Starting phenix.real_space_refine
on Fri Jul 25 18:22:17 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8zt2_60445/07_2025/8zt2_60445.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8zt2_60445/07_2025/8zt2_60445.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.31
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8zt2_60445/07_2025/8zt2_60445.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8zt2_60445/07_2025/8zt2_60445.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8zt2_60445/07_2025/8zt2_60445.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8zt2_60445/07_2025/8zt2_60445.cif"
  }
  resolution = 2.31
  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      1      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 11 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: 7994
  Number of models: 1
  Model: ""
    Number of chains: 9
    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: 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: 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: "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: 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: "A"
      Number of atoms: 2
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 2
          Classifications: {'water': 2}
          Link IDs: {None: 1}
    Chain: "B"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Classifications: {'water': 1}
    Chain: "C"
      Number of atoms: 4
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 4
          Classifications: {'water': 4}
          Link IDs: {None: 3}
  Time building chain proxies: 5.48, per 1000 atoms: 0.69
  Number of scatterers: 7994
  At special positions: 0
  Unit cell: (88.168, 84.048, 120.304, 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      1     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 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
    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

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Links applied
    NAG-ASN
      " NAG A 502 " - " ASN A 210 "
      " NAG A 503 " - " ASN A 153 "
      " NAG A 504 " - " ASN A 184 "
      " NAG B 503 " - " ASN B 210 "
      " NAG B 504 " - " ASN B 153 "
      " NAG B 505 " - " 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: 2.14
  Conformation dependent library (CDL) restraints added in 851.2 milliseconds
  

