Starting phenix.real_space_refine
on Fri Mar 14 07:26:47 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7wut_32841/03_2025/7wut_32841.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7wut_32841/03_2025/7wut_32841.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.5
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7wut_32841/03_2025/7wut_32841.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7wut_32841/03_2025/7wut_32841.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7wut_32841/03_2025/7wut_32841.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7wut_32841/03_2025/7wut_32841.cif"
  }
  resolution = 3.5
  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
-------------------------------------------------------------------------------
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=  -0.000 sd=   1.000
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 128 atoms to isotropic.
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: 4
    Type Number    sf(0)   Gaussians
     S      76      5.16       5
     C    6100      2.51       5
     N    1728      2.21       5
     O    1828      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 32 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 9732
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 2433
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 316, 2433
          Classifications: {'peptide': 316}
          Incomplete info: {'truncation_to_alanine': 22}
          Link IDs: {'CIS': 15, 'PCIS': 2, 'PTRANS': 14, 'TRANS': 284}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 107
          Unresolved non-hydrogen angles: 142
          Unresolved non-hydrogen dihedrals: 98
          Unresolved non-hydrogen chiralities: 6
          Planarities with less than four sites: {'GLN:plan1': 3, 'TYR:plan': 2, 'ASN:plan1': 1, 'TRP:plan': 2, 'ASP:plan': 1, 'PHE:plan': 3, 'GLU:plan': 2}
          Unresolved non-hydrogen planarities: 76
    Chain: "B"
      Number of atoms: 2433
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 316, 2433
          Classifications: {'peptide': 316}
          Incomplete info: {'truncation_to_alanine': 22}
          Link IDs: {'CIS': 15, 'PCIS': 2, 'PTRANS': 14, 'TRANS': 284}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 107
          Unresolved non-hydrogen angles: 142
          Unresolved non-hydrogen dihedrals: 98
          Unresolved non-hydrogen chiralities: 6
          Planarities with less than four sites: {'GLN:plan1': 3, 'TYR:plan': 2, 'ASN:plan1': 1, 'TRP:plan': 2, 'ASP:plan': 1, 'PHE:plan': 3, 'GLU:plan': 2}
          Unresolved non-hydrogen planarities: 76
    Chain: "C"
      Number of atoms: 2433
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 316, 2433
          Classifications: {'peptide': 316}
          Incomplete info: {'truncation_to_alanine': 22}
          Link IDs: {'CIS': 15, 'PCIS': 2, 'PTRANS': 14, 'TRANS': 284}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 107
          Unresolved non-hydrogen angles: 142
          Unresolved non-hydrogen dihedrals: 98
          Unresolved non-hydrogen chiralities: 6
          Planarities with less than four sites: {'GLN:plan1': 3, 'TYR:plan': 2, 'ASN:plan1': 1, 'TRP:plan': 2, 'ASP:plan': 1, 'PHE:plan': 3, 'GLU:plan': 2}
          Unresolved non-hydrogen planarities: 76
    Chain: "D"
      Number of atoms: 2433
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 316, 2433
          Classifications: {'peptide': 316}
          Incomplete info: {'truncation_to_alanine': 22}
          Link IDs: {'CIS': 15, 'PCIS': 2, 'PTRANS': 14, 'TRANS': 284}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 107
          Unresolved non-hydrogen angles: 142
          Unresolved non-hydrogen dihedrals: 98
          Unresolved non-hydrogen chiralities: 6
          Planarities with less than four sites: {'GLN:plan1': 3, 'TYR:plan': 2, 'ASN:plan1': 1, 'TRP:plan': 2, 'ASP:plan': 1, 'PHE:plan': 3, 'GLU:plan': 2}
          Unresolved non-hydrogen planarities: 76
  Time building chain proxies: 5.41, per 1000 atoms: 0.56
  Number of scatterers: 9732
  At special positions: 0
  Unit cell: (114.84, 85.8, 85.8, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      76     16.00
     O    1828      8.00
     N    1728      7.00
     C    6100      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=20, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  55 " - pdb=" SG  CYS A 143 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 179 " - pdb=" SG  CYS A 223 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 280 " - pdb=" SG  CYS A 329 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 291 " - pdb=" SG  CYS A 312 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 313 " - pdb=" SG  CYS A 316 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  55 " - pdb=" SG  CYS B 143 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 179 " - pdb=" SG  CYS B 223 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 280 " - pdb=" SG  CYS B 329 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 291 " - pdb=" SG  CYS B 312 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 313 " - pdb=" SG  CYS B 316 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C  55 " - pdb=" SG  CYS C 143 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 179 " - pdb=" SG  CYS C 223 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 280 " - pdb=" SG  CYS C 329 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 291 " - pdb=" SG  CYS C 312 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 313 " - pdb=" SG  CYS C 316 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D  55 " - pdb=" SG  CYS D 143 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D 179 " - pdb=" SG  CYS D 223 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D 280 " - pdb=" SG  CYS D 329 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D 291 " - pdb=" SG  CYS D 312 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D 313 " - pdb=" SG  CYS D 316 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.27
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  2496 Ramachandran restraints generated.
    1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2344

  Finding SS restraints...
    Secondary structure from input PDB file:
      28 helices and 14 sheets defined
      17.4% alpha, 11.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.04
  Creating SS restraints...
    Processing helix  chain 'A' and resid 38 through 51
      removed outlier: 4.326A  pdb=" N   LEU A  42 " --> pdb=" O   SER A  38 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 61 through 78
      Proline residue:  A  73  - end of helix
    Processing helix  chain 'A' and resid 79 through 83
    Processing helix  chain 'A' and resid 144 through 146
      No H-bonds generated for 'chain 'A' and resid 144 through 146'
    Processing helix  chain 'A' and resid 226 through 230
    Processing helix  chain 'A' and resid 244 through 248
    Processing helix  chain 'A' and resid 252 through 256
    Processing helix  chain 'B' and resid 38 through 51
      removed outlier: 4.313A  pdb=" N   LEU B  42 " --> pdb=" O   SER B  38 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 61 through 79
      Proline residue:  B  73  - end of helix
      removed outlier: 3.596A  pdb=" N   LEU B  79 " --> pdb=" O   LEU B  75 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 80 through 83
    Processing helix  chain 'B' and resid 144 through 146
      No H-bonds generated for 'chain 'B' and resid 144 through 146'
    Processing helix  chain 'B' and resid 226 through 230
    Processing helix  chain 'B' and resid 244 through 248
    Processing helix  chain 'B' and resid 252 through 256
    Processing helix  chain 'C' and resid 38 through 51
      removed outlier: 4.290A  pdb=" N   LEU C  42 " --> pdb=" O   SER C  38 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 61 through 79
      Proline residue:  C  73  - end of helix
      removed outlier: 3.587A  pdb=" N   LEU C  79 " --> pdb=" O   LEU C  75 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 80 through 83
    Processing helix  chain 'C' and resid 144 through 146
      No H-bonds generated for 'chain 'C' and resid 144 through 146'
    Processing helix  chain 'C' and resid 226 through 230
    Processing helix  chain 'C' and resid 244 through 248
    Processing helix  chain 'C' and resid 252 through 256
    Processing helix  chain 'D' and resid 38 through 51
      removed outlier: 4.288A  pdb=" N   LEU D  42 " --> pdb=" O   SER D  38 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 61 through 79
      Proline residue:  D  73  - end of helix
      removed outlier: 3.588A  pdb=" N   LEU D  79 " --> pdb=" O   LEU D  75 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 80 through 83
    Processing helix  chain 'D' and resid 144 through 146
      No H-bonds generated for 'chain 'D' and resid 144 through 146'
    Processing helix  chain 'D' and resid 226 through 230
    Processing helix  chain 'D' and resid 244 through 248
    Processing helix  chain 'D' and resid 252 through 256
    Processing sheet with id=AA1, first strand: chain 'A' and resid 56 through 57
      removed outlier: 6.812A  pdb=" N   GLY A  56 " --> pdb=" O   ALA A 149 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'A' and resid 153 through 154
    Processing sheet with id=AA3, first strand: chain 'A' and resid 329 through 331
      removed outlier: 4.041A  pdb=" N   ASP A 276 " --> pdb=" O   ARG A 322 " (cutoff:3.500A)
      removed outlier: 3.555A  pdb=" N   ARG A 324 " --> pdb=" O   GLU A 274 " (cutoff:3.500A)
      removed outlier: 4.065A  pdb=" N   PHE A 277 " --> pdb=" O   GLU A 213 " (cutoff:3.500A)
      removed outlier: 8.978A  pdb=" N   GLU A 213 " --> pdb=" O   PHE A 277 " (cutoff:3.500A)
      removed outlier: 5.288A  pdb=" N   ILE A 212 " --> pdb=" O   ALA A 205 " (cutoff:3.500A)
      removed outlier: 5.688A  pdb=" N   ALA A 205 " --> pdb=" O   ILE A 212 " (cutoff:3.500A)
      removed outlier: 3.567A  pdb=" N   SER A 216 " --> pdb=" O   TRP A 201 " (cutoff:3.500A)
      removed outlier: 3.890A  pdb=" N   ARG A 192 " --> pdb=" O   LYS A 189 " (cutoff:3.500A)
      removed outlier: 3.890A  pdb=" N   ARG C 192 " --> pdb=" O   LYS C 189 " (cutoff:3.500A)
      removed outlier: 3.564A  pdb=" N   SER C 216 " --> pdb=" O   TRP C 201 " (cutoff:3.500A)
      removed outlier: 5.682A  pdb=" N   ALA C 205 " --> pdb=" O   ILE C 212 " (cutoff:3.500A)
      removed outlier: 5.276A  pdb=" N   ILE C 212 " --> pdb=" O   ALA C 205 " (cutoff:3.500A)
      removed outlier: 8.979A  pdb=" N   GLU C 213 " --> pdb=" O   PHE C 277 " (cutoff:3.500A)
      removed outlier: 4.065A  pdb=" N   PHE C 277 " --> pdb=" O   GLU C 213 " (cutoff:3.500A)
      removed outlier: 3.550A  pdb=" N   ARG C 324 " --> pdb=" O   GLU C 274 " (cutoff:3.500A)
      removed outlier: 4.046A  pdb=" N   ASP C 276 " --> pdb=" O   ARG C 322 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 286 through 287
      removed outlier: 6.973A  pdb=" N   VAL A 286 " --> pdb=" O   CYS A 313 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 56 through 57
      removed outlier: 6.775A  pdb=" N   GLY B  56 " --> pdb=" O   ALA B 149 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA5
    Processing sheet with id=AA6, first strand: chain 'B' and resid 153 through 154
    Processing sheet with id=AA7, first strand: chain 'B' and resid 329 through 331
      removed outlier: 4.046A  pdb=" N   ASP B 276 " --> pdb=" O   ARG B 322 " (cutoff:3.500A)
      removed outlier: 3.557A  pdb=" N   ARG B 324 " --> pdb=" O   GLU B 274 " (cutoff:3.500A)
      removed outlier: 4.060A  pdb=" N   PHE B 277 " --> pdb=" O   GLU B 213 " (cutoff:3.500A)
      removed outlier: 8.975A  pdb=" N   GLU B 213 " --> pdb=" O   PHE B 277 " (cutoff:3.500A)
      removed outlier: 5.284A  pdb=" N   ILE B 212 " --> pdb=" O   ALA B 205 " (cutoff:3.500A)
      removed outlier: 5.675A  pdb=" N   ALA B 205 " --> pdb=" O   ILE B 212 " (cutoff:3.500A)
      removed outlier: 3.560A  pdb=" N   SER B 216 " --> pdb=" O   TRP B 201 " (cutoff:3.500A)
      removed outlier: 3.889A  pdb=" N   ARG B 192 " --> pdb=" O   LYS B 189 " (cutoff:3.500A)
      removed outlier: 3.889A  pdb=" N   ARG D 192 " --> pdb=" O   LYS D 189 " (cutoff:3.500A)
      removed outlier: 3.564A  pdb=" N   SER D 216 " --> pdb=" O   TRP D 201 " (cutoff:3.500A)
      removed outlier: 5.694A  pdb=" N   ALA D 205 " --> pdb=" O   ILE D 212 " (cutoff:3.500A)
      removed outlier: 5.272A  pdb=" N   ILE D 212 " --> pdb=" O   ALA D 205 " (cutoff:3.500A)
      removed outlier: 8.975A  pdb=" N   GLU D 213 " --> pdb=" O   PHE D 277 " (cutoff:3.500A)
      removed outlier: 4.063A  pdb=" N   PHE D 277 " --> pdb=" O   GLU D 213 " (cutoff:3.500A)
      removed outlier: 3.554A  pdb=" N   ARG D 324 " --> pdb=" O   GLU D 274 " (cutoff:3.500A)
      removed outlier: 4.045A  pdb=" N   ASP D 276 " --> pdb=" O   ARG D 322 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 286 through 287
      removed outlier: 6.972A  pdb=" N   VAL B 286 " --> pdb=" O   CYS B 313 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'C' and resid 56 through 57
      removed outlier: 6.765A  pdb=" N   GLY C  56 " --> pdb=" O   ALA C 149 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA9
    Processing sheet with id=AB1, first strand: chain 'C' and resid 153 through 154
    Processing sheet with id=AB2, first strand: chain 'C' and resid 286 through 287
      removed outlier: 6.984A  pdb=" N   VAL C 286 " --> pdb=" O   CYS C 313 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'D' and resid 56 through 57
      removed outlier: 6.770A  pdb=" N   GLY D  56 " --> pdb=" O   ALA D 149 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB3
    Processing sheet with id=AB4, first strand: chain 'D' and resid 153 through 154
    Processing sheet with id=AB5, first strand: chain 'D' and resid 286 through 287
      removed outlier: 6.977A  pdb=" N   VAL D 286 " --> pdb=" O   CYS D 313 " (cutoff:3.500A)

