Starting phenix.real_space_refine
on Fri Jul 25 11:20:31 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8jv5_36668/07_2025/8jv5_36668.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8jv5_36668/07_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_36668/07_2025/8jv5_36668.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8jv5_36668/07_2025/8jv5_36668.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8jv5_36668/07_2025/8jv5_36668.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8jv5_36668/07_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-5711/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: 5.01, per 1000 atoms: 0.67
  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: 1.88
  Conformation dependent library (CDL) restraints added in 1.0 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: 0.83
  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: 1.86

  Time building geometry restraints manager: 2.13 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:             1.030
  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:             0.000
  Extract box with map and model:          0.360
  Check model and map are aligned:         0.060
  Set scattering table:                    0.090
  Process input model:                     20.670
  Find NCS groups from input model:        0.280
  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:2.810
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   25.330
-------------------------------------------------------------------------------
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   7675  Z= 0.235
  Angle     :  0.635   7.026  10495  Z= 0.322
  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 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00248 (    9)
  link_NAG-ASN         : angle       1.10061 (   27)
  hydrogen bonds       : bond        0.12802 (  270)
  hydrogen bonds       : angle       5.68562 (  774)
  SS BOND              : bond        0.00306 (   15)
  SS BOND              : angle       1.44619 (   30)
  covalent geometry    : bond        0.00486 ( 7651)
  covalent geometry    : angle       0.62938 (10438)

*********************** 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  : 0.777 
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: 0.2555
  time to fit residues: 49.9013
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  : 0.810 
-------------------------------------------------------------------------------
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:    7.9990
   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   7675  Z= 0.167
  Angle     :  0.586   6.217  10495  Z= 0.307
  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 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00311 (    9)
  link_NAG-ASN         : angle       1.06962 (   27)
  hydrogen bonds       : bond        0.03677 (  270)
  hydrogen bonds       : angle       5.02094 (  774)
  SS BOND              : bond        0.00348 (   15)
  SS BOND              : angle       1.77469 (   30)
  covalent geometry    : bond        0.00397 ( 7651)
  covalent geometry    : angle       0.57678 (10438)

*********************** 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  : 0.847 
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: 0.2339
  time to fit residues: 31.7836
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  : 0.767 
-------------------------------------------------------------------------------
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:    8.9990
   chunk 6 optimal weight:    1.9990
   chunk 61 optimal weight:    7.9990
   overall best weight:    2.1788

-------------------------------------------------------------------------------
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 = 0.4020 r_free = 0.4020 target = 0.181085 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3302 r_free = 0.3302 target = 0.116821 restraints weight = 6910.360|
|-----------------------------------------------------------------------------|
r_work (start): 0.3287 rms_B_bonded: 2.74
r_work: 0.3126 rms_B_bonded: 3.19 restraints_weight: 0.5000
r_work: 0.2954 rms_B_bonded: 4.91 restraints_weight: 0.2500
r_work (final): 0.2954
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7890
moved from start:          0.2146

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.046   7675  Z= 0.230
  Angle     :  0.631   7.532  10495  Z= 0.332
  Chirality :  0.047   0.133   1190
  Planarity :  0.005   0.039   1354
  Dihedral  :  6.878  50.673   1231
  Min Nonbonded Distance : 2.474

Molprobity Statistics.
  All-atom Clashscore : 6.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.65 %
    Favored  : 97.35 %
  Rotamer:
    Outliers :  2.53 %
    Allowed  : 12.15 %
    Favored  : 85.32 %
  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:  0.47 (0.27), residues: 943
  helix:  1.04 (0.42), residues: 183
  sheet:  0.97 (0.28), residues: 336
  loop : -0.52 (0.27), residues: 424

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.003   TRP B 167 
 HIS   0.000   0.000   HIS A 132 
 PHE   0.016   0.002   PHE B 103 
 TYR   0.012   0.002   TYR C  57 
 ARG   0.003   0.001   ARG A 281 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00383 (    9)
  link_NAG-ASN         : angle       1.64678 (   27)
  hydrogen bonds       : bond        0.03863 (  270)
  hydrogen bonds       : angle       5.23067 (  774)
  SS BOND              : bond        0.00516 (   15)
  SS BOND              : angle       1.50722 (   30)
  covalent geometry    : bond        0.00565 ( 7651)
  covalent geometry    : angle       0.62226 (10438)