  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:
      23 helices and 21 sheets defined
      27.2% alpha, 46.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.04
  Creating SS restraints...
    Processing helix  chain 'A' and resid 26 through 47
      removed outlier: 3.893A  pdb=" N   GLY A  30 " --> pdb=" O   ASN A  26 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 86 through 91
    Processing helix  chain 'A' and resid 179 through 184
      removed outlier: 3.724A  pdb=" N   ASN A 184 " --> pdb=" O   GLU A 181 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 210 through 216
      removed outlier: 3.585A  pdb=" N   LYS A 216 " --> pdb=" O   THR A 212 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 232 through 240
    Processing helix  chain 'A' and resid 242 through 250
      removed outlier: 3.712A  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
    Processing helix  chain 'B' and resid 27 through 47
    Processing helix  chain 'B' and resid 86 through 91
    Processing helix  chain 'B' and resid 128 through 132
    Processing helix  chain 'B' and resid 179 through 184
      removed outlier: 3.717A  pdb=" N   ASN B 184 " --> pdb=" O   GLU B 181 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 210 through 216
      removed outlier: 3.689A  pdb=" N   LYS B 216 " --> pdb=" O   THR B 212 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 232 through 240
    Processing helix  chain 'B' and resid 242 through 250
      removed outlier: 3.593A  pdb=" N   LEU B 246 " --> pdb=" O   ASP B 242 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 327 through 355
      removed outlier: 3.552A  pdb=" N   THR B 331 " --> pdb=" O   ASP B 327 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 27 through 46
    Processing helix  chain 'C' and resid 86 through 91
    Processing helix  chain 'C' and resid 179 through 184
      removed outlier: 3.814A  pdb=" N   ASN C 184 " --> pdb=" O   GLU C 181 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 232 through 240
    Processing helix  chain 'C' and resid 242 through 250
      removed outlier: 3.558A  pdb=" N   LEU C 246 " --> pdb=" O   ASP C 242 " (cutoff:3.500A)
      removed outlier: 3.675A  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
    Processing sheet with id=AA1, first strand: chain 'A' and resid 56 through 59
      removed outlier: 3.511A  pdb=" N   SER A  59 " --> pdb=" O   ALA A 323 " (cutoff:3.500A)
      removed outlier: 3.779A  pdb=" N   ALA A 323 " --> pdb=" O   SER A  59 " (cutoff:3.500A)
      removed outlier: 7.240A  pdb=" N   CYS A 261 " --> pdb=" O   GLY A 324 " (cutoff:3.500A)
      removed outlier: 9.166A  pdb=" N   PHE A 326 " --> pdb=" O   CYS A 261 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 62 through 70
      removed outlier: 3.985A  pdb=" N   THR A 186 " --> pdb=" O   LYS A  70 " (cutoff:3.500A)
      removed outlier: 3.514A  pdb=" N   VAL A 200 " --> pdb=" O   PHE A 195 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 62 through 70
      removed outlier: 3.985A  pdb=" N   THR A 186 " --> pdb=" O   LYS A  70 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 73 through 75
    Processing sheet with id=AA5, first strand: chain 'A' and resid 99 through 112
      removed outlier: 5.467A  pdb=" N   SER A  99 " --> pdb=" O   ILE A 317 " (cutoff:3.500A)
      removed outlier: 7.317A  pdb=" N   ILE A 317 " --> pdb=" O   SER A  99 " (cutoff:3.500A)
      removed outlier: 5.457A  pdb=" N   VAL A 101 " --> pdb=" O   PHE A 315 " (cutoff:3.500A)
      removed outlier: 7.005A  pdb=" N   PHE A 315 " --> pdb=" O   VAL A 101 " (cutoff:3.500A)
      removed outlier: 5.816A  pdb=" N   MET A 103 " --> pdb=" O   ILE A 313 " (cutoff:3.500A)
      removed outlier: 6.381A  pdb=" N   ILE A 313 " --> pdb=" O   MET A 103 " (cutoff:3.500A)
      removed outlier: 3.536A  pdb=" N   GLN A 111 " --> pdb=" O   ARG A 305 " (cutoff:3.500A)
      removed outlier: 6.200A  pdb=" N   ARG A 305 " --> pdb=" O   GLN A 111 " (cutoff:3.500A)
      removed outlier: 3.946A  pdb=" N   VAL A 252 " --> pdb=" O   LEU A 279 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 99 through 112
      removed outlier: 5.467A  pdb=" N   SER A  99 " --> pdb=" O   ILE A 317 " (cutoff:3.500A)
      removed outlier: 7.317A  pdb=" N   ILE A 317 " --> pdb=" O   SER A  99 " (cutoff:3.500A)
      removed outlier: 5.457A  pdb=" N   VAL A 101 " --> pdb=" O   PHE A 315 " (cutoff:3.500A)
      removed outlier: 7.005A  pdb=" N   PHE A 315 " --> pdb=" O   VAL A 101 " (cutoff:3.500A)
      removed outlier: 5.816A  pdb=" N   MET A 103 " --> pdb=" O   ILE A 313 " (cutoff:3.500A)
      removed outlier: 6.381A  pdb=" N   ILE A 313 " --> pdb=" O   MET A 103 " (cutoff:3.500A)
      removed outlier: 3.536A  pdb=" N   GLN A 111 " --> pdb=" O   ARG A 305 " (cutoff:3.500A)
      removed outlier: 6.200A  pdb=" N   ARG A 305 " --> pdb=" O   GLN A 111 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 114 through 118
      removed outlier: 5.181A  pdb=" N   ASN A 148 " --> pdb=" O   GLU A 160 " (cutoff:3.500A)
      removed outlier: 8.801A  pdb=" N   PHE A 162 " --> pdb=" O   THR A 146 " (cutoff:3.500A)
      removed outlier: 8.230A  pdb=" N   THR A 146 " --> pdb=" O   PHE A 162 " (cutoff:3.500A)
      removed outlier: 9.417A  pdb=" N   TRP A 164 " --> pdb=" O   ILE A 144 " (cutoff:3.500A)
      removed outlier: 9.558A  pdb=" N   ILE A 144 " --> pdb=" O   TRP A 164 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 56 through 59
      removed outlier: 3.519A  pdb=" N   LYS B 325 " --> pdb=" O   THR B  57 " (cutoff:3.500A)
      removed outlier: 3.579A  pdb=" N   SER B  59 " --> pdb=" O   ALA B 323 " (cutoff:3.500A)
      removed outlier: 3.757A  pdb=" N   ALA B 323 " --> pdb=" O   SER B  59 " (cutoff:3.500A)
      removed outlier: 7.548A  pdb=" N   CYS B 261 " --> pdb=" O   GLY B 324 " (cutoff:3.500A)
      removed outlier: 9.522A  pdb=" N   PHE B 326 " --> pdb=" O   CYS B 261 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 62 through 70
      removed outlier: 3.541A  pdb=" N   THR B 186 " --> pdb=" O   LYS B  70 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'B' and resid 62 through 70
      removed outlier: 3.541A  pdb=" N   THR B 186 " --> pdb=" O   LYS B  70 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'B' and resid 73 through 75
    Processing sheet with id=AB3, first strand: chain 'B' and resid 99 through 112
      removed outlier: 5.497A  pdb=" N   SER B  99 " --> pdb=" O   ILE B 317 " (cutoff:3.500A)
      removed outlier: 7.338A  pdb=" N   ILE B 317 " --> pdb=" O   SER B  99 " (cutoff:3.500A)
      removed outlier: 5.451A  pdb=" N   VAL B 101 " --> pdb=" O   PHE B 315 " (cutoff:3.500A)
      removed outlier: 6.995A  pdb=" N   PHE B 315 " --> pdb=" O   VAL B 101 " (cutoff:3.500A)
      removed outlier: 5.899A  pdb=" N   MET B 103 " --> pdb=" O   ILE B 313 " (cutoff:3.500A)
      removed outlier: 6.541A  pdb=" N   ILE B 313 " --> pdb=" O   MET B 103 " (cutoff:3.500A)
      removed outlier: 3.572A  pdb=" N   GLN B 111 " --> pdb=" O   ARG B 305 " (cutoff:3.500A)
      removed outlier: 6.026A  pdb=" N   ARG B 305 " --> pdb=" O   GLN B 111 " (cutoff:3.500A)
      removed outlier: 3.624A  pdb=" N   GLY B 251 " --> pdb=" O   GLY B 312 " (cutoff:3.500A)
      removed outlier: 3.835A  pdb=" N   VAL B 252 " --> pdb=" O   LEU B 279 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'B' and resid 99 through 112
      removed outlier: 5.497A  pdb=" N   SER B  99 " --> pdb=" O   ILE B 317 " (cutoff:3.500A)
      removed outlier: 7.338A  pdb=" N   ILE B 317 " --> pdb=" O   SER B  99 " (cutoff:3.500A)
      removed outlier: 5.451A  pdb=" N   VAL B 101 " --> pdb=" O   PHE B 315 " (cutoff:3.500A)
      removed outlier: 6.995A  pdb=" N   PHE B 315 " --> pdb=" O   VAL B 101 " (cutoff:3.500A)
      removed outlier: 5.899A  pdb=" N   MET B 103 " --> pdb=" O   ILE B 313 " (cutoff:3.500A)
      removed outlier: 6.541A  pdb=" N   ILE B 313 " --> pdb=" O   MET B 103 " (cutoff:3.500A)
      removed outlier: 3.572A  pdb=" N   GLN B 111 " --> pdb=" O   ARG B 305 " (cutoff:3.500A)
      removed outlier: 6.026A  pdb=" N   ARG B 305 " --> pdb=" O   GLN B 111 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'B' and resid 114 through 118
      removed outlier: 5.174A  pdb=" N   ASN B 148 " --> pdb=" O   GLU B 160 " (cutoff:3.500A)
      removed outlier: 8.530A  pdb=" N   PHE B 162 " --> pdb=" O   THR B 146 " (cutoff:3.500A)
      removed outlier: 7.759A  pdb=" N   THR B 146 " --> pdb=" O   PHE B 162 " (cutoff:3.500A)
      removed outlier: 9.239A  pdb=" N   TRP B 164 " --> pdb=" O   ILE B 144 " (cutoff:3.500A)
      removed outlier: 9.453A  pdb=" N   ILE B 144 " --> pdb=" O   TRP B 164 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'C' and resid 56 through 59
      removed outlier: 3.821A  pdb=" N   SER C  59 " --> pdb=" O   ALA C 323 " (cutoff:3.500A)
      removed outlier: 3.947A  pdb=" N   ALA C 323 " --> pdb=" O   SER C  59 " (cutoff:3.500A)
      removed outlier: 7.324A  pdb=" N   CYS C 261 " --> pdb=" O   GLY C 324 " (cutoff:3.500A)
      removed outlier: 9.300A  pdb=" N   PHE C 326 " --> pdb=" O   CYS C 261 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'C' and resid 62 through 70
    Processing sheet with id=AB8, first strand: chain 'C' and resid 62 through 70
    Processing sheet with id=AB9, first strand: chain 'C' and resid 73 through 76
    Processing sheet with id=AC1, first strand: chain 'C' and resid 99 through 112
      removed outlier: 5.462A  pdb=" N   SER C  99 " --> pdb=" O   ILE C 317 " (cutoff:3.500A)
      removed outlier: 7.254A  pdb=" N   ILE C 317 " --> pdb=" O   SER C  99 " (cutoff:3.500A)
      removed outlier: 5.545A  pdb=" N   VAL C 101 " --> pdb=" O   PHE C 315 " (cutoff:3.500A)
      removed outlier: 6.821A  pdb=" N   PHE C 315 " --> pdb=" O   VAL C 101 " (cutoff:3.500A)
      removed outlier: 5.348A  pdb=" N   MET C 103 " --> pdb=" O   ILE C 313 " (cutoff:3.500A)
      removed outlier: 6.187A  pdb=" N   ILE C 313 " --> pdb=" O   MET C 103 " (cutoff:3.500A)
      removed outlier: 6.014A  pdb=" N   ARG C 305 " --> pdb=" O   GLN C 111 " (cutoff:3.500A)
      removed outlier: 3.573A  pdb=" N   GLY C 251 " --> pdb=" O   GLY C 312 " (cutoff:3.500A)
      removed outlier: 3.972A  pdb=" N   VAL C 252 " --> pdb=" O   LEU C 279 " (cutoff:3.500A)
    Processing sheet with id=AC2, first strand: chain 'C' and resid 99 through 112
      removed outlier: 5.462A  pdb=" N   SER C  99 " --> pdb=" O   ILE C 317 " (cutoff:3.500A)
      removed outlier: 7.254A  pdb=" N   ILE C 317 " --> pdb=" O   SER C  99 " (cutoff:3.500A)
      removed outlier: 5.545A  pdb=" N   VAL C 101 " --> pdb=" O   PHE C 315 " (cutoff:3.500A)
      removed outlier: 6.821A  pdb=" N   PHE C 315 " --> pdb=" O   VAL C 101 " (cutoff:3.500A)
      removed outlier: 5.348A  pdb=" N   MET C 103 " --> pdb=" O   ILE C 313 " (cutoff:3.500A)
      removed outlier: 6.187A  pdb=" N   ILE C 313 " --> pdb=" O   MET C 103 " (cutoff:3.500A)
      removed outlier: 6.014A  pdb=" N   ARG C 305 " --> pdb=" O   GLN C 111 " (cutoff:3.500A)
    Processing sheet with id=AC3, first strand: chain 'C' and resid 114 through 118
      removed outlier: 5.143A  pdb=" N   ASN C 148 " --> pdb=" O   GLU C 160 " (cutoff:3.500A)
      removed outlier: 8.561A  pdb=" N   PHE C 162 " --> pdb=" O   THR C 146 " (cutoff:3.500A)
      removed outlier: 7.784A  pdb=" N   THR C 146 " --> pdb=" O   PHE C 162 " (cutoff:3.500A)
      removed outlier: 9.293A  pdb=" N   TRP C 164 " --> pdb=" O   ILE C 144 " (cutoff:3.500A)
      removed outlier: 9.547A  pdb=" N   ILE C 144 " --> pdb=" O   TRP C 164 " (cutoff:3.500A)

    400 hydrogen bonds defined for protein.
    1089 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: 2.28

