Starting phenix.real_space_refine
on Wed Sep 17 09:19:41 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9bpd_44772/09_2025/9bpd_44772.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9bpd_44772/09_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 {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9bpd_44772/09_2025/9bpd_44772.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9bpd_44772/09_2025/9bpd_44772.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9bpd_44772/09_2025/9bpd_44772.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9bpd_44772/09_2025/9bpd_44772.map"
  }
  resolution = 3.63
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 2.38, per 1000 atoms: 0.32
  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: 0.66
  Conformation dependent library (CDL) restraints added in 439.7 milliseconds
  
  Enol-peptide restraints added in 1.4 microseconds
  

  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: 0.29
  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: 1.12

  Time building geometry restraints manager: 0.90 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: 0.02
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:             1.240
  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:          0.080
  Check model and map are aligned:         0.010
  Set scattering table:                    0.020
  Process input model:                     9.140
  Find NCS groups from input model:        0.180
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.320
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   12.020
-------------------------------------------------------------------------------
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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  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
 ARG   0.002   0.000   ARG C 199 
 TYR   0.019   0.001   TYR C  75 
 PHE   0.015   0.001   PHE A 166 
 TRP   0.007   0.001   TRP A 240 
 HIS   0.002   0.001   HIS C 201 

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

*********************** 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  : 0.293 
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: B  201 HIS cc_start: 0.6571 (t-90) cc_final: 0.6282 (t-170)
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: 0.0822
  time to fit residues: 13.4182
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  : 0.294 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 49 optimal weight:    0.9990
   chunk 53 optimal weight:    4.9990
   chunk 5 optimal weight:    0.0010
   chunk 33 optimal weight:    2.9990
   chunk 65 optimal weight:    1.9990
   chunk 62 optimal weight:    5.9990
   chunk 51 optimal weight:    1.9990
   chunk 38 optimal weight:    7.9990
   chunk 61 optimal weight:    0.0070
   chunk 45 optimal weight:    0.9980
   chunk 74 optimal weight:    0.9990
   overall best weight:    0.6008

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

Flipped N/Q/H residues before XYZ refinement:
A  80 GLN
A  99 GLN
B  80 GLN
B  99 GLN
C  80 GLN
C  99 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4129 r_free = 0.4129 target = 0.173310 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3528 r_free = 0.3528 target = 0.117133 restraints weight = 11045.755|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3583 r_free = 0.3583 target = 0.121915 restraints weight = 6129.012|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3618 r_free = 0.3618 target = 0.124952 restraints weight = 4448.134|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 42)----------------|
| r_work = 0.3639 r_free = 0.3639 target = 0.126730 restraints weight = 3731.149|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3646 r_free = 0.3646 target = 0.127380 restraints weight = 3389.265|
|-----------------------------------------------------------------------------|
r_work (final): 0.3657
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7305
moved from start:          0.1078

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   7758  Z= 0.134
  Angle     :  0.616   6.051  10557  Z= 0.314
  Chirality :  0.051   0.279   1188
  Planarity :  0.004   0.043   1305
  Dihedral  :  9.090  54.624   1419
  Min Nonbonded Distance : 1.898

Molprobity Statistics.
  All-atom Clashscore : 8.69
  Ramachandran Plot:
    Outliers :  0.33 %
    Allowed  : 11.40 %
    Favored  : 88.27 %
  Rotamer:
    Outliers :  3.14 %
    Allowed  : 28.68 %
    Favored  : 68.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.48 (0.26), residues: 912
  helix: -1.36 (0.36), residues: 213
  sheet: -0.01 (0.29), residues: 294
  loop : -3.14 (0.25), residues: 405

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 259 
 TYR   0.014   0.002   TYR A 289 
 PHE   0.026   0.002   PHE B 166 
 TRP   0.006   0.001   TRP B 147 
 HIS   0.001   0.001   HIS B 201 

Details of bonding type rmsd
  covalent geometry    : bond        0.00301 ( 7728)
  covalent geometry    : angle       0.59314 (10482)
  SS BOND              : bond        0.00245 (   15)
  SS BOND              : angle       1.24478 (   30)
  hydrogen bonds       : bond        0.03354 (  251)
  hydrogen bonds       : angle       5.17116 (  753)
  link_BETA1-4         : bond        0.00344 (    6)
  link_BETA1-4         : angle       2.15882 (   18)
  link_NAG-ASN         : bond        0.00805 (    9)
  link_NAG-ASN         : angle       2.59268 (   27)