*********************** 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
  119 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 99
  time to evaluate  : 0.834 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   61 ASP cc_start: 0.8129 (t0) cc_final: 0.7896 (t0)
REVERT: A   79 THR cc_start: 0.7858 (t) cc_final: 0.7394 (p)
REVERT: A  164 VAL cc_start: 0.6531 (m) cc_final: 0.6201 (m)
REVERT: A  166 SER cc_start: 0.7637 (t) cc_final: 0.7317 (m)
REVERT: A  276 ARG cc_start: 0.7222 (mtp85) cc_final: 0.6406 (mtm-85)
REVERT: B  164 VAL cc_start: 0.6705 (m) cc_final: 0.6437 (m)
REVERT: B  276 ARG cc_start: 0.7679 (mpp80) cc_final: 0.7440 (mtm-85)
REVERT: B  286 ASP cc_start: 0.7376 (t70) cc_final: 0.6966 (t0)
REVERT: C   61 ASP cc_start: 0.8147 (t0) cc_final: 0.7932 (t0)
REVERT: C   79 THR cc_start: 0.7788 (t) cc_final: 0.7393 (p)
REVERT: C  164 VAL cc_start: 0.6733 (m) cc_final: 0.6484 (m)
REVERT: C  285 LYS cc_start: 0.7713 (mtpt) cc_final: 0.7498 (ttmm)
REVERT: C  301 LYS cc_start: 0.8554 (mttp) cc_final: 0.8325 (mttm)
REVERT: C  325 MET cc_start: 0.8401 (mtp) cc_final: 0.8163 (mtm)
  outliers start: 20
  outliers final: 14
  residues processed: 108
  average time/residue: 0.2117
  time to fit residues: 30.3793
Evaluate side-chains
  108 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 94
  time to evaluate  : 0.776 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   86 ILE
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 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:    5.9990
   chunk 88 optimal weight:    7.9990
   chunk 54 optimal weight:    0.9980
   chunk 63 optimal weight:    0.0170
   chunk 31 optimal weight:    0.9990
   chunk 32 optimal weight:    5.9990
   chunk 1 optimal weight:    6.9990
   chunk 90 optimal weight:    0.9990
   chunk 47 optimal weight:    0.6980
   chunk 8 optimal weight:   30.0000
   chunk 9 optimal weight:    1.9990
   overall best weight:    0.7422

-------------------------------------------------------------------------------
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 = 0.4053 r_free = 0.4053 target = 0.184067 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3346 r_free = 0.3346 target = 0.120104 restraints weight = 6790.675|
|-----------------------------------------------------------------------------|
r_work (start): 0.3321 rms_B_bonded: 2.73
r_work: 0.3176 rms_B_bonded: 3.09 restraints_weight: 0.5000
r_work: 0.3011 rms_B_bonded: 4.79 restraints_weight: 0.2500
r_work (final): 0.3011
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7857
moved from start:          0.2232

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   7675  Z= 0.121
  Angle     :  0.563   9.752  10495  Z= 0.293
  Chirality :  0.044   0.142   1190
  Planarity :  0.004   0.036   1354
  Dihedral  :  6.443  52.351   1231
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 5.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.86 %
    Favored  : 97.14 %
  Rotamer:
    Outliers :  2.78 %
    Allowed  : 12.66 %
    Favored  : 84.56 %
  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:  0.84 (0.27), residues: 943
  helix:  1.94 (0.45), residues: 165
  sheet:  1.33 (0.29), residues: 315
  loop : -0.52 (0.26), residues: 463

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   0.010   0.001   PHE C 103 
 TYR   0.008   0.001   TYR B  92 
 ARG   0.003   0.000   ARG C 261 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00212 (    9)
  link_NAG-ASN         : angle       1.36369 (   27)
  hydrogen bonds       : bond        0.03226 (  270)
  hydrogen bonds       : angle       4.97281 (  774)
  SS BOND              : bond        0.00495 (   15)
  SS BOND              : angle       1.68349 (   30)
  covalent geometry    : bond        0.00278 ( 7651)
  covalent geometry    : angle       0.55333 (10438)

*********************** 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
  120 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 98
  time to evaluate  : 0.735 
Fit side-chains
   revert: symmetry clash
REVERT: A   61 ASP cc_start: 0.7960 (t0) cc_final: 0.7737 (t0)
REVERT: A   72 LYS cc_start: 0.7750 (mtmm) cc_final: 0.7403 (mtpp)
REVERT: A   79 THR cc_start: 0.7894 (t) cc_final: 0.7395 (p)
REVERT: A  108 MET cc_start: 0.8726 (ptp) cc_final: 0.8399 (ptp)
REVERT: A  164 VAL cc_start: 0.6619 (m) cc_final: 0.6413 (m)
REVERT: A  166 SER cc_start: 0.7631 (t) cc_final: 0.7297 (m)
REVERT: A  276 ARG cc_start: 0.7119 (mtp85) cc_final: 0.6289 (mtm-85)
REVERT: B  286 ASP cc_start: 0.7367 (t70) cc_final: 0.6967 (t0)
REVERT: C   61 ASP cc_start: 0.7928 (t0) cc_final: 0.7712 (t0)
REVERT: C   79 THR cc_start: 0.7827 (t) cc_final: 0.7353 (p)
REVERT: C  285 LYS cc_start: 0.7634 (mtpt) cc_final: 0.7422 (ttmm)
REVERT: C  286 ASP cc_start: 0.7157 (t70) cc_final: 0.6867 (t0)
REVERT: C  325 MET cc_start: 0.8436 (mtp) cc_final: 0.8187 (mtm)
  outliers start: 22
  outliers final: 15
  residues processed: 108
  average time/residue: 0.2273
  time to fit residues: 32.2299
Evaluate side-chains
  109 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 94
  time to evaluate  : 0.837 
-------------------------------------------------------------------------------
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  129 CYS
Chi-restraints excluded: chain B residue  152 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=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 50 optimal weight:    3.9990
   chunk 79 optimal weight:    2.9990
   chunk 20 optimal weight:    1.9990
   chunk 53 optimal weight:    3.9990
   chunk 31 optimal weight:    8.9990
   chunk 92 optimal weight:    6.9990
   chunk 74 optimal weight:    3.9990
   chunk 87 optimal weight:    1.9990
   chunk 67 optimal weight:    0.4980
   chunk 1 optimal weight:    8.9990
   chunk 25 optimal weight:    0.9980
   overall best weight:    1.6986

