Starting phenix.real_space_refine
on Wed Mar 12 07:33:57 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8jv5_36668/03_2025/8jv5_36668.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8jv5_36668/03_2025/8jv5_36668.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.23
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8jv5_36668/03_2025/8jv5_36668.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8jv5_36668/03_2025/8jv5_36668.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8jv5_36668/03_2025/8jv5_36668.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8jv5_36668/03_2025/8jv5_36668.cif"
  }
  resolution = 3.23
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.001 sd=   0.094
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     Br      6      7.06       5
     S      51      5.16       5
     C    4733      2.51       5
     N    1249      2.21       5
     O    1441      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 5 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 7480
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 2428
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 316, 2428
          Classifications: {'peptide': 316}
          Incomplete info: {'truncation_to_alanine': 14}
          Link IDs: {'PCIS': 3, 'PTRANS': 15, 'TRANS': 297}
          Unresolved non-hydrogen bonds: 59
          Unresolved non-hydrogen angles: 70
          Unresolved non-hydrogen dihedrals: 50
          Unresolved non-hydrogen chiralities: 4
          Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 3, 'ASN:plan1': 1, 'HIS:plan': 1}
          Unresolved non-hydrogen planarities: 27
    Chain: "B"
      Number of atoms: 2428
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 316, 2428
          Classifications: {'peptide': 316}
          Incomplete info: {'truncation_to_alanine': 14}
          Link IDs: {'PCIS': 3, 'PTRANS': 15, 'TRANS': 297}
          Unresolved non-hydrogen bonds: 59
          Unresolved non-hydrogen angles: 70
          Unresolved non-hydrogen dihedrals: 50
          Unresolved non-hydrogen chiralities: 4
          Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 3, 'ASN:plan1': 1, 'HIS:plan': 1}
          Unresolved non-hydrogen planarities: 27
    Chain: "C"
      Number of atoms: 2435
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 317, 2435
          Classifications: {'peptide': 317}
          Incomplete info: {'truncation_to_alanine': 14}
          Link IDs: {'PCIS': 3, 'PTRANS': 15, 'TRANS': 298}
          Unresolved non-hydrogen bonds: 59
          Unresolved non-hydrogen angles: 70
          Unresolved non-hydrogen dihedrals: 50
          Unresolved non-hydrogen chiralities: 4
          Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 3, 'ASN:plan1': 1, 'HIS:plan': 1}
          Unresolved non-hydrogen planarities: 27
    Chain: "A"
      Number of atoms: 63
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 63
          Unusual residues: {'NAG': 3, 'P73': 1}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 9
          Unresolved non-hydrogen chiralities: 3
    Chain: "B"
      Number of atoms: 63
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 63
          Unusual residues: {'NAG': 3, 'P73': 1}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 9
          Unresolved non-hydrogen chiralities: 3
    Chain: "C"
      Number of atoms: 63
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 63
          Unusual residues: {'NAG': 3, 'P73': 1}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 9
          Unresolved non-hydrogen chiralities: 3
  Time building chain proxies: 5.41, per 1000 atoms: 0.72
  Number of scatterers: 7480
  At special positions: 0
  Unit cell: (91.3, 85.49, 113.71, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     Br      6     34.99
     S      51     16.00
     O    1441      8.00
     N    1249      7.00
     C    4733      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=15, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 119 " - pdb=" SG  CYS A 168 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 129 " - pdb=" SG  CYS A 152 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 135 " - pdb=" SG  CYS A 162 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 220 " - pdb=" SG  CYS A 230 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 264 " - pdb=" SG  CYS A 273 " distance=2.02
    Simple disulfide: pdb=" SG  CYS B 119 " - pdb=" SG  CYS B 168 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 129 " - pdb=" SG  CYS B 152 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 135 " - pdb=" SG  CYS B 162 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 220 " - pdb=" SG  CYS B 230 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 264 " - pdb=" SG  CYS B 273 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 119 " - pdb=" SG  CYS C 168 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 129 " - pdb=" SG  CYS C 152 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 135 " - pdb=" SG  CYS C 162 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 220 " - pdb=" SG  CYS C 230 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 264 " - pdb=" SG  CYS C 273 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Links applied
    NAG-ASN
      " NAG A 502 " - " ASN A 213 "
      " NAG A 503 " - " ASN A 187 "
      " NAG A 504 " - " ASN A  78 "
      " NAG B 502 " - " ASN B 213 "
      " NAG B 503 " - " ASN B 187 "
      " NAG B 504 " - " ASN B  78 "
      " NAG C 502 " - " ASN C 213 "
      " NAG C 503 " - " ASN C 187 "
      " NAG C 504 " - " ASN C  78 "
  Time building additional restraints: 1.87
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  1886 Ramachandran restraints generated.
    943 Oldfield, 0 Emsley, 943 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1760

