-01 2.50e+01 5.95e-01
  ... (remaining 1841 not shown)

  Planarity restraints: 2078
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ARG A  96 "    0.075 5.00e-02 4.00e+02   1.14e-01 2.10e+01
        pdb=" N   PRO A  97 "   -0.198 5.00e-02 4.00e+02
        pdb=" CA  PRO A  97 "    0.062 5.00e-02 4.00e+02
        pdb=" CD  PRO A  97 "    0.061 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ARG F  96 "   -0.075 5.00e-02 4.00e+02   1.14e-01 2.09e+01
        pdb=" N   PRO F  97 "    0.198 5.00e-02 4.00e+02
        pdb=" CA  PRO F  97 "   -0.061 5.00e-02 4.00e+02
        pdb=" CD  PRO F  97 "   -0.061 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR A  91 "   -0.032 5.00e-02 4.00e+02   4.83e-02 3.73e+00
        pdb=" N   PRO A  92 "    0.084 5.00e-02 4.00e+02
        pdb=" CA  PRO A  92 "   -0.025 5.00e-02 4.00e+02
        pdb=" CD  PRO A  92 "   -0.027 5.00e-02 4.00e+02
  ... (remaining 2075 not shown)

  Histogram of nonbonded interaction distances:
        2.28 -     2.80: 2837
        2.80 -     3.33: 9646
        3.33 -     3.85: 17971
        3.85 -     4.38: 20008
        4.38 -     4.90: 36855
  Nonbonded interactions: 87317
  Sorted by model distance:
  nonbonded pdb=" OE1 GLN C   7 "
            pdb=" OG1 THR C 103 "
     model   vdw
     2.277 3.040
  nonbonded pdb=" OE1 GLN E   7 "
            pdb=" OG1 THR E 103 "
     model   vdw
     2.277 3.040
  nonbonded pdb=" NZ  LYS F  11 "
            pdb=" OE2 GLU H 349 "
     model   vdw
     2.279 3.120
  nonbonded pdb=" O   PHE E 140 "
            pdb=" OG1 THR E 173 "
     model   vdw
     2.282 3.040
  nonbonded pdb=" O   PHE C 140 "
            pdb=" OG1 THR C 173 "
     model   vdw
     2.282 3.040
  ... (remaining 87312 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: 0.06
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'F'
}
ncs_group {
  reference = chain 'G'
  selection = chain 'H'
}
ncs_group {
  reference = chain 'B'
  selection = chain 'D'
}
ncs_group {
  reference = chain 'C'
  selection = chain 'E'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.65 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.010
  Normalize map: mean=0, sd=1:             0.960
  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:          0.480
  Check model and map are aligned:         0.090
  Set scattering table:                    0.130
  Process input model:                     27.720
  Find NCS groups from input model:        0.190
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:2.570
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   32.210
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7782
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      :  0.003   0.108  11936  Z= 0.152
  Angle     :  0.554  12.092  16262  Z= 0.275
  Chirality :  0.042   0.177   1844
  Planarity :  0.006   0.114   2078
  Dihedral  : 13.071  89.963   4286
  Min Nonbonded Distance : 2.277

Molprobity Statistics.
  All-atom Clashscore : 5.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.23 %
    Favored  : 94.77 %
  Rotamer:
    Outliers :  0.32 %
    Allowed  :  0.24 %
    Favored  : 99.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 14.89 %
    Cis-general     : 0.14 %
    Twisted Proline : 2.13 %
    Twisted General : 0.14 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.51 (0.23), residues: 1472
  helix:  2.08 (0.60), residues: 80
  sheet:  1.27 (0.22), residues: 656
  loop : -0.77 (0.23), residues: 736

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP B  50 
 HIS   0.002   0.000   HIS F 346 
 PHE   0.008   0.001   PHE F 278 
 TYR   0.006   0.001   TYR A 250 
 ARG   0.007   0.000   ARG E  25 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.22647 (  434)
  hydrogen bonds       : angle       9.36260 ( 1242)
  SS BOND              : bond        0.00197 (    6)
  SS BOND              : angle       0.23271 (   12)
  covalent geometry    : bond        0.00307 (11930)
  covalent geometry    : angle       0.55415 (16250)

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

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

  2944 Ramachandran restraints generated.
    1472 Oldfield, 0 Emsley, 1472 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2944 Ramachandran restraints generated.
    1472 Oldfield, 0 Emsley, 1472 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 1326 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 124
  time to evaluate  : 1.250 
Fit side-chains
REVERT: A  108 LYS cc_start: 0.8357 (OUTLIER) cc_final: 0.7923 (tttm)
REVERT: B   77 THR cc_start: 0.8264 (p) cc_final: 0.8018 (p)
REVERT: B  185 LEU cc_start: 0.7506 (mm) cc_final: 0.7219 (mm)
REVERT: D   22 ARG cc_start: 0.7345 (ttt-90) cc_final: 0.7120 (tpt-90)
REVERT: D  132 PHE cc_start: 0.6250 (m-10) cc_final: 0.5801 (m-80)
REVERT: D  151 LEU cc_start: 0.7352 (tt) cc_final: 0.7145 (tt)
REVERT: F  108 LYS cc_start: 0.8195 (OUTLIER) cc_final: 0.7960 (ttpt)
  outliers start: 4
  outliers final: 1
  residues processed: 128
  average time/residue: 0.2583
  time to fit residues: 46.5152
Evaluate side-chains
  107 residues out of total 1326 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 104
  time to evaluate  : 1.389 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  108 LYS
Chi-restraints excluded: chain F residue  108 LYS
Chi-restraints excluded: chain F residue  295 LYS
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 126 optimal weight:    0.7980
   chunk 113 optimal weight:    0.9980
   chunk 63 optimal weight:    3.9990
   chunk 38 optimal weight:    3.9990
   chunk 76 optimal weight:    1.9990
   chunk 60 optimal weight:    0.0570
   chunk 117 optimal weight:    2.9990
   chunk 45 optimal weight:    1.9990
   chunk 71 optimal weight:    0.1980
   chunk 87 optimal weight:    4.9990
   chunk 136 optimal weight:    0.8980
   overall best weight:    0.5898