-------------------------------------------------------------------------------
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 = 0.3998 r_free = 0.3998 target = 0.179180 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3283 r_free = 0.3283 target = 0.115263 restraints weight = 6619.004|
|-----------------------------------------------------------------------------|
r_work (start): 0.3296 rms_B_bonded: 2.70
r_work: 0.3134 rms_B_bonded: 3.20 restraints_weight: 0.5000
r_work: 0.2961 rms_B_bonded: 4.94 restraints_weight: 0.2500
r_work (final): 0.2961
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7842
moved from start:          0.2499

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.053   7675  Z= 0.190
  Angle     :  0.618  10.588  10495  Z= 0.320
  Chirality :  0.045   0.130   1190
  Planarity :  0.004   0.034   1354
  Dihedral  :  6.216  48.382   1231
  Min Nonbonded Distance : 2.596

Molprobity Statistics.
  All-atom Clashscore : 5.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.44 %
    Favored  : 97.56 %
  Rotamer:
    Outliers :  3.42 %
    Allowed  : 13.16 %
    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:  0.47 (0.27), residues: 943
  helix:  1.09 (0.42), residues: 185
  sheet:  1.00 (0.29), residues: 322
  loop : -0.53 (0.27), residues: 436

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP A 167 
 HIS   0.001   0.000   HIS A 132 
 PHE   0.016   0.002   PHE B 103 
 TYR   0.010   0.001   TYR C 216 
 ARG   0.005   0.001   ARG B 276 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00283 (    9)
  link_NAG-ASN         : angle       1.70339 (   27)
  hydrogen bonds       : bond        0.03492 (  270)
  hydrogen bonds       : angle       5.03787 (  774)
  SS BOND              : bond        0.00457 (   15)
  SS BOND              : angle       1.85076 (   30)
  covalent geometry    : bond        0.00467 ( 7651)
  covalent geometry    : angle       0.60503 (10438)

*********************** 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
  119 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 92
  time to evaluate  : 0.772 
Fit side-chains
   revert: symmetry clash
REVERT: A   61 ASP cc_start: 0.8065 (t0) cc_final: 0.7838 (t0)
REVERT: A   72 LYS cc_start: 0.7707 (mtmm) cc_final: 0.7316 (mtpp)
REVERT: A   79 THR cc_start: 0.7736 (t) cc_final: 0.7217 (p)
REVERT: A  166 SER cc_start: 0.7481 (t) cc_final: 0.7174 (m)
REVERT: A  276 ARG cc_start: 0.7180 (mtp85) cc_final: 0.6281 (mtm-85)
REVERT: A  286 ASP cc_start: 0.7268 (t70) cc_final: 0.6877 (t0)
REVERT: B  191 LEU cc_start: 0.8257 (OUTLIER) cc_final: 0.7875 (tp)
REVERT: B  286 ASP cc_start: 0.7484 (t70) cc_final: 0.7007 (t0)
REVERT: C   61 ASP cc_start: 0.8125 (t0) cc_final: 0.7902 (t0)
REVERT: C   79 THR cc_start: 0.7649 (t) cc_final: 0.7159 (p)
REVERT: C  147 VAL cc_start: 0.8633 (m) cc_final: 0.8293 (p)
REVERT: C  191 LEU cc_start: 0.8293 (OUTLIER) cc_final: 0.7856 (tp)
REVERT: C  285 LYS cc_start: 0.7801 (mtpt) cc_final: 0.7585 (ttmm)
REVERT: C  286 ASP cc_start: 0.7230 (t70) cc_final: 0.6899 (t0)
REVERT: C  325 MET cc_start: 0.8474 (mtp) cc_final: 0.8209 (mtm)
  outliers start: 27
  outliers final: 18
  residues processed: 108
  average time/residue: 0.2237
  time to fit residues: 31.8307
Evaluate side-chains
  110 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 90
  time to evaluate  : 0.867 
-------------------------------------------------------------------------------
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   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  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=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 87 optimal weight:    0.9990
   chunk 10 optimal weight:    5.9990
   chunk 31 optimal weight:    8.9990
   chunk 67 optimal weight:    0.4980
   chunk 23 optimal weight:    1.9990
   chunk 29 optimal weight:    7.9990
   chunk 90 optimal weight:    0.8980
   chunk 44 optimal weight:    0.0470
   chunk 35 optimal weight:    0.6980
   chunk 76 optimal weight:    0.9990
   chunk 88 optimal weight:    4.9990
   overall best weight:    0.6280

