Starting phenix.real_space_refine
on Sun May 11 06:04:50 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9bpd_44772/05_2025/9bpd_44772.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9bpd_44772/05_2025/9bpd_44772.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.63
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9bpd_44772/05_2025/9bpd_44772.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9bpd_44772/05_2025/9bpd_44772.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9bpd_44772/05_2025/9bpd_44772.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9bpd_44772/05_2025/9bpd_44772.cif"
  }
  resolution = 3.63
  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=   0.002 sd=   0.029
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: 6
    Type Number    sf(0)   Gaussians
     P       9      5.49       5
     Mg      3      5.21       5
     S      54      5.16       5
     C    4809      2.51       5
     N    1248      2.21       5
     O    1428      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 15 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 7551
  Number of models: 1
  Model: ""
    Number of chains: 12
    Chain: "A"
      Number of atoms: 2415
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 306, 2415
          Classifications: {'peptide': 306}
          Link IDs: {'PTRANS': 15, 'TRANS': 290}
    Chain: "B"
      Number of atoms: 2415
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 306, 2415
          Classifications: {'peptide': 306}
          Link IDs: {'PTRANS': 15, 'TRANS': 290}
    Chain: "C"
      Number of atoms: 2415
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 306, 2415
          Classifications: {'peptide': 306}
          Link IDs: {'PTRANS': 15, 'TRANS': 290}
    Chain: "D"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "E"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "F"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "G"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "H"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "I"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "A"
      Number of atoms: 46
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 46
          Unusual residues: {' MG': 1, 'ATP': 1, 'NAG': 1}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 1
    Chain: "B"
      Number of atoms: 46
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 46
          Unusual residues: {' MG': 1, 'ATP': 1, 'NAG': 1}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 1
    Chain: "C"
      Number of atoms: 46
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 46
          Unusual residues: {' MG': 1, 'ATP': 1, 'NAG': 1}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 1
  Time building chain proxies: 5.06, per 1000 atoms: 0.67
  Number of scatterers: 7551
  At special positions: 0
  Unit cell: (88.536, 87.482, 111.724, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S      54     16.00
     P       9     15.00
     Mg      3     11.99
     O    1428      8.00
     N    1248      7.00
     C    4809      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=15, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 102 " - pdb=" SG  CYS A 148 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 111 " - pdb=" SG  CYS A 132 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 117 " - pdb=" SG  CYS A 142 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 198 " - pdb=" SG  CYS A 208 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 242 " - pdb=" SG  CYS A 251 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 102 " - pdb=" SG  CYS B 148 " distance=2.04
    Simple disulfide: pdb=" SG  CYS B 111 " - pdb=" SG  CYS B 132 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 117 " - pdb=" SG  CYS B 142 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 198 " - pdb=" SG  CYS B 208 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 242 " - pdb=" SG  CYS B 251 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 102 " - pdb=" SG  CYS C 148 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 111 " - pdb=" SG  CYS C 132 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 117 " - pdb=" SG  CYS C 142 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 198 " - pdb=" SG  CYS C 208 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 242 " - pdb=" SG  CYS C 251 " 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
    BETA1-4
      " NAG D   1 " - " NAG D   2 "
      " NAG E   1 " - " NAG E   2 "
      " NAG F   1 " - " NAG F   2 "
      " NAG G   1 " - " NAG G   2 "
      " NAG H   1 " - " NAG H   2 "
      " NAG I   1 " - " NAG I   2 "
    NAG-ASN
      " NAG A 401 " - " ASN A 285 "
      " NAG B 401 " - " ASN B 285 "
      " NAG C 402 " - " ASN C 285 "
      " NAG D   1 " - " ASN A 165 "
      " NAG E   1 " - " ASN A 189 "
      " NAG F   1 " - " ASN B 165 "
      " NAG G   1 " - " ASN B 189 "
      " NAG H   1 " - " ASN C 165 "
      " NAG I   1 " - " ASN C 189 "
  Time building additional restraints: 2.03
  Conformation dependent library (CDL) restraints added in 927.5 milliseconds
  

