Starting phenix.real_space_refine
on Wed Apr 30 22:52:58 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6zgd_11202/04_2025/6zgd_11202.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6zgd_11202/04_2025/6zgd_11202.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.1
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6zgd_11202/04_2025/6zgd_11202.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6zgd_11202/04_2025/6zgd_11202.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6zgd_11202/04_2025/6zgd_11202.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6zgd_11202/04_2025/6zgd_11202.cif"
  }
  resolution = 4.1
  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=   0.003
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      20      5.16       5
     C    6745      2.51       5
     N    1685      2.21       5
     O    1725      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 64 residue(s): 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib"
  Total number of atoms: 10175
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 2035
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 288, 2035
          Classifications: {'peptide': 288}
          Incomplete info: {'truncation_to_alanine': 96}
          Link IDs: {'PTRANS': 17, 'TRANS': 270}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 308
          Unresolved non-hydrogen angles: 395
          Unresolved non-hydrogen dihedrals: 238
          Unresolved non-hydrogen chiralities: 36
          Planarities with less than four sites: {'GLN:plan1': 3, 'TYR:plan': 2, 'ASN:plan1': 5, 'TRP:plan': 1, 'ASP:plan': 12, 'PHE:plan': 2, 'GLU:plan': 12, 'ARG:plan': 4}
          Unresolved non-hydrogen planarities: 166
    Chain: "B"
      Number of atoms: 2035
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 288, 2035
          Classifications: {'peptide': 288}
          Incomplete info: {'truncation_to_alanine': 96}
          Link IDs: {'PTRANS': 17, 'TRANS': 270}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 308
          Unresolved non-hydrogen angles: 395
          Unresolved non-hydrogen dihedrals: 238
          Unresolved non-hydrogen chiralities: 36
          Planarities with less than four sites: {'GLN:plan1': 3, 'TYR:plan': 2, 'ASN:plan1': 5, 'TRP:plan': 1, 'ASP:plan': 12, 'PHE:plan': 2, 'GLU:plan': 12, 'ARG:plan': 4}
          Unresolved non-hydrogen planarities: 166
    Chain: "C"
      Number of atoms: 2035
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 288, 2035
          Classifications: {'peptide': 288}
          Incomplete info: {'truncation_to_alanine': 96}
          Link IDs: {'PTRANS': 17, 'TRANS': 270}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 308
          Unresolved non-hydrogen angles: 395
          Unresolved non-hydrogen dihedrals: 238
          Unresolved non-hydrogen chiralities: 36
          Planarities with less than four sites: {'GLN:plan1': 3, 'TYR:plan': 2, 'ASN:plan1': 5, 'TRP:plan': 1, 'ASP:plan': 12, 'PHE:plan': 2, 'GLU:plan': 12, 'ARG:plan': 4}
          Unresolved non-hydrogen planarities: 166
    Chain: "D"
      Number of atoms: 2035
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 288, 2035
          Classifications: {'peptide': 288}
          Incomplete info: {'truncation_to_alanine': 96}
          Link IDs: {'PTRANS': 17, 'TRANS': 270}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 308
          Unresolved non-hydrogen angles: 395
          Unresolved non-hydrogen dihedrals: 238
          Unresolved non-hydrogen chiralities: 36
          Planarities with less than four sites: {'GLN:plan1': 3, 'TYR:plan': 2, 'ASN:plan1': 5, 'TRP:plan': 1, 'ASP:plan': 12, 'PHE:plan': 2, 'GLU:plan': 12, 'ARG:plan': 4}
          Unresolved non-hydrogen planarities: 166
    Chain: "E"
      Number of atoms: 2035
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 288, 2035
          Classifications: {'peptide': 288}
          Incomplete info: {'truncation_to_alanine': 96}
          Link IDs: {'PTRANS': 17, 'TRANS': 270}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 308
          Unresolved non-hydrogen angles: 395
          Unresolved non-hydrogen dihedrals: 238
          Unresolved non-hydrogen chiralities: 36
          Planarities with less than four sites: {'GLN:plan1': 3, 'TYR:plan': 2, 'ASN:plan1': 5, 'TRP:plan': 1, 'ASP:plan': 12, 'PHE:plan': 2, 'GLU:plan': 12, 'ARG:plan': 4}
          Unresolved non-hydrogen planarities: 166
  Time building chain proxies: 6.36, per 1000 atoms: 0.63
  Number of scatterers: 10175
  At special positions: 0
  Unit cell: (89.38, 87.74, 112.34, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      20     16.00
     O    1725      8.00
     N    1685      7.00
     C    6745      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.53
  Conformation dependent library (CDL) restraints added in 1.3 seconds
  