*********************** 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
  139 residues out of total 795 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 114
  time to evaluate  : 0.298 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   98 MET cc_start: 0.8044 (ttt) cc_final: 0.7743 (ttm)
REVERT: A  109 TYR cc_start: 0.6988 (m-80) cc_final: 0.6313 (m-80)
REVERT: A  201 HIS cc_start: 0.7148 (t-90) cc_final: 0.6584 (t70)
REVERT: B  109 TYR cc_start: 0.6793 (m-80) cc_final: 0.5617 (m-80)
REVERT: B  201 HIS cc_start: 0.7236 (t-90) cc_final: 0.6922 (t-170)
REVERT: C   75 TYR cc_start: 0.8922 (p90) cc_final: 0.8603 (p90)
REVERT: C  201 HIS cc_start: 0.7342 (t-90) cc_final: 0.7077 (t-170)
  outliers start: 25
  outliers final: 10
  residues processed: 138
  average time/residue: 0.0784
  time to fit residues: 15.0737
Evaluate side-chains
  120 residues out of total 795 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 110
  time to evaluate  : 0.217 
-------------------------------------------------------------------------------
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   51 ILE
Chi-restraints excluded: chain B residue   69 VAL
Chi-restraints excluded: chain B residue   72 VAL
Chi-restraints excluded: chain C residue   51 ILE
Chi-restraints excluded: chain C residue   69 VAL
Chi-restraints excluded: chain C residue   72 VAL
Chi-restraints excluded: chain C residue  160 MET
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 85 optimal weight:    0.4980
   chunk 54 optimal weight:    0.2980
   chunk 75 optimal weight:    1.9990
   chunk 70 optimal weight:    5.9990
   chunk 71 optimal weight:    4.9990
   chunk 31 optimal weight:    8.9990
   chunk 13 optimal weight:   10.0000
   chunk 10 optimal weight:    0.9990
   chunk 43 optimal weight:    0.7980
   chunk 53 optimal weight:    0.8980
   chunk 68 optimal weight:    5.9990
   overall best weight:    0.6982

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

Flipped N/Q/H residues before XYZ refinement:
** B  80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  80 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 = 0.4124 r_free = 0.4124 target = 0.172636 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3515 r_free = 0.3515 target = 0.115898 restraints weight = 10992.541|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3570 r_free = 0.3570 target = 0.120634 restraints weight = 6146.250|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3605 r_free = 0.3605 target = 0.123613 restraints weight = 4478.417|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3619 r_free = 0.3619 target = 0.125091 restraints weight = 3761.708|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 45)----------------|
| r_work = 0.3636 r_free = 0.3636 target = 0.126326 restraints weight = 3440.753|
|-----------------------------------------------------------------------------|
r_work (final): 0.3642
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7325
moved from start:          0.1273

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   7758  Z= 0.133
  Angle     :  0.619   6.545  10557  Z= 0.313
  Chirality :  0.052   0.286   1188
  Planarity :  0.004   0.052   1305
  Dihedral  :  9.018  56.710   1419
  Min Nonbonded Distance : 1.971

Molprobity Statistics.
  All-atom Clashscore : 9.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.29 %
    Favored  : 88.71 %
  Rotamer:
    Outliers :  2.26 %
    Allowed  : 29.81 %
    Favored  : 67.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.25 (0.27), residues: 912
  helix: -1.16 (0.37), residues: 213
  sheet:  0.23 (0.30), residues: 294
  loop : -3.10 (0.26), residues: 405

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C 121 
 TYR   0.034   0.001   TYR B 289 
 PHE   0.032   0.001   PHE B 166 
 TRP   0.010   0.001   TRP C  36 
 HIS   0.006   0.001   HIS C  40 

Details of bonding type rmsd
  covalent geometry    : bond        0.00304 ( 7728)
  covalent geometry    : angle       0.59668 (10482)
  SS BOND              : bond        0.00213 (   15)
  SS BOND              : angle       1.12593 (   30)
  hydrogen bonds       : bond        0.03149 (  251)
  hydrogen bonds       : angle       4.74072 (  753)
  link_BETA1-4         : bond        0.00454 (    6)
  link_BETA1-4         : angle       2.13714 (   18)
  link_NAG-ASN         : bond        0.00796 (    9)
  link_NAG-ASN         : angle       2.64015 (   27)

*********************** 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
  140 residues out of total 795 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 122
  time to evaluate  : 0.279 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   98 MET cc_start: 0.7986 (ttt) cc_final: 0.7673 (ttm)
REVERT: A  109 TYR cc_start: 0.6670 (m-80) cc_final: 0.6314 (m-80)
REVERT: A  201 HIS cc_start: 0.7199 (t-90) cc_final: 0.6583 (t70)
REVERT: B   75 TYR cc_start: 0.9008 (p90) cc_final: 0.8666 (p90)
REVERT: B  201 HIS cc_start: 0.7206 (t-90) cc_final: 0.6847 (t-170)
REVERT: B  250 GLN cc_start: 0.8306 (mt0) cc_final: 0.7855 (mt0)
REVERT: C   75 TYR cc_start: 0.8986 (p90) cc_final: 0.8706 (p90)
REVERT: C  201 HIS cc_start: 0.7355 (t-90) cc_final: 0.7128 (t-170)
  outliers start: 18
  outliers final: 8
  residues processed: 138
  average time/residue: 0.0695
  time to fit residues: 13.6770
Evaluate side-chains
  120 residues out of total 795 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 112
  time to evaluate  : 0.284 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   72 VAL
Chi-restraints excluded: chain A residue  258 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  191 THR
Chi-restraints excluded: chain C residue   69 VAL
Chi-restraints excluded: chain C residue   72 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 74 optimal weight:    0.0000
   chunk 8 optimal weight:    3.9990
   chunk 52 optimal weight:    0.6980
   chunk 58 optimal weight:    2.9990
   chunk 3 optimal weight:    3.9990
   chunk 17 optimal weight:    5.9990
   chunk 0 optimal weight:   30.0000
   chunk 23 optimal weight:    2.9990
   chunk 68 optimal weight:    9.9990
   chunk 14 optimal weight:    0.7980
   chunk 85 optimal weight:    0.8980
   overall best weight:    1.0786