    213 hydrogen bonds defined for protein.
    492 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: 2.23

  Time building geometry restraints manager: 2.71 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 3226
        1.34 -     1.46: 2163
        1.46 -     1.58: 4467
        1.58 -     1.69: 0
        1.69 -     1.81: 108
  Bond restraints: 9964
  Sorted by residual:
  bond pdb=" N   GLN C  31 "
       pdb=" CA  GLN C  31 "
    ideal  model  delta    sigma   weight residual
    1.458  1.486 -0.028 1.90e-02 2.77e+03 2.11e+00
  bond pdb=" N   GLN B  31 "
       pdb=" CA  GLN B  31 "
    ideal  model  delta    sigma   weight residual
    1.458  1.485 -0.027 1.90e-02 2.77e+03 2.08e+00
  bond pdb=" N   GLN D  31 "
       pdb=" CA  GLN D  31 "
    ideal  model  delta    sigma   weight residual
    1.458  1.485 -0.027 1.90e-02 2.77e+03 2.06e+00
  bond pdb=" N   GLN A  31 "
       pdb=" CA  GLN A  31 "
    ideal  model  delta    sigma   weight residual
    1.458  1.485 -0.027 1.90e-02 2.77e+03 2.05e+00
  bond pdb=" N   GLU A 156 "
       pdb=" CA  GLU A 156 "
    ideal  model  delta    sigma   weight residual
    1.458  1.485 -0.027 1.90e-02 2.77e+03 1.99e+00
  ... (remaining 9959 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.10: 13158
        2.10 -     4.21: 274
        4.21 -     6.31: 48
        6.31 -     8.41: 17
        8.41 -    10.52: 23
  Bond angle restraints: 13520
  Sorted by residual:
  angle pdb=" C   VAL B 155 "
        pdb=" N   GLU B 156 "
        pdb=" CA  GLU B 156 "
      ideal   model   delta    sigma   weight residual
     121.70  131.51   -9.81 1.80e+00 3.09e-01 2.97e+01
  angle pdb=" C   VAL D 155 "
        pdb=" N   GLU D 156 "
        pdb=" CA  GLU D 156 "
      ideal   model   delta    sigma   weight residual
     121.70  131.50   -9.80 1.80e+00 3.09e-01 2.97e+01
  angle pdb=" C   VAL C 155 "
        pdb=" N   GLU C 156 "
        pdb=" CA  GLU C 156 "
      ideal   model   delta    sigma   weight residual
     121.70  131.48   -9.78 1.80e+00 3.09e-01 2.95e+01
  angle pdb=" C   GLU A  30 "
        pdb=" N   GLN A  31 "
        pdb=" CA  GLN A  31 "
      ideal   model   delta    sigma   weight residual
     121.70  131.45   -9.75 1.80e+00 3.09e-01 2.94e+01
  angle pdb=" C   GLU C  30 "
        pdb=" N   GLN C  31 "
        pdb=" CA  GLN C  31 "
      ideal   model   delta    sigma   weight residual
     121.70  131.44   -9.74 1.80e+00 3.09e-01 2.93e+01
  ... (remaining 13515 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.62: 5050
       15.62 -    31.23: 678
       31.23 -    46.85: 199
       46.85 -    62.47: 73
       62.47 -    78.08: 16
  Dihedral angle restraints: 6016
    sinusoidal: 2392
      harmonic: 3624
  Sorted by residual:
  dihedral pdb=" CB  CYS D 313 "
           pdb=" SG  CYS D 313 "
           pdb=" SG  CYS D 316 "
           pdb=" CB  CYS D 316 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   38.82   54.18     1      1.00e+01 1.00e-02 3.98e+01
  dihedral pdb=" CB  CYS B 313 "
           pdb=" SG  CYS B 313 "
           pdb=" SG  CYS B 316 "
           pdb=" CB  CYS B 316 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   38.89   54.11     1      1.00e+01 1.00e-02 3.97e+01
  dihedral pdb=" CB  CYS A 313 "
           pdb=" SG  CYS A 313 "
           pdb=" SG  CYS A 316 "
           pdb=" CB  CYS A 316 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   39.05   53.95     1      1.00e+01 1.00e-02 3.95e+01
  ... (remaining 6013 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.035: 959
       0.035 -    0.070: 339
       0.070 -    0.105: 119
       0.105 -    0.141: 54
       0.141 -    0.176: 9
  Chirality restraints: 1480
  Sorted by residual:
  chirality pdb=" CA  THR C  72 "
            pdb=" N   THR C  72 "
            pdb=" C   THR C  72 "
            pdb=" CB  THR C  72 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.35    0.18 2.00e-01 2.50e+01 7.72e-01
  chirality pdb=" CA  THR B  72 "
            pdb=" N   THR B  72 "
            pdb=" C   THR B  72 "
            pdb=" CB  THR B  72 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.36    0.17 2.00e-01 2.50e+01 6.97e-01
  chirality pdb=" CA  THR D  72 "
            pdb=" N   THR D  72 "
            pdb=" C   THR D  72 "
            pdb=" CB  THR D  72 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.36    0.17 2.00e-01 2.50e+01 6.88e-01
  ... (remaining 1477 not shown)

  Planarity restraints: 1740
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR D  72 "   -0.024 5.00e-02 4.00e+02   3.63e-02 2.11e+00
        pdb=" N   PRO D  73 "    0.063 5.00e-02 4.00e+02
        pdb=" CA  PRO D  73 "   -0.018 5.00e-02 4.00e+02
        pdb=" CD  PRO D  73 "   -0.021 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR C  72 "    0.024 5.00e-02 4.00e+02   3.58e-02 2.05e+00
        pdb=" N   PRO C  73 "   -0.062 5.00e-02 4.00e+02
        pdb=" CA  PRO C  73 "    0.017 5.00e-02 4.00e+02
        pdb=" CD  PRO C  73 "    0.020 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR A  72 "   -0.024 5.00e-02 4.00e+02   3.56e-02 2.03e+00
        pdb=" N   PRO A  73 "    0.062 5.00e-02 4.00e+02
        pdb=" CA  PRO A  73 "   -0.017 5.00e-02 4.00e+02
        pdb=" CD  PRO A  73 "   -0.020 5.00e-02 4.00e+02
  ... (remaining 1737 not shown)

  Histogram of nonbonded interaction distances:
        2.14 -     2.69: 333
        2.69 -     3.24: 9875
        3.24 -     3.80: 15637
        3.80 -     4.35: 19508
        4.35 -     4.90: 31111
  Nonbonded interactions: 76464
  Sorted by model distance:
  nonbonded pdb=" OD2 ASP B  23 "
            pdb=" OG  SER B 185 "
     model   vdw
     2.139 3.040
  nonbonded pdb=" OD2 ASP A  23 "
            pdb=" OG  SER A 185 "
     model   vdw
     2.151 3.040
  nonbonded pdb=" OD2 ASP C  23 "
            pdb=" OG  SER C 185 "
     model   vdw
     2.160 3.040
  nonbonded pdb=" OD2 ASP D  23 "
            pdb=" OG  SER D 185 "
     model   vdw
     2.190 3.040
  nonbonded pdb=" OG1 THR B 300 "
            pdb=" O   CYS B 329 "
     model   vdw
     2.267 3.040
  ... (remaining 76459 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: 0.07
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'C'
  selection = chain 'B'
  selection = chain 'D'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.240
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.050
  Construct map_model_manager:             0.020
  Extract box with map and model:          0.340
  Check model and map are aligned:         0.060
  Set scattering table:                    0.090
  Process input model:                     22.520
  Find NCS groups from input model:        0.190
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.890
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   26.430
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7741
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   9964  Z= 0.193
  Angle     :  0.833  10.516  13520  Z= 0.418
  Chirality :  0.046   0.176   1480
  Planarity :  0.004   0.036   1740
  Dihedral  : 16.782  78.083   3612
  Min Nonbonded Distance : 2.139

