Starting phenix.real_space_refine
on Tue May 13 09:01:45 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8j7f_36039/05_2025/8j7f_36039_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8j7f_36039/05_2025/8j7f_36039.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.6
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8j7f_36039/05_2025/8j7f_36039.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8j7f_36039/05_2025/8j7f_36039.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8j7f_36039/05_2025/8j7f_36039_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8j7f_36039/05_2025/8j7f_36039_neut.cif"
  }
  resolution = 2.6
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.001 sd=   0.101
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
     Ca      4      9.91       5
     P       4      5.49       5
     S      54      5.16       5
     C    6665      2.51       5
     N    1513      2.21       5
     O    1721      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 28 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 9961
  Number of models: 1
  Model: ""
    Number of chains: 13
    Chain: "A"
      Number of atoms: 2331
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 289, 2331
          Classifications: {'peptide': 289}
          Incomplete info: {'truncation_to_alanine': 3}
          Link IDs: {'PTRANS': 7, 'TRANS': 281}
          Unresolved non-hydrogen bonds: 21
          Unresolved non-hydrogen angles: 28
          Unresolved non-hydrogen dihedrals: 23
          Planarities with less than four sites: {'PHE:plan': 1, 'TRP:plan': 1}
          Unresolved non-hydrogen planarities: 15
    Chain: "B"
      Number of atoms: 2334
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 289, 2334
          Classifications: {'peptide': 289}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 7, 'TRANS': 281}
          Unresolved non-hydrogen bonds: 18
          Unresolved non-hydrogen angles: 25
          Unresolved non-hydrogen dihedrals: 20
          Planarities with less than four sites: {'PHE:plan': 1, 'TRP:plan': 1}
          Unresolved non-hydrogen planarities: 15
    Chain: "C"
      Number of atoms: 2340
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 289, 2340
          Classifications: {'peptide': 289}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 7, 'TRANS': 281}
          Unresolved non-hydrogen bonds: 11
          Unresolved non-hydrogen angles: 16
          Unresolved non-hydrogen dihedrals: 13
          Planarities with less than four sites: {'TRP:plan': 1}
          Unresolved non-hydrogen planarities: 9
    Chain: "D"
      Number of atoms: 2337
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 289, 2337
          Classifications: {'peptide': 289}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 7, 'TRANS': 281}
          Unresolved non-hydrogen bonds: 14
          Unresolved non-hydrogen angles: 19
          Unresolved non-hydrogen dihedrals: 16
          Planarities with less than four sites: {'TRP:plan': 1}
          Unresolved non-hydrogen planarities: 9
    Chain: "E"
      Number of atoms: 153
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 20, 153
          Classifications: {'peptide': 20}
          Link IDs: {'TRANS': 19}
    Chain: "A"
      Number of atoms: 114
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 5, 114
          Unusual residues: {' CA': 1, 'CLR': 3, 'POV': 1}
          Classifications: {'undetermined': 5}
          Link IDs: {None: 4}
          Unresolved non-hydrogen bonds: 23
          Unresolved non-hydrogen angles: 26
          Unresolved non-hydrogen dihedrals: 21
          Planarities with less than four sites: {'POV:plan-1': 1}
          Unresolved non-hydrogen planarities: 4
    Chain: "B"
      Number of atoms: 114
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 5, 114
          Unusual residues: {' CA': 1, 'CLR': 3, 'POV': 1}
          Classifications: {'undetermined': 5}
          Link IDs: {None: 4}
          Unresolved non-hydrogen bonds: 23
          Unresolved non-hydrogen angles: 26
          Unresolved non-hydrogen dihedrals: 21
          Planarities with less than four sites: {'POV:plan-1': 1}
          Unresolved non-hydrogen planarities: 4
    Chain: "C"
      Number of atoms: 115
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 6, 115
          Unusual residues: {' CA': 2, 'CLR': 3, 'POV': 1}
          Classifications: {'undetermined': 6}
          Link IDs: {None: 5}
          Unresolved non-hydrogen bonds: 23
          Unresolved non-hydrogen angles: 26
          Unresolved non-hydrogen dihedrals: 21
          Planarities with less than four sites: {'POV:plan-1': 1}
          Unresolved non-hydrogen planarities: 4
    Chain: "D"
      Number of atoms: 113
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 113
          Unusual residues: {'CLR': 3, 'POV': 1}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}
          Unresolved non-hydrogen bonds: 23
          Unresolved non-hydrogen angles: 26
          Unresolved non-hydrogen dihedrals: 21
          Planarities with less than four sites: {'POV:plan-1': 1}
          Unresolved non-hydrogen planarities: 4
    Chain: "A"
      Number of atoms: 2
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 2
          Classifications: {'water': 2}
          Link IDs: {None: 1}
    Chain: "B"
      Number of atoms: 3
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 3
          Classifications: {'water': 3}
          Link IDs: {None: 2}
    Chain: "C"
      Number of atoms: 3
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 3
          Classifications: {'water': 3}
          Link IDs: {None: 2}
    Chain: "D"
      Number of atoms: 2
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 2
          Classifications: {'water': 2}
          Link IDs: {None: 1}
  Time building chain proxies: 6.50, per 1000 atoms: 0.65
  Number of scatterers: 9961
  At special positions: 0
  Unit cell: (121.68, 121.68, 94.64, 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)
     Ca      4     19.99
     S      54     16.00
     P       4     15.00
     O    1721      8.00
     N    1513      7.00
     C    6665      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  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=1, symmetry=0
  Number of additional bonds: simple=1, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 2.67
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  2332 Ramachandran restraints generated.
    1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2192