  Time building geometry restraints manager: 2.51 seconds

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

  Histogram of bond lengths:
        1.23 -     1.35: 2531
        1.35 -     1.46: 2009
        1.46 -     1.58: 3578
        1.58 -     1.70: 15
        1.70 -     1.82: 57
  Bond restraints: 8190
  Sorted by residual:
  bond pdb=" C4  ATP A 501 "
       pdb=" C5  ATP A 501 "
    ideal  model  delta    sigma   weight residual
    1.388  1.467 -0.079 1.00e-02 1.00e+04 6.26e+01
  bond pdb=" C4  ATP B 502 "
       pdb=" C5  ATP B 502 "
    ideal  model  delta    sigma   weight residual
    1.388  1.467 -0.079 1.00e-02 1.00e+04 6.26e+01
  bond pdb=" C4  ATP C 502 "
       pdb=" C5  ATP C 502 "
    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 A 501 "
       pdb=" C6  ATP A 501 "
    ideal  model  delta    sigma   weight residual
    1.409  1.480 -0.071 1.00e-02 1.00e+04 5.01e+01
  bond pdb=" C5  ATP B 502 "
       pdb=" C6  ATP B 502 "
    ideal  model  delta    sigma   weight residual
    1.409  1.479 -0.070 1.00e-02 1.00e+04 4.96e+01
  ... (remaining 8185 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.37: 11042
        3.37 -     6.73: 64
        6.73 -    10.10: 9
       10.10 -    13.46: 0
       13.46 -    16.83: 6
  Bond angle restraints: 11121
  Sorted by residual:
  angle pdb=" PB  ATP B 502 "
        pdb=" O3B ATP B 502 "
        pdb=" PG  ATP B 502 "
      ideal   model   delta    sigma   weight residual
     139.87  123.04   16.83 1.00e+00 1.00e+00 2.83e+02
  angle pdb=" PB  ATP C 502 "
        pdb=" O3B ATP C 502 "
        pdb=" PG  ATP C 502 "
      ideal   model   delta    sigma   weight residual
     139.87  123.24   16.63 1.00e+00 1.00e+00 2.77e+02
  angle pdb=" PB  ATP A 501 "
        pdb=" O3B ATP A 501 "
        pdb=" PG  ATP A 501 "
      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 C 502 "
        pdb=" O3A ATP C 502 "
        pdb=" PB  ATP C 502 "
      ideal   model   delta    sigma   weight residual
     136.83  122.45   14.38 1.00e+00 1.00e+00 2.07e+02
  angle pdb=" PA  ATP B 502 "
        pdb=" O3A ATP B 502 "
        pdb=" PB  ATP B 502 "
      ideal   model   delta    sigma   weight residual
     136.83  122.50   14.33 1.00e+00 1.00e+00 2.05e+02
  ... (remaining 11116 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    14.59: 4678
       14.59 -    29.18: 200
       29.18 -    43.78: 32
       43.78 -    58.37: 30
       58.37 -    72.96: 7
  Dihedral angle restraints: 4947
    sinusoidal: 2157
      harmonic: 2790
  Sorted by residual:
  dihedral pdb=" CA  CYS C 117 "
           pdb=" CB  CYS C 117 "
           pdb=" SG  CYS C 117 "
           pdb=" SG  CYS C 165 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -73.00 -124.73   51.73     1      2.00e+01 2.50e-03 9.13e+00
  dihedral pdb=" N   ASN C 120 "
           pdb=" CA  ASN C 120 "
           pdb=" CB  ASN C 120 "
           pdb=" CG  ASN C 120 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -180.00 -131.38  -48.62     3      1.50e+01 4.44e-03 8.66e+00
  dihedral pdb=" CA  LYS B  28 "
           pdb=" CB  LYS B  28 "
           pdb=" CG  LYS B  28 "
           pdb=" CD  LYS B  28 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00 -107.43   47.43     3      1.50e+01 4.44e-03 8.49e+00
  ... (remaining 4944 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.057: 1053
       0.057 -    0.115: 170
       0.115 -    0.172: 16
       0.172 -    0.229: 0
       0.229 -    0.287: 3
  Chirality restraints: 1242
  Sorted by residual:
  chirality pdb=" C1  NAG A 504 "
            pdb=" ND2 ASN A 184 "
            pdb=" C2  NAG A 504 "
            pdb=" O5  NAG A 504 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.11   -0.29 2.00e-01 2.50e+01 2.06e+00
  chirality pdb=" C1  NAG C 505 "
            pdb=" ND2 ASN C 184 "
            pdb=" C2  NAG C 505 "
            pdb=" O5  NAG C 505 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.12   -0.28 2.00e-01 2.50e+01 2.02e+00
  chirality pdb=" C1  NAG B 505 "
            pdb=" ND2 ASN B 184 "
            pdb=" C2  NAG B 505 "
            pdb=" O5  NAG B 505 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.12   -0.28 2.00e-01 2.50e+01 1.97e+00
  ... (remaining 1239 not shown)

  Planarity restraints: 1407
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   CYS C 165 "    0.026 5.00e-02 4.00e+02   3.92e-02 2.46e+00
        pdb=" N   PRO C 166 "   -0.068 5.00e-02 4.00e+02
        pdb=" CA  PRO C 166 "    0.020 5.00e-02 4.00e+02
        pdb=" CD  PRO C 166 "    0.022 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE C  92 "    0.022 5.00e-02 4.00e+02   3.39e-02 1.84e+00
        pdb=" N   PRO C  93 "   -0.059 5.00e-02 4.00e+02
        pdb=" CA  PRO C  93 "    0.017 5.00e-02 4.00e+02
        pdb=" CD  PRO C  93 "    0.019 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE B  92 "   -0.022 5.00e-02 4.00e+02   3.37e-02 1.82e+00
        pdb=" N   PRO B  93 "    0.058 5.00e-02 4.00e+02
        pdb=" CA  PRO B  93 "   -0.017 5.00e-02 4.00e+02
        pdb=" CD  PRO B  93 "   -0.019 5.00e-02 4.00e+02
  ... (remaining 1404 not shown)

  Histogram of nonbonded interaction distances:
        1.93 -     2.52: 34
        2.52 -     3.12: 5866
        3.12 -     3.71: 12121
        3.71 -     4.31: 17735
        4.31 -     4.90: 29443
  Nonbonded interactions: 65199
  Sorted by model distance:
  nonbonded pdb=" O3G ATP A 501 "
            pdb="MG    MG B 501 "
     model   vdw
     1.928 2.170
  nonbonded pdb="MG    MG A 505 "
            pdb=" O3G ATP C 502 "
     model   vdw
     2.025 2.170
  nonbonded pdb=" O3G ATP B 502 "
            pdb="MG    MG C 501 "
     model   vdw
     2.048 2.170
  nonbonded pdb=" O   VAL C 298 "
            pdb=" O   HOH C 601 "
     model   vdw
     2.253 3.040
  nonbonded pdb=" O   VAL B 298 "
            pdb=" O   HOH C 601 "
     model   vdw
     2.283 3.040
  ... (remaining 65194 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 503 through 504))
  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:             0.770
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.300
  Check model and map are aligned:         0.050
  Set scattering table:                    0.070
  Process input model:                     22.040
  Find NCS groups from input model:        0.370
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:12.900
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   36.540
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6646
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= 0.311
  Angle     :  0.744  16.831  11166  Z= 0.539
  Chirality :  0.044   0.287   1242
  Planarity :  0.003   0.039   1398
  Dihedral  :  9.506  72.962   3144
  Min Nonbonded Distance : 1.928

Molprobity Statistics.
  All-atom Clashscore : 5.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.91 %
    Favored  : 99.09 %
  Rotamer:
    Outliers :  1.06 %
    Allowed  :  2.60 %
    Favored  : 96.34 %
  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: -0.61 (0.25), residues: 984
  helix: -0.63 (0.30), residues: 294
  sheet:  1.65 (0.30), residues: 240
  loop : -1.40 (0.25), residues: 450

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.000   TRP C  47 
 HIS   0.002   0.000   HIS A 306 
 PHE   0.005   0.001   PHE C 342 
 TYR   0.008   0.001   TYR A  90 
 ARG   0.002   0.000   ARG B 244 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00759 (    9)
  link_NAG-ASN         : angle       3.21971 (   27)
  hydrogen bonds       : bond        0.22036 (  353)
  hydrogen bonds       : angle       8.24364 ( 1089)
  SS BOND              : bond        0.00248 (    9)
  SS BOND              : angle       0.98478 (   18)
  covalent geometry    : bond        0.00398 ( 8190)
  covalent geometry    : angle       0.72728 (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
  202 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 193
  time to evaluate  : 0.863 
Fit side-chains
  outliers start: 9
  outliers final: 0
  residues processed: 200
  average time/residue: 1.3711
  time to fit residues: 287.4494
Evaluate side-chains
  94 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 94
  time to evaluate  : 0.797 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 83 optimal weight:    0.8980
   chunk 75 optimal weight:    0.0980
   chunk 41 optimal weight:    5.9990
   chunk 25 optimal weight:    0.9990
   chunk 50 optimal weight:    0.7980
   chunk 40 optimal weight:    0.9990
   chunk 77 optimal weight:    0.6980
   chunk 30 optimal weight:    0.9980
   chunk 47 optimal weight:    0.9990
   chunk 57 optimal weight:    2.9990
   chunk 89 optimal weight:    0.3980
   overall best weight:    0.5780