  Finding SS restraints...
    Secondary structure from input PDB file:
      21 helices and 15 sheets defined
      20.8% alpha, 47.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.90
  Creating SS restraints...
    Processing helix  chain 'A' and resid 43 through 50
      removed outlier: 3.702A  pdb=" N   ILE A  47 " --> pdb=" O   ILE A  43 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 182 through 187
    Processing helix  chain 'A' and resid 213 through 219
      removed outlier: 3.910A  pdb=" N   HIS A 219 " --> pdb=" O   SER A 215 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 235 through 241
    Processing helix  chain 'A' and resid 245 through 253
      removed outlier: 4.102A  pdb=" N   ARG A 252 " --> pdb=" O   ILE A 248 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 269 through 273
    Processing helix  chain 'A' and resid 335 through 358
    Processing helix  chain 'B' and resid 44 through 50
    Processing helix  chain 'B' and resid 182 through 187
    Processing helix  chain 'B' and resid 213 through 219
      removed outlier: 3.905A  pdb=" N   HIS B 219 " --> pdb=" O   SER B 215 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 235 through 241
    Processing helix  chain 'B' and resid 245 through 253
      removed outlier: 4.105A  pdb=" N   ARG B 252 " --> pdb=" O   ILE B 248 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 269 through 273
    Processing helix  chain 'B' and resid 335 through 358
    Processing helix  chain 'C' and resid 43 through 50
      removed outlier: 3.803A  pdb=" N   ILE C  47 " --> pdb=" O   ILE C  43 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 182 through 187
    Processing helix  chain 'C' and resid 213 through 219
      removed outlier: 3.902A  pdb=" N   HIS C 219 " --> pdb=" O   SER C 215 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 235 through 241
    Processing helix  chain 'C' and resid 245 through 253
      removed outlier: 4.110A  pdb=" N   ARG C 252 " --> pdb=" O   ILE C 248 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 269 through 273
    Processing helix  chain 'C' and resid 335 through 358
    Processing sheet with id=AA1, first strand: chain 'A' and resid 58 through 62
      removed outlier: 6.784A  pdb=" N   GLY A 254 " --> pdb=" O   ARG A 321 " (cutoff:3.500A)
      removed outlier: 8.083A  pdb=" N   ASP A 323 " --> pdb=" O   GLY A 254 " (cutoff:3.500A)
      removed outlier: 6.761A  pdb=" N   MET A 256 " --> pdb=" O   ASP A 323 " (cutoff:3.500A)
      removed outlier: 7.632A  pdb=" N   MET A 325 " --> pdb=" O   MET A 256 " (cutoff:3.500A)
      removed outlier: 6.202A  pdb=" N   VAL A 258 " --> pdb=" O   MET A 325 " (cutoff:3.500A)
      removed outlier: 7.515A  pdb=" N   PHE A 327 " --> pdb=" O   VAL A 258 " (cutoff:3.500A)
      removed outlier: 5.928A  pdb=" N   ILE A 260 " --> pdb=" O   PHE A 327 " (cutoff:3.500A)
      removed outlier: 8.176A  pdb=" N   GLN A 329 " --> pdb=" O   ILE A 260 " (cutoff:3.500A)
      removed outlier: 6.710A  pdb=" N   TRP A 262 " --> pdb=" O   GLN A 329 " (cutoff:3.500A)
      removed outlier: 7.757A  pdb=" N   GLY A 331 " --> pdb=" O   TRP A 262 " (cutoff:3.500A)
      removed outlier: 7.314A  pdb=" N   CYS A 264 " --> pdb=" O   GLY A 331 " (cutoff:3.500A)
      removed outlier: 9.272A  pdb=" N   PHE A 333 " --> pdb=" O   CYS A 264 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 147 through 153
      removed outlier: 10.061A  pdb=" N   VAL A 147 " --> pdb=" O   TRP A 167 " (cutoff:3.500A)
      removed outlier: 9.497A  pdb=" N   TRP A 167 " --> pdb=" O   VAL A 147 " (cutoff:3.500A)
      removed outlier: 8.180A  pdb=" N   THR A 149 " --> pdb=" O   LEU A 165 " (cutoff:3.500A)
      removed outlier: 8.417A  pdb=" N   LEU A 165 " --> pdb=" O   THR A 149 " (cutoff:3.500A)
      removed outlier: 5.832A  pdb=" N   ARG A 151 " --> pdb=" O   GLU A 163 " (cutoff:3.500A)
      removed outlier: 6.233A  pdb=" N   SER A 101 " --> pdb=" O   VAL A 324 " (cutoff:3.500A)
      removed outlier: 7.295A  pdb=" N   VAL A 324 " --> pdb=" O   SER A 101 " (cutoff:3.500A)
      removed outlier: 5.562A  pdb=" N   PHE A 103 " --> pdb=" O   PHE A 322 " (cutoff:3.500A)
      removed outlier: 7.125A  pdb=" N   PHE A 322 " --> pdb=" O   PHE A 103 " (cutoff:3.500A)
      removed outlier: 5.747A  pdb=" N   LEU A 105 " --> pdb=" O   ILE A 320 " (cutoff:3.500A)
      removed outlier: 6.330A  pdb=" N   ILE A 320 " --> pdb=" O   LEU A 105 " (cutoff:3.500A)
      removed outlier: 3.643A  pdb=" N   ASN A 113 " --> pdb=" O   ARG A 312 " (cutoff:3.500A)
      removed outlier: 6.011A  pdb=" N   ARG A 312 " --> pdb=" O   ASN A 113 " (cutoff:3.500A)
      removed outlier: 5.270A  pdb=" N   THR A 115 " --> pdb=" O   GLU A 310 " (cutoff:3.500A)
      removed outlier: 8.963A  pdb=" N   GLU A 310 " --> pdb=" O   THR A 115 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 64 through 72
    Processing sheet with id=AA4, first strand: chain 'A' and resid 64 through 72
    Processing sheet with id=AA5, first strand: chain 'A' and resid 75 through 77
    Processing sheet with id=AA6, first strand: chain 'B' and resid 58 through 62
      removed outlier: 6.784A  pdb=" N   GLY B 254 " --> pdb=" O   ARG B 321 " (cutoff:3.500A)
      removed outlier: 8.087A  pdb=" N   ASP B 323 " --> pdb=" O   GLY B 254 " (cutoff:3.500A)
      removed outlier: 6.763A  pdb=" N   MET B 256 " --> pdb=" O   ASP B 323 " (cutoff:3.500A)
      removed outlier: 7.635A  pdb=" N   MET B 325 " --> pdb=" O   MET B 256 " (cutoff:3.500A)
      removed outlier: 6.204A  pdb=" N   VAL B 258 " --> pdb=" O   MET B 325 " (cutoff:3.500A)
      removed outlier: 7.513A  pdb=" N   PHE B 327 " --> pdb=" O   VAL B 258 " (cutoff:3.500A)
      removed outlier: 5.932A  pdb=" N   ILE B 260 " --> pdb=" O   PHE B 327 " (cutoff:3.500A)
      removed outlier: 8.179A  pdb=" N   GLN B 329 " --> pdb=" O   ILE B 260 " (cutoff:3.500A)
      removed outlier: 6.705A  pdb=" N   TRP B 262 " --> pdb=" O   GLN B 329 " (cutoff:3.500A)
      removed outlier: 7.751A  pdb=" N   GLY B 331 " --> pdb=" O   TRP B 262 " (cutoff:3.500A)
      removed outlier: 7.319A  pdb=" N   CYS B 264 " --> pdb=" O   GLY B 331 " (cutoff:3.500A)
      removed outlier: 9.269A  pdb=" N   PHE B 333 " --> pdb=" O   CYS B 264 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 147 through 153
      removed outlier: 10.057A  pdb=" N   VAL B 147 " --> pdb=" O   TRP B 167 " (cutoff:3.500A)
      removed outlier: 9.493A  pdb=" N   TRP B 167 " --> pdb=" O   VAL B 147 " (cutoff:3.500A)
      removed outlier: 8.179A  pdb=" N   THR B 149 " --> pdb=" O   LEU B 165 " (cutoff:3.500A)
      removed outlier: 8.417A  pdb=" N   LEU B 165 " --> pdb=" O   THR B 149 " (cutoff:3.500A)
      removed outlier: 5.841A  pdb=" N   ARG B 151 " --> pdb=" O   GLU B 163 " (cutoff:3.500A)
      removed outlier: 6.228A  pdb=" N   SER B 101 " --> pdb=" O   VAL B 324 " (cutoff:3.500A)
      removed outlier: 7.296A  pdb=" N   VAL B 324 " --> pdb=" O   SER B 101 " (cutoff:3.500A)
      removed outlier: 5.563A  pdb=" N   PHE B 103 " --> pdb=" O   PHE B 322 " (cutoff:3.500A)
      removed outlier: 7.126A  pdb=" N   PHE B 322 " --> pdb=" O   PHE B 103 " (cutoff:3.500A)
      removed outlier: 5.743A  pdb=" N   LEU B 105 " --> pdb=" O   ILE B 320 " (cutoff:3.500A)
      removed outlier: 6.334A  pdb=" N   ILE B 320 " --> pdb=" O   LEU B 105 " (cutoff:3.500A)
      removed outlier: 3.635A  pdb=" N   ASN B 113 " --> pdb=" O   ARG B 312 " (cutoff:3.500A)
      removed outlier: 6.010A  pdb=" N   ARG B 312 " --> pdb=" O   ASN B 113 " (cutoff:3.500A)
      removed outlier: 5.264A  pdb=" N   THR B 115 " --> pdb=" O   GLU B 310 " (cutoff:3.500A)
      removed outlier: 8.957A  pdb=" N   GLU B 310 " --> pdb=" O   THR B 115 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 64 through 72
    Processing sheet with id=AA9, first strand: chain 'B' and resid 64 through 72
    Processing sheet with id=AB1, first strand: chain 'B' and resid 75 through 77
    Processing sheet with id=AB2, first strand: chain 'C' and resid 58 through 62
      removed outlier: 6.769A  pdb=" N   GLY C 254 " --> pdb=" O   ARG C 321 " (cutoff:3.500A)
      removed outlier: 8.076A  pdb=" N   ASP C 323 " --> pdb=" O   GLY C 254 " (cutoff:3.500A)
      removed outlier: 6.756A  pdb=" N   MET C 256 " --> pdb=" O   ASP C 323 " (cutoff:3.500A)
      removed outlier: 7.632A  pdb=" N   MET C 325 " --> pdb=" O   MET C 256 " (cutoff:3.500A)
      removed outlier: 6.200A  pdb=" N   VAL C 258 " --> pdb=" O   MET C 325 " (cutoff:3.500A)
      removed outlier: 7.512A  pdb=" N   PHE C 327 " --> pdb=" O   VAL C 258 " (cutoff:3.500A)
      removed outlier: 5.925A  pdb=" N   ILE C 260 " --> pdb=" O   PHE C 327 " (cutoff:3.500A)
      removed outlier: 8.169A  pdb=" N   GLN C 329 " --> pdb=" O   ILE C 260 " (cutoff:3.500A)
      removed outlier: 6.704A  pdb=" N   TRP C 262 " --> pdb=" O   GLN C 329 " (cutoff:3.500A)
      removed outlier: 7.742A  pdb=" N   GLY C 331 " --> pdb=" O   TRP C 262 " (cutoff:3.500A)
      removed outlier: 7.316A  pdb=" N   CYS C 264 " --> pdb=" O   GLY C 331 " (cutoff:3.500A)
      removed outlier: 9.268A  pdb=" N   PHE C 333 " --> pdb=" O   CYS C 264 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'C' and resid 147 through 153
      removed outlier: 10.058A  pdb=" N   VAL C 147 " --> pdb=" O   TRP C 167 " (cutoff:3.500A)
      removed outlier: 9.498A  pdb=" N   TRP C 167 " --> pdb=" O   VAL C 147 " (cutoff:3.500A)
      removed outlier: 8.185A  pdb=" N   THR C 149 " --> pdb=" O   LEU C 165 " (cutoff:3.500A)
      removed outlier: 8.423A  pdb=" N   LEU C 165 " --> pdb=" O   THR C 149 " (cutoff:3.500A)
      removed outlier: 5.838A  pdb=" N   ARG C 151 " --> pdb=" O   GLU C 163 " (cutoff:3.500A)
      removed outlier: 6.230A  pdb=" N   SER C 101 " --> pdb=" O   VAL C 324 " (cutoff:3.500A)
      removed outlier: 7.300A  pdb=" N   VAL C 324 " --> pdb=" O   SER C 101 " (cutoff:3.500A)
      removed outlier: 5.568A  pdb=" N   PHE C 103 " --> pdb=" O   PHE C 322 " (cutoff:3.500A)
      removed outlier: 7.123A  pdb=" N   PHE C 322 " --> pdb=" O   PHE C 103 " (cutoff:3.500A)
      removed outlier: 5.741A  pdb=" N   LEU C 105 " --> pdb=" O   ILE C 320 " (cutoff:3.500A)
      removed outlier: 6.333A  pdb=" N   ILE C 320 " --> pdb=" O   LEU C 105 " (cutoff:3.500A)
      removed outlier: 3.645A  pdb=" N   ASN C 113 " --> pdb=" O   ARG C 312 " (cutoff:3.500A)
      removed outlier: 6.009A  pdb=" N   ARG C 312 " --> pdb=" O   ASN C 113 " (cutoff:3.500A)
      removed outlier: 5.264A  pdb=" N   THR C 115 " --> pdb=" O   GLU C 310 " (cutoff:3.500A)
      removed outlier: 8.955A  pdb=" N   GLU C 310 " --> pdb=" O   THR C 115 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'C' and resid 64 through 72
    Processing sheet with id=AB5, first strand: chain 'C' and resid 64 through 72
    Processing sheet with id=AB6, first strand: chain 'C' and resid 75 through 77