  Finding SS restraints...
    Secondary structure from input PDB file:
      53 helices and 4 sheets defined
      76.8% alpha, 2.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.79
  Creating SS restraints...
    Processing helix  chain 'A' and resid 72 through 81
      removed outlier: 3.933A  pdb=" N   VAL A  76 " --> pdb=" O   HIS A  72 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 82 through 107
    Processing helix  chain 'A' and resid 114 through 139
      removed outlier: 3.692A  pdb=" N   TRP A 118 " --> pdb=" O   TYR A 114 " (cutoff:3.500A)
      removed outlier: 3.728A  pdb=" N   GLY A 139 " --> pdb=" O   ILE A 135 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 148 through 172
      removed outlier: 4.358A  pdb=" N   GLY A 172 " --> pdb=" O   GLU A 168 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 179 through 191
      removed outlier: 3.519A  pdb=" N   ILE A 182 " --> pdb=" O   MET A 179 " (cutoff:3.500A)
      removed outlier: 3.671A  pdb=" N   ASN A 184 " --> pdb=" O   LEU A 181 " (cutoff:3.500A)
      removed outlier: 4.224A  pdb=" N   ARG A 186 " --> pdb=" O   ARG A 183 " (cutoff:3.500A)
      removed outlier: 3.755A  pdb=" N   ALA A 187 " --> pdb=" O   ASN A 184 " (cutoff:3.500A)
      removed outlier: 3.858A  pdb=" N   ILE A 190 " --> pdb=" O   ALA A 187 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 192 through 197
      removed outlier: 3.502A  pdb=" N   ARG A 196 " --> pdb=" O   ARG A 192 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 197 through 237
      Proline residue:  A 212  - end of helix
      removed outlier: 4.618A  pdb=" N   ASN A 216 " --> pdb=" O   PRO A 212 " (cutoff:3.500A)
      removed outlier: 4.776A  pdb=" N   ALA A 217 " --> pdb=" O   GLY A 213 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 258 through 264
    Processing helix  chain 'A' and resid 282 through 289
    Processing helix  chain 'A' and resid 290 through 304
    Processing helix  chain 'A' and resid 311 through 319
      removed outlier: 3.848A  pdb=" N   ALA A 315 " --> pdb=" O   VAL A 311 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 323 through 337
    Processing helix  chain 'A' and resid 338 through 357
    Processing helix  chain 'B' and resid 72 through 81
      removed outlier: 3.932A  pdb=" N   VAL B  76 " --> pdb=" O   HIS B  72 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 82 through 107
    Processing helix  chain 'B' and resid 114 through 141
      removed outlier: 3.702A  pdb=" N   TRP B 118 " --> pdb=" O   TYR B 114 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 148 through 172
      removed outlier: 4.358A  pdb=" N   GLY B 172 " --> pdb=" O   GLU B 168 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 179 through 191
      removed outlier: 3.519A  pdb=" N   ILE B 182 " --> pdb=" O   MET B 179 " (cutoff:3.500A)
      removed outlier: 3.670A  pdb=" N   ASN B 184 " --> pdb=" O   LEU B 181 " (cutoff:3.500A)
      removed outlier: 4.224A  pdb=" N   ARG B 186 " --> pdb=" O   ARG B 183 " (cutoff:3.500A)
      removed outlier: 3.755A  pdb=" N   ALA B 187 " --> pdb=" O   ASN B 184 " (cutoff:3.500A)
      removed outlier: 3.857A  pdb=" N   ILE B 190 " --> pdb=" O   ALA B 187 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 192 through 197
      removed outlier: 3.502A  pdb=" N   ARG B 196 " --> pdb=" O   ARG B 192 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 197 through 237
      Proline residue:  B 212  - end of helix
      removed outlier: 4.617A  pdb=" N   ASN B 216 " --> pdb=" O   PRO B 212 " (cutoff:3.500A)
      removed outlier: 4.775A  pdb=" N   ALA B 217 " --> pdb=" O   GLY B 213 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 258 through 264
    Processing helix  chain 'B' and resid 282 through 289
    Processing helix  chain 'B' and resid 290 through 304
    Processing helix  chain 'B' and resid 311 through 319
      removed outlier: 3.848A  pdb=" N   ALA B 315 " --> pdb=" O   VAL B 311 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 323 through 338
    Processing helix  chain 'B' and resid 340 through 357
    Processing helix  chain 'C' and resid 72 through 81
      removed outlier: 3.932A  pdb=" N   VAL C  76 " --> pdb=" O   HIS C  72 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 82 through 107
    Processing helix  chain 'C' and resid 114 through 139
      removed outlier: 3.701A  pdb=" N   TRP C 118 " --> pdb=" O   TYR C 114 " (cutoff:3.500A)
      removed outlier: 3.727A  pdb=" N   GLY C 139 " --> pdb=" O   ILE C 135 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 148 through 172
      removed outlier: 4.357A  pdb=" N   GLY C 172 " --> pdb=" O   GLU C 168 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 179 through 191
      removed outlier: 3.519A  pdb=" N   ILE C 182 " --> pdb=" O   MET C 179 " (cutoff:3.500A)
      removed outlier: 3.671A  pdb=" N   ASN C 184 " --> pdb=" O   LEU C 181 " (cutoff:3.500A)
      removed outlier: 4.224A  pdb=" N   ARG C 186 " --> pdb=" O   ARG C 183 " (cutoff:3.500A)
      removed outlier: 3.755A  pdb=" N   ALA C 187 " --> pdb=" O   ASN C 184 " (cutoff:3.500A)
      removed outlier: 3.858A  pdb=" N   ILE C 190 " --> pdb=" O   ALA C 187 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 192 through 197
      removed outlier: 3.503A  pdb=" N   ARG C 196 " --> pdb=" O   ARG C 192 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 197 through 237
      Proline residue:  C 212  - end of helix
      removed outlier: 4.618A  pdb=" N   ASN C 216 " --> pdb=" O   PRO C 212 " (cutoff:3.500A)
      removed outlier: 4.775A  pdb=" N   ALA C 217 " --> pdb=" O   GLY C 213 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 258 through 264
    Processing helix  chain 'C' and resid 282 through 289
    Processing helix  chain 'C' and resid 290 through 304
    Processing helix  chain 'C' and resid 311 through 319
      removed outlier: 3.848A  pdb=" N   ALA C 315 " --> pdb=" O   VAL C 311 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 323 through 337
    Processing helix  chain 'C' and resid 338 through 357
    Processing helix  chain 'D' and resid 72 through 81
      removed outlier: 3.932A  pdb=" N   VAL D  76 " --> pdb=" O   HIS D  72 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 82 through 107
    Processing helix  chain 'D' and resid 114 through 139
      removed outlier: 3.701A  pdb=" N   TRP D 118 " --> pdb=" O   TYR D 114 " (cutoff:3.500A)
      removed outlier: 3.728A  pdb=" N   GLY D 139 " --> pdb=" O   ILE D 135 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 148 through 172
      removed outlier: 4.358A  pdb=" N   GLY D 172 " --> pdb=" O   GLU D 168 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 179 through 191
      removed outlier: 3.519A  pdb=" N   ILE D 182 " --> pdb=" O   MET D 179 " (cutoff:3.500A)
      removed outlier: 3.671A  pdb=" N   ASN D 184 " --> pdb=" O   LEU D 181 " (cutoff:3.500A)
      removed outlier: 4.224A  pdb=" N   ARG D 186 " --> pdb=" O   ARG D 183 " (cutoff:3.500A)
      removed outlier: 3.755A  pdb=" N   ALA D 187 " --> pdb=" O   ASN D 184 " (cutoff:3.500A)
      removed outlier: 3.857A  pdb=" N   ILE D 190 " --> pdb=" O   ALA D 187 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 192 through 197
      removed outlier: 3.503A  pdb=" N   ARG D 196 " --> pdb=" O   ARG D 192 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 197 through 237
      Proline residue:  D 212  - end of helix
      removed outlier: 4.618A  pdb=" N   ASN D 216 " --> pdb=" O   PRO D 212 " (cutoff:3.500A)
      removed outlier: 4.775A  pdb=" N   ALA D 217 " --> pdb=" O   GLY D 213 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 258 through 264
    Processing helix  chain 'D' and resid 282 through 289
    Processing helix  chain 'D' and resid 290 through 304
    Processing helix  chain 'D' and resid 311 through 319
      removed outlier: 3.848A  pdb=" N   ALA D 315 " --> pdb=" O   VAL D 311 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 323 through 337
    Processing helix  chain 'D' and resid 339 through 357
    Processing helix  chain 'E' and resid 3 through 21
    Processing sheet with id=AA1, first strand: chain 'A' and resid 244 through 248
    Processing sheet with id=AA2, first strand: chain 'B' and resid 244 through 248
    Processing sheet with id=AA3, first strand: chain 'C' and resid 244 through 248
    Processing sheet with id=AA4, first strand: chain 'D' and resid 244 through 248

    648 hydrogen bonds defined for protein.
    1884 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.53

  Time building geometry restraints manager: 3.09 seconds

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

  Histogram of bond lengths:
        1.18 -     1.30: 1487
        1.30 -     1.43: 2955
        1.43 -     1.56: 5706
        1.56 -     1.68: 10
        1.68 -     1.81: 84
  Bond restraints: 10242
  Sorted by residual:
  bond pdb=" C21 POV C 403 "
       pdb=" O21 POV C 403 "
    ideal  model  delta    sigma   weight residual
    1.330  1.455 -0.125 2.00e-02 2.50e+03 3.90e+01
  bond pdb=" C21 POV A 402 "
       pdb=" O21 POV A 402 "
    ideal  model  delta    sigma   weight residual
    1.330  1.454 -0.124 2.00e-02 2.50e+03 3.86e+01
  bond pdb=" C21 POV B 402 "
       pdb=" O21 POV B 402 "
    ideal  model  delta    sigma   weight residual
    1.330  1.454 -0.124 2.00e-02 2.50e+03 3.86e+01
  bond pdb=" C21 POV D1101 "
       pdb=" O21 POV D1101 "
    ideal  model  delta    sigma   weight residual
    1.330  1.453 -0.123 2.00e-02 2.50e+03 3.79e+01
  bond pdb=" C31 POV C 403 "
       pdb=" O31 POV C 403 "
    ideal  model  delta    sigma   weight residual
    1.327  1.450 -0.123 2.00e-02 2.50e+03 3.78e+01
  ... (remaining 10237 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.10: 13581
        3.10 -     6.21: 329
        6.21 -     9.31: 48
        9.31 -    12.41: 10
       12.41 -    15.52: 3
  Bond angle restraints: 13971
  Sorted by residual:
  angle pdb=" N   ILE B 339 "
        pdb=" CA  ILE B 339 "
        pdb=" C   ILE B 339 "
      ideal   model   delta    sigma   weight residual
     111.05  124.82  -13.77 1.25e+00 6.40e-01 1.21e+02
  angle pdb=" N   GLN B 338 "
        pdb=" CA  GLN B 338 "
        pdb=" C   GLN B 338 "
      ideal   model   delta    sigma   weight residual
     112.04  127.56  -15.52 1.44e+00 4.82e-01 1.16e+02
  angle pdb=" N   VAL B 340 "
        pdb=" CA  VAL B 340 "
        pdb=" C   VAL B 340 "
      ideal   model   delta    sigma   weight residual
     111.56  119.81   -8.25 8.60e-01 1.35e+00 9.21e+01
  angle pdb=" N   TYR B 138 "
        pdb=" CA  TYR B 138 "
        pdb=" C   TYR B 138 "
      ideal   model   delta    sigma   weight residual
     111.14  100.78   10.36 1.08e+00 8.57e-01 9.20e+01
  angle pdb=" C   GLN B 338 "
        pdb=" CA  GLN B 338 "
        pdb=" CB  GLN B 338 "
      ideal   model   delta    sigma   weight residual
     110.56   97.70   12.86 1.83e+00 2.99e-01 4.94e+01
  ... (remaining 13966 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    26.04: 5949
       26.04 -    52.08: 416
       52.08 -    78.12: 48
       78.12 -   104.15: 14
      104.15 -   130.19: 2
  Dihedral angle restraints: 6429
    sinusoidal: 2998
      harmonic: 3431
  Sorted by residual:
  dihedral pdb=" CA  GLU B 355 "
           pdb=" C   GLU B 355 "
           pdb=" N   GLU B 356 "
           pdb=" CA  GLU B 356 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  151.91   28.09     0      5.00e+00 4.00e-02 3.16e+01
  dihedral pdb=" CA  GLU A 355 "
           pdb=" C   GLU A 355 "
           pdb=" N   GLU A 356 "
           pdb=" CA  GLU A 356 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  151.97   28.03     0      5.00e+00 4.00e-02 3.14e+01
  dihedral pdb=" CA  GLU C 355 "
           pdb=" C   GLU C 355 "
           pdb=" N   GLU C 356 "
           pdb=" CA  GLU C 356 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  151.98   28.02     0      5.00e+00 4.00e-02 3.14e+01
  ... (remaining 6426 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.096: 1403
       0.096 -    0.193: 112
       0.193 -    0.289: 26
       0.289 -    0.385: 14
       0.385 -    0.482: 3
  Chirality restraints: 1558
  Sorted by residual:
  chirality pdb=" CA  GLU C 305 "
            pdb=" N   GLU C 305 "
            pdb=" C   GLU C 305 "
            pdb=" CB  GLU C 305 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.03    0.48 2.00e-01 2.50e+01 5.80e+00
  chirality pdb=" CA  ARG B 279 "
            pdb=" N   ARG B 279 "
            pdb=" C   ARG B 279 "
            pdb=" CB  ARG B 279 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.06    0.45 2.00e-01 2.50e+01 5.15e+00
  chirality pdb=" CA  CYS B 337 "
            pdb=" N   CYS B 337 "
            pdb=" C   CYS B 337 "
            pdb=" CB  CYS B 337 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.10    0.41 2.00e-01 2.50e+01 4.27e+00
  ... (remaining 1555 not shown)