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

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4106 r_free = 0.4106 target = 0.171186 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3469 r_free = 0.3469 target = 0.112525 restraints weight = 11457.747|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3530 r_free = 0.3530 target = 0.117615 restraints weight = 6186.265|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3567 r_free = 0.3567 target = 0.120705 restraints weight = 4454.790|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3583 r_free = 0.3583 target = 0.122320 restraints weight = 3745.873|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3599 r_free = 0.3599 target = 0.123496 restraints weight = 3419.977|
|-----------------------------------------------------------------------------|
r_work (final): 0.3586
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7445
moved from start:          0.1704

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   7758  Z= 0.169
  Angle     :  0.651   7.411  10557  Z= 0.328
  Chirality :  0.053   0.300   1188
  Planarity :  0.004   0.059   1305
  Dihedral  :  8.974  59.597   1419
  Min Nonbonded Distance : 1.916

Molprobity Statistics.
  All-atom Clashscore : 10.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.51 %
    Favored  : 88.49 %
  Rotamer:
    Outliers :  3.52 %
    Allowed  : 28.30 %
    Favored  : 68.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.23 (0.27), residues: 912
  helix: -1.26 (0.36), residues: 213
  sheet:  0.28 (0.30), residues: 294
  loop : -3.05 (0.27), residues: 405

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A 121 
 TYR   0.026   0.002   TYR B 289 
 PHE   0.030   0.002   PHE B 166 
 TRP   0.009   0.001   TRP A  36 
 HIS   0.006   0.001   HIS A  40 

Details of bonding type rmsd
  covalent geometry    : bond        0.00396 ( 7728)
  covalent geometry    : angle       0.62940 (10482)
  SS BOND              : bond        0.00192 (   15)
  SS BOND              : angle       1.13634 (   30)
  hydrogen bonds       : bond        0.03159 (  251)
  hydrogen bonds       : angle       4.63911 (  753)
  link_BETA1-4         : bond        0.00379 (    6)
  link_BETA1-4         : angle       2.09596 (   18)
  link_NAG-ASN         : bond        0.00652 (    9)
  link_NAG-ASN         : angle       2.75900 (   27)

*********************** 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
  143 residues out of total 795 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 115
  time to evaluate  : 0.286 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   28 LEU cc_start: 0.7745 (OUTLIER) cc_final: 0.7489 (mt)
REVERT: A   70 MET cc_start: 0.8601 (ptp) cc_final: 0.8255 (mtm)
REVERT: A   98 MET cc_start: 0.8023 (ttt) cc_final: 0.7734 (ttm)
REVERT: A  201 HIS cc_start: 0.7215 (t-90) cc_final: 0.6456 (t70)
REVERT: B  201 HIS cc_start: 0.7228 (t-90) cc_final: 0.6800 (t-170)
REVERT: C   28 LEU cc_start: 0.7861 (OUTLIER) cc_final: 0.7606 (mt)
REVERT: C  201 HIS cc_start: 0.7393 (t-90) cc_final: 0.7154 (t-170)
REVERT: C  250 GLN cc_start: 0.8262 (mt0) cc_final: 0.7866 (mt0)
  outliers start: 28
  outliers final: 13
  residues processed: 141
  average time/residue: 0.0840
  time to fit residues: 16.2654
Evaluate side-chains
  123 residues out of total 795 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 108
  time to evaluate  : 0.309 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   28 LEU
Chi-restraints excluded: chain A residue   69 VAL
Chi-restraints excluded: chain A residue   72 VAL
Chi-restraints excluded: chain A residue  191 THR
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  161 MET
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   72 VAL
Chi-restraints excluded: chain C residue  191 THR
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 21 optimal weight:    2.9990
   chunk 73 optimal weight:    3.9990
   chunk 31 optimal weight:   10.0000
   chunk 26 optimal weight:    0.6980
   chunk 10 optimal weight:    0.0670
   chunk 30 optimal weight:   10.0000
   chunk 19 optimal weight:    0.9990
   chunk 55 optimal weight:    0.9990
   chunk 17 optimal weight:    5.9990
   chunk 7 optimal weight:    0.9980
   chunk 87 optimal weight:    3.9990
   overall best weight:    0.7522

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4130 r_free = 0.4130 target = 0.170008 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3498 r_free = 0.3498 target = 0.114424 restraints weight = 11103.339|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3553 r_free = 0.3553 target = 0.119159 restraints weight = 6049.971|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3588 r_free = 0.3588 target = 0.122159 restraints weight = 4376.284|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.3610 r_free = 0.3610 target = 0.123932 restraints weight = 3657.679|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3615 r_free = 0.3615 target = 0.124386 restraints weight = 3320.550|
|-----------------------------------------------------------------------------|
r_work (final): 0.3603
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7390
moved from start:          0.1829