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

Flipped N/Q/H residues before XYZ refinement:
A  56 GLN
A 112 GLN
A 180 HIS
A 191 ASN
A 220 HIS
A 290 ASN
B 112 GLN
B 180 HIS
B 191 ASN
B 220 HIS
B 290 ASN
C 112 GLN
C 180 HIS
C 191 ASN
C 220 HIS

Total number of N/Q/H flips: 15

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3951 r_free = 0.3951 target = 0.137238 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3539 r_free = 0.3539 target = 0.102631 restraints weight = 12044.378|
|-----------------------------------------------------------------------------|
r_work (start): 0.3495 rms_B_bonded: 2.48
r_work: 0.3409 rms_B_bonded: 2.83 restraints_weight: 0.5000
r_work: 0.3313 rms_B_bonded: 4.54 restraints_weight: 0.2500
r_work (final): 0.3313
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8512
moved from start:          0.2462

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   8208  Z= 0.130
  Angle     :  0.630  13.248  11166  Z= 0.308
  Chirality :  0.048   0.323   1242
  Planarity :  0.004   0.037   1398
  Dihedral  :  8.313  88.662   1347
  Min Nonbonded Distance : 1.955

Molprobity Statistics.
  All-atom Clashscore : 4.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.74 %
    Favored  : 97.26 %
  Rotamer:
    Outliers :  1.77 %
    Allowed  : 10.76 %
    Favored  : 87.47 %
  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:  0.44 (0.27), residues: 984
  helix:  0.63 (0.33), residues: 276
  sheet:  1.33 (0.28), residues: 321
  loop : -0.83 (0.30), residues: 387

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP C  47 
 HIS   0.003   0.001   HIS A 306 
 PHE   0.018   0.001   PHE A 326 
 TYR   0.024   0.002   TYR C  90 
 ARG   0.007   0.001   ARG B 197 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.01419 (    9)
  link_NAG-ASN         : angle       4.50098 (   27)
  hydrogen bonds       : bond        0.03252 (  353)
  hydrogen bonds       : angle       5.17319 ( 1089)
  SS BOND              : bond        0.00308 (    9)
  SS BOND              : angle       1.67077 (   18)
  covalent geometry    : bond        0.00275 ( 8190)
  covalent geometry    : angle       0.58769 (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
  118 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 103
  time to evaluate  : 0.892 
Fit side-chains
   revert: symmetry clash
REVERT: A  332 MET cc_start: 0.8336 (mmm) cc_final: 0.7991 (mtm)
REVERT: B   51 TYR cc_start: 0.8611 (t80) cc_final: 0.7804 (t80)
REVERT: C  208 GLU cc_start: 0.8395 (mp0) cc_final: 0.8030 (mp0)
  outliers start: 15
  outliers final: 4
  residues processed: 116
  average time/residue: 1.1958
  time to fit residues: 147.3775
Evaluate side-chains
  90 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 86
  time to evaluate  : 0.895 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  210 ASN
Chi-restraints excluded: chain A residue  245 SER
Chi-restraints excluded: chain B residue  226 LEU
Chi-restraints excluded: chain C residue  258 ASP
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 66 optimal weight:   60.0000
   chunk 89 optimal weight:    0.0470
   chunk 68 optimal weight:    0.2980
   chunk 28 optimal weight:    6.9990
   chunk 83 optimal weight:    1.9990
   chunk 91 optimal weight:    0.9990
   chunk 63 optimal weight:    1.9990
   chunk 57 optimal weight:    3.9990
   chunk 74 optimal weight:    7.9990
   chunk 27 optimal weight:    0.8980
   chunk 31 optimal weight:    7.9990
   overall best weight:    0.8482

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

Flipped N/Q/H residues before XYZ refinement:
A 120 ASN
A 180 HIS
B 180 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3888 r_free = 0.3888 target = 0.132069 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3436 r_free = 0.3436 target = 0.095983 restraints weight = 12178.351|
|-----------------------------------------------------------------------------|
r_work (start): 0.3356 rms_B_bonded: 2.54
r_work: 0.3263 rms_B_bonded: 2.86 restraints_weight: 0.5000
r_work: 0.3161 rms_B_bonded: 4.58 restraints_weight: 0.2500
r_work (final): 0.3161
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8666
moved from start:          0.3027

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   8208  Z= 0.131
  Angle     :  0.614  13.338  11166  Z= 0.302
  Chirality :  0.050   0.397   1242
  Planarity :  0.004   0.039   1398
  Dihedral  :  8.023  79.902   1347
  Min Nonbonded Distance : 1.917

Molprobity Statistics.
  All-atom Clashscore : 4.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.34 %
    Favored  : 97.66 %
  Rotamer:
    Outliers :  1.42 %
    Allowed  : 13.48 %
    Favored  : 85.11 %
  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:  0.71 (0.27), residues: 984
  helix:  0.93 (0.33), residues: 276
  sheet:  1.34 (0.28), residues: 324
  loop : -0.60 (0.32), residues: 384

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP C  47 
 HIS   0.003   0.001   HIS B 116 
 PHE   0.017   0.002   PHE B  92 
 TYR   0.019   0.001   TYR C  90 
 ARG   0.008   0.001   ARG C 197 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00803 (    9)
  link_NAG-ASN         : angle       5.19891 (   27)
  hydrogen bonds       : bond        0.03146 (  353)
  hydrogen bonds       : angle       4.73142 ( 1089)
  SS BOND              : bond        0.00275 (    9)
  SS BOND              : angle       1.76885 (   18)
  covalent geometry    : bond        0.00292 ( 8190)
  covalent geometry    : angle       0.55483 (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
  109 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 97
  time to evaluate  : 0.896 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   49 PHE cc_start: 0.8213 (OUTLIER) cc_final: 0.7773 (m-80)
REVERT: A  332 MET cc_start: 0.8334 (mmm) cc_final: 0.7992 (mtm)
REVERT: B   51 TYR cc_start: 0.8640 (t80) cc_final: 0.7836 (t80)
REVERT: B  208 GLU cc_start: 0.8389 (OUTLIER) cc_final: 0.8082 (pm20)
REVERT: C   76 GLN cc_start: 0.8643 (tp40) cc_final: 0.8366 (tp-100)
REVERT: C  116 HIS cc_start: 0.7765 (m-70) cc_final: 0.7529 (m90)
REVERT: C  208 GLU cc_start: 0.8555 (mp0) cc_final: 0.8211 (mp0)
  outliers start: 12
  outliers final: 4
  residues processed: 107
  average time/residue: 1.2873
  time to fit residues: 145.9968
Evaluate side-chains
  92 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 86
  time to evaluate  : 1.020 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   49 PHE
Chi-restraints excluded: chain A residue  122 GLU
Chi-restraints excluded: chain A residue  210 ASN
Chi-restraints excluded: chain B residue  208 GLU
Chi-restraints excluded: chain B residue  226 LEU
Chi-restraints excluded: chain B residue  267 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 82 optimal weight:    3.9990
   chunk 65 optimal weight:    5.9990
   chunk 41 optimal weight:    5.9990
   chunk 24 optimal weight:    2.9990
   chunk 63 optimal weight:    0.8980
   chunk 34 optimal weight:    9.9990
   chunk 67 optimal weight:    9.9990
   chunk 11 optimal weight:    6.9990
   chunk 87 optimal weight:    0.6980
   chunk 72 optimal weight:    3.9990
   chunk 32 optimal weight:   20.0000
   overall best weight:    2.5186