Molprobity Statistics.
  All-atom Clashscore : 13.93
  Ramachandran Plot:
    Outliers :  0.32 %
    Allowed  : 13.30 %
    Favored  : 86.38 %
  Rotamer:
    Outliers :  0.20 %
    Allowed  : 32.13 %
    Favored  : 67.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.50 %
    Cis-general     : 5.03 %
    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: -1.82 (0.24), residues: 1248
  helix:  0.09 (0.48), residues: 128
  sheet:  0.00 (0.77), residues: 60
  loop : -1.61 (0.20), residues: 1060

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP D 225 
 HIS   0.004   0.001   HIS A 254 
 PHE   0.005   0.001   PHE A 217 
 TYR   0.006   0.001   TYR D 256 
 ARG   0.006   0.000   ARG A 294 

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

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

  2496 Ramachandran restraints generated.
    1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2496 Ramachandran restraints generated.
    1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  76 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 74
  time to evaluate  : 1.045 
Fit side-chains
REVERT: A  136 ASP cc_start: 0.8745 (t0) cc_final: 0.7851 (t70)
REVERT: A  241 MET cc_start: 0.8010 (mmm) cc_final: 0.7703 (mtt)
REVERT: B   86 LEU cc_start: 0.8778 (pp) cc_final: 0.8501 (tp)
REVERT: C   86 LEU cc_start: 0.8739 (pp) cc_final: 0.8499 (tp)
REVERT: D   86 LEU cc_start: 0.8729 (pp) cc_final: 0.8488 (tp)
  outliers start: 2
  outliers final: 1
  residues processed: 74
  average time/residue: 0.1722
  time to fit residues: 20.6053
Evaluate side-chains
  73 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 72
  time to evaluate  : 1.225 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  113 TYR
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 104 optimal weight:    0.0370
   chunk 93 optimal weight:    9.9990
   chunk 52 optimal weight:   10.0000
   chunk 32 optimal weight:    8.9990
   chunk 63 optimal weight:   20.0000
   chunk 50 optimal weight:    9.9990
   chunk 97 optimal weight:    6.9990
   chunk 37 optimal weight:    3.9990
   chunk 59 optimal weight:    4.9990
   chunk 72 optimal weight:   50.0000
   chunk 112 optimal weight:    7.9990
   overall best weight:    4.8066

-------------------------------------------------------------------------------
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 = 0.4231 r_free = 0.4231 target = 0.113040 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3765 r_free = 0.3765 target = 0.075428 restraints weight = 33569.457|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3808 r_free = 0.3808 target = 0.078294 restraints weight = 17902.782|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3838 r_free = 0.3838 target = 0.080244 restraints weight = 12338.464|
|-----------------------------------------------------------------------------|
r_work (final): 0.3763
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7920
moved from start:          0.1250

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.041   9964  Z= 0.359
  Angle     :  0.852   9.870  13520  Z= 0.443
  Chirality :  0.047   0.178   1480
  Planarity :  0.004   0.032   1740
  Dihedral  :  5.537  34.528   1342
  Min Nonbonded Distance : 2.556

Molprobity Statistics.
  All-atom Clashscore : 15.83
  Ramachandran Plot:
    Outliers :  0.32 %
    Allowed  : 14.18 %
    Favored  : 85.50 %
  Rotamer:
    Outliers :  5.66 %
    Allowed  : 29.20 %
    Favored  : 65.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.50 %
    Cis-general     : 5.03 %
    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: -1.95 (0.24), residues: 1248
  helix: -0.05 (0.45), residues: 144
  sheet: -1.13 (0.57), residues: 100
  loop : -1.65 (0.21), residues: 1004

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP A 225 
 HIS   0.005   0.001   HIS B 254 
 PHE   0.010   0.001   PHE D 217 
 TYR   0.009   0.001   TYR A 323 
 ARG   0.004   0.000   ARG A 294 

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

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

  2496 Ramachandran restraints generated.
    1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2496 Ramachandran restraints generated.
    1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  131 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 58
    poor density    : 73
  time to evaluate  : 1.143 
Fit side-chains
REVERT: A  190 ASP cc_start: 0.9143 (OUTLIER) cc_final: 0.8772 (p0)
REVERT: A  195 HIS cc_start: 0.8771 (OUTLIER) cc_final: 0.8123 (m90)
REVERT: A  227 LYS cc_start: 0.9246 (OUTLIER) cc_final: 0.8972 (mmmt)
REVERT: A  310 GLU cc_start: 0.8694 (OUTLIER) cc_final: 0.8484 (pp20)
REVERT: B  190 ASP cc_start: 0.9144 (OUTLIER) cc_final: 0.8761 (p0)
REVERT: B  195 HIS cc_start: 0.8741 (OUTLIER) cc_final: 0.8181 (m90)
REVERT: B  227 LYS cc_start: 0.9242 (OUTLIER) cc_final: 0.8983 (mmmt)
REVERT: B  242 ILE cc_start: 0.9324 (OUTLIER) cc_final: 0.8977 (mm)
REVERT: B  310 GLU cc_start: 0.8679 (OUTLIER) cc_final: 0.8475 (pp20)
REVERT: C  190 ASP cc_start: 0.9151 (OUTLIER) cc_final: 0.8779 (p0)
REVERT: C  195 HIS cc_start: 0.8798 (OUTLIER) cc_final: 0.8148 (m90)
REVERT: C  242 ILE cc_start: 0.9329 (OUTLIER) cc_final: 0.8984 (mm)
REVERT: C  310 GLU cc_start: 0.8675 (OUTLIER) cc_final: 0.8468 (pp20)
REVERT: D  190 ASP cc_start: 0.9124 (OUTLIER) cc_final: 0.8740 (p0)
REVERT: D  195 HIS cc_start: 0.8770 (OUTLIER) cc_final: 0.8121 (m90)
REVERT: D  227 LYS cc_start: 0.9237 (OUTLIER) cc_final: 0.8932 (mmmt)
REVERT: D  310 GLU cc_start: 0.8688 (OUTLIER) cc_final: 0.8474 (pp20)
  outliers start: 58
  outliers final: 20
  residues processed: 112
  average time/residue: 0.1649
  time to fit residues: 28.8249
Evaluate side-chains
  114 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 77
  time to evaluate  : 1.050 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  113 TYR
Chi-restraints excluded: chain A residue  190 ASP
Chi-restraints excluded: chain A residue  194 VAL
Chi-restraints excluded: chain A residue  195 HIS
Chi-restraints excluded: chain A residue  227 LYS
Chi-restraints excluded: chain A residue  264 THR
Chi-restraints excluded: chain A residue  273 LEU
Chi-restraints excluded: chain A residue  310 GLU
Chi-restraints excluded: chain A residue  329 CYS
Chi-restraints excluded: chain B residue  113 TYR
Chi-restraints excluded: chain B residue  190 ASP
Chi-restraints excluded: chain B residue  194 VAL
Chi-restraints excluded: chain B residue  195 HIS
Chi-restraints excluded: chain B residue  227 LYS
Chi-restraints excluded: chain B residue  242 ILE
Chi-restraints excluded: chain B residue  273 LEU
Chi-restraints excluded: chain B residue  310 GLU
Chi-restraints excluded: chain B residue  329 CYS
Chi-restraints excluded: chain B residue  333 MET
Chi-restraints excluded: chain C residue  190 ASP
Chi-restraints excluded: chain C residue  194 VAL
Chi-restraints excluded: chain C residue  195 HIS
Chi-restraints excluded: chain C residue  242 ILE
Chi-restraints excluded: chain C residue  273 LEU
Chi-restraints excluded: chain C residue  310 GLU
Chi-restraints excluded: chain C residue  329 CYS
Chi-restraints excluded: chain C residue  333 MET
Chi-restraints excluded: chain D residue  113 TYR
Chi-restraints excluded: chain D residue  190 ASP
Chi-restraints excluded: chain D residue  194 VAL
Chi-restraints excluded: chain D residue  195 HIS
Chi-restraints excluded: chain D residue  227 LYS
Chi-restraints excluded: chain D residue  264 THR
Chi-restraints excluded: chain D residue  283 THR
Chi-restraints excluded: chain D residue  310 GLU
Chi-restraints excluded: chain D residue  329 CYS
Chi-restraints excluded: chain D residue  333 MET
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 24 optimal weight:    0.6980
   chunk 77 optimal weight:    5.9990
   chunk 104 optimal weight:    8.9990
   chunk 66 optimal weight:    8.9990
   chunk 1 optimal weight:   20.0000
   chunk 94 optimal weight:    0.9980
   chunk 33 optimal weight:    9.9990
   chunk 50 optimal weight:    4.9990
   chunk 35 optimal weight:    7.9990
   chunk 19 optimal weight:    3.9990
   chunk 80 optimal weight:    0.6980
   overall best weight:    2.2784

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

Flipped N/Q/H residues before XYZ refinement:
** A  65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4279 r_free = 0.4279 target = 0.114194 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3783 r_free = 0.3783 target = 0.076462 restraints weight = 34421.204|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3830 r_free = 0.3830 target = 0.079510 restraints weight = 17645.404|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 57)----------------|
| r_work = 0.3862 r_free = 0.3862 target = 0.081565 restraints weight = 12124.761|
|-----------------------------------------------------------------------------|
r_work (final): 0.3788
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7839
moved from start:          0.1316

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   9964  Z= 0.226
  Angle     :  0.806   9.906  13520  Z= 0.414
  Chirality :  0.046   0.176   1480
  Planarity :  0.004   0.031   1740
  Dihedral  :  5.339  33.731   1342
  Min Nonbonded Distance : 2.584