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= 0.138
  Angle     :  0.631   6.852  10557  Z= 0.316
  Chirality :  0.052   0.293   1188
  Planarity :  0.004   0.052   1305
  Dihedral  :  8.827  58.701   1419
  Min Nonbonded Distance : 1.969

Molprobity Statistics.
  All-atom Clashscore : 9.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.62 %
    Favored  : 88.38 %
  Rotamer:
    Outliers :  2.14 %
    Allowed  : 29.18 %
    Favored  : 68.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.22 (0.27), residues: 912
  helix: -1.19 (0.37), residues: 213
  sheet:  0.27 (0.30), residues: 294
  loop : -3.07 (0.27), residues: 405

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 121 
 TYR   0.014   0.001   TYR B 289 
 PHE   0.033   0.001   PHE C 166 
 TRP   0.010   0.001   TRP A  36 
 HIS   0.001   0.000   HIS C 201 

Details of bonding type rmsd
  covalent geometry    : bond        0.00316 ( 7728)
  covalent geometry    : angle       0.60973 (10482)
  SS BOND              : bond        0.00194 (   15)
  SS BOND              : angle       1.10463 (   30)
  hydrogen bonds       : bond        0.03055 (  251)
  hydrogen bonds       : angle       4.53529 (  753)
  link_BETA1-4         : bond        0.00468 (    6)
  link_BETA1-4         : angle       2.04102 (   18)
  link_NAG-ASN         : bond        0.00719 (    9)
  link_NAG-ASN         : angle       2.65442 (   27)

*********************** 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
  128 residues out of total 795 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 111
  time to evaluate  : 0.287 
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: 0.7986 (ttt) cc_final: 0.7682 (ttm)
REVERT: A  201 HIS cc_start: 0.7305 (t-90) cc_final: 0.6641 (t70)
REVERT: B   80 GLN cc_start: 0.8235 (mm-40) cc_final: 0.7982 (mp10)
REVERT: B  201 HIS cc_start: 0.7265 (t-90) cc_final: 0.6882 (t-170)
REVERT: C  201 HIS cc_start: 0.7326 (t-90) cc_final: 0.7035 (t-170)
  outliers start: 17
  outliers final: 15
  residues processed: 125
  average time/residue: 0.0703
  time to fit residues: 12.7766
Evaluate side-chains
  122 residues out of total 795 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 107
  time to evaluate  : 0.283 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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   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   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=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 4 optimal weight:    3.9990
   chunk 36 optimal weight:    0.7980
   chunk 10 optimal weight:    2.9990
   chunk 35 optimal weight:    0.6980
   chunk 40 optimal weight:    5.9990
   chunk 11 optimal weight:    0.9980
   chunk 77 optimal weight:    0.9990
   chunk 5 optimal weight:    0.2980
   chunk 75 optimal weight:    0.9990
   chunk 14 optimal weight:    0.9980
   chunk 52 optimal weight:    0.6980
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
** B  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 = 0.4129 r_free = 0.4129 target = 0.170040 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3497 r_free = 0.3497 target = 0.114380 restraints weight = 11048.575|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3553 r_free = 0.3553 target = 0.119168 restraints weight = 6037.494|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3588 r_free = 0.3588 target = 0.122192 restraints weight = 4355.081|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3603 r_free = 0.3603 target = 0.123671 restraints weight = 3642.738|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 43)----------------|
| r_work = 0.3621 r_free = 0.3621 target = 0.124908 restraints weight = 3326.259|
|-----------------------------------------------------------------------------|
r_work (final): 0.3612
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7379
moved from start:          0.1940

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   7758  Z= 0.134
  Angle     :  0.620   6.686  10557  Z= 0.311
  Chirality :  0.052   0.289   1188
  Planarity :  0.003   0.048   1305
  Dihedral  :  8.689  57.903   1419
  Min Nonbonded Distance : 1.968

Molprobity Statistics.
  All-atom Clashscore : 9.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.73 %
    Favored  : 88.27 %
  Rotamer:
    Outliers :  3.02 %
    Allowed  : 28.18 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.21 (0.27), residues: 912
  helix: -1.16 (0.37), residues: 213
  sheet:  0.24 (0.30), residues: 294
  loop : -3.04 (0.28), residues: 405

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 199 
 TYR   0.014   0.001   TYR B 289 
 PHE   0.031   0.001   PHE B 166 
 TRP   0.012   0.001   TRP C  36 
 HIS   0.001   0.000   HIS B 201 

Details of bonding type rmsd
  covalent geometry    : bond        0.00307 ( 7728)
  covalent geometry    : angle       0.59926 (10482)
  SS BOND              : bond        0.00189 (   15)
  SS BOND              : angle       1.05658 (   30)
  hydrogen bonds       : bond        0.02995 (  251)
  hydrogen bonds       : angle       4.48869 (  753)
  link_BETA1-4         : bond        0.00434 (    6)
  link_BETA1-4         : angle       2.02657 (   18)
  link_NAG-ASN         : bond        0.00684 (    9)
  link_NAG-ASN         : angle       2.60359 (   27)