  Planarity restraints: 1668
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLN B 338 "   -0.017 2.00e-02 2.50e+03   3.28e-02 1.08e+01
        pdb=" C   GLN B 338 "    0.057 2.00e-02 2.50e+03
        pdb=" O   GLN B 338 "   -0.021 2.00e-02 2.50e+03
        pdb=" N   ILE B 339 "   -0.019 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLN C 338 "    0.015 2.00e-02 2.50e+03   3.08e-02 9.46e+00
        pdb=" C   GLN C 338 "   -0.053 2.00e-02 2.50e+03
        pdb=" O   GLN C 338 "    0.020 2.00e-02 2.50e+03
        pdb=" N   ILE C 339 "    0.018 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLN A 338 "   -0.015 2.00e-02 2.50e+03   3.05e-02 9.32e+00
        pdb=" C   GLN A 338 "    0.053 2.00e-02 2.50e+03
        pdb=" O   GLN A 338 "   -0.020 2.00e-02 2.50e+03
        pdb=" N   ILE A 339 "   -0.018 2.00e-02 2.50e+03
  ... (remaining 1665 not shown)

  Histogram of nonbonded interaction distances:
        1.81 -     2.43: 41
        2.43 -     3.05: 6730
        3.05 -     3.66: 15075
        3.66 -     4.28: 24491
        4.28 -     4.90: 39081
  Nonbonded interactions: 85418
  Sorted by model distance:
  nonbonded pdb=" O   GLN D 338 "
            pdb=" CG2 ILE D 342 "
     model   vdw
     1.812 3.460
  nonbonded pdb=" O   GLN A 338 "
            pdb=" CG2 ILE A 342 "
     model   vdw
     1.964 3.460
  nonbonded pdb=" O   GLN C 338 "
            pdb=" CG2 ILE C 342 "
     model   vdw
     1.964 3.460
  nonbonded pdb=" NH2 ARG A 279 "
            pdb=" OE2 GLU A 286 "
     model   vdw
     1.992 3.120
  nonbonded pdb=" NE2 GLN B 300 "
            pdb=" OE1 GLU B 305 "
     model   vdw
     2.027 3.120
  ... (remaining 85413 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'A' and (resid 69 through 357 or resid 404))
  selection = (chain 'B' and (resid 69 through 174 or (resid 175 and (name N or name CA or nam \ 
e C or name O or name CB )) or resid 176 through 357 or resid 404))
  selection = (chain 'C' and (resid 69 through 173 or (resid 174 through 175 and (name N or na \ 
me CA or name C or name O or name CB )) or resid 176 through 357 or resid 404))
  selection = (chain 'D' and (resid 69 through 173 or (resid 174 through 175 and (name N or na \ 
me CA or name C or name O or name CB )) or resid 176 through 357 or resid 1104)) \ 

}

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=0.45 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.310
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.320
  Check model and map are aligned:         0.070
  Set scattering table:                    0.090
  Process input model:                     24.310
  Find NCS groups from input model:        0.470
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:11.370
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   37.990
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7257
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      :  0.009   0.125  10243  Z= 0.442
  Angle     :  1.115  15.518  13971  Z= 0.601
  Chirality :  0.070   0.482   1558
  Planarity :  0.005   0.033   1668
  Dihedral  : 16.629 130.192   4237
  Min Nonbonded Distance : 1.812

Molprobity Statistics.
  All-atom Clashscore : 21.63
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  4.55 %
    Favored  : 95.37 %
  Rotamer:
    Outliers :  0.40 %
    Allowed  : 15.16 %
    Favored  : 84.44 %
  Cbeta Deviations :  0.09 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.36 (0.22), residues: 1166
  helix: -1.38 (0.15), residues: 806
  sheet: -1.33 (0.61), residues: 48
  loop : -1.56 (0.38), residues: 312

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP A 106 
 HIS   0.004   0.001   HIS C 237 
 PHE   0.029   0.002   PHE C 144 
 TYR   0.025   0.003   TYR A 288 
 ARG   0.005   0.001   ARG E   9 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.13614 (  648)
  hydrogen bonds       : angle       7.08100 ( 1884)
  covalent geometry    : bond        0.00868 (10242)
  covalent geometry    : angle       1.11534 (13971)
  Misc. bond           : bond        0.00150 (    1)

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

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

  2332 Ramachandran restraints generated.
    1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2332 Ramachandran restraints generated.
    1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  184 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 180
  time to evaluate  : 1.066 
Fit side-chains
   revert: symmetry clash
REVERT: A  195 LYS cc_start: 0.6971 (ttpt) cc_final: 0.6631 (ttpt)
REVERT: B  247 THR cc_start: 0.8216 (m) cc_final: 0.7981 (p)
REVERT: B  349 LEU cc_start: 0.7889 (tp) cc_final: 0.7652 (tp)
REVERT: C  179 MET cc_start: 0.6358 (mmm) cc_final: 0.5684 (mpm)
REVERT: C  225 MET cc_start: 0.8036 (mtp) cc_final: 0.7829 (ttm)
REVERT: D  111 ASP cc_start: 0.7359 (m-30) cc_final: 0.6996 (m-30)
REVERT: D  189 ARG cc_start: 0.7735 (mtt180) cc_final: 0.7524 (mtp85)
REVERT: D  225 MET cc_start: 0.7746 (mtp) cc_final: 0.7537 (ttm)
REVERT: D  238 MET cc_start: 0.8607 (mmm) cc_final: 0.8298 (tpt)
REVERT: E   10 ARG cc_start: 0.6520 (OUTLIER) cc_final: 0.5511 (ttm170)
  outliers start: 4
  outliers final: 3
  residues processed: 183
  average time/residue: 1.0865
  time to fit residues: 215.2849
Evaluate side-chains
  127 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 123
  time to evaluate  : 0.989 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  342 ILE
Chi-restraints excluded: chain C residue  161 ILE
Chi-restraints excluded: chain D residue  342 ILE
Chi-restraints excluded: chain E residue   10 ARG
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 96 optimal weight:    0.1980
   chunk 86 optimal weight:    0.9980
   chunk 47 optimal weight:    3.9990
   chunk 29 optimal weight:    2.9990
   chunk 58 optimal weight:    0.5980
   chunk 46 optimal weight:    0.3980
   chunk 89 optimal weight:    2.9990
   chunk 34 optimal weight:    0.7980
   chunk 54 optimal weight:    0.7980
   chunk 66 optimal weight:    8.9990
   chunk 103 optimal weight:    3.9990
   overall best weight:    0.5580

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

Flipped N/Q/H residues before XYZ refinement:
A  96 ASN
A 343 ASN
B  96 ASN
D  96 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4243 r_free = 0.4243 target = 0.196760 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3875 r_free = 0.3875 target = 0.155597 restraints weight = 9504.346|
|-----------------------------------------------------------------------------|
r_work (start): 0.3829 rms_B_bonded: 1.34
r_work: 0.3647 rms_B_bonded: 2.33 restraints_weight: 0.5000
r_work: 0.3554 rms_B_bonded: 3.69 restraints_weight: 0.2500
r_work (final): 0.3554
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3553
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3553 r_free = 0.3553    target_work(ls_wunit_k1) = 0.132         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3552 r_free = 0.3552    target_work(ls_wunit_k1) = 0.132         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
r_final: 0.3552
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7577
moved from start:          0.1617

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.065  10243  Z= 0.154
  Angle     :  0.635   8.718  13971  Z= 0.323
  Chirality :  0.043   0.332   1558
  Planarity :  0.004   0.034   1668
  Dihedral  : 10.927  88.857   2172
  Min Nonbonded Distance : 2.307

Molprobity Statistics.
  All-atom Clashscore : 7.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.77 %
    Favored  : 96.23 %
  Rotamer:
    Outliers :  2.61 %
    Allowed  : 17.77 %
    Favored  : 79.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.22 (0.25), residues: 1166
  helix:  0.11 (0.18), residues: 802
  sheet: -0.48 (0.68), residues: 48
  loop : -0.37 (0.42), residues: 316

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP C 307 
 HIS   0.003   0.001   HIS C 237 
 PHE   0.025   0.002   PHE D 144 
 TYR   0.013   0.002   TYR C 114 
 ARG   0.006   0.001   ARG C 119 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04657 (  648)
  hydrogen bonds       : angle       5.62673 ( 1884)
  covalent geometry    : bond        0.00330 (10242)
  covalent geometry    : angle       0.63523 (13971)
  Misc. bond           : bond        0.00363 (    1)