Molprobity Statistics.
  All-atom Clashscore : 12.40
  Ramachandran Plot:
    Outliers :  0.32 %
    Allowed  : 13.54 %
    Favored  : 86.14 %
  Rotamer:
    Outliers :  3.91 %
    Allowed  : 30.86 %
    Favored  : 65.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.50 %
    Cis-general     : 5.03 %
    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: -1.88 (0.24), residues: 1248
  helix:  0.06 (0.45), residues: 144
  sheet: -1.06 (0.56), residues: 96
  loop : -1.60 (0.20), residues: 1008

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP B 225 
 HIS   0.004   0.001   HIS C 195 
 PHE   0.009   0.001   PHE B 277 
 TYR   0.012   0.001   TYR A 323 
 ARG   0.003   0.000   ARG A 294 

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

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

  2496 Ramachandran restraints generated.
    1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2496 Ramachandran restraints generated.
    1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 80
  time to evaluate  : 1.060 
Fit side-chains
REVERT: A  190 ASP cc_start: 0.9032 (OUTLIER) cc_final: 0.8643 (p0)
REVERT: A  221 LYS cc_start: 0.7301 (OUTLIER) cc_final: 0.7069 (pttt)
REVERT: A  242 ILE cc_start: 0.9334 (OUTLIER) cc_final: 0.8985 (mm)
REVERT: A  310 GLU cc_start: 0.8706 (OUTLIER) cc_final: 0.8477 (pp20)
REVERT: B   42 LEU cc_start: 0.9560 (tt) cc_final: 0.9094 (mp)
REVERT: B  184 MET cc_start: 0.7699 (mmm) cc_final: 0.7408 (mtp)
REVERT: B  190 ASP cc_start: 0.9032 (OUTLIER) cc_final: 0.8637 (p0)
REVERT: B  221 LYS cc_start: 0.7315 (OUTLIER) cc_final: 0.7061 (ptpt)
REVERT: B  310 GLU cc_start: 0.8692 (OUTLIER) cc_final: 0.8401 (pp20)
REVERT: C   42 LEU cc_start: 0.9535 (tt) cc_final: 0.9054 (mp)
REVERT: C  190 ASP cc_start: 0.9046 (OUTLIER) cc_final: 0.8633 (p0)
REVERT: C  221 LYS cc_start: 0.7479 (OUTLIER) cc_final: 0.7214 (ptpt)
REVERT: C  310 GLU cc_start: 0.8699 (OUTLIER) cc_final: 0.8473 (pp20)
REVERT: D   42 LEU cc_start: 0.9532 (tt) cc_final: 0.9053 (mp)
REVERT: D  190 ASP cc_start: 0.9031 (OUTLIER) cc_final: 0.8638 (p0)
REVERT: D  221 LYS cc_start: 0.7322 (OUTLIER) cc_final: 0.7102 (pttt)
REVERT: D  238 GLU cc_start: 0.8908 (OUTLIER) cc_final: 0.8706 (mt-10)
REVERT: D  242 ILE cc_start: 0.9286 (OUTLIER) cc_final: 0.8911 (mm)
  outliers start: 40
  outliers final: 14
  residues processed: 113
  average time/residue: 0.1736
  time to fit residues: 30.3123
Evaluate side-chains
  102 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 74
  time to evaluate  : 1.025 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   72 THR
Chi-restraints excluded: chain A residue  113 TYR
Chi-restraints excluded: chain A residue  188 ILE
Chi-restraints excluded: chain A residue  190 ASP
Chi-restraints excluded: chain A residue  221 LYS
Chi-restraints excluded: chain A residue  242 ILE
Chi-restraints excluded: chain A residue  310 GLU
Chi-restraints excluded: chain A residue  329 CYS
Chi-restraints excluded: chain B residue  190 ASP
Chi-restraints excluded: chain B residue  221 LYS
Chi-restraints excluded: chain B residue  310 GLU
Chi-restraints excluded: chain B residue  329 CYS
Chi-restraints excluded: chain B residue  333 MET
Chi-restraints excluded: chain C residue  113 TYR
Chi-restraints excluded: chain C residue  188 ILE
Chi-restraints excluded: chain C residue  190 ASP
Chi-restraints excluded: chain C residue  221 LYS
Chi-restraints excluded: chain C residue  310 GLU
Chi-restraints excluded: chain C residue  329 CYS
Chi-restraints excluded: chain C residue  333 MET
Chi-restraints excluded: chain D residue  113 TYR
Chi-restraints excluded: chain D residue  188 ILE
Chi-restraints excluded: chain D residue  190 ASP
Chi-restraints excluded: chain D residue  221 LYS
Chi-restraints excluded: chain D residue  238 GLU
Chi-restraints excluded: chain D residue  242 ILE
Chi-restraints excluded: chain D residue  329 CYS
Chi-restraints excluded: chain D residue  333 MET
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 38 optimal weight:    7.9990
   chunk 64 optimal weight:    9.9990
   chunk 58 optimal weight:   20.0000
   chunk 19 optimal weight:    4.9990
   chunk 60 optimal weight:    9.9990
   chunk 13 optimal weight:   20.0000
   chunk 65 optimal weight:    4.9990
   chunk 72 optimal weight:   50.0000
   chunk 96 optimal weight:    5.9990
   chunk 51 optimal weight:    2.9990
   chunk 112 optimal weight:    9.9990
   overall best weight:    5.3990

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

Flipped N/Q/H residues before XYZ refinement:
** A  65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4224 r_free = 0.4224 target = 0.103553 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3873 r_free = 0.3873 target = 0.077974 restraints weight = 31270.165|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3824 r_free = 0.3824 target = 0.081209 restraints weight = 18061.088|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3826 r_free = 0.3826 target = 0.081508 restraints weight = 10210.246|
|-----------------------------------------------------------------------------|
r_work (final): 0.3813
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7847
moved from start:          0.1819

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.040   9964  Z= 0.389
  Angle     :  0.879  10.359  13520  Z= 0.454
  Chirality :  0.048   0.168   1480
  Planarity :  0.004   0.031   1740
  Dihedral  :  5.604  21.306   1340
  Min Nonbonded Distance : 2.518

Molprobity Statistics.
  All-atom Clashscore : 16.72
  Ramachandran Plot:
    Outliers :  0.32 %
    Allowed  : 15.71 %
    Favored  : 83.97 %
  Rotamer:
    Outliers :  6.35 %
    Allowed  : 29.00 %
    Favored  : 64.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.50 %
    Cis-general     : 5.03 %
    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: -1.90 (0.25), residues: 1248
  helix:  0.42 (0.47), residues: 144
  sheet: -0.98 (0.59), residues: 104
  loop : -1.70 (0.20), residues: 1000

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP B 225 
 HIS   0.007   0.002   HIS C 195 
 PHE   0.012   0.002   PHE C 217 
 TYR   0.008   0.001   TYR B 323 
 ARG   0.003   0.000   ARG A 294 

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

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

  2496 Ramachandran restraints generated.
    1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2496 Ramachandran restraints generated.
    1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  140 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 65
    poor density    : 75
  time to evaluate  : 1.083 
Fit side-chains
REVERT: A  238 GLU cc_start: 0.8826 (OUTLIER) cc_final: 0.8582 (mt-10)
REVERT: A  242 ILE cc_start: 0.9346 (OUTLIER) cc_final: 0.8975 (mm)
REVERT: A  260 TYR cc_start: 0.8327 (OUTLIER) cc_final: 0.8124 (m-10)
REVERT: A  310 GLU cc_start: 0.8769 (OUTLIER) cc_final: 0.8477 (pp20)
REVERT: B  227 LYS cc_start: 0.9092 (OUTLIER) cc_final: 0.8793 (mmmt)
REVERT: B  238 GLU cc_start: 0.8788 (OUTLIER) cc_final: 0.8575 (mt-10)
REVERT: B  241 MET cc_start: 0.8770 (mmm) cc_final: 0.8249 (mtt)
REVERT: B  242 ILE cc_start: 0.9327 (OUTLIER) cc_final: 0.8970 (mm)
REVERT: B  275 MET cc_start: 0.8746 (mmp) cc_final: 0.8298 (mmt)
REVERT: B  310 GLU cc_start: 0.8779 (OUTLIER) cc_final: 0.8513 (pp20)
REVERT: B  323 TYR cc_start: 0.7285 (m-80) cc_final: 0.6663 (m-80)
REVERT: B  333 MET cc_start: 0.8168 (OUTLIER) cc_final: 0.7798 (ptp)
REVERT: C   26 HIS cc_start: 0.8111 (OUTLIER) cc_final: 0.7369 (t-90)
REVERT: C  227 LYS cc_start: 0.9222 (OUTLIER) cc_final: 0.8922 (mmmm)
REVERT: C  238 GLU cc_start: 0.8770 (OUTLIER) cc_final: 0.8565 (mt-10)
REVERT: C  242 ILE cc_start: 0.9332 (OUTLIER) cc_final: 0.8973 (mm)
REVERT: C  275 MET cc_start: 0.8728 (mmp) cc_final: 0.8294 (mmt)
REVERT: C  310 GLU cc_start: 0.8778 (OUTLIER) cc_final: 0.8509 (pp20)
REVERT: C  323 TYR cc_start: 0.7305 (m-80) cc_final: 0.6685 (m-80)
REVERT: C  333 MET cc_start: 0.8098 (OUTLIER) cc_final: 0.7789 (ptp)
REVERT: D  227 LYS cc_start: 0.9106 (OUTLIER) cc_final: 0.8794 (mmmm)
REVERT: D  238 GLU cc_start: 0.8809 (OUTLIER) cc_final: 0.8602 (mt-10)
REVERT: D  242 ILE cc_start: 0.9338 (OUTLIER) cc_final: 0.8963 (mm)
REVERT: D  275 MET cc_start: 0.8737 (mmp) cc_final: 0.8309 (mmt)
REVERT: D  323 TYR cc_start: 0.7319 (m-80) cc_final: 0.6681 (m-80)
  outliers start: 65
  outliers final: 32
  residues processed: 130
  average time/residue: 0.1861
  time to fit residues: 35.9416
Evaluate side-chains
  125 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 75
  time to evaluate  : 1.086 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   72 THR
Chi-restraints excluded: chain A residue  113 TYR
Chi-restraints excluded: chain A residue  135 ILE
Chi-restraints excluded: chain A residue  188 ILE
Chi-restraints excluded: chain A residue  194 VAL
Chi-restraints excluded: chain A residue  232 TRP
Chi-restraints excluded: chain A residue  238 GLU
Chi-restraints excluded: chain A residue  242 ILE
Chi-restraints excluded: chain A residue  260 TYR
Chi-restraints excluded: chain A residue  273 LEU
Chi-restraints excluded: chain A residue  283 THR
Chi-restraints excluded: chain A residue  310 GLU
Chi-restraints excluded: chain A residue  329 CYS
Chi-restraints excluded: chain B residue   72 THR
Chi-restraints excluded: chain B residue  188 ILE
Chi-restraints excluded: chain B residue  194 VAL
Chi-restraints excluded: chain B residue  227 LYS
Chi-restraints excluded: chain B residue  232 TRP
Chi-restraints excluded: chain B residue  238 GLU
Chi-restraints excluded: chain B residue  242 ILE
Chi-restraints excluded: chain B residue  273 LEU
Chi-restraints excluded: chain B residue  283 THR
Chi-restraints excluded: chain B residue  310 GLU
Chi-restraints excluded: chain B residue  329 CYS
Chi-restraints excluded: chain B residue  333 MET
Chi-restraints excluded: chain C residue   26 HIS
Chi-restraints excluded: chain C residue   40 SER
Chi-restraints excluded: chain C residue   72 THR
Chi-restraints excluded: chain C residue  113 TYR
Chi-restraints excluded: chain C residue  188 ILE
Chi-restraints excluded: chain C residue  194 VAL
Chi-restraints excluded: chain C residue  227 LYS
Chi-restraints excluded: chain C residue  232 TRP
Chi-restraints excluded: chain C residue  238 GLU
Chi-restraints excluded: chain C residue  242 ILE
Chi-restraints excluded: chain C residue  273 LEU
Chi-restraints excluded: chain C residue  283 THR
Chi-restraints excluded: chain C residue  310 GLU
Chi-restraints excluded: chain C residue  329 CYS
Chi-restraints excluded: chain C residue  333 MET
Chi-restraints excluded: chain D residue   40 SER
Chi-restraints excluded: chain D residue   72 THR
Chi-restraints excluded: chain D residue  188 ILE
Chi-restraints excluded: chain D residue  194 VAL
Chi-restraints excluded: chain D residue  227 LYS
Chi-restraints excluded: chain D residue  232 TRP
Chi-restraints excluded: chain D residue  238 GLU
Chi-restraints excluded: chain D residue  242 ILE
Chi-restraints excluded: chain D residue  329 CYS
Chi-restraints excluded: chain D residue  333 MET
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 99 optimal weight:   20.0000
   chunk 75 optimal weight:    0.6980
   chunk 57 optimal weight:    3.9990
   chunk 94 optimal weight:    6.9990
   chunk 116 optimal weight:    3.9990
   chunk 104 optimal weight:   20.0000
   chunk 120 optimal weight:    5.9990
   chunk 25 optimal weight:    8.9990
   chunk 108 optimal weight:    3.9990
   chunk 4 optimal weight:    7.9990
   chunk 105 optimal weight:    4.9990
   overall best weight:    3.5388

