Starting phenix.real_space_refine
on Fri Jul 25 17:23:48 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8zt5_60447/07_2025/8zt5_60447.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8zt5_60447/07_2025/8zt5_60447.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.35
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8zt5_60447/07_2025/8zt5_60447.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8zt5_60447/07_2025/8zt5_60447.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8zt5_60447/07_2025/8zt5_60447.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8zt5_60447/07_2025/8zt5_60447.cif"
  }
  resolution = 2.35
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.052
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: 7
    Type Number    sf(0)   Gaussians
     Ca      3      9.91       5
     P       9      5.49       5
     Mg      3      5.21       5
     S      45      5.16       5
     C    5118      2.51       5
     N    1359      2.21       5
     O    1459      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 12 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: 7996
  Number of models: 1
  Model: ""
    Number of chains: 9
    Chain: "B"
      Number of atoms: 2588
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 330, 2588
          Classifications: {'peptide': 330}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 15, 'TRANS': 314}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 4
    Chain: "C"
      Number of atoms: 2588
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 330, 2588
          Classifications: {'peptide': 330}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 15, 'TRANS': 314}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 4
    Chain: "A"
      Number of atoms: 2588
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 330, 2588
          Classifications: {'peptide': 330}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 15, 'TRANS': 314}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 4
    Chain: "B"
      Number of atoms: 74
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 5, 74
          Unusual residues: {' MG': 1, 'ATP': 1, 'NAG': 3}
          Classifications: {'undetermined': 5}
          Link IDs: {None: 4}
          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: 75
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 6, 75
          Unusual residues: {' CA': 1, ' MG': 1, 'ATP': 1, 'NAG': 3}
          Classifications: {'undetermined': 6}
          Link IDs: {None: 5}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 9
          Unresolved non-hydrogen chiralities: 3
    Chain: "A"
      Number of atoms: 76
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 7, 76
          Unusual residues: {' CA': 2, ' MG': 1, 'ATP': 1, 'NAG': 3}
          Classifications: {'undetermined': 7}
          Link IDs: {None: 6}
          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: 3
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 3
          Classifications: {'water': 3}
          Link IDs: {None: 2}
    Chain: "C"
      Number of atoms: 2
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 2
          Classifications: {'water': 2}
          Link IDs: {None: 1}
    Chain: "A"
      Number of atoms: 2
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 2
          Classifications: {'water': 2}
          Link IDs: {None: 1}
  Time building chain proxies: 5.77, per 1000 atoms: 0.72
  Number of scatterers: 7996
  At special positions: 0
  Unit cell: (87.48, 85.05, 119.88, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 7
    Type Number    sf(0)
     Ca      3     19.99
     S      45     16.00
     P       9     15.00
     Mg      3     11.99
     O    1459      8.00
     N    1359      7.00
     C    5118      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=9, symmetry=0
    Simple disulfide: pdb=" SG  CYS B 117 " - pdb=" SG  CYS B 165 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 126 " - pdb=" SG  CYS B 149 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 217 " - pdb=" SG  CYS B 227 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 117 " - pdb=" SG  CYS C 165 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 126 " - pdb=" SG  CYS C 149 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 217 " - pdb=" SG  CYS C 227 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 117 " - pdb=" SG  CYS A 165 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 126 " - pdb=" SG  CYS A 149 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 217 " - pdb=" SG  CYS A 227 " distance=2.04

  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 503 " - " ASN A 210 "
      " NAG A 504 " - " ASN A 153 "
      " NAG A 505 " - " ASN A 184 "
      " NAG B 402 " - " ASN B 210 "
      " NAG B 403 " - " ASN B 153 "
      " NAG B 404 " - " ASN B 184 "
      " NAG C 503 " - " ASN C 210 "
      " NAG C 504 " - " ASN C 153 "
      " NAG C 505 " - " ASN C 184 "
  Time building additional restraints: 2.29
  Conformation dependent library (CDL) restraints added in 1.0 seconds
  