  2800 Ramachandran restraints generated.
    1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2840

  Finding SS restraints...
    Secondary structure from input PDB file:
      30 helices and 15 sheets defined
      38.5% alpha, 25.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.05
  Creating SS restraints...
    Processing helix  chain 'A' and resid 152 through 156
    Processing helix  chain 'A' and resid 196 through 201
    Processing helix  chain 'A' and resid 201 through 214
      removed outlier: 3.714A  pdb=" N   MET A 205 " --> pdb=" O   ILE A 201 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 220 through 244
      removed outlier: 4.300A  pdb=" N   THR A 226 " --> pdb=" O   GLU A 222 " (cutoff:3.500A)
      removed outlier: 4.102A  pdb=" N   THR A 231 " --> pdb=" O   LEU A 227 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 253 through 282
      removed outlier: 3.887A  pdb=" N   PHE A 260 " --> pdb=" O   GLY A 256 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 284 through 314
      Proline residue:  A 300  - end of helix
    Processing helix  chain 'B' and resid 152 through 156
    Processing helix  chain 'B' and resid 196 through 201
    Processing helix  chain 'B' and resid 201 through 214
      removed outlier: 3.714A  pdb=" N   MET B 205 " --> pdb=" O   ILE B 201 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 220 through 244
      removed outlier: 4.299A  pdb=" N   THR B 226 " --> pdb=" O   GLU B 222 " (cutoff:3.500A)
      removed outlier: 4.102A  pdb=" N   THR B 231 " --> pdb=" O   LEU B 227 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 253 through 282
      removed outlier: 3.887A  pdb=" N   PHE B 260 " --> pdb=" O   GLY B 256 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 284 through 314
      Proline residue:  B 300  - end of helix
    Processing helix  chain 'C' and resid 152 through 156
    Processing helix  chain 'C' and resid 196 through 201
    Processing helix  chain 'C' and resid 201 through 214
      removed outlier: 3.714A  pdb=" N   MET C 205 " --> pdb=" O   ILE C 201 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 220 through 244
      removed outlier: 4.300A  pdb=" N   THR C 226 " --> pdb=" O   GLU C 222 " (cutoff:3.500A)
      removed outlier: 4.101A  pdb=" N   THR C 231 " --> pdb=" O   LEU C 227 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 253 through 282
      removed outlier: 3.887A  pdb=" N   PHE C 260 " --> pdb=" O   GLY C 256 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 284 through 314
      Proline residue:  C 300  - end of helix
    Processing helix  chain 'D' and resid 152 through 156
    Processing helix  chain 'D' and resid 196 through 201
    Processing helix  chain 'D' and resid 201 through 214
      removed outlier: 3.714A  pdb=" N   MET D 205 " --> pdb=" O   ILE D 201 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 220 through 244
      removed outlier: 4.299A  pdb=" N   THR D 226 " --> pdb=" O   GLU D 222 " (cutoff:3.500A)
      removed outlier: 4.102A  pdb=" N   THR D 231 " --> pdb=" O   LEU D 227 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 253 through 282
      removed outlier: 3.887A  pdb=" N   PHE D 260 " --> pdb=" O   GLY D 256 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 284 through 314
      Proline residue:  D 300  - end of helix
    Processing helix  chain 'E' and resid 152 through 156
    Processing helix  chain 'E' and resid 196 through 201
    Processing helix  chain 'E' and resid 201 through 214
      removed outlier: 3.714A  pdb=" N   MET E 205 " --> pdb=" O   ILE E 201 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 220 through 244
      removed outlier: 4.299A  pdb=" N   THR E 226 " --> pdb=" O   GLU E 222 " (cutoff:3.500A)
      removed outlier: 4.101A  pdb=" N   THR E 231 " --> pdb=" O   LEU E 227 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 253 through 282
      removed outlier: 3.887A  pdb=" N   PHE E 260 " --> pdb=" O   GLY E 256 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 284 through 314
      Proline residue:  E 300  - end of helix
    Processing sheet with id=AA1, first strand: chain 'A' and resid 86 through 94
      removed outlier: 5.265A  pdb=" N   ALA A  87 " --> pdb=" O   SER A 107 " (cutoff:3.500A)
      removed outlier: 6.765A  pdb=" N   SER A 107 " --> pdb=" O   ALA A  87 " (cutoff:3.500A)
      removed outlier: 4.895A  pdb=" N   VAL A  89 " --> pdb=" O   ARG A 105 " (cutoff:3.500A)
      removed outlier: 5.640A  pdb=" N   ARG A 105 " --> pdb=" O   VAL A  89 " (cutoff:3.500A)
      removed outlier: 3.515A  pdb=" N   PHE A  37 " --> pdb=" O   VAL A 110 " (cutoff:3.500A)
      removed outlier: 7.736A  pdb=" N   THR A  36 " --> pdb=" O   SER A  29 " (cutoff:3.500A)
      removed outlier: 7.377A  pdb=" N   SER A  29 " --> pdb=" O   THR A  36 " (cutoff:3.500A)
      removed outlier: 6.625A  pdb=" N   LYS A  38 " --> pdb=" O   CYS A  27 " (cutoff:3.500A)
      removed outlier: 5.076A  pdb=" N   CYS A  27 " --> pdb=" O   LYS A  38 " (cutoff:3.500A)
      removed outlier: 7.236A  pdb=" N   ASN A  40 " --> pdb=" O   ILE A  25 " (cutoff:3.500A)
      removed outlier: 3.804A  pdb=" N   ILE A  25 " --> pdb=" O   ASN A  40 " (cutoff:3.500A)
      removed outlier: 3.797A  pdb=" N   PHE A  42 " --> pdb=" O   TYR A  23 " (cutoff:3.500A)
      removed outlier: 3.914A  pdb=" N   VAL A  18 " --> pdb=" O   VAL A 141 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 76 through 78
    Processing sheet with id=AA3, first strand: chain 'A' and resid 125 through 128
      removed outlier: 6.472A  pdb=" N   LYS A 183 " --> pdb=" O   VAL A 169 " (cutoff:3.500A)
      removed outlier: 4.739A  pdb=" N   VAL A 169 " --> pdb=" O   LYS A 183 " (cutoff:3.500A)
      removed outlier: 6.707A  pdb=" N   ASP A 185 " --> pdb=" O   ALA A 167 " (cutoff:3.500A)
      removed outlier: 4.467A  pdb=" N   ALA A 167 " --> pdb=" O   ASP A 185 " (cutoff:3.500A)
      removed outlier: 6.494A  pdb=" N   GLN A 187 " --> pdb=" O   PHE A 165 " (cutoff:3.500A)
      removed outlier: 4.188A  pdb=" N   PHE A 165 " --> pdb=" O   GLN A 187 " (cutoff:3.500A)
      removed outlier: 6.674A  pdb=" N   ARG A 189 " --> pdb=" O   GLU A 163 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 86 through 94
      removed outlier: 5.265A  pdb=" N   ALA B  87 " --> pdb=" O   SER B 107 " (cutoff:3.500A)
      removed outlier: 6.766A  pdb=" N   SER B 107 " --> pdb=" O   ALA B  87 " (cutoff:3.500A)
      removed outlier: 4.895A  pdb=" N   VAL B  89 " --> pdb=" O   ARG B 105 " (cutoff:3.500A)
      removed outlier: 5.640A  pdb=" N   ARG B 105 " --> pdb=" O   VAL B  89 " (cutoff:3.500A)
      removed outlier: 3.515A  pdb=" N   PHE B  37 " --> pdb=" O   VAL B 110 " (cutoff:3.500A)
      removed outlier: 7.737A  pdb=" N   THR B  36 " --> pdb=" O   SER B  29 " (cutoff:3.500A)
      removed outlier: 7.377A  pdb=" N   SER B  29 " --> pdb=" O   THR B  36 " (cutoff:3.500A)
      removed outlier: 6.625A  pdb=" N   LYS B  38 " --> pdb=" O   CYS B  27 " (cutoff:3.500A)
      removed outlier: 5.075A  pdb=" N   CYS B  27 " --> pdb=" O   LYS B  38 " (cutoff:3.500A)
      removed outlier: 7.236A  pdb=" N   ASN B  40 " --> pdb=" O   ILE B  25 " (cutoff:3.500A)
      removed outlier: 3.805A  pdb=" N   ILE B  25 " --> pdb=" O   ASN B  40 " (cutoff:3.500A)
      removed outlier: 3.798A  pdb=" N   PHE B  42 " --> pdb=" O   TYR B  23 " (cutoff:3.500A)
      removed outlier: 3.914A  pdb=" N   VAL B  18 " --> pdb=" O   VAL B 141 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 76 through 78
    Processing sheet with id=AA6, first strand: chain 'B' and resid 125 through 128
      removed outlier: 6.473A  pdb=" N   LYS B 183 " --> pdb=" O   VAL B 169 " (cutoff:3.500A)
      removed outlier: 4.739A  pdb=" N   VAL B 169 " --> pdb=" O   LYS B 183 " (cutoff:3.500A)
      removed outlier: 6.708A  pdb=" N   ASP B 185 " --> pdb=" O   ALA B 167 " (cutoff:3.500A)
      removed outlier: 4.466A  pdb=" N   ALA B 167 " --> pdb=" O   ASP B 185 " (cutoff:3.500A)
      removed outlier: 6.494A  pdb=" N   GLN B 187 " --> pdb=" O   PHE B 165 " (cutoff:3.500A)
      removed outlier: 4.188A  pdb=" N   PHE B 165 " --> pdb=" O   GLN B 187 " (cutoff:3.500A)
      removed outlier: 6.673A  pdb=" N   ARG B 189 " --> pdb=" O   GLU B 163 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'C' and resid 86 through 94
      removed outlier: 5.265A  pdb=" N   ALA C  87 " --> pdb=" O   SER C 107 " (cutoff:3.500A)
      removed outlier: 6.766A  pdb=" N   SER C 107 " --> pdb=" O   ALA C  87 " (cutoff:3.500A)
      removed outlier: 4.895A  pdb=" N   VAL C  89 " --> pdb=" O   ARG C 105 " (cutoff:3.500A)
      removed outlier: 5.640A  pdb=" N   ARG C 105 " --> pdb=" O   VAL C  89 " (cutoff:3.500A)
      removed outlier: 3.515A  pdb=" N   PHE C  37 " --> pdb=" O   VAL C 110 " (cutoff:3.500A)
      removed outlier: 7.736A  pdb=" N   THR C  36 " --> pdb=" O   SER C  29 " (cutoff:3.500A)
      removed outlier: 7.377A  pdb=" N   SER C  29 " --> pdb=" O   THR C  36 " (cutoff:3.500A)
      removed outlier: 6.625A  pdb=" N   LYS C  38 " --> pdb=" O   CYS C  27 " (cutoff:3.500A)
      removed outlier: 5.076A  pdb=" N   CYS C  27 " --> pdb=" O   LYS C  38 " (cutoff:3.500A)
      removed outlier: 7.236A  pdb=" N   ASN C  40 " --> pdb=" O   ILE C  25 " (cutoff:3.500A)
      removed outlier: 3.804A  pdb=" N   ILE C  25 " --> pdb=" O   ASN C  40 " (cutoff:3.500A)
      removed outlier: 3.797A  pdb=" N   PHE C  42 " --> pdb=" O   TYR C  23 " (cutoff:3.500A)
      removed outlier: 3.914A  pdb=" N   VAL C  18 " --> pdb=" O   VAL C 141 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'C' and resid 76 through 78
    Processing sheet with id=AA9, first strand: chain 'C' and resid 125 through 128
      removed outlier: 6.472A  pdb=" N   LYS C 183 " --> pdb=" O   VAL C 169 " (cutoff:3.500A)
      removed outlier: 4.740A  pdb=" N   VAL C 169 " --> pdb=" O   LYS C 183 " (cutoff:3.500A)
      removed outlier: 6.708A  pdb=" N   ASP C 185 " --> pdb=" O   ALA C 167 " (cutoff:3.500A)
      removed outlier: 4.467A  pdb=" N   ALA C 167 " --> pdb=" O   ASP C 185 " (cutoff:3.500A)
      removed outlier: 6.494A  pdb=" N   GLN C 187 " --> pdb=" O   PHE C 165 " (cutoff:3.500A)
      removed outlier: 4.189A  pdb=" N   PHE C 165 " --> pdb=" O   GLN C 187 " (cutoff:3.500A)
      removed outlier: 6.673A  pdb=" N   ARG C 189 " --> pdb=" O   GLU C 163 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'D' and resid 86 through 94
      removed outlier: 5.265A  pdb=" N   ALA D  87 " --> pdb=" O   SER D 107 " (cutoff:3.500A)
      removed outlier: 6.766A  pdb=" N   SER D 107 " --> pdb=" O   ALA D  87 " (cutoff:3.500A)
      removed outlier: 4.895A  pdb=" N   VAL D  89 " --> pdb=" O   ARG D 105 " (cutoff:3.500A)
      removed outlier: 5.641A  pdb=" N   ARG D 105 " --> pdb=" O   VAL D  89 " (cutoff:3.500A)
      removed outlier: 3.516A  pdb=" N   PHE D  37 " --> pdb=" O   VAL D 110 " (cutoff:3.500A)
      removed outlier: 7.737A  pdb=" N   THR D  36 " --> pdb=" O   SER D  29 " (cutoff:3.500A)
      removed outlier: 7.377A  pdb=" N   SER D  29 " --> pdb=" O   THR D  36 " (cutoff:3.500A)
      removed outlier: 6.625A  pdb=" N   LYS D  38 " --> pdb=" O   CYS D  27 " (cutoff:3.500A)
      removed outlier: 5.076A  pdb=" N   CYS D  27 " --> pdb=" O   LYS D  38 " (cutoff:3.500A)
      removed outlier: 7.236A  pdb=" N   ASN D  40 " --> pdb=" O   ILE D  25 " (cutoff:3.500A)
      removed outlier: 3.805A  pdb=" N   ILE D  25 " --> pdb=" O   ASN D  40 " (cutoff:3.500A)
      removed outlier: 3.797A  pdb=" N   PHE D  42 " --> pdb=" O   TYR D  23 " (cutoff:3.500A)
      removed outlier: 3.914A  pdb=" N   VAL D  18 " --> pdb=" O   VAL D 141 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'D' and resid 76 through 78
    Processing sheet with id=AB3, first strand: chain 'D' and resid 125 through 128
      removed outlier: 6.472A  pdb=" N   LYS D 183 " --> pdb=" O   VAL D 169 " (cutoff:3.500A)
      removed outlier: 4.739A  pdb=" N   VAL D 169 " --> pdb=" O   LYS D 183 " (cutoff:3.500A)
      removed outlier: 6.708A  pdb=" N   ASP D 185 " --> pdb=" O   ALA D 167 " (cutoff:3.500A)
      removed outlier: 4.466A  pdb=" N   ALA D 167 " --> pdb=" O   ASP D 185 " (cutoff:3.500A)
      removed outlier: 6.493A  pdb=" N   GLN D 187 " --> pdb=" O   PHE D 165 " (cutoff:3.500A)
      removed outlier: 4.188A  pdb=" N   PHE D 165 " --> pdb=" O   GLN D 187 " (cutoff:3.500A)
      removed outlier: 6.674A  pdb=" N   ARG D 189 " --> pdb=" O   GLU D 163 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'E' and resid 86 through 94
      removed outlier: 5.265A  pdb=" N   ALA E  87 " --> pdb=" O   SER E 107 " (cutoff:3.500A)
      removed outlier: 6.766A  pdb=" N   SER E 107 " --> pdb=" O   ALA E  87 " (cutoff:3.500A)
      removed outlier: 4.895A  pdb=" N   VAL E  89 " --> pdb=" O   ARG E 105 " (cutoff:3.500A)
      removed outlier: 5.640A  pdb=" N   ARG E 105 " --> pdb=" O   VAL E  89 " (cutoff:3.500A)
      removed outlier: 3.515A  pdb=" N   PHE E  37 " --> pdb=" O   VAL E 110 " (cutoff:3.500A)
      removed outlier: 7.736A  pdb=" N   THR E  36 " --> pdb=" O   SER E  29 " (cutoff:3.500A)
      removed outlier: 7.376A  pdb=" N   SER E  29 " --> pdb=" O   THR E  36 " (cutoff:3.500A)
      removed outlier: 6.625A  pdb=" N   LYS E  38 " --> pdb=" O   CYS E  27 " (cutoff:3.500A)
      removed outlier: 5.076A  pdb=" N   CYS E  27 " --> pdb=" O   LYS E  38 " (cutoff:3.500A)
      removed outlier: 7.235A  pdb=" N   ASN E  40 " --> pdb=" O   ILE E  25 " (cutoff:3.500A)
      removed outlier: 3.804A  pdb=" N   ILE E  25 " --> pdb=" O   ASN E  40 " (cutoff:3.500A)
      removed outlier: 3.798A  pdb=" N   PHE E  42 " --> pdb=" O   TYR E  23 " (cutoff:3.500A)
      removed outlier: 3.913A  pdb=" N   VAL E  18 " --> pdb=" O   VAL E 141 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'E' and resid 76 through 78
    Processing sheet with id=AB6, first strand: chain 'E' and resid 125 through 128
      removed outlier: 6.472A  pdb=" N   LYS E 183 " --> pdb=" O   VAL E 169 " (cutoff:3.500A)
      removed outlier: 4.740A  pdb=" N   VAL E 169 " --> pdb=" O   LYS E 183 " (cutoff:3.500A)
      removed outlier: 6.708A  pdb=" N   ASP E 185 " --> pdb=" O   ALA E 167 " (cutoff:3.500A)
      removed outlier: 4.466A  pdb=" N   ALA E 167 " --> pdb=" O   ASP E 185 " (cutoff:3.500A)
      removed outlier: 6.493A  pdb=" N   GLN E 187 " --> pdb=" O   PHE E 165 " (cutoff:3.500A)
      removed outlier: 4.188A  pdb=" N   PHE E 165 " --> pdb=" O   GLN E 187 " (cutoff:3.500A)
      removed outlier: 6.674A  pdb=" N   ARG E 189 " --> pdb=" O   GLU E 163 " (cutoff:3.500A)