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

Flipped N/Q/H residues before XYZ refinement:
B 202 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4076 r_free = 0.4076 target = 0.186187 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3371 r_free = 0.3371 target = 0.122311 restraints weight = 6724.832|
|-----------------------------------------------------------------------------|
r_work (start): 0.3330 rms_B_bonded: 2.75
r_work: 0.3169 rms_B_bonded: 3.25 restraints_weight: 0.5000
r_work (final): 0.3169
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7677
moved from start:          0.2505

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   7675  Z= 0.111
  Angle     :  0.552   9.148  10495  Z= 0.285
  Chirality :  0.044   0.139   1190
  Planarity :  0.004   0.035   1354
  Dihedral  :  5.786  47.336   1231
  Min Nonbonded Distance : 2.599

Molprobity Statistics.
  All-atom Clashscore : 5.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.33 %
    Favored  : 97.67 %
  Rotamer:
    Outliers :  2.78 %
    Allowed  : 14.43 %
    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:  0.84 (0.27), residues: 943
  helix:  1.88 (0.44), residues: 165
  sheet:  1.36 (0.29), residues: 309
  loop : -0.49 (0.27), residues: 469

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP A 167 
 HIS   0.000   0.000   HIS A 132 
 PHE   0.011   0.001   PHE C 103 
 TYR   0.012   0.001   TYR A 318 
 ARG   0.005   0.000   ARG C 261 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00211 (    9)
  link_NAG-ASN         : angle       1.47811 (   27)
  hydrogen bonds       : bond        0.03092 (  270)
  hydrogen bonds       : angle       4.80662 (  774)
  SS BOND              : bond        0.00341 (   15)
  SS BOND              : angle       1.62277 (   30)
  covalent geometry    : bond        0.00256 ( 7651)
  covalent geometry    : angle       0.54115 (10438)

*********************** 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
  117 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 95
  time to evaluate  : 0.861 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   61 ASP cc_start: 0.7777 (t0) cc_final: 0.7564 (t0)
REVERT: A   79 THR cc_start: 0.7796 (t) cc_final: 0.7246 (p)
REVERT: A  108 MET cc_start: 0.8667 (ptp) cc_final: 0.8324 (ptp)
REVERT: A  166 SER cc_start: 0.7359 (t) cc_final: 0.7019 (m)
REVERT: A  276 ARG cc_start: 0.6897 (mtp85) cc_final: 0.6078 (mtm-85)
REVERT: A  286 ASP cc_start: 0.7165 (t70) cc_final: 0.6827 (t0)
REVERT: B  286 ASP cc_start: 0.7424 (t70) cc_final: 0.7010 (t0)
REVERT: C   61 ASP cc_start: 0.7800 (t0) cc_final: 0.7591 (t0)
REVERT: C   79 THR cc_start: 0.7675 (t) cc_final: 0.7163 (p)
REVERT: C  147 VAL cc_start: 0.8405 (m) cc_final: 0.8011 (p)
REVERT: C  286 ASP cc_start: 0.7168 (t70) cc_final: 0.6870 (t0)
REVERT: C  325 MET cc_start: 0.8370 (mtp) cc_final: 0.8131 (mtm)
  outliers start: 22
  outliers final: 17
  residues processed: 107
  average time/residue: 0.2180
  time to fit residues: 31.0249
Evaluate side-chains
  107 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 90
  time to evaluate  : 0.862 
-------------------------------------------------------------------------------
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   74 ILE
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  214 SER
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=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 34 optimal weight:    8.9990
   chunk 29 optimal weight:    7.9990
   chunk 62 optimal weight:    0.0170
   chunk 39 optimal weight:   20.0000
   chunk 69 optimal weight:    2.9990
   chunk 15 optimal weight:    1.9990
   chunk 28 optimal weight:    4.9990
   chunk 30 optimal weight:    0.9990
   chunk 9 optimal weight:   10.0000
   chunk 91 optimal weight:    3.9990
   chunk 86 optimal weight:    3.9990
   overall best weight:    2.0026

-------------------------------------------------------------------------------
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 = 0.4030 r_free = 0.4030 target = 0.182035 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3314 r_free = 0.3314 target = 0.117996 restraints weight = 6749.923|
|-----------------------------------------------------------------------------|
r_work (start): 0.3286 rms_B_bonded: 2.74
r_work: 0.3142 rms_B_bonded: 3.08 restraints_weight: 0.5000
r_work: 0.2976 rms_B_bonded: 4.76 restraints_weight: 0.2500
r_work (final): 0.2976
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7913
moved from start:          0.2826