  1968 Ramachandran restraints generated.
    984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1776

  Finding SS restraints...
    Secondary structure from input PDB file:
      24 helices and 21 sheets defined
      27.9% alpha, 47.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.08
  Creating SS restraints...
    Processing helix  chain 'B' and resid 26 through 47
      removed outlier: 3.503A  pdb=" N   GLY B  30 " --> pdb=" O   ASN B  26 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 86 through 91
    Processing helix  chain 'B' and resid 179 through 184
    Processing helix  chain 'B' and resid 210 through 216
      removed outlier: 3.676A  pdb=" N   LYS B 216 " --> pdb=" O   THR B 212 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 232 through 239
    Processing helix  chain 'B' and resid 242 through 250
      removed outlier: 3.530A  pdb=" N   LEU B 246 " --> pdb=" O   ASP B 242 " (cutoff:3.500A)
      removed outlier: 3.631A  pdb=" N   LYS B 249 " --> pdb=" O   SER B 245 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 266 through 270
    Processing helix  chain 'B' and resid 327 through 355
      removed outlier: 3.613A  pdb=" N   THR B 331 " --> pdb=" O   ASP B 327 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 27 through 47
    Processing helix  chain 'C' and resid 86 through 91
      removed outlier: 3.594A  pdb=" N   VAL C  91 " --> pdb=" O   VAL C  87 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 179 through 184
    Processing helix  chain 'C' and resid 210 through 217
      removed outlier: 3.808A  pdb=" N   LYS C 216 " --> pdb=" O   THR C 212 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 232 through 240
    Processing helix  chain 'C' and resid 242 through 250
      removed outlier: 3.512A  pdb=" N   GLU C 248 " --> pdb=" O   ARG C 244 " (cutoff:3.500A)
      removed outlier: 3.985A  pdb=" N   LYS C 249 " --> pdb=" O   SER C 245 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 266 through 270
    Processing helix  chain 'C' and resid 327 through 355
      removed outlier: 3.601A  pdb=" N   THR C 331 " --> pdb=" O   ASP C 327 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 27 through 47
    Processing helix  chain 'A' and resid 86 through 91
    Processing helix  chain 'A' and resid 179 through 184
    Processing helix  chain 'A' and resid 210 through 216
      removed outlier: 3.610A  pdb=" N   LYS A 216 " --> pdb=" O   THR A 212 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 232 through 239
    Processing helix  chain 'A' and resid 242 through 250
      removed outlier: 3.513A  pdb=" N   LEU A 246 " --> pdb=" O   ASP A 242 " (cutoff:3.500A)
      removed outlier: 3.575A  pdb=" N   LYS A 249 " --> pdb=" O   SER A 245 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 266 through 270
    Processing helix  chain 'A' and resid 327 through 355
      removed outlier: 3.537A  pdb=" N   THR A 331 " --> pdb=" O   ASP A 327 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'B' and resid 56 through 60
      removed outlier: 7.053A  pdb=" N   CYS B 261 " --> pdb=" O   GLY B 324 " (cutoff:3.500A)
      removed outlier: 9.058A  pdb=" N   PHE B 326 " --> pdb=" O   CYS B 261 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 62 through 70
    Processing sheet with id=AA3, first strand: chain 'B' and resid 62 through 70
    Processing sheet with id=AA4, first strand: chain 'B' and resid 73 through 76
    Processing sheet with id=AA5, first strand: chain 'B' and resid 99 through 112
      removed outlier: 8.078A  pdb=" N   PHE B 100 " --> pdb=" O   ILE B 317 " (cutoff:3.500A)
      removed outlier: 7.490A  pdb=" N   ILE B 317 " --> pdb=" O   PHE B 100 " (cutoff:3.500A)
      removed outlier: 7.536A  pdb=" N   VAL B 102 " --> pdb=" O   PHE B 315 " (cutoff:3.500A)
      removed outlier: 7.564A  pdb=" N   PHE B 315 " --> pdb=" O   VAL B 102 " (cutoff:3.500A)
      removed outlier: 7.235A  pdb=" N   THR B 104 " --> pdb=" O   ILE B 313 " (cutoff:3.500A)
      removed outlier: 8.047A  pdb=" N   ILE B 313 " --> pdb=" O   THR B 104 " (cutoff:3.500A)
      removed outlier: 5.361A  pdb=" N   PHE B 106 " --> pdb=" O   PHE B 311 " (cutoff:3.500A)
      removed outlier: 7.025A  pdb=" N   PHE B 311 " --> pdb=" O   PHE B 106 " (cutoff:3.500A)
      removed outlier: 5.655A  pdb=" N   MET B 108 " --> pdb=" O   LYS B 309 " (cutoff:3.500A)
      removed outlier: 7.244A  pdb=" N   LYS B 309 " --> pdb=" O   MET B 108 " (cutoff:3.500A)
      removed outlier: 6.384A  pdb=" N   LEU B 307 " --> pdb=" O   PRO B 110 " (cutoff:3.500A)
      removed outlier: 6.780A  pdb=" N   GLY B 251 " --> pdb=" O   ARG B 314 " (cutoff:3.500A)
      removed outlier: 8.001A  pdb=" N   ASP B 316 " --> pdb=" O   GLY B 251 " (cutoff:3.500A)
      removed outlier: 6.745A  pdb=" N   VAL B 253 " --> pdb=" O   ASP B 316 " (cutoff:3.500A)
      removed outlier: 7.964A  pdb=" N   LEU B 318 " --> pdb=" O   VAL B 253 " (cutoff:3.500A)
      removed outlier: 6.238A  pdb=" N   ILE B 255 " --> pdb=" O   LEU B 318 " (cutoff:3.500A)
      removed outlier: 7.548A  pdb=" N   ASP B 320 " --> pdb=" O   ILE B 255 " (cutoff:3.500A)
      removed outlier: 5.788A  pdb=" N   ILE B 257 " --> pdb=" O   ASP B 320 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 99 through 112
      removed outlier: 8.078A  pdb=" N   PHE B 100 " --> pdb=" O   ILE B 317 " (cutoff:3.500A)
      removed outlier: 7.490A  pdb=" N   ILE B 317 " --> pdb=" O   PHE B 100 " (cutoff:3.500A)
      removed outlier: 7.536A  pdb=" N   VAL B 102 " --> pdb=" O   PHE B 315 " (cutoff:3.500A)
      removed outlier: 7.564A  pdb=" N   PHE B 315 " --> pdb=" O   VAL B 102 " (cutoff:3.500A)
      removed outlier: 7.235A  pdb=" N   THR B 104 " --> pdb=" O   ILE B 313 " (cutoff:3.500A)
      removed outlier: 8.047A  pdb=" N   ILE B 313 " --> pdb=" O   THR B 104 " (cutoff:3.500A)
      removed outlier: 5.361A  pdb=" N   PHE B 106 " --> pdb=" O   PHE B 311 " (cutoff:3.500A)
      removed outlier: 7.025A  pdb=" N   PHE B 311 " --> pdb=" O   PHE B 106 " (cutoff:3.500A)
      removed outlier: 5.655A  pdb=" N   MET B 108 " --> pdb=" O   LYS B 309 " (cutoff:3.500A)
      removed outlier: 7.244A  pdb=" N   LYS B 309 " --> pdb=" O   MET B 108 " (cutoff:3.500A)
      removed outlier: 6.384A  pdb=" N   LEU B 307 " --> pdb=" O   PRO B 110 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 114 through 118
      removed outlier: 6.767A  pdb=" N   THR B 158 " --> pdb=" O   ASN B 148 " (cutoff:3.500A)
      removed outlier: 6.858A  pdb=" N   ASN B 148 " --> pdb=" O   THR B 158 " (cutoff:3.500A)
      removed outlier: 7.483A  pdb=" N   GLU B 160 " --> pdb=" O   THR B 146 " (cutoff:3.500A)
      removed outlier: 3.577A  pdb=" N   ILE B 144 " --> pdb=" O   PHE B 162 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'C' and resid 56 through 60
      removed outlier: 3.640A  pdb=" N   GLY C 324 " --> pdb=" O   CYS C 261 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'C' and resid 62 through 70
    Processing sheet with id=AB1, first strand: chain 'C' and resid 62 through 70
    Processing sheet with id=AB2, first strand: chain 'C' and resid 73 through 76
    Processing sheet with id=AB3, first strand: chain 'C' and resid 99 through 112
      removed outlier: 8.109A  pdb=" N   PHE C 100 " --> pdb=" O   ILE C 317 " (cutoff:3.500A)
      removed outlier: 7.513A  pdb=" N   ILE C 317 " --> pdb=" O   PHE C 100 " (cutoff:3.500A)
      removed outlier: 7.509A  pdb=" N   VAL C 102 " --> pdb=" O   PHE C 315 " (cutoff:3.500A)
      removed outlier: 7.506A  pdb=" N   PHE C 315 " --> pdb=" O   VAL C 102 " (cutoff:3.500A)
      removed outlier: 6.967A  pdb=" N   THR C 104 " --> pdb=" O   ILE C 313 " (cutoff:3.500A)
      removed outlier: 7.826A  pdb=" N   ILE C 313 " --> pdb=" O   THR C 104 " (cutoff:3.500A)
      removed outlier: 5.325A  pdb=" N   PHE C 106 " --> pdb=" O   PHE C 311 " (cutoff:3.500A)
      removed outlier: 7.012A  pdb=" N   PHE C 311 " --> pdb=" O   PHE C 106 " (cutoff:3.500A)
      removed outlier: 5.632A  pdb=" N   MET C 108 " --> pdb=" O   LYS C 309 " (cutoff:3.500A)
      removed outlier: 7.252A  pdb=" N   LYS C 309 " --> pdb=" O   MET C 108 " (cutoff:3.500A)
      removed outlier: 6.382A  pdb=" N   LEU C 307 " --> pdb=" O   PRO C 110 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'C' and resid 99 through 112
      removed outlier: 8.109A  pdb=" N   PHE C 100 " --> pdb=" O   ILE C 317 " (cutoff:3.500A)
      removed outlier: 7.513A  pdb=" N   ILE C 317 " --> pdb=" O   PHE C 100 " (cutoff:3.500A)
      removed outlier: 7.509A  pdb=" N   VAL C 102 " --> pdb=" O   PHE C 315 " (cutoff:3.500A)
      removed outlier: 7.506A  pdb=" N   PHE C 315 " --> pdb=" O   VAL C 102 " (cutoff:3.500A)
      removed outlier: 6.967A  pdb=" N   THR C 104 " --> pdb=" O   ILE C 313 " (cutoff:3.500A)
      removed outlier: 7.826A  pdb=" N   ILE C 313 " --> pdb=" O   THR C 104 " (cutoff:3.500A)
      removed outlier: 5.325A  pdb=" N   PHE C 106 " --> pdb=" O   PHE C 311 " (cutoff:3.500A)
      removed outlier: 7.012A  pdb=" N   PHE C 311 " --> pdb=" O   PHE C 106 " (cutoff:3.500A)
      removed outlier: 5.632A  pdb=" N   MET C 108 " --> pdb=" O   LYS C 309 " (cutoff:3.500A)
      removed outlier: 7.252A  pdb=" N   LYS C 309 " --> pdb=" O   MET C 108 " (cutoff:3.500A)
      removed outlier: 6.382A  pdb=" N   LEU C 307 " --> pdb=" O   PRO C 110 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'C' and resid 114 through 118
      removed outlier: 4.909A  pdb=" N   ASN C 148 " --> pdb=" O   GLU C 160 " (cutoff:3.500A)
      removed outlier: 8.436A  pdb=" N   PHE C 162 " --> pdb=" O   THR C 146 " (cutoff:3.500A)
      removed outlier: 7.676A  pdb=" N   THR C 146 " --> pdb=" O   PHE C 162 " (cutoff:3.500A)
      removed outlier: 9.302A  pdb=" N   TRP C 164 " --> pdb=" O   ILE C 144 " (cutoff:3.500A)
      removed outlier: 9.738A  pdb=" N   ILE C 144 " --> pdb=" O   TRP C 164 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'A' and resid 56 through 59
      removed outlier: 7.172A  pdb=" N   CYS A 261 " --> pdb=" O   GLY A 324 " (cutoff:3.500A)
      removed outlier: 9.142A  pdb=" N   PHE A 326 " --> pdb=" O   CYS A 261 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'A' and resid 62 through 70
    Processing sheet with id=AB8, first strand: chain 'A' and resid 62 through 70
    Processing sheet with id=AB9, first strand: chain 'A' and resid 73 through 76
    Processing sheet with id=AC1, first strand: chain 'A' and resid 99 through 112
      removed outlier: 8.106A  pdb=" N   PHE A 100 " --> pdb=" O   ILE A 317 " (cutoff:3.500A)
      removed outlier: 7.502A  pdb=" N   ILE A 317 " --> pdb=" O   PHE A 100 " (cutoff:3.500A)
      removed outlier: 7.533A  pdb=" N   VAL A 102 " --> pdb=" O   PHE A 315 " (cutoff:3.500A)
      removed outlier: 7.569A  pdb=" N   PHE A 315 " --> pdb=" O   VAL A 102 " (cutoff:3.500A)
      removed outlier: 7.281A  pdb=" N   THR A 104 " --> pdb=" O   ILE A 313 " (cutoff:3.500A)
      removed outlier: 8.057A  pdb=" N   ILE A 313 " --> pdb=" O   THR A 104 " (cutoff:3.500A)
      removed outlier: 5.354A  pdb=" N   PHE A 106 " --> pdb=" O   PHE A 311 " (cutoff:3.500A)
      removed outlier: 7.028A  pdb=" N   PHE A 311 " --> pdb=" O   PHE A 106 " (cutoff:3.500A)
      removed outlier: 5.664A  pdb=" N   MET A 108 " --> pdb=" O   LYS A 309 " (cutoff:3.500A)
      removed outlier: 7.232A  pdb=" N   LYS A 309 " --> pdb=" O   MET A 108 " (cutoff:3.500A)
      removed outlier: 6.270A  pdb=" N   LEU A 307 " --> pdb=" O   PRO A 110 " (cutoff:3.500A)
      removed outlier: 6.732A  pdb=" N   GLY A 251 " --> pdb=" O   ARG A 314 " (cutoff:3.500A)
      removed outlier: 7.997A  pdb=" N   ASP A 316 " --> pdb=" O   GLY A 251 " (cutoff:3.500A)
      removed outlier: 6.742A  pdb=" N   VAL A 253 " --> pdb=" O   ASP A 316 " (cutoff:3.500A)
      removed outlier: 7.908A  pdb=" N   LEU A 318 " --> pdb=" O   VAL A 253 " (cutoff:3.500A)
      removed outlier: 6.211A  pdb=" N   ILE A 255 " --> pdb=" O   LEU A 318 " (cutoff:3.500A)
      removed outlier: 7.656A  pdb=" N   ASP A 320 " --> pdb=" O   ILE A 255 " (cutoff:3.500A)
      removed outlier: 5.937A  pdb=" N   ILE A 257 " --> pdb=" O   ASP A 320 " (cutoff:3.500A)
    Processing sheet with id=AC2, first strand: chain 'A' and resid 99 through 112
      removed outlier: 8.106A  pdb=" N   PHE A 100 " --> pdb=" O   ILE A 317 " (cutoff:3.500A)
      removed outlier: 7.502A  pdb=" N   ILE A 317 " --> pdb=" O   PHE A 100 " (cutoff:3.500A)
      removed outlier: 7.533A  pdb=" N   VAL A 102 " --> pdb=" O   PHE A 315 " (cutoff:3.500A)
      removed outlier: 7.569A  pdb=" N   PHE A 315 " --> pdb=" O   VAL A 102 " (cutoff:3.500A)
      removed outlier: 7.281A  pdb=" N   THR A 104 " --> pdb=" O   ILE A 313 " (cutoff:3.500A)
      removed outlier: 8.057A  pdb=" N   ILE A 313 " --> pdb=" O   THR A 104 " (cutoff:3.500A)
      removed outlier: 5.354A  pdb=" N   PHE A 106 " --> pdb=" O   PHE A 311 " (cutoff:3.500A)
      removed outlier: 7.028A  pdb=" N   PHE A 311 " --> pdb=" O   PHE A 106 " (cutoff:3.500A)
      removed outlier: 5.664A  pdb=" N   MET A 108 " --> pdb=" O   LYS A 309 " (cutoff:3.500A)
      removed outlier: 7.232A  pdb=" N   LYS A 309 " --> pdb=" O   MET A 108 " (cutoff:3.500A)
      removed outlier: 6.270A  pdb=" N   LEU A 307 " --> pdb=" O   PRO A 110 " (cutoff:3.500A)
    Processing sheet with id=AC3, first strand: chain 'A' and resid 114 through 118
      removed outlier: 4.982A  pdb=" N   ASN A 148 " --> pdb=" O   GLU A 160 " (cutoff:3.500A)
      removed outlier: 8.642A  pdb=" N   PHE A 162 " --> pdb=" O   THR A 146 " (cutoff:3.500A)
      removed outlier: 8.017A  pdb=" N   THR A 146 " --> pdb=" O   PHE A 162 " (cutoff:3.500A)
      removed outlier: 9.354A  pdb=" N   TRP A 164 " --> pdb=" O   ILE A 144 " (cutoff:3.500A)
      removed outlier: 9.663A  pdb=" N   ILE A 144 " --> pdb=" O   TRP A 164 " (cutoff:3.500A)