  1824 Ramachandran restraints generated.
    912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1692

  Finding SS restraints...
    Secondary structure from input PDB file:
      33 helices and 18 sheets defined
      27.9% alpha, 45.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.88
  Creating SS restraints...
    Processing helix  chain 'A' and resid 21 through 34
      removed outlier: 3.520A  pdb=" N   VAL A  25 " --> pdb=" O   ILE A  21 " (cutoff:3.500A)
      removed outlier: 3.749A  pdb=" N   LEU A  27 " --> pdb=" O   ARG A  23 " (cutoff:3.500A)
      removed outlier: 4.026A  pdb=" N   ILE A  30 " --> pdb=" O   GLN A  26 " (cutoff:3.500A)
      removed outlier: 3.633A  pdb=" N   TYR A  32 " --> pdb=" O   LEU A  28 " (cutoff:3.500A)
      removed outlier: 3.850A  pdb=" N   PHE A  33 " --> pdb=" O   ILE A  29 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 71 through 76
      removed outlier: 3.609A  pdb=" N   TYR A  75 " --> pdb=" O   ASP A  71 " (cutoff:3.500A)
      removed outlier: 3.500A  pdb=" N   VAL A  76 " --> pdb=" O   VAL A  72 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 71 through 76'
    Processing helix  chain 'A' and resid 106 through 110
      removed outlier: 3.944A  pdb=" N   ARG A 110 " --> pdb=" O   GLU A 107 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 113 through 118
      removed outlier: 3.687A  pdb=" N   GLN A 116 " --> pdb=" O   SER A 113 " (cutoff:3.500A)
      removed outlier: 4.071A  pdb=" N   GLY A 118 " --> pdb=" O   SER A 115 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 160 through 165
      removed outlier: 3.871A  pdb=" N   GLU A 164 " --> pdb=" O   MET A 161 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 191 through 197
      removed outlier: 4.202A  pdb=" N   THR A 197 " --> pdb=" O   ALA A 193 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 212 through 221
    Processing helix  chain 'A' and resid 223 through 231
      removed outlier: 3.657A  pdb=" N   LEU A 227 " --> pdb=" O   ASP A 223 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 247 through 251
      removed outlier: 3.687A  pdb=" N   CYS A 251 " --> pdb=" O   TRP A 248 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 261 through 264
    Processing helix  chain 'A' and resid 313 through 326
      removed outlier: 4.154A  pdb=" N   ILE A 317 " --> pdb=" O   ILE A 313 " (cutoff:3.500A)
      removed outlier: 3.555A  pdb=" N   ILE A 318 " --> pdb=" O   ILE A 314 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 22 through 34
      removed outlier: 3.749A  pdb=" N   LEU B  27 " --> pdb=" O   ARG B  23 " (cutoff:3.500A)
      removed outlier: 4.025A  pdb=" N   ILE B  30 " --> pdb=" O   GLN B  26 " (cutoff:3.500A)
      removed outlier: 3.632A  pdb=" N   TYR B  32 " --> pdb=" O   LEU B  28 " (cutoff:3.500A)
      removed outlier: 3.850A  pdb=" N   PHE B  33 " --> pdb=" O   ILE B  29 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 71 through 76
      removed outlier: 3.608A  pdb=" N   TYR B  75 " --> pdb=" O   ASP B  71 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 106 through 110
      removed outlier: 3.942A  pdb=" N   ARG B 110 " --> pdb=" O   GLU B 107 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 113 through 118
      removed outlier: 3.688A  pdb=" N   GLN B 116 " --> pdb=" O   SER B 113 " (cutoff:3.500A)
      removed outlier: 4.070A  pdb=" N   GLY B 118 " --> pdb=" O   SER B 115 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 160 through 165
      removed outlier: 3.870A  pdb=" N   GLU B 164 " --> pdb=" O   MET B 161 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 191 through 197
      removed outlier: 4.202A  pdb=" N   THR B 197 " --> pdb=" O   ALA B 193 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 212 through 221
    Processing helix  chain 'B' and resid 223 through 231
      removed outlier: 3.657A  pdb=" N   LEU B 227 " --> pdb=" O   ASP B 223 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 247 through 251
      removed outlier: 3.688A  pdb=" N   CYS B 251 " --> pdb=" O   TRP B 248 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 261 through 264
    Processing helix  chain 'B' and resid 313 through 326
      removed outlier: 4.153A  pdb=" N   ILE B 317 " --> pdb=" O   ILE B 313 " (cutoff:3.500A)
      removed outlier: 3.555A  pdb=" N   ILE B 318 " --> pdb=" O   ILE B 314 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 22 through 34
      removed outlier: 3.749A  pdb=" N   LEU C  27 " --> pdb=" O   ARG C  23 " (cutoff:3.500A)
      removed outlier: 4.026A  pdb=" N   ILE C  30 " --> pdb=" O   GLN C  26 " (cutoff:3.500A)
      removed outlier: 3.633A  pdb=" N   TYR C  32 " --> pdb=" O   LEU C  28 " (cutoff:3.500A)
      removed outlier: 3.850A  pdb=" N   PHE C  33 " --> pdb=" O   ILE C  29 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 71 through 76
      removed outlier: 3.609A  pdb=" N   TYR C  75 " --> pdb=" O   ASP C  71 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 106 through 110
      removed outlier: 3.943A  pdb=" N   ARG C 110 " --> pdb=" O   GLU C 107 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 113 through 118
      removed outlier: 3.688A  pdb=" N   GLN C 116 " --> pdb=" O   SER C 113 " (cutoff:3.500A)
      removed outlier: 4.070A  pdb=" N   GLY C 118 " --> pdb=" O   SER C 115 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 160 through 165
      removed outlier: 3.870A  pdb=" N   GLU C 164 " --> pdb=" O   MET C 161 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 191 through 197
      removed outlier: 4.201A  pdb=" N   THR C 197 " --> pdb=" O   ALA C 193 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 212 through 221
    Processing helix  chain 'C' and resid 223 through 231
      removed outlier: 3.657A  pdb=" N   LEU C 227 " --> pdb=" O   ASP C 223 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 247 through 251
      removed outlier: 3.687A  pdb=" N   CYS C 251 " --> pdb=" O   TRP C 248 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 261 through 264
    Processing helix  chain 'C' and resid 313 through 326
      removed outlier: 4.154A  pdb=" N   ILE C 317 " --> pdb=" O   ILE C 313 " (cutoff:3.500A)
      removed outlier: 3.555A  pdb=" N   ILE C 318 " --> pdb=" O   ILE C 314 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 52 through 59
    Processing sheet with id=AA2, first strand: chain 'A' and resid 52 through 59
    Processing sheet with id=AA3, first strand: chain 'A' and resid 63 through 65
    Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 97
      removed outlier: 6.815A  pdb=" N   PHE A 296 " --> pdb=" O   THR A  89 " (cutoff:3.500A)
      removed outlier: 4.441A  pdb=" N   MET A  91 " --> pdb=" O   LYS A 294 " (cutoff:3.500A)
      removed outlier: 6.492A  pdb=" N   LYS A 294 " --> pdb=" O   MET A  91 " (cutoff:3.500A)
      removed outlier: 4.328A  pdb=" N   VAL A  93 " --> pdb=" O   LEU A 292 " (cutoff:3.500A)
      removed outlier: 6.708A  pdb=" N   LEU A 292 " --> pdb=" O   VAL A  93 " (cutoff:3.500A)
      removed outlier: 5.570A  pdb=" N   GLU A  95 " --> pdb=" O   ARG A 290 " (cutoff:3.500A)
      removed outlier: 7.568A  pdb=" N   ARG A 290 " --> pdb=" O   GLU A  95 " (cutoff:3.500A)
      removed outlier: 6.964A  pdb=" N   GLN A  97 " --> pdb=" O   GLU A 288 " (cutoff:3.500A)
      removed outlier: 7.330A  pdb=" N   GLU A 288 " --> pdb=" O   GLN A  97 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 84 through 97
      removed outlier: 6.815A  pdb=" N   PHE A 296 " --> pdb=" O   THR A  89 " (cutoff:3.500A)
      removed outlier: 4.441A  pdb=" N   MET A  91 " --> pdb=" O   LYS A 294 " (cutoff:3.500A)
      removed outlier: 6.492A  pdb=" N   LYS A 294 " --> pdb=" O   MET A  91 " (cutoff:3.500A)
      removed outlier: 4.328A  pdb=" N   VAL A  93 " --> pdb=" O   LEU A 292 " (cutoff:3.500A)
      removed outlier: 6.708A  pdb=" N   LEU A 292 " --> pdb=" O   VAL A  93 " (cutoff:3.500A)
      removed outlier: 5.570A  pdb=" N   GLU A  95 " --> pdb=" O   ARG A 290 " (cutoff:3.500A)
      removed outlier: 7.568A  pdb=" N   ARG A 290 " --> pdb=" O   GLU A  95 " (cutoff:3.500A)
      removed outlier: 6.964A  pdb=" N   GLN A  97 " --> pdb=" O   GLU A 288 " (cutoff:3.500A)
      removed outlier: 7.330A  pdb=" N   GLU A 288 " --> pdb=" O   GLN A  97 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 99 through 102
      removed outlier: 5.032A  pdb=" N   ARG A 131 " --> pdb=" O   GLU A 143 " (cutoff:3.500A)
      removed outlier: 8.737A  pdb=" N   GLN A 145 " --> pdb=" O   THR A 129 " (cutoff:3.500A)
      removed outlier: 7.962A  pdb=" N   THR A 129 " --> pdb=" O   GLN A 145 " (cutoff:3.500A)
      removed outlier: 9.333A  pdb=" N   TRP A 147 " --> pdb=" O   ILE A 127 " (cutoff:3.500A)
      removed outlier: 9.131A  pdb=" N   ILE A 127 " --> pdb=" O   TRP A 147 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 52 through 59
    Processing sheet with id=AA8, first strand: chain 'B' and resid 52 through 59
    Processing sheet with id=AA9, first strand: chain 'B' and resid 63 through 65
    Processing sheet with id=AB1, first strand: chain 'B' and resid 84 through 97
      removed outlier: 6.816A  pdb=" N   PHE B 296 " --> pdb=" O   THR B  89 " (cutoff:3.500A)
      removed outlier: 4.440A  pdb=" N   MET B  91 " --> pdb=" O   LYS B 294 " (cutoff:3.500A)
      removed outlier: 6.492A  pdb=" N   LYS B 294 " --> pdb=" O   MET B  91 " (cutoff:3.500A)
      removed outlier: 4.329A  pdb=" N   VAL B  93 " --> pdb=" O   LEU B 292 " (cutoff:3.500A)
      removed outlier: 6.707A  pdb=" N   LEU B 292 " --> pdb=" O   VAL B  93 " (cutoff:3.500A)
      removed outlier: 5.570A  pdb=" N   GLU B  95 " --> pdb=" O   ARG B 290 " (cutoff:3.500A)
      removed outlier: 7.568A  pdb=" N   ARG B 290 " --> pdb=" O   GLU B  95 " (cutoff:3.500A)
      removed outlier: 6.964A  pdb=" N   GLN B  97 " --> pdb=" O   GLU B 288 " (cutoff:3.500A)
      removed outlier: 7.330A  pdb=" N   GLU B 288 " --> pdb=" O   GLN B  97 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'B' and resid 84 through 97
      removed outlier: 6.816A  pdb=" N   PHE B 296 " --> pdb=" O   THR B  89 " (cutoff:3.500A)
      removed outlier: 4.440A  pdb=" N   MET B  91 " --> pdb=" O   LYS B 294 " (cutoff:3.500A)
      removed outlier: 6.492A  pdb=" N   LYS B 294 " --> pdb=" O   MET B  91 " (cutoff:3.500A)
      removed outlier: 4.329A  pdb=" N   VAL B  93 " --> pdb=" O   LEU B 292 " (cutoff:3.500A)
      removed outlier: 6.707A  pdb=" N   LEU B 292 " --> pdb=" O   VAL B  93 " (cutoff:3.500A)
      removed outlier: 5.570A  pdb=" N   GLU B  95 " --> pdb=" O   ARG B 290 " (cutoff:3.500A)
      removed outlier: 7.568A  pdb=" N   ARG B 290 " --> pdb=" O   GLU B  95 " (cutoff:3.500A)
      removed outlier: 6.964A  pdb=" N   GLN B  97 " --> pdb=" O   GLU B 288 " (cutoff:3.500A)
      removed outlier: 7.330A  pdb=" N   GLU B 288 " --> pdb=" O   GLN B  97 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'B' and resid 99 through 102
      removed outlier: 5.032A  pdb=" N   ARG B 131 " --> pdb=" O   GLU B 143 " (cutoff:3.500A)
      removed outlier: 8.737A  pdb=" N   GLN B 145 " --> pdb=" O   THR B 129 " (cutoff:3.500A)
      removed outlier: 7.962A  pdb=" N   THR B 129 " --> pdb=" O   GLN B 145 " (cutoff:3.500A)
      removed outlier: 9.333A  pdb=" N   TRP B 147 " --> pdb=" O   ILE B 127 " (cutoff:3.500A)
      removed outlier: 9.131A  pdb=" N   ILE B 127 " --> pdb=" O   TRP B 147 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'C' and resid 52 through 59
    Processing sheet with id=AB5, first strand: chain 'C' and resid 52 through 59
    Processing sheet with id=AB6, first strand: chain 'C' and resid 63 through 65
    Processing sheet with id=AB7, first strand: chain 'C' and resid 84 through 97
      removed outlier: 6.815A  pdb=" N   PHE C 296 " --> pdb=" O   THR C  89 " (cutoff:3.500A)
      removed outlier: 4.440A  pdb=" N   MET C  91 " --> pdb=" O   LYS C 294 " (cutoff:3.500A)
      removed outlier: 6.491A  pdb=" N   LYS C 294 " --> pdb=" O   MET C  91 " (cutoff:3.500A)
      removed outlier: 4.329A  pdb=" N   VAL C  93 " --> pdb=" O   LEU C 292 " (cutoff:3.500A)
      removed outlier: 6.708A  pdb=" N   LEU C 292 " --> pdb=" O   VAL C  93 " (cutoff:3.500A)
      removed outlier: 5.571A  pdb=" N   GLU C  95 " --> pdb=" O   ARG C 290 " (cutoff:3.500A)
      removed outlier: 7.568A  pdb=" N   ARG C 290 " --> pdb=" O   GLU C  95 " (cutoff:3.500A)
      removed outlier: 6.965A  pdb=" N   GLN C  97 " --> pdb=" O   GLU C 288 " (cutoff:3.500A)
      removed outlier: 7.330A  pdb=" N   GLU C 288 " --> pdb=" O   GLN C  97 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'C' and resid 84 through 97
      removed outlier: 6.815A  pdb=" N   PHE C 296 " --> pdb=" O   THR C  89 " (cutoff:3.500A)
      removed outlier: 4.440A  pdb=" N   MET C  91 " --> pdb=" O   LYS C 294 " (cutoff:3.500A)
      removed outlier: 6.491A  pdb=" N   LYS C 294 " --> pdb=" O   MET C  91 " (cutoff:3.500A)
      removed outlier: 4.329A  pdb=" N   VAL C  93 " --> pdb=" O   LEU C 292 " (cutoff:3.500A)
      removed outlier: 6.708A  pdb=" N   LEU C 292 " --> pdb=" O   VAL C  93 " (cutoff:3.500A)
      removed outlier: 5.571A  pdb=" N   GLU C  95 " --> pdb=" O   ARG C 290 " (cutoff:3.500A)
      removed outlier: 7.568A  pdb=" N   ARG C 290 " --> pdb=" O   GLU C  95 " (cutoff:3.500A)
      removed outlier: 6.965A  pdb=" N   GLN C  97 " --> pdb=" O   GLU C 288 " (cutoff:3.500A)
      removed outlier: 7.330A  pdb=" N   GLU C 288 " --> pdb=" O   GLN C  97 " (cutoff:3.500A)
    Processing sheet with id=AB9, first strand: chain 'C' and resid 99 through 102
      removed outlier: 5.032A  pdb=" N   ARG C 131 " --> pdb=" O   GLU C 143 " (cutoff:3.500A)
      removed outlier: 8.737A  pdb=" N   GLN C 145 " --> pdb=" O   THR C 129 " (cutoff:3.500A)
      removed outlier: 7.962A  pdb=" N   THR C 129 " --> pdb=" O   GLN C 145 " (cutoff:3.500A)
      removed outlier: 9.334A  pdb=" N   TRP C 147 " --> pdb=" O   ILE C 127 " (cutoff:3.500A)
      removed outlier: 9.130A  pdb=" N   ILE C 127 " --> pdb=" O   TRP C 147 " (cutoff:3.500A)