    560 hydrogen bonds defined for protein.
    1635 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: 3.17

  Time building geometry restraints manager: 3.00 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: 3180
        1.34 -     1.46: 2421
        1.46 -     1.57: 4819
        1.57 -     1.69: 0
        1.69 -     1.81: 35
  Bond restraints: 10455
  Sorted by residual:
  bond pdb=" CG1 ILE A 233 "
       pdb=" CD1 ILE A 233 "
    ideal  model  delta    sigma   weight residual
    1.513  1.448  0.065 3.90e-02 6.57e+02 2.78e+00
  bond pdb=" CG1 ILE C 233 "
       pdb=" CD1 ILE C 233 "
    ideal  model  delta    sigma   weight residual
    1.513  1.448  0.065 3.90e-02 6.57e+02 2.74e+00
  bond pdb=" CG1 ILE E 233 "
       pdb=" CD1 ILE E 233 "
    ideal  model  delta    sigma   weight residual
    1.513  1.448  0.065 3.90e-02 6.57e+02 2.74e+00
  bond pdb=" CG1 ILE B 233 "
       pdb=" CD1 ILE B 233 "
    ideal  model  delta    sigma   weight residual
    1.513  1.449  0.064 3.90e-02 6.57e+02 2.71e+00
  bond pdb=" CG1 ILE D 233 "
       pdb=" CD1 ILE D 233 "
    ideal  model  delta    sigma   weight residual
    1.513  1.449  0.064 3.90e-02 6.57e+02 2.68e+00
  ... (remaining 10450 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.14: 13575
        1.14 -     2.29: 671
        2.29 -     3.43: 124
        3.43 -     4.58: 20
        4.58 -     5.72: 30
  Bond angle restraints: 14420
  Sorted by residual:
  angle pdb=" N   VAL D 155 "
        pdb=" CA  VAL D 155 "
        pdb=" C   VAL D 155 "
      ideal   model   delta    sigma   weight residual
     111.91  109.26    2.65 8.90e-01 1.26e+00 8.90e+00
  angle pdb=" N   VAL B 155 "
        pdb=" CA  VAL B 155 "
        pdb=" C   VAL B 155 "
      ideal   model   delta    sigma   weight residual
     111.91  109.27    2.64 8.90e-01 1.26e+00 8.82e+00
  angle pdb=" N   VAL C 155 "
        pdb=" CA  VAL C 155 "
        pdb=" C   VAL C 155 "
      ideal   model   delta    sigma   weight residual
     111.91  109.28    2.63 8.90e-01 1.26e+00 8.75e+00
  angle pdb=" N   VAL E 155 "
        pdb=" CA  VAL E 155 "
        pdb=" C   VAL E 155 "
      ideal   model   delta    sigma   weight residual
     111.91  109.30    2.61 8.90e-01 1.26e+00 8.58e+00
  angle pdb=" N   VAL A 155 "
        pdb=" CA  VAL A 155 "
        pdb=" C   VAL A 155 "
      ideal   model   delta    sigma   weight residual
     111.91  109.31    2.60 8.90e-01 1.26e+00 8.56e+00
  ... (remaining 14415 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    10.11: 5273
       10.11 -    20.23: 491
       20.23 -    30.34: 226
       30.34 -    40.46: 35
       40.46 -    50.57: 25
  Dihedral angle restraints: 6050
    sinusoidal: 1730
      harmonic: 4320
  Sorted by residual:
  dihedral pdb=" CA  PRO E   9 "
           pdb=" C   PRO E   9 "
           pdb=" N   PRO E  10 "
           pdb=" CA  PRO E  10 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -159.38  -20.62     0      5.00e+00 4.00e-02 1.70e+01
  dihedral pdb=" CA  PRO A   9 "
           pdb=" C   PRO A   9 "
           pdb=" N   PRO A  10 "
           pdb=" CA  PRO A  10 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -159.40  -20.60     0      5.00e+00 4.00e-02 1.70e+01
  dihedral pdb=" CA  PRO C   9 "
           pdb=" C   PRO C   9 "
           pdb=" N   PRO C  10 "
           pdb=" CA  PRO C  10 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -159.41  -20.59     0      5.00e+00 4.00e-02 1.70e+01
  ... (remaining 6047 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.046: 1285
       0.046 -    0.092: 333
       0.092 -    0.137: 132
       0.137 -    0.183: 5
       0.183 -    0.229: 5
  Chirality restraints: 1760
  Sorted by residual:
  chirality pdb=" CA  PHE A 299 "
            pdb=" N   PHE A 299 "
            pdb=" C   PHE A 299 "
            pdb=" CB  PHE A 299 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.28    0.23 2.00e-01 2.50e+01 1.31e+00
  chirality pdb=" CA  PHE B 299 "
            pdb=" N   PHE B 299 "
            pdb=" C   PHE B 299 "
            pdb=" CB  PHE B 299 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.28    0.23 2.00e-01 2.50e+01 1.30e+00
  chirality pdb=" CA  PHE C 299 "
            pdb=" N   PHE C 299 "
            pdb=" C   PHE C 299 "
            pdb=" CB  PHE C 299 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.28    0.23 2.00e-01 2.50e+01 1.29e+00
  ... (remaining 1757 not shown)