    369 hydrogen bonds defined for protein.
    972 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: 2.48

  Time building geometry restraints manager: 2.70 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2480
        1.34 -     1.46: 1585
        1.46 -     1.58: 4053
        1.58 -     1.70: 15
        1.70 -     1.82: 57
  Bond restraints: 8190
  Sorted by residual:
  bond pdb=" C4  ATP A 502 "
       pdb=" C5  ATP A 502 "
    ideal  model  delta    sigma   weight residual
    1.388  1.467 -0.079 1.00e-02 1.00e+04 6.17e+01
  bond pdb=" C4  ATP C 502 "
       pdb=" C5  ATP C 502 "
    ideal  model  delta    sigma   weight residual
    1.388  1.467 -0.079 1.00e-02 1.00e+04 6.17e+01
  bond pdb=" C4  ATP B 401 "
       pdb=" C5  ATP B 401 "
    ideal  model  delta    sigma   weight residual
    1.388  1.466 -0.078 1.00e-02 1.00e+04 6.16e+01
  bond pdb=" C5  ATP B 401 "
       pdb=" C6  ATP B 401 "
    ideal  model  delta    sigma   weight residual
    1.409  1.478 -0.069 1.00e-02 1.00e+04 4.80e+01
  bond pdb=" C5  ATP A 502 "
       pdb=" C6  ATP A 502 "
    ideal  model  delta    sigma   weight residual
    1.409  1.478 -0.069 1.00e-02 1.00e+04 4.78e+01
  ... (remaining 8185 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.36: 11017
        3.36 -     6.71: 85
        6.71 -    10.07: 13
       10.07 -    13.42: 0
       13.42 -    16.78: 6
  Bond angle restraints: 11121
  Sorted by residual:
  angle pdb=" PB  ATP C 502 "
        pdb=" O3B ATP C 502 "
        pdb=" PG  ATP C 502 "
      ideal   model   delta    sigma   weight residual
     139.87  123.09   16.78 1.00e+00 1.00e+00 2.81e+02
  angle pdb=" PB  ATP A 502 "
        pdb=" O3B ATP A 502 "
        pdb=" PG  ATP A 502 "
      ideal   model   delta    sigma   weight residual
     139.87  123.53   16.34 1.00e+00 1.00e+00 2.67e+02
  angle pdb=" PB  ATP B 401 "
        pdb=" O3B ATP B 401 "
        pdb=" PG  ATP B 401 "
      ideal   model   delta    sigma   weight residual
     139.87  123.72   16.15 1.00e+00 1.00e+00 2.61e+02
  angle pdb=" PA  ATP A 502 "
        pdb=" O3A ATP A 502 "
        pdb=" PB  ATP A 502 "
      ideal   model   delta    sigma   weight residual
     136.83  122.14   14.69 1.00e+00 1.00e+00 2.16e+02
  angle pdb=" PA  ATP C 502 "
        pdb=" O3A ATP C 502 "
        pdb=" PB  ATP C 502 "
      ideal   model   delta    sigma   weight residual
     136.83  122.53   14.30 1.00e+00 1.00e+00 2.05e+02
  ... (remaining 11116 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.07: 4666
       16.07 -    32.14: 209
       32.14 -    48.22: 47
       48.22 -    64.29: 17
       64.29 -    80.36: 8
  Dihedral angle restraints: 4947
    sinusoidal: 2157
      harmonic: 2790
  Sorted by residual:
  dihedral pdb=" C   PHE C  92 "
           pdb=" N   PHE C  92 "
           pdb=" CA  PHE C  92 "
           pdb=" CB  PHE C  92 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -140.35   17.75     0      2.50e+00 1.60e-01 5.04e+01
  dihedral pdb=" N   PHE C  92 "
           pdb=" C   PHE C  92 "
           pdb=" CA  PHE C  92 "
           pdb=" CB  PHE C  92 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80  138.34  -15.54     0      2.50e+00 1.60e-01 3.86e+01
  dihedral pdb=" CA  LEU A  72 "
           pdb=" CB  LEU A  72 "
           pdb=" CG  LEU A  72 "
           pdb=" CD1 LEU A  72 "
      ideal   model   delta sinusoidal    sigma   weight residual
     180.00  120.50   59.50     3      1.50e+01 4.44e-03 9.48e+00
  ... (remaining 4944 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.153: 1229
       0.153 -    0.306: 9
       0.306 -    0.458: 3
       0.458 -    0.611: 0
       0.611 -    0.764: 1
  Chirality restraints: 1242
  Sorted by residual:
  chirality pdb=" CA  PHE C  92 "
            pdb=" N   PHE C  92 "
            pdb=" C   PHE C  92 "
            pdb=" CB  PHE C  92 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.75    0.76 2.00e-01 2.50e+01 1.46e+01
  chirality pdb=" C1  NAG A 505 "
            pdb=" ND2 ASN A 184 "
            pdb=" C2  NAG A 505 "
            pdb=" O5  NAG A 505 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -1.99   -0.41 2.00e-01 2.50e+01 4.28e+00
  chirality pdb=" C1  NAG B 404 "
            pdb=" ND2 ASN B 184 "
            pdb=" C2  NAG B 404 "
            pdb=" O5  NAG B 404 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.01   -0.39 2.00e-01 2.50e+01 3.81e+00
  ... (remaining 1239 not shown)

  Planarity restraints: 1407
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE C  92 "   -0.050 5.00e-02 4.00e+02   7.63e-02 9.31e+00
        pdb=" N   PRO C  93 "    0.132 5.00e-02 4.00e+02
        pdb=" CA  PRO C  93 "   -0.037 5.00e-02 4.00e+02
        pdb=" CD  PRO C  93 "   -0.044 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN B 120 "   -0.030 5.00e-02 4.00e+02   4.60e-02 3.38e+00
        pdb=" N   PRO B 121 "    0.079 5.00e-02 4.00e+02
        pdb=" CA  PRO B 121 "   -0.024 5.00e-02 4.00e+02
        pdb=" CD  PRO B 121 "   -0.025 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PHE A 185 "   -0.008 2.00e-02 2.50e+03   1.66e-02 2.76e+00
        pdb=" C   PHE A 185 "    0.029 2.00e-02 2.50e+03
        pdb=" O   PHE A 185 "   -0.011 2.00e-02 2.50e+03
        pdb=" N   THR A 186 "   -0.010 2.00e-02 2.50e+03
  ... (remaining 1404 not shown)