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

Flipped N/Q/H residues before XYZ refinement:
** A  65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4244 r_free = 0.4244 target = 0.112962 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3768 r_free = 0.3768 target = 0.075601 restraints weight = 34156.217|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3813 r_free = 0.3813 target = 0.078524 restraints weight = 18116.007|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3842 r_free = 0.3842 target = 0.080483 restraints weight = 12522.368|
|-----------------------------------------------------------------------------|
r_work (final): 0.3773
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7893
moved from start:          0.1798

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   9964  Z= 0.286
  Angle     :  0.846  10.072  13520  Z= 0.433
  Chirality :  0.047   0.172   1480
  Planarity :  0.004   0.031   1740
  Dihedral  :  5.480  22.039   1340
  Min Nonbonded Distance : 2.544

Molprobity Statistics.
  All-atom Clashscore : 15.09
  Ramachandran Plot:
    Outliers :  0.32 %
    Allowed  : 14.34 %
    Favored  : 85.34 %
  Rotamer:
    Outliers :  6.15 %
    Allowed  : 28.71 %
    Favored  : 65.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.50 %
    Cis-general     : 5.03 %
    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: -1.90 (0.25), residues: 1248
  helix:  0.49 (0.48), residues: 144
  sheet: -0.81 (0.63), residues: 100
  loop : -1.73 (0.20), residues: 1004

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP B 225 
 HIS   0.003   0.001   HIS D 195 
 PHE   0.011   0.002   PHE D 217 
 TYR   0.013   0.001   TYR A 323 
 ARG   0.003   0.000   ARG A 294 

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

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

  2496 Ramachandran restraints generated.
    1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2496 Ramachandran restraints generated.
    1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  142 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 63
    poor density    : 79
  time to evaluate  : 1.198 
Fit side-chains
REVERT: A  190 ASP cc_start: 0.9025 (OUTLIER) cc_final: 0.8672 (p0)
REVERT: A  195 HIS cc_start: 0.8698 (OUTLIER) cc_final: 0.8432 (m170)
REVERT: A  227 LYS cc_start: 0.9189 (OUTLIER) cc_final: 0.8907 (mmmm)
REVERT: A  238 GLU cc_start: 0.8866 (OUTLIER) cc_final: 0.8638 (mt-10)
REVERT: A  242 ILE cc_start: 0.9364 (OUTLIER) cc_final: 0.9026 (mm)
REVERT: A  275 MET cc_start: 0.8716 (mmp) cc_final: 0.8403 (mmt)
REVERT: A  310 GLU cc_start: 0.8741 (OUTLIER) cc_final: 0.8470 (pp20)
REVERT: B  190 ASP cc_start: 0.9016 (OUTLIER) cc_final: 0.8665 (p0)
REVERT: B  195 HIS cc_start: 0.8639 (OUTLIER) cc_final: 0.8387 (m170)
REVERT: B  227 LYS cc_start: 0.9178 (OUTLIER) cc_final: 0.8871 (mmmt)
REVERT: B  238 GLU cc_start: 0.8841 (OUTLIER) cc_final: 0.8615 (mt-10)
REVERT: B  241 MET cc_start: 0.8714 (mmm) cc_final: 0.8110 (mtt)
REVERT: B  242 ILE cc_start: 0.9315 (OUTLIER) cc_final: 0.8963 (mm)
REVERT: B  275 MET cc_start: 0.8772 (mmp) cc_final: 0.8371 (mmt)
REVERT: B  310 GLU cc_start: 0.8722 (OUTLIER) cc_final: 0.8465 (pp20)
REVERT: B  323 TYR cc_start: 0.7393 (m-80) cc_final: 0.6791 (m-80)
REVERT: B  333 MET cc_start: 0.7966 (OUTLIER) cc_final: 0.7593 (ptp)
REVERT: C  190 ASP cc_start: 0.9030 (OUTLIER) cc_final: 0.8685 (p0)
REVERT: C  227 LYS cc_start: 0.9255 (OUTLIER) cc_final: 0.9020 (mmmm)
REVERT: C  238 GLU cc_start: 0.8856 (OUTLIER) cc_final: 0.8619 (mt-10)
REVERT: C  242 ILE cc_start: 0.9316 (OUTLIER) cc_final: 0.8964 (mm)
REVERT: C  275 MET cc_start: 0.8772 (mmp) cc_final: 0.8371 (mmt)
REVERT: C  310 GLU cc_start: 0.8725 (OUTLIER) cc_final: 0.8476 (pp20)
REVERT: C  323 TYR cc_start: 0.7405 (m-80) cc_final: 0.6791 (m-80)
REVERT: C  333 MET cc_start: 0.7936 (OUTLIER) cc_final: 0.7689 (ptp)
REVERT: D  190 ASP cc_start: 0.9023 (OUTLIER) cc_final: 0.8665 (p0)
REVERT: D  195 HIS cc_start: 0.8683 (OUTLIER) cc_final: 0.8384 (m170)
REVERT: D  238 GLU cc_start: 0.8839 (OUTLIER) cc_final: 0.8623 (mt-10)
REVERT: D  241 MET cc_start: 0.8626 (mtt) cc_final: 0.7967 (mtt)
REVERT: D  242 ILE cc_start: 0.9316 (OUTLIER) cc_final: 0.8974 (mm)
REVERT: D  275 MET cc_start: 0.8774 (mmp) cc_final: 0.8356 (mmt)
REVERT: D  323 TYR cc_start: 0.7399 (m-80) cc_final: 0.6782 (m-80)
  outliers start: 63
  outliers final: 30
  residues processed: 130
  average time/residue: 0.2097
  time to fit residues: 41.3721
Evaluate side-chains
  131 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 53
    poor density    : 78
  time to evaluate  : 1.183 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   72 THR
Chi-restraints excluded: chain A residue  113 TYR
Chi-restraints excluded: chain A residue  188 ILE
Chi-restraints excluded: chain A residue  190 ASP
Chi-restraints excluded: chain A residue  194 VAL
Chi-restraints excluded: chain A residue  195 HIS
Chi-restraints excluded: chain A residue  212 ILE
Chi-restraints excluded: chain A residue  227 LYS
Chi-restraints excluded: chain A residue  232 TRP
Chi-restraints excluded: chain A residue  238 GLU
Chi-restraints excluded: chain A residue  242 ILE
Chi-restraints excluded: chain A residue  283 THR
Chi-restraints excluded: chain A residue  310 GLU
Chi-restraints excluded: chain A residue  329 CYS
Chi-restraints excluded: chain B residue   72 THR
Chi-restraints excluded: chain B residue  188 ILE
Chi-restraints excluded: chain B residue  190 ASP
Chi-restraints excluded: chain B residue  194 VAL
Chi-restraints excluded: chain B residue  195 HIS
Chi-restraints excluded: chain B residue  212 ILE
Chi-restraints excluded: chain B residue  227 LYS
Chi-restraints excluded: chain B residue  232 TRP
Chi-restraints excluded: chain B residue  238 GLU
Chi-restraints excluded: chain B residue  242 ILE
Chi-restraints excluded: chain B residue  283 THR
Chi-restraints excluded: chain B residue  310 GLU
Chi-restraints excluded: chain B residue  329 CYS
Chi-restraints excluded: chain B residue  333 MET
Chi-restraints excluded: chain C residue   72 THR
Chi-restraints excluded: chain C residue   87 THR
Chi-restraints excluded: chain C residue  113 TYR
Chi-restraints excluded: chain C residue  188 ILE
Chi-restraints excluded: chain C residue  190 ASP
Chi-restraints excluded: chain C residue  194 VAL
Chi-restraints excluded: chain C residue  227 LYS
Chi-restraints excluded: chain C residue  232 TRP
Chi-restraints excluded: chain C residue  238 GLU
Chi-restraints excluded: chain C residue  242 ILE
Chi-restraints excluded: chain C residue  283 THR
Chi-restraints excluded: chain C residue  310 GLU
Chi-restraints excluded: chain C residue  329 CYS
Chi-restraints excluded: chain C residue  333 MET
Chi-restraints excluded: chain D residue   72 THR
Chi-restraints excluded: chain D residue  113 TYR
Chi-restraints excluded: chain D residue  188 ILE
Chi-restraints excluded: chain D residue  190 ASP
Chi-restraints excluded: chain D residue  194 VAL
Chi-restraints excluded: chain D residue  195 HIS
Chi-restraints excluded: chain D residue  232 TRP
Chi-restraints excluded: chain D residue  238 GLU
Chi-restraints excluded: chain D residue  242 ILE
Chi-restraints excluded: chain D residue  329 CYS
Chi-restraints excluded: chain D residue  333 MET
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 46 optimal weight:    9.9990
   chunk 77 optimal weight:    3.9990
   chunk 116 optimal weight:    5.9990
   chunk 106 optimal weight:   20.0000
   chunk 15 optimal weight:    0.9990
   chunk 123 optimal weight:    1.9990
   chunk 104 optimal weight:    9.9990
   chunk 111 optimal weight:    1.9990
   chunk 44 optimal weight:    0.0770
   chunk 87 optimal weight:   10.0000
   chunk 60 optimal weight:    4.9990
   overall best weight:    1.8146