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.055   7675  Z= 0.218
  Angle     :  0.648   9.837  10495  Z= 0.335
  Chirality :  0.046   0.132   1190
  Planarity :  0.005   0.033   1354
  Dihedral  :  5.610  34.840   1231
  Min Nonbonded Distance : 2.557

Molprobity Statistics.
  All-atom Clashscore : 6.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.44 %
    Favored  : 97.56 %
  Rotamer:
    Outliers :  4.05 %
    Allowed  : 14.30 %
    Favored  : 81.65 %
  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:  0.40 (0.27), residues: 943
  helix:  1.30 (0.43), residues: 177
  sheet:  0.79 (0.29), residues: 330
  loop : -0.54 (0.28), residues: 436

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.003   TRP B 272 
 HIS   0.001   0.000   HIS A 132 
 PHE   0.017   0.002   PHE B 103 
 TYR   0.010   0.002   TYR C 216 
 ARG   0.006   0.001   ARG C 261 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00367 (    9)
  link_NAG-ASN         : angle       1.87195 (   27)
  hydrogen bonds       : bond        0.03653 (  270)
  hydrogen bonds       : angle       5.02709 (  774)
  SS BOND              : bond        0.00563 (   15)
  SS BOND              : angle       1.99945 (   30)
  covalent geometry    : bond        0.00536 ( 7651)
  covalent geometry    : angle       0.63394 (10438)

*********************** 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
  118 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 86
  time to evaluate  : 0.855 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   61 ASP cc_start: 0.8071 (t0) cc_final: 0.7846 (t0)
REVERT: A   79 THR cc_start: 0.7866 (t) cc_final: 0.7262 (p)
REVERT: A  166 SER cc_start: 0.7596 (t) cc_final: 0.7268 (m)
REVERT: A  191 LEU cc_start: 0.8314 (OUTLIER) cc_final: 0.7927 (tp)
REVERT: A  276 ARG cc_start: 0.7230 (mtp85) cc_final: 0.6395 (mtm-85)
REVERT: A  286 ASP cc_start: 0.7349 (t70) cc_final: 0.6948 (t0)
REVERT: B  191 LEU cc_start: 0.8303 (OUTLIER) cc_final: 0.7912 (tp)
REVERT: B  286 ASP cc_start: 0.7614 (t70) cc_final: 0.7158 (t0)
REVERT: C   61 ASP cc_start: 0.8100 (t0) cc_final: 0.7890 (t0)
REVERT: C   79 THR cc_start: 0.7647 (t) cc_final: 0.7097 (p)
REVERT: C  191 LEU cc_start: 0.8341 (OUTLIER) cc_final: 0.7882 (tp)
REVERT: C  286 ASP cc_start: 0.7429 (t70) cc_final: 0.7068 (t0)
REVERT: C  325 MET cc_start: 0.8507 (mtp) cc_final: 0.8258 (mtm)
  outliers start: 32
  outliers final: 23
  residues processed: 108
  average time/residue: 0.2168
  time to fit residues: 30.8415
Evaluate side-chains
  109 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 83
  time to evaluate  : 0.788 
-------------------------------------------------------------------------------
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  191 LEU
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  291 VAL
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  191 LEU
Chi-restraints excluded: chain B residue  196 ILE
Chi-restraints excluded: chain B residue  214 SER
Chi-restraints excluded: chain B residue  221 VAL
Chi-restraints excluded: chain B residue  291 VAL
Chi-restraints excluded: chain C residue   74 ILE
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
Chi-restraints excluded: chain C residue  291 VAL
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:    0.7980
   chunk 24 optimal weight:    0.9980
   chunk 18 optimal weight:    0.0980
   chunk 73 optimal weight:    9.9990
   chunk 23 optimal weight:    0.7980
   chunk 89 optimal weight:    3.9990
   chunk 68 optimal weight:    3.9990
   chunk 48 optimal weight:    6.9990
   chunk 50 optimal weight:    0.9980
   overall best weight:    0.7380

-------------------------------------------------------------------------------
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 = 0.4044 r_free = 0.4044 target = 0.183723 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3342 r_free = 0.3342 target = 0.120267 restraints weight = 6745.915|
|-----------------------------------------------------------------------------|
r_work (start): 0.3316 rms_B_bonded: 2.72
r_work: 0.3170 rms_B_bonded: 3.11 restraints_weight: 0.5000
r_work: 0.3002 rms_B_bonded: 4.86 restraints_weight: 0.2500
r_work (final): 0.3002
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7892
moved from start:          0.2801

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048   7675  Z= 0.121
  Angle     :  0.566   9.688  10495  Z= 0.292
  Chirality :  0.044   0.141   1190
  Planarity :  0.004   0.035   1354
  Dihedral  :  5.087  26.960   1231
  Min Nonbonded Distance : 2.602