  Histogram of nonbonded interaction distances:
        1.33 -     2.04: 2
        2.04 -     2.76: 1047
        2.76 -     3.47: 10976
        3.47 -     4.19: 19668
        4.19 -     4.90: 33970
  Nonbonded interactions: 65663
  Sorted by model distance:
  nonbonded pdb=" O3G ATP C 502 "
            pdb="MG    MG A 501 "
     model   vdw
     1.329 2.170
  nonbonded pdb=" O3G ATP B 401 "
            pdb="MG    MG C 501 "
     model   vdw
     1.879 2.170
  nonbonded pdb="MG    MG B 405 "
            pdb=" O3G ATP A 502 "
     model   vdw
     2.084 2.170
  nonbonded pdb=" OD1 ASP A 170 "
            pdb="MG    MG A 501 "
     model   vdw
     2.278 2.170
  nonbonded pdb=" O   VAL B 298 "
            pdb=" O   HOH B 501 "
     model   vdw
     2.296 3.040
  ... (remaining 65658 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' and (resid 26 through 355 or resid 503 through 504))
  selection = (chain 'B' and (resid 26 through 355 or resid 403 through 404))
  selection = (chain 'C' and (resid 26 through 355 or resid 503 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:             0.830
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.320
  Check model and map are aligned:         0.060
  Set scattering table:                    0.090
  Process input model:                     23.540
  Find NCS groups from input model:        0.360
  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:13.350
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   38.590
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6967
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.079   8208  Z= 0.334
  Angle     :  0.852  16.778  11166  Z= 0.602
  Chirality :  0.055   0.764   1242
  Planarity :  0.004   0.076   1398
  Dihedral  : 10.436  80.361   3144
  Min Nonbonded Distance : 1.329

Molprobity Statistics.
  All-atom Clashscore : 6.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.73 %
    Favored  : 98.27 %
  Rotamer:
    Outliers :  2.25 %
    Allowed  :  3.90 %
    Favored  : 93.85 %
  Cbeta Deviations :  0.11 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.33 (0.25), residues: 984
  helix: -0.02 (0.32), residues: 270
  sheet:  0.84 (0.29), residues: 279
  loop : -1.02 (0.26), residues: 435

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.000   TRP B 164 
 HIS   0.001   0.000   HIS C 355 
 PHE   0.027   0.001   PHE C  92 
 TYR   0.011   0.001   TYR C  55 
 ARG   0.006   0.000   ARG A 292 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00718 (    9)
  link_NAG-ASN         : angle       3.66369 (   27)
  hydrogen bonds       : bond        0.12995 (  333)
  hydrogen bonds       : angle       5.39096 (  972)
  SS BOND              : bond        0.00235 (    9)
  SS BOND              : angle       0.94770 (   18)
  covalent geometry    : bond        0.00435 ( 8190)
  covalent geometry    : angle       0.83343 (11121)

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

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

  1968 Ramachandran restraints generated.
    984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1968 Ramachandran restraints generated.
    984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  244 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 225
  time to evaluate  : 0.878 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  292 ARG cc_start: 0.8555 (OUTLIER) cc_final: 0.8119 (mtm180)
  outliers start: 19
  outliers final: 1
  residues processed: 238
  average time/residue: 1.1549
  time to fit residues: 290.9216
Evaluate side-chains
  112 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 110
  time to evaluate  : 0.923 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   72 LEU
Chi-restraints excluded: chain A residue  292 ARG
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 83 optimal weight:    3.9990
   chunk 75 optimal weight:    2.9990
   chunk 41 optimal weight:    5.9990
   chunk 25 optimal weight:    0.5980
   chunk 50 optimal weight:    0.9980
   chunk 40 optimal weight:    3.9990
   chunk 77 optimal weight:    2.9990
   chunk 30 optimal weight:    5.9990
   chunk 47 optimal weight:    5.9990
   chunk 57 optimal weight:    3.9990
   chunk 89 optimal weight:    0.5980
   overall best weight:    1.6384

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

Flipped N/Q/H residues before XYZ refinement:
B 191 ASN
B 220 HIS
B 299 GLN
C 191 ASN
C 220 HIS
C 299 GLN
A  56 GLN
A 148 ASN
A 191 ASN
A 220 HIS
A 299 GLN

Total number of N/Q/H flips: 11

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3535 r_free = 0.3535 target = 0.112787 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3047 r_free = 0.3047 target = 0.080192 restraints weight = 11154.159|
|-----------------------------------------------------------------------------|
r_work (start): 0.3013 rms_B_bonded: 2.56
r_work: 0.2880 rms_B_bonded: 2.86 restraints_weight: 0.5000
r_work: 0.2758 rms_B_bonded: 4.53 restraints_weight: 0.2500
r_work (final): 0.2758
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8728
moved from start:          0.2961

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.056   8208  Z= 0.188
  Angle     :  0.723  17.416  11166  Z= 0.353
  Chirality :  0.054   0.602   1242
  Planarity :  0.005   0.040   1398
  Dihedral  :  9.128  86.787   1353
  Min Nonbonded Distance : 1.949

Molprobity Statistics.
  All-atom Clashscore : 4.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.03 %
    Favored  : 97.97 %
  Rotamer:
    Outliers :  3.78 %
    Allowed  : 13.48 %
    Favored  : 82.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.40 (0.26), residues: 984
  helix:  0.95 (0.34), residues: 264
  sheet:  1.14 (0.27), residues: 327
  loop : -0.96 (0.30), residues: 393

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A  47 
 HIS   0.005   0.001   HIS C  95 
 PHE   0.037   0.002   PHE C  92 
 TYR   0.030   0.002   TYR A  90 
 ARG   0.006   0.001   ARG B 244 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00861 (    9)
  link_NAG-ASN         : angle       5.81704 (   27)
  hydrogen bonds       : bond        0.03115 (  333)
  hydrogen bonds       : angle       4.55415 (  972)
  SS BOND              : bond        0.00356 (    9)
  SS BOND              : angle       2.17540 (   18)
  covalent geometry    : bond        0.00433 ( 8190)
  covalent geometry    : angle       0.65983 (11121)

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

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

  1968 Ramachandran restraints generated.
    984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1968 Ramachandran restraints generated.
    984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  146 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 114
  time to evaluate  : 0.910 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   76 GLN cc_start: 0.8813 (OUTLIER) cc_final: 0.8595 (mm-40)
REVERT: B  197 ARG cc_start: 0.8994 (OUTLIER) cc_final: 0.8719 (ttm-80)
REVERT: B  258 ASP cc_start: 0.9122 (m-30) cc_final: 0.8402 (t70)
REVERT: C   52 GLU cc_start: 0.8552 (OUTLIER) cc_final: 0.8153 (mp0)
REVERT: C  258 ASP cc_start: 0.9041 (m-30) cc_final: 0.8415 (t70)
REVERT: C  260 GLU cc_start: 0.7872 (OUTLIER) cc_final: 0.7014 (mm-30)
REVERT: A   45 ILE cc_start: 0.8626 (tt) cc_final: 0.8333 (tp)
REVERT: A  221 LYS cc_start: 0.9250 (OUTLIER) cc_final: 0.8998 (mtmm)
REVERT: A  258 ASP cc_start: 0.9084 (m-30) cc_final: 0.8383 (t70)
REVERT: A  268 ARG cc_start: 0.8413 (ptp90) cc_final: 0.8037 (ptm-80)
  outliers start: 32
  outliers final: 8
  residues processed: 137
  average time/residue: 1.2655
  time to fit residues: 183.5003
Evaluate side-chains
  108 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 95
  time to evaluate  : 0.892 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   76 GLN
Chi-restraints excluded: chain B residue  197 ARG
Chi-restraints excluded: chain C residue   52 GLU
Chi-restraints excluded: chain C residue   66 SER
Chi-restraints excluded: chain C residue  167 VAL
Chi-restraints excluded: chain C residue  260 GLU
Chi-restraints excluded: chain C residue  337 SER
Chi-restraints excluded: chain A residue   42 VAL
Chi-restraints excluded: chain A residue  122 GLU
Chi-restraints excluded: chain A residue  167 VAL
Chi-restraints excluded: chain A residue  214 MET
Chi-restraints excluded: chain A residue  221 LYS
Chi-restraints excluded: chain A residue  337 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 68 optimal weight:    4.9990
   chunk 28 optimal weight:    5.9990
   chunk 83 optimal weight:    6.9990
   chunk 91 optimal weight:    0.0970
   chunk 63 optimal weight:    3.9990
   chunk 57 optimal weight:    0.8980
   chunk 74 optimal weight:    6.9990
   chunk 27 optimal weight:    0.7980
   chunk 31 optimal weight:    9.9990
   chunk 16 optimal weight:    2.9990
   chunk 42 optimal weight:    0.5980
   overall best weight:    1.0780

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

Flipped N/Q/H residues before XYZ refinement:
B 116 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3523 r_free = 0.3523 target = 0.111784 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3029 r_free = 0.3029 target = 0.078989 restraints weight = 11372.450|
|-----------------------------------------------------------------------------|
r_work (start): 0.2994 rms_B_bonded: 2.59
r_work: 0.2861 rms_B_bonded: 2.88 restraints_weight: 0.5000
r_work: 0.2735 rms_B_bonded: 4.58 restraints_weight: 0.2500
r_work (final): 0.2735
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8747
moved from start:          0.3229