*********************** 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
  139 residues out of total 795 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 115
  time to evaluate  : 0.282 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   28 LEU cc_start: 0.7695 (OUTLIER) cc_final: 0.7483 (mt)
REVERT: A  201 HIS cc_start: 0.7371 (t-90) cc_final: 0.6635 (t70)
REVERT: A  270 SER cc_start: 0.8519 (OUTLIER) cc_final: 0.8164 (p)
REVERT: B  201 HIS cc_start: 0.7256 (t-90) cc_final: 0.6828 (t-170)
REVERT: B  270 SER cc_start: 0.8448 (OUTLIER) cc_final: 0.8128 (p)
REVERT: C   28 LEU cc_start: 0.7709 (OUTLIER) cc_final: 0.7500 (mt)
REVERT: C  201 HIS cc_start: 0.7444 (t-90) cc_final: 0.7184 (t-170)
REVERT: C  270 SER cc_start: 0.8399 (OUTLIER) cc_final: 0.8025 (p)
  outliers start: 24
  outliers final: 17
  residues processed: 135
  average time/residue: 0.0702
  time to fit residues: 13.7314
Evaluate side-chains
  129 residues out of total 795 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 107
  time to evaluate  : 0.268 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   28 LEU
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 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 B residue  270 SER
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  270 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 77 optimal weight:    1.9990
   chunk 48 optimal weight:    0.0670
   chunk 7 optimal weight:    1.9990
   chunk 82 optimal weight:    1.9990
   chunk 71 optimal weight:    3.9990
   chunk 28 optimal weight:    1.9990
   chunk 21 optimal weight:    0.7980
   chunk 39 optimal weight:    3.9990
   chunk 29 optimal weight:    6.9990
   chunk 35 optimal weight:    0.7980
   chunk 4 optimal weight:    1.9990
   overall best weight:    1.1322

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

Flipped N/Q/H residues before XYZ refinement:
** B  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 = 0.4111 r_free = 0.4111 target = 0.167939 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3468 r_free = 0.3468 target = 0.112448 restraints weight = 11022.909|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3522 r_free = 0.3522 target = 0.116974 restraints weight = 6221.205|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3555 r_free = 0.3555 target = 0.119784 restraints weight = 4567.176|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3570 r_free = 0.3570 target = 0.121177 restraints weight = 3864.709|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 52)----------------|
| r_work = 0.3586 r_free = 0.3586 target = 0.122273 restraints weight = 3547.385|
|-----------------------------------------------------------------------------|
r_work (final): 0.3576
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7477
moved from start:          0.2123

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= 0.171
  Angle     :  0.656   7.245  10557  Z= 0.331
  Chirality :  0.053   0.294   1188
  Planarity :  0.004   0.044   1305
  Dihedral  :  8.751  59.727   1419
  Min Nonbonded Distance : 1.930

Molprobity Statistics.
  All-atom Clashscore : 9.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.86 %
    Favored  : 89.14 %
  Rotamer:
    Outliers :  3.77 %
    Allowed  : 27.67 %
    Favored  : 68.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.25 (0.27), residues: 912
  helix: -1.27 (0.36), residues: 213
  sheet:  0.34 (0.31), residues: 288
  loop : -3.08 (0.28), residues: 411

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 199 
 TYR   0.012   0.001   TYR C 281 
 PHE   0.034   0.002   PHE B 166 
 TRP   0.012   0.001   TRP A  36 
 HIS   0.001   0.000   HIS C 201 

Details of bonding type rmsd
  covalent geometry    : bond        0.00399 ( 7728)
  covalent geometry    : angle       0.63525 (10482)
  SS BOND              : bond        0.00194 (   15)
  SS BOND              : angle       1.12071 (   30)
  hydrogen bonds       : bond        0.03098 (  251)
  hydrogen bonds       : angle       4.56831 (  753)
  link_BETA1-4         : bond        0.00396 (    6)
  link_BETA1-4         : angle       2.01696 (   18)
  link_NAG-ASN         : bond        0.00609 (    9)
  link_NAG-ASN         : angle       2.74574 (   27)