  Planarity restraints: 1825
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE B 198 "   -0.045 5.00e-02 4.00e+02   6.86e-02 7.53e+00
        pdb=" N   PRO B 199 "    0.119 5.00e-02 4.00e+02
        pdb=" CA  PRO B 199 "   -0.036 5.00e-02 4.00e+02
        pdb=" CD  PRO B 199 "   -0.038 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE D 198 "    0.045 5.00e-02 4.00e+02   6.85e-02 7.51e+00
        pdb=" N   PRO D 199 "   -0.118 5.00e-02 4.00e+02
        pdb=" CA  PRO D 199 "    0.035 5.00e-02 4.00e+02
        pdb=" CD  PRO D 199 "    0.038 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE A 198 "   -0.045 5.00e-02 4.00e+02   6.84e-02 7.48e+00
        pdb=" N   PRO A 199 "    0.118 5.00e-02 4.00e+02
        pdb=" CA  PRO A 199 "   -0.035 5.00e-02 4.00e+02
        pdb=" CD  PRO A 199 "   -0.038 5.00e-02 4.00e+02
  ... (remaining 1822 not shown)

  Histogram of nonbonded interaction distances:
        2.14 -     2.69: 182
        2.69 -     3.24: 10400
        3.24 -     3.79: 15383
        3.79 -     4.35: 17375
        4.35 -     4.90: 30233
  Nonbonded interactions: 73573
  Sorted by model distance:
  nonbonded pdb=" O   LEU E 209 "
            pdb=" OG  SER E 212 "
     model   vdw
     2.137 3.040
  nonbonded pdb=" O   LEU D 209 "
            pdb=" OG  SER D 212 "
     model   vdw
     2.137 3.040
  nonbonded pdb=" O   LEU C 209 "
            pdb=" OG  SER C 212 "
     model   vdw
     2.137 3.040
  nonbonded pdb=" O   LEU B 209 "
            pdb=" OG  SER B 212 "
     model   vdw
     2.138 3.040
  nonbonded pdb=" O   LEU A 209 "
            pdb=" OG  SER A 212 "
     model   vdw
     2.138 3.040
  ... (remaining 73568 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: 0.09
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'C'
  selection = chain 'B'
  selection = chain 'E'
  selection = chain 'D'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.290
  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:          0.430
  Check model and map are aligned:         0.090
  Set scattering table:                    0.110
  Process input model:                     25.770
  Find NCS groups from input model:        0.230
  Set up NCS constraints:                  0.050
  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:3.230
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   31.220
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8202
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      :  0.006   0.065  10455  Z= 0.247
  Angle     :  0.622   5.723  14420  Z= 0.352
  Chirality :  0.048   0.229   1760
  Planarity :  0.006   0.069   1825
  Dihedral  : 10.928  50.574   3210
  Min Nonbonded Distance : 2.137

Molprobity Statistics.
  All-atom Clashscore : 10.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.64 %
    Favored  : 95.36 %
  Rotamer:
    Outliers :  0.61 %
    Allowed  :  0.00 %
    Favored  : 99.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.11 (0.21), residues: 1400
  helix:  0.93 (0.21), residues: 515
  sheet: -1.41 (0.26), residues: 335
  loop : -1.88 (0.25), residues: 550

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP D 160 
 HIS   0.005   0.002   HIS A 235 
 PHE   0.025   0.002   PHE E 299 
 TYR   0.011   0.002   TYR D 251 
 ARG   0.007   0.001   ARG C 287 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.10907 (  560)
  hydrogen bonds       : angle       6.73060 ( 1635)
  covalent geometry    : bond        0.00586 (10455)
  covalent geometry    : angle       0.62183 (14420)

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

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

  2800 Ramachandran restraints generated.
    1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2800 Ramachandran restraints generated.
    1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  289 residues out of total 1300 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 284
  time to evaluate  : 1.148 
Fit side-chains
REVERT: A   38 LYS cc_start: 0.7893 (mttm) cc_final: 0.7588 (ttmm)
REVERT: A  117 ARG cc_start: 0.7693 (mtm180) cc_final: 0.7303 (mmm-85)
REVERT: A  287 ARG cc_start: 0.8701 (mtp85) cc_final: 0.8472 (mmm-85)
REVERT: B  117 ARG cc_start: 0.7648 (mtm180) cc_final: 0.7333 (mmm-85)
REVERT: B  238 PHE cc_start: 0.9275 (t80) cc_final: 0.8904 (t80)
REVERT: B  287 ARG cc_start: 0.8783 (mtp85) cc_final: 0.8487 (mmm-85)
REVERT: C  117 ARG cc_start: 0.7847 (mtm180) cc_final: 0.7432 (mmm-85)
REVERT: C  287 ARG cc_start: 0.8755 (mtp85) cc_final: 0.8492 (mmm-85)
REVERT: D   38 LYS cc_start: 0.7831 (mttm) cc_final: 0.7578 (ttmm)
REVERT: D  187 GLN cc_start: 0.7847 (mt0) cc_final: 0.7621 (tt0)
REVERT: D  239 ASN cc_start: 0.8713 (t0) cc_final: 0.8485 (t0)
REVERT: E  287 ARG cc_start: 0.8734 (mtp85) cc_final: 0.8465 (mmm-85)
  outliers start: 5
  outliers final: 0
  residues processed: 284
  average time/residue: 0.2353
  time to fit residues: 91.1258
Evaluate side-chains
  202 residues out of total 1300 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 202
  time to evaluate  : 1.181 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 118 optimal weight:    7.9990
   chunk 106 optimal weight:    0.6980
   chunk 58 optimal weight:   20.0000
   chunk 36 optimal weight:    6.9990
   chunk 71 optimal weight:    7.9990
   chunk 56 optimal weight:   10.0000
   chunk 109 optimal weight:    3.9990
   chunk 42 optimal weight:   30.0000
   chunk 66 optimal weight:    0.9990
   chunk 81 optimal weight:    3.9990
   chunk 127 optimal weight:   20.0000
   overall best weight:    3.3388

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

Flipped N/Q/H residues before XYZ refinement:
A  80 ASN
** A 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  80 ASN
D  80 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3677 r_free = 0.3677 target = 0.139692 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3121 r_free = 0.3121 target = 0.101156 restraints weight = 17554.144|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3159 r_free = 0.3159 target = 0.103613 restraints weight = 11456.769|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3186 r_free = 0.3186 target = 0.105322 restraints weight = 8596.418|
|-----------------------------------------------------------------------------|
r_work (final): 0.3162
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8264
moved from start:          0.1724