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049   8208  Z= 0.140
  Angle     :  0.645  14.569  11166  Z= 0.313
  Chirality :  0.050   0.536   1242
  Planarity :  0.004   0.040   1398
  Dihedral  :  8.906  82.731   1347
  Min Nonbonded Distance : 1.953

Molprobity Statistics.
  All-atom Clashscore : 3.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.34 %
    Favored  : 97.66 %
  Rotamer:
    Outliers :  3.66 %
    Allowed  : 14.18 %
    Favored  : 82.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.68 (0.27), residues: 984
  helix:  1.16 (0.34), residues: 270
  sheet:  1.23 (0.27), residues: 327
  loop : -0.75 (0.31), residues: 387

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A  47 
 HIS   0.003   0.001   HIS B 116 
 PHE   0.026   0.002   PHE C  92 
 TYR   0.018   0.001   TYR B  90 
 ARG   0.008   0.001   ARG A 244 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00831 (    9)
  link_NAG-ASN         : angle       5.00350 (   27)
  hydrogen bonds       : bond        0.02800 (  333)
  hydrogen bonds       : angle       4.36606 (  972)
  SS BOND              : bond        0.00248 (    9)
  SS BOND              : angle       2.39429 (   18)
  covalent geometry    : bond        0.00323 ( 8190)
  covalent geometry    : angle       0.58944 (11121)

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

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

  1968 Ramachandran restraints generated.
    984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1968 Ramachandran restraints generated.
    984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 99
  time to evaluate  : 0.866 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   76 GLN cc_start: 0.8823 (mm-40) cc_final: 0.8605 (mm-40)
REVERT: B  197 ARG cc_start: 0.8972 (ttm-80) cc_final: 0.8719 (ttm-80)
REVERT: B  258 ASP cc_start: 0.9135 (m-30) cc_final: 0.8443 (t70)
REVERT: C  258 ASP cc_start: 0.9031 (m-30) cc_final: 0.8453 (t70)
REVERT: A   45 ILE cc_start: 0.8628 (OUTLIER) cc_final: 0.8348 (tp)
REVERT: A  215 LYS cc_start: 0.8927 (OUTLIER) cc_final: 0.8714 (mtpt)
REVERT: A  258 ASP cc_start: 0.9102 (m-30) cc_final: 0.8383 (t70)
REVERT: A  268 ARG cc_start: 0.8451 (ptp90) cc_final: 0.8075 (ptm-80)
REVERT: A  275 GLN cc_start: 0.8881 (OUTLIER) cc_final: 0.8644 (mt0)
  outliers start: 31
  outliers final: 11
  residues processed: 119
  average time/residue: 1.1514
  time to fit residues: 145.7663
Evaluate side-chains
  104 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 90
  time to evaluate  : 0.857 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   66 SER
Chi-restraints excluded: chain B residue  328 ILE
Chi-restraints excluded: chain C residue   66 SER
Chi-restraints excluded: chain C residue  155 THR
Chi-restraints excluded: chain C residue  167 VAL
Chi-restraints excluded: chain C residue  328 ILE
Chi-restraints excluded: chain C residue  337 SER
Chi-restraints excluded: chain A residue   42 VAL
Chi-restraints excluded: chain A residue   45 ILE
Chi-restraints excluded: chain A residue  155 THR
Chi-restraints excluded: chain A residue  167 VAL
Chi-restraints excluded: chain A residue  215 LYS
Chi-restraints excluded: chain A residue  275 GLN
Chi-restraints excluded: chain A residue  337 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 63 optimal weight:    0.0470
   chunk 34 optimal weight:    0.9980
   chunk 67 optimal weight:    2.9990
   chunk 11 optimal weight:    6.9990
   chunk 87 optimal weight:    4.9990
   chunk 72 optimal weight:    0.9990
   chunk 32 optimal weight:    9.9990
   chunk 31 optimal weight:    3.9990
   chunk 58 optimal weight:    3.9990
   chunk 29 optimal weight:    6.9990
   chunk 68 optimal weight:    4.9990
   overall best weight:    1.8084

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

Flipped N/Q/H residues before XYZ refinement:
B 114 GLN
B 116 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3457 r_free = 0.3457 target = 0.107495 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.2941 r_free = 0.2941 target = 0.074263 restraints weight = 11369.435|
|-----------------------------------------------------------------------------|
r_work (start): 0.2905 rms_B_bonded: 2.57
r_work: 0.2767 rms_B_bonded: 2.82 restraints_weight: 0.5000
r_work: 0.2639 rms_B_bonded: 4.45 restraints_weight: 0.2500
r_work (final): 0.2639
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8823
moved from start:          0.3700

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.055   8208  Z= 0.191
  Angle     :  0.688  11.695  11166  Z= 0.336
  Chirality :  0.047   0.253   1242
  Planarity :  0.005   0.042   1398
  Dihedral  :  9.911  85.464   1347
  Min Nonbonded Distance : 1.916

Molprobity Statistics.
  All-atom Clashscore : 3.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.74 %
    Favored  : 97.26 %
  Rotamer:
    Outliers :  4.37 %
    Allowed  : 14.30 %
    Favored  : 81.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.83 (0.27), residues: 984
  helix:  1.43 (0.35), residues: 264
  sheet:  1.33 (0.27), residues: 327
  loop : -0.74 (0.31), residues: 393

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A  47 
 HIS   0.004   0.001   HIS B 116 
 PHE   0.038   0.002   PHE C  92 
 TYR   0.017   0.002   TYR A  90 
 ARG   0.009   0.001   ARG C 244 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00331 (    9)
  link_NAG-ASN         : angle       3.47100 (   27)
  hydrogen bonds       : bond        0.03035 (  333)
  hydrogen bonds       : angle       4.40909 (  972)
  SS BOND              : bond        0.00353 (    9)
  SS BOND              : angle       2.26725 (   18)
  covalent geometry    : bond        0.00439 ( 8190)
  covalent geometry    : angle       0.66172 (11121)

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

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

  1968 Ramachandran restraints generated.
    984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1968 Ramachandran restraints generated.
    984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 99
  time to evaluate  : 0.842 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  138 GLU cc_start: 0.8810 (pm20) cc_final: 0.8588 (mp0)
REVERT: B  197 ARG cc_start: 0.8999 (ttm-80) cc_final: 0.8738 (ttm-80)
REVERT: B  258 ASP cc_start: 0.9127 (m-30) cc_final: 0.8481 (t70)
REVERT: C  244 ARG cc_start: 0.8828 (mtp-110) cc_final: 0.8481 (mtp85)
REVERT: C  261 CYS cc_start: 0.8657 (p) cc_final: 0.8437 (p)
REVERT: A   45 ILE cc_start: 0.8638 (OUTLIER) cc_final: 0.8384 (tp)
REVERT: A  214 MET cc_start: 0.9425 (OUTLIER) cc_final: 0.9054 (ttp)
REVERT: A  215 LYS cc_start: 0.8932 (OUTLIER) cc_final: 0.8696 (mtpt)
REVERT: A  258 ASP cc_start: 0.9119 (m-30) cc_final: 0.8490 (t70)
  outliers start: 37
  outliers final: 13
  residues processed: 124
  average time/residue: 1.1687
  time to fit residues: 153.8278
Evaluate side-chains
  107 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 91
  time to evaluate  : 0.842 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   48 VAL
Chi-restraints excluded: chain B residue   66 SER
Chi-restraints excluded: chain C residue   66 SER
Chi-restraints excluded: chain C residue  167 VAL
Chi-restraints excluded: chain C residue  214 MET
Chi-restraints excluded: chain C residue  275 GLN
Chi-restraints excluded: chain C residue  337 SER
Chi-restraints excluded: chain A residue   42 VAL
Chi-restraints excluded: chain A residue   45 ILE
Chi-restraints excluded: chain A residue  122 GLU
Chi-restraints excluded: chain A residue  155 THR
Chi-restraints excluded: chain A residue  167 VAL
Chi-restraints excluded: chain A residue  214 MET
Chi-restraints excluded: chain A residue  215 LYS
Chi-restraints excluded: chain A residue  328 ILE
Chi-restraints excluded: chain A residue  337 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 38 optimal weight:    0.2980
   chunk 26 optimal weight:    1.9990
   chunk 89 optimal weight:    4.9990
   chunk 35 optimal weight:    0.9980
   chunk 92 optimal weight:    0.7980
   chunk 79 optimal weight:    5.9990
   chunk 34 optimal weight:    1.9990
   chunk 97 optimal weight:   10.0000
   chunk 55 optimal weight:    7.9990
   chunk 9 optimal weight:    0.8980
   chunk 84 optimal weight:    0.9990
   overall best weight:    0.7982

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

Flipped N/Q/H residues before XYZ refinement:
B 114 GLN
B 116 HIS
** A  76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3483 r_free = 0.3483 target = 0.109397 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.2981 r_free = 0.2981 target = 0.076401 restraints weight = 11239.259|
|-----------------------------------------------------------------------------|
r_work (start): 0.2946 rms_B_bonded: 2.55
r_work: 0.2811 rms_B_bonded: 2.82 restraints_weight: 0.5000
r_work: 0.2685 rms_B_bonded: 4.47 restraints_weight: 0.2500
r_work (final): 0.2685
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8794
moved from start:          0.3709