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

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3756 r_free = 0.3756 target = 0.121976 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3266 r_free = 0.3266 target = 0.084946 restraints weight = 12183.031|
|-----------------------------------------------------------------------------|
r_work (start): 0.3213 rms_B_bonded: 2.45
r_work: 0.3115 rms_B_bonded: 2.71 restraints_weight: 0.5000
r_work: 0.3011 rms_B_bonded: 4.24 restraints_weight: 0.2500
r_work (final): 0.3011
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8836
moved from start:          0.4005

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.083   8208  Z= 0.259
  Angle     :  0.754  14.587  11166  Z= 0.380
  Chirality :  0.056   0.476   1242
  Planarity :  0.005   0.036   1398
  Dihedral  :  9.855  75.107   1347
  Min Nonbonded Distance : 1.921

Molprobity Statistics.
  All-atom Clashscore : 3.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.64 %
    Favored  : 97.36 %
  Rotamer:
    Outliers :  2.01 %
    Allowed  : 13.59 %
    Favored  : 84.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.01 (0.28), residues: 984
  helix:  1.90 (0.35), residues: 249
  sheet:  0.91 (0.27), residues: 336
  loop : -0.28 (0.33), residues: 399

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP C 259 
 HIS   0.004   0.001   HIS C 306 
 PHE   0.038   0.003   PHE A  92 
 TYR   0.021   0.002   TYR C  90 
 ARG   0.011   0.001   ARG A 197 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00724 (    9)
  link_NAG-ASN         : angle       5.82969 (   27)
  hydrogen bonds       : bond        0.03876 (  353)
  hydrogen bonds       : angle       4.80199 ( 1089)
  SS BOND              : bond        0.00410 (    9)
  SS BOND              : angle       2.96954 (   18)
  covalent geometry    : bond        0.00594 ( 8190)
  covalent geometry    : angle       0.68861 (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
  107 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 90
  time to evaluate  : 0.901 
Fit side-chains
   revert: symmetry clash
REVERT: A   49 PHE cc_start: 0.8464 (OUTLIER) cc_final: 0.7749 (m-80)
REVERT: A  149 CYS cc_start: 0.6724 (t) cc_final: 0.6522 (t)
REVERT: A  332 MET cc_start: 0.8372 (mmm) cc_final: 0.8091 (mtm)
REVERT: B   51 TYR cc_start: 0.8659 (t80) cc_final: 0.8284 (t80)
REVERT: B  216 LYS cc_start: 0.8507 (OUTLIER) cc_final: 0.8282 (pptt)
REVERT: C   76 GLN cc_start: 0.8647 (tp40) cc_final: 0.8328 (tp-100)
REVERT: C  314 ARG cc_start: 0.8989 (OUTLIER) cc_final: 0.8702 (ptm160)
  outliers start: 17
  outliers final: 8
  residues processed: 102
  average time/residue: 1.3289
  time to fit residues: 143.6933
Evaluate side-chains
  91 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 80
  time to evaluate  : 0.884 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   49 PHE
Chi-restraints excluded: chain A residue  122 GLU
Chi-restraints excluded: chain A residue  210 ASN
Chi-restraints excluded: chain A residue  245 SER
Chi-restraints excluded: chain B residue  208 GLU
Chi-restraints excluded: chain B residue  216 LYS
Chi-restraints excluded: chain B residue  226 LEU
Chi-restraints excluded: chain B residue  267 VAL
Chi-restraints excluded: chain C residue   48 VAL
Chi-restraints excluded: chain C residue  245 SER
Chi-restraints excluded: chain C residue  314 ARG
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 67 optimal weight:   10.0000
   chunk 93 optimal weight:    1.9990
   chunk 70 optimal weight:    5.9990
   chunk 8 optimal weight:    5.9990
   chunk 75 optimal weight:    0.8980
   chunk 94 optimal weight:    3.9990
   chunk 38 optimal weight:    0.3980
   chunk 26 optimal weight:    1.9990
   chunk 89 optimal weight:    0.2980
   chunk 35 optimal weight:    0.7980
   chunk 92 optimal weight:    0.9990
   overall best weight:    0.6782

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3699 r_free = 0.3699 target = 0.121200 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3100 r_free = 0.3100 target = 0.081291 restraints weight = 11348.737|
|-----------------------------------------------------------------------------|
r_work (start): 0.3092 rms_B_bonded: 2.64
r_work: 0.2964 rms_B_bonded: 2.89 restraints_weight: 0.5000
r_work: 0.2843 rms_B_bonded: 4.53 restraints_weight: 0.2500
r_work (final): 0.2843
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8635
moved from start:          0.3977

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   8208  Z= 0.139
  Angle     :  0.700  16.553  11166  Z= 0.338
  Chirality :  0.053   0.479   1242
  Planarity :  0.005   0.044   1398
  Dihedral  :  9.811  68.552   1347
  Min Nonbonded Distance : 1.980

Molprobity Statistics.
  All-atom Clashscore : 3.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.64 %
    Favored  : 97.36 %
  Rotamer:
    Outliers :  1.65 %
    Allowed  : 14.89 %
    Favored  : 83.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.21 %

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:  0.96 (0.27), residues: 984
  helix:  1.83 (0.35), residues: 249
  sheet:  1.04 (0.28), residues: 321
  loop : -0.39 (0.31), residues: 414

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 164 
 HIS   0.002   0.000   HIS B 116 
 PHE   0.020   0.002   PHE A  92 
 TYR   0.020   0.001   TYR C  90 
 ARG   0.010   0.001   ARG A 197 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.01200 (    9)
  link_NAG-ASN         : angle       6.16173 (   27)
  hydrogen bonds       : bond        0.02926 (  353)
  hydrogen bonds       : angle       4.54034 ( 1089)
  SS BOND              : bond        0.00340 (    9)
  SS BOND              : angle       2.07679 (   18)
  covalent geometry    : bond        0.00295 ( 8190)
  covalent geometry    : angle       0.62674 (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
  101 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 87
  time to evaluate  : 0.937 
Fit side-chains
   revert: symmetry clash
REVERT: A   49 PHE cc_start: 0.8266 (OUTLIER) cc_final: 0.7579 (m-80)
REVERT: A  275 GLN cc_start: 0.8380 (mm110) cc_final: 0.8018 (mt0)
REVERT: A  304 ARG cc_start: 0.8179 (OUTLIER) cc_final: 0.7910 (mtt180)
REVERT: A  332 MET cc_start: 0.8273 (mmm) cc_final: 0.7990 (mtm)
REVERT: B   51 TYR cc_start: 0.8621 (t80) cc_final: 0.8269 (t80)
REVERT: B  172 LYS cc_start: 0.8069 (tppt) cc_final: 0.7835 (mmmt)
REVERT: B  275 GLN cc_start: 0.8272 (mm110) cc_final: 0.7878 (mt0)
REVERT: B  328 ILE cc_start: 0.8681 (mp) cc_final: 0.8460 (mm)
REVERT: C   76 GLN cc_start: 0.8733 (tp40) cc_final: 0.8429 (mm110)
REVERT: C  328 ILE cc_start: 0.8556 (mp) cc_final: 0.8119 (OUTLIER)
REVERT: C  332 MET cc_start: 0.8355 (mmm) cc_final: 0.8135 (mtm)
  outliers start: 14
  outliers final: 7
  residues processed: 99
  average time/residue: 1.2644
  time to fit residues: 132.7510
Evaluate side-chains
  90 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 82
  time to evaluate  : 0.822 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   49 PHE
Chi-restraints excluded: chain A residue  122 GLU
Chi-restraints excluded: chain A residue  210 ASN
Chi-restraints excluded: chain A residue  245 SER
Chi-restraints excluded: chain A residue  304 ARG
Chi-restraints excluded: chain B residue  208 GLU
Chi-restraints excluded: chain B residue  267 VAL
Chi-restraints excluded: chain C residue  245 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 40 optimal weight:    4.9990
   chunk 67 optimal weight:    9.9990
   chunk 6 optimal weight:    1.9990
   chunk 12 optimal weight:    3.9990
   chunk 29 optimal weight:    1.9990
   chunk 56 optimal weight:    0.5980
   chunk 57 optimal weight:    1.9990
   chunk 22 optimal weight:    0.6980
   chunk 42 optimal weight:    0.6980
   chunk 73 optimal weight:    5.9990
   chunk 63 optimal weight:    0.8980
   overall best weight:    0.9782