*********************** 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
  135 residues out of total 795 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 105
  time to evaluate  : 0.239 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   98 MET cc_start: 0.7971 (ttt) cc_final: 0.7668 (ttm)
REVERT: A  250 GLN cc_start: 0.8446 (mt0) cc_final: 0.8036 (mt0)
REVERT: A  270 SER cc_start: 0.8580 (OUTLIER) cc_final: 0.8171 (p)
REVERT: B   80 GLN cc_start: 0.8165 (mm-40) cc_final: 0.7947 (mp10)
REVERT: B  201 HIS cc_start: 0.7232 (t-90) cc_final: 0.6793 (t-170)
REVERT: B  250 GLN cc_start: 0.8464 (mt0) cc_final: 0.8063 (mt0)
REVERT: B  270 SER cc_start: 0.8499 (OUTLIER) cc_final: 0.8137 (p)
REVERT: C   28 LEU cc_start: 0.7709 (OUTLIER) cc_final: 0.7457 (mt)
REVERT: C  250 GLN cc_start: 0.8326 (mt0) cc_final: 0.8001 (mt0)
REVERT: C  270 SER cc_start: 0.8494 (OUTLIER) cc_final: 0.8075 (p)
  outliers start: 30
  outliers final: 22
  residues processed: 132
  average time/residue: 0.0772
  time to fit residues: 14.1487
Evaluate side-chains
  126 residues out of total 795 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 100
  time to evaluate  : 0.252 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  270 SER
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 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   75 TYR
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  281 TYR
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 57 optimal weight:    4.9990
   chunk 31 optimal weight:    3.9990
   chunk 53 optimal weight:    0.8980
   chunk 14 optimal weight:    0.9990
   chunk 89 optimal weight:    7.9990
   chunk 6 optimal weight:    1.9990
   chunk 15 optimal weight:    0.6980
   chunk 45 optimal weight:    0.8980
   chunk 8 optimal weight:    6.9990
   chunk 26 optimal weight:    0.0980
   chunk 63 optimal weight:    0.7980
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
** B  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 = 0.4121 r_free = 0.4121 target = 0.168933 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3481 r_free = 0.3481 target = 0.113240 restraints weight = 11063.426|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3536 r_free = 0.3536 target = 0.117992 restraints weight = 6035.732|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3571 r_free = 0.3571 target = 0.120954 restraints weight = 4357.641|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3586 r_free = 0.3586 target = 0.122413 restraints weight = 3651.834|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3602 r_free = 0.3602 target = 0.123503 restraints weight = 3344.148|
|-----------------------------------------------------------------------------|
r_work (final): 0.3595
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7395
moved from start:          0.2146

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   7758  Z= 0.137
  Angle     :  0.645   6.579  10557  Z= 0.324
  Chirality :  0.052   0.287   1188
  Planarity :  0.003   0.028   1305
  Dihedral  :  8.631  58.667   1419
  Min Nonbonded Distance : 1.976

Molprobity Statistics.
  All-atom Clashscore : 10.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.29 %
    Favored  : 88.71 %
  Rotamer:
    Outliers :  3.27 %
    Allowed  : 28.05 %
    Favored  : 68.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.22 (0.28), residues: 912
  helix: -1.18 (0.37), residues: 213
  sheet:  0.35 (0.31), residues: 288
  loop : -3.10 (0.28), residues: 411

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 199 
 TYR   0.013   0.001   TYR C  75 
 PHE   0.034   0.001   PHE C 166 
 TRP   0.012   0.001   TRP C  36 
 HIS   0.001   0.000   HIS B 201 

Details of bonding type rmsd
  covalent geometry    : bond        0.00315 ( 7728)
  covalent geometry    : angle       0.62458 (10482)
  SS BOND              : bond        0.00186 (   15)
  SS BOND              : angle       1.05237 (   30)
  hydrogen bonds       : bond        0.02991 (  251)
  hydrogen bonds       : angle       4.47658 (  753)
  link_BETA1-4         : bond        0.00443 (    6)
  link_BETA1-4         : angle       1.97141 (   18)
  link_NAG-ASN         : bond        0.00750 (    9)
  link_NAG-ASN         : angle       2.69345 (   27)

*********************** 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
  129 residues out of total 795 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 103
  time to evaluate  : 0.282 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  250 GLN cc_start: 0.8440 (mt0) cc_final: 0.8013 (mt0)
REVERT: A  270 SER cc_start: 0.8566 (OUTLIER) cc_final: 0.8184 (p)
REVERT: B   80 GLN cc_start: 0.8162 (mm-40) cc_final: 0.7962 (mp10)
REVERT: B  109 TYR cc_start: 0.6906 (m-80) cc_final: 0.5870 (m-80)
REVERT: B  199 ARG cc_start: 0.7691 (mmt180) cc_final: 0.7487 (mpt180)
REVERT: B  270 SER cc_start: 0.8442 (OUTLIER) cc_final: 0.8107 (p)
REVERT: C   28 LEU cc_start: 0.7713 (OUTLIER) cc_final: 0.7500 (mt)
REVERT: C  250 GLN cc_start: 0.8359 (mt0) cc_final: 0.7990 (mt0)
REVERT: C  270 SER cc_start: 0.8403 (OUTLIER) cc_final: 0.8048 (p)
  outliers start: 26
  outliers final: 20
  residues processed: 126
  average time/residue: 0.0813
  time to fit residues: 14.3732
Evaluate side-chains
  124 residues out of total 795 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 100
  time to evaluate  : 0.356 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  270 SER
Chi-restraints excluded: chain A residue  281 TYR
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 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  281 TYR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 53 optimal weight:    3.9990
   chunk 83 optimal weight:    0.9980
   chunk 59 optimal weight:    0.8980
   chunk 25 optimal weight:    1.9990
   chunk 2 optimal weight:    0.9980
   chunk 11 optimal weight:    8.9990
   chunk 23 optimal weight:    2.9990
   chunk 68 optimal weight:    9.9990
   chunk 21 optimal weight:    0.7980
   chunk 65 optimal weight:    0.1980
   chunk 4 optimal weight:    0.0870
   overall best weight:    0.5958