    290 hydrogen bonds defined for protein.
    753 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: 2.17

  Time building geometry restraints manager: 2.34 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2352
        1.34 -     1.46: 1952
        1.46 -     1.59: 3334
        1.59 -     1.71: 12
        1.71 -     1.83: 78
  Bond restraints: 7728
  Sorted by residual:
  bond pdb=" C1  NAG E   2 "
       pdb=" O5  NAG E   2 "
    ideal  model  delta    sigma   weight residual
    1.406  1.438 -0.032 2.00e-02 2.50e+03 2.63e+00
  bond pdb=" C1  NAG D   2 "
       pdb=" O5  NAG D   2 "
    ideal  model  delta    sigma   weight residual
    1.406  1.438 -0.032 2.00e-02 2.50e+03 2.62e+00
  bond pdb=" C1  NAG H   2 "
       pdb=" O5  NAG H   2 "
    ideal  model  delta    sigma   weight residual
    1.406  1.438 -0.032 2.00e-02 2.50e+03 2.61e+00
  bond pdb=" C1  NAG G   2 "
       pdb=" O5  NAG G   2 "
    ideal  model  delta    sigma   weight residual
    1.406  1.438 -0.032 2.00e-02 2.50e+03 2.61e+00
  bond pdb=" C1  NAG F   2 "
       pdb=" O5  NAG F   2 "
    ideal  model  delta    sigma   weight residual
    1.406  1.438 -0.032 2.00e-02 2.50e+03 2.54e+00
  ... (remaining 7723 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.03: 9590
        1.03 -     2.06: 690
        2.06 -     3.10: 136
        3.10 -     4.13: 39
        4.13 -     5.16: 27
  Bond angle restraints: 10482
  Sorted by residual:
  angle pdb=" N   ASP C 203 "
        pdb=" CA  ASP C 203 "
        pdb=" C   ASP C 203 "
      ideal   model   delta    sigma   weight residual
     114.62  109.96    4.66 1.14e+00 7.69e-01 1.67e+01
  angle pdb=" N   ASP A 203 "
        pdb=" CA  ASP A 203 "
        pdb=" C   ASP A 203 "
      ideal   model   delta    sigma   weight residual
     114.62  109.98    4.64 1.14e+00 7.69e-01 1.66e+01
  angle pdb=" N   ASP B 203 "
        pdb=" CA  ASP B 203 "
        pdb=" C   ASP B 203 "
      ideal   model   delta    sigma   weight residual
     114.62  109.99    4.63 1.14e+00 7.69e-01 1.65e+01
  angle pdb=" CA  ASP B 203 "
        pdb=" C   ASP B 203 "
        pdb=" N   LYS B 204 "
      ideal   model   delta    sigma   weight residual
     119.71  116.31    3.40 1.17e+00 7.31e-01 8.43e+00
  angle pdb=" CA  ASP C 203 "
        pdb=" C   ASP C 203 "
        pdb=" N   LYS C 204 "
      ideal   model   delta    sigma   weight residual
     119.71  116.34    3.37 1.17e+00 7.31e-01 8.27e+00
  ... (remaining 10477 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    18.04: 4086
       18.04 -    36.07: 561
       36.07 -    54.11: 177
       54.11 -    72.14: 18
       72.14 -    90.18: 27
  Dihedral angle restraints: 4869
    sinusoidal: 2226
      harmonic: 2643
  Sorted by residual:
  dihedral pdb=" CB  CYS C 117 "
           pdb=" SG  CYS C 117 "
           pdb=" SG  CYS C 142 "
           pdb=" CB  CYS C 142 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00 -176.82  -90.18     1      1.00e+01 1.00e-02 9.63e+01
  dihedral pdb=" CB  CYS A 117 "
           pdb=" SG  CYS A 117 "
           pdb=" SG  CYS A 142 "
           pdb=" CB  CYS A 142 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00 -176.83  -90.17     1      1.00e+01 1.00e-02 9.63e+01
  dihedral pdb=" CB  CYS B 117 "
           pdb=" SG  CYS B 117 "
           pdb=" SG  CYS B 142 "
           pdb=" CB  CYS B 142 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00 -176.86  -90.14     1      1.00e+01 1.00e-02 9.62e+01
  ... (remaining 4866 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.071: 1023
       0.071 -    0.141: 153
       0.141 -    0.212: 3
       0.212 -    0.282: 3
       0.282 -    0.353: 6
  Chirality restraints: 1188
  Sorted by residual:
  chirality pdb=" C1  NAG F   1 "
            pdb=" ND2 ASN B 165 "
            pdb=" C2  NAG F   1 "
            pdb=" O5  NAG F   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.05   -0.35 2.00e-01 2.50e+01 3.11e+00
  chirality pdb=" C1  NAG D   1 "
            pdb=" ND2 ASN A 165 "
            pdb=" C2  NAG D   1 "
            pdb=" O5  NAG D   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.05   -0.35 2.00e-01 2.50e+01 3.10e+00
  chirality pdb=" C1  NAG H   1 "
            pdb=" ND2 ASN C 165 "
            pdb=" C2  NAG H   1 "
            pdb=" O5  NAG H   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.05   -0.35 2.00e-01 2.50e+01 3.09e+00
  ... (remaining 1185 not shown)

  Planarity restraints: 1314
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA B 205 "   -0.045 5.00e-02 4.00e+02   6.82e-02 7.44e+00
        pdb=" N   PRO B 206 "    0.118 5.00e-02 4.00e+02
        pdb=" CA  PRO B 206 "   -0.035 5.00e-02 4.00e+02
        pdb=" CD  PRO B 206 "   -0.038 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA C 205 "    0.045 5.00e-02 4.00e+02   6.79e-02 7.37e+00
        pdb=" N   PRO C 206 "   -0.117 5.00e-02 4.00e+02
        pdb=" CA  PRO C 206 "    0.035 5.00e-02 4.00e+02
        pdb=" CD  PRO C 206 "    0.038 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA A 205 "    0.045 5.00e-02 4.00e+02   6.78e-02 7.36e+00
        pdb=" N   PRO A 206 "   -0.117 5.00e-02 4.00e+02
        pdb=" CA  PRO A 206 "    0.035 5.00e-02 4.00e+02
        pdb=" CD  PRO A 206 "    0.038 5.00e-02 4.00e+02
  ... (remaining 1311 not shown)

  Histogram of nonbonded interaction distances:
        2.05 -     2.62: 111
        2.62 -     3.19: 6498
        3.19 -     3.76: 11174
        3.76 -     4.33: 15124
        4.33 -     4.90: 24877
  Nonbonded interactions: 57784
  Sorted by model distance:
  nonbonded pdb="MG    MG A 402 "
            pdb=" O3B ATP C 401 "
     model   vdw
     2.046 2.170
  nonbonded pdb=" O3B ATP B 403 "
            pdb="MG    MG C 403 "
     model   vdw
     2.047 2.170
  nonbonded pdb=" O3B ATP A 403 "
            pdb="MG    MG B 402 "
     model   vdw
     2.047 2.170
  nonbonded pdb=" O3G ATP A 403 "
            pdb="MG    MG B 402 "
     model   vdw
     2.100 2.170
  nonbonded pdb=" O3G ATP B 403 "
            pdb="MG    MG C 403 "
     model   vdw
     2.100 2.170
  ... (remaining 57779 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 21 through 326)
  selection = (chain 'B' and resid 21 through 326)
  selection = (chain 'C' and resid 21 through 326)
}
ncs_group {
  reference = chain 'D'
  selection = chain 'E'
  selection = chain 'F'
  selection = chain 'G'
  selection = chain 'H'
  selection = chain 'I'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.040
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.270
  Check model and map are aligned:         0.050
  Set scattering table:                    0.080
  Process input model:                     20.330
  Find NCS groups from input model:        0.390
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:2.790
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   25.000
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6879
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      :  0.003   0.032   7758  Z= 0.170
  Angle     :  0.683   7.232  10557  Z= 0.360
  Chirality :  0.054   0.353   1188
  Planarity :  0.004   0.068   1305
  Dihedral  : 17.660  86.216   3132
  Min Nonbonded Distance : 2.046