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

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

  2332 Ramachandran restraints generated.
    1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2332 Ramachandran restraints generated.
    1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  172 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 146
  time to evaluate  : 0.950 
Fit side-chains
REVERT: A  132 GLU cc_start: 0.6487 (OUTLIER) cc_final: 0.5816 (pp20)
REVERT: A  195 LYS cc_start: 0.7202 (ttpt) cc_final: 0.6920 (ttpt)
REVERT: B  119 ARG cc_start: 0.6928 (mtm110) cc_final: 0.6645 (ttp80)
REVERT: B  195 LYS cc_start: 0.7265 (ttpt) cc_final: 0.7031 (ttpt)
REVERT: B  353 MET cc_start: 0.7382 (mtp) cc_final: 0.6865 (mtp)
REVERT: C  123 PHE cc_start: 0.7357 (t80) cc_final: 0.7049 (t80)
REVERT: C  179 MET cc_start: 0.6700 (mmm) cc_final: 0.5706 (mpm)
REVERT: C  195 LYS cc_start: 0.7497 (ttpt) cc_final: 0.7128 (ttpt)
REVERT: C  353 MET cc_start: 0.7300 (mtp) cc_final: 0.6754 (mtp)
REVERT: D  111 ASP cc_start: 0.8154 (m-30) cc_final: 0.7698 (m-30)
REVERT: D  119 ARG cc_start: 0.6894 (mtm110) cc_final: 0.6687 (ttp80)
REVERT: D  189 ARG cc_start: 0.8060 (mtt180) cc_final: 0.7665 (mtp180)
REVERT: D  238 MET cc_start: 0.8427 (mmm) cc_final: 0.8193 (tpt)
REVERT: D  286 GLU cc_start: 0.8444 (OUTLIER) cc_final: 0.6840 (tp30)
REVERT: D  353 MET cc_start: 0.7214 (mtp) cc_final: 0.6727 (mtp)
REVERT: E   10 ARG cc_start: 0.6739 (OUTLIER) cc_final: 0.5914 (ttm170)
REVERT: E   13 ARG cc_start: 0.5856 (OUTLIER) cc_final: 0.5321 (mpt-90)
  outliers start: 26
  outliers final: 10
  residues processed: 157
  average time/residue: 1.1416
  time to fit residues: 192.9817
Evaluate side-chains
  147 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 133
  time to evaluate  : 1.005 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  132 GLU
Chi-restraints excluded: chain A residue  182 ILE
Chi-restraints excluded: chain A residue  247 THR
Chi-restraints excluded: chain A residue  342 ILE
Chi-restraints excluded: chain B residue  114 TYR
Chi-restraints excluded: chain B residue  342 ILE
Chi-restraints excluded: chain C residue  114 TYR
Chi-restraints excluded: chain C residue  247 THR
Chi-restraints excluded: chain C residue  342 ILE
Chi-restraints excluded: chain D residue  114 TYR
Chi-restraints excluded: chain D residue  247 THR
Chi-restraints excluded: chain D residue  286 GLU
Chi-restraints excluded: chain E residue   10 ARG
Chi-restraints excluded: chain E residue   13 ARG
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 56 optimal weight:    7.9990
   chunk 19 optimal weight:    3.9990
   chunk 35 optimal weight:    0.7980
   chunk 76 optimal weight:    0.0770
   chunk 95 optimal weight:    0.0570
   chunk 71 optimal weight:    1.9990
   chunk 87 optimal weight:    0.5980
   chunk 21 optimal weight:    0.7980
   chunk 67 optimal weight:    0.2980
   chunk 17 optimal weight:    1.9990
   chunk 104 optimal weight:    0.7980
   overall best weight:    0.3656

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

Flipped N/Q/H residues before XYZ refinement:
A  96 ASN
A 136 ASN
B 136 ASN
B 152 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4262 r_free = 0.4262 target = 0.198280 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3910 r_free = 0.3910 target = 0.158512 restraints weight = 9674.164|
|-----------------------------------------------------------------------------|
r_work (start): 0.3863 rms_B_bonded: 1.34
r_work: 0.3667 rms_B_bonded: 2.37 restraints_weight: 0.5000
r_work: 0.3571 rms_B_bonded: 3.81 restraints_weight: 0.2500
r_work (final): 0.3571
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3576
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3576 r_free = 0.3576    target_work(ls_wunit_k1) = 0.133         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3576 r_free = 0.3576    target_work(ls_wunit_k1) = 0.133         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
r_final: 0.3576
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7543
moved from start:          0.2119

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  10243  Z= 0.126
  Angle     :  0.562   7.831  13971  Z= 0.289
  Chirality :  0.041   0.237   1558
  Planarity :  0.003   0.026   1668
  Dihedral  :  9.667  82.259   2168
  Min Nonbonded Distance : 2.413

Molprobity Statistics.
  All-atom Clashscore : 7.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.00 %
    Favored  : 97.00 %
  Rotamer:
    Outliers :  3.61 %
    Allowed  : 18.37 %
    Favored  : 78.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.35 (0.25), residues: 1166
  helix:  0.63 (0.18), residues: 810
  sheet:  0.00 (0.77), residues: 48
  loop : -0.51 (0.42), residues: 308

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP D 307 
 HIS   0.003   0.001   HIS D 237 
 PHE   0.020   0.001   PHE D 144 
 TYR   0.017   0.002   TYR D 109 
 ARG   0.006   0.000   ARG C 119 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04167 (  648)
  hydrogen bonds       : angle       5.36574 ( 1884)
  covalent geometry    : bond        0.00262 (10242)
  covalent geometry    : angle       0.56245 (13971)
  Misc. bond           : bond        0.00133 (    1)

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

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

  2332 Ramachandran restraints generated.
    1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2332 Ramachandran restraints generated.
    1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  185 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 149
  time to evaluate  : 1.013 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  195 LYS cc_start: 0.7225 (ttpt) cc_final: 0.6916 (ttpt)
REVERT: A  242 ASP cc_start: 0.7857 (t0) cc_final: 0.7646 (t0)
REVERT: A  353 MET cc_start: 0.7188 (mtp) cc_final: 0.6679 (mtp)
REVERT: B  189 ARG cc_start: 0.8095 (mtt180) cc_final: 0.7555 (mtp85)
REVERT: B  195 LYS cc_start: 0.7206 (ttpt) cc_final: 0.6971 (ttpt)
REVERT: B  353 MET cc_start: 0.7336 (mtp) cc_final: 0.6875 (mtp)
REVERT: C  123 PHE cc_start: 0.7348 (t80) cc_final: 0.7105 (t80)
REVERT: C  179 MET cc_start: 0.6654 (mmm) cc_final: 0.5783 (mpm)
REVERT: C  195 LYS cc_start: 0.7471 (ttpt) cc_final: 0.7092 (ttpt)
REVERT: C  242 ASP cc_start: 0.7784 (t0) cc_final: 0.7568 (t0)
REVERT: C  353 MET cc_start: 0.7529 (mtp) cc_final: 0.7080 (mtp)
REVERT: D  111 ASP cc_start: 0.8184 (m-30) cc_final: 0.7824 (m-30)
REVERT: D  189 ARG cc_start: 0.8035 (mtt180) cc_final: 0.7637 (mtp180)
REVERT: D  353 MET cc_start: 0.7395 (mtp) cc_final: 0.6929 (mtp)
  outliers start: 36
  outliers final: 12
  residues processed: 169
  average time/residue: 1.1321
  time to fit residues: 206.0748
Evaluate side-chains
  148 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 136
  time to evaluate  : 1.063 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  114 TYR
Chi-restraints excluded: chain A residue  186 ARG
Chi-restraints excluded: chain A residue  247 THR
Chi-restraints excluded: chain A residue  342 ILE
Chi-restraints excluded: chain B residue  114 TYR
Chi-restraints excluded: chain B residue  186 ARG
Chi-restraints excluded: chain B residue  342 ILE
Chi-restraints excluded: chain C residue  114 TYR
Chi-restraints excluded: chain C residue  186 ARG
Chi-restraints excluded: chain C residue  247 THR
Chi-restraints excluded: chain C residue  342 ILE
Chi-restraints excluded: chain D residue  247 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 13 optimal weight:    0.0870
   chunk 54 optimal weight:    3.9990
   chunk 16 optimal weight:    0.6980
   chunk 107 optimal weight:    0.0870
   chunk 35 optimal weight:    3.9990
   chunk 73 optimal weight:    2.9990
   chunk 66 optimal weight:    0.4980
   chunk 59 optimal weight:    2.9990
   chunk 75 optimal weight:    3.9990
   chunk 6 optimal weight:    2.9990
   chunk 57 optimal weight:    3.9990
   overall best weight:    0.8738

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

Flipped N/Q/H residues before XYZ refinement:
A 136 ASN
C 343 ASN
D 152 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4224 r_free = 0.4224 target = 0.194363 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3866 r_free = 0.3866 target = 0.154813 restraints weight = 9528.791|
|-----------------------------------------------------------------------------|
r_work (start): 0.3829 rms_B_bonded: 1.40
r_work: 0.3626 rms_B_bonded: 2.28 restraints_weight: 0.5000
r_work: 0.3529 rms_B_bonded: 3.63 restraints_weight: 0.2500
r_work (final): 0.3529
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3537
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3537 r_free = 0.3537    target_work(ls_wunit_k1) = 0.130         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3537 r_free = 0.3537    target_work(ls_wunit_k1) = 0.130         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
r_final: 0.3537
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7599
moved from start:          0.2296

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034  10243  Z= 0.167
  Angle     :  0.605   8.596  13971  Z= 0.310
  Chirality :  0.043   0.237   1558
  Planarity :  0.004   0.027   1668
  Dihedral  :  9.492  80.245   2164
  Min Nonbonded Distance : 2.444

Molprobity Statistics.
  All-atom Clashscore : 8.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.83 %
    Favored  : 97.17 %
  Rotamer:
    Outliers :  3.61 %
    Allowed  : 18.47 %
    Favored  : 77.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.69 (0.25), residues: 1166
  helix:  0.90 (0.18), residues: 810
  sheet:  0.15 (0.82), residues: 48
  loop : -0.46 (0.40), residues: 308

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP D 307 
 HIS   0.003   0.001   HIS E   6 
 PHE   0.020   0.002   PHE A 144 
 TYR   0.020   0.002   TYR A 109 
 ARG   0.006   0.001   ARG C 119 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04487 (  648)
  hydrogen bonds       : angle       5.43292 ( 1884)
  covalent geometry    : bond        0.00374 (10242)
  covalent geometry    : angle       0.60459 (13971)
  Misc. bond           : bond        0.00147 (    1)