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

Flipped N/Q/H residues before XYZ refinement:
** B  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 = 0.4129 r_free = 0.4129 target = 0.169788 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3495 r_free = 0.3495 target = 0.114209 restraints weight = 10993.862|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3549 r_free = 0.3549 target = 0.118936 restraints weight = 6004.524|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3583 r_free = 0.3583 target = 0.121894 restraints weight = 4347.018|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3604 r_free = 0.3604 target = 0.123590 restraints weight = 3646.774|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3609 r_free = 0.3609 target = 0.124017 restraints weight = 3323.201|
|-----------------------------------------------------------------------------|
r_work (final): 0.3598
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7392
moved from start:          0.2235

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   7758  Z= 0.133
  Angle     :  0.651   6.379  10557  Z= 0.327
  Chirality :  0.051   0.281   1188
  Planarity :  0.003   0.041   1305
  Dihedral  :  8.515  57.397   1419
  Min Nonbonded Distance : 1.982

Molprobity Statistics.
  All-atom Clashscore : 9.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.42 %
    Favored  : 89.58 %
  Rotamer:
    Outliers :  3.27 %
    Allowed  : 28.05 %
    Favored  : 68.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.20 (0.28), residues: 912
  helix: -1.12 (0.37), residues: 213
  sheet:  0.36 (0.31), residues: 288
  loop : -3.10 (0.28), residues: 411

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B 121 
 TYR   0.012   0.001   TYR C  75 
 PHE   0.032   0.001   PHE B 166 
 TRP   0.013   0.002   TRP C  36 
 HIS   0.000   0.000   HIS B  40 

Details of bonding type rmsd
  covalent geometry    : bond        0.00309 ( 7728)
  covalent geometry    : angle       0.63278 (10482)
  SS BOND              : bond        0.00185 (   15)
  SS BOND              : angle       1.04109 (   30)
  hydrogen bonds       : bond        0.02945 (  251)
  hydrogen bonds       : angle       4.43744 (  753)
  link_BETA1-4         : bond        0.00456 (    6)
  link_BETA1-4         : angle       1.95125 (   18)
  link_NAG-ASN         : bond        0.00706 (    9)
  link_NAG-ASN         : angle       2.58475 (   27)

*********************** 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
  130 residues out of total 795 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 104
  time to evaluate  : 0.271 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  250 GLN cc_start: 0.8445 (mt0) cc_final: 0.8010 (mt0)
REVERT: A  270 SER cc_start: 0.8500 (OUTLIER) cc_final: 0.8139 (p)
REVERT: B   80 GLN cc_start: 0.8158 (mm-40) cc_final: 0.7935 (mp10)
REVERT: B  143 GLU cc_start: 0.7610 (tp30) cc_final: 0.7241 (tp30)
REVERT: B  199 ARG cc_start: 0.7616 (mmt180) cc_final: 0.7368 (mpt180)
REVERT: B  201 HIS cc_start: 0.7175 (t-90) cc_final: 0.6805 (t-90)
REVERT: B  270 SER cc_start: 0.8396 (OUTLIER) cc_final: 0.8081 (p)
REVERT: C   28 LEU cc_start: 0.7712 (OUTLIER) cc_final: 0.7501 (mt)
REVERT: C  250 GLN cc_start: 0.8356 (mt0) cc_final: 0.7980 (mt0)
REVERT: C  270 SER cc_start: 0.8364 (OUTLIER) cc_final: 0.8039 (p)
  outliers start: 26
  outliers final: 22
  residues processed: 126
  average time/residue: 0.0771
  time to fit residues: 13.8308
Evaluate side-chains
  127 residues out of total 795 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 101
  time to evaluate  : 0.265 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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 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 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  281 TYR
Chi-restraints excluded: chain C residue  289 TYR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 23 optimal weight:    2.9990
   chunk 6 optimal weight:    0.9990
   chunk 56 optimal weight:    0.4980
   chunk 31 optimal weight:    2.9990
   chunk 60 optimal weight:   30.0000
   chunk 15 optimal weight:    0.9980
   chunk 25 optimal weight:    0.0970
   chunk 59 optimal weight:    0.0970
   chunk 10 optimal weight:    0.8980
   chunk 54 optimal weight:    0.4980
   chunk 3 optimal weight:    0.5980
   overall best weight:    0.3576

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

Flipped N/Q/H residues before XYZ refinement:
** B  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 = 0.4116 r_free = 0.4116 target = 0.171547 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3499 r_free = 0.3499 target = 0.114780 restraints weight = 11079.264|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3554 r_free = 0.3554 target = 0.119561 restraints weight = 6088.687|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.3589 r_free = 0.3589 target = 0.122614 restraints weight = 4432.677|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3603 r_free = 0.3603 target = 0.124004 restraints weight = 3721.545|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.3619 r_free = 0.3619 target = 0.125220 restraints weight = 3413.054|
|-----------------------------------------------------------------------------|
r_work (final): 0.3629
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7354
moved from start:          0.2207

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   7758  Z= 0.120
  Angle     :  0.635   6.914  10557  Z= 0.319
  Chirality :  0.051   0.275   1188
  Planarity :  0.003   0.062   1305
  Dihedral  :  8.331  55.733   1419
  Min Nonbonded Distance : 2.006