Molprobity Statistics.
  All-atom Clashscore : 13.38
  Ramachandran Plot:
    Outliers :  0.33 %
    Allowed  : 11.95 %
    Favored  : 87.72 %
  Rotamer:
    Outliers :  0.38 %
    Allowed  : 33.58 %
    Favored  : 66.04 %
  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: -2.62 (0.26), residues: 912
  helix: -1.28 (0.37), residues: 195
  sheet: -0.06 (0.31), residues: 264
  loop : -3.12 (0.23), residues: 453

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 240 
 HIS   0.002   0.001   HIS C 201 
 PHE   0.015   0.001   PHE A 166 
 TYR   0.019   0.001   TYR C  75 
 ARG   0.002   0.000   ARG C 199 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.01211 (    9)
  link_NAG-ASN         : angle       2.62826 (   27)
  link_BETA1-4         : bond        0.00617 (    6)
  link_BETA1-4         : angle       3.78410 (   18)
  hydrogen bonds       : bond        0.19105 (  251)
  hydrogen bonds       : angle       8.01670 (  753)
  SS BOND              : bond        0.00247 (   15)
  SS BOND              : angle       1.46109 (   30)
  covalent geometry    : bond        0.00344 ( 7728)
  covalent geometry    : angle       0.64933 (10482)

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

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

  1824 Ramachandran restraints generated.
    912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1824 Ramachandran restraints generated.
    912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 795 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 113
  time to evaluate  : 0.768 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   98 MET cc_start: 0.7823 (ttt) cc_final: 0.7530 (ttm)
REVERT: A  201 HIS cc_start: 0.6467 (t-90) cc_final: 0.6064 (t70)
REVERT: A  283 MET cc_start: 0.8631 (mmm) cc_final: 0.8322 (mmm)
REVERT: C   98 MET cc_start: 0.7688 (ttt) cc_final: 0.7462 (ttm)
REVERT: C  201 HIS cc_start: 0.6676 (t-90) cc_final: 0.6390 (t-170)
REVERT: C  283 MET cc_start: 0.8765 (mmm) cc_final: 0.8428 (mmt)
  outliers start: 3
  outliers final: 0
  residues processed: 116
  average time/residue: 0.1682
  time to fit residues: 27.2007
Evaluate side-chains
  107 residues out of total 795 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 107
  time to evaluate  : 0.732 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 75 optimal weight:    3.9990
   chunk 68 optimal weight:    8.9990
   chunk 37 optimal weight:    1.9990
   chunk 23 optimal weight:    1.9990
   chunk 46 optimal weight:    1.9990
   chunk 36 optimal weight:    0.7980
   chunk 70 optimal weight:    0.6980
   chunk 27 optimal weight:    2.9990
   chunk 42 optimal weight:    6.9990
   chunk 52 optimal weight:    2.9990
   chunk 81 optimal weight:    0.7980
   overall best weight:    1.2584

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

Flipped N/Q/H residues before XYZ refinement:
** A  80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A  97 GLN
** A  99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  97 GLN
** B  99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 201 HIS
C  97 GLN
** C  99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4112 r_free = 0.4112 target = 0.168473 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3477 r_free = 0.3477 target = 0.113105 restraints weight = 10968.839|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3533 r_free = 0.3533 target = 0.117748 restraints weight = 6104.070|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3569 r_free = 0.3569 target = 0.120596 restraints weight = 4428.147|
|-----------------------------------------------------------------------------|
r_work (final): 0.3561
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7474
moved from start:          0.1391

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   7758  Z= 0.188
  Angle     :  0.663   6.991  10557  Z= 0.340
  Chirality :  0.054   0.309   1188
  Planarity :  0.004   0.044   1305
  Dihedral  :  9.222  58.557   1419
  Min Nonbonded Distance : 1.869

Molprobity Statistics.
  All-atom Clashscore : 9.50
  Ramachandran Plot:
    Outliers :  0.33 %
    Allowed  : 11.29 %
    Favored  : 88.38 %
  Rotamer:
    Outliers :  2.89 %
    Allowed  : 28.81 %
    Favored  : 68.30 %
  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: -2.54 (0.26), residues: 912
  helix: -1.64 (0.34), residues: 213
  sheet:  0.00 (0.30), residues: 294
  loop : -3.08 (0.26), residues: 405

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B 240 
 HIS   0.004   0.001   HIS B 201 
 PHE   0.032   0.002   PHE C 166 
 TYR   0.015   0.002   TYR A 289 
 ARG   0.002   0.000   ARG B 259 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00833 (    9)
  link_NAG-ASN         : angle       2.81342 (   27)
  link_BETA1-4         : bond        0.00272 (    6)
  link_BETA1-4         : angle       2.02152 (   18)
  hydrogen bonds       : bond        0.03574 (  251)
  hydrogen bonds       : angle       5.14365 (  753)
  SS BOND              : bond        0.00236 (   15)
  SS BOND              : angle       1.33748 (   30)
  covalent geometry    : bond        0.00440 ( 7728)
  covalent geometry    : angle       0.64050 (10482)

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

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

  1824 Ramachandran restraints generated.
    912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1824 Ramachandran restraints generated.
    912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 795 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 114
  time to evaluate  : 0.824 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   98 MET cc_start: 0.8100 (ttt) cc_final: 0.7805 (ttm)
REVERT: A  109 TYR cc_start: 0.7117 (m-80) cc_final: 0.6340 (m-80)
REVERT: A  201 HIS cc_start: 0.7252 (t-90) cc_final: 0.6656 (t70)
REVERT: C   75 TYR cc_start: 0.9031 (p90) cc_final: 0.8712 (p90)
  outliers start: 23
  outliers final: 9
  residues processed: 136
  average time/residue: 0.1837
  time to fit residues: 34.1778
Evaluate side-chains
  115 residues out of total 795 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 106
  time to evaluate  : 0.831 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   51 ILE
Chi-restraints excluded: chain A residue   69 VAL
Chi-restraints excluded: chain A residue   72 VAL
Chi-restraints excluded: chain B residue   69 VAL
Chi-restraints excluded: chain B residue   72 VAL
Chi-restraints excluded: chain B residue  121 ARG
Chi-restraints excluded: chain C residue   69 VAL
Chi-restraints excluded: chain C residue   72 VAL
Chi-restraints excluded: chain C residue  141 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 79 optimal weight:    1.9990
   chunk 29 optimal weight:    0.0970
   chunk 74 optimal weight:    6.9990
   chunk 84 optimal weight:    2.9990
   chunk 33 optimal weight:    2.9990
   chunk 22 optimal weight:    0.8980
   chunk 56 optimal weight:    3.9990
   chunk 2 optimal weight:    5.9990
   chunk 89 optimal weight:    1.9990
   chunk 24 optimal weight:    4.9990
   chunk 39 optimal weight:    7.9990
   overall best weight:    1.5984

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

Flipped N/Q/H residues before XYZ refinement:
** A  99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 201 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4087 r_free = 0.4087 target = 0.165730 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3435 r_free = 0.3435 target = 0.109938 restraints weight = 11023.468|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3489 r_free = 0.3489 target = 0.114448 restraints weight = 6112.397|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3523 r_free = 0.3523 target = 0.117276 restraints weight = 4442.109|
|-----------------------------------------------------------------------------|
r_work (final): 0.3511
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7521
moved from start:          0.1745

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.040   7758  Z= 0.217
  Angle     :  0.693   8.295  10557  Z= 0.351
  Chirality :  0.055   0.322   1188
  Planarity :  0.004   0.059   1305
  Dihedral  :  9.417  59.929   1419
  Min Nonbonded Distance : 1.913

Molprobity Statistics.
  All-atom Clashscore : 9.83
  Ramachandran Plot:
    Outliers :  0.33 %
    Allowed  : 10.86 %
    Favored  : 88.82 %
  Rotamer:
    Outliers :  4.78 %
    Allowed  : 27.67 %
    Favored  : 67.55 %
  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: -2.42 (0.27), residues: 912
  helix: -1.60 (0.33), residues: 213
  sheet:  0.33 (0.31), residues: 288
  loop : -3.14 (0.26), residues: 411

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP C  36 
 HIS   0.008   0.002   HIS C  40 
 PHE   0.040   0.002   PHE B 166 
 TYR   0.029   0.002   TYR C 289 
 ARG   0.005   0.000   ARG C 121 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00586 (    9)
  link_NAG-ASN         : angle       2.94422 (   27)
  link_BETA1-4         : bond        0.00472 (    6)
  link_BETA1-4         : angle       2.17081 (   18)
  hydrogen bonds       : bond        0.03559 (  251)
  hydrogen bonds       : angle       4.99810 (  753)
  SS BOND              : bond        0.00232 (   15)
  SS BOND              : angle       1.31029 (   30)
  covalent geometry    : bond        0.00508 ( 7728)
  covalent geometry    : angle       0.66961 (10482)