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.068  10455  Z= 0.277
  Angle     :  0.628   5.635  14420  Z= 0.347
  Chirality :  0.049   0.189   1760
  Planarity :  0.006   0.051   1825
  Dihedral  :  4.500  19.533   1525
  Min Nonbonded Distance : 2.443

Molprobity Statistics.
  All-atom Clashscore : 10.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.50 %
    Favored  : 94.50 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  7.44 %
    Favored  : 92.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.14 (0.22), residues: 1400
  helix:  0.99 (0.22), residues: 495
  sheet: -1.10 (0.27), residues: 320
  loop : -2.11 (0.25), residues: 585

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP C 160 
 HIS   0.007   0.002   HIS D 235 
 PHE   0.023   0.002   PHE C 238 
 TYR   0.009   0.002   TYR A 251 
 ARG   0.005   0.001   ARG D 287 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04057 (  560)
  hydrogen bonds       : angle       5.29730 ( 1635)
  covalent geometry    : bond        0.00654 (10455)
  covalent geometry    : angle       0.62836 (14420)

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

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

  2800 Ramachandran restraints generated.
    1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2800 Ramachandran restraints generated.
    1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  251 residues out of total 1300 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 251
  time to evaluate  : 1.047 
Fit side-chains
REVERT: A   38 LYS cc_start: 0.8007 (mttm) cc_final: 0.7584 (ttmm)
REVERT: A  200 ASN cc_start: 0.8696 (t0) cc_final: 0.8485 (t0)
REVERT: B  200 ASN cc_start: 0.8780 (t0) cc_final: 0.8530 (t0)
REVERT: B  238 PHE cc_start: 0.9313 (t80) cc_final: 0.9085 (t80)
REVERT: B  239 ASN cc_start: 0.8902 (t0) cc_final: 0.8502 (t0)
REVERT: C  200 ASN cc_start: 0.8628 (t0) cc_final: 0.8306 (t0)
REVERT: C  261 MET cc_start: 0.7981 (mmt) cc_final: 0.7694 (mmm)
REVERT: C  287 ARG cc_start: 0.8873 (mtp85) cc_final: 0.8605 (mmm-85)
REVERT: C  307 ASN cc_start: 0.8203 (t0) cc_final: 0.8000 (t0)
REVERT: D   38 LYS cc_start: 0.7897 (mttm) cc_final: 0.7557 (ttmm)
REVERT: D  243 GLU cc_start: 0.7477 (tp30) cc_final: 0.7234 (tp30)
REVERT: D  307 ASN cc_start: 0.8162 (t0) cc_final: 0.7942 (t0)
REVERT: E  192 ARG cc_start: 0.9232 (mtt-85) cc_final: 0.9012 (tpp80)
REVERT: E  287 ARG cc_start: 0.8897 (mtp85) cc_final: 0.8625 (mmm-85)
  outliers start: 0
  outliers final: 0
  residues processed: 251
  average time/residue: 0.2292
  time to fit residues: 79.3898
Evaluate side-chains
  197 residues out of total 1300 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 197
  time to evaluate  : 1.249 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 8 optimal weight:    5.9990
   chunk 0 optimal weight:   10.0000
   chunk 99 optimal weight:    6.9990
   chunk 118 optimal weight:    0.0980
   chunk 3 optimal weight:    1.9990
   chunk 78 optimal weight:    1.9990
   chunk 124 optimal weight:    9.9990
   chunk 53 optimal weight:    0.9980
   chunk 55 optimal weight:    4.9990
   chunk 81 optimal weight:    0.9980
   chunk 92 optimal weight:    9.9990
   overall best weight:    1.2184

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3753 r_free = 0.3753 target = 0.146204 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3260 r_free = 0.3260 target = 0.110858 restraints weight = 17020.492|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3276 r_free = 0.3276 target = 0.111921 restraints weight = 10831.729|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3292 r_free = 0.3292 target = 0.113108 restraints weight = 7775.376|
|-----------------------------------------------------------------------------|
r_work (final): 0.3259
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8116
moved from start:          0.2164

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.051  10455  Z= 0.146
  Angle     :  0.561   5.569  14420  Z= 0.300
  Chirality :  0.046   0.166   1760
  Planarity :  0.005   0.044   1825
  Dihedral  :  4.247  18.090   1525
  Min Nonbonded Distance : 2.497

Molprobity Statistics.
  All-atom Clashscore : 8.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.64 %
    Favored  : 97.36 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.78 %
    Favored  : 96.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.79 (0.22), residues: 1400
  helix:  1.43 (0.22), residues: 500
  sheet: -1.12 (0.27), residues: 340
  loop : -1.95 (0.26), residues: 560

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP B 213 
 HIS   0.005   0.001   HIS B 235 
 PHE   0.016   0.001   PHE C  37 
 TYR   0.008   0.001   TYR D 251 
 ARG   0.007   0.000   ARG D 287 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03279 (  560)
  hydrogen bonds       : angle       4.71120 ( 1635)
  covalent geometry    : bond        0.00358 (10455)
  covalent geometry    : angle       0.56057 (14420)

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

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

  2800 Ramachandran restraints generated.
    1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2800 Ramachandran restraints generated.
    1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  255 residues out of total 1300 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 255
  time to evaluate  : 1.065 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   38 LYS cc_start: 0.8001 (mttm) cc_final: 0.7619 (ttmm)
REVERT: A  200 ASN cc_start: 0.8601 (t0) cc_final: 0.8386 (t0)
REVERT: B  200 ASN cc_start: 0.8602 (t0) cc_final: 0.8281 (t0)
REVERT: C  192 ARG cc_start: 0.9253 (tpp80) cc_final: 0.8996 (tpp80)
REVERT: C  200 ASN cc_start: 0.8504 (t0) cc_final: 0.8065 (t0)
REVERT: C  287 ARG cc_start: 0.8904 (mtp85) cc_final: 0.8634 (mmm-85)
REVERT: C  307 ASN cc_start: 0.8172 (t0) cc_final: 0.7899 (t0)
REVERT: D   38 LYS cc_start: 0.7879 (mttm) cc_final: 0.7503 (ttmm)
REVERT: D  307 ASN cc_start: 0.8153 (t0) cc_final: 0.7858 (t0)
REVERT: E  192 ARG cc_start: 0.9172 (mtt-85) cc_final: 0.8962 (tpp80)
REVERT: E  200 ASN cc_start: 0.8711 (t0) cc_final: 0.8509 (t0)
REVERT: E  287 ARG cc_start: 0.8900 (mtp85) cc_final: 0.8613 (mmm-85)
  outliers start: 0
  outliers final: 0
  residues processed: 255
  average time/residue: 0.2878
  time to fit residues: 104.4795
Evaluate side-chains
  214 residues out of total 1300 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 214
  time to evaluate  : 1.161 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 84 optimal weight:   10.0000
   chunk 34 optimal weight:   20.0000
   chunk 96 optimal weight:   20.0000
   chunk 102 optimal weight:    0.5980
   chunk 68 optimal weight:   20.0000
   chunk 6 optimal weight:    8.9990
   chunk 60 optimal weight:    9.9990
   chunk 13 optimal weight:    7.9990
   chunk 76 optimal weight:    0.6980
   chunk 117 optimal weight:   10.0000
   chunk 128 optimal weight:    7.9990
   overall best weight:    5.2586

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

Flipped N/Q/H residues before XYZ refinement:
** D 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3618 r_free = 0.3618 target = 0.135677 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3060 r_free = 0.3060 target = 0.097210 restraints weight = 17647.980|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3100 r_free = 0.3100 target = 0.099686 restraints weight = 11188.952|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3127 r_free = 0.3127 target = 0.101429 restraints weight = 8289.601|
|-----------------------------------------------------------------------------|
r_work (final): 0.3099
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8317
moved from start:          0.2526

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.010   0.080  10455  Z= 0.420
  Angle     :  0.743   7.345  14420  Z= 0.417
  Chirality :  0.051   0.173   1760
  Planarity :  0.006   0.059   1825
  Dihedral  :  4.967  19.355   1525
  Min Nonbonded Distance : 2.462

Molprobity Statistics.
  All-atom Clashscore : 10.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.79 %
    Favored  : 92.21 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  8.29 %
    Favored  : 91.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.42 (0.22), residues: 1400
  helix:  0.71 (0.22), residues: 500
  sheet: -1.30 (0.26), residues: 325
  loop : -2.21 (0.27), residues: 575

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.003   TRP B 160 
 HIS   0.008   0.003   HIS A 235 
 PHE   0.025   0.003   PHE E 238 
 TYR   0.026   0.003   TYR D 278 
 ARG   0.006   0.000   ARG B 287 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04783 (  560)
  hydrogen bonds       : angle       5.54206 ( 1635)
  covalent geometry    : bond        0.00972 (10455)
  covalent geometry    : angle       0.74281 (14420)