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

Flipped N/Q/H residues before XYZ refinement:
A  65 ASN
C  65 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4281 r_free = 0.4281 target = 0.114109 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3792 r_free = 0.3792 target = 0.075955 restraints weight = 34305.987|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3839 r_free = 0.3839 target = 0.079052 restraints weight = 17846.998|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3871 r_free = 0.3871 target = 0.081145 restraints weight = 12218.079|
|-----------------------------------------------------------------------------|
r_work (final): 0.3806
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7835
moved from start:          0.1757

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   9964  Z= 0.211
  Angle     :  0.816  10.266  13520  Z= 0.413
  Chirality :  0.046   0.173   1480
  Planarity :  0.004   0.031   1740
  Dihedral  :  5.210  22.473   1340
  Min Nonbonded Distance : 2.581

Molprobity Statistics.
  All-atom Clashscore : 12.56
  Ramachandran Plot:
    Outliers :  0.32 %
    Allowed  : 14.02 %
    Favored  : 85.66 %
  Rotamer:
    Outliers :  4.10 %
    Allowed  : 30.76 %
    Favored  : 65.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.50 %
    Cis-general     : 5.03 %
    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: -1.91 (0.25), residues: 1248
  helix:  0.40 (0.49), residues: 144
  sheet: -1.27 (0.48), residues: 124
  loop : -1.67 (0.21), residues: 980

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP B 225 
 HIS   0.002   0.001   HIS A  77 
 PHE   0.009   0.001   PHE C 277 
 TYR   0.013   0.001   TYR A 323 
 ARG   0.002   0.000   ARG A 257 

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

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

  2496 Ramachandran restraints generated.
    1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2496 Ramachandran restraints generated.
    1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 78
  time to evaluate  : 1.059 
Fit side-chains
REVERT: A  136 ASP cc_start: 0.9111 (t0) cc_final: 0.8360 (t70)
REVERT: A  190 ASP cc_start: 0.9005 (OUTLIER) cc_final: 0.8678 (p0)
REVERT: A  238 GLU cc_start: 0.8897 (OUTLIER) cc_final: 0.8673 (mt-10)
REVERT: A  242 ILE cc_start: 0.9293 (OUTLIER) cc_final: 0.8912 (mm)
REVERT: A  310 GLU cc_start: 0.8772 (OUTLIER) cc_final: 0.8494 (pp20)
REVERT: B  190 ASP cc_start: 0.9004 (OUTLIER) cc_final: 0.8673 (p0)
REVERT: B  225 TRP cc_start: 0.7901 (t-100) cc_final: 0.7621 (t-100)
REVERT: B  227 LYS cc_start: 0.9157 (OUTLIER) cc_final: 0.8905 (mmmt)
REVERT: B  242 ILE cc_start: 0.9334 (OUTLIER) cc_final: 0.9007 (mm)
REVERT: B  275 MET cc_start: 0.8799 (mmp) cc_final: 0.8369 (mmt)
REVERT: B  310 GLU cc_start: 0.8752 (OUTLIER) cc_final: 0.8470 (pp20)
REVERT: B  323 TYR cc_start: 0.7419 (m-80) cc_final: 0.6858 (m-80)
REVERT: B  333 MET cc_start: 0.7908 (OUTLIER) cc_final: 0.7557 (ptp)
REVERT: C  190 ASP cc_start: 0.9017 (OUTLIER) cc_final: 0.8692 (p0)
REVERT: C  242 ILE cc_start: 0.9339 (OUTLIER) cc_final: 0.9005 (mm)
REVERT: C  275 MET cc_start: 0.8802 (mmp) cc_final: 0.8425 (mmt)
REVERT: C  310 GLU cc_start: 0.8754 (OUTLIER) cc_final: 0.8482 (pp20)
REVERT: C  333 MET cc_start: 0.7787 (OUTLIER) cc_final: 0.7492 (ptp)
REVERT: D  190 ASP cc_start: 0.9011 (OUTLIER) cc_final: 0.8681 (p0)
REVERT: D  241 MET cc_start: 0.8589 (mtt) cc_final: 0.8309 (mtt)
REVERT: D  242 ILE cc_start: 0.9334 (OUTLIER) cc_final: 0.9007 (mm)
REVERT: D  275 MET cc_start: 0.8799 (mmp) cc_final: 0.8432 (mmt)
  outliers start: 42
  outliers final: 26
  residues processed: 112
  average time/residue: 0.1577
  time to fit residues: 28.0229
Evaluate side-chains
  113 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 72
  time to evaluate  : 1.167 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   72 THR
Chi-restraints excluded: chain A residue  113 TYR
Chi-restraints excluded: chain A residue  188 ILE
Chi-restraints excluded: chain A residue  190 ASP
Chi-restraints excluded: chain A residue  232 TRP
Chi-restraints excluded: chain A residue  238 GLU
Chi-restraints excluded: chain A residue  242 ILE
Chi-restraints excluded: chain A residue  310 GLU
Chi-restraints excluded: chain A residue  329 CYS
Chi-restraints excluded: chain A residue  333 MET
Chi-restraints excluded: chain B residue   72 THR
Chi-restraints excluded: chain B residue  113 TYR
Chi-restraints excluded: chain B residue  188 ILE
Chi-restraints excluded: chain B residue  190 ASP
Chi-restraints excluded: chain B residue  227 LYS
Chi-restraints excluded: chain B residue  232 TRP
Chi-restraints excluded: chain B residue  242 ILE
Chi-restraints excluded: chain B residue  310 GLU
Chi-restraints excluded: chain B residue  329 CYS
Chi-restraints excluded: chain B residue  333 MET
Chi-restraints excluded: chain C residue   72 THR
Chi-restraints excluded: chain C residue   87 THR
Chi-restraints excluded: chain C residue  113 TYR
Chi-restraints excluded: chain C residue  188 ILE
Chi-restraints excluded: chain C residue  190 ASP
Chi-restraints excluded: chain C residue  212 ILE
Chi-restraints excluded: chain C residue  232 TRP
Chi-restraints excluded: chain C residue  242 ILE
Chi-restraints excluded: chain C residue  283 THR
Chi-restraints excluded: chain C residue  310 GLU
Chi-restraints excluded: chain C residue  329 CYS
Chi-restraints excluded: chain C residue  333 MET
Chi-restraints excluded: chain D residue   72 THR
Chi-restraints excluded: chain D residue  113 TYR
Chi-restraints excluded: chain D residue  188 ILE
Chi-restraints excluded: chain D residue  190 ASP
Chi-restraints excluded: chain D residue  232 TRP
Chi-restraints excluded: chain D residue  242 ILE
Chi-restraints excluded: chain D residue  283 THR
Chi-restraints excluded: chain D residue  329 CYS
Chi-restraints excluded: chain D residue  333 MET
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 81 optimal weight:    0.9990
   chunk 120 optimal weight:   10.0000
   chunk 23 optimal weight:    1.9990
   chunk 104 optimal weight:    7.9990
   chunk 31 optimal weight:   30.0000
   chunk 17 optimal weight:    5.9990
   chunk 62 optimal weight:    8.9990
   chunk 18 optimal weight:    3.9990
   chunk 66 optimal weight:    2.9990
   chunk 8 optimal weight:    8.9990
   chunk 28 optimal weight:    7.9990
   overall best weight:    3.1990

-------------------------------------------------------------------------------
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 = 0.4264 r_free = 0.4264 target = 0.111938 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3739 r_free = 0.3739 target = 0.074126 restraints weight = 34818.828|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3787 r_free = 0.3787 target = 0.077172 restraints weight = 18643.958|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3818 r_free = 0.3818 target = 0.079178 restraints weight = 12988.077|
|-----------------------------------------------------------------------------|
r_work (final): 0.3755
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7851
moved from start:          0.1865

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   9964  Z= 0.269
  Angle     :  0.833  10.109  13520  Z= 0.422
  Chirality :  0.046   0.169   1480
  Planarity :  0.004   0.031   1740
  Dihedral  :  5.266  21.997   1340
  Min Nonbonded Distance : 2.565

Molprobity Statistics.
  All-atom Clashscore : 14.51
  Ramachandran Plot:
    Outliers :  0.32 %
    Allowed  : 14.02 %
    Favored  : 85.66 %
  Rotamer:
    Outliers :  5.08 %
    Allowed  : 30.18 %
    Favored  : 64.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.50 %
    Cis-general     : 5.03 %
    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: -1.91 (0.25), residues: 1248
  helix:  0.35 (0.49), residues: 144
  sheet: -0.93 (0.51), residues: 120
  loop : -1.71 (0.21), residues: 984

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP B 225 
 HIS   0.003   0.001   HIS C 261 
 PHE   0.011   0.001   PHE D 217 
 TYR   0.011   0.001   TYR A 323 
 ARG   0.003   0.000   ARG B 257 