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

Flipped N/Q/H residues before XYZ refinement:
B  85 GLN
B  87 ASN
C   7 GLN
D  87 ASN
E   7 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4094 r_free = 0.4094 target = 0.179373 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 91)----------------|
| r_work = 0.3445 r_free = 0.3445 target = 0.123026 restraints weight = 13935.825|
|-----------------------------------------------------------------------------|
r_work (start): 0.3302 rms_B_bonded: 2.63
r_work: 0.3149 rms_B_bonded: 2.83 restraints_weight: 0.5000
r_work: 0.2999 rms_B_bonded: 4.36 restraints_weight: 0.2500
r_work (final): 0.2999
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3007
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3007 r_free = 0.3007    target_work(ls_wunit_k1) = 0.089         |
| occupancies: max = 1.00  min = 0.65   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3007 r_free = 0.3007    target_work(ls_wunit_k1) = 0.089         |
| occupancies: max = 1.00  min = 0.53   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3007
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8006
moved from start:          0.1271

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  11936  Z= 0.126
  Angle     :  0.531   7.596  16262  Z= 0.272
  Chirality :  0.044   0.148   1844
  Planarity :  0.005   0.091   2078
  Dihedral  :  5.799  62.750   1688
  Min Nonbonded Distance : 2.513

Molprobity Statistics.
  All-atom Clashscore : 5.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.14 %
    Favored  : 95.86 %
  Rotamer:
    Outliers :  1.20 %
    Allowed  :  5.50 %
    Favored  : 93.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 14.89 %
    Cis-general     : 0.28 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.45 (0.23), residues: 1472
  helix:  2.06 (0.59), residues: 84
  sheet:  1.11 (0.21), residues: 672
  loop : -0.73 (0.24), residues: 716

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B  50 
 HIS   0.002   0.001   HIS F 199 
 PHE   0.022   0.001   PHE F  81 
 TYR   0.013   0.001   TYR E  92 
 ARG   0.006   0.000   ARG E  25 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03374 (  434)
  hydrogen bonds       : angle       6.00925 ( 1242)
  SS BOND              : bond        0.00437 (    6)
  SS BOND              : angle       0.36730 (   12)
  covalent geometry    : bond        0.00295 (11930)
  covalent geometry    : angle       0.53138 (16250)

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

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

  2944 Ramachandran restraints generated.
    1472 Oldfield, 0 Emsley, 1472 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2944 Ramachandran restraints generated.
    1472 Oldfield, 0 Emsley, 1472 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  131 residues out of total 1326 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 116
  time to evaluate  : 1.412 
Fit side-chains
REVERT: A  308 LYS cc_start: 0.7436 (ptpp) cc_final: 0.7070 (mtpp)
REVERT: C   25 ARG cc_start: 0.8029 (ttm110) cc_final: 0.7367 (mmm160)
REVERT: C   28 GLN cc_start: 0.8096 (mp10) cc_final: 0.7828 (mm-40)
REVERT: D  185 LEU cc_start: 0.7076 (mm) cc_final: 0.6255 (mm)
REVERT: E  106 GLU cc_start: 0.8285 (pm20) cc_final: 0.8071 (pm20)
REVERT: F  153 LYS cc_start: 0.8503 (mtmm) cc_final: 0.8243 (mttp)
REVERT: F  230 LYS cc_start: 0.7080 (mtmm) cc_final: 0.6705 (mtpp)
REVERT: F  308 LYS cc_start: 0.7444 (ptpp) cc_final: 0.7057 (mtpp)
  outliers start: 15
  outliers final: 13
  residues processed: 124
  average time/residue: 0.2887
  time to fit residues: 49.3233
Evaluate side-chains
  111 residues out of total 1326 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 98
  time to evaluate  : 1.395 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  147 ILE
Chi-restraints excluded: chain A residue  296 HIS
Chi-restraints excluded: chain A residue  405 LEU
Chi-restraints excluded: chain B residue  151 LEU
Chi-restraints excluded: chain C residue   64 SER
Chi-restraints excluded: chain E residue   64 SER
Chi-restraints excluded: chain E residue   77 SER
Chi-restraints excluded: chain F residue  295 LYS
Chi-restraints excluded: chain F residue  296 HIS
Chi-restraints excluded: chain F residue  299 THR
Chi-restraints excluded: chain F residue  405 LEU
Chi-restraints excluded: chain G residue  349 GLU
Chi-restraints excluded: chain H residue  349 GLU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 16 optimal weight:    2.9990
   chunk 7 optimal weight:    0.1980
   chunk 2 optimal weight:    1.9990
   chunk 32 optimal weight:    2.9990
   chunk 125 optimal weight:    0.3980
   chunk 8 optimal weight:    3.9990
   chunk 103 optimal weight:    1.9990
   chunk 83 optimal weight:    0.9990
   chunk 136 optimal weight:    0.6980
   chunk 128 optimal weight:    1.9990
   chunk 38 optimal weight:    2.9990
   overall best weight:    0.8584

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

Flipped N/Q/H residues before XYZ refinement:
B  87 ASN
D  87 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4067 r_free = 0.4067 target = 0.176557 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 71)----------------|
| r_work = 0.3427 r_free = 0.3427 target = 0.122623 restraints weight = 14228.543|
|-----------------------------------------------------------------------------|
r_work (start): 0.3298 rms_B_bonded: 2.78
r_work: 0.3099 rms_B_bonded: 3.04 restraints_weight: 0.5000
r_work: 0.2945 rms_B_bonded: 4.69 restraints_weight: 0.2500
r_work (final): 0.2945
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2941
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2941 r_free = 0.2941    target_work(ls_wunit_k1) = 0.085         |
| occupancies: max = 1.00  min = 0.53   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2941 r_free = 0.2941    target_work(ls_wunit_k1) = 0.085         |
| occupancies: max = 1.00  min = 0.55   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2941
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8070
moved from start:          0.1731