Molprobity Statistics.
  All-atom Clashscore : 5.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.33 %
    Favored  : 97.67 %
  Rotamer:
    Outliers :  2.53 %
    Allowed  : 15.82 %
    Favored  : 81.65 %
  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:  0.77 (0.27), residues: 943
  helix:  1.83 (0.45), residues: 165
  sheet:  1.20 (0.29), residues: 314
  loop : -0.45 (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 A 132 
 PHE   0.011   0.001   PHE C 103 
 TYR   0.008   0.001   TYR B  92 
 ARG   0.006   0.001   ARG B 276 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00157 (    9)
  link_NAG-ASN         : angle       1.61695 (   27)
  hydrogen bonds       : bond        0.03154 (  270)
  hydrogen bonds       : angle       4.80481 (  774)
  SS BOND              : bond        0.00288 (   15)
  SS BOND              : angle       1.64504 (   30)
  covalent geometry    : bond        0.00287 ( 7651)
  covalent geometry    : angle       0.55435 (10438)

*********************** 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: 20
    poor density    : 94
  time to evaluate  : 0.832 
Fit side-chains
   revert: symmetry clash
REVERT: A   61 ASP cc_start: 0.7891 (t0) cc_final: 0.7681 (t0)
REVERT: A   79 THR cc_start: 0.7801 (t) cc_final: 0.7176 (p)
REVERT: A  108 MET cc_start: 0.8729 (ptp) cc_final: 0.8422 (ptp)
REVERT: A  166 SER cc_start: 0.7611 (t) cc_final: 0.7243 (m)
REVERT: A  276 ARG cc_start: 0.7148 (mtp85) cc_final: 0.6328 (mtm-85)
REVERT: A  286 ASP cc_start: 0.7355 (t70) cc_final: 0.7001 (t0)
REVERT: B  286 ASP cc_start: 0.7594 (t70) cc_final: 0.7169 (t0)
REVERT: C   61 ASP cc_start: 0.7899 (t0) cc_final: 0.7678 (t0)
REVERT: C   79 THR cc_start: 0.7671 (t) cc_final: 0.7085 (p)
REVERT: C  147 VAL cc_start: 0.8569 (m) cc_final: 0.8210 (p)
REVERT: C  286 ASP cc_start: 0.7381 (t70) cc_final: 0.7074 (t0)
REVERT: C  288 ASP cc_start: 0.8145 (m-30) cc_final: 0.7504 (t70)
  outliers start: 20
  outliers final: 19
  residues processed: 105
  average time/residue: 0.2210
  time to fit residues: 30.8544
Evaluate side-chains
  110 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 91
  time to evaluate  : 0.808 
-------------------------------------------------------------------------------
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  291 VAL
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  182 LEU
Chi-restraints excluded: chain B residue  196 ILE
Chi-restraints excluded: chain B residue  221 VAL
Chi-restraints excluded: chain B residue  291 VAL
Chi-restraints excluded: chain C residue   74 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=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 38 optimal weight:    8.9990
   chunk 0 optimal weight:   10.0000
   chunk 12 optimal weight:    4.9990
   chunk 29 optimal weight:    0.9980
   chunk 32 optimal weight:    0.5980
   chunk 6 optimal weight:    1.9990
   chunk 19 optimal weight:    1.9990
   chunk 42 optimal weight:    8.9990
   chunk 3 optimal weight:    8.9990
   chunk 47 optimal weight:    2.9990
   chunk 87 optimal weight:    0.9980
   overall best weight:    1.3184

-------------------------------------------------------------------------------
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 = 0.4034 r_free = 0.4034 target = 0.182650 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3328 r_free = 0.3328 target = 0.119168 restraints weight = 6761.060|
|-----------------------------------------------------------------------------|
r_work (start): 0.3306 rms_B_bonded: 2.72
r_work: 0.3162 rms_B_bonded: 3.08 restraints_weight: 0.5000
r_work: 0.2995 rms_B_bonded: 4.78 restraints_weight: 0.2500
r_work (final): 0.2995
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7885
moved from start:          0.2881

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.052   7675  Z= 0.157
  Angle     :  0.590   9.511  10495  Z= 0.305
  Chirality :  0.044   0.139   1190
  Planarity :  0.004   0.033   1354
  Dihedral  :  5.072  26.969   1231
  Min Nonbonded Distance : 2.609

Molprobity Statistics.
  All-atom Clashscore : 5.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.91 %
    Favored  : 98.09 %
  Rotamer:
    Outliers :  3.16 %
    Allowed  : 15.44 %
    Favored  : 81.39 %
  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:  0.73 (0.27), residues: 943
  helix:  1.81 (0.44), residues: 167
  sheet:  1.04 (0.29), residues: 318
  loop : -0.40 (0.28), residues: 458

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP C 272 
 HIS   0.000   0.000   HIS C 132 
 PHE   0.012   0.002   PHE B 103 
 TYR   0.008   0.001   TYR C 216 
 ARG   0.007   0.001   ARG C 261 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00190 (    9)
  link_NAG-ASN         : angle       1.74166 (   27)
  hydrogen bonds       : bond        0.03281 (  270)
  hydrogen bonds       : angle       4.81471 (  774)
  SS BOND              : bond        0.00337 (   15)
  SS BOND              : angle       1.71244 (   30)
  covalent geometry    : bond        0.00385 ( 7651)
  covalent geometry    : angle       0.57734 (10438)