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.053   8208  Z= 0.127
  Angle     :  0.627   9.807  11166  Z= 0.307
  Chirality :  0.045   0.234   1242
  Planarity :  0.004   0.044   1398
  Dihedral  :  9.010  72.329   1347
  Min Nonbonded Distance : 1.973

Molprobity Statistics.
  All-atom Clashscore : 3.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.95 %
    Favored  : 97.05 %
  Rotamer:
    Outliers :  2.60 %
    Allowed  : 15.25 %
    Favored  : 82.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.84 (0.27), residues: 984
  helix:  1.35 (0.35), residues: 270
  sheet:  1.35 (0.27), residues: 327
  loop : -0.72 (0.32), residues: 387

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP C 164 
 HIS   0.003   0.000   HIS B 116 
 PHE   0.024   0.001   PHE C  92 
 TYR   0.017   0.001   TYR B  90 
 ARG   0.009   0.001   ARG A 244 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00977 (    9)
  link_NAG-ASN         : angle       3.03353 (   27)
  hydrogen bonds       : bond        0.02583 (  333)
  hydrogen bonds       : angle       4.28158 (  972)
  SS BOND              : bond        0.00427 (    9)
  SS BOND              : angle       2.50677 (   18)
  covalent geometry    : bond        0.00290 ( 8190)
  covalent geometry    : angle       0.60181 (11121)

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

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

  1968 Ramachandran restraints generated.
    984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1968 Ramachandran restraints generated.
    984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 96
  time to evaluate  : 0.841 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  138 GLU cc_start: 0.8796 (pm20) cc_final: 0.8563 (mp0)
REVERT: B  197 ARG cc_start: 0.8953 (ttm-80) cc_final: 0.8702 (ttm-80)
REVERT: B  258 ASP cc_start: 0.9119 (m-30) cc_final: 0.8457 (t70)
REVERT: C   45 ILE cc_start: 0.8740 (tp) cc_final: 0.8504 (tp)
REVERT: C  244 ARG cc_start: 0.8818 (mtp-110) cc_final: 0.8617 (mpt180)
REVERT: C  261 CYS cc_start: 0.8599 (p) cc_final: 0.8396 (p)
REVERT: A   45 ILE cc_start: 0.8640 (OUTLIER) cc_final: 0.8390 (tp)
REVERT: A  214 MET cc_start: 0.9434 (OUTLIER) cc_final: 0.9027 (ttp)
REVERT: A  258 ASP cc_start: 0.9081 (m-30) cc_final: 0.8452 (t70)
REVERT: A  268 ARG cc_start: 0.8472 (ptp90) cc_final: 0.8044 (ptm-80)
  outliers start: 22
  outliers final: 9
  residues processed: 110
  average time/residue: 1.1788
  time to fit residues: 137.8635
Evaluate side-chains
  100 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 89
  time to evaluate  : 0.835 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  328 ILE
Chi-restraints excluded: chain C residue  167 VAL
Chi-restraints excluded: chain C residue  214 MET
Chi-restraints excluded: chain C residue  328 ILE
Chi-restraints excluded: chain C residue  332 MET
Chi-restraints excluded: chain C residue  337 SER
Chi-restraints excluded: chain A residue   42 VAL
Chi-restraints excluded: chain A residue   45 ILE
Chi-restraints excluded: chain A residue  167 VAL
Chi-restraints excluded: chain A residue  214 MET
Chi-restraints excluded: chain A residue  328 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 73 optimal weight:    3.9990
   chunk 63 optimal weight:    0.8980
   chunk 87 optimal weight:    5.9990
   chunk 51 optimal weight:    6.9990
   chunk 88 optimal weight:    2.9990
   chunk 59 optimal weight:    3.9990
   chunk 89 optimal weight:    0.8980
   chunk 44 optimal weight:    5.9990
   chunk 3 optimal weight:    0.9980
   chunk 86 optimal weight:    3.9990
   chunk 85 optimal weight:    0.7980
   overall best weight:    1.3182

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

Flipped N/Q/H residues before XYZ refinement:
B 114 GLN
B 116 HIS
** A  76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3472 r_free = 0.3472 target = 0.108374 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.2960 r_free = 0.2960 target = 0.075152 restraints weight = 11327.952|
|-----------------------------------------------------------------------------|
r_work (start): 0.2917 rms_B_bonded: 2.58
r_work: 0.2780 rms_B_bonded: 2.83 restraints_weight: 0.5000
r_work: 0.2652 rms_B_bonded: 4.47 restraints_weight: 0.2500
r_work (final): 0.2652
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8808
moved from start:          0.3816

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.065   8208  Z= 0.154
  Angle     :  0.654  10.760  11166  Z= 0.323
  Chirality :  0.045   0.245   1242
  Planarity :  0.004   0.051   1398
  Dihedral  :  8.872  74.448   1347
  Min Nonbonded Distance : 1.939

Molprobity Statistics.
  All-atom Clashscore : 4.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.25 %
    Favored  : 96.75 %
  Rotamer:
    Outliers :  2.84 %
    Allowed  : 15.37 %
    Favored  : 81.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.88 (0.27), residues: 984
  helix:  1.40 (0.35), residues: 270
  sheet:  1.38 (0.27), residues: 327
  loop : -0.71 (0.32), residues: 387

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP C 259 
 HIS   0.003   0.001   HIS B 116 
 PHE   0.031   0.002   PHE C  92 
 TYR   0.016   0.001   TYR A  90 
 ARG   0.011   0.001   ARG B 244 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00982 (    9)
  link_NAG-ASN         : angle       3.04567 (   27)
  hydrogen bonds       : bond        0.02743 (  333)
  hydrogen bonds       : angle       4.27796 (  972)
  SS BOND              : bond        0.00247 (    9)
  SS BOND              : angle       3.19489 (   18)
  covalent geometry    : bond        0.00356 ( 8190)
  covalent geometry    : angle       0.62458 (11121)

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

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

  1968 Ramachandran restraints generated.
    984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1968 Ramachandran restraints generated.
    984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 95
  time to evaluate  : 0.915 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  258 ASP cc_start: 0.9115 (m-30) cc_final: 0.8437 (t70)
REVERT: C   76 GLN cc_start: 0.8919 (mm-40) cc_final: 0.8705 (mm-40)
REVERT: C  261 CYS cc_start: 0.8633 (p) cc_final: 0.8432 (p)
REVERT: A   45 ILE cc_start: 0.8647 (OUTLIER) cc_final: 0.8406 (tp)
REVERT: A  197 ARG cc_start: 0.9035 (ttm-80) cc_final: 0.8748 (ttt-90)
REVERT: A  208 GLU cc_start: 0.8708 (OUTLIER) cc_final: 0.8160 (mt-10)
REVERT: A  214 MET cc_start: 0.9436 (OUTLIER) cc_final: 0.9070 (ttp)
REVERT: A  258 ASP cc_start: 0.9081 (m-30) cc_final: 0.8463 (t70)
REVERT: A  268 ARG cc_start: 0.8484 (ptp90) cc_final: 0.8061 (ptm-80)
  outliers start: 24
  outliers final: 12
  residues processed: 107
  average time/residue: 1.2448
  time to fit residues: 141.3425
Evaluate side-chains
  103 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 88
  time to evaluate  : 0.913 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   48 VAL
Chi-restraints excluded: chain B residue   66 SER
Chi-restraints excluded: chain C residue   66 SER
Chi-restraints excluded: chain C residue  167 VAL
Chi-restraints excluded: chain C residue  275 GLN
Chi-restraints excluded: chain C residue  328 ILE
Chi-restraints excluded: chain C residue  337 SER
Chi-restraints excluded: chain A residue   42 VAL
Chi-restraints excluded: chain A residue   45 ILE
Chi-restraints excluded: chain A residue  122 GLU
Chi-restraints excluded: chain A residue  167 VAL
Chi-restraints excluded: chain A residue  208 GLU
Chi-restraints excluded: chain A residue  214 MET
Chi-restraints excluded: chain A residue  328 ILE
Chi-restraints excluded: chain A residue  337 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 45 optimal weight:    5.9990
   chunk 12 optimal weight:    0.9980
   chunk 28 optimal weight:    5.9990
   chunk 14 optimal weight:    6.9990
   chunk 97 optimal weight:   10.0000
   chunk 1 optimal weight:    1.9990
   chunk 85 optimal weight:    0.4980
   chunk 61 optimal weight:    4.9990
   chunk 4 optimal weight:    2.9990
   chunk 62 optimal weight:    3.9990
   chunk 88 optimal weight:    4.9990
   overall best weight:    2.0986

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

Flipped N/Q/H residues before XYZ refinement:
B 116 HIS
C 241 GLN
** A  76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 127 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3476 r_free = 0.3476 target = 0.107723 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3010 r_free = 0.3010 target = 0.075571 restraints weight = 11790.480|
|-----------------------------------------------------------------------------|
r_work (start): 0.2963 rms_B_bonded: 2.49
r_work: 0.2846 rms_B_bonded: 2.69 restraints_weight: 0.5000
r_work: 0.2729 rms_B_bonded: 4.28 restraints_weight: 0.2500
r_work (final): 0.2729
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8895
moved from start:          0.4070