    300 hydrogen bonds defined for protein.
    774 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: 1.90

  Time building geometry restraints manager: 2.23 seconds

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

  Histogram of bond lengths:
        1.18 -     1.33: 2065
        1.33 -     1.48: 2359
        1.48 -     1.63: 3155
        1.63 -     1.79: 7
        1.79 -     1.94: 65
  Bond restraints: 7651
  Sorted by residual:
  bond pdb=" C10 P73 A 501 "
       pdb=" N11 P73 A 501 "
    ideal  model  delta    sigma   weight residual
    1.373  1.454 -0.081 2.00e-02 2.50e+03 1.64e+01
  bond pdb=" C10 P73 B 501 "
       pdb=" N11 P73 B 501 "
    ideal  model  delta    sigma   weight residual
    1.373  1.453 -0.080 2.00e-02 2.50e+03 1.62e+01
  bond pdb=" C10 P73 C 501 "
       pdb=" N11 P73 C 501 "
    ideal  model  delta    sigma   weight residual
    1.373  1.452 -0.079 2.00e-02 2.50e+03 1.58e+01
  bond pdb=" C10 P73 B 501 "
       pdb=" N09 P73 B 501 "
    ideal  model  delta    sigma   weight residual
    1.377  1.454 -0.077 2.00e-02 2.50e+03 1.49e+01
  bond pdb=" C10 P73 C 501 "
       pdb=" N09 P73 C 501 "
    ideal  model  delta    sigma   weight residual
    1.377  1.453 -0.076 2.00e-02 2.50e+03 1.46e+01
  ... (remaining 7646 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.41: 10043
        1.41 -     2.81: 314
        2.81 -     4.22: 65
        4.22 -     5.62: 10
        5.62 -     7.03: 6
  Bond angle restraints: 10438
  Sorted by residual:
  angle pdb=" C   ASP B 229 "
        pdb=" N   CYS B 230 "
        pdb=" CA  CYS B 230 "
      ideal   model   delta    sigma   weight residual
     120.67  117.43    3.24 1.34e+00 5.57e-01 5.84e+00
  angle pdb=" C   ASP C 229 "
        pdb=" N   CYS C 230 "
        pdb=" CA  CYS C 230 "
      ideal   model   delta    sigma   weight residual
     120.67  117.48    3.19 1.34e+00 5.57e-01 5.68e+00
  angle pdb=" CA  CYS B 220 "
        pdb=" CB  CYS B 220 "
        pdb=" SG  CYS B 220 "
      ideal   model   delta    sigma   weight residual
     114.40  119.86   -5.46 2.30e+00 1.89e-01 5.64e+00
  angle pdb=" CA  CYS C 220 "
        pdb=" CB  CYS C 220 "
        pdb=" SG  CYS C 220 "
      ideal   model   delta    sigma   weight residual
     114.40  119.85   -5.45 2.30e+00 1.89e-01 5.61e+00
  angle pdb=" N09 P73 C 501 "
        pdb=" C10 P73 C 501 "
        pdb=" N11 P73 C 501 "
      ideal   model   delta    sigma   weight residual
     113.26  120.29   -7.03 3.00e+00 1.11e-01 5.48e+00
  ... (remaining 10433 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.23: 4215
       15.23 -    30.47: 341
       30.47 -    45.70: 80
       45.70 -    60.94: 24
       60.94 -    76.17: 12
  Dihedral angle restraints: 4672
    sinusoidal: 1927
      harmonic: 2745
  Sorted by residual:
  dihedral pdb=" CB  CYS C 220 "
           pdb=" SG  CYS C 220 "
           pdb=" SG  CYS C 230 "
           pdb=" CB  CYS C 230 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  157.49  -64.49     1      1.00e+01 1.00e-02 5.47e+01
  dihedral pdb=" CB  CYS A 220 "
           pdb=" SG  CYS A 220 "
           pdb=" SG  CYS A 230 "
           pdb=" CB  CYS A 230 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  157.43  -64.43     1      1.00e+01 1.00e-02 5.46e+01
  dihedral pdb=" CB  CYS B 220 "
           pdb=" SG  CYS B 220 "
           pdb=" SG  CYS B 230 "
           pdb=" CB  CYS B 230 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  157.33  -64.33     1      1.00e+01 1.00e-02 5.44e+01
  ... (remaining 4669 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.026: 638
       0.026 -    0.053: 315
       0.053 -    0.079: 106
       0.079 -    0.106: 85
       0.106 -    0.132: 46
  Chirality restraints: 1190
  Sorted by residual:
  chirality pdb=" CA  ILE B  94 "
            pdb=" N   ILE B  94 "
            pdb=" C   ILE B  94 "
            pdb=" CB  ILE B  94 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.13 2.00e-01 2.50e+01 4.38e-01
  chirality pdb=" C1  NAG A 504 "
            pdb=" ND2 ASN A  78 "
            pdb=" C2  NAG A 504 "
            pdb=" O5  NAG A 504 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.27   -0.13 2.00e-01 2.50e+01 4.29e-01
  chirality pdb=" CA  ILE C  94 "
            pdb=" N   ILE C  94 "
            pdb=" C   ILE C  94 "
            pdb=" CB  ILE C  94 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.28e-01
  ... (remaining 1187 not shown)

  Planarity restraints: 1363
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TYR C 198 "    0.029 5.00e-02 4.00e+02   4.40e-02 3.10e+00
        pdb=" N   PRO C 199 "   -0.076 5.00e-02 4.00e+02
        pdb=" CA  PRO C 199 "    0.023 5.00e-02 4.00e+02
        pdb=" CD  PRO C 199 "    0.025 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TYR A 198 "    0.028 5.00e-02 4.00e+02   4.29e-02 2.94e+00
        pdb=" N   PRO A 199 "   -0.074 5.00e-02 4.00e+02
        pdb=" CA  PRO A 199 "    0.022 5.00e-02 4.00e+02
        pdb=" CD  PRO A 199 "    0.024 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TYR B 198 "    0.027 5.00e-02 4.00e+02   4.17e-02 2.78e+00
        pdb=" N   PRO B 199 "   -0.072 5.00e-02 4.00e+02
        pdb=" CA  PRO B 199 "    0.021 5.00e-02 4.00e+02
        pdb=" CD  PRO B 199 "    0.023 5.00e-02 4.00e+02
  ... (remaining 1360 not shown)

  Histogram of nonbonded interaction distances:
        2.31 -     2.83: 2290
        2.83 -     3.35: 6419
        3.35 -     3.86: 11685
        3.86 -     4.38: 13688
        4.38 -     4.90: 24128
  Nonbonded interactions: 58210
  Sorted by model distance:
  nonbonded pdb=" NE  ARG B 281 "
            pdb=" OD1 ASP B 283 "
     model   vdw
     2.312 3.120
  nonbonded pdb=" NE  ARG A 281 "
            pdb=" OD1 ASP A 283 "
     model   vdw
     2.318 3.120
  nonbonded pdb=" OD2 ASP B  99 "
            pdb=" OH  TYR C 295 "
     model   vdw
     2.322 3.040
  nonbonded pdb=" NE  ARG C 281 "
            pdb=" OD1 ASP C 283 "
     model   vdw
     2.322 3.120
  nonbonded pdb=" OD2 ASP A  99 "
            pdb=" OH  TYR B 295 "
     model   vdw
     2.326 3.040
  ... (remaining 58205 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = (chain 'C' and (resid 43 through 358 or resid 501 through 504))
}

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 individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.690
  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:          0.330
  Check model and map are aligned:         0.060
  Set scattering table:                    0.070
  Process input model:                     21.330
  Find NCS groups from input model:        0.270
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.910
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   26.700
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7755
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.081   7651  Z= 0.340
  Angle     :  0.629   7.026  10438  Z= 0.320
  Chirality :  0.045   0.132   1190
  Planarity :  0.005   0.044   1354
  Dihedral  : 12.601  76.169   2867
  Min Nonbonded Distance : 2.312

Molprobity Statistics.
  All-atom Clashscore : 5.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.86 %
    Favored  : 97.14 %
  Rotamer:
    Outliers :  0.76 %
    Allowed  :  3.29 %
    Favored  : 95.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 16.67 %
    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:  0.88 (0.27), residues: 943
  helix:  1.17 (0.44), residues: 174
  sheet:  1.29 (0.29), residues: 330
  loop : -0.16 (0.27), residues: 439