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

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

  2332 Ramachandran restraints generated.
    1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2332 Ramachandran restraints generated.
    1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  179 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 143
  time to evaluate  : 1.014 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  132 GLU cc_start: 0.5914 (OUTLIER) cc_final: 0.5676 (pt0)
REVERT: A  353 MET cc_start: 0.7192 (mtp) cc_final: 0.6705 (mtp)
REVERT: B  111 ASP cc_start: 0.8123 (m-30) cc_final: 0.7911 (m-30)
REVERT: B  166 MET cc_start: 0.7154 (OUTLIER) cc_final: 0.6908 (mtp)
REVERT: B  189 ARG cc_start: 0.8074 (mtt180) cc_final: 0.7614 (mtp85)
REVERT: B  353 MET cc_start: 0.7468 (mtp) cc_final: 0.6996 (mtp)
REVERT: C  195 LYS cc_start: 0.7450 (ttpt) cc_final: 0.7060 (ttpt)
REVERT: C  353 MET cc_start: 0.7712 (mtp) cc_final: 0.7248 (mtp)
REVERT: D  119 ARG cc_start: 0.6980 (mtm110) cc_final: 0.6706 (ttp80)
REVERT: D  189 ARG cc_start: 0.8143 (mtt180) cc_final: 0.7657 (mtp85)
REVERT: D  191 PHE cc_start: 0.8569 (m-10) cc_final: 0.8344 (m-10)
REVERT: D  353 MET cc_start: 0.7540 (mtp) cc_final: 0.6948 (mtp)
REVERT: E   10 ARG cc_start: 0.6807 (OUTLIER) cc_final: 0.5930 (ttm170)
REVERT: E   13 ARG cc_start: 0.5908 (OUTLIER) cc_final: 0.5488 (mpt-90)
  outliers start: 36
  outliers final: 12
  residues processed: 165
  average time/residue: 1.1037
  time to fit residues: 196.3656
Evaluate side-chains
  145 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 129
  time to evaluate  : 0.921 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  114 TYR
Chi-restraints excluded: chain A residue  132 GLU
Chi-restraints excluded: chain A residue  182 ILE
Chi-restraints excluded: chain A residue  247 THR
Chi-restraints excluded: chain A residue  273 VAL
Chi-restraints excluded: chain B residue  114 TYR
Chi-restraints excluded: chain B residue  166 MET
Chi-restraints excluded: chain B residue  186 ARG
Chi-restraints excluded: chain B residue  247 THR
Chi-restraints excluded: chain B residue  342 ILE
Chi-restraints excluded: chain C residue  186 ARG
Chi-restraints excluded: chain C residue  247 THR
Chi-restraints excluded: chain D residue  114 TYR
Chi-restraints excluded: chain D residue  247 THR
Chi-restraints excluded: chain E residue   10 ARG
Chi-restraints excluded: chain E residue   13 ARG
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 77 optimal weight:    0.7980
   chunk 29 optimal weight:    2.9990
   chunk 3 optimal weight:    2.9990
   chunk 74 optimal weight:    0.8980
   chunk 91 optimal weight:    0.0060
   chunk 96 optimal weight:    2.9990
   chunk 27 optimal weight:    0.7980
   chunk 22 optimal weight:    0.9990
   chunk 65 optimal weight:    4.9990
   chunk 111 optimal weight:    0.8980
   chunk 98 optimal weight:    1.9990
   overall best weight:    0.6796

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

Flipped N/Q/H residues before XYZ refinement:
A 152 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4234 r_free = 0.4234 target = 0.195439 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3877 r_free = 0.3877 target = 0.155735 restraints weight = 9589.668|
|-----------------------------------------------------------------------------|
r_work (start): 0.3836 rms_B_bonded: 1.33
r_work: 0.3638 rms_B_bonded: 2.30 restraints_weight: 0.5000
r_work: 0.3542 rms_B_bonded: 3.65 restraints_weight: 0.2500
r_work (final): 0.3542
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3550
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3550 r_free = 0.3550    target_work(ls_wunit_k1) = 0.131         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3550 r_free = 0.3550    target_work(ls_wunit_k1) = 0.131         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
r_final: 0.3550
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7585
moved from start:          0.2516

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031  10243  Z= 0.144
  Angle     :  0.571   8.353  13971  Z= 0.296
  Chirality :  0.041   0.219   1558
  Planarity :  0.004   0.032   1668
  Dihedral  :  9.282  77.324   2162
  Min Nonbonded Distance : 2.447

Molprobity Statistics.
  All-atom Clashscore : 7.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.26 %
    Favored  : 96.74 %
  Rotamer:
    Outliers :  2.91 %
    Allowed  : 18.67 %
    Favored  : 78.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.89 (0.25), residues: 1166
  helix:  1.04 (0.18), residues: 810
  sheet:  0.12 (0.82), residues: 48
  loop : -0.32 (0.41), residues: 308

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP D 307 
 HIS   0.002   0.001   HIS E   6 
 PHE   0.020   0.001   PHE A 144 
 TYR   0.023   0.002   TYR A 109 
 ARG   0.006   0.001   ARG C 119 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04259 (  648)
  hydrogen bonds       : angle       5.32729 ( 1884)
  covalent geometry    : bond        0.00316 (10242)
  covalent geometry    : angle       0.57087 (13971)
  Misc. bond           : bond        0.00045 (    1)

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

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

  2332 Ramachandran restraints generated.
    1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2332 Ramachandran restraints generated.
    1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  157 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 128
  time to evaluate  : 1.085 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  109 TYR cc_start: 0.6914 (m-80) cc_final: 0.6675 (m-80)
REVERT: A  195 LYS cc_start: 0.7154 (ttpt) cc_final: 0.6869 (ttpt)
REVERT: A  353 MET cc_start: 0.7324 (mtp) cc_final: 0.6834 (mtp)
REVERT: B  189 ARG cc_start: 0.8112 (mtt180) cc_final: 0.7656 (mtp85)
REVERT: B  195 LYS cc_start: 0.7194 (ttpt) cc_final: 0.6961 (ttpt)
REVERT: B  353 MET cc_start: 0.7420 (mtp) cc_final: 0.7032 (mtp)
REVERT: C  195 LYS cc_start: 0.7418 (ttpt) cc_final: 0.7039 (ttpt)
REVERT: C  221 MET cc_start: 0.7470 (OUTLIER) cc_final: 0.6715 (mtp)
REVERT: C  353 MET cc_start: 0.7637 (mtp) cc_final: 0.7168 (mtp)
REVERT: D  189 ARG cc_start: 0.8125 (mtt180) cc_final: 0.7651 (mtp85)
REVERT: D  353 MET cc_start: 0.7493 (mtp) cc_final: 0.6898 (mtp)
  outliers start: 29
  outliers final: 17
  residues processed: 147
  average time/residue: 1.1028
  time to fit residues: 175.5758
Evaluate side-chains
  141 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 123
  time to evaluate  : 0.948 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  114 TYR
Chi-restraints excluded: chain A residue  247 THR
Chi-restraints excluded: chain A residue  267 CYS
Chi-restraints excluded: chain A residue  273 VAL
Chi-restraints excluded: chain A residue  342 ILE
Chi-restraints excluded: chain B residue  114 TYR
Chi-restraints excluded: chain B residue  186 ARG
Chi-restraints excluded: chain B residue  250 ASP
Chi-restraints excluded: chain B residue  267 CYS
Chi-restraints excluded: chain B residue  342 ILE
Chi-restraints excluded: chain C residue  114 TYR
Chi-restraints excluded: chain C residue  186 ARG
Chi-restraints excluded: chain C residue  221 MET
Chi-restraints excluded: chain C residue  247 THR
Chi-restraints excluded: chain C residue  267 CYS
Chi-restraints excluded: chain D residue  114 TYR
Chi-restraints excluded: chain D residue  247 THR
Chi-restraints excluded: chain D residue  267 CYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 83 optimal weight:    0.8980
   chunk 60 optimal weight:    0.8980
   chunk 74 optimal weight:    1.9990
   chunk 69 optimal weight:    1.9990
   chunk 109 optimal weight:    1.9990
   chunk 49 optimal weight:    0.8980
   chunk 100 optimal weight:    0.5980
   chunk 0 optimal weight:    6.9990
   chunk 23 optimal weight:    0.9990
   chunk 31 optimal weight:    3.9990
   chunk 87 optimal weight:    1.9990
   overall best weight:    0.8582

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

Flipped N/Q/H residues before XYZ refinement:
A  73 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4225 r_free = 0.4225 target = 0.194337 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3867 r_free = 0.3867 target = 0.155080 restraints weight = 9595.221|
|-----------------------------------------------------------------------------|
r_work (start): 0.3830 rms_B_bonded: 1.29
r_work: 0.3629 rms_B_bonded: 2.25 restraints_weight: 0.5000
r_work: 0.3534 rms_B_bonded: 3.55 restraints_weight: 0.2500
r_work (final): 0.3534
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3544
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3544 r_free = 0.3544    target_work(ls_wunit_k1) = 0.131         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3544 r_free = 0.3544    target_work(ls_wunit_k1) = 0.131         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
r_final: 0.3544
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7601
moved from start:          0.2625

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034  10243  Z= 0.161
  Angle     :  0.581   7.962  13971  Z= 0.301
  Chirality :  0.042   0.220   1558
  Planarity :  0.004   0.038   1668
  Dihedral  :  9.265  76.251   2162
  Min Nonbonded Distance : 2.513

Molprobity Statistics.
  All-atom Clashscore : 7.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.00 %
    Favored  : 97.00 %
  Rotamer:
    Outliers :  3.41 %
    Allowed  : 18.07 %
    Favored  : 78.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.87 (0.25), residues: 1166
  helix:  1.02 (0.18), residues: 822
  sheet:  0.08 (0.81), residues: 48
  loop : -0.37 (0.41), residues: 296