*********************** 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
  119 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 94
  time to evaluate  : 0.797 
Fit side-chains
   revert: symmetry clash
REVERT: A   61 ASP cc_start: 0.7953 (t0) cc_final: 0.7743 (t0)
REVERT: A   79 THR cc_start: 0.7773 (t) cc_final: 0.7137 (p)
REVERT: A  166 SER cc_start: 0.7546 (t) cc_final: 0.7205 (m)
REVERT: A  276 ARG cc_start: 0.7185 (mtp85) cc_final: 0.6353 (mtm-85)
REVERT: A  286 ASP cc_start: 0.7414 (t70) cc_final: 0.6994 (t0)
REVERT: B  191 LEU cc_start: 0.8257 (OUTLIER) cc_final: 0.7895 (tp)
REVERT: B  286 ASP cc_start: 0.7632 (t70) cc_final: 0.7200 (t0)
REVERT: B  288 ASP cc_start: 0.8134 (m-30) cc_final: 0.7507 (t70)
REVERT: C   61 ASP cc_start: 0.7982 (t0) cc_final: 0.7760 (t0)
REVERT: C   79 THR cc_start: 0.7696 (t) cc_final: 0.7131 (p)
REVERT: C  147 VAL cc_start: 0.8630 (m) cc_final: 0.8266 (p)
REVERT: C  191 LEU cc_start: 0.8307 (OUTLIER) cc_final: 0.7856 (tp)
REVERT: C  286 ASP cc_start: 0.7385 (t70) cc_final: 0.7059 (t0)
REVERT: C  288 ASP cc_start: 0.8174 (m-30) cc_final: 0.7522 (t70)
  outliers start: 25
  outliers final: 22
  residues processed: 110
  average time/residue: 0.2201
  time to fit residues: 32.2602
Evaluate side-chains
  115 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 91
  time to evaluate  : 0.751 
-------------------------------------------------------------------------------
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  291 VAL
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  191 LEU
Chi-restraints excluded: chain B residue  196 ILE
Chi-restraints excluded: chain B residue  214 SER
Chi-restraints excluded: chain B residue  221 VAL
Chi-restraints excluded: chain B residue  291 VAL
Chi-restraints excluded: chain C residue   74 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
Chi-restraints excluded: chain C residue  291 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 18 optimal weight:    1.9990
   chunk 49 optimal weight:    3.9990
   chunk 87 optimal weight:    0.0570
   chunk 76 optimal weight:    0.9990
   chunk 23 optimal weight:    0.6980
   chunk 7 optimal weight:    5.9990
   chunk 58 optimal weight:    4.9990
   chunk 10 optimal weight:    9.9990
   chunk 25 optimal weight:    0.2980
   chunk 11 optimal weight:   20.0000
   chunk 56 optimal weight:    0.7980
   overall best weight:    0.5700

-------------------------------------------------------------------------------
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 = 0.4071 r_free = 0.4071 target = 0.186175 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3377 r_free = 0.3377 target = 0.123013 restraints weight = 6659.924|
|-----------------------------------------------------------------------------|
r_work (start): 0.3331 rms_B_bonded: 2.72
r_work: 0.3186 rms_B_bonded: 3.09 restraints_weight: 0.5000
r_work: 0.3020 rms_B_bonded: 4.81 restraints_weight: 0.2500
r_work (final): 0.3020
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7805
moved from start:          0.2900

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   7675  Z= 0.113
  Angle     :  0.560   9.073  10495  Z= 0.290
  Chirality :  0.044   0.140   1190
  Planarity :  0.004   0.034   1354
  Dihedral  :  4.821  26.744   1231
  Min Nonbonded Distance : 2.604

Molprobity Statistics.
  All-atom Clashscore : 5.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.44 %
    Favored  : 97.56 %
  Rotamer:
    Outliers :  3.16 %
    Allowed  : 15.70 %
    Favored  : 81.14 %
  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:  0.84 (0.27), residues: 943
  helix:  1.81 (0.44), residues: 167
  sheet:  1.27 (0.29), residues: 314
  loop : -0.40 (0.28), residues: 462

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP A 167 
 HIS   0.000   0.000   HIS A 132 
 PHE   0.011   0.001   PHE C 103 
 TYR   0.008   0.001   TYR B  92 
 ARG   0.006   0.000   ARG C 261 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00159 (    9)
  link_NAG-ASN         : angle       1.56888 (   27)
  hydrogen bonds       : bond        0.03033 (  270)
  hydrogen bonds       : angle       4.70158 (  774)
  SS BOND              : bond        0.00216 (   15)
  SS BOND              : angle       1.49754 (   30)
  covalent geometry    : bond        0.00265 ( 7651)
  covalent geometry    : angle       0.54982 (10438)