Molprobity Statistics.
  All-atom Clashscore : 9.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.18 %
    Favored  : 88.82 %
  Rotamer:
    Outliers :  2.89 %
    Allowed  : 28.55 %
    Favored  : 68.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.17 (0.28), residues: 912
  helix: -1.02 (0.38), residues: 213
  sheet:  0.24 (0.31), residues: 294
  loop : -3.06 (0.28), residues: 405

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 199 
 TYR   0.014   0.001   TYR B 109 
 PHE   0.030   0.001   PHE C 166 
 TRP   0.015   0.002   TRP C  36 
 HIS   0.001   0.000   HIS C 201 

Details of bonding type rmsd
  covalent geometry    : bond        0.00276 ( 7728)
  covalent geometry    : angle       0.61696 (10482)
  SS BOND              : bond        0.00218 (   15)
  SS BOND              : angle       1.04518 (   30)
  hydrogen bonds       : bond        0.02880 (  251)
  hydrogen bonds       : angle       4.41737 (  753)
  link_BETA1-4         : bond        0.00449 (    6)
  link_BETA1-4         : angle       1.92107 (   18)
  link_NAG-ASN         : bond        0.00799 (    9)
  link_NAG-ASN         : angle       2.48532 (   27)

********************** 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
  128 residues out of total 795 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 105
  time to evaluate  : 0.308 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   80 GLN cc_start: 0.8145 (mm-40) cc_final: 0.7910 (mp10)
REVERT: B  199 ARG cc_start: 0.7665 (mmt180) cc_final: 0.7431 (mpt180)
REVERT: B  201 HIS cc_start: 0.7286 (t-90) cc_final: 0.6909 (t-90)
REVERT: C   28 LEU cc_start: 0.7719 (OUTLIER) cc_final: 0.7507 (mt)
REVERT: C  270 SER cc_start: 0.8248 (OUTLIER) cc_final: 0.7961 (p)
  outliers start: 23
  outliers final: 20
  residues processed: 123
  average time/residue: 0.0800
  time to fit residues: 14.0017
Evaluate side-chains
  124 residues out of total 795 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 102
  time to evaluate  : 0.284 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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 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
Chi-restraints excluded: chain C residue  191 THR
Chi-restraints excluded: chain C residue  270 SER
Chi-restraints excluded: chain C residue  281 TYR
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 44 optimal weight:    0.5980
   chunk 46 optimal weight:    0.9980
   chunk 84 optimal weight:    0.6980
   chunk 34 optimal weight:    0.6980
   chunk 56 optimal weight:    0.0570
   chunk 64 optimal weight:    0.6980
   chunk 3 optimal weight:    1.9990
   chunk 26 optimal weight:    1.9990
   chunk 65 optimal weight:    0.0670
   chunk 60 optimal weight:   30.0000
   chunk 88 optimal weight:    0.9990
   overall best weight:    0.4236

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

Flipped N/Q/H residues before XYZ refinement:
** B  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 = 0.4118 r_free = 0.4118 target = 0.171834 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3504 r_free = 0.3504 target = 0.115043 restraints weight = 10991.478|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3558 r_free = 0.3558 target = 0.119794 restraints weight = 6111.819|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3592 r_free = 0.3592 target = 0.122717 restraints weight = 4466.595|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3614 r_free = 0.3614 target = 0.124580 restraints weight = 3771.740|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3621 r_free = 0.3621 target = 0.125378 restraints weight = 3420.092|
|-----------------------------------------------------------------------------|
r_work (final): 0.3628
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7357
moved from start:          0.2292

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   7758  Z= 0.120
  Angle     :  0.628   6.903  10557  Z= 0.316
  Chirality :  0.051   0.273   1188
  Planarity :  0.003   0.039   1305
  Dihedral  :  8.221  56.334   1419
  Min Nonbonded Distance : 1.987

Molprobity Statistics.
  All-atom Clashscore : 9.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.75 %
    Favored  : 89.25 %
  Rotamer:
    Outliers :  2.77 %
    Allowed  : 28.81 %
    Favored  : 68.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.14 (0.28), residues: 912
  helix: -1.01 (0.38), residues: 213
  sheet:  0.28 (0.31), residues: 294
  loop : -3.06 (0.28), residues: 405

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 199 
 TYR   0.014   0.001   TYR B 109 
 PHE   0.031   0.001   PHE B 166 
 TRP   0.015   0.002   TRP C  36 
 HIS   0.001   0.000   HIS A 201 

Details of bonding type rmsd
  covalent geometry    : bond        0.00279 ( 7728)
  covalent geometry    : angle       0.61091 (10482)
  SS BOND              : bond        0.00203 (   15)
  SS BOND              : angle       1.01443 (   30)
  hydrogen bonds       : bond        0.02838 (  251)
  hydrogen bonds       : angle       4.32241 (  753)
  link_BETA1-4         : bond        0.00466 (    6)
  link_BETA1-4         : angle       1.91224 (   18)
  link_NAG-ASN         : bond        0.00741 (    9)
  link_NAG-ASN         : angle       2.44462 (   27)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1477.51 seconds
wall clock time: 26 minutes 10.74 seconds (1570.74 seconds total)