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 262 
 HIS   0.000   0.000   HIS B 132 
 PHE   0.011   0.001   PHE B 327 
 TYR   0.008   0.001   TYR C 318 
 ARG   0.003   0.001   ARG B 276 

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

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

  1886 Ramachandran restraints generated.
    943 Oldfield, 0 Emsley, 943 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1886 Ramachandran restraints generated.
    943 Oldfield, 0 Emsley, 943 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  161 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 155
  time to evaluate  : 0.766 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  276 ARG cc_start: 0.6841 (mtp85) cc_final: 0.6515 (mtm180)
REVERT: B   72 LYS cc_start: 0.7822 (mtmm) cc_final: 0.7578 (mtpp)
  outliers start: 6
  outliers final: 0
  residues processed: 155
  average time/residue: 0.2337
  time to fit residues: 46.3628
Evaluate side-chains
  95 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 95
  time to evaluate  : 0.739 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 78 optimal weight:    2.9990
   chunk 70 optimal weight:    8.9990
   chunk 39 optimal weight:   30.0000
   chunk 24 optimal weight:    0.2980
   chunk 47 optimal weight:    1.9990
   chunk 37 optimal weight:    2.9990
   chunk 72 optimal weight:    5.9990
   chunk 28 optimal weight:    4.9990
   chunk 44 optimal weight:    6.9990
   chunk 54 optimal weight:    0.9980
   chunk 84 optimal weight:    0.5980
   overall best weight:    1.3784

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

Flipped N/Q/H residues before XYZ refinement:
A  54 ASN
A 247 GLN
B 247 GLN
** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 247 GLN
** C 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4094 r_free = 0.4094 target = 0.186375 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3393 r_free = 0.3393 target = 0.122904 restraints weight = 6889.522|
|-----------------------------------------------------------------------------|
r_work (start): 0.3395 rms_B_bonded: 2.66
r_work: 0.3214 rms_B_bonded: 3.22 restraints_weight: 0.5000
r_work: 0.3044 rms_B_bonded: 4.97 restraints_weight: 0.2500
r_work (final): 0.3044
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7799
moved from start:          0.1427

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   7651  Z= 0.261
  Angle     :  0.577   6.217  10438  Z= 0.304
  Chirality :  0.045   0.152   1190
  Planarity :  0.004   0.038   1354
  Dihedral  :  7.106  53.858   1231
  Min Nonbonded Distance : 2.319

Molprobity Statistics.
  All-atom Clashscore : 6.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.55 %
    Favored  : 97.45 %
  Rotamer:
    Outliers :  0.63 %
    Allowed  : 10.38 %
    Favored  : 88.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 16.67 %
    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:  0.74 (0.27), residues: 943
  helix:  0.97 (0.42), residues: 194
  sheet:  1.30 (0.29), residues: 335
  loop : -0.39 (0.28), residues: 414

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.003   TRP C 262 
 HIS   0.000   0.000   HIS A 132 
 PHE   0.011   0.002   PHE B 103 
 TYR   0.008   0.001   TYR C 318 
 ARG   0.003   0.001   ARG B 298 

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

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

  1886 Ramachandran restraints generated.
    943 Oldfield, 0 Emsley, 943 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1886 Ramachandran restraints generated.
    943 Oldfield, 0 Emsley, 943 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 102
  time to evaluate  : 0.753 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   61 ASP cc_start: 0.7855 (t0) cc_final: 0.7617 (t0)
REVERT: A  166 SER cc_start: 0.7485 (t) cc_final: 0.7272 (m)
REVERT: A  200 LYS cc_start: 0.8627 (ttmm) cc_final: 0.8326 (ttmm)
REVERT: A  276 ARG cc_start: 0.7012 (mtp85) cc_final: 0.6188 (mtm-85)
REVERT: B   72 LYS cc_start: 0.7658 (mtmm) cc_final: 0.7353 (mtpp)
REVERT: C  325 MET cc_start: 0.8432 (mtp) cc_final: 0.8201 (mtm)
  outliers start: 5
  outliers final: 4
  residues processed: 103
  average time/residue: 0.2220
  time to fit residues: 29.7825
Evaluate side-chains
  97 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 93
  time to evaluate  : 0.866 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  221 VAL
Chi-restraints excluded: chain A residue  227 ASP
Chi-restraints excluded: chain B residue  221 VAL
Chi-restraints excluded: chain C residue  221 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 52 optimal weight:    3.9990
   chunk 13 optimal weight:    1.9990
   chunk 8 optimal weight:   30.0000
   chunk 78 optimal weight:    2.9990
   chunk 53 optimal weight:    3.9990
   chunk 90 optimal weight:    0.8980
   chunk 19 optimal weight:    2.9990
   chunk 21 optimal weight:    2.9990
   chunk 72 optimal weight:    0.0270
   chunk 6 optimal weight:    1.9990
   chunk 61 optimal weight:    7.9990
   overall best weight:    1.5844

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

Flipped N/Q/H residues before XYZ refinement:
A  54 ASN
** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4065 r_free = 0.4065 target = 0.185730 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3335 r_free = 0.3335 target = 0.119759 restraints weight = 6952.138|
|-----------------------------------------------------------------------------|
r_work (start): 0.3289 rms_B_bonded: 2.87
r_work: 0.3131 rms_B_bonded: 3.28 restraints_weight: 0.5000
r_work (final): 0.3131
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7691
moved from start:          0.1938

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   7651  Z= 0.283
  Angle     :  0.572   7.685  10438  Z= 0.302
  Chirality :  0.045   0.138   1190
  Planarity :  0.004   0.037   1354
  Dihedral  :  6.838  53.991   1231
  Min Nonbonded Distance : 2.474

Molprobity Statistics.
  All-atom Clashscore : 6.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.55 %
    Favored  : 97.45 %
  Rotamer:
    Outliers :  2.53 %
    Allowed  : 11.77 %
    Favored  : 85.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 16.67 %
    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:  0.56 (0.27), residues: 943
  helix:  1.18 (0.42), residues: 183
  sheet:  1.02 (0.29), residues: 336
  loop : -0.49 (0.27), residues: 424

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP B 262 
 HIS   0.000   0.000   HIS B 132 
 PHE   0.012   0.002   PHE A 103 
 TYR   0.009   0.001   TYR A 216 
 ARG   0.002   0.001   ARG B 261 

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

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

  1886 Ramachandran restraints generated.
    943 Oldfield, 0 Emsley, 943 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1886 Ramachandran restraints generated.
    943 Oldfield, 0 Emsley, 943 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 96
  time to evaluate  : 1.016 
Fit side-chains
   revert: symmetry clash
REVERT: A   61 ASP cc_start: 0.7983 (t0) cc_final: 0.7759 (t0)
REVERT: A  108 MET cc_start: 0.8779 (ptp) cc_final: 0.8407 (ptp)
REVERT: A  166 SER cc_start: 0.7430 (t) cc_final: 0.7137 (m)
REVERT: A  276 ARG cc_start: 0.6907 (mtp85) cc_final: 0.6125 (mtm-85)
REVERT: B  164 VAL cc_start: 0.6475 (m) cc_final: 0.6213 (m)
REVERT: B  285 LYS cc_start: 0.7542 (mttm) cc_final: 0.7319 (mttp)
REVERT: C   61 ASP cc_start: 0.7921 (t0) cc_final: 0.7704 (t0)
REVERT: C   79 THR cc_start: 0.7842 (t) cc_final: 0.7438 (p)
REVERT: C  164 VAL cc_start: 0.6497 (m) cc_final: 0.6256 (m)
REVERT: C  285 LYS cc_start: 0.7580 (mtpt) cc_final: 0.7369 (ttmm)
REVERT: C  325 MET cc_start: 0.8386 (mtp) cc_final: 0.8122 (mtm)
  outliers start: 20
  outliers final: 14
  residues processed: 103
  average time/residue: 0.2248
  time to fit residues: 30.6321
Evaluate side-chains
  105 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 91
  time to evaluate  : 0.805 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  196 ILE
Chi-restraints excluded: chain A residue  221 VAL
Chi-restraints excluded: chain A residue  278 THR
Chi-restraints excluded: chain B residue  129 CYS
Chi-restraints excluded: chain B residue  152 CYS
Chi-restraints excluded: chain B residue  182 LEU
Chi-restraints excluded: chain B residue  221 VAL
Chi-restraints excluded: chain B residue  278 THR
Chi-restraints excluded: chain C residue   86 ILE
Chi-restraints excluded: chain C residue  129 CYS
Chi-restraints excluded: chain C residue  152 CYS
Chi-restraints excluded: chain C residue  196 ILE
Chi-restraints excluded: chain C residue  221 VAL
Chi-restraints excluded: chain C residue  278 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 70 optimal weight:    0.0070
   chunk 88 optimal weight:    4.9990
   chunk 54 optimal weight:    1.9990
   chunk 63 optimal weight:    9.9990
   chunk 31 optimal weight:   10.0000
   chunk 32 optimal weight:    0.5980
   chunk 1 optimal weight:    7.9990
   chunk 90 optimal weight:    0.9980
   chunk 47 optimal weight:    0.9990
   chunk 8 optimal weight:   30.0000
   chunk 9 optimal weight:    0.9990
   overall best weight:    0.7202