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039  11936  Z= 0.157
  Angle     :  0.540   6.677  16262  Z= 0.276
  Chirality :  0.044   0.159   1844
  Planarity :  0.005   0.065   2078
  Dihedral  :  5.825  64.068   1680
  Min Nonbonded Distance : 2.534

Molprobity Statistics.
  All-atom Clashscore : 5.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.89 %
    Favored  : 95.11 %
  Rotamer:
    Outliers :  1.83 %
    Allowed  :  7.97 %
    Favored  : 90.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 14.89 %
    Cis-general     : 0.14 %
    Twisted Proline : 0.00 %
    Twisted General : 0.14 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.37 (0.23), residues: 1472
  helix:  2.22 (0.59), residues: 82
  sheet:  0.97 (0.20), residues: 690
  loop : -0.75 (0.24), residues: 700

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B  50 
 HIS   0.003   0.001   HIS B  38 
 PHE   0.022   0.002   PHE F 269 
 TYR   0.016   0.002   TYR C  92 
 ARG   0.004   0.000   ARG B  22 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03198 (  434)
  hydrogen bonds       : angle       5.53529 ( 1242)
  SS BOND              : bond        0.00422 (    6)
  SS BOND              : angle       0.24657 (   12)
  covalent geometry    : bond        0.00375 (11930)
  covalent geometry    : angle       0.54011 (16250)

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

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

  2944 Ramachandran restraints generated.
    1472 Oldfield, 0 Emsley, 1472 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2944 Ramachandran restraints generated.
    1472 Oldfield, 0 Emsley, 1472 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 1326 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 106
  time to evaluate  : 1.236 
Fit side-chains
REVERT: A  308 LYS cc_start: 0.7322 (ptpp) cc_final: 0.7086 (mtpp)
REVERT: C   25 ARG cc_start: 0.8155 (ttm110) cc_final: 0.7365 (mtp85)
REVERT: C   28 GLN cc_start: 0.8149 (mp10) cc_final: 0.7854 (mm-40)
REVERT: C  106 GLU cc_start: 0.8266 (pm20) cc_final: 0.7777 (pm20)
REVERT: D   22 ARG cc_start: 0.7912 (tpt-90) cc_final: 0.7639 (tpt-90)
REVERT: E  106 GLU cc_start: 0.8077 (pm20) cc_final: 0.7569 (pm20)
REVERT: F  153 LYS cc_start: 0.8518 (mtmm) cc_final: 0.8297 (mttp)
REVERT: F  230 LYS cc_start: 0.7096 (mtmm) cc_final: 0.6701 (mtpp)
REVERT: F  308 LYS cc_start: 0.7371 (ptpp) cc_final: 0.7108 (mtpp)
  outliers start: 23
  outliers final: 20
  residues processed: 122
  average time/residue: 0.2719
  time to fit residues: 46.0113
Evaluate side-chains
  121 residues out of total 1326 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 101
  time to evaluate  : 1.473 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  147 ILE
Chi-restraints excluded: chain A residue  205 ASP
Chi-restraints excluded: chain A residue  296 HIS
Chi-restraints excluded: chain A residue  405 LEU
Chi-restraints excluded: chain B residue   24 SER
Chi-restraints excluded: chain B residue   81 THR
Chi-restraints excluded: chain B residue  151 LEU
Chi-restraints excluded: chain C residue   64 SER
Chi-restraints excluded: chain C residue  107 ILE
Chi-restraints excluded: chain D residue   24 SER
Chi-restraints excluded: chain D residue   81 THR
Chi-restraints excluded: chain E residue   64 SER
Chi-restraints excluded: chain E residue   77 SER
Chi-restraints excluded: chain E residue  107 ILE
Chi-restraints excluded: chain F residue  147 ILE
Chi-restraints excluded: chain F residue  205 ASP
Chi-restraints excluded: chain F residue  299 THR
Chi-restraints excluded: chain F residue  405 LEU
Chi-restraints excluded: chain G residue  349 GLU
Chi-restraints excluded: chain H residue  349 GLU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 139 optimal weight:    1.9990
   chunk 138 optimal weight:    0.7980
   chunk 96 optimal weight:    1.9990
   chunk 56 optimal weight:    2.9990
   chunk 114 optimal weight:    0.9980
   chunk 20 optimal weight:    0.8980
   chunk 18 optimal weight:    7.9990
   chunk 65 optimal weight:    0.6980
   chunk 133 optimal weight:    0.9980
   chunk 12 optimal weight:    0.9990
   chunk 103 optimal weight:    0.0670
   overall best weight:    0.6918

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

Flipped N/Q/H residues before XYZ refinement:
B  87 ASN
D  87 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4075 r_free = 0.4075 target = 0.177159 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 70)----------------|
| r_work = 0.3436 r_free = 0.3436 target = 0.122416 restraints weight = 14132.481|
|-----------------------------------------------------------------------------|
r_work (start): 0.3276 rms_B_bonded: 2.70
r_work: 0.3087 rms_B_bonded: 2.85 restraints_weight: 0.5000
r_work: 0.2937 rms_B_bonded: 4.37 restraints_weight: 0.2500
r_work (final): 0.2937
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2959
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2959 r_free = 0.2959    target_work(ls_wunit_k1) = 0.086         |
| occupancies: max = 1.00  min = 0.55   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2959 r_free = 0.2959    target_work(ls_wunit_k1) = 0.086         |
| occupancies: max = 1.00  min = 0.51   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2959
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7996
moved from start:          0.1908

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  11936  Z= 0.131
  Angle     :  0.516   6.560  16262  Z= 0.262
  Chirality :  0.044   0.151   1844
  Planarity :  0.005   0.089   2078
  Dihedral  :  5.695  65.043   1676
  Min Nonbonded Distance : 2.534

Molprobity Statistics.
  All-atom Clashscore : 5.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.62 %
    Favored  : 95.38 %
  Rotamer:
    Outliers :  1.67 %
    Allowed  :  9.81 %
    Favored  : 88.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 14.89 %
    Cis-general     : 0.14 %
    Twisted Proline : 0.00 %
    Twisted General : 0.14 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.35 (0.23), residues: 1472
  helix:  2.19 (0.60), residues: 84
  sheet:  0.93 (0.20), residues: 690
  loop : -0.74 (0.24), residues: 698