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP D 307 
 HIS   0.002   0.001   HIS B 237 
 PHE   0.019   0.002   PHE C 144 
 TYR   0.023   0.002   TYR D 109 
 ARG   0.006   0.001   ARG E   9 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04379 (  648)
  hydrogen bonds       : angle       5.36438 ( 1884)
  covalent geometry    : bond        0.00363 (10242)
  covalent geometry    : angle       0.58148 (13971)
  Misc. bond           : bond        0.00118 (    1)

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

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

  2332 Ramachandran restraints generated.
    1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2332 Ramachandran restraints generated.
    1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  164 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 130
  time to evaluate  : 1.073 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  195 LYS cc_start: 0.7143 (ttpt) cc_final: 0.6859 (ttpt)
REVERT: A  242 ASP cc_start: 0.7631 (t0) cc_final: 0.7398 (t0)
REVERT: A  353 MET cc_start: 0.7365 (mtp) cc_final: 0.6855 (mtp)
REVERT: B  109 TYR cc_start: 0.6912 (m-80) cc_final: 0.6683 (m-80)
REVERT: B  166 MET cc_start: 0.7093 (OUTLIER) cc_final: 0.6789 (mtp)
REVERT: B  189 ARG cc_start: 0.8159 (mtt180) cc_final: 0.7699 (mtp85)
REVERT: B  195 LYS cc_start: 0.7177 (ttpt) cc_final: 0.6961 (ttpt)
REVERT: B  353 MET cc_start: 0.7412 (mtp) cc_final: 0.6968 (mtp)
REVERT: C  195 LYS cc_start: 0.7398 (ttpt) cc_final: 0.7017 (ttpt)
REVERT: C  221 MET cc_start: 0.7513 (OUTLIER) cc_final: 0.6722 (mtp)
REVERT: C  242 ASP cc_start: 0.7670 (t0) cc_final: 0.7442 (t0)
REVERT: C  353 MET cc_start: 0.7614 (mtp) cc_final: 0.7150 (mtp)
REVERT: D  119 ARG cc_start: 0.7003 (mtm110) cc_final: 0.6724 (ttp80)
REVERT: D  189 ARG cc_start: 0.8163 (mtt180) cc_final: 0.7677 (mtp85)
REVERT: D  191 PHE cc_start: 0.8571 (m-10) cc_final: 0.8322 (m-10)
REVERT: D  221 MET cc_start: 0.7435 (OUTLIER) cc_final: 0.6652 (mtp)
REVERT: D  353 MET cc_start: 0.7517 (mtp) cc_final: 0.6948 (mtp)
  outliers start: 34
  outliers final: 15
  residues processed: 150
  average time/residue: 1.0611
  time to fit residues: 173.4008
Evaluate side-chains
  144 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 126
  time to evaluate  : 0.987 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  114 TYR
Chi-restraints excluded: chain A residue  247 THR
Chi-restraints excluded: chain A residue  267 CYS
Chi-restraints excluded: chain A residue  273 VAL
Chi-restraints excluded: chain A residue  342 ILE
Chi-restraints excluded: chain B residue  114 TYR
Chi-restraints excluded: chain B residue  166 MET
Chi-restraints excluded: chain B residue  186 ARG
Chi-restraints excluded: chain B residue  247 THR
Chi-restraints excluded: chain B residue  267 CYS
Chi-restraints excluded: chain B residue  342 ILE
Chi-restraints excluded: chain C residue  221 MET
Chi-restraints excluded: chain C residue  247 THR
Chi-restraints excluded: chain C residue  267 CYS
Chi-restraints excluded: chain D residue  114 TYR
Chi-restraints excluded: chain D residue  221 MET
Chi-restraints excluded: chain D residue  247 THR
Chi-restraints excluded: chain D residue  267 CYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 102 optimal weight:    1.9990
   chunk 55 optimal weight:    0.5980
   chunk 73 optimal weight:    1.9990
   chunk 113 optimal weight:    2.9990
   chunk 48 optimal weight:    1.9990
   chunk 23 optimal weight:    0.6980
   chunk 107 optimal weight:    0.9990
   chunk 42 optimal weight:    0.9990
   chunk 7 optimal weight:    1.9990
   chunk 103 optimal weight:    5.9990
   chunk 95 optimal weight:    2.9990
   overall best weight:    1.0586

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4171 r_free = 0.4171 target = 0.190839 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3818 r_free = 0.3818 target = 0.152013 restraints weight = 9796.279|
|-----------------------------------------------------------------------------|
r_work (start): 0.3775 rms_B_bonded: 1.67
r_work: 0.3517 rms_B_bonded: 2.74 restraints_weight: 0.5000
r_work: 0.3416 rms_B_bonded: 4.35 restraints_weight: 0.2500
r_work (final): 0.3416
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3429
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3429 r_free = 0.3429    target_work(ls_wunit_k1) = 0.122         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3429 r_free = 0.3429    target_work(ls_wunit_k1) = 0.122         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
r_final: 0.3429
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7647
moved from start:          0.2707

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036  10243  Z= 0.183
  Angle     :  0.605   8.796  13971  Z= 0.314
  Chirality :  0.043   0.223   1558
  Planarity :  0.004   0.040   1668
  Dihedral  :  9.344  76.754   2162
  Min Nonbonded Distance : 2.519

Molprobity Statistics.
  All-atom Clashscore : 7.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.43 %
    Favored  : 96.57 %
  Rotamer:
    Outliers :  2.81 %
    Allowed  : 18.17 %
    Favored  : 79.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.78 (0.25), residues: 1166
  helix:  0.95 (0.17), residues: 822
  sheet:  0.07 (0.80), residues: 48
  loop : -0.39 (0.40), residues: 296

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 120 
 HIS   0.003   0.001   HIS B 237 
 PHE   0.019   0.002   PHE A 144 
 TYR   0.030   0.002   TYR A 109 
 ARG   0.007   0.001   ARG C 119 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04599 (  648)
  hydrogen bonds       : angle       5.42381 ( 1884)
  covalent geometry    : bond        0.00415 (10242)
  covalent geometry    : angle       0.60493 (13971)
  Misc. bond           : bond        0.00040 (    1)

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

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

  2332 Ramachandran restraints generated.
    1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2332 Ramachandran restraints generated.
    1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  159 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 131
  time to evaluate  : 0.939 
Fit side-chains
   revert: symmetry clash
REVERT: A  152 ASN cc_start: 0.8066 (m110) cc_final: 0.7774 (m110)
REVERT: A  195 LYS cc_start: 0.7192 (ttpt) cc_final: 0.6889 (ttpt)
REVERT: A  242 ASP cc_start: 0.7830 (t0) cc_final: 0.7599 (t0)
REVERT: A  353 MET cc_start: 0.7520 (mtp) cc_final: 0.7014 (mtp)
REVERT: B  161 ILE cc_start: 0.7755 (mm) cc_final: 0.7521 (mp)
REVERT: B  166 MET cc_start: 0.7161 (OUTLIER) cc_final: 0.6720 (mtp)
REVERT: B  175 MET cc_start: 0.5563 (tpt) cc_final: 0.4997 (tpp)
REVERT: B  189 ARG cc_start: 0.8207 (mtt180) cc_final: 0.7734 (mtp85)
REVERT: B  242 ASP cc_start: 0.7816 (t0) cc_final: 0.7580 (t0)
REVERT: B  353 MET cc_start: 0.7574 (mtp) cc_final: 0.7212 (mtp)
REVERT: C  195 LYS cc_start: 0.7410 (ttpt) cc_final: 0.7010 (ttpt)
REVERT: C  221 MET cc_start: 0.7599 (OUTLIER) cc_final: 0.6780 (mtp)
REVERT: C  242 ASP cc_start: 0.7853 (t0) cc_final: 0.7604 (t0)
REVERT: C  353 MET cc_start: 0.7710 (mtp) cc_final: 0.7251 (mtp)
REVERT: D  189 ARG cc_start: 0.8233 (mtt180) cc_final: 0.7738 (mtp85)
REVERT: D  191 PHE cc_start: 0.8605 (m-10) cc_final: 0.8370 (m-10)
REVERT: D  221 MET cc_start: 0.7494 (OUTLIER) cc_final: 0.6685 (mtp)
REVERT: D  353 MET cc_start: 0.7585 (mtp) cc_final: 0.7074 (mtp)
  outliers start: 28
  outliers final: 13
  residues processed: 146
  average time/residue: 0.9702
  time to fit residues: 154.3942
Evaluate side-chains
  144 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 128
  time to evaluate  : 1.180 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  114 TYR
Chi-restraints excluded: chain A residue  267 CYS
Chi-restraints excluded: chain A residue  273 VAL
Chi-restraints excluded: chain A residue  342 ILE
Chi-restraints excluded: chain B residue  114 TYR
Chi-restraints excluded: chain B residue  166 MET
Chi-restraints excluded: chain B residue  186 ARG
Chi-restraints excluded: chain B residue  247 THR
Chi-restraints excluded: chain B residue  267 CYS
Chi-restraints excluded: chain B residue  342 ILE
Chi-restraints excluded: chain C residue  221 MET
Chi-restraints excluded: chain C residue  247 THR
Chi-restraints excluded: chain C residue  267 CYS
Chi-restraints excluded: chain D residue  114 TYR
Chi-restraints excluded: chain D residue  221 MET
Chi-restraints excluded: chain D residue  267 CYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 109 optimal weight:    1.9990
   chunk 7 optimal weight:    2.9990
   chunk 5 optimal weight:    0.9990
   chunk 96 optimal weight:    1.9990
   chunk 50 optimal weight:    0.5980
   chunk 105 optimal weight:    0.5980
   chunk 90 optimal weight:    1.9990
   chunk 89 optimal weight:    0.7980
   chunk 44 optimal weight:    0.3980
   chunk 76 optimal weight:    0.7980
   chunk 52 optimal weight:    0.6980
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
A 136 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4186 r_free = 0.4186 target = 0.192576 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3837 r_free = 0.3837 target = 0.153993 restraints weight = 9777.556|
|-----------------------------------------------------------------------------|
r_work (start): 0.3801 rms_B_bonded: 1.67
r_work: 0.3570 rms_B_bonded: 2.48 restraints_weight: 0.5000
r_work: 0.3468 rms_B_bonded: 3.99 restraints_weight: 0.2500
r_work (final): 0.3468
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3479
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3479 r_free = 0.3479    target_work(ls_wunit_k1) = 0.126         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3479 r_free = 0.3479    target_work(ls_wunit_k1) = 0.126         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
r_final: 0.3479
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7576
moved from start:          0.2847