-------------------------------------------------------------------------------
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 = 0.4086 r_free = 0.4086 target = 0.187576 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3364 r_free = 0.3364 target = 0.122033 restraints weight = 6840.457|
|-----------------------------------------------------------------------------|
r_work (start): 0.3315 rms_B_bonded: 2.85
r_work: 0.3170 rms_B_bonded: 3.17 restraints_weight: 0.5000
r_work: 0.3001 rms_B_bonded: 4.94 restraints_weight: 0.2500
r_work (final): 0.3001
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7773
moved from start:          0.2090

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   7651  Z= 0.179
  Angle     :  0.550   9.977  10438  Z= 0.285
  Chirality :  0.044   0.146   1190
  Planarity :  0.004   0.036   1354
  Dihedral  :  6.612  57.979   1231
  Min Nonbonded Distance : 2.523

Molprobity Statistics.
  All-atom Clashscore : 5.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.55 %
    Favored  : 97.45 %
  Rotamer:
    Outliers :  2.03 %
    Allowed  : 13.29 %
    Favored  : 84.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 16.67 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.76 (0.27), residues: 943
  helix:  1.53 (0.43), residues: 179
  sheet:  1.38 (0.29), residues: 315
  loop : -0.57 (0.27), residues: 449

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP A 167 
 HIS   0.000   0.000   HIS B 132 
 PHE   0.009   0.001   PHE C 103 
 TYR   0.007   0.001   TYR B  92 
 ARG   0.004   0.000   ARG A 281 

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

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

  1886 Ramachandran restraints generated.
    943 Oldfield, 0 Emsley, 943 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1886 Ramachandran restraints generated.
    943 Oldfield, 0 Emsley, 943 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  109 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 93
  time to evaluate  : 0.789 
Fit side-chains
REVERT: A   61 ASP cc_start: 0.7949 (t0) cc_final: 0.7717 (t0)
REVERT: A  164 VAL cc_start: 0.6349 (m) cc_final: 0.6126 (m)
REVERT: A  166 SER cc_start: 0.7477 (t) cc_final: 0.7129 (m)
REVERT: A  276 ARG cc_start: 0.7063 (mtp85) cc_final: 0.6154 (mtm-85)
REVERT: B  261 ARG cc_start: 0.8386 (ttt-90) cc_final: 0.8112 (ttt-90)
REVERT: B  276 ARG cc_start: 0.7525 (mpp80) cc_final: 0.7303 (mtm-85)
REVERT: B  285 LYS cc_start: 0.7581 (mttm) cc_final: 0.7336 (mttp)
REVERT: C   61 ASP cc_start: 0.7980 (t0) cc_final: 0.7772 (t0)
REVERT: C   79 THR cc_start: 0.7831 (t) cc_final: 0.7413 (p)
REVERT: C  270 GLN cc_start: 0.7845 (pp30) cc_final: 0.6943 (pm20)
REVERT: C  285 LYS cc_start: 0.7593 (mtpt) cc_final: 0.7386 (ttmm)
REVERT: C  325 MET cc_start: 0.8431 (mtp) cc_final: 0.8170 (mtm)
  outliers start: 16
  outliers final: 15
  residues processed: 100
  average time/residue: 0.2179
  time to fit residues: 28.8433
Evaluate side-chains
  103 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 88
  time to evaluate  : 0.780 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  152 CYS
Chi-restraints excluded: chain A residue  196 ILE
Chi-restraints excluded: chain A residue  221 VAL
Chi-restraints excluded: chain A residue  278 THR
Chi-restraints excluded: chain B residue  129 CYS
Chi-restraints excluded: chain B residue  152 CYS
Chi-restraints excluded: chain B residue  168 CYS
Chi-restraints excluded: chain B residue  221 VAL
Chi-restraints excluded: chain B residue  278 THR
Chi-restraints excluded: chain B residue  325 MET
Chi-restraints excluded: chain C residue  129 CYS
Chi-restraints excluded: chain C residue  152 CYS
Chi-restraints excluded: chain C residue  196 ILE
Chi-restraints excluded: chain C residue  221 VAL
Chi-restraints excluded: chain C residue  278 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 50 optimal weight:    3.9990
   chunk 79 optimal weight:    0.4980
   chunk 20 optimal weight:    1.9990
   chunk 53 optimal weight:    3.9990
   chunk 31 optimal weight:    0.0070
   chunk 92 optimal weight:    6.9990
   chunk 74 optimal weight:    0.5980
   chunk 87 optimal weight:    1.9990
   chunk 67 optimal weight:    0.0010
   chunk 1 optimal weight:    8.9990
   chunk 25 optimal weight:    0.8980
   overall best weight:    0.4004

-------------------------------------------------------------------------------
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 = 0.4062 r_free = 0.4062 target = 0.184991 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3372 r_free = 0.3372 target = 0.121990 restraints weight = 6602.822|
|-----------------------------------------------------------------------------|
r_work (start): 0.3355 rms_B_bonded: 2.67
r_work: 0.3194 rms_B_bonded: 3.19 restraints_weight: 0.5000
r_work: 0.3026 rms_B_bonded: 4.92 restraints_weight: 0.2500
r_work (final): 0.3026
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7759
moved from start:          0.2195

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032   7651  Z= 0.147
  Angle     :  0.521   9.648  10438  Z= 0.271
  Chirality :  0.044   0.154   1190
  Planarity :  0.004   0.034   1354
  Dihedral  :  6.104  54.766   1231
  Min Nonbonded Distance : 2.599

Molprobity Statistics.
  All-atom Clashscore : 5.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.12 %
    Favored  : 97.88 %
  Rotamer:
    Outliers :  2.28 %
    Allowed  : 13.29 %
    Favored  : 84.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 16.67 %
    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:  0.99 (0.27), residues: 943
  helix:  1.97 (0.44), residues: 167
  sheet:  1.47 (0.29), residues: 315
  loop : -0.43 (0.27), residues: 461

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP A 167 
 HIS   0.000   0.000   HIS A 132 
 PHE   0.009   0.001   PHE C 103 
 TYR   0.011   0.001   TYR C 318 
 ARG   0.004   0.000   ARG C 261 

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

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

  1886 Ramachandran restraints generated.
    943 Oldfield, 0 Emsley, 943 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1886 Ramachandran restraints generated.
    943 Oldfield, 0 Emsley, 943 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  109 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 91
  time to evaluate  : 0.705 
Fit side-chains
   revert: symmetry clash
REVERT: A   61 ASP cc_start: 0.7850 (t0) cc_final: 0.7601 (t0)
REVERT: A  166 SER cc_start: 0.7436 (t) cc_final: 0.7060 (m)
REVERT: A  276 ARG cc_start: 0.7018 (mtp85) cc_final: 0.6133 (mtm-85)
REVERT: A  286 ASP cc_start: 0.7123 (t70) cc_final: 0.6743 (t0)
REVERT: B  261 ARG cc_start: 0.8392 (ttt-90) cc_final: 0.8162 (ttt-90)
REVERT: B  285 LYS cc_start: 0.7502 (mttm) cc_final: 0.7295 (mttp)
REVERT: C   79 THR cc_start: 0.7751 (t) cc_final: 0.7300 (p)
REVERT: C  147 VAL cc_start: 0.8485 (m) cc_final: 0.8111 (p)
REVERT: C  276 ARG cc_start: 0.7561 (mtm180) cc_final: 0.7333 (mtm-85)
  outliers start: 18
  outliers final: 15
  residues processed: 100
  average time/residue: 0.2246
  time to fit residues: 29.2630
Evaluate side-chains
  98 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 83
  time to evaluate  : 0.784 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  152 CYS
Chi-restraints excluded: chain A residue  196 ILE
Chi-restraints excluded: chain A residue  221 VAL
Chi-restraints excluded: chain A residue  278 THR
Chi-restraints excluded: chain B residue  129 CYS
Chi-restraints excluded: chain B residue  152 CYS
Chi-restraints excluded: chain B residue  168 CYS
Chi-restraints excluded: chain B residue  196 ILE
Chi-restraints excluded: chain B residue  221 VAL
Chi-restraints excluded: chain B residue  278 THR
Chi-restraints excluded: chain C residue  129 CYS
Chi-restraints excluded: chain C residue  152 CYS
Chi-restraints excluded: chain C residue  196 ILE
Chi-restraints excluded: chain C residue  221 VAL
Chi-restraints excluded: chain C residue  278 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 87 optimal weight:    0.9980
   chunk 10 optimal weight:    6.9990
   chunk 31 optimal weight:    6.9990
   chunk 67 optimal weight:    4.9990
   chunk 23 optimal weight:    3.9990
   chunk 29 optimal weight:    7.9990
   chunk 90 optimal weight:    0.8980
   chunk 44 optimal weight:    0.0270
   chunk 35 optimal weight:    0.9980
   chunk 76 optimal weight:    4.9990
   chunk 88 optimal weight:    0.0030
   overall best weight:    0.5848