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3695 r_free = 0.3695 target = 0.120809 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3086 r_free = 0.3086 target = 0.080482 restraints weight = 11320.866|
|-----------------------------------------------------------------------------|
r_work (start): 0.3046 rms_B_bonded: 2.67
r_work: 0.2916 rms_B_bonded: 2.91 restraints_weight: 0.5000
r_work: 0.2793 rms_B_bonded: 4.55 restraints_weight: 0.2500
r_work (final): 0.2793
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8648
moved from start:          0.4006

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.059   8208  Z= 0.142
  Angle     :  0.666  14.899  11166  Z= 0.330
  Chirality :  0.051   0.427   1242
  Planarity :  0.005   0.045   1398
  Dihedral  :  9.799  65.339   1347
  Min Nonbonded Distance : 1.934

Molprobity Statistics.
  All-atom Clashscore : 4.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.35 %
    Favored  : 96.65 %
  Rotamer:
    Outliers :  1.77 %
    Allowed  : 16.31 %
    Favored  : 81.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.21 %

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:  0.72 (0.27), residues: 984
  helix:  1.37 (0.35), residues: 267
  sheet:  1.07 (0.29), residues: 303
  loop : -0.53 (0.30), residues: 414

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 164 
 HIS   0.003   0.001   HIS B 116 
 PHE   0.024   0.002   PHE B 326 
 TYR   0.018   0.001   TYR C  90 
 ARG   0.010   0.001   ARG A 197 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00986 (    9)
  link_NAG-ASN         : angle       5.27135 (   27)
  hydrogen bonds       : bond        0.02876 (  353)
  hydrogen bonds       : angle       4.47658 ( 1089)
  SS BOND              : bond        0.00317 (    9)
  SS BOND              : angle       2.79754 (   18)
  covalent geometry    : bond        0.00318 ( 8190)
  covalent geometry    : angle       0.60486 (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
  105 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 90
  time to evaluate  : 0.881 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   49 PHE cc_start: 0.8264 (OUTLIER) cc_final: 0.7482 (m-80)
REVERT: A  275 GLN cc_start: 0.8402 (mm110) cc_final: 0.8019 (mt0)
REVERT: A  304 ARG cc_start: 0.8249 (OUTLIER) cc_final: 0.7980 (mtt180)
REVERT: A  328 ILE cc_start: 0.8543 (mp) cc_final: 0.8056 (OUTLIER)
REVERT: A  332 MET cc_start: 0.8297 (mmm) cc_final: 0.7975 (mtm)
REVERT: B   51 TYR cc_start: 0.8603 (t80) cc_final: 0.8276 (t80)
REVERT: B  172 LYS cc_start: 0.8103 (tppt) cc_final: 0.7872 (mmmt)
REVERT: B  275 GLN cc_start: 0.8276 (mm110) cc_final: 0.7899 (mt0)
REVERT: C   76 GLN cc_start: 0.8759 (tp40) cc_final: 0.8518 (mm110)
  outliers start: 15
  outliers final: 8
  residues processed: 102
  average time/residue: 1.2585
  time to fit residues: 136.1013
Evaluate side-chains
  89 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 80
  time to evaluate  : 0.873 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   49 PHE
Chi-restraints excluded: chain A residue  210 ASN
Chi-restraints excluded: chain A residue  245 SER
Chi-restraints excluded: chain A residue  304 ARG
Chi-restraints excluded: chain B residue  208 GLU
Chi-restraints excluded: chain B residue  245 SER
Chi-restraints excluded: chain B residue  267 VAL
Chi-restraints excluded: chain C residue   48 VAL
Chi-restraints excluded: chain C residue  210 ASN
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 30 optimal weight:    3.9990
   chunk 27 optimal weight:    2.9990
   chunk 51 optimal weight:    1.9990
   chunk 55 optimal weight:    5.9990
   chunk 83 optimal weight:    1.9990
   chunk 24 optimal weight:    0.9990
   chunk 11 optimal weight:    0.0980
   chunk 89 optimal weight:    3.9990
   chunk 71 optimal weight:    2.9990
   chunk 61 optimal weight:    5.9990
   chunk 44 optimal weight:    4.9990
   overall best weight:    1.6188

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3786 r_free = 0.3786 target = 0.124473 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3278 r_free = 0.3278 target = 0.086478 restraints weight = 12032.729|
|-----------------------------------------------------------------------------|
r_work (start): 0.3208 rms_B_bonded: 2.53
r_work: 0.3109 rms_B_bonded: 2.81 restraints_weight: 0.5000
r_work: 0.3004 rms_B_bonded: 4.39 restraints_weight: 0.2500
r_work (final): 0.3004
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8828
moved from start:          0.4232

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.067   8208  Z= 0.186
  Angle     :  0.701  13.893  11166  Z= 0.349
  Chirality :  0.054   0.570   1242
  Planarity :  0.005   0.051   1398
  Dihedral  : 10.245  85.165   1347
  Min Nonbonded Distance : 1.944

Molprobity Statistics.
  All-atom Clashscore : 4.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.25 %
    Favored  : 96.75 %
  Rotamer:
    Outliers :  2.48 %
    Allowed  : 15.25 %
    Favored  : 82.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.21 %

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:  0.67 (0.27), residues: 984
  helix:  1.39 (0.35), residues: 267
  sheet:  0.89 (0.28), residues: 315
  loop : -0.50 (0.31), residues: 402

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP C 259 
 HIS   0.002   0.001   HIS A 306 
 PHE   0.030   0.002   PHE C  92 
 TYR   0.018   0.002   TYR C  90 
 ARG   0.012   0.001   ARG A 197 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00920 (    9)
  link_NAG-ASN         : angle       5.32408 (   27)
  hydrogen bonds       : bond        0.03205 (  353)
  hydrogen bonds       : angle       4.54647 ( 1089)
  SS BOND              : bond        0.00319 (    9)
  SS BOND              : angle       2.75477 (   18)
  covalent geometry    : bond        0.00420 ( 8190)
  covalent geometry    : angle       0.64213 (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
  112 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 91
  time to evaluate  : 0.930 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   49 PHE cc_start: 0.8499 (OUTLIER) cc_final: 0.7608 (m-80)
REVERT: A  258 ASP cc_start: 0.9009 (OUTLIER) cc_final: 0.8502 (t0)
REVERT: A  275 GLN cc_start: 0.8493 (mm110) cc_final: 0.8250 (mt0)
REVERT: A  304 ARG cc_start: 0.8440 (OUTLIER) cc_final: 0.8204 (mtt180)
REVERT: A  328 ILE cc_start: 0.8707 (mp) cc_final: 0.8236 (OUTLIER)
REVERT: A  332 MET cc_start: 0.8398 (mmm) cc_final: 0.8109 (mtm)
REVERT: B   51 TYR cc_start: 0.8661 (t80) cc_final: 0.8387 (t80)
REVERT: B  172 LYS cc_start: 0.8289 (tppt) cc_final: 0.7691 (tptt)
REVERT: B  275 GLN cc_start: 0.8379 (mm110) cc_final: 0.8169 (mt0)
REVERT: C   76 GLN cc_start: 0.8684 (tp40) cc_final: 0.8350 (tp-100)
REVERT: C  314 ARG cc_start: 0.8985 (OUTLIER) cc_final: 0.8718 (ptm160)
REVERT: C  328 ILE cc_start: 0.8633 (mp) cc_final: 0.8087 (OUTLIER)
  outliers start: 21
  outliers final: 12
  residues processed: 108
  average time/residue: 1.2685
  time to fit residues: 145.9269
Evaluate side-chains
  99 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 85
  time to evaluate  : 0.899 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   49 PHE
Chi-restraints excluded: chain A residue  165 CYS
Chi-restraints excluded: chain A residue  210 ASN
Chi-restraints excluded: chain A residue  245 SER
Chi-restraints excluded: chain A residue  258 ASP
Chi-restraints excluded: chain A residue  304 ARG
Chi-restraints excluded: chain B residue  208 GLU
Chi-restraints excluded: chain B residue  245 SER
Chi-restraints excluded: chain B residue  267 VAL
Chi-restraints excluded: chain C residue   48 VAL
Chi-restraints excluded: chain C residue  210 ASN
Chi-restraints excluded: chain C residue  245 SER
Chi-restraints excluded: chain C residue  258 ASP
Chi-restraints excluded: chain C residue  314 ARG
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 38 optimal weight:    1.9990
   chunk 45 optimal weight:    0.9980
   chunk 75 optimal weight:    0.8980
   chunk 19 optimal weight:    5.9990
   chunk 52 optimal weight:    6.9990
   chunk 91 optimal weight:    5.9990
   chunk 61 optimal weight:    5.9990
   chunk 3 optimal weight:    6.9990
   chunk 57 optimal weight:    2.9990
   chunk 23 optimal weight:    0.9990
   chunk 32 optimal weight:   20.0000
   overall best weight:    1.5786