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

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

  1824 Ramachandran restraints generated.
    912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1824 Ramachandran restraints generated.
    912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  147 residues out of total 795 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 109
  time to evaluate  : 0.776 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   98 MET cc_start: 0.8077 (ttt) cc_final: 0.7777 (ttm)
REVERT: A  201 HIS cc_start: 0.7252 (t-90) cc_final: 0.6573 (t70)
REVERT: A  250 GLN cc_start: 0.8437 (mt0) cc_final: 0.7952 (mt0)
REVERT: A  270 SER cc_start: 0.8702 (OUTLIER) cc_final: 0.8293 (p)
REVERT: B   28 LEU cc_start: 0.7807 (OUTLIER) cc_final: 0.7589 (mt)
REVERT: B  109 TYR cc_start: 0.6879 (m-80) cc_final: 0.5412 (m-80)
REVERT: B  250 GLN cc_start: 0.8337 (mt0) cc_final: 0.7900 (mp10)
REVERT: B  270 SER cc_start: 0.8755 (OUTLIER) cc_final: 0.8362 (p)
REVERT: C   28 LEU cc_start: 0.7903 (OUTLIER) cc_final: 0.7640 (mt)
REVERT: C   75 TYR cc_start: 0.9103 (p90) cc_final: 0.8873 (p90)
REVERT: C  270 SER cc_start: 0.8597 (OUTLIER) cc_final: 0.8117 (p)
  outliers start: 38
  outliers final: 17
  residues processed: 144
  average time/residue: 0.1887
  time to fit residues: 36.5798
Evaluate side-chains
  123 residues out of total 795 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 101
  time to evaluate  : 0.762 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   51 ILE
Chi-restraints excluded: chain A residue   69 VAL
Chi-restraints excluded: chain A residue   70 MET
Chi-restraints excluded: chain A residue   72 VAL
Chi-restraints excluded: chain A residue  191 THR
Chi-restraints excluded: chain A residue  258 THR
Chi-restraints excluded: chain A residue  270 SER
Chi-restraints excluded: chain A residue  291 THR
Chi-restraints excluded: chain B residue   28 LEU
Chi-restraints excluded: chain B residue   69 VAL
Chi-restraints excluded: chain B residue   70 MET
Chi-restraints excluded: chain B residue   72 VAL
Chi-restraints excluded: chain B residue  191 THR
Chi-restraints excluded: chain B residue  258 THR
Chi-restraints excluded: chain B residue  270 SER
Chi-restraints excluded: chain B residue  291 THR
Chi-restraints excluded: chain C residue   28 LEU
Chi-restraints excluded: chain C residue   69 VAL
Chi-restraints excluded: chain C residue   72 VAL
Chi-restraints excluded: chain C residue  191 THR
Chi-restraints excluded: chain C residue  270 SER
Chi-restraints excluded: chain C residue  291 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 71 optimal weight:    4.9990
   chunk 69 optimal weight:    8.9990
   chunk 49 optimal weight:    0.9990
   chunk 11 optimal weight:    4.9990
   chunk 19 optimal weight:    0.9990
   chunk 41 optimal weight:    3.9990
   chunk 75 optimal weight:    0.8980
   chunk 78 optimal weight:    0.0670
   chunk 29 optimal weight:    6.9990
   chunk 60 optimal weight:   30.0000
   chunk 18 optimal weight:    2.9990
   overall best weight:    1.1924

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

Flipped N/Q/H residues before XYZ refinement:
** A  99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4088 r_free = 0.4088 target = 0.166003 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3441 r_free = 0.3441 target = 0.110392 restraints weight = 10981.276|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3495 r_free = 0.3495 target = 0.114992 restraints weight = 6038.501|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3529 r_free = 0.3529 target = 0.117783 restraints weight = 4388.197|
|-----------------------------------------------------------------------------|
r_work (final): 0.3522
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7516
moved from start:          0.1988

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   7758  Z= 0.178
  Angle     :  0.675   7.740  10557  Z= 0.337
  Chirality :  0.054   0.307   1188
  Planarity :  0.004   0.046   1305
  Dihedral  :  9.254  59.905   1419
  Min Nonbonded Distance : 1.926

Molprobity Statistics.
  All-atom Clashscore : 9.90
  Ramachandran Plot:
    Outliers :  0.33 %
    Allowed  : 10.96 %
    Favored  : 88.71 %
  Rotamer:
    Outliers :  3.77 %
    Allowed  : 26.42 %
    Favored  : 69.81 %
  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: -2.46 (0.27), residues: 912
  helix: -1.52 (0.34), residues: 213
  sheet:  0.24 (0.31), residues: 288
  loop : -3.19 (0.27), residues: 411

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP C  36 
 HIS   0.001   0.000   HIS A 201 
 PHE   0.037   0.002   PHE C 166 
 TYR   0.010   0.001   TYR A 281 
 ARG   0.007   0.001   ARG B 121 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00751 (    9)
  link_NAG-ASN         : angle       2.92900 (   27)
  link_BETA1-4         : bond        0.00422 (    6)
  link_BETA1-4         : angle       2.12669 (   18)
  hydrogen bonds       : bond        0.03216 (  251)
  hydrogen bonds       : angle       4.82548 (  753)
  SS BOND              : bond        0.00170 (   15)
  SS BOND              : angle       1.19032 (   30)
  covalent geometry    : bond        0.00413 ( 7728)
  covalent geometry    : angle       0.65145 (10482)

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

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

  1824 Ramachandran restraints generated.
    912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1824 Ramachandran restraints generated.
    912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  131 residues out of total 795 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 101
  time to evaluate  : 0.831 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   98 MET cc_start: 0.8104 (ttt) cc_final: 0.7796 (ttm)
REVERT: A  201 HIS cc_start: 0.7333 (t-90) cc_final: 0.6599 (t70)
REVERT: A  250 GLN cc_start: 0.8517 (mt0) cc_final: 0.8058 (mt0)
REVERT: A  270 SER cc_start: 0.8679 (OUTLIER) cc_final: 0.8261 (p)
REVERT: B  270 SER cc_start: 0.8731 (OUTLIER) cc_final: 0.8332 (p)
REVERT: C  270 SER cc_start: 0.8584 (OUTLIER) cc_final: 0.8117 (p)
  outliers start: 30
  outliers final: 19
  residues processed: 127
  average time/residue: 0.1693
  time to fit residues: 30.1702
Evaluate side-chains
  117 residues out of total 795 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 95
  time to evaluate  : 0.793 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   51 ILE
Chi-restraints excluded: chain A residue   69 VAL
Chi-restraints excluded: chain A residue   70 MET
Chi-restraints excluded: chain A residue   72 VAL
Chi-restraints excluded: chain A residue  102 CYS
Chi-restraints excluded: chain A residue  258 THR
Chi-restraints excluded: chain A residue  270 SER
Chi-restraints excluded: chain A residue  291 THR
Chi-restraints excluded: chain B residue   69 VAL
Chi-restraints excluded: chain B residue   70 MET
Chi-restraints excluded: chain B residue   72 VAL
Chi-restraints excluded: chain B residue  102 CYS
Chi-restraints excluded: chain B residue  191 THR
Chi-restraints excluded: chain B residue  258 THR
Chi-restraints excluded: chain B residue  270 SER
Chi-restraints excluded: chain B residue  291 THR
Chi-restraints excluded: chain C residue   69 VAL
Chi-restraints excluded: chain C residue   70 MET
Chi-restraints excluded: chain C residue   72 VAL
Chi-restraints excluded: chain C residue  102 CYS
Chi-restraints excluded: chain C residue  270 SER
Chi-restraints excluded: chain C residue  291 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 73 optimal weight:    0.0050
   chunk 10 optimal weight:    2.9990
   chunk 1 optimal weight:    4.9990
   chunk 24 optimal weight:    0.9980
   chunk 63 optimal weight:    0.7980
   chunk 18 optimal weight:    0.2980
   chunk 40 optimal weight:    2.9990
   chunk 82 optimal weight:    0.9990
   chunk 35 optimal weight:    0.9990
   chunk 49 optimal weight:    1.9990
   chunk 56 optimal weight:    0.6980
   overall best weight:    0.5594

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

Flipped N/Q/H residues before XYZ refinement:
** A  99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4081 r_free = 0.4081 target = 0.168383 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3457 r_free = 0.3457 target = 0.111757 restraints weight = 10970.789|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 50)----------------|
| r_work = 0.3513 r_free = 0.3513 target = 0.116500 restraints weight = 6087.824|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3543 r_free = 0.3543 target = 0.119231 restraints weight = 4441.436|
|-----------------------------------------------------------------------------|
r_work (final): 0.3550
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7492
moved from start:          0.1991

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   7758  Z= 0.129
  Angle     :  0.634   6.990  10557  Z= 0.318
  Chirality :  0.053   0.304   1188
  Planarity :  0.003   0.035   1305
  Dihedral  :  9.008  58.059   1419
  Min Nonbonded Distance : 1.984

Molprobity Statistics.
  All-atom Clashscore : 9.43
  Ramachandran Plot:
    Outliers :  0.33 %
    Allowed  : 11.29 %
    Favored  : 88.38 %
  Rotamer:
    Outliers :  3.02 %
    Allowed  : 27.17 %
    Favored  : 69.81 %
  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: -2.31 (0.27), residues: 912
  helix: -1.28 (0.36), residues: 213
  sheet:  0.33 (0.31), residues: 288
  loop : -3.17 (0.27), residues: 411

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP C  36 
 HIS   0.001   0.000   HIS A 201 
 PHE   0.038   0.001   PHE C 166 
 TYR   0.014   0.001   TYR B 289 
 ARG   0.004   0.000   ARG B 199 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00830 (    9)
  link_NAG-ASN         : angle       2.79646 (   27)
  link_BETA1-4         : bond        0.00496 (    6)
  link_BETA1-4         : angle       2.06668 (   18)
  hydrogen bonds       : bond        0.03074 (  251)
  hydrogen bonds       : angle       4.65333 (  753)
  SS BOND              : bond        0.00339 (   15)
  SS BOND              : angle       1.30376 (   30)
  covalent geometry    : bond        0.00290 ( 7728)
  covalent geometry    : angle       0.61078 (10482)