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

Flipped N/Q/H residues before XYZ refinement:
C 341 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4106 r_free = 0.4106 target = 0.187303 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.3432 r_free = 0.3432 target = 0.125748 restraints weight = 6597.261|
|-----------------------------------------------------------------------------|
r_work (start): 0.3452 rms_B_bonded: 2.54
r_work: 0.3269 rms_B_bonded: 3.12 restraints_weight: 0.5000
r_work: 0.3108 rms_B_bonded: 4.77 restraints_weight: 0.2500
r_work (final): 0.3108
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7792
moved from start:          0.2326

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033   7651  Z= 0.164
  Angle     :  0.535   8.970  10438  Z= 0.272
  Chirality :  0.044   0.163   1190
  Planarity :  0.004   0.032   1354
  Dihedral  :  5.500  42.959   1231
  Min Nonbonded Distance : 2.590

Molprobity Statistics.
  All-atom Clashscore : 5.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.01 %
    Favored  : 97.99 %
  Rotamer:
    Outliers :  3.16 %
    Allowed  : 13.04 %
    Favored  : 83.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 16.67 %
    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:  1.03 (0.28), residues: 943
  helix:  2.06 (0.44), residues: 167
  sheet:  1.46 (0.30), residues: 309
  loop : -0.37 (0.27), residues: 467

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 167 
 HIS   0.000   0.000   HIS A 132 
 PHE   0.008   0.001   PHE C 103 
 TYR   0.011   0.001   TYR A 318 
 ARG   0.005   0.000   ARG C 261 

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

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

  1886 Ramachandran restraints generated.
    943 Oldfield, 0 Emsley, 943 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1886 Ramachandran restraints generated.
    943 Oldfield, 0 Emsley, 943 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 87
  time to evaluate  : 0.715 
Fit side-chains
   revert: symmetry clash
REVERT: A   61 ASP cc_start: 0.7744 (t0) cc_final: 0.7499 (t0)
REVERT: A  166 SER cc_start: 0.7434 (t) cc_final: 0.7061 (m)
REVERT: A  276 ARG cc_start: 0.7070 (mtp85) cc_final: 0.6209 (mtm-85)
REVERT: A  286 ASP cc_start: 0.7124 (t70) cc_final: 0.6765 (t0)
REVERT: B  261 ARG cc_start: 0.8393 (ttt-90) cc_final: 0.8154 (ttt-90)
REVERT: C   76 LEU cc_start: 0.8544 (OUTLIER) cc_final: 0.8335 (tp)
REVERT: C  147 VAL cc_start: 0.8542 (m) cc_final: 0.8226 (p)
  outliers start: 25
  outliers final: 17
  residues processed: 101
  average time/residue: 0.2269
  time to fit residues: 30.0182
Evaluate side-chains
  101 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 83
  time to evaluate  : 0.783 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  152 CYS
Chi-restraints excluded: chain A residue  196 ILE
Chi-restraints excluded: chain A residue  221 VAL
Chi-restraints excluded: chain A residue  278 THR
Chi-restraints excluded: chain B residue  152 CYS
Chi-restraints excluded: chain B residue  168 CYS
Chi-restraints excluded: chain B residue  182 LEU
Chi-restraints excluded: chain B residue  196 ILE
Chi-restraints excluded: chain B residue  221 VAL
Chi-restraints excluded: chain B residue  278 THR
Chi-restraints excluded: chain B residue  325 MET
Chi-restraints excluded: chain C residue   76 LEU
Chi-restraints excluded: chain C residue   86 ILE
Chi-restraints excluded: chain C residue  129 CYS
Chi-restraints excluded: chain C residue  152 CYS
Chi-restraints excluded: chain C residue  196 ILE
Chi-restraints excluded: chain C residue  221 VAL
Chi-restraints excluded: chain C residue  278 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 34 optimal weight:    8.9990
   chunk 29 optimal weight:    1.9990
   chunk 62 optimal weight:    5.9990
   chunk 39 optimal weight:   20.0000
   chunk 69 optimal weight:    1.9990
   chunk 15 optimal weight:    1.9990
   chunk 28 optimal weight:    4.9990
   chunk 30 optimal weight:    1.9990
   chunk 9 optimal weight:   10.0000
   chunk 91 optimal weight:    0.9980
   chunk 86 optimal weight:    5.9990
   overall best weight:    1.7988

-------------------------------------------------------------------------------
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 = 0.4095 r_free = 0.4095 target = 0.187220 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3399 r_free = 0.3399 target = 0.124150 restraints weight = 6781.535|
|-----------------------------------------------------------------------------|
r_work (start): 0.3378 rms_B_bonded: 2.63
r_work: 0.3200 rms_B_bonded: 3.18 restraints_weight: 0.5000
r_work: 0.3032 rms_B_bonded: 4.91 restraints_weight: 0.2500
r_work (final): 0.3032
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7893
moved from start:          0.2585

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.054   7651  Z= 0.318
  Angle     :  0.604  10.020  10438  Z= 0.314
  Chirality :  0.046   0.152   1190
  Planarity :  0.004   0.032   1354
  Dihedral  :  5.617  36.728   1231
  Min Nonbonded Distance : 2.578

Molprobity Statistics.
  All-atom Clashscore : 5.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.33 %
    Favored  : 97.67 %
  Rotamer:
    Outliers :  3.29 %
    Allowed  : 13.29 %
    Favored  : 83.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 16.67 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.62 (0.28), residues: 943
  helix:  1.42 (0.43), residues: 179
  sheet:  0.95 (0.29), residues: 330
  loop : -0.40 (0.28), residues: 434

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP A 272 
 HIS   0.000   0.000   HIS C 132 
 PHE   0.016   0.002   PHE B 103 
 TYR   0.012   0.001   TYR C 318 
 ARG   0.005   0.001   ARG C 261 

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

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

  1886 Ramachandran restraints generated.
    943 Oldfield, 0 Emsley, 943 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1886 Ramachandran restraints generated.
    943 Oldfield, 0 Emsley, 943 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 88
  time to evaluate  : 0.728 
Fit side-chains
   revert: symmetry clash
REVERT: A   61 ASP cc_start: 0.7982 (t0) cc_final: 0.7740 (t0)
REVERT: A   79 THR cc_start: 0.7794 (t) cc_final: 0.7232 (p)
REVERT: A  166 SER cc_start: 0.7575 (t) cc_final: 0.7241 (m)
REVERT: A  276 ARG cc_start: 0.7247 (mtp85) cc_final: 0.6399 (mtm-85)
REVERT: A  286 ASP cc_start: 0.7303 (t70) cc_final: 0.6913 (t0)
REVERT: B  286 ASP cc_start: 0.7571 (t70) cc_final: 0.7190 (t0)
REVERT: C   61 ASP cc_start: 0.8021 (t0) cc_final: 0.7800 (t0)
REVERT: C   79 THR cc_start: 0.7655 (t) cc_final: 0.7132 (p)
REVERT: C  286 ASP cc_start: 0.7329 (t70) cc_final: 0.6985 (t0)
  outliers start: 26
  outliers final: 18
  residues processed: 101
  average time/residue: 0.2140
  time to fit residues: 28.5734
Evaluate side-chains
  102 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 84
  time to evaluate  : 0.751 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   86 ILE
Chi-restraints excluded: chain A residue  152 CYS
Chi-restraints excluded: chain A residue  196 ILE
Chi-restraints excluded: chain A residue  221 VAL
Chi-restraints excluded: chain A residue  278 THR
Chi-restraints excluded: chain B residue   74 ILE
Chi-restraints excluded: chain B residue   86 ILE
Chi-restraints excluded: chain B residue  152 CYS
Chi-restraints excluded: chain B residue  168 CYS
Chi-restraints excluded: chain B residue  182 LEU
Chi-restraints excluded: chain B residue  196 ILE
Chi-restraints excluded: chain B residue  221 VAL
Chi-restraints excluded: chain C residue   86 ILE
Chi-restraints excluded: chain C residue  129 CYS
Chi-restraints excluded: chain C residue  152 CYS
Chi-restraints excluded: chain C residue  196 ILE
Chi-restraints excluded: chain C residue  221 VAL
Chi-restraints excluded: chain C residue  278 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 30 optimal weight:    4.9990
   chunk 46 optimal weight:    1.9990
   chunk 70 optimal weight:    0.2980
   chunk 24 optimal weight:    1.9990
   chunk 18 optimal weight:    6.9990
   chunk 73 optimal weight:    3.9990
   chunk 23 optimal weight:    0.9990
   chunk 89 optimal weight:    3.9990
   chunk 68 optimal weight:    0.7980
   chunk 48 optimal weight:    0.0270
   chunk 50 optimal weight:    0.8980
   overall best weight:    0.6040