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

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

  2496 Ramachandran restraints generated.
    1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2496 Ramachandran restraints generated.
    1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  125 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 52
    poor density    : 73
  time to evaluate  : 1.080 
Fit side-chains
REVERT: A  190 ASP cc_start: 0.8984 (OUTLIER) cc_final: 0.8658 (p0)
REVERT: A  242 ILE cc_start: 0.9332 (OUTLIER) cc_final: 0.8987 (mm)
REVERT: A  310 GLU cc_start: 0.8754 (OUTLIER) cc_final: 0.8469 (pp20)
REVERT: B  190 ASP cc_start: 0.9022 (OUTLIER) cc_final: 0.8706 (p0)
REVERT: B  225 TRP cc_start: 0.7924 (t-100) cc_final: 0.7690 (t-100)
REVERT: B  238 GLU cc_start: 0.8973 (OUTLIER) cc_final: 0.8694 (mt-10)
REVERT: B  242 ILE cc_start: 0.9323 (OUTLIER) cc_final: 0.8970 (mm)
REVERT: B  275 MET cc_start: 0.8878 (mmp) cc_final: 0.8514 (mmt)
REVERT: B  310 GLU cc_start: 0.8745 (OUTLIER) cc_final: 0.8470 (pp20)
REVERT: B  323 TYR cc_start: 0.7424 (m-80) cc_final: 0.6842 (m-80)
REVERT: B  333 MET cc_start: 0.7874 (OUTLIER) cc_final: 0.7469 (ptp)
REVERT: C  190 ASP cc_start: 0.8995 (OUTLIER) cc_final: 0.8666 (p0)
REVERT: C  227 LYS cc_start: 0.9157 (OUTLIER) cc_final: 0.8849 (mmmm)
REVERT: C  238 GLU cc_start: 0.8897 (OUTLIER) cc_final: 0.8682 (mt-10)
REVERT: C  242 ILE cc_start: 0.9323 (OUTLIER) cc_final: 0.8971 (mm)
REVERT: C  275 MET cc_start: 0.8919 (mmp) cc_final: 0.8494 (mmt)
REVERT: C  310 GLU cc_start: 0.8748 (OUTLIER) cc_final: 0.8466 (pp20)
REVERT: C  323 TYR cc_start: 0.7341 (m-80) cc_final: 0.6747 (m-80)
REVERT: C  333 MET cc_start: 0.7855 (OUTLIER) cc_final: 0.7485 (ptp)
REVERT: D  190 ASP cc_start: 0.9003 (OUTLIER) cc_final: 0.8675 (p0)
REVERT: D  241 MET cc_start: 0.8661 (mtt) cc_final: 0.8368 (mtt)
REVERT: D  242 ILE cc_start: 0.9362 (OUTLIER) cc_final: 0.9032 (mm)
REVERT: D  275 MET cc_start: 0.8915 (mmp) cc_final: 0.8489 (mmt)
REVERT: D  323 TYR cc_start: 0.7431 (m-80) cc_final: 0.6801 (m-80)
  outliers start: 52
  outliers final: 30
  residues processed: 115
  average time/residue: 0.1604
  time to fit residues: 29.2108
Evaluate side-chains
  119 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 73
  time to evaluate  : 1.083 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   72 THR
Chi-restraints excluded: chain A residue  113 TYR
Chi-restraints excluded: chain A residue  188 ILE
Chi-restraints excluded: chain A residue  190 ASP
Chi-restraints excluded: chain A residue  212 ILE
Chi-restraints excluded: chain A residue  232 TRP
Chi-restraints excluded: chain A residue  242 ILE
Chi-restraints excluded: chain A residue  283 THR
Chi-restraints excluded: chain A residue  310 GLU
Chi-restraints excluded: chain A residue  329 CYS
Chi-restraints excluded: chain A residue  333 MET
Chi-restraints excluded: chain B residue   72 THR
Chi-restraints excluded: chain B residue   87 THR
Chi-restraints excluded: chain B residue  113 TYR
Chi-restraints excluded: chain B residue  188 ILE
Chi-restraints excluded: chain B residue  190 ASP
Chi-restraints excluded: chain B residue  232 TRP
Chi-restraints excluded: chain B residue  238 GLU
Chi-restraints excluded: chain B residue  242 ILE
Chi-restraints excluded: chain B residue  283 THR
Chi-restraints excluded: chain B residue  310 GLU
Chi-restraints excluded: chain B residue  329 CYS
Chi-restraints excluded: chain B residue  333 MET
Chi-restraints excluded: chain C residue   72 THR
Chi-restraints excluded: chain C residue   87 THR
Chi-restraints excluded: chain C residue  113 TYR
Chi-restraints excluded: chain C residue  188 ILE
Chi-restraints excluded: chain C residue  190 ASP
Chi-restraints excluded: chain C residue  212 ILE
Chi-restraints excluded: chain C residue  227 LYS
Chi-restraints excluded: chain C residue  232 TRP
Chi-restraints excluded: chain C residue  238 GLU
Chi-restraints excluded: chain C residue  242 ILE
Chi-restraints excluded: chain C residue  283 THR
Chi-restraints excluded: chain C residue  310 GLU
Chi-restraints excluded: chain C residue  329 CYS
Chi-restraints excluded: chain C residue  333 MET
Chi-restraints excluded: chain D residue   72 THR
Chi-restraints excluded: chain D residue  113 TYR
Chi-restraints excluded: chain D residue  188 ILE
Chi-restraints excluded: chain D residue  190 ASP
Chi-restraints excluded: chain D residue  232 TRP
Chi-restraints excluded: chain D residue  242 ILE
Chi-restraints excluded: chain D residue  283 THR
Chi-restraints excluded: chain D residue  329 CYS
Chi-restraints excluded: chain D residue  333 MET
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 86 optimal weight:    3.9990
   chunk 76 optimal weight:   10.0000
   chunk 114 optimal weight:    0.7980
   chunk 78 optimal weight:    7.9990
   chunk 105 optimal weight:    0.9990
   chunk 113 optimal weight:    0.6980
   chunk 50 optimal weight:    7.9990
   chunk 97 optimal weight:    3.9990
   chunk 96 optimal weight:    5.9990
   chunk 33 optimal weight:    5.9990
   chunk 52 optimal weight:    0.8980
   overall best weight:    1.4784

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

Flipped N/Q/H residues before XYZ refinement:
B  77 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4294 r_free = 0.4294 target = 0.115020 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3810 r_free = 0.3810 target = 0.077022 restraints weight = 34538.988|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3860 r_free = 0.3860 target = 0.080220 restraints weight = 17968.975|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3892 r_free = 0.3892 target = 0.082309 restraints weight = 12224.861|
|-----------------------------------------------------------------------------|
r_work (final): 0.3829
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7820
moved from start:          0.1904

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   9964  Z= 0.199
  Angle     :  0.808  10.211  13520  Z= 0.407
  Chirality :  0.046   0.171   1480
  Planarity :  0.004   0.030   1740
  Dihedral  :  5.075  22.411   1340
  Min Nonbonded Distance : 2.596

Molprobity Statistics.
  All-atom Clashscore : 12.19
  Ramachandran Plot:
    Outliers :  0.32 %
    Allowed  : 13.62 %
    Favored  : 86.06 %
  Rotamer:
    Outliers :  3.71 %
    Allowed  : 31.35 %
    Favored  : 64.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.50 %
    Cis-general     : 5.03 %
    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: -1.73 (0.25), residues: 1248
  helix:  0.32 (0.50), residues: 132
  sheet: -0.80 (0.48), residues: 112
  loop : -1.52 (0.21), residues: 1004

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP B 225 
 HIS   0.002   0.001   HIS B 229 
 PHE   0.008   0.001   PHE D 217 
 TYR   0.014   0.001   TYR A 323 
 ARG   0.002   0.000   ARG A 257 

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

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

  2496 Ramachandran restraints generated.
    1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2496 Ramachandran restraints generated.
    1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 76
  time to evaluate  : 1.677 
Fit side-chains
REVERT: A  136 ASP cc_start: 0.9111 (t0) cc_final: 0.8318 (t70)
REVERT: A  190 ASP cc_start: 0.8969 (OUTLIER) cc_final: 0.8641 (p0)
REVERT: A  242 ILE cc_start: 0.9333 (OUTLIER) cc_final: 0.9005 (mm)
REVERT: A  310 GLU cc_start: 0.8743 (OUTLIER) cc_final: 0.8473 (pp20)
REVERT: B  136 ASP cc_start: 0.9082 (t0) cc_final: 0.8268 (t70)
REVERT: B  190 ASP cc_start: 0.8967 (OUTLIER) cc_final: 0.8635 (p0)
REVERT: B  241 MET cc_start: 0.8485 (mtt) cc_final: 0.8221 (mtt)
REVERT: B  242 ILE cc_start: 0.9327 (OUTLIER) cc_final: 0.9009 (mm)
REVERT: B  275 MET cc_start: 0.8855 (mmp) cc_final: 0.8490 (mmt)
REVERT: B  310 GLU cc_start: 0.8725 (OUTLIER) cc_final: 0.8465 (pp20)
REVERT: B  323 TYR cc_start: 0.7742 (m-80) cc_final: 0.7178 (m-80)
REVERT: B  333 MET cc_start: 0.7871 (OUTLIER) cc_final: 0.7524 (ptp)
REVERT: C   26 HIS cc_start: 0.8132 (OUTLIER) cc_final: 0.7486 (t-90)
REVERT: C  136 ASP cc_start: 0.9018 (t0) cc_final: 0.8218 (t70)
REVERT: C  190 ASP cc_start: 0.8984 (OUTLIER) cc_final: 0.8654 (p0)
REVERT: C  242 ILE cc_start: 0.9329 (OUTLIER) cc_final: 0.8996 (mm)
REVERT: C  310 GLU cc_start: 0.8727 (OUTLIER) cc_final: 0.8479 (pp20)
REVERT: C  333 MET cc_start: 0.7832 (OUTLIER) cc_final: 0.7549 (ptp)
REVERT: D  136 ASP cc_start: 0.9078 (t0) cc_final: 0.8251 (t70)
REVERT: D  190 ASP cc_start: 0.8983 (OUTLIER) cc_final: 0.8652 (p0)
REVERT: D  241 MET cc_start: 0.8676 (mtt) cc_final: 0.8276 (mtt)
REVERT: D  275 MET cc_start: 0.8849 (mmp) cc_final: 0.8553 (mmt)
  outliers start: 38
  outliers final: 24
  residues processed: 106
  average time/residue: 0.1613
  time to fit residues: 27.4522
Evaluate side-chains
  112 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 75
  time to evaluate  : 1.159 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  113 TYR
Chi-restraints excluded: chain A residue  188 ILE
Chi-restraints excluded: chain A residue  190 ASP
Chi-restraints excluded: chain A residue  232 TRP
Chi-restraints excluded: chain A residue  242 ILE
Chi-restraints excluded: chain A residue  310 GLU
Chi-restraints excluded: chain A residue  329 CYS
Chi-restraints excluded: chain A residue  333 MET
Chi-restraints excluded: chain B residue   72 THR
Chi-restraints excluded: chain B residue  113 TYR
Chi-restraints excluded: chain B residue  188 ILE
Chi-restraints excluded: chain B residue  190 ASP
Chi-restraints excluded: chain B residue  232 TRP
Chi-restraints excluded: chain B residue  242 ILE
Chi-restraints excluded: chain B residue  310 GLU
Chi-restraints excluded: chain B residue  329 CYS
Chi-restraints excluded: chain B residue  333 MET
Chi-restraints excluded: chain C residue   26 HIS
Chi-restraints excluded: chain C residue   72 THR
Chi-restraints excluded: chain C residue  113 TYR
Chi-restraints excluded: chain C residue  188 ILE
Chi-restraints excluded: chain C residue  190 ASP
Chi-restraints excluded: chain C residue  212 ILE
Chi-restraints excluded: chain C residue  232 TRP
Chi-restraints excluded: chain C residue  242 ILE
Chi-restraints excluded: chain C residue  283 THR
Chi-restraints excluded: chain C residue  310 GLU
Chi-restraints excluded: chain C residue  329 CYS
Chi-restraints excluded: chain C residue  333 MET
Chi-restraints excluded: chain D residue   72 THR
Chi-restraints excluded: chain D residue   87 THR
Chi-restraints excluded: chain D residue  113 TYR
Chi-restraints excluded: chain D residue  190 ASP
Chi-restraints excluded: chain D residue  212 ILE
Chi-restraints excluded: chain D residue  232 TRP
Chi-restraints excluded: chain D residue  329 CYS
Chi-restraints excluded: chain D residue  333 MET
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 71 optimal weight:    9.9990
   chunk 63 optimal weight:    0.7980
   chunk 94 optimal weight:    7.9990
   chunk 99 optimal weight:    0.9980
   chunk 25 optimal weight:    9.9990
   chunk 35 optimal weight:    0.9990
   chunk 34 optimal weight:    5.9990
   chunk 49 optimal weight:    0.9980
   chunk 5 optimal weight:    8.9990
   chunk 119 optimal weight:    7.9990
   chunk 17 optimal weight:    0.9990
   overall best weight:    0.9584