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP D  50 
 HIS   0.003   0.001   HIS F 199 
 PHE   0.014   0.001   PHE F  81 
 TYR   0.015   0.001   TYR E  92 
 ARG   0.003   0.000   ARG B  22 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02757 (  434)
  hydrogen bonds       : angle       5.17325 ( 1242)
  SS BOND              : bond        0.00381 (    6)
  SS BOND              : angle       0.17961 (   12)
  covalent geometry    : bond        0.00315 (11930)
  covalent geometry    : angle       0.51662 (16250)

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

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

  2944 Ramachandran restraints generated.
    1472 Oldfield, 0 Emsley, 1472 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2944 Ramachandran restraints generated.
    1472 Oldfield, 0 Emsley, 1472 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 1326 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 105
  time to evaluate  : 1.295 
Fit side-chains
REVERT: A  308 LYS cc_start: 0.7346 (ptpp) cc_final: 0.6994 (mtpp)
REVERT: C   25 ARG cc_start: 0.8073 (ttm110) cc_final: 0.7237 (mtp85)
REVERT: C   28 GLN cc_start: 0.8193 (mp10) cc_final: 0.7865 (mm-40)
REVERT: C  106 GLU cc_start: 0.8209 (pm20) cc_final: 0.7745 (pm20)
REVERT: D   22 ARG cc_start: 0.7925 (tpt-90) cc_final: 0.7599 (tpt-90)
REVERT: D  185 LEU cc_start: 0.6672 (mm) cc_final: 0.5814 (mm)
REVERT: E  106 GLU cc_start: 0.8411 (pm20) cc_final: 0.8138 (pm20)
REVERT: F  153 LYS cc_start: 0.8487 (mtmm) cc_final: 0.8279 (mttp)
REVERT: F  230 LYS cc_start: 0.7051 (mtmm) cc_final: 0.6679 (mtpp)
REVERT: F  308 LYS cc_start: 0.7470 (ptpp) cc_final: 0.7007 (mtpp)
  outliers start: 21
  outliers final: 16
  residues processed: 118
  average time/residue: 0.3038
  time to fit residues: 49.4102
Evaluate side-chains
  108 residues out of total 1326 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 92
  time to evaluate  : 1.283 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  147 ILE
Chi-restraints excluded: chain A residue  205 ASP
Chi-restraints excluded: chain A residue  405 LEU
Chi-restraints excluded: chain B residue   24 SER
Chi-restraints excluded: chain B residue   77 THR
Chi-restraints excluded: chain B residue  151 LEU
Chi-restraints excluded: chain D residue   24 SER
Chi-restraints excluded: chain E residue    5 MET
Chi-restraints excluded: chain E residue   77 SER
Chi-restraints excluded: chain E residue  107 ILE
Chi-restraints excluded: chain F residue  147 ILE
Chi-restraints excluded: chain F residue  205 ASP
Chi-restraints excluded: chain F residue  299 THR
Chi-restraints excluded: chain F residue  405 LEU
Chi-restraints excluded: chain G residue  349 GLU
Chi-restraints excluded: chain H residue  349 GLU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 26 optimal weight:    0.0070
   chunk 1 optimal weight:    1.9990
   chunk 125 optimal weight:    0.4980
   chunk 143 optimal weight:    0.5980
   chunk 75 optimal weight:    3.9990
   chunk 101 optimal weight:    2.9990
   chunk 7 optimal weight:    1.9990
   chunk 88 optimal weight:    2.9990
   chunk 42 optimal weight:    0.9980
   chunk 92 optimal weight:    5.9990
   chunk 9 optimal weight:    0.9980
   overall best weight:    0.6198

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

Flipped N/Q/H residues before XYZ refinement:
A 190 HIS
B  87 ASN
D  87 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4093 r_free = 0.4093 target = 0.178642 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 75)----------------|
| r_work = 0.3435 r_free = 0.3435 target = 0.122258 restraints weight = 14030.822|
|-----------------------------------------------------------------------------|
r_work (start): 0.3262 rms_B_bonded: 2.77
r_work: 0.3097 rms_B_bonded: 2.86 restraints_weight: 0.5000
r_work: 0.2942 rms_B_bonded: 4.43 restraints_weight: 0.2500
r_work (final): 0.2942
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2956
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2956 r_free = 0.2956    target_work(ls_wunit_k1) = 0.086         |
| occupancies: max = 1.00  min = 0.51   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2956 r_free = 0.2956    target_work(ls_wunit_k1) = 0.086         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2956
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7985
moved from start:          0.2062

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  11936  Z= 0.123
  Angle     :  0.510   6.395  16262  Z= 0.259
  Chirality :  0.043   0.150   1844
  Planarity :  0.005   0.076   2078
  Dihedral  :  5.652  65.650   1676
  Min Nonbonded Distance : 2.530

Molprobity Statistics.
  All-atom Clashscore : 5.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.96 %
    Favored  : 95.04 %
  Rotamer:
    Outliers :  2.15 %
    Allowed  : 10.85 %
    Favored  : 87.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 14.89 %
    Cis-general     : 0.14 %
    Twisted Proline : 0.00 %
    Twisted General : 0.14 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.34 (0.23), residues: 1472
  helix:  2.30 (0.59), residues: 84
  sheet:  0.87 (0.20), residues: 692
  loop : -0.71 (0.24), residues: 696

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B  50 
 HIS   0.002   0.000   HIS A 346 
 PHE   0.012   0.001   PHE F  81 
 TYR   0.014   0.001   TYR A 250 
 ARG   0.004   0.000   ARG B  22 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02698 (  434)
  hydrogen bonds       : angle       4.88483 ( 1242)
  SS BOND              : bond        0.00371 (    6)
  SS BOND              : angle       0.23500 (   12)
  covalent geometry    : bond        0.00296 (11930)
  covalent geometry    : angle       0.50988 (16250)