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

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

  1824 Ramachandran restraints generated.
    912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1824 Ramachandran restraints generated.
    912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 795 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 109
  time to evaluate  : 0.895 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   98 MET cc_start: 0.8030 (ttt) cc_final: 0.7738 (ttm)
REVERT: A  143 GLU cc_start: 0.7731 (tp30) cc_final: 0.7495 (tp30)
REVERT: A  201 HIS cc_start: 0.7373 (t-90) cc_final: 0.6692 (t70)
REVERT: B   28 LEU cc_start: 0.7806 (OUTLIER) cc_final: 0.7585 (mt)
REVERT: C   28 LEU cc_start: 0.7745 (OUTLIER) cc_final: 0.7496 (mt)
  outliers start: 24
  outliers final: 17
  residues processed: 130
  average time/residue: 0.1670
  time to fit residues: 30.8681
Evaluate side-chains
  115 residues out of total 795 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 96
  time to evaluate  : 0.791 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   51 ILE
Chi-restraints excluded: chain A residue   69 VAL
Chi-restraints excluded: chain A residue   72 VAL
Chi-restraints excluded: chain A residue  102 CYS
Chi-restraints excluded: chain A residue  258 THR
Chi-restraints excluded: chain B residue   28 LEU
Chi-restraints excluded: chain B residue   69 VAL
Chi-restraints excluded: chain B residue   70 MET
Chi-restraints excluded: chain B residue   72 VAL
Chi-restraints excluded: chain B residue  102 CYS
Chi-restraints excluded: chain B residue  258 THR
Chi-restraints excluded: chain B residue  291 THR
Chi-restraints excluded: chain C residue   28 LEU
Chi-restraints excluded: chain C residue   69 VAL
Chi-restraints excluded: chain C residue   70 MET
Chi-restraints excluded: chain C residue   72 VAL
Chi-restraints excluded: chain C residue  102 CYS
Chi-restraints excluded: chain C residue  191 THR
Chi-restraints excluded: chain C residue  291 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 62 optimal weight:   10.0000
   chunk 7 optimal weight:    0.6980
   chunk 10 optimal weight:    2.9990
   chunk 17 optimal weight:    5.9990
   chunk 40 optimal weight:    0.0670
   chunk 22 optimal weight:    3.9990
   chunk 37 optimal weight:    3.9990
   chunk 67 optimal weight:    0.9990
   chunk 4 optimal weight:    1.9990
   chunk 31 optimal weight:    9.9990
   chunk 6 optimal weight:    0.7980
   overall best weight:    0.9122

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

Flipped N/Q/H residues before XYZ refinement:
** A  99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4098 r_free = 0.4098 target = 0.166844 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3458 r_free = 0.3458 target = 0.111636 restraints weight = 10984.539|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3512 r_free = 0.3512 target = 0.116306 restraints weight = 5986.677|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3547 r_free = 0.3547 target = 0.119174 restraints weight = 4324.202|
|-----------------------------------------------------------------------------|
r_work (final): 0.3539
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7487
moved from start:          0.2119

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   7758  Z= 0.151
  Angle     :  0.645   7.346  10557  Z= 0.324
  Chirality :  0.053   0.310   1188
  Planarity :  0.003   0.028   1305
  Dihedral  :  8.922  59.057   1419
  Min Nonbonded Distance : 1.942

Molprobity Statistics.
  All-atom Clashscore : 9.23
  Ramachandran Plot:
    Outliers :  0.33 %
    Allowed  : 11.29 %
    Favored  : 88.38 %
  Rotamer:
    Outliers :  3.52 %
    Allowed  : 27.30 %
    Favored  : 69.18 %
  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: -2.34 (0.27), residues: 912
  helix: -1.31 (0.36), residues: 213
  sheet:  0.16 (0.31), residues: 294
  loop : -3.08 (0.28), residues: 405

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP C  36 
 HIS   0.009   0.001   HIS A  40 
 PHE   0.035   0.002   PHE C 166 
 TYR   0.024   0.001   TYR B 289 
 ARG   0.005   0.000   ARG B 199 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00649 (    9)
  link_NAG-ASN         : angle       2.84120 (   27)
  link_BETA1-4         : bond        0.00477 (    6)
  link_BETA1-4         : angle       2.07610 (   18)
  hydrogen bonds       : bond        0.03076 (  251)
  hydrogen bonds       : angle       4.61263 (  753)
  SS BOND              : bond        0.00211 (   15)
  SS BOND              : angle       1.16527 (   30)
  covalent geometry    : bond        0.00348 ( 7728)
  covalent geometry    : angle       0.62236 (10482)

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

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

  1824 Ramachandran restraints generated.
    912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1824 Ramachandran restraints generated.
    912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 795 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 99
  time to evaluate  : 0.822 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   98 MET cc_start: 0.8083 (ttt) cc_final: 0.7799 (ttm)
REVERT: B   28 LEU cc_start: 0.7813 (OUTLIER) cc_final: 0.7586 (mt)
REVERT: C   28 LEU cc_start: 0.7744 (OUTLIER) cc_final: 0.7531 (mt)
REVERT: C  199 ARG cc_start: 0.7473 (mpt180) cc_final: 0.7159 (mpt180)
  outliers start: 28
  outliers final: 23
  residues processed: 123
  average time/residue: 0.1772
  time to fit residues: 30.3567
Evaluate side-chains
  114 residues out of total 795 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 89
  time to evaluate  : 0.857 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   51 ILE
Chi-restraints excluded: chain A residue   69 VAL
Chi-restraints excluded: chain A residue   70 MET
Chi-restraints excluded: chain A residue   72 VAL
Chi-restraints excluded: chain A residue  102 CYS
Chi-restraints excluded: chain A residue  167 THR
Chi-restraints excluded: chain A residue  191 THR
Chi-restraints excluded: chain A residue  258 THR
Chi-restraints excluded: chain A residue  281 TYR
Chi-restraints excluded: chain A residue  291 THR
Chi-restraints excluded: chain B residue   28 LEU
Chi-restraints excluded: chain B residue   69 VAL
Chi-restraints excluded: chain B residue   70 MET
Chi-restraints excluded: chain B residue   72 VAL
Chi-restraints excluded: chain B residue  102 CYS
Chi-restraints excluded: chain B residue  191 THR
Chi-restraints excluded: chain B residue  258 THR
Chi-restraints excluded: chain B residue  291 THR
Chi-restraints excluded: chain C residue   28 LEU
Chi-restraints excluded: chain C residue   69 VAL
Chi-restraints excluded: chain C residue   70 MET
Chi-restraints excluded: chain C residue   72 VAL
Chi-restraints excluded: chain C residue  102 CYS
Chi-restraints excluded: chain C residue  191 THR
Chi-restraints excluded: chain C residue  291 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 89 optimal weight:    7.9990
   chunk 15 optimal weight:    0.6980
   chunk 83 optimal weight:    1.9990
   chunk 19 optimal weight:    0.7980
   chunk 74 optimal weight:    0.7980
   chunk 56 optimal weight:    3.9990
   chunk 87 optimal weight:    4.9990
   chunk 22 optimal weight:    2.9990
   chunk 47 optimal weight:    1.9990
   chunk 25 optimal weight:    1.9990
   chunk 2 optimal weight:    0.2980
   overall best weight:    0.9182

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

Flipped N/Q/H residues before XYZ refinement:
** A  99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4069 r_free = 0.4069 target = 0.167022 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3432 r_free = 0.3432 target = 0.109883 restraints weight = 10974.991|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3490 r_free = 0.3490 target = 0.114691 restraints weight = 5878.903|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3527 r_free = 0.3527 target = 0.117721 restraints weight = 4228.779|
|-----------------------------------------------------------------------------|
r_work (final): 0.3523
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7469
moved from start:          0.2196

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   7758  Z= 0.153
  Angle     :  0.651   7.434  10557  Z= 0.327
  Chirality :  0.053   0.310   1188
  Planarity :  0.004   0.059   1305
  Dihedral  :  8.865  59.111   1419
  Min Nonbonded Distance : 1.953

Molprobity Statistics.
  All-atom Clashscore : 9.50
  Ramachandran Plot:
    Outliers :  0.33 %
    Allowed  : 11.18 %
    Favored  : 88.49 %
  Rotamer:
    Outliers :  3.65 %
    Allowed  : 27.55 %
    Favored  : 68.81 %
  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: -2.34 (0.27), residues: 912
  helix: -1.30 (0.36), residues: 213
  sheet:  0.14 (0.31), residues: 294
  loop : -3.08 (0.28), residues: 405

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP C  36 
 HIS   0.001   0.000   HIS A 201 
 PHE   0.039   0.002   PHE C 166 
 TYR   0.024   0.001   TYR B 289 
 ARG   0.010   0.000   ARG A 121 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00720 (    9)
  link_NAG-ASN         : angle       2.84266 (   27)
  link_BETA1-4         : bond        0.00440 (    6)
  link_BETA1-4         : angle       2.02180 (   18)
  hydrogen bonds       : bond        0.03057 (  251)
  hydrogen bonds       : angle       4.61326 (  753)
  SS BOND              : bond        0.00184 (   15)
  SS BOND              : angle       1.09226 (   30)
  covalent geometry    : bond        0.00352 ( 7728)
  covalent geometry    : angle       0.62938 (10482)