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

Flipped N/Q/H residues before XYZ refinement:
** B 259 GLN ** 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 = 0.4118 r_free = 0.4118 target = 0.189276 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 62)----------------|
| r_work = 0.3436 r_free = 0.3436 target = 0.126919 restraints weight = 6799.440|
|-----------------------------------------------------------------------------|
r_work (start): 0.3428 rms_B_bonded: 2.62
r_work: 0.3266 rms_B_bonded: 3.03 restraints_weight: 0.5000
r_work: 0.3098 rms_B_bonded: 4.76 restraints_weight: 0.2500
r_work (final): 0.3098
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7844
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   0.045   7651  Z= 0.172
  Angle     :  0.535   9.278  10438  Z= 0.279
  Chirality :  0.044   0.158   1190
  Planarity :  0.004   0.033   1354
  Dihedral  :  5.090  27.109   1231
  Min Nonbonded Distance : 2.605

Molprobity Statistics.
  All-atom Clashscore : 5.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.44 %
    Favored  : 97.56 %
  Rotamer:
    Outliers :  2.66 %
    Allowed  : 14.18 %
    Favored  : 83.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 16.67 %
    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 (0.27), residues: 943
  helix:  1.96 (0.44), residues: 167
  sheet:  1.32 (0.30), residues: 312
  loop : -0.36 (0.27), residues: 464

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP A 167 
 HIS   0.000   0.000   HIS C 132 
 PHE   0.009   0.001   PHE C 103 
 TYR   0.007   0.001   TYR B  92 
 ARG   0.005   0.000   ARG C 261 

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

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

  1886 Ramachandran restraints generated.
    943 Oldfield, 0 Emsley, 943 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1886 Ramachandran restraints generated.
    943 Oldfield, 0 Emsley, 943 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 93
  time to evaluate  : 0.766 
Fit side-chains
   revert: symmetry clash
REVERT: A   61 ASP cc_start: 0.7800 (t0) cc_final: 0.7569 (t0)
REVERT: A   79 THR cc_start: 0.7824 (t) cc_final: 0.7242 (p)
REVERT: A  166 SER cc_start: 0.7545 (t) cc_final: 0.7218 (m)
REVERT: A  276 ARG cc_start: 0.7150 (mtp85) cc_final: 0.6314 (mtm-85)
REVERT: A  286 ASP cc_start: 0.7211 (t70) cc_final: 0.6869 (t0)
REVERT: B  118 LYS cc_start: 0.7666 (ttmm) cc_final: 0.7328 (mptt)
REVERT: B  191 LEU cc_start: 0.8256 (OUTLIER) cc_final: 0.7914 (tp)
REVERT: B  276 ARG cc_start: 0.7592 (mpp80) cc_final: 0.7332 (mtm-85)
REVERT: B  286 ASP cc_start: 0.7570 (t70) cc_final: 0.7186 (t0)
REVERT: C   61 ASP cc_start: 0.7845 (t0) cc_final: 0.7643 (t0)
REVERT: C   76 LEU cc_start: 0.8604 (OUTLIER) cc_final: 0.8387 (tp)
REVERT: C   79 THR cc_start: 0.7699 (t) cc_final: 0.7150 (p)
REVERT: C  108 MET cc_start: 0.8616 (ptp) cc_final: 0.8387 (ptp)
REVERT: C  147 VAL cc_start: 0.8642 (m) cc_final: 0.8265 (p)
REVERT: C  191 LEU cc_start: 0.8310 (OUTLIER) cc_final: 0.7854 (tp)
REVERT: C  286 ASP cc_start: 0.7311 (t70) cc_final: 0.6970 (t0)
  outliers start: 21
  outliers final: 18
  residues processed: 104
  average time/residue: 0.2114
  time to fit residues: 29.3537
Evaluate side-chains
  108 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 87
  time to evaluate  : 0.825 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   74 ILE
Chi-restraints excluded: chain A residue  152 CYS
Chi-restraints excluded: chain A residue  196 ILE
Chi-restraints excluded: chain A residue  221 VAL
Chi-restraints excluded: chain A residue  278 THR
Chi-restraints excluded: chain A residue  325 MET
Chi-restraints excluded: chain B residue   74 ILE
Chi-restraints excluded: chain B residue  152 CYS
Chi-restraints excluded: chain B residue  168 CYS
Chi-restraints excluded: chain B residue  182 LEU
Chi-restraints excluded: chain B residue  191 LEU
Chi-restraints excluded: chain B residue  196 ILE
Chi-restraints excluded: chain B residue  221 VAL
Chi-restraints excluded: chain C residue   76 LEU
Chi-restraints excluded: chain C residue   86 ILE
Chi-restraints excluded: chain C residue  129 CYS
Chi-restraints excluded: chain C residue  152 CYS
Chi-restraints excluded: chain C residue  191 LEU
Chi-restraints excluded: chain C residue  196 ILE
Chi-restraints excluded: chain C residue  221 VAL
Chi-restraints excluded: chain C residue  278 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 38 optimal weight:   10.0000
   chunk 0 optimal weight:   10.0000
   chunk 12 optimal weight:    0.7980
   chunk 29 optimal weight:    1.9990
   chunk 32 optimal weight:    6.9990
   chunk 6 optimal weight:    0.8980
   chunk 19 optimal weight:    3.9990
   chunk 42 optimal weight:    9.9990
   chunk 3 optimal weight:    8.9990
   chunk 47 optimal weight:    1.9990
   chunk 87 optimal weight:    0.9990
   overall best weight:    1.3386

-------------------------------------------------------------------------------
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 = 0.4101 r_free = 0.4101 target = 0.187791 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3410 r_free = 0.3410 target = 0.125000 restraints weight = 6848.484|
|-----------------------------------------------------------------------------|
r_work (start): 0.3390 rms_B_bonded: 2.67
r_work: 0.3214 rms_B_bonded: 3.19 restraints_weight: 0.5000
r_work: 0.3045 rms_B_bonded: 4.93 restraints_weight: 0.2500
r_work (final): 0.3045
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7882
moved from start:          0.2756

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.052   7651  Z= 0.260
  Angle     :  0.581   9.320  10438  Z= 0.303
  Chirality :  0.045   0.149   1190
  Planarity :  0.004   0.032   1354
  Dihedral  :  5.027  26.735   1231
  Min Nonbonded Distance : 2.612

Molprobity Statistics.
  All-atom Clashscore : 5.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.44 %
    Favored  : 97.56 %
  Rotamer:
    Outliers :  3.04 %
    Allowed  : 14.56 %
    Favored  : 82.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 16.67 %
    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:  0.74 (0.27), residues: 943
  helix:  1.75 (0.43), residues: 167
  sheet:  1.00 (0.29), residues: 322
  loop : -0.33 (0.28), residues: 454

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP C 272 
 HIS   0.000   0.000   HIS B 132 
 PHE   0.012   0.002   PHE B 103 
 TYR   0.010   0.001   TYR C 318 
 ARG   0.006   0.001   ARG C 261 