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

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

  2944 Ramachandran restraints generated.
    1472 Oldfield, 0 Emsley, 1472 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2944 Ramachandran restraints generated.
    1472 Oldfield, 0 Emsley, 1472 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 1326 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 99
  time to evaluate  : 1.242 
Fit side-chains
REVERT: A   48 TYR cc_start: 0.7051 (t80) cc_final: 0.6846 (t80)
REVERT: A   63 ARG cc_start: 0.7875 (mtp85) cc_final: 0.7642 (mtp85)
REVERT: A  106 LEU cc_start: 0.7825 (mm) cc_final: 0.7622 (mm)
REVERT: A  308 LYS cc_start: 0.7503 (ptpp) cc_final: 0.6888 (mtpp)
REVERT: C   25 ARG cc_start: 0.8063 (ttm110) cc_final: 0.7256 (ttm-80)
REVERT: C   28 GLN cc_start: 0.8204 (mp10) cc_final: 0.7849 (mm-40)
REVERT: D   22 ARG cc_start: 0.7879 (tpt-90) cc_final: 0.7560 (tpt-90)
REVERT: F   63 ARG cc_start: 0.7888 (mtp85) cc_final: 0.7662 (mtp85)
REVERT: F  106 LEU cc_start: 0.7823 (mm) cc_final: 0.7496 (mp)
REVERT: F  230 LYS cc_start: 0.6970 (mtmm) cc_final: 0.6609 (mtpp)
REVERT: F  308 LYS cc_start: 0.7486 (ptpp) cc_final: 0.6916 (mtpp)
  outliers start: 27
  outliers final: 22
  residues processed: 117
  average time/residue: 0.3056
  time to fit residues: 48.3999
Evaluate side-chains
  114 residues out of total 1326 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 92
  time to evaluate  : 1.343 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  147 ILE
Chi-restraints excluded: chain A residue  165 VAL
Chi-restraints excluded: chain A residue  205 ASP
Chi-restraints excluded: chain A residue  219 VAL
Chi-restraints excluded: chain A residue  405 LEU
Chi-restraints excluded: chain B residue   24 SER
Chi-restraints excluded: chain B residue   77 THR
Chi-restraints excluded: chain B residue  151 LEU
Chi-restraints excluded: chain C residue  107 ILE
Chi-restraints excluded: chain D residue   24 SER
Chi-restraints excluded: chain D residue   77 THR
Chi-restraints excluded: chain E residue    5 MET
Chi-restraints excluded: chain E residue   77 SER
Chi-restraints excluded: chain E residue  107 ILE
Chi-restraints excluded: chain F residue  147 ILE
Chi-restraints excluded: chain F residue  165 VAL
Chi-restraints excluded: chain F residue  205 ASP
Chi-restraints excluded: chain F residue  219 VAL
Chi-restraints excluded: chain F residue  299 THR
Chi-restraints excluded: chain F residue  405 LEU
Chi-restraints excluded: chain G residue  349 GLU
Chi-restraints excluded: chain H residue  349 GLU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 91 optimal weight:   10.0000
   chunk 7 optimal weight:    1.9990
   chunk 72 optimal weight:    4.9990
   chunk 9 optimal weight:    6.9990
   chunk 117 optimal weight:    0.8980
   chunk 134 optimal weight:    5.9990
   chunk 130 optimal weight:    8.9990
   chunk 8 optimal weight:    3.9990
   chunk 146 optimal weight:    0.9980
   chunk 54 optimal weight:   20.0000
   chunk 26 optimal weight:    0.0270
   overall best weight:    1.5842

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

Flipped N/Q/H residues before XYZ refinement:
B  87 ASN
D  87 ASN
D 174 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4020 r_free = 0.4020 target = 0.171724 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 124)---------------|
| r_work = 0.3458 r_free = 0.3458 target = 0.123824 restraints weight = 14267.220|
|-----------------------------------------------------------------------------|
r_work (start): 0.3341 rms_B_bonded: 2.12
r_work: 0.3099 rms_B_bonded: 2.48 restraints_weight: 0.5000
r_work: 0.2956 rms_B_bonded: 3.79 restraints_weight: 0.2500
r_work (final): 0.2956
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2948
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2948 r_free = 0.2948    target_work(ls_wunit_k1) = 0.086         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2948 r_free = 0.2948    target_work(ls_wunit_k1) = 0.086         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2948
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8077
moved from start:          0.2430

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.078  11936  Z= 0.256
  Angle     :  0.629   8.209  16262  Z= 0.325
  Chirality :  0.047   0.173   1844
  Planarity :  0.005   0.091   2078
  Dihedral  :  6.143  70.604   1676
  Min Nonbonded Distance : 2.527

Molprobity Statistics.
  All-atom Clashscore : 6.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.66 %
    Favored  : 93.34 %
  Rotamer:
    Outliers :  2.23 %
    Allowed  : 11.40 %
    Favored  : 86.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 14.89 %
    Cis-general     : 0.14 %
    Twisted Proline : 0.00 %
    Twisted General : 0.14 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.07 (0.23), residues: 1472
  helix:  2.25 (0.60), residues: 84
  sheet:  0.77 (0.20), residues: 676
  loop : -0.96 (0.24), residues: 712

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP B  50 
 HIS   0.006   0.001   HIS A 211 
 PHE   0.014   0.002   PHE B 105 
 TYR   0.026   0.002   TYR E  92 
 ARG   0.003   0.001   ARG D 101 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03335 (  434)
  hydrogen bonds       : angle       5.41839 ( 1242)
  SS BOND              : bond        0.00544 (    6)
  SS BOND              : angle       0.42644 (   12)
  covalent geometry    : bond        0.00620 (11930)
  covalent geometry    : angle       0.62915 (16250)