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

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

  2800 Ramachandran restraints generated.
    1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2800 Ramachandran restraints generated.
    1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  222 residues out of total 1300 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 222
  time to evaluate  : 1.553 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   38 LYS cc_start: 0.7952 (mttm) cc_final: 0.7271 (mtpp)
REVERT: A   42 PHE cc_start: 0.7529 (p90) cc_final: 0.7222 (p90)
REVERT: A  200 ASN cc_start: 0.8891 (t0) cc_final: 0.8578 (t0)
REVERT: B   42 PHE cc_start: 0.7505 (p90) cc_final: 0.7261 (p90)
REVERT: B  200 ASN cc_start: 0.8929 (t0) cc_final: 0.8588 (t0)
REVERT: B  239 ASN cc_start: 0.9195 (t0) cc_final: 0.8813 (t0)
REVERT: C   42 PHE cc_start: 0.7522 (p90) cc_final: 0.7246 (p90)
REVERT: C  200 ASN cc_start: 0.8778 (t0) cc_final: 0.8407 (t0)
REVERT: C  224 ASN cc_start: 0.8874 (m-40) cc_final: 0.8166 (t0)
REVERT: C  287 ARG cc_start: 0.8971 (mtp85) cc_final: 0.8753 (mmm-85)
REVERT: C  307 ASN cc_start: 0.8288 (t0) cc_final: 0.8065 (t0)
REVERT: D   38 LYS cc_start: 0.7833 (mttm) cc_final: 0.7168 (mtpp)
REVERT: D  200 ASN cc_start: 0.8760 (t0) cc_final: 0.8287 (t0)
REVERT: D  274 THR cc_start: 0.9742 (m) cc_final: 0.9290 (t)
REVERT: D  307 ASN cc_start: 0.8259 (t0) cc_final: 0.8045 (t0)
REVERT: D  312 PHE cc_start: 0.8669 (t80) cc_final: 0.8270 (t80)
REVERT: E   42 PHE cc_start: 0.7306 (p90) cc_final: 0.7024 (p90)
REVERT: E  200 ASN cc_start: 0.8996 (t0) cc_final: 0.8625 (t0)
REVERT: E  274 THR cc_start: 0.9577 (p) cc_final: 0.9276 (t)
REVERT: E  287 ARG cc_start: 0.8958 (mtp85) cc_final: 0.8694 (mmm-85)
  outliers start: 0
  outliers final: 0
  residues processed: 222
  average time/residue: 0.2737
  time to fit residues: 84.0965
Evaluate side-chains
  188 residues out of total 1300 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 188
  time to evaluate  : 1.074 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 44 optimal weight:    2.9990
   chunk 22 optimal weight:    0.8980
   chunk 124 optimal weight:    9.9990
   chunk 95 optimal weight:   30.0000
   chunk 114 optimal weight:   30.0000
   chunk 117 optimal weight:    0.0270
   chunk 63 optimal weight:    4.9990
   chunk 71 optimal weight:   20.0000
   chunk 37 optimal weight:    2.9990
   chunk 136 optimal weight:    0.7980
   chunk 24 optimal weight:    0.8980
   overall best weight:    1.1240

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

Flipped N/Q/H residues before XYZ refinement:
C 200 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3737 r_free = 0.3737 target = 0.144749 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3183 r_free = 0.3183 target = 0.105547 restraints weight = 17287.385|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3226 r_free = 0.3226 target = 0.108383 restraints weight = 10555.699|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3257 r_free = 0.3257 target = 0.110394 restraints weight = 7651.987|
|-----------------------------------------------------------------------------|
r_work (final): 0.3236
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8140
moved from start:          0.2606

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.053  10455  Z= 0.141
  Angle     :  0.579   6.791  14420  Z= 0.306
  Chirality :  0.047   0.190   1760
  Planarity :  0.005   0.050   1825
  Dihedral  :  4.404  18.319   1525
  Min Nonbonded Distance : 2.534

Molprobity Statistics.
  All-atom Clashscore : 8.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.07 %
    Favored  : 97.93 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.90 %
    Favored  : 96.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.02 (0.22), residues: 1400
  helix:  1.19 (0.22), residues: 500
  sheet: -1.05 (0.27), residues: 325
  loop : -2.15 (0.26), residues: 575

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP B 213 
 HIS   0.006   0.002   HIS B 235 
 PHE   0.015   0.001   PHE C  37 
 TYR   0.009   0.001   TYR C 186 
 ARG   0.005   0.000   ARG D 287 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03396 (  560)
  hydrogen bonds       : angle       4.81747 ( 1635)
  covalent geometry    : bond        0.00342 (10455)
  covalent geometry    : angle       0.57853 (14420)

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

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

  2800 Ramachandran restraints generated.
    1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2800 Ramachandran restraints generated.
    1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  242 residues out of total 1300 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 242
  time to evaluate  : 1.264 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   38 LYS cc_start: 0.7929 (mttm) cc_final: 0.7294 (mtpp)
REVERT: A  200 ASN cc_start: 0.8675 (t0) cc_final: 0.8391 (t0)
REVERT: B  200 ASN cc_start: 0.8722 (t0) cc_final: 0.8450 (t0)
REVERT: B  239 ASN cc_start: 0.8964 (t0) cc_final: 0.8495 (t0)
REVERT: C  200 ASN cc_start: 0.8335 (t0) cc_final: 0.7986 (t0)
REVERT: C  224 ASN cc_start: 0.8795 (m-40) cc_final: 0.8065 (t0)
REVERT: C  248 LYS cc_start: 0.7109 (mmmt) cc_final: 0.5985 (mmtt)
REVERT: C  287 ARG cc_start: 0.9004 (mtp85) cc_final: 0.8772 (mmm-85)
REVERT: C  307 ASN cc_start: 0.8170 (t0) cc_final: 0.7896 (t0)
REVERT: D   38 LYS cc_start: 0.7838 (mttm) cc_final: 0.7186 (mtpp)
REVERT: D  200 ASN cc_start: 0.8431 (t0) cc_final: 0.7943 (t0)
REVERT: D  307 ASN cc_start: 0.8191 (t0) cc_final: 0.7930 (t0)
REVERT: E  192 ARG cc_start: 0.9195 (mtt-85) cc_final: 0.8720 (tpp80)
REVERT: E  200 ASN cc_start: 0.8780 (t0) cc_final: 0.8514 (t0)
REVERT: E  287 ARG cc_start: 0.8968 (mtp85) cc_final: 0.8734 (mmm-85)
  outliers start: 0
  outliers final: 0
  residues processed: 242
  average time/residue: 0.2536
  time to fit residues: 85.6724
Evaluate side-chains
  207 residues out of total 1300 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 207
  time to evaluate  : 1.045 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 122 optimal weight:    9.9990
   chunk 12 optimal weight:   20.0000
   chunk 2 optimal weight:    0.0870
   chunk 115 optimal weight:    9.9990
   chunk 47 optimal weight:    0.7980
   chunk 50 optimal weight:    6.9990
   chunk 91 optimal weight:   10.0000
   chunk 74 optimal weight:    0.5980
   chunk 125 optimal weight:    0.9990
   chunk 52 optimal weight:    2.9990
   chunk 126 optimal weight:    0.9990
   overall best weight:    0.6962

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

Flipped N/Q/H residues before XYZ refinement:
A 187 GLN
C 187 GLN
D 187 GLN
D 200 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3763 r_free = 0.3763 target = 0.147135 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3204 r_free = 0.3204 target = 0.107126 restraints weight = 17433.695|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3252 r_free = 0.3252 target = 0.110200 restraints weight = 10543.193|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3279 r_free = 0.3279 target = 0.112110 restraints weight = 7553.697|
|-----------------------------------------------------------------------------|
r_work (final): 0.3260
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8072
moved from start:          0.2861

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045  10455  Z= 0.121
  Angle     :  0.552   6.617  14420  Z= 0.287
  Chirality :  0.046   0.154   1760
  Planarity :  0.005   0.046   1825
  Dihedral  :  4.165  17.336   1525
  Min Nonbonded Distance : 2.501

Molprobity Statistics.
  All-atom Clashscore : 8.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.86 %
    Favored  : 97.14 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.95 %
    Favored  : 98.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.79 (0.22), residues: 1400
  helix:  1.39 (0.22), residues: 500
  sheet: -1.11 (0.26), residues: 350
  loop : -1.92 (0.27), residues: 550

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP A 213 
 HIS   0.005   0.002   HIS D 235 
 PHE   0.013   0.001   PHE C  37 
 TYR   0.009   0.001   TYR E 221 
 ARG   0.006   0.000   ARG B 287 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03027 (  560)
  hydrogen bonds       : angle       4.51993 ( 1635)
  covalent geometry    : bond        0.00288 (10455)
  covalent geometry    : angle       0.55236 (14420)