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.071   8208  Z= 0.212
  Angle     :  0.682  10.140  11166  Z= 0.341
  Chirality :  0.047   0.260   1242
  Planarity :  0.005   0.058   1398
  Dihedral  :  9.116  76.562   1347
  Min Nonbonded Distance : 1.928

Molprobity Statistics.
  All-atom Clashscore : 3.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.15 %
    Favored  : 96.85 %
  Rotamer:
    Outliers :  3.07 %
    Allowed  : 15.25 %
    Favored  : 81.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.83 (0.27), residues: 984
  helix:  1.52 (0.35), residues: 264
  sheet:  1.24 (0.27), residues: 333
  loop : -0.75 (0.32), residues: 387

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A  47 
 HIS   0.003   0.001   HIS B 116 
 PHE   0.038   0.002   PHE C  92 
 TYR   0.016   0.002   TYR B  90 
 ARG   0.012   0.001   ARG B 244 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.01067 (    9)
  link_NAG-ASN         : angle       2.97144 (   27)
  hydrogen bonds       : bond        0.03023 (  333)
  hydrogen bonds       : angle       4.37253 (  972)
  SS BOND              : bond        0.00331 (    9)
  SS BOND              : angle       2.83677 (   18)
  covalent geometry    : bond        0.00492 ( 8190)
  covalent geometry    : angle       0.65770 (11121)

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

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

  1968 Ramachandran restraints generated.
    984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1968 Ramachandran restraints generated.
    984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 89
  time to evaluate  : 0.952 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  258 ASP cc_start: 0.9061 (m-30) cc_final: 0.8469 (t70)
REVERT: C   45 ILE cc_start: 0.8861 (tp) cc_final: 0.8613 (tp)
REVERT: A   45 ILE cc_start: 0.8747 (OUTLIER) cc_final: 0.8496 (tp)
REVERT: A  197 ARG cc_start: 0.9066 (ttm-80) cc_final: 0.8812 (ttt-90)
REVERT: A  208 GLU cc_start: 0.8820 (OUTLIER) cc_final: 0.8272 (mt-10)
REVERT: A  258 ASP cc_start: 0.9054 (m-30) cc_final: 0.8495 (t70)
REVERT: A  260 GLU cc_start: 0.8239 (mm-30) cc_final: 0.7794 (mm-30)
REVERT: A  268 ARG cc_start: 0.8536 (ptp90) cc_final: 0.8117 (ptm-80)
  outliers start: 26
  outliers final: 14
  residues processed: 105
  average time/residue: 1.2513
  time to fit residues: 139.7174
Evaluate side-chains
  101 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 85
  time to evaluate  : 0.966 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   48 VAL
Chi-restraints excluded: chain B residue   66 SER
Chi-restraints excluded: chain C residue   66 SER
Chi-restraints excluded: chain C residue  167 VAL
Chi-restraints excluded: chain C residue  214 MET
Chi-restraints excluded: chain C residue  328 ILE
Chi-restraints excluded: chain C residue  332 MET
Chi-restraints excluded: chain C residue  337 SER
Chi-restraints excluded: chain A residue   42 VAL
Chi-restraints excluded: chain A residue   45 ILE
Chi-restraints excluded: chain A residue  122 GLU
Chi-restraints excluded: chain A residue  167 VAL
Chi-restraints excluded: chain A residue  208 GLU
Chi-restraints excluded: chain A residue  221 LYS
Chi-restraints excluded: chain A residue  328 ILE
Chi-restraints excluded: chain A residue  337 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 82 optimal weight:    2.9990
   chunk 47 optimal weight:    0.6980
   chunk 90 optimal weight:    0.9990
   chunk 44 optimal weight:    7.9990
   chunk 88 optimal weight:    5.9990
   chunk 64 optimal weight:    8.9990
   chunk 25 optimal weight:    1.9990
   chunk 65 optimal weight:    5.9990
   chunk 46 optimal weight:    2.9990
   chunk 8 optimal weight:    4.9990
   chunk 50 optimal weight:    0.9980
   overall best weight:    1.5386

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

Flipped N/Q/H residues before XYZ refinement:
B 114 GLN
B 116 HIS
** A  76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3490 r_free = 0.3490 target = 0.108670 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3029 r_free = 0.3029 target = 0.076685 restraints weight = 11847.359|
|-----------------------------------------------------------------------------|
r_work (start): 0.2983 rms_B_bonded: 2.48
r_work: 0.2868 rms_B_bonded: 2.71 restraints_weight: 0.5000
r_work: 0.2752 rms_B_bonded: 4.30 restraints_weight: 0.2500
r_work (final): 0.2752
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8883
moved from start:          0.4089

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.061   8208  Z= 0.169
  Angle     :  0.656   9.114  11166  Z= 0.327
  Chirality :  0.046   0.234   1242
  Planarity :  0.004   0.059   1398
  Dihedral  :  9.045  74.973   1347
  Min Nonbonded Distance : 1.959

Molprobity Statistics.
  All-atom Clashscore : 4.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.35 %
    Favored  : 96.65 %
  Rotamer:
    Outliers :  2.72 %
    Allowed  : 16.90 %
    Favored  : 80.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.82 (0.27), residues: 984
  helix:  1.55 (0.35), residues: 264
  sheet:  1.24 (0.28), residues: 333
  loop : -0.79 (0.31), residues: 387

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP C 259 
 HIS   0.003   0.001   HIS B 116 
 PHE   0.032   0.002   PHE C  92 
 TYR   0.017   0.001   TYR C  90 
 ARG   0.013   0.001   ARG B 244 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00859 (    9)
  link_NAG-ASN         : angle       2.90780 (   27)
  hydrogen bonds       : bond        0.02818 (  333)
  hydrogen bonds       : angle       4.28004 (  972)
  SS BOND              : bond        0.00282 (    9)
  SS BOND              : angle       2.58182 (   18)
  covalent geometry    : bond        0.00391 ( 8190)
  covalent geometry    : angle       0.63351 (11121)

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

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

  1968 Ramachandran restraints generated.
    984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1968 Ramachandran restraints generated.
    984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  110 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 87
  time to evaluate  : 0.859 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  244 ARG cc_start: 0.8129 (mtp-110) cc_final: 0.7908 (mtp85)
REVERT: C   45 ILE cc_start: 0.8855 (tp) cc_final: 0.8590 (tp)
REVERT: A   45 ILE cc_start: 0.8748 (OUTLIER) cc_final: 0.8502 (tp)
REVERT: A  197 ARG cc_start: 0.9038 (ttm-80) cc_final: 0.8779 (ttt-90)
REVERT: A  258 ASP cc_start: 0.9050 (m-30) cc_final: 0.8489 (t70)
REVERT: A  268 ARG cc_start: 0.8533 (ptp90) cc_final: 0.8110 (ptm-80)
  outliers start: 23
  outliers final: 16
  residues processed: 99
  average time/residue: 1.2098
  time to fit residues: 127.5642
Evaluate side-chains
  101 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 84
  time to evaluate  : 1.034 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   48 VAL
Chi-restraints excluded: chain B residue   66 SER
Chi-restraints excluded: chain B residue  193 ILE
Chi-restraints excluded: chain C residue   66 SER
Chi-restraints excluded: chain C residue  167 VAL
Chi-restraints excluded: chain C residue  214 MET
Chi-restraints excluded: chain C residue  275 GLN
Chi-restraints excluded: chain C residue  328 ILE
Chi-restraints excluded: chain C residue  332 MET
Chi-restraints excluded: chain C residue  337 SER
Chi-restraints excluded: chain A residue   42 VAL
Chi-restraints excluded: chain A residue   45 ILE
Chi-restraints excluded: chain A residue  122 GLU
Chi-restraints excluded: chain A residue  167 VAL
Chi-restraints excluded: chain A residue  221 LYS
Chi-restraints excluded: chain A residue  328 ILE
Chi-restraints excluded: chain A residue  337 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 12 optimal weight:    1.9990
   chunk 93 optimal weight:    2.9990
   chunk 25 optimal weight:    2.9990
   chunk 3 optimal weight:    0.9990
   chunk 46 optimal weight:    0.9980
   chunk 2 optimal weight:    0.5980
   chunk 60 optimal weight:    0.4980
   chunk 92 optimal weight:    2.9990
   chunk 42 optimal weight:    1.9990
   chunk 38 optimal weight:    2.9990
   chunk 66 optimal weight:   30.0000
   overall best weight:    1.0184

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

Flipped N/Q/H residues before XYZ refinement:
B 116 HIS
** A  76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 127 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3505 r_free = 0.3505 target = 0.109836 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3052 r_free = 0.3052 target = 0.078017 restraints weight = 11940.426|
|-----------------------------------------------------------------------------|
r_work (start): 0.3003 rms_B_bonded: 2.49
r_work: 0.2887 rms_B_bonded: 2.74 restraints_weight: 0.5000
r_work: 0.2772 rms_B_bonded: 4.34 restraints_weight: 0.2500
r_work (final): 0.2772
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8864
moved from start:          0.4060

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.052   8208  Z= 0.131
  Angle     :  0.608   8.921  11166  Z= 0.304
  Chirality :  0.044   0.207   1242
  Planarity :  0.004   0.054   1398
  Dihedral  :  8.913  85.712   1347
  Min Nonbonded Distance : 1.981