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

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

  2944 Ramachandran restraints generated.
    1472 Oldfield, 0 Emsley, 1472 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2944 Ramachandran restraints generated.
    1472 Oldfield, 0 Emsley, 1472 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 1326 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 94
  time to evaluate  : 1.420 
Fit side-chains
REVERT: A   63 ARG cc_start: 0.7985 (mtp85) cc_final: 0.7497 (mtp85)
REVERT: A  230 LYS cc_start: 0.6820 (mtmm) cc_final: 0.6491 (mtpp)
REVERT: A  308 LYS cc_start: 0.7682 (ptpp) cc_final: 0.7005 (mtpp)
REVERT: C   28 GLN cc_start: 0.8202 (mp10) cc_final: 0.7963 (mm-40)
REVERT: C   43 LYS cc_start: 0.8547 (mmtt) cc_final: 0.8327 (mmmt)
REVERT: C  109 ARG cc_start: 0.7628 (ptm160) cc_final: 0.7302 (ptm160)
REVERT: D   22 ARG cc_start: 0.7683 (tpt-90) cc_final: 0.7342 (tpt-90)
REVERT: F   63 ARG cc_start: 0.7992 (mtp85) cc_final: 0.7504 (mtp85)
REVERT: F  230 LYS cc_start: 0.7117 (mtmm) cc_final: 0.6583 (mtpp)
REVERT: F  308 LYS cc_start: 0.7648 (ptpp) cc_final: 0.7089 (mtpp)
  outliers start: 28
  outliers final: 26
  residues processed: 114
  average time/residue: 0.3105
  time to fit residues: 47.5562
Evaluate side-chains
  116 residues out of total 1326 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 90
  time to evaluate  : 1.263 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  147 ILE
Chi-restraints excluded: chain A residue  165 VAL
Chi-restraints excluded: chain A residue  200 LEU
Chi-restraints excluded: chain A residue  219 VAL
Chi-restraints excluded: chain A residue  336 VAL
Chi-restraints excluded: chain A residue  405 LEU
Chi-restraints excluded: chain B residue   24 SER
Chi-restraints excluded: chain B residue   77 THR
Chi-restraints excluded: chain B residue   81 THR
Chi-restraints excluded: chain B residue  151 LEU
Chi-restraints excluded: chain C residue   64 SER
Chi-restraints excluded: chain C residue  107 ILE
Chi-restraints excluded: chain D residue   24 SER
Chi-restraints excluded: chain E residue    5 MET
Chi-restraints excluded: chain E residue   64 SER
Chi-restraints excluded: chain E residue   77 SER
Chi-restraints excluded: chain E residue  107 ILE
Chi-restraints excluded: chain F residue  147 ILE
Chi-restraints excluded: chain F residue  165 VAL
Chi-restraints excluded: chain F residue  200 LEU
Chi-restraints excluded: chain F residue  219 VAL
Chi-restraints excluded: chain F residue  299 THR
Chi-restraints excluded: chain F residue  336 VAL
Chi-restraints excluded: chain F residue  405 LEU
Chi-restraints excluded: chain G residue  349 GLU
Chi-restraints excluded: chain H residue  349 GLU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 115 optimal weight:    2.9990
   chunk 58 optimal weight:    2.9990
   chunk 22 optimal weight:    0.9990
   chunk 50 optimal weight:    0.6980
   chunk 8 optimal weight:    3.9990
   chunk 107 optimal weight:    0.9980
   chunk 26 optimal weight:    0.6980
   chunk 35 optimal weight:    1.9990
   chunk 130 optimal weight:   10.0000
   chunk 47 optimal weight:    0.7980
   chunk 87 optimal weight:    1.9990
   overall best weight:    0.8382

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

Flipped N/Q/H residues before XYZ refinement:
B  87 ASN
D  87 ASN
D 174 HIS
E  28 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4055 r_free = 0.4055 target = 0.174966 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3691 r_free = 0.3691 target = 0.141116 restraints weight = 14307.336|
|-----------------------------------------------------------------------------|
r_work (start): 0.3699 rms_B_bonded: 1.66
r_work: 0.3316 rms_B_bonded: 2.37 restraints_weight: 0.5000
r_work: 0.3162 rms_B_bonded: 3.90 restraints_weight: 0.2500
r_work (final): 0.3162
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3134
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3134 r_free = 0.3134    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3134 r_free = 0.3134    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.62   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3134
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8135
moved from start:          0.2421

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039  11936  Z= 0.153
  Angle     :  0.556   7.588  16262  Z= 0.284
  Chirality :  0.045   0.146   1844
  Planarity :  0.005   0.084   2078
  Dihedral  :  5.971  68.441   1676
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 6.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.82 %
    Favored  : 95.18 %
  Rotamer:
    Outliers :  2.55 %
    Allowed  : 11.72 %
    Favored  : 85.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 14.89 %
    Cis-general     : 0.14 %
    Twisted Proline : 0.00 %
    Twisted General : 0.14 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.11 (0.23), residues: 1472
  helix:  2.32 (0.60), residues: 84
  sheet:  0.79 (0.20), residues: 676
  loop : -0.93 (0.24), residues: 712

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B  50 
 HIS   0.002   0.001   HIS F 346 
 PHE   0.011   0.001   PHE F  81 
 TYR   0.016   0.001   TYR E  92 
 ARG   0.013   0.000   ARG C  25 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02770 (  434)
  hydrogen bonds       : angle       5.07558 ( 1242)
  SS BOND              : bond        0.00389 (    6)
  SS BOND              : angle       0.27148 (   12)
  covalent geometry    : bond        0.00368 (11930)
  covalent geometry    : angle       0.55602 (16250)