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

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

  2800 Ramachandran restraints generated.
    1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2800 Ramachandran restraints generated.
    1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  256 residues out of total 1300 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 256
  time to evaluate  : 1.046 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   38 LYS cc_start: 0.7920 (mttm) cc_final: 0.7271 (mtpp)
REVERT: A  200 ASN cc_start: 0.8590 (t0) cc_final: 0.8336 (t0)
REVERT: B  200 ASN cc_start: 0.8627 (t0) cc_final: 0.8336 (t0)
REVERT: B  239 ASN cc_start: 0.8845 (t0) cc_final: 0.8458 (t0)
REVERT: C  192 ARG cc_start: 0.9075 (mmt90) cc_final: 0.8874 (mmm-85)
REVERT: C  200 ASN cc_start: 0.8187 (t0) cc_final: 0.7879 (t0)
REVERT: C  224 ASN cc_start: 0.8794 (m-40) cc_final: 0.8221 (t0)
REVERT: C  287 ARG cc_start: 0.8969 (mtp85) cc_final: 0.8725 (mmm-85)
REVERT: C  307 ASN cc_start: 0.8128 (t0) cc_final: 0.7859 (t0)
REVERT: D   38 LYS cc_start: 0.7835 (mttm) cc_final: 0.7171 (mtpp)
REVERT: D  200 ASN cc_start: 0.8158 (t0) cc_final: 0.7757 (t0)
REVERT: D  307 ASN cc_start: 0.8157 (t0) cc_final: 0.7839 (t0)
REVERT: E  187 GLN cc_start: 0.8519 (mt0) cc_final: 0.7865 (tt0)
REVERT: E  200 ASN cc_start: 0.8683 (t0) cc_final: 0.8417 (t0)
REVERT: E  287 ARG cc_start: 0.8968 (mtp85) cc_final: 0.8731 (mmm-85)
  outliers start: 0
  outliers final: 0
  residues processed: 256
  average time/residue: 0.2089
  time to fit residues: 74.4721
Evaluate side-chains
  212 residues out of total 1300 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 212
  time to evaluate  : 1.037 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 64 optimal weight:    6.9990
   chunk 57 optimal weight:    9.9990
   chunk 92 optimal weight:   10.0000
   chunk 120 optimal weight:    8.9990
   chunk 84 optimal weight:   10.0000
   chunk 134 optimal weight:    2.9990
   chunk 112 optimal weight:    9.9990
   chunk 79 optimal weight:    0.7980
   chunk 119 optimal weight:    0.6980
   chunk 34 optimal weight:    8.9990
   chunk 107 optimal weight:    0.5980
   overall best weight:    2.4184

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

Flipped N/Q/H residues before XYZ refinement:
C 187 GLN
D 127 HIS
D 200 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3708 r_free = 0.3708 target = 0.142347 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.3135 r_free = 0.3135 target = 0.102348 restraints weight = 17813.879|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3177 r_free = 0.3177 target = 0.105100 restraints weight = 10934.705|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3207 r_free = 0.3207 target = 0.107010 restraints weight = 7969.205|
|-----------------------------------------------------------------------------|
r_work (final): 0.3197
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8179
moved from start:          0.2802

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.057  10455  Z= 0.213
  Angle     :  0.594   7.415  14420  Z= 0.319
  Chirality :  0.047   0.180   1760
  Planarity :  0.005   0.056   1825
  Dihedral  :  4.276  19.652   1525
  Min Nonbonded Distance : 2.484

Molprobity Statistics.
  All-atom Clashscore : 9.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.64 %
    Favored  : 96.36 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.02 %
    Favored  : 95.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.87 (0.22), residues: 1400
  helix:  1.34 (0.22), residues: 500
  sheet: -1.23 (0.26), residues: 350
  loop : -1.93 (0.27), residues: 550

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP A 160 
 HIS   0.006   0.002   HIS E 235 
 PHE   0.017   0.002   PHE E  37 
 TYR   0.012   0.001   TYR D 278 
 ARG   0.006   0.000   ARG B 287 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03538 (  560)
  hydrogen bonds       : angle       4.72554 ( 1635)
  covalent geometry    : bond        0.00510 (10455)
  covalent geometry    : angle       0.59385 (14420)

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

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

  2800 Ramachandran restraints generated.
    1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2800 Ramachandran restraints generated.
    1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  230 residues out of total 1300 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 230
  time to evaluate  : 1.032 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   38 LYS cc_start: 0.7910 (mttm) cc_final: 0.7278 (mtpp)
REVERT: A  200 ASN cc_start: 0.8761 (t0) cc_final: 0.8451 (t0)
REVERT: A  274 THR cc_start: 0.9583 (m) cc_final: 0.8983 (t)
REVERT: B  200 ASN cc_start: 0.8778 (t0) cc_final: 0.8482 (t0)
REVERT: B  239 ASN cc_start: 0.9064 (t0) cc_final: 0.8666 (t0)
REVERT: C  200 ASN cc_start: 0.8392 (t0) cc_final: 0.8164 (t0)
REVERT: C  224 ASN cc_start: 0.8835 (m-40) cc_final: 0.8161 (t0)
REVERT: C  287 ARG cc_start: 0.8974 (mtp85) cc_final: 0.8742 (mmm-85)
REVERT: C  307 ASN cc_start: 0.8225 (t0) cc_final: 0.7930 (t0)
REVERT: D   38 LYS cc_start: 0.7817 (mttm) cc_final: 0.7167 (mtpp)
REVERT: D  200 ASN cc_start: 0.8556 (t0) cc_final: 0.7903 (t0)
REVERT: D  307 ASN cc_start: 0.8166 (t0) cc_final: 0.7883 (t0)
REVERT: E  200 ASN cc_start: 0.8829 (t0) cc_final: 0.8537 (t0)
REVERT: E  287 ARG cc_start: 0.8979 (mtp85) cc_final: 0.8756 (mmm-85)
  outliers start: 0
  outliers final: 0
  residues processed: 230
  average time/residue: 0.2163
  time to fit residues: 69.1386
Evaluate side-chains
  196 residues out of total 1300 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 196
  time to evaluate  : 1.039 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 9 optimal weight:    5.9990
   chunk 60 optimal weight:   10.0000
   chunk 96 optimal weight:   20.0000
   chunk 97 optimal weight:    0.9980
   chunk 111 optimal weight:    5.9990
   chunk 33 optimal weight:    7.9990
   chunk 24 optimal weight:    0.7980
   chunk 58 optimal weight:    6.9990
   chunk 135 optimal weight:    0.6980
   chunk 69 optimal weight:    6.9990
   chunk 113 optimal weight:    5.9990
   overall best weight:    2.8984

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

Flipped N/Q/H residues before XYZ refinement:
D 200 ASN
E 187 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3848 r_free = 0.3848 target = 0.152130 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3316 r_free = 0.3316 target = 0.113416 restraints weight = 17496.409|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3370 r_free = 0.3370 target = 0.116881 restraints weight = 9671.298|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3405 r_free = 0.3405 target = 0.119178 restraints weight = 6600.623|
|-----------------------------------------------------------------------------|
r_work (final): 0.3275
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8190
moved from start:          0.2825

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.062  10455  Z= 0.246
  Angle     :  0.626   7.696  14420  Z= 0.339
  Chirality :  0.049   0.229   1760
  Planarity :  0.006   0.070   1825
  Dihedral  :  4.439  19.260   1525
  Min Nonbonded Distance : 2.483

Molprobity Statistics.
  All-atom Clashscore : 9.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.07 %
    Favored  : 95.93 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.59 %
    Favored  : 98.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.08 (0.22), residues: 1400
  helix:  1.12 (0.21), residues: 495
  sheet: -1.09 (0.27), residues: 325
  loop : -2.14 (0.26), residues: 580

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.002   TRP A 213 
 HIS   0.006   0.002   HIS D 235 
 PHE   0.022   0.002   PHE A 299 
 TYR   0.013   0.002   TYR D 278 
 ARG   0.007   0.000   ARG D 287 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03772 (  560)
  hydrogen bonds       : angle       4.94106 ( 1635)
  covalent geometry    : bond        0.00585 (10455)
  covalent geometry    : angle       0.62582 (14420)