********************** 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
  122 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 97
  time to evaluate  : 0.806 
Fit side-chains
   revert: symmetry clash
REVERT: A   61 ASP cc_start: 0.7892 (t0) cc_final: 0.7672 (t0)
REVERT: A   79 THR cc_start: 0.7766 (t) cc_final: 0.7102 (p)
REVERT: A  108 MET cc_start: 0.8715 (ptp) cc_final: 0.8386 (ptp)
REVERT: A  166 SER cc_start: 0.7451 (t) cc_final: 0.7101 (m)
REVERT: A  276 ARG cc_start: 0.7107 (mtp85) cc_final: 0.6202 (mtm-85)
REVERT: A  286 ASP cc_start: 0.7300 (t70) cc_final: 0.6956 (t0)
REVERT: A  288 ASP cc_start: 0.8202 (m-30) cc_final: 0.7580 (t70)
REVERT: B  147 VAL cc_start: 0.8457 (m) cc_final: 0.8113 (p)
REVERT: B  286 ASP cc_start: 0.7561 (t70) cc_final: 0.7130 (t0)
REVERT: B  288 ASP cc_start: 0.8174 (m-30) cc_final: 0.7622 (t70)
REVERT: C   61 ASP cc_start: 0.7930 (t0) cc_final: 0.7718 (t0)
REVERT: C   79 THR cc_start: 0.7670 (t) cc_final: 0.7088 (p)
REVERT: C  147 VAL cc_start: 0.8535 (m) cc_final: 0.8187 (p)
REVERT: C  286 ASP cc_start: 0.7298 (t70) cc_final: 0.6965 (t0)
REVERT: C  288 ASP cc_start: 0.8194 (m-30) cc_final: 0.7529 (t70)
  outliers start: 25
  outliers final: 23
  residues processed: 110
  average time/residue: 0.2174
  time to fit residues: 31.8592
Evaluate side-chains
  118 residues out of total 832 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 95
  time to evaluate  : 0.788 
-------------------------------------------------------------------------------
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  291 VAL
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  182 LEU
Chi-restraints excluded: chain B residue  196 ILE
Chi-restraints excluded: chain B residue  214 SER
Chi-restraints excluded: chain B residue  221 VAL
Chi-restraints excluded: chain B residue  291 VAL
Chi-restraints excluded: chain B residue  325 MET
Chi-restraints excluded: chain C residue   74 ILE
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
Chi-restraints excluded: chain C residue  291 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 90 optimal weight:    2.9990
   chunk 86 optimal weight:    3.9990
   chunk 15 optimal weight:    1.9990
   chunk 44 optimal weight:    0.0870
   chunk 36 optimal weight:    3.9990
   chunk 9 optimal weight:    2.9990
   chunk 3 optimal weight:    7.9990
   chunk 65 optimal weight:    5.9990
   chunk 55 optimal weight:    3.9990
   chunk 43 optimal weight:    0.0370
   chunk 16 optimal weight:    0.7980
   overall best weight:    1.1840

-------------------------------------------------------------------------------
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 = 0.4042 r_free = 0.4042 target = 0.183323 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3340 r_free = 0.3340 target = 0.119961 restraints weight = 6707.600|
|-----------------------------------------------------------------------------|
r_work (start): 0.3316 rms_B_bonded: 2.70
r_work: 0.3172 rms_B_bonded: 3.05 restraints_weight: 0.5000
r_work: 0.3007 rms_B_bonded: 4.76 restraints_weight: 0.2500
r_work (final): 0.3007
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7912
moved from start:          0.2973

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.049   7675  Z= 0.148
  Angle     :  0.591   9.101  10495  Z= 0.304
  Chirality :  0.044   0.139   1190
  Planarity :  0.004   0.033   1354
  Dihedral  :  4.907  26.395   1231
  Min Nonbonded Distance : 2.610

Molprobity Statistics.
  All-atom Clashscore : 5.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.91 %
    Favored  : 98.09 %
  Rotamer:
    Outliers :  3.42 %
    Allowed  : 15.70 %
    Favored  : 80.89 %
  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:  0.80 (0.27), residues: 943
  helix:  1.76 (0.44), residues: 167
  sheet:  1.18 (0.29), residues: 316
  loop : -0.39 (0.28), residues: 460

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP C 272 
 HIS   0.000   0.000   HIS C 132 
 PHE   0.011   0.002   PHE B 103 
 TYR   0.008   0.001   TYR C 216 
 ARG   0.005   0.001   ARG C 276 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00176 (    9)
  link_NAG-ASN         : angle       1.72664 (   27)
  hydrogen bonds       : bond        0.03199 (  270)
  hydrogen bonds       : angle       4.70791 (  774)
  SS BOND              : bond        0.00309 (   15)
  SS BOND              : angle       1.62512 (   30)
  covalent geometry    : bond        0.00361 ( 7651)
  covalent geometry    : angle       0.57950 (10438)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4493.73 seconds
wall clock time: 77 minutes 46.06 seconds (4666.06 seconds total)