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

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

  2944 Ramachandran restraints generated.
    1472 Oldfield, 0 Emsley, 1472 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2944 Ramachandran restraints generated.
    1472 Oldfield, 0 Emsley, 1472 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  123 residues out of total 1326 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 91
  time to evaluate  : 1.283 
Fit side-chains
REVERT: A   63 ARG cc_start: 0.7888 (mtp85) cc_final: 0.7661 (mtp85)
REVERT: A  230 LYS cc_start: 0.6909 (mtmm) cc_final: 0.6598 (mtpp)
REVERT: A  308 LYS cc_start: 0.7699 (ptpp) cc_final: 0.7095 (mtpp)
REVERT: C   25 ARG cc_start: 0.8241 (ttm110) cc_final: 0.7751 (ttm-80)
REVERT: C   28 GLN cc_start: 0.8277 (mp10) cc_final: 0.8074 (mm-40)
REVERT: D   22 ARG cc_start: 0.7549 (tpt-90) cc_final: 0.7310 (tpt-90)
REVERT: E   25 ARG cc_start: 0.7828 (ttm110) cc_final: 0.7599 (ttm110)
REVERT: F   63 ARG cc_start: 0.7907 (mtp85) cc_final: 0.7679 (mtp85)
REVERT: F  308 LYS cc_start: 0.7654 (ptpp) cc_final: 0.7035 (mtpp)
  outliers start: 32
  outliers final: 30
  residues processed: 113
  average time/residue: 0.3047
  time to fit residues: 46.2746
Evaluate side-chains
  116 residues out of total 1326 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 86
  time to evaluate  : 1.268 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   60 VAL
Chi-restraints excluded: chain A residue  147 ILE
Chi-restraints excluded: chain A residue  165 VAL
Chi-restraints excluded: chain A residue  200 LEU
Chi-restraints excluded: chain A residue  219 VAL
Chi-restraints excluded: chain A residue  336 VAL
Chi-restraints excluded: chain A residue  405 LEU
Chi-restraints excluded: chain B residue   24 SER
Chi-restraints excluded: chain B residue   77 THR
Chi-restraints excluded: chain B residue  151 LEU
Chi-restraints excluded: chain C residue   64 SER
Chi-restraints excluded: chain C residue  107 ILE
Chi-restraints excluded: chain D residue   24 SER
Chi-restraints excluded: chain D residue   77 THR
Chi-restraints excluded: chain D residue   81 THR
Chi-restraints excluded: chain E residue    5 MET
Chi-restraints excluded: chain E residue   28 GLN
Chi-restraints excluded: chain E residue   64 SER
Chi-restraints excluded: chain E residue   77 SER
Chi-restraints excluded: chain E residue  107 ILE
Chi-restraints excluded: chain F residue   60 VAL
Chi-restraints excluded: chain F residue  147 ILE
Chi-restraints excluded: chain F residue  165 VAL
Chi-restraints excluded: chain F residue  200 LEU
Chi-restraints excluded: chain F residue  219 VAL
Chi-restraints excluded: chain F residue  299 THR
Chi-restraints excluded: chain F residue  336 VAL
Chi-restraints excluded: chain F residue  405 LEU
Chi-restraints excluded: chain G residue  349 GLU
Chi-restraints excluded: chain H residue  349 GLU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 16 optimal weight:    0.9980
   chunk 35 optimal weight:    0.8980
   chunk 131 optimal weight:    4.9990
   chunk 90 optimal weight:    0.9980
   chunk 126 optimal weight:    1.9990
   chunk 1 optimal weight:    0.8980
   chunk 66 optimal weight:    0.6980
   chunk 50 optimal weight:    0.6980
   chunk 5 optimal weight:    2.9990
   chunk 82 optimal weight:    0.6980
   chunk 87 optimal weight:    1.9990
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
B  87 ASN
D  87 ASN
E  28 GLN
F 190 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4061 r_free = 0.4061 target = 0.175421 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3696 r_free = 0.3696 target = 0.141433 restraints weight = 14230.556|
|-----------------------------------------------------------------------------|
r_work (start): 0.3675 rms_B_bonded: 1.66
r_work: 0.3300 rms_B_bonded: 2.36 restraints_weight: 0.5000
r_work: 0.3152 rms_B_bonded: 3.86 restraints_weight: 0.2500
r_work (final): 0.3152
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3016
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3016 r_free = 0.3016    target_work(ls_wunit_k1) = 0.091         |
| occupancies: max = 1.00  min = 0.62   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3016 r_free = 0.3016    target_work(ls_wunit_k1) = 0.091         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3016
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8127
moved from start:          0.2469

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041  11936  Z= 0.146
  Angle     :  0.545   7.726  16262  Z= 0.279
  Chirality :  0.044   0.152   1844
  Planarity :  0.005   0.074   2078
  Dihedral  :  5.927  68.655   1676
  Min Nonbonded Distance : 2.526

Molprobity Statistics.
  All-atom Clashscore : 6.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.96 %
    Favored  : 95.04 %
  Rotamer:
    Outliers :  2.71 %
    Allowed  : 11.96 %
    Favored  : 85.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 14.89 %
    Cis-general     : 0.14 %
    Twisted Proline : 0.00 %
    Twisted General : 0.14 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.13 (0.23), residues: 1472
  helix:  2.33 (0.60), residues: 84
  sheet:  0.81 (0.20), residues: 676
  loop : -0.92 (0.24), residues: 712

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP D  50 
 HIS   0.002   0.001   HIS F 346 
 PHE   0.011   0.001   PHE F  81 
 TYR   0.015   0.001   TYR E  92 
 ARG   0.010   0.000   ARG C  25 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02672 (  434)
  hydrogen bonds       : angle       4.97785 ( 1242)
  SS BOND              : bond        0.00397 (    6)
  SS BOND              : angle       0.27169 (   12)
  covalent geometry    : bond        0.00353 (11930)
  covalent geometry    : angle       0.54559 (16250)