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030  10243  Z= 0.139
  Angle     :  0.559   8.501  13971  Z= 0.289
  Chirality :  0.041   0.204   1558
  Planarity :  0.004   0.041   1668
  Dihedral  :  9.119  74.777   2162
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 7.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.92 %
    Favored  : 97.08 %
  Rotamer:
    Outliers :  2.31 %
    Allowed  : 18.98 %
    Favored  : 78.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.33 (0.25), residues: 1166
  helix:  1.23 (0.18), residues: 802
  sheet:  0.02 (0.79), residues: 48
  loop :  0.37 (0.42), residues: 316

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP D 307 
 HIS   0.002   0.001   HIS B 237 
 PHE   0.018   0.001   PHE A 144 
 TYR   0.028   0.002   TYR D 109 
 ARG   0.007   0.001   ARG D 119 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04229 (  648)
  hydrogen bonds       : angle       5.30118 ( 1884)
  covalent geometry    : bond        0.00303 (10242)
  covalent geometry    : angle       0.55899 (13971)
  Misc. bond           : bond        0.00040 (    1)

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

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

  2332 Ramachandran restraints generated.
    1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2332 Ramachandran restraints generated.
    1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  151 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 128
  time to evaluate  : 0.983 
Fit side-chains
   revert: symmetry clash
REVERT: A  195 LYS cc_start: 0.7052 (ttpt) cc_final: 0.6759 (ttpt)
REVERT: A  353 MET cc_start: 0.7431 (mtp) cc_final: 0.6882 (mtp)
REVERT: B  119 ARG cc_start: 0.6849 (mtm110) cc_final: 0.6547 (ttp80)
REVERT: B  166 MET cc_start: 0.6938 (OUTLIER) cc_final: 0.6645 (mtp)
REVERT: B  179 MET cc_start: 0.6087 (mmt) cc_final: 0.5676 (tpp)
REVERT: B  189 ARG cc_start: 0.8134 (mtt180) cc_final: 0.7631 (mtp85)
REVERT: B  195 LYS cc_start: 0.7149 (ttpt) cc_final: 0.6783 (ttpt)
REVERT: B  242 ASP cc_start: 0.7825 (t0) cc_final: 0.7620 (t0)
REVERT: B  353 MET cc_start: 0.7505 (mtp) cc_final: 0.7159 (mtp)
REVERT: C  119 ARG cc_start: 0.7222 (ttm-80) cc_final: 0.6861 (ttp80)
REVERT: C  164 LEU cc_start: 0.8042 (mt) cc_final: 0.7495 (tt)
REVERT: C  195 LYS cc_start: 0.7238 (ttpt) cc_final: 0.6852 (ttpt)
REVERT: C  221 MET cc_start: 0.7559 (OUTLIER) cc_final: 0.6754 (mtp)
REVERT: C  353 MET cc_start: 0.7646 (mtp) cc_final: 0.7155 (mtp)
REVERT: D  119 ARG cc_start: 0.6926 (mtm110) cc_final: 0.6635 (ttp80)
REVERT: D  189 ARG cc_start: 0.8103 (mtt180) cc_final: 0.7563 (mtp85)
REVERT: D  353 MET cc_start: 0.7494 (mtp) cc_final: 0.6868 (mtp)
  outliers start: 23
  outliers final: 13
  residues processed: 144
  average time/residue: 0.9901
  time to fit residues: 155.4923
Evaluate side-chains
  142 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 127
  time to evaluate  : 0.990 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  114 TYR
Chi-restraints excluded: chain A residue  247 THR
Chi-restraints excluded: chain A residue  267 CYS
Chi-restraints excluded: chain A residue  273 VAL
Chi-restraints excluded: chain B residue  114 TYR
Chi-restraints excluded: chain B residue  166 MET
Chi-restraints excluded: chain B residue  186 ARG
Chi-restraints excluded: chain B residue  267 CYS
Chi-restraints excluded: chain B residue  342 ILE
Chi-restraints excluded: chain C residue  221 MET
Chi-restraints excluded: chain C residue  247 THR
Chi-restraints excluded: chain C residue  267 CYS
Chi-restraints excluded: chain D residue  114 TYR
Chi-restraints excluded: chain D residue  247 THR
Chi-restraints excluded: chain D residue  267 CYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 14 optimal weight:    0.8980
   chunk 28 optimal weight:    6.9990
   chunk 26 optimal weight:    3.9990
   chunk 83 optimal weight:    0.9980
   chunk 24 optimal weight:    0.9980
   chunk 40 optimal weight:    1.9990
   chunk 74 optimal weight:    0.9990
   chunk 49 optimal weight:    0.9990
   chunk 25 optimal weight:    0.7980
   chunk 58 optimal weight:    0.9990
   chunk 96 optimal weight:    2.9990
   overall best weight:    0.9382

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

Flipped N/Q/H residues before XYZ refinement:
A 136 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4173 r_free = 0.4173 target = 0.191213 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3819 r_free = 0.3819 target = 0.152228 restraints weight = 9740.809|
|-----------------------------------------------------------------------------|
r_work (start): 0.3785 rms_B_bonded: 1.65
r_work: 0.3551 rms_B_bonded: 2.52 restraints_weight: 0.5000
r_work: 0.3450 rms_B_bonded: 4.03 restraints_weight: 0.2500
r_work (final): 0.3450
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3456
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3456 r_free = 0.3456    target_work(ls_wunit_k1) = 0.125         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3456 r_free = 0.3456    target_work(ls_wunit_k1) = 0.125         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
r_final: 0.3456
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7619
moved from start:          0.2888

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035  10243  Z= 0.172
  Angle     :  0.608   8.319  13971  Z= 0.316
  Chirality :  0.043   0.210   1558
  Planarity :  0.004   0.043   1668
  Dihedral  :  9.168  74.984   2162
  Min Nonbonded Distance : 2.412

Molprobity Statistics.
  All-atom Clashscore : 7.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.60 %
    Favored  : 96.40 %
  Rotamer:
    Outliers :  2.11 %
    Allowed  : 19.38 %
    Favored  : 78.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.96 (0.25), residues: 1166
  helix:  1.09 (0.17), residues: 822
  sheet: -0.17 (0.80), residues: 48
  loop : -0.29 (0.41), residues: 296

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 120 
 HIS   0.002   0.001   HIS B 237 
 PHE   0.019   0.002   PHE A 144 
 TYR   0.032   0.002   TYR B 109 
 ARG   0.007   0.001   ARG C 119 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04470 (  648)
  hydrogen bonds       : angle       5.38947 ( 1884)
  covalent geometry    : bond        0.00390 (10242)
  covalent geometry    : angle       0.60826 (13971)
  Misc. bond           : bond        0.00049 (    1)

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

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

  2332 Ramachandran restraints generated.
    1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2332 Ramachandran restraints generated.
    1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  146 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 125
  time to evaluate  : 1.069 
Fit side-chains
   revert: symmetry clash
REVERT: A  152 ASN cc_start: 0.8049 (m110) cc_final: 0.7679 (m110)
REVERT: A  195 LYS cc_start: 0.7092 (ttpt) cc_final: 0.6803 (ttpt)
REVERT: A  353 MET cc_start: 0.7498 (mtp) cc_final: 0.6964 (mtp)
REVERT: B  166 MET cc_start: 0.7043 (OUTLIER) cc_final: 0.6677 (mtp)
REVERT: B  175 MET cc_start: 0.5462 (tpt) cc_final: 0.4758 (tpp)
REVERT: B  179 MET cc_start: 0.6028 (mmt) cc_final: 0.5496 (tpp)
REVERT: B  189 ARG cc_start: 0.8191 (mtt180) cc_final: 0.7706 (mtp85)
REVERT: B  195 LYS cc_start: 0.7171 (ttpt) cc_final: 0.6791 (ttpt)
REVERT: B  353 MET cc_start: 0.7557 (mtp) cc_final: 0.7159 (mtp)
REVERT: C  161 ILE cc_start: 0.7552 (mm) cc_final: 0.7349 (mp)
REVERT: C  179 MET cc_start: 0.5960 (mmt) cc_final: 0.5517 (tpp)
REVERT: C  195 LYS cc_start: 0.7296 (ttpt) cc_final: 0.6921 (ttpt)
REVERT: C  221 MET cc_start: 0.7585 (OUTLIER) cc_final: 0.6751 (mtp)
REVERT: C  353 MET cc_start: 0.7670 (mtp) cc_final: 0.7178 (mtp)
REVERT: D  119 ARG cc_start: 0.7007 (mtm110) cc_final: 0.6681 (ttp80)
REVERT: D  189 ARG cc_start: 0.8191 (mtt180) cc_final: 0.7674 (mtp85)
REVERT: D  191 PHE cc_start: 0.8599 (m-10) cc_final: 0.8390 (m-10)
REVERT: D  221 MET cc_start: 0.7448 (OUTLIER) cc_final: 0.6621 (mtp)
REVERT: D  353 MET cc_start: 0.7553 (mtp) cc_final: 0.7005 (mtp)
  outliers start: 21
  outliers final: 11
  residues processed: 137
  average time/residue: 1.0451
  time to fit residues: 155.5443
Evaluate side-chains
  138 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 124
  time to evaluate  : 1.038 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  114 TYR
Chi-restraints excluded: chain A residue  267 CYS
Chi-restraints excluded: chain A residue  273 VAL
Chi-restraints excluded: chain B residue  114 TYR
Chi-restraints excluded: chain B residue  166 MET
Chi-restraints excluded: chain B residue  186 ARG
Chi-restraints excluded: chain B residue  267 CYS
Chi-restraints excluded: chain B residue  342 ILE
Chi-restraints excluded: chain C residue  221 MET
Chi-restraints excluded: chain C residue  247 THR
Chi-restraints excluded: chain C residue  267 CYS
Chi-restraints excluded: chain D residue  114 TYR
Chi-restraints excluded: chain D residue  221 MET
Chi-restraints excluded: chain D residue  267 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 24 optimal weight:    1.9990
   chunk 76 optimal weight:    2.9990
   chunk 74 optimal weight:    0.6980
   chunk 86 optimal weight:    0.6980
   chunk 95 optimal weight:    5.9990
   chunk 61 optimal weight:    0.8980
   chunk 42 optimal weight:    0.9990
   chunk 85 optimal weight:    0.9980
   chunk 84 optimal weight:    3.9990
   chunk 0 optimal weight:    6.9990
   chunk 54 optimal weight:    1.9990
   overall best weight:    0.8582