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3772 r_free = 0.3772 target = 0.123201 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3274 r_free = 0.3274 target = 0.085446 restraints weight = 12260.710|
|-----------------------------------------------------------------------------|
r_work (start): 0.3213 rms_B_bonded: 2.55
r_work: 0.3115 rms_B_bonded: 2.78 restraints_weight: 0.5000
r_work: 0.3010 rms_B_bonded: 4.41 restraints_weight: 0.2500
r_work (final): 0.3010
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8824
moved from start:          0.4279

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= 0.183
  Angle     :  0.698  13.879  11166  Z= 0.348
  Chirality :  0.053   0.490   1242
  Planarity :  0.005   0.056   1398
  Dihedral  : 10.206  82.235   1347
  Min Nonbonded Distance : 1.980

Molprobity Statistics.
  All-atom Clashscore : 4.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.15 %
    Favored  : 96.85 %
  Rotamer:
    Outliers :  2.13 %
    Allowed  : 16.55 %
    Favored  : 81.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.21 %

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:  0.63 (0.27), residues: 984
  helix:  1.42 (0.35), residues: 267
  sheet:  0.80 (0.29), residues: 309
  loop : -0.50 (0.31), residues: 408

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP C 259 
 HIS   0.002   0.001   HIS C 306 
 PHE   0.028   0.002   PHE C  92 
 TYR   0.018   0.002   TYR C  90 
 ARG   0.013   0.001   ARG A 197 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00808 (    9)
  link_NAG-ASN         : angle       5.28401 (   27)
  hydrogen bonds       : bond        0.03156 (  353)
  hydrogen bonds       : angle       4.54213 ( 1089)
  SS BOND              : bond        0.00295 (    9)
  SS BOND              : angle       2.46442 (   18)
  covalent geometry    : bond        0.00415 ( 8190)
  covalent geometry    : angle       0.64103 (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
  107 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 89
  time to evaluate  : 0.863 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   49 PHE cc_start: 0.8508 (OUTLIER) cc_final: 0.7595 (m-80)
REVERT: A  275 GLN cc_start: 0.8507 (mm110) cc_final: 0.8258 (mt0)
REVERT: A  304 ARG cc_start: 0.8433 (OUTLIER) cc_final: 0.8198 (mtt180)
REVERT: A  328 ILE cc_start: 0.8702 (mp) cc_final: 0.8225 (OUTLIER)
REVERT: A  332 MET cc_start: 0.8384 (mmm) cc_final: 0.8104 (mtm)
REVERT: B   51 TYR cc_start: 0.8659 (t80) cc_final: 0.8385 (t80)
REVERT: B  275 GLN cc_start: 0.8381 (mm110) cc_final: 0.8147 (mt0)
REVERT: B  328 ILE cc_start: 0.8788 (mp) cc_final: 0.8354 (mm)
REVERT: C   76 GLN cc_start: 0.8728 (tp40) cc_final: 0.8497 (mm110)
REVERT: C  314 ARG cc_start: 0.8981 (OUTLIER) cc_final: 0.8751 (ptm160)
REVERT: C  328 ILE cc_start: 0.8646 (mp) cc_final: 0.8269 (OUTLIER)
REVERT: C  332 MET cc_start: 0.8414 (mmm) cc_final: 0.8157 (mtm)
  outliers start: 18
  outliers final: 12
  residues processed: 103
  average time/residue: 1.2520
  time to fit residues: 137.0180
Evaluate side-chains
  103 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 90
  time to evaluate  : 0.833 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   49 PHE
Chi-restraints excluded: chain A residue  210 ASN
Chi-restraints excluded: chain A residue  245 SER
Chi-restraints excluded: chain A residue  258 ASP
Chi-restraints excluded: chain A residue  304 ARG
Chi-restraints excluded: chain B residue  208 GLU
Chi-restraints excluded: chain B residue  245 SER
Chi-restraints excluded: chain B residue  267 VAL
Chi-restraints excluded: chain C residue   48 VAL
Chi-restraints excluded: chain C residue  210 ASN
Chi-restraints excluded: chain C residue  245 SER
Chi-restraints excluded: chain C residue  258 ASP
Chi-restraints excluded: chain C residue  314 ARG
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 3 optimal weight:    6.9990
   chunk 29 optimal weight:    2.9990
   chunk 75 optimal weight:    0.9990
   chunk 45 optimal weight:    0.8980
   chunk 33 optimal weight:   40.0000
   chunk 36 optimal weight:    4.9990
   chunk 27 optimal weight:    1.9990
   chunk 84 optimal weight:    0.0010
   chunk 80 optimal weight:    4.9990
   chunk 25 optimal weight:    4.9990
   chunk 11 optimal weight:    5.9990
   overall best weight:    1.3792

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3778 r_free = 0.3778 target = 0.123572 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3282 r_free = 0.3282 target = 0.085916 restraints weight = 12363.441|
|-----------------------------------------------------------------------------|
r_work (start): 0.3235 rms_B_bonded: 2.51
r_work: 0.3138 rms_B_bonded: 2.75 restraints_weight: 0.5000
r_work: 0.3033 rms_B_bonded: 4.34 restraints_weight: 0.2500
r_work (final): 0.3033
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8820
moved from start:          0.4341

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.058   8208  Z= 0.167
  Angle     :  0.690  13.730  11166  Z= 0.342
  Chirality :  0.053   0.472   1242
  Planarity :  0.005   0.059   1398
  Dihedral  : 10.148  87.452   1347
  Min Nonbonded Distance : 2.052

Molprobity Statistics.
  All-atom Clashscore : 4.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.05 %
    Favored  : 96.95 %
  Rotamer:
    Outliers :  2.13 %
    Allowed  : 16.43 %
    Favored  : 81.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.21 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.62 (0.27), residues: 984
  helix:  1.41 (0.35), residues: 267
  sheet:  0.81 (0.29), residues: 309
  loop : -0.53 (0.31), residues: 408