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

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

  2944 Ramachandran restraints generated.
    1472 Oldfield, 0 Emsley, 1472 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2944 Ramachandran restraints generated.
    1472 Oldfield, 0 Emsley, 1472 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 1326 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 87
  time to evaluate  : 1.358 
Fit side-chains
REVERT: A   63 ARG cc_start: 0.7863 (mtp85) cc_final: 0.7660 (mtp85)
REVERT: A  230 LYS cc_start: 0.6927 (mtmm) cc_final: 0.6611 (mtpp)
REVERT: A  308 LYS cc_start: 0.7696 (ptpp) cc_final: 0.7110 (mtpp)
REVERT: C   28 GLN cc_start: 0.8356 (mp10) cc_final: 0.8076 (mm-40)
REVERT: D   22 ARG cc_start: 0.7497 (tpt-90) cc_final: 0.7273 (tpt-90)
REVERT: F   63 ARG cc_start: 0.7884 (mtp85) cc_final: 0.7683 (mtp85)
REVERT: F   74 LEU cc_start: 0.7505 (OUTLIER) cc_final: 0.7303 (mp)
REVERT: F  308 LYS cc_start: 0.7651 (ptpp) cc_final: 0.7001 (mtpp)
  outliers start: 34
  outliers final: 32
  residues processed: 111
  average time/residue: 0.3046
  time to fit residues: 45.7301
Evaluate side-chains
  120 residues out of total 1326 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 87
  time to evaluate  : 1.211 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   59 THR
Chi-restraints excluded: chain A residue   60 VAL
Chi-restraints excluded: chain A residue  147 ILE
Chi-restraints excluded: chain A residue  165 VAL
Chi-restraints excluded: chain A residue  200 LEU
Chi-restraints excluded: chain A residue  219 VAL
Chi-restraints excluded: chain A residue  336 VAL
Chi-restraints excluded: chain A residue  405 LEU
Chi-restraints excluded: chain B residue   24 SER
Chi-restraints excluded: chain B residue   77 THR
Chi-restraints excluded: chain B residue  151 LEU
Chi-restraints excluded: chain C residue   64 SER
Chi-restraints excluded: chain C residue  107 ILE
Chi-restraints excluded: chain D residue   24 SER
Chi-restraints excluded: chain D residue   53 SER
Chi-restraints excluded: chain D residue   77 THR
Chi-restraints excluded: chain D residue   81 THR
Chi-restraints excluded: chain E residue    5 MET
Chi-restraints excluded: chain E residue   28 GLN
Chi-restraints excluded: chain E residue   64 SER
Chi-restraints excluded: chain E residue  107 ILE
Chi-restraints excluded: chain F residue   59 THR
Chi-restraints excluded: chain F residue   60 VAL
Chi-restraints excluded: chain F residue   74 LEU
Chi-restraints excluded: chain F residue  147 ILE
Chi-restraints excluded: chain F residue  165 VAL
Chi-restraints excluded: chain F residue  200 LEU
Chi-restraints excluded: chain F residue  219 VAL
Chi-restraints excluded: chain F residue  299 THR
Chi-restraints excluded: chain F residue  336 VAL
Chi-restraints excluded: chain F residue  405 LEU
Chi-restraints excluded: chain G residue  349 GLU
Chi-restraints excluded: chain H residue  349 GLU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Traceback (most recent call last):
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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-5687/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program
    task.run()
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run
    log         = self.logger)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__
    log                   = log)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller
    func()
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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-5687/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-5687/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-5687/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-5687/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-5687/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-5687/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-5687/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-5687/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run
    line_search)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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-5687/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-5687/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-5687/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-5687/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: 63.0394 > 50:
  distance: 39 - 127:   4.554
  distance: 42 - 124:  10.468
  distance: 53 - 116:   8.401
  distance: 56 - 113:  13.174
  distance: 90 - 92:  29.000
  distance: 92 - 93:  41.489
  distance: 93 - 94:  21.114
  distance: 93 - 96:  25.439
  distance: 94 - 95:   5.731
  distance: 94 - 97:  36.055
  distance: 97 - 98:  25.518
  distance: 97 - 225:  25.114
  distance: 98 - 99:  17.135
  distance: 98 - 101:  19.268
  distance: 99 - 100:  12.402
  distance: 99 - 102:  12.733
  distance: 100 - 222:  21.032
  distance: 102 - 103:   3.908
  distance: 103 - 104:  16.783
  distance: 103 - 106:   8.563
  distance: 104 - 105:  10.055
  distance: 104 - 108:   6.119
  distance: 106 - 107:   5.113
  distance: 108 - 109:   3.464
  distance: 108 - 212:   9.107
  distance: 109 - 110:   9.424
  distance: 109 - 112:   4.040
  distance: 110 - 111:  14.159
  distance: 110 - 113:  10.137
  distance: 111 - 209:   8.153
  distance: 113 - 114:   5.813
  distance: 114 - 115:   5.716
  distance: 114 - 117:   8.181
  distance: 115 - 116:   8.715
  distance: 115 - 118:  11.895
  distance: 118 - 119:   4.206
  distance: 118 - 200:  13.315
  distance: 119 - 120:   7.881
  distance: 119 - 122:  11.700
  distance: 120 - 121:   6.090
  distance: 120 - 124:   4.897
  distance: 121 - 197:  10.810
  distance: 122 - 123:   6.749
  distance: 124 - 125:   9.292
  distance: 125 - 126:   5.473
  distance: 125 - 128:   9.650
  distance: 126 - 127:   4.797
  distance: 126 - 132:   9.947
  distance: 128 - 129:  23.627
  distance: 129 - 130:  16.808
  distance: 129 - 131:  24.342
  distance: 132 - 133:  11.533
  distance: 132 - 188:  11.128
  distance: 133 - 134:   7.511
  distance: 133 - 136:   6.492
  distance: 134 - 135:   7.328
  distance: 134 - 140:  13.211
  distance: 135 - 185:   9.022
  distance: 136 - 137:   7.641
  distance: 137 - 138:   7.163
  distance: 140 - 141:   9.217
  distance: 141 - 142:   6.161
  distance: 141 - 144:  25.006
  distance: 142 - 143:  11.160
  distance: 142 - 148:  11.633
  distance: 144 - 145:  17.023
  distance: 145 - 146:  14.788
  distance: 145 - 147:  18.085
  distance: 148 - 149:   4.129
  distance: 148 - 178:  14.353
  distance: 149 - 150:  13.124
  distance: 149 - 152:  17.400
  distance: 150 - 151:  24.545
  distance: 150 - 156:   4.570
  distance: 152 - 153:   8.235
  distance: 153 - 154:   3.141
  distance: 153 - 155:  10.645