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

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

  1886 Ramachandran restraints generated.
    943 Oldfield, 0 Emsley, 943 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1886 Ramachandran restraints generated.
    943 Oldfield, 0 Emsley, 943 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  111 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 87
  time to evaluate  : 0.813 
Fit side-chains
   revert: symmetry clash
REVERT: A   61 ASP cc_start: 0.7937 (t0) cc_final: 0.7690 (t0)
REVERT: A   79 THR cc_start: 0.7823 (t) cc_final: 0.7252 (p)
REVERT: A  166 SER cc_start: 0.7576 (t) cc_final: 0.7250 (m)
REVERT: A  276 ARG cc_start: 0.7235 (mtp85) cc_final: 0.6383 (mtm-85)
REVERT: A  286 ASP cc_start: 0.7401 (t70) cc_final: 0.7044 (t0)
REVERT: B  191 LEU cc_start: 0.8260 (OUTLIER) cc_final: 0.7898 (tp)
REVERT: B  276 ARG cc_start: 0.7662 (mpp80) cc_final: 0.7428 (mtm-85)
REVERT: B  286 ASP cc_start: 0.7626 (t70) cc_final: 0.7224 (t0)
REVERT: C   61 ASP cc_start: 0.7983 (t0) cc_final: 0.7756 (t0)
REVERT: C   79 THR cc_start: 0.7688 (t) cc_final: 0.7125 (p)
REVERT: C  147 VAL cc_start: 0.8631 (m) cc_final: 0.8288 (p)
REVERT: C  191 LEU cc_start: 0.8310 (OUTLIER) cc_final: 0.7852 (tp)
REVERT: C  286 ASP cc_start: 0.7359 (t70) cc_final: 0.7011 (t0)
  outliers start: 24
  outliers final: 20
  residues processed: 100
  average time/residue: 0.2171
  time to fit residues: 28.7894
Evaluate side-chains
  106 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 84
  time to evaluate  : 0.778 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   74 ILE
Chi-restraints excluded: chain A residue   86 ILE
Chi-restraints excluded: chain A residue  152 CYS
Chi-restraints excluded: chain A residue  196 ILE
Chi-restraints excluded: chain A residue  221 VAL
Chi-restraints excluded: chain A residue  278 THR
Chi-restraints excluded: chain A residue  325 MET
Chi-restraints excluded: chain B residue   74 ILE
Chi-restraints excluded: chain B residue  152 CYS
Chi-restraints excluded: chain B residue  168 CYS
Chi-restraints excluded: chain B residue  182 LEU
Chi-restraints excluded: chain B residue  191 LEU
Chi-restraints excluded: chain B residue  196 ILE
Chi-restraints excluded: chain B residue  221 VAL
Chi-restraints excluded: chain B residue  325 MET
Chi-restraints excluded: chain C residue   86 ILE
Chi-restraints excluded: chain C residue  129 CYS
Chi-restraints excluded: chain C residue  152 CYS
Chi-restraints excluded: chain C residue  191 LEU
Chi-restraints excluded: chain C residue  196 ILE
Chi-restraints excluded: chain C residue  221 VAL
Chi-restraints excluded: chain C residue  278 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 18 optimal weight:    0.9990
   chunk 49 optimal weight:    3.9990
   chunk 87 optimal weight:    0.8980
   chunk 76 optimal weight:    2.9990
   chunk 23 optimal weight:    2.9990
   chunk 7 optimal weight:    9.9990
   chunk 58 optimal weight:    0.9980
   chunk 10 optimal weight:    7.9990
   chunk 25 optimal weight:    3.9990
   chunk 11 optimal weight:    5.9990
   chunk 56 optimal weight:    0.8980
   overall best weight:    1.3584

-------------------------------------------------------------------------------
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 = 0.4101 r_free = 0.4101 target = 0.187834 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3419 r_free = 0.3419 target = 0.125868 restraints weight = 6816.429|
|-----------------------------------------------------------------------------|
r_work (start): 0.3410 rms_B_bonded: 2.60
r_work: 0.3230 rms_B_bonded: 3.13 restraints_weight: 0.5000
r_work: 0.3061 rms_B_bonded: 4.86 restraints_weight: 0.2500
r_work (final): 0.3061
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7897
moved from start:          0.2877

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.051   7651  Z= 0.257
  Angle     :  0.579   9.290  10438  Z= 0.302
  Chirality :  0.045   0.144   1190
  Planarity :  0.004   0.033   1354
  Dihedral  :  4.918  26.915   1231
  Min Nonbonded Distance : 2.611

Molprobity Statistics.
  All-atom Clashscore : 5.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.23 %
    Favored  : 97.77 %
  Rotamer:
    Outliers :  2.91 %
    Allowed  : 14.43 %
    Favored  : 82.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 16.67 %
    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:  0.71 (0.27), residues: 943
  helix:  1.74 (0.43), residues: 167
  sheet:  0.94 (0.29), residues: 322
  loop : -0.32 (0.28), residues: 454

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP C 272 
 HIS   0.000   0.000   HIS A 132 
 PHE   0.011   0.001   PHE B 103 
 TYR   0.008   0.001   TYR B 216 
 ARG   0.005   0.001   ARG C 276 

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

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

  1886 Ramachandran restraints generated.
    943 Oldfield, 0 Emsley, 943 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1886 Ramachandran restraints generated.
    943 Oldfield, 0 Emsley, 943 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 93
  time to evaluate  : 0.851 
Fit side-chains
   revert: symmetry clash
REVERT: A   61 ASP cc_start: 0.7952 (t0) cc_final: 0.7709 (t0)
REVERT: A   79 THR cc_start: 0.7816 (t) cc_final: 0.7250 (p)
REVERT: A  166 SER cc_start: 0.7576 (t) cc_final: 0.7249 (m)
REVERT: A  276 ARG cc_start: 0.7228 (mtp85) cc_final: 0.6403 (mtm-85)
REVERT: A  286 ASP cc_start: 0.7450 (t70) cc_final: 0.7159 (t0)
REVERT: A  288 ASP cc_start: 0.8128 (m-30) cc_final: 0.7618 (t70)
REVERT: B  191 LEU cc_start: 0.8268 (OUTLIER) cc_final: 0.7896 (tp)
REVERT: B  276 ARG cc_start: 0.7684 (mpp80) cc_final: 0.7445 (mtm-85)
REVERT: B  286 ASP cc_start: 0.7617 (t70) cc_final: 0.7245 (t0)
REVERT: B  288 ASP cc_start: 0.8181 (m-30) cc_final: 0.7620 (t70)
REVERT: C   61 ASP cc_start: 0.7963 (t0) cc_final: 0.7743 (t0)
REVERT: C   79 THR cc_start: 0.7675 (t) cc_final: 0.7087 (p)
REVERT: C  147 VAL cc_start: 0.8768 (m) cc_final: 0.8439 (p)
REVERT: C  181 LEU cc_start: 0.7784 (mt) cc_final: 0.7573 (mp)
REVERT: C  191 LEU cc_start: 0.8312 (OUTLIER) cc_final: 0.7851 (tp)
REVERT: C  286 ASP cc_start: 0.7410 (t70) cc_final: 0.7106 (t0)
REVERT: C  288 ASP cc_start: 0.8183 (m-30) cc_final: 0.7529 (t70)
  outliers start: 23
  outliers final: 19
  residues processed: 105
  average time/residue: 0.2123
  time to fit residues: 29.7105
Evaluate side-chains
  113 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 92
  time to evaluate  : 0.747 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   74 ILE
Chi-restraints excluded: chain A residue  152 CYS
Chi-restraints excluded: chain A residue  196 ILE
Chi-restraints excluded: chain A residue  221 VAL
Chi-restraints excluded: chain A residue  278 THR
Chi-restraints excluded: chain A residue  325 MET
Chi-restraints excluded: chain B residue   74 ILE
Chi-restraints excluded: chain B residue  152 CYS
Chi-restraints excluded: chain B residue  168 CYS
Chi-restraints excluded: chain B residue  182 LEU
Chi-restraints excluded: chain B residue  191 LEU
Chi-restraints excluded: chain B residue  196 ILE
Chi-restraints excluded: chain B residue  221 VAL
Chi-restraints excluded: chain B residue  278 THR
Chi-restraints excluded: chain C residue   86 ILE
Chi-restraints excluded: chain C residue  129 CYS
Chi-restraints excluded: chain C residue  152 CYS
Chi-restraints excluded: chain C residue  191 LEU
Chi-restraints excluded: chain C residue  196 ILE
Chi-restraints excluded: chain C residue  221 VAL
Chi-restraints excluded: chain C residue  278 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 90 optimal weight:    0.6980
   chunk 86 optimal weight:    2.9990
   chunk 15 optimal weight:    1.9990
   chunk 44 optimal weight:    0.1980
   chunk 36 optimal weight:    0.9990
   chunk 9 optimal weight:    4.9990
   chunk 3 optimal weight:    7.9990
   chunk 65 optimal weight:    0.8980
   chunk 55 optimal weight:    0.4980
   chunk 43 optimal weight:    0.6980
   chunk 16 optimal weight:    0.4980
   overall best weight:    0.5180

-------------------------------------------------------------------------------
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 = 0.4125 r_free = 0.4125 target = 0.190041 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3449 r_free = 0.3449 target = 0.127892 restraints weight = 6825.111|
|-----------------------------------------------------------------------------|
r_work (start): 0.3440 rms_B_bonded: 2.65
r_work: 0.3279 rms_B_bonded: 3.03 restraints_weight: 0.5000
r_work: 0.3114 rms_B_bonded: 4.76 restraints_weight: 0.2500
r_work (final): 0.3114
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7830
moved from start:          0.2852

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   7651  Z= 0.167
  Angle     :  0.536   8.864  10438  Z= 0.279
  Chirality :  0.044   0.142   1190
  Planarity :  0.004   0.034   1354
  Dihedral  :  4.636  26.285   1231
  Min Nonbonded Distance : 2.607

Molprobity Statistics.
  All-atom Clashscore : 5.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.12 %
    Favored  : 97.88 %
  Rotamer:
    Outliers :  3.04 %
    Allowed  : 14.18 %
    Favored  : 82.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 16.67 %
    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:  0.95 (0.28), residues: 943
  helix:  1.87 (0.44), residues: 167
  sheet:  1.29 (0.30), residues: 312
  loop : -0.27 (0.28), residues: 464

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP A 167 
 HIS   0.000   0.000   HIS B 132 
 PHE   0.010   0.001   PHE C 103 
 TYR   0.011   0.001   TYR C 318 
 ARG   0.006   0.000   ARG C 261 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4357.15 seconds
wall clock time: 75 minutes 7.09 seconds (4507.09 seconds total)