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP C 259 
 HIS   0.004   0.001   HIS A 116 
 PHE   0.026   0.002   PHE B  92 
 TYR   0.018   0.002   TYR C  90 
 ARG   0.015   0.001   ARG A 197 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00827 (    9)
  link_NAG-ASN         : angle       5.13655 (   27)
  hydrogen bonds       : bond        0.03045 (  353)
  hydrogen bonds       : angle       4.46767 ( 1089)
  SS BOND              : bond        0.00338 (    9)
  SS BOND              : angle       2.37168 (   18)
  covalent geometry    : bond        0.00379 ( 8190)
  covalent geometry    : angle       0.63592 (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
  108 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 90
  time to evaluate  : 0.817 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   49 PHE cc_start: 0.8550 (OUTLIER) cc_final: 0.7636 (m-80)
REVERT: A  275 GLN cc_start: 0.8501 (mm110) cc_final: 0.8255 (mt0)
REVERT: A  304 ARG cc_start: 0.8418 (OUTLIER) cc_final: 0.8180 (mtt180)
REVERT: A  328 ILE cc_start: 0.8737 (mp) cc_final: 0.8244 (OUTLIER)
REVERT: A  332 MET cc_start: 0.8381 (mmm) cc_final: 0.8105 (mtm)
REVERT: B   51 TYR cc_start: 0.8637 (t80) cc_final: 0.8371 (t80)
REVERT: B  275 GLN cc_start: 0.8361 (mm110) cc_final: 0.8150 (mt0)
REVERT: B  328 ILE cc_start: 0.8774 (mp) cc_final: 0.8353 (mm)
REVERT: C  314 ARG cc_start: 0.8982 (OUTLIER) cc_final: 0.8770 (ptm160)
REVERT: C  328 ILE cc_start: 0.8609 (mp) cc_final: 0.8217 (OUTLIER)
REVERT: C  332 MET cc_start: 0.8403 (mmm) cc_final: 0.8150 (mtm)
  outliers start: 18
  outliers final: 13
  residues processed: 104
  average time/residue: 1.2092
  time to fit residues: 133.4061
Evaluate side-chains
  102 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 88
  time to evaluate  : 0.927 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   49 PHE
Chi-restraints excluded: chain A residue  210 ASN
Chi-restraints excluded: chain A residue  245 SER
Chi-restraints excluded: chain A residue  246 LEU
Chi-restraints excluded: chain A residue  258 ASP
Chi-restraints excluded: chain A residue  304 ARG
Chi-restraints excluded: chain B residue  208 GLU
Chi-restraints excluded: chain B residue  245 SER
Chi-restraints excluded: chain B residue  267 VAL
Chi-restraints excluded: chain C residue   48 VAL
Chi-restraints excluded: chain C residue  210 ASN
Chi-restraints excluded: chain C residue  245 SER
Chi-restraints excluded: chain C residue  258 ASP
Chi-restraints excluded: chain C residue  314 ARG
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 71 optimal weight:    0.0270
   chunk 20 optimal weight:    4.9990
   chunk 43 optimal weight:    0.7980
   chunk 29 optimal weight:    5.9990
   chunk 55 optimal weight:    0.9990
   chunk 12 optimal weight:    0.9980
   chunk 38 optimal weight:    4.9990
   chunk 28 optimal weight:    3.9990
   chunk 65 optimal weight:    5.9990
   chunk 30 optimal weight:    0.8980
   chunk 37 optimal weight:    3.9990
   overall best weight:    0.7440

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3805 r_free = 0.3805 target = 0.125503 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3321 r_free = 0.3321 target = 0.088150 restraints weight = 12113.204|
|-----------------------------------------------------------------------------|
r_work (start): 0.3259 rms_B_bonded: 2.54
r_work: 0.3164 rms_B_bonded: 2.80 restraints_weight: 0.5000
r_work: 0.3057 rms_B_bonded: 4.45 restraints_weight: 0.2500
r_work (final): 0.3057
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8785
moved from start:          0.4266

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048   8208  Z= 0.129
  Angle     :  0.660  13.471  11166  Z= 0.326
  Chirality :  0.051   0.441   1242
  Planarity :  0.005   0.063   1398
  Dihedral  :  9.812  88.289   1347
  Min Nonbonded Distance : 2.074

Molprobity Statistics.
  All-atom Clashscore : 4.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.25 %
    Favored  : 96.75 %
  Rotamer:
    Outliers :  1.54 %
    Allowed  : 17.49 %
    Favored  : 80.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.11 %

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:  0.64 (0.27), residues: 984
  helix:  1.44 (0.35), residues: 267
  sheet:  0.86 (0.29), residues: 309
  loop : -0.56 (0.31), residues: 408

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP C  47 
 HIS   0.004   0.000   HIS A 116 
 PHE   0.031   0.002   PHE B 326 
 TYR   0.019   0.001   TYR C  90 
 ARG   0.015   0.001   ARG A 197 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00987 (    9)
  link_NAG-ASN         : angle       4.88053 (   27)
  hydrogen bonds       : bond        0.02687 (  353)
  hydrogen bonds       : angle       4.36394 ( 1089)
  SS BOND              : bond        0.00306 (    9)
  SS BOND              : angle       2.13635 (   18)
  covalent geometry    : bond        0.00290 ( 8190)
  covalent geometry    : angle       0.60951 (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
  102 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 89
  time to evaluate  : 0.933 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   49 PHE cc_start: 0.8547 (OUTLIER) cc_final: 0.7686 (m-80)
REVERT: A  258 ASP cc_start: 0.9030 (OUTLIER) cc_final: 0.8775 (m-30)
REVERT: A  275 GLN cc_start: 0.8505 (mm110) cc_final: 0.8249 (mt0)
REVERT: A  304 ARG cc_start: 0.8312 (OUTLIER) cc_final: 0.8063 (mtt180)
REVERT: A  328 ILE cc_start: 0.8755 (mp) cc_final: 0.8255 (OUTLIER)
REVERT: A  332 MET cc_start: 0.8367 (mmm) cc_final: 0.8091 (mtm)
REVERT: B   51 TYR cc_start: 0.8618 (t80) cc_final: 0.8349 (t80)
REVERT: B  275 GLN cc_start: 0.8352 (mm110) cc_final: 0.8144 (mt0)
REVERT: B  328 ILE cc_start: 0.8781 (mp) cc_final: 0.8535 (mm)
REVERT: C  328 ILE cc_start: 0.8600 (mp) cc_final: 0.8180 (OUTLIER)
REVERT: C  332 MET cc_start: 0.8405 (mmm) cc_final: 0.8142 (mtm)
  outliers start: 13
  outliers final: 8
  residues processed: 99
  average time/residue: 1.2413
  time to fit residues: 130.7091
Evaluate side-chains
  96 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 87
  time to evaluate  : 0.909 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   49 PHE
Chi-restraints excluded: chain A residue  210 ASN
Chi-restraints excluded: chain A residue  245 SER
Chi-restraints excluded: chain A residue  258 ASP
Chi-restraints excluded: chain A residue  304 ARG
Chi-restraints excluded: chain B residue  184 ASN
Chi-restraints excluded: chain B residue  245 SER
Chi-restraints excluded: chain B residue  267 VAL
Chi-restraints excluded: chain C residue  210 ASN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 89 optimal weight:    1.9990
   chunk 81 optimal weight:    0.0370
   chunk 47 optimal weight:    1.9990
   chunk 71 optimal weight:    0.9980
   chunk 38 optimal weight:    3.9990
   chunk 51 optimal weight:    0.5980
   chunk 12 optimal weight:    1.9990
   chunk 64 optimal weight:    4.9990
   chunk 34 optimal weight:    0.9990
   chunk 26 optimal weight:    3.9990
   chunk 4 optimal weight:    1.9990
   overall best weight:    0.9262

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3794 r_free = 0.3794 target = 0.124754 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3302 r_free = 0.3302 target = 0.087118 restraints weight = 12187.874|
|-----------------------------------------------------------------------------|
r_work (start): 0.3245 rms_B_bonded: 2.57
r_work: 0.3150 rms_B_bonded: 2.82 restraints_weight: 0.5000
r_work: 0.3045 rms_B_bonded: 4.45 restraints_weight: 0.2500
r_work (final): 0.3045
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8795
moved from start:          0.4309

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   8208  Z= 0.138
  Angle     :  0.668  13.853  11166  Z= 0.328
  Chirality :  0.051   0.629   1242
  Planarity :  0.005   0.063   1398
  Dihedral  :  9.735  83.194   1347
  Min Nonbonded Distance : 2.080

Molprobity Statistics.
  All-atom Clashscore : 4.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.95 %
    Favored  : 97.05 %
  Rotamer:
    Outliers :  1.65 %
    Allowed  : 17.26 %
    Favored  : 81.09 %
  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:  0.64 (0.27), residues: 984
  helix:  1.41 (0.35), residues: 267
  sheet:  0.84 (0.29), residues: 309
  loop : -0.52 (0.31), residues: 408

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP C  47 
 HIS   0.004   0.001   HIS B 116 
 PHE   0.021   0.002   PHE B  92 
 TYR   0.018   0.001   TYR C  90 
 ARG   0.015   0.001   ARG C 197 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00965 (    9)
  link_NAG-ASN         : angle       5.39343 (   27)
  hydrogen bonds       : bond        0.02760 (  353)
  hydrogen bonds       : angle       4.35787 ( 1089)
  SS BOND              : bond        0.00299 (    9)
  SS BOND              : angle       2.08600 (   18)
  covalent geometry    : bond        0.00312 ( 8190)
  covalent geometry    : angle       0.60848 (11121)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 8282.41 seconds
wall clock time: 142 minutes 7.57 seconds (8527.57 seconds total)