Molprobity Statistics.
  All-atom Clashscore : 4.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.15 %
    Favored  : 96.85 %
  Rotamer:
    Outliers :  2.01 %
    Allowed  : 17.73 %
    Favored  : 80.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.86 (0.27), residues: 984
  helix:  1.42 (0.35), residues: 270
  sheet:  1.37 (0.27), residues: 327
  loop : -0.76 (0.31), residues: 387

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP C 259 
 HIS   0.003   0.000   HIS B 116 
 PHE   0.026   0.002   PHE C  92 
 TYR   0.017   0.001   TYR C  90 
 ARG   0.012   0.001   ARG B 244 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00744 (    9)
  link_NAG-ASN         : angle       2.28569 (   27)
  hydrogen bonds       : bond        0.02565 (  333)
  hydrogen bonds       : angle       4.18710 (  972)
  SS BOND              : bond        0.00291 (    9)
  SS BOND              : angle       2.36889 (   18)
  covalent geometry    : bond        0.00303 ( 8190)
  covalent geometry    : angle       0.59104 (11121)

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

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

  1968 Ramachandran restraints generated.
    984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1968 Ramachandran restraints generated.
    984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 87
  time to evaluate  : 0.863 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  244 ARG cc_start: 0.8095 (mtp-110) cc_final: 0.7895 (mtp85)
REVERT: C   45 ILE cc_start: 0.8853 (tp) cc_final: 0.8593 (tp)
REVERT: C  216 LYS cc_start: 0.8925 (mmtt) cc_final: 0.8673 (pptt)
REVERT: A  197 ARG cc_start: 0.9022 (ttm-80) cc_final: 0.8761 (ttt-90)
REVERT: A  258 ASP cc_start: 0.9052 (m-30) cc_final: 0.8487 (t70)
REVERT: A  268 ARG cc_start: 0.8516 (ptp90) cc_final: 0.8101 (ptm-80)
  outliers start: 17
  outliers final: 11
  residues processed: 97
  average time/residue: 1.2246
  time to fit residues: 126.3201
Evaluate side-chains
  96 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 85
  time to evaluate  : 0.921 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   48 VAL
Chi-restraints excluded: chain B residue   66 SER
Chi-restraints excluded: chain B residue  193 ILE
Chi-restraints excluded: chain C residue   66 SER
Chi-restraints excluded: chain C residue  167 VAL
Chi-restraints excluded: chain C residue  328 ILE
Chi-restraints excluded: chain C residue  337 SER
Chi-restraints excluded: chain A residue   42 VAL
Chi-restraints excluded: chain A residue  167 VAL
Chi-restraints excluded: chain A residue  328 ILE
Chi-restraints excluded: chain A residue  337 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 50 optimal weight:    0.9990
   chunk 84 optimal weight:    0.9990
   chunk 10 optimal weight:    8.9990
   chunk 95 optimal weight:    3.9990
   chunk 43 optimal weight:   10.0000
   chunk 82 optimal weight:    1.9990
   chunk 39 optimal weight:    0.9990
   chunk 47 optimal weight:    0.7980
   chunk 59 optimal weight:    1.9990
   chunk 6 optimal weight:    0.7980
   chunk 33 optimal weight:   30.0000
   overall best weight:    0.9186

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

Flipped N/Q/H residues before XYZ refinement:
B 116 HIS
** A  76 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 = 0.3512 r_free = 0.3512 target = 0.110290 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3060 r_free = 0.3060 target = 0.078399 restraints weight = 11801.499|
|-----------------------------------------------------------------------------|
r_work (start): 0.3011 rms_B_bonded: 2.49
r_work: 0.2895 rms_B_bonded: 2.74 restraints_weight: 0.5000
r_work: 0.2780 rms_B_bonded: 4.35 restraints_weight: 0.2500
r_work (final): 0.2780
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8859
moved from start:          0.4074

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049   8208  Z= 0.127
  Angle     :  0.606   8.984  11166  Z= 0.304
  Chirality :  0.044   0.198   1242
  Planarity :  0.004   0.051   1398
  Dihedral  :  8.850  89.036   1347
  Min Nonbonded Distance : 1.987

Molprobity Statistics.
  All-atom Clashscore : 4.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.15 %
    Favored  : 96.85 %
  Rotamer:
    Outliers :  1.42 %
    Allowed  : 18.44 %
    Favored  : 80.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.91 (0.27), residues: 984
  helix:  1.47 (0.35), residues: 270
  sheet:  1.37 (0.27), residues: 327
  loop : -0.71 (0.31), residues: 387

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP C 259 
 HIS   0.003   0.000   HIS B 116 
 PHE   0.026   0.002   PHE C  92 
 TYR   0.016   0.001   TYR C  90 
 ARG   0.012   0.001   ARG B 244 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00633 (    9)
  link_NAG-ASN         : angle       2.03254 (   27)
  hydrogen bonds       : bond        0.02519 (  333)
  hydrogen bonds       : angle       4.17708 (  972)
  SS BOND              : bond        0.00282 (    9)
  SS BOND              : angle       2.34316 (   18)
  covalent geometry    : bond        0.00295 ( 8190)
  covalent geometry    : angle       0.59097 (11121)

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

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

  1968 Ramachandran restraints generated.
    984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1968 Ramachandran restraints generated.
    984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 89
  time to evaluate  : 0.936 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   45 ILE cc_start: 0.8865 (tp) cc_final: 0.8601 (tp)
REVERT: C  216 LYS cc_start: 0.8935 (mmtt) cc_final: 0.8707 (pptt)
REVERT: A   45 ILE cc_start: 0.8744 (tp) cc_final: 0.8502 (tp)
REVERT: A  197 ARG cc_start: 0.9021 (ttm-80) cc_final: 0.8757 (ttt-90)
REVERT: A  258 ASP cc_start: 0.9069 (m-30) cc_final: 0.8498 (t70)
REVERT: A  268 ARG cc_start: 0.8500 (ptp90) cc_final: 0.8062 (ptm-80)
  outliers start: 12
  outliers final: 11
  residues processed: 96
  average time/residue: 1.2019
  time to fit residues: 122.8941
Evaluate side-chains
  98 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 87
  time to evaluate  : 0.916 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   48 VAL
Chi-restraints excluded: chain B residue   66 SER
Chi-restraints excluded: chain B residue  193 ILE
Chi-restraints excluded: chain C residue   66 SER
Chi-restraints excluded: chain C residue  167 VAL
Chi-restraints excluded: chain C residue  275 GLN
Chi-restraints excluded: chain C residue  328 ILE
Chi-restraints excluded: chain C residue  337 SER
Chi-restraints excluded: chain A residue   42 VAL
Chi-restraints excluded: chain A residue  167 VAL
Chi-restraints excluded: chain A residue  328 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 92 optimal weight:    0.9980
   chunk 70 optimal weight:    4.9990
   chunk 22 optimal weight:    2.9990
   chunk 74 optimal weight:    0.8980
   chunk 10 optimal weight:    3.9990
   chunk 48 optimal weight:    3.9990
   chunk 88 optimal weight:    0.9980
   chunk 31 optimal weight:    0.9990
   chunk 1 optimal weight:    0.9990
   chunk 27 optimal weight:    0.8980
   chunk 41 optimal weight:    3.9990
   overall best weight:    0.9582

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

Flipped N/Q/H residues before XYZ refinement:
B 116 HIS
** A  76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 127 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3512 r_free = 0.3512 target = 0.110343 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3062 r_free = 0.3062 target = 0.078486 restraints weight = 11942.816|
|-----------------------------------------------------------------------------|
r_work (start): 0.3012 rms_B_bonded: 2.50
r_work: 0.2896 rms_B_bonded: 2.75 restraints_weight: 0.5000
r_work: 0.2781 rms_B_bonded: 4.36 restraints_weight: 0.2500
r_work (final): 0.2781
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8859
moved from start:          0.4096

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049   8208  Z= 0.128
  Angle     :  0.600   9.284  11166  Z= 0.303
  Chirality :  0.044   0.197   1242
  Planarity :  0.004   0.038   1398
  Dihedral  :  8.563  84.397   1347
  Min Nonbonded Distance : 1.994

Molprobity Statistics.
  All-atom Clashscore : 4.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.25 %
    Favored  : 96.75 %
  Rotamer:
    Outliers :  1.89 %
    Allowed  : 18.09 %
    Favored  : 80.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.92 (0.27), residues: 984
  helix:  1.51 (0.35), residues: 270
  sheet:  1.37 (0.27), residues: 327
  loop : -0.71 (0.31), residues: 387

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A  47 
 HIS   0.003   0.000   HIS B 116 
 PHE   0.026   0.002   PHE C  92 
 TYR   0.016   0.001   TYR A  90 
 ARG   0.007   0.000   ARG C 197 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00592 (    9)
  link_NAG-ASN         : angle       1.84998 (   27)
  hydrogen bonds       : bond        0.02519 (  333)
  hydrogen bonds       : angle       4.16529 (  972)
  SS BOND              : bond        0.00397 (    9)
  SS BOND              : angle       2.27916 (   18)
  covalent geometry    : bond        0.00296 ( 8190)
  covalent geometry    : angle       0.58730 (11121)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 7586.82 seconds
wall clock time: 129 minutes 40.08 seconds (7780.08 seconds total)