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

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

  1824 Ramachandran restraints generated.
    912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1824 Ramachandran restraints generated.
    912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  125 residues out of total 795 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 96
  time to evaluate  : 0.863 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   98 MET cc_start: 0.8085 (ttt) cc_final: 0.7796 (ttm)
REVERT: B   28 LEU cc_start: 0.7827 (OUTLIER) cc_final: 0.7599 (mt)
REVERT: B  270 SER cc_start: 0.8478 (OUTLIER) cc_final: 0.8124 (p)
REVERT: B  289 TYR cc_start: 0.8908 (p90) cc_final: 0.8674 (p90)
REVERT: C   28 LEU cc_start: 0.7755 (OUTLIER) cc_final: 0.7544 (mt)
REVERT: C  270 SER cc_start: 0.8431 (OUTLIER) cc_final: 0.8059 (p)
  outliers start: 29
  outliers final: 23
  residues processed: 121
  average time/residue: 0.1682
  time to fit residues: 28.8390
Evaluate side-chains
  120 residues out of total 795 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 93
  time to evaluate  : 0.764 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   51 ILE
Chi-restraints excluded: chain A residue   69 VAL
Chi-restraints excluded: chain A residue   70 MET
Chi-restraints excluded: chain A residue   72 VAL
Chi-restraints excluded: chain A residue  102 CYS
Chi-restraints excluded: chain A residue  167 THR
Chi-restraints excluded: chain A residue  191 THR
Chi-restraints excluded: chain A residue  258 THR
Chi-restraints excluded: chain A residue  281 TYR
Chi-restraints excluded: chain A residue  291 THR
Chi-restraints excluded: chain B residue   28 LEU
Chi-restraints excluded: chain B residue   69 VAL
Chi-restraints excluded: chain B residue   70 MET
Chi-restraints excluded: chain B residue   72 VAL
Chi-restraints excluded: chain B residue  102 CYS
Chi-restraints excluded: chain B residue  191 THR
Chi-restraints excluded: chain B residue  258 THR
Chi-restraints excluded: chain B residue  270 SER
Chi-restraints excluded: chain B residue  291 THR
Chi-restraints excluded: chain C residue   28 LEU
Chi-restraints excluded: chain C residue   69 VAL
Chi-restraints excluded: chain C residue   70 MET
Chi-restraints excluded: chain C residue   72 VAL
Chi-restraints excluded: chain C residue  102 CYS
Chi-restraints excluded: chain C residue  191 THR
Chi-restraints excluded: chain C residue  270 SER
Chi-restraints excluded: chain C residue  291 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 79 optimal weight:    1.9990
   chunk 43 optimal weight:    0.0770
   chunk 21 optimal weight:    0.5980
   chunk 60 optimal weight:   30.0000
   chunk 44 optimal weight:    2.9990
   chunk 18 optimal weight:    0.0470
   chunk 28 optimal weight:    1.9990
   chunk 63 optimal weight:    2.9990
   chunk 15 optimal weight:    0.8980
   chunk 0 optimal weight:   30.0000
   chunk 5 optimal weight:    0.0370
   overall best weight:    0.3314

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

Flipped N/Q/H residues before XYZ refinement:
** A  99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4103 r_free = 0.4103 target = 0.170327 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3488 r_free = 0.3488 target = 0.113941 restraints weight = 11121.543|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3542 r_free = 0.3542 target = 0.118720 restraints weight = 6123.571|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3577 r_free = 0.3577 target = 0.121750 restraints weight = 4450.908|
|-----------------------------------------------------------------------------|
r_work (final): 0.3584
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7451
moved from start:          0.2160

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   7758  Z= 0.117
  Angle     :  0.622   6.262  10557  Z= 0.312
  Chirality :  0.051   0.282   1188
  Planarity :  0.003   0.023   1305
  Dihedral  :  8.533  55.320   1419
  Min Nonbonded Distance : 2.026

Molprobity Statistics.
  All-atom Clashscore : 9.43
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  : 10.86 %
    Favored  : 89.04 %
  Rotamer:
    Outliers :  2.77 %
    Allowed  : 28.18 %
    Favored  : 69.06 %
  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: -2.25 (0.28), residues: 912
  helix: -1.07 (0.38), residues: 213
  sheet:  0.14 (0.31), residues: 294
  loop : -3.08 (0.28), residues: 405

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP C  36 
 HIS   0.001   0.000   HIS A 201 
 PHE   0.031   0.001   PHE C 166 
 TYR   0.020   0.001   TYR B 289 
 ARG   0.006   0.000   ARG B 199 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00783 (    9)
  link_NAG-ASN         : angle       2.52417 (   27)
  link_BETA1-4         : bond        0.00469 (    6)
  link_BETA1-4         : angle       1.96238 (   18)
  hydrogen bonds       : bond        0.02910 (  251)
  hydrogen bonds       : angle       4.48095 (  753)
  SS BOND              : bond        0.00161 (   15)
  SS BOND              : angle       1.01967 (   30)
  covalent geometry    : bond        0.00267 ( 7728)
  covalent geometry    : angle       0.60279 (10482)

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

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

  1824 Ramachandran restraints generated.
    912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1824 Ramachandran restraints generated.
    912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 795 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 110
  time to evaluate  : 0.867 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   98 MET cc_start: 0.7962 (ttt) cc_final: 0.7691 (ttm)
REVERT: B  199 ARG cc_start: 0.7612 (mmt180) cc_final: 0.7379 (mpt180)
REVERT: B  287 SER cc_start: 0.7395 (p) cc_final: 0.6927 (m)
REVERT: C   28 LEU cc_start: 0.7728 (OUTLIER) cc_final: 0.7484 (mt)
  outliers start: 22
  outliers final: 19
  residues processed: 128
  average time/residue: 0.1760
  time to fit residues: 31.4857
Evaluate side-chains
  117 residues out of total 795 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 97
  time to evaluate  : 0.861 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   51 ILE
Chi-restraints excluded: chain A residue   69 VAL
Chi-restraints excluded: chain A residue   72 VAL
Chi-restraints excluded: chain A residue  102 CYS
Chi-restraints excluded: chain A residue  191 THR
Chi-restraints excluded: chain A residue  258 THR
Chi-restraints excluded: chain A residue  281 TYR
Chi-restraints excluded: chain A residue  291 THR
Chi-restraints excluded: chain B residue   69 VAL
Chi-restraints excluded: chain B residue   70 MET
Chi-restraints excluded: chain B residue   72 VAL
Chi-restraints excluded: chain B residue  102 CYS
Chi-restraints excluded: chain B residue  161 MET
Chi-restraints excluded: chain B residue  191 THR
Chi-restraints excluded: chain B residue  258 THR
Chi-restraints excluded: chain C residue   28 LEU
Chi-restraints excluded: chain C residue   69 VAL
Chi-restraints excluded: chain C residue   70 MET
Chi-restraints excluded: chain C residue   72 VAL
Chi-restraints excluded: chain C residue  102 CYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 15 optimal weight:    2.9990
   chunk 38 optimal weight:    9.9990
   chunk 21 optimal weight:    1.9990
   chunk 71 optimal weight:    0.9980
   chunk 87 optimal weight:    2.9990
   chunk 44 optimal weight:    6.9990
   chunk 88 optimal weight:    0.5980
   chunk 30 optimal weight:   30.0000
   chunk 79 optimal weight:    1.9990
   chunk 47 optimal weight:    0.9980
   chunk 29 optimal weight:    7.9990
   overall best weight:    1.3184

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

Flipped N/Q/H residues before XYZ refinement:
** A  99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4070 r_free = 0.4070 target = 0.167244 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3420 r_free = 0.3420 target = 0.108938 restraints weight = 11413.484|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3477 r_free = 0.3477 target = 0.113772 restraints weight = 6173.589|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3513 r_free = 0.3513 target = 0.116751 restraints weight = 4459.389|
|-----------------------------------------------------------------------------|
r_work (final): 0.3507
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7528
moved from start:          0.2379

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.054   7758  Z= 0.192
  Angle     :  0.678   7.146  10557  Z= 0.341
  Chirality :  0.053   0.305   1188
  Planarity :  0.003   0.026   1305
  Dihedral  :  8.709  59.952   1419
  Min Nonbonded Distance : 1.914

Molprobity Statistics.
  All-atom Clashscore : 9.30
  Ramachandran Plot:
    Outliers :  0.33 %
    Allowed  : 11.40 %
    Favored  : 88.27 %
  Rotamer:
    Outliers :  3.27 %
    Allowed  : 28.68 %
    Favored  : 68.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.32 (0.27), residues: 912
  helix: -1.29 (0.36), residues: 213
  sheet:  0.14 (0.31), residues: 294
  loop : -3.06 (0.28), residues: 405

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP C  36 
 HIS   0.001   0.000   HIS A  40 
 PHE   0.040   0.002   PHE C 166 
 TYR   0.012   0.002   TYR C 289 
 ARG   0.006   0.000   ARG A 199 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00544 (    9)
  link_NAG-ASN         : angle       2.80202 (   27)
  link_BETA1-4         : bond        0.00390 (    6)
  link_BETA1-4         : angle       2.04362 (   18)
  hydrogen bonds       : bond        0.03164 (  251)
  hydrogen bonds       : angle       4.59434 (  753)
  SS BOND              : bond        0.00205 (   15)
  SS BOND              : angle       1.10159 (   30)
  covalent geometry    : bond        0.00452 ( 7728)
  covalent geometry    : angle       0.65731 (10482)