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

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

  2800 Ramachandran restraints generated.
    1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2800 Ramachandran restraints generated.
    1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  230 residues out of total 1300 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 230
  time to evaluate  : 1.045 
Fit side-chains
REVERT: A   38 LYS cc_start: 0.7906 (mttm) cc_final: 0.7275 (mtpp)
REVERT: A  187 GLN cc_start: 0.8244 (tt0) cc_final: 0.8023 (mt0)
REVERT: A  200 ASN cc_start: 0.8772 (t0) cc_final: 0.8493 (t0)
REVERT: A  238 PHE cc_start: 0.9273 (t80) cc_final: 0.9000 (t80)
REVERT: A  274 THR cc_start: 0.9619 (m) cc_final: 0.9047 (t)
REVERT: B  200 ASN cc_start: 0.8869 (t0) cc_final: 0.8536 (t0)
REVERT: B  239 ASN cc_start: 0.9008 (t0) cc_final: 0.8685 (t0)
REVERT: B  248 LYS cc_start: 0.6826 (mmmt) cc_final: 0.6470 (mmmt)
REVERT: B  274 THR cc_start: 0.9428 (p) cc_final: 0.9086 (t)
REVERT: C   80 ASN cc_start: 0.9260 (m110) cc_final: 0.9047 (m-40)
REVERT: C  200 ASN cc_start: 0.8555 (t0) cc_final: 0.8194 (t0)
REVERT: C  224 ASN cc_start: 0.8865 (m-40) cc_final: 0.8161 (t0)
REVERT: C  287 ARG cc_start: 0.8966 (mtp85) cc_final: 0.8727 (mmm-85)
REVERT: C  307 ASN cc_start: 0.8217 (t0) cc_final: 0.7933 (t0)
REVERT: D   38 LYS cc_start: 0.7851 (mttm) cc_final: 0.7186 (mtpp)
REVERT: D  200 ASN cc_start: 0.8556 (t0) cc_final: 0.8070 (t0)
REVERT: D  243 GLU cc_start: 0.7415 (tp30) cc_final: 0.7109 (tp30)
REVERT: D  245 ASN cc_start: 0.8595 (t0) cc_final: 0.8340 (t0)
REVERT: D  307 ASN cc_start: 0.8197 (t0) cc_final: 0.7915 (t0)
REVERT: E  187 GLN cc_start: 0.8538 (mt0) cc_final: 0.7943 (mm110)
REVERT: E  200 ASN cc_start: 0.8845 (t0) cc_final: 0.8511 (t0)
REVERT: E  287 ARG cc_start: 0.8968 (mtp85) cc_final: 0.8728 (mmm-85)
  outliers start: 0
  outliers final: 0
  residues processed: 230
  average time/residue: 0.2135
  time to fit residues: 68.2434
Evaluate side-chains
  198 residues out of total 1300 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 198
  time to evaluate  : 1.036 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 90 optimal weight:    9.9990
   chunk 2 optimal weight:    0.9980
   chunk 76 optimal weight:    0.6980
   chunk 108 optimal weight:    1.9990
   chunk 51 optimal weight:    0.6980
   chunk 62 optimal weight:    7.9990
   chunk 84 optimal weight:    9.9990
   chunk 64 optimal weight:    6.9990
   chunk 123 optimal weight:   30.0000
   chunk 87 optimal weight:    7.9990
   chunk 118 optimal weight:    0.7980
   overall best weight:    1.0382

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

Flipped N/Q/H residues before XYZ refinement:
C 187 GLN
D 200 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3736 r_free = 0.3736 target = 0.144917 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3181 r_free = 0.3181 target = 0.105365 restraints weight = 17595.440|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3224 r_free = 0.3224 target = 0.108244 restraints weight = 10497.075|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3256 r_free = 0.3256 target = 0.110293 restraints weight = 7508.395|
|-----------------------------------------------------------------------------|
r_work (final): 0.3243
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8109
moved from start:          0.3018

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049  10455  Z= 0.139
  Angle     :  0.572   7.635  14420  Z= 0.300
  Chirality :  0.046   0.200   1760
  Planarity :  0.005   0.057   1825
  Dihedral  :  4.267  18.275   1525
  Min Nonbonded Distance : 2.475

Molprobity Statistics.
  All-atom Clashscore : 8.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.07 %
    Favored  : 96.93 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.98 %
    Favored  : 99.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.94 (0.22), residues: 1400
  helix:  1.29 (0.22), residues: 495
  sheet: -1.11 (0.27), residues: 345
  loop : -2.06 (0.26), residues: 560

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.043   0.002   TRP A 213 
 HIS   0.006   0.002   HIS D 235 
 PHE   0.021   0.001   PHE B 299 
 TYR   0.008   0.001   TYR A 186 
 ARG   0.007   0.000   ARG D 287 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03209 (  560)
  hydrogen bonds       : angle       4.63264 ( 1635)
  covalent geometry    : bond        0.00341 (10455)
  covalent geometry    : angle       0.57176 (14420)

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

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

  2800 Ramachandran restraints generated.
    1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2800 Ramachandran restraints generated.
    1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  231 residues out of total 1300 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 231
  time to evaluate  : 1.044 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   38 LYS cc_start: 0.7861 (mttm) cc_final: 0.7240 (mtpp)
REVERT: A  187 GLN cc_start: 0.8224 (tt0) cc_final: 0.7928 (mt0)
REVERT: A  200 ASN cc_start: 0.8710 (t0) cc_final: 0.8392 (t0)
REVERT: B  200 ASN cc_start: 0.8763 (t0) cc_final: 0.8424 (t0)
REVERT: B  239 ASN cc_start: 0.8912 (t0) cc_final: 0.8497 (t0)
REVERT: C  200 ASN cc_start: 0.8420 (t0) cc_final: 0.8063 (t0)
REVERT: C  224 ASN cc_start: 0.8838 (m-40) cc_final: 0.8165 (t0)
REVERT: C  287 ARG cc_start: 0.8974 (mtp85) cc_final: 0.8733 (mmm-85)
REVERT: C  307 ASN cc_start: 0.8211 (t0) cc_final: 0.7895 (t0)
REVERT: D   38 LYS cc_start: 0.7756 (mttm) cc_final: 0.7102 (mtpp)
REVERT: D  117 ARG cc_start: 0.7885 (mtp180) cc_final: 0.7315 (mmm-85)
REVERT: D  200 ASN cc_start: 0.8407 (t0) cc_final: 0.7790 (t0)
REVERT: D  243 GLU cc_start: 0.7452 (tp30) cc_final: 0.6825 (tp30)
REVERT: D  248 LYS cc_start: 0.6287 (mmtt) cc_final: 0.5909 (mmtt)
REVERT: D  307 ASN cc_start: 0.8117 (t0) cc_final: 0.7840 (t0)
REVERT: E  200 ASN cc_start: 0.8661 (t0) cc_final: 0.8339 (t0)
REVERT: E  287 ARG cc_start: 0.8999 (mtp85) cc_final: 0.8767 (mmm-85)
  outliers start: 0
  outliers final: 0
  residues processed: 231
  average time/residue: 0.2211
  time to fit residues: 70.6347
Evaluate side-chains
  196 residues out of total 1300 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 196
  time to evaluate  : 1.138 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Traceback (most recent call last):
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/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-5669/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program
    task.run()
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run
    log         = self.logger)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__
    log                   = log)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/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-5669/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller
    func()
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/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-5669/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-5669/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-5669/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-5669/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-5669/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-5669/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-5669/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-5669/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run
    line_search)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/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-5669/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-5669/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-5669/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-5669/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: 68.982 > 50:
  distance: 7 - 100:  34.032
  distance: 10 - 97:  32.727
  distance: 19 - 90:  31.771
  distance: 22 - 87:  34.727
  distance: 48 - 112:  34.790
  distance: 50 - 53:  34.694
  distance: 51 - 109:  37.011
  distance: 53 - 54:  39.770
  distance: 54 - 57:  39.708
  distance: 55 - 56:  56.905
  distance: 58 - 95:  54.338
  distance: 60 - 63:  40.995
  distance: 64 - 65:  40.418
  distance: 64 - 67:  39.456
  distance: 68 - 69:  40.404
  distance: 69 - 70:  39.933
  distance: 69 - 72:  40.662
  distance: 70 - 71:  39.846
  distance: 73 - 79:  40.548
  distance: 74 - 77:  40.936
  distance: 75 - 76:  56.744
  distance: 81 - 84:  39.522
  distance: 82 - 83:  39.211
  distance: 84 - 85:  39.901
  distance: 84 - 86:  41.070
  distance: 87 - 88:  40.519
  distance: 89 - 90:  40.637
  distance: 93 - 94:  55.891
  distance: 94 - 95:  57.752
  distance: 98 - 99:  55.619
  distance: 98 - 101:  39.250
  distance: 99 - 100:  40.997
  distance: 99 - 109:  68.982
  distance: 102 - 103:  40.523
  distance: 102 - 104:  40.880
  distance: 109 - 110:  38.653
  distance: 111 - 112:  39.741
  distance: 111 - 114:  34.675