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

Flipped N/Q/H residues before XYZ refinement:
A 136 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4116 r_free = 0.4116 target = 0.186755 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3744 r_free = 0.3744 target = 0.146323 restraints weight = 9875.512|
|-----------------------------------------------------------------------------|
r_work (start): 0.3719 rms_B_bonded: 1.89
r_work: 0.3480 rms_B_bonded: 2.50 restraints_weight: 0.5000
r_work: 0.3369 rms_B_bonded: 4.05 restraints_weight: 0.2500
r_work (final): 0.3369
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3378
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3378 r_free = 0.3378    target_work(ls_wunit_k1) = 0.120         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3378 r_free = 0.3378    target_work(ls_wunit_k1) = 0.120         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
r_final: 0.3378
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7544
moved from start:          0.2937

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034  10243  Z= 0.163
  Angle     :  0.596   8.335  13971  Z= 0.310
  Chirality :  0.042   0.208   1558
  Planarity :  0.004   0.043   1668
  Dihedral  :  9.127  75.092   2162
  Min Nonbonded Distance : 2.426

Molprobity Statistics.
  All-atom Clashscore : 7.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.17 %
    Favored  : 96.83 %
  Rotamer:
    Outliers :  1.41 %
    Allowed  : 19.98 %
    Favored  : 78.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.99 (0.25), residues: 1166
  helix:  1.09 (0.17), residues: 822
  sheet: -0.09 (0.79), residues: 48
  loop : -0.22 (0.41), residues: 296

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 120 
 HIS   0.002   0.001   HIS B 237 
 PHE   0.019   0.002   PHE A 144 
 TYR   0.029   0.002   TYR B 109 
 ARG   0.007   0.001   ARG C 119 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04403 (  648)
  hydrogen bonds       : angle       5.37239 ( 1884)
  covalent geometry    : bond        0.00366 (10242)
  covalent geometry    : angle       0.59557 (13971)
  Misc. bond           : bond        0.00043 (    1)

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

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

  2332 Ramachandran restraints generated.
    1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2332 Ramachandran restraints generated.
    1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  143 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 129
  time to evaluate  : 1.000 
Fit side-chains
   revert: symmetry clash
REVERT: A  152 ASN cc_start: 0.7913 (m110) cc_final: 0.7539 (m110)
REVERT: A  195 LYS cc_start: 0.6859 (ttpt) cc_final: 0.6534 (ttpt)
REVERT: A  353 MET cc_start: 0.7352 (mtp) cc_final: 0.6767 (mtp)
REVERT: B  119 ARG cc_start: 0.6836 (mtm110) cc_final: 0.6488 (ttp80)
REVERT: B  166 MET cc_start: 0.6879 (OUTLIER) cc_final: 0.6557 (mtp)
REVERT: B  175 MET cc_start: 0.5669 (tpt) cc_final: 0.5011 (tpp)
REVERT: B  179 MET cc_start: 0.5893 (mmt) cc_final: 0.5378 (tpp)
REVERT: B  189 ARG cc_start: 0.8132 (mtt180) cc_final: 0.7606 (mtp85)
REVERT: B  195 LYS cc_start: 0.7016 (ttpt) cc_final: 0.6608 (ttpt)
REVERT: B  353 MET cc_start: 0.7398 (mtp) cc_final: 0.6919 (mtp)
REVERT: C  119 ARG cc_start: 0.7211 (ttm-80) cc_final: 0.6790 (ttp80)
REVERT: C  179 MET cc_start: 0.5940 (mmt) cc_final: 0.5599 (tpp)
REVERT: C  195 LYS cc_start: 0.7105 (ttpt) cc_final: 0.6688 (ttpt)
REVERT: C  221 MET cc_start: 0.7514 (OUTLIER) cc_final: 0.6629 (mtp)
REVERT: C  353 MET cc_start: 0.7521 (mtp) cc_final: 0.6991 (mtp)
REVERT: D  119 ARG cc_start: 0.6872 (mtm110) cc_final: 0.6528 (ttp80)
REVERT: D  189 ARG cc_start: 0.8093 (mtt180) cc_final: 0.7524 (mtp85)
REVERT: D  191 PHE cc_start: 0.8594 (m-10) cc_final: 0.8390 (m-10)
REVERT: D  221 MET cc_start: 0.7427 (OUTLIER) cc_final: 0.6637 (mtp)
REVERT: D  353 MET cc_start: 0.7398 (mtp) cc_final: 0.6758 (mtp)
  outliers start: 14
  outliers final: 11
  residues processed: 136
  average time/residue: 1.0276
  time to fit residues: 152.0846
Evaluate side-chains
  142 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 128
  time to evaluate  : 1.143 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  114 TYR
Chi-restraints excluded: chain A residue  267 CYS
Chi-restraints excluded: chain A residue  273 VAL
Chi-restraints excluded: chain B residue  114 TYR
Chi-restraints excluded: chain B residue  166 MET
Chi-restraints excluded: chain B residue  186 ARG
Chi-restraints excluded: chain B residue  267 CYS
Chi-restraints excluded: chain B residue  342 ILE
Chi-restraints excluded: chain C residue  221 MET
Chi-restraints excluded: chain C residue  247 THR
Chi-restraints excluded: chain C residue  267 CYS
Chi-restraints excluded: chain D residue  114 TYR
Chi-restraints excluded: chain D residue  221 MET
Chi-restraints excluded: chain D residue  267 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 20 optimal weight:    0.9980
   chunk 1 optimal weight:    3.9990
   chunk 99 optimal weight:    0.6980
   chunk 71 optimal weight:    0.5980
   chunk 4 optimal weight:    1.9990
   chunk 68 optimal weight:    0.8980
   chunk 23 optimal weight:    0.0980
   chunk 28 optimal weight:    6.9990
   chunk 38 optimal weight:    8.9990
   chunk 45 optimal weight:    1.9990
   chunk 25 optimal weight:    0.7980
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
A 136 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4188 r_free = 0.4188 target = 0.192871 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3842 r_free = 0.3842 target = 0.154113 restraints weight = 9760.785|
|-----------------------------------------------------------------------------|
r_work (start): 0.3803 rms_B_bonded: 1.67
r_work: 0.3550 rms_B_bonded: 2.74 restraints_weight: 0.5000
r_work: 0.3445 rms_B_bonded: 4.42 restraints_weight: 0.2500
r_work (final): 0.3445
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3443
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3443 r_free = 0.3443    target_work(ls_wunit_k1) = 0.123         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3443 r_free = 0.3443    target_work(ls_wunit_k1) = 0.123         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
r_final: 0.3443
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7604
moved from start:          0.3038

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030  10243  Z= 0.142
  Angle     :  0.579   8.305  13971  Z= 0.302
  Chirality :  0.041   0.194   1558
  Planarity :  0.004   0.044   1668
  Dihedral  :  8.940  73.453   2162
  Min Nonbonded Distance : 2.429

Molprobity Statistics.
  All-atom Clashscore : 7.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.43 %
    Favored  : 96.57 %
  Rotamer:
    Outliers :  2.01 %
    Allowed  : 19.58 %
    Favored  : 78.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.38 (0.25), residues: 1166
  helix:  1.26 (0.18), residues: 802
  sheet: -0.10 (0.80), residues: 48
  loop :  0.46 (0.42), residues: 316

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP A 120 
 HIS   0.002   0.001   HIS B 237 
 PHE   0.018   0.001   PHE A 144 
 TYR   0.026   0.002   TYR B 109 
 ARG   0.007   0.001   ARG C 119 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04174 (  648)
  hydrogen bonds       : angle       5.30082 ( 1884)
  covalent geometry    : bond        0.00309 (10242)
  covalent geometry    : angle       0.57935 (13971)
  Misc. bond           : bond        0.00031 (    1)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 7906.11 seconds
wall clock time: 136 minutes 39.77 seconds (8199.77 seconds total)