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

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

  1824 Ramachandran restraints generated.
    912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1824 Ramachandran restraints generated.
    912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 795 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 95
  time to evaluate  : 0.892 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   98 MET cc_start: 0.8029 (ttt) cc_final: 0.7751 (ttm)
REVERT: A  250 GLN cc_start: 0.8421 (mt0) cc_final: 0.7998 (mt0)
REVERT: A  270 SER cc_start: 0.8571 (OUTLIER) cc_final: 0.8163 (p)
REVERT: B   28 LEU cc_start: 0.7835 (OUTLIER) cc_final: 0.7605 (mt)
REVERT: B  250 GLN cc_start: 0.8490 (mt0) cc_final: 0.8052 (mt0)
REVERT: C   28 LEU cc_start: 0.7774 (OUTLIER) cc_final: 0.7566 (mt)
REVERT: C  270 SER cc_start: 0.8423 (OUTLIER) cc_final: 0.8082 (p)
REVERT: C  288 GLU cc_start: 0.8320 (pm20) cc_final: 0.7958 (pt0)
  outliers start: 26
  outliers final: 21
  residues processed: 119
  average time/residue: 0.1729
  time to fit residues: 29.2588
Evaluate side-chains
  118 residues out of total 795 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 93
  time to evaluate  : 0.755 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   51 ILE
Chi-restraints excluded: chain A residue   69 VAL
Chi-restraints excluded: chain A residue   72 VAL
Chi-restraints excluded: chain A residue  102 CYS
Chi-restraints excluded: chain A residue  167 THR
Chi-restraints excluded: chain A residue  191 THR
Chi-restraints excluded: chain A residue  258 THR
Chi-restraints excluded: chain A residue  270 SER
Chi-restraints excluded: chain A residue  281 TYR
Chi-restraints excluded: chain A residue  291 THR
Chi-restraints excluded: chain B residue   28 LEU
Chi-restraints excluded: chain B residue   69 VAL
Chi-restraints excluded: chain B residue   70 MET
Chi-restraints excluded: chain B residue   72 VAL
Chi-restraints excluded: chain B residue  102 CYS
Chi-restraints excluded: chain B residue  191 THR
Chi-restraints excluded: chain B residue  258 THR
Chi-restraints excluded: chain B residue  269 VAL
Chi-restraints excluded: chain C residue   28 LEU
Chi-restraints excluded: chain C residue   69 VAL
Chi-restraints excluded: chain C residue   72 VAL
Chi-restraints excluded: chain C residue  102 CYS
Chi-restraints excluded: chain C residue  191 THR
Chi-restraints excluded: chain C residue  270 SER
Chi-restraints excluded: chain C residue  291 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 3 optimal weight:    1.9990
   chunk 77 optimal weight:    0.0770
   chunk 7 optimal weight:    0.8980
   chunk 67 optimal weight:    5.9990
   chunk 23 optimal weight:    0.7980
   chunk 33 optimal weight:    2.9990
   chunk 13 optimal weight:    2.9990
   chunk 72 optimal weight:    2.9990
   chunk 34 optimal weight:    0.6980
   chunk 52 optimal weight:    1.9990
   chunk 84 optimal weight:    0.0170
   overall best weight:    0.4976

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

Flipped N/Q/H residues before XYZ refinement:
** A  99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4119 r_free = 0.4119 target = 0.168769 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3490 r_free = 0.3490 target = 0.113810 restraints weight = 10977.173|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3544 r_free = 0.3544 target = 0.118503 restraints weight = 5976.876|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3577 r_free = 0.3577 target = 0.121363 restraints weight = 4315.630|
|-----------------------------------------------------------------------------|
r_work (final): 0.3568
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7460
moved from start:          0.2310

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   7758  Z= 0.127
  Angle     :  0.634   6.479  10557  Z= 0.318
  Chirality :  0.052   0.282   1188
  Planarity :  0.003   0.022   1305
  Dihedral  :  8.500  57.323   1419
  Min Nonbonded Distance : 2.008

Molprobity Statistics.
  All-atom Clashscore : 9.43
  Ramachandran Plot:
    Outliers :  0.22 %
    Allowed  : 11.18 %
    Favored  : 88.60 %
  Rotamer:
    Outliers :  2.89 %
    Allowed  : 28.81 %
    Favored  : 68.30 %
  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: -2.25 (0.28), residues: 912
  helix: -1.11 (0.37), residues: 213
  sheet:  0.17 (0.31), residues: 294
  loop : -3.07 (0.28), residues: 405

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP C  36 
 HIS   0.001   0.000   HIS A 201 
 PHE   0.032   0.001   PHE C 166 
 TYR   0.006   0.001   TYR B 280 
 ARG   0.005   0.000   ARG A 199 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00737 (    9)
  link_NAG-ASN         : angle       2.56662 (   27)
  link_BETA1-4         : bond        0.00434 (    6)
  link_BETA1-4         : angle       1.89635 (   18)
  hydrogen bonds       : bond        0.02991 (  251)
  hydrogen bonds       : angle       4.46770 (  753)
  SS BOND              : bond        0.00160 (   15)
  SS BOND              : angle       1.01891 (   30)
  covalent geometry    : bond        0.00293 ( 7728)
  covalent geometry    : angle       0.61498 (10482)

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

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

  1824 Ramachandran restraints generated.
    912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1824 Ramachandran restraints generated.
    912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 795 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 103
  time to evaluate  : 0.797 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   98 MET cc_start: 0.7883 (ttt) cc_final: 0.7601 (ttm)
REVERT: A  199 ARG cc_start: 0.7662 (mmt180) cc_final: 0.7451 (mmt180)
REVERT: B   28 LEU cc_start: 0.7809 (OUTLIER) cc_final: 0.7577 (mt)
REVERT: B  143 GLU cc_start: 0.7589 (tp30) cc_final: 0.7147 (tp30)
REVERT: C   28 LEU cc_start: 0.7741 (OUTLIER) cc_final: 0.7530 (mt)
  outliers start: 23
  outliers final: 21
  residues processed: 124
  average time/residue: 0.1715
  time to fit residues: 30.1470
Evaluate side-chains
  116 residues out of total 795 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 93
  time to evaluate  : 0.835 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   44 TYR
Chi-restraints excluded: chain A residue   51 ILE
Chi-restraints excluded: chain A residue   69 VAL
Chi-restraints excluded: chain A residue   72 VAL
Chi-restraints excluded: chain A residue  102 CYS
Chi-restraints excluded: chain A residue  167 THR
Chi-restraints excluded: chain A residue  191 THR
Chi-restraints excluded: chain A residue  258 THR
Chi-restraints excluded: chain A residue  291 THR
Chi-restraints excluded: chain B residue   28 LEU
Chi-restraints excluded: chain B residue   69 VAL
Chi-restraints excluded: chain B residue   70 MET
Chi-restraints excluded: chain B residue   72 VAL
Chi-restraints excluded: chain B residue  102 CYS
Chi-restraints excluded: chain B residue  191 THR
Chi-restraints excluded: chain B residue  258 THR
Chi-restraints excluded: chain B residue  269 VAL
Chi-restraints excluded: chain C residue   28 LEU
Chi-restraints excluded: chain C residue   44 TYR
Chi-restraints excluded: chain C residue   69 VAL
Chi-restraints excluded: chain C residue   72 VAL
Chi-restraints excluded: chain C residue  102 CYS
Chi-restraints excluded: chain C residue  191 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 31 optimal weight:    9.9990
   chunk 10 optimal weight:    0.0270
   chunk 74 optimal weight:    0.0970
   chunk 73 optimal weight:    3.9990
   chunk 37 optimal weight:    1.9990
   chunk 41 optimal weight:    9.9990
   chunk 83 optimal weight:    0.9980
   chunk 87 optimal weight:    4.9990
   chunk 59 optimal weight:    2.9990
   chunk 42 optimal weight:    3.9990
   chunk 69 optimal weight:    7.9990
   overall best weight:    1.2240

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

Flipped N/Q/H residues before XYZ refinement:
** A  99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4069 r_free = 0.4069 target = 0.167073 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3421 r_free = 0.3421 target = 0.109025 restraints weight = 11207.454|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3478 r_free = 0.3478 target = 0.113815 restraints weight = 6081.421|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3513 r_free = 0.3513 target = 0.116742 restraints weight = 4408.585|
|-----------------------------------------------------------------------------|
r_work (final): 0.3504
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7506
moved from start:          0.2483

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048   7758  Z= 0.180
  Angle     :  0.667   7.196  10557  Z= 0.337
  Chirality :  0.053   0.301   1188
  Planarity :  0.004   0.065   1305
  Dihedral  :  8.649  59.961   1419
  Min Nonbonded Distance : 1.916

Molprobity Statistics.
  All-atom Clashscore : 9.30
  Ramachandran Plot:
    Outliers :  0.22 %
    Allowed  : 12.17 %
    Favored  : 87.61 %
  Rotamer:
    Outliers :  3.77 %
    Allowed  : 28.18 %
    Favored  : 68.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.29 (0.27), residues: 912
  helix: -1.26 (0.36), residues: 213
  sheet:  0.27 (0.31), residues: 288
  loop : -3.10 (0.28), residues: 411

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP C  36 
 HIS   0.001   0.000   HIS B 201 
 PHE   0.039   0.002   PHE C 166 
 TYR   0.011   0.001   TYR A 281 
 ARG   0.005   0.000   ARG A 199 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00563 (    9)
  link_NAG-ASN         : angle       2.77343 (   27)
  link_BETA1-4         : bond        0.00437 (    6)
  link_BETA1-4         : angle       2.01257 (   18)
  hydrogen bonds       : bond        0.03132 (  251)
  hydrogen bonds       : angle       4.59376 (  753)
  SS BOND              : bond        0.00216 (   15)
  SS BOND              : angle       1.11347 (   30)
  covalent geometry    : bond        0.00422 ( 7728)
  covalent geometry    : angle       0.64656 (10482)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2538.66 seconds
wall clock time: 45 minutes 13.00 seconds (2713.00 seconds total)