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

Flipped N/Q/H residues before XYZ refinement:
B 195 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4323 r_free = 0.4323 target = 0.115982 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3837 r_free = 0.3837 target = 0.078973 restraints weight = 34397.198|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3884 r_free = 0.3884 target = 0.082278 restraints weight = 18085.354|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3916 r_free = 0.3916 target = 0.084460 restraints weight = 12436.050|
|-----------------------------------------------------------------------------|
r_work (final): 0.3849
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7781
moved from start:          0.2087

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   9964  Z= 0.183
  Angle     :  0.797  10.566  13520  Z= 0.397
  Chirality :  0.046   0.169   1480
  Planarity :  0.004   0.031   1740
  Dihedral  :  4.845  22.849   1340
  Min Nonbonded Distance : 2.603

Molprobity Statistics.
  All-atom Clashscore : 11.50
  Ramachandran Plot:
    Outliers :  0.32 %
    Allowed  : 12.82 %
    Favored  : 86.86 %
  Rotamer:
    Outliers :  4.10 %
    Allowed  : 30.66 %
    Favored  : 65.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.50 %
    Cis-general     : 5.03 %
    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: -1.70 (0.25), residues: 1248
  helix:  0.27 (0.50), residues: 132
  sheet: -0.99 (0.46), residues: 112
  loop : -1.46 (0.21), residues: 1004

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.034   0.001   TRP B 225 
 HIS   0.004   0.001   HIS B  77 
 PHE   0.008   0.001   PHE A 277 
 TYR   0.015   0.001   TYR A 323 
 ARG   0.002   0.000   ARG A 257 

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

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

  2496 Ramachandran restraints generated.
    1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2496 Ramachandran restraints generated.
    1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 77
  time to evaluate  : 1.087 
Fit side-chains
REVERT: A  136 ASP cc_start: 0.9064 (t0) cc_final: 0.8287 (t70)
REVERT: A  190 ASP cc_start: 0.8929 (OUTLIER) cc_final: 0.8606 (p0)
REVERT: A  242 ILE cc_start: 0.9338 (OUTLIER) cc_final: 0.9023 (mm)
REVERT: A  310 GLU cc_start: 0.8702 (OUTLIER) cc_final: 0.8435 (pp20)
REVERT: B  136 ASP cc_start: 0.9060 (t0) cc_final: 0.8281 (t70)
REVERT: B  190 ASP cc_start: 0.8924 (OUTLIER) cc_final: 0.8612 (p0)
REVERT: B  241 MET cc_start: 0.8427 (mtt) cc_final: 0.8146 (mtt)
REVERT: B  242 ILE cc_start: 0.9325 (OUTLIER) cc_final: 0.9010 (mm)
REVERT: B  310 GLU cc_start: 0.8693 (OUTLIER) cc_final: 0.8425 (pp20)
REVERT: B  333 MET cc_start: 0.8010 (OUTLIER) cc_final: 0.7734 (ptp)
REVERT: C   26 HIS cc_start: 0.8085 (OUTLIER) cc_final: 0.7462 (t-90)
REVERT: C  136 ASP cc_start: 0.9042 (t0) cc_final: 0.8426 (t70)
REVERT: C  190 ASP cc_start: 0.8935 (OUTLIER) cc_final: 0.8609 (p0)
REVERT: C  242 ILE cc_start: 0.9328 (OUTLIER) cc_final: 0.9019 (mm)
REVERT: C  310 GLU cc_start: 0.8688 (OUTLIER) cc_final: 0.8427 (pp20)
REVERT: C  323 TYR cc_start: 0.7415 (m-80) cc_final: 0.7174 (m-80)
REVERT: C  333 MET cc_start: 0.7870 (OUTLIER) cc_final: 0.7606 (ptp)
REVERT: D  136 ASP cc_start: 0.9075 (t0) cc_final: 0.8305 (t70)
REVERT: D  190 ASP cc_start: 0.8938 (OUTLIER) cc_final: 0.8612 (p0)
REVERT: D  241 MET cc_start: 0.8523 (mtt) cc_final: 0.8114 (mtt)
REVERT: D  275 MET cc_start: 0.8845 (mmp) cc_final: 0.8572 (mmp)
  outliers start: 42
  outliers final: 26
  residues processed: 111
  average time/residue: 0.1559
  time to fit residues: 27.3355
Evaluate side-chains
  115 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 76
  time to evaluate  : 1.082 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   72 THR
Chi-restraints excluded: chain A residue  113 TYR
Chi-restraints excluded: chain A residue  190 ASP
Chi-restraints excluded: chain A residue  232 TRP
Chi-restraints excluded: chain A residue  242 ILE
Chi-restraints excluded: chain A residue  310 GLU
Chi-restraints excluded: chain A residue  329 CYS
Chi-restraints excluded: chain A residue  333 MET
Chi-restraints excluded: chain B residue   72 THR
Chi-restraints excluded: chain B residue  113 TYR
Chi-restraints excluded: chain B residue  188 ILE
Chi-restraints excluded: chain B residue  190 ASP
Chi-restraints excluded: chain B residue  195 HIS
Chi-restraints excluded: chain B residue  212 ILE
Chi-restraints excluded: chain B residue  232 TRP
Chi-restraints excluded: chain B residue  242 ILE
Chi-restraints excluded: chain B residue  310 GLU
Chi-restraints excluded: chain B residue  329 CYS
Chi-restraints excluded: chain B residue  333 MET
Chi-restraints excluded: chain C residue   26 HIS
Chi-restraints excluded: chain C residue   72 THR
Chi-restraints excluded: chain C residue   87 THR
Chi-restraints excluded: chain C residue  113 TYR
Chi-restraints excluded: chain C residue  190 ASP
Chi-restraints excluded: chain C residue  212 ILE
Chi-restraints excluded: chain C residue  232 TRP
Chi-restraints excluded: chain C residue  242 ILE
Chi-restraints excluded: chain C residue  283 THR
Chi-restraints excluded: chain C residue  310 GLU
Chi-restraints excluded: chain C residue  329 CYS
Chi-restraints excluded: chain C residue  333 MET
Chi-restraints excluded: chain D residue   72 THR
Chi-restraints excluded: chain D residue   87 THR
Chi-restraints excluded: chain D residue  113 TYR
Chi-restraints excluded: chain D residue  188 ILE
Chi-restraints excluded: chain D residue  190 ASP
Chi-restraints excluded: chain D residue  232 TRP
Chi-restraints excluded: chain D residue  329 CYS
Chi-restraints excluded: chain D residue  333 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 55 optimal weight:   10.0000
   chunk 33 optimal weight:   10.0000
   chunk 63 optimal weight:    0.0570
   chunk 69 optimal weight:   20.0000
   chunk 98 optimal weight:    9.9990
   chunk 117 optimal weight:    0.0370
   chunk 9 optimal weight:    0.8980
   chunk 25 optimal weight:    9.9990
   chunk 74 optimal weight:    0.0000
   chunk 31 optimal weight:   30.0000
   chunk 20 optimal weight:    3.9990
   overall best weight:    0.9982

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

Flipped N/Q/H residues before XYZ refinement:
B 195 HIS
C  77 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4324 r_free = 0.4324 target = 0.116165 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3842 r_free = 0.3842 target = 0.079070 restraints weight = 34579.362|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3889 r_free = 0.3889 target = 0.082380 restraints weight = 18087.292|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3921 r_free = 0.3921 target = 0.084576 restraints weight = 12391.967|
|-----------------------------------------------------------------------------|
r_work (final): 0.3852
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7778
moved from start:          0.2190

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   9964  Z= 0.185
  Angle     :  0.798  10.973  13520  Z= 0.397
  Chirality :  0.046   0.169   1480
  Planarity :  0.004   0.032   1740
  Dihedral  :  4.802  22.670   1340
  Min Nonbonded Distance : 2.615

Molprobity Statistics.
  All-atom Clashscore : 11.34
  Ramachandran Plot:
    Outliers :  0.32 %
    Allowed  : 12.66 %
    Favored  : 87.02 %
  Rotamer:
    Outliers :  3.81 %
    Allowed  : 30.86 %
    Favored  : 65.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.50 %
    Cis-general     : 5.03 %
    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: -1.66 (0.24), residues: 1248
  helix:  0.19 (0.49), residues: 132
  sheet: -0.92 (0.47), residues: 112
  loop : -1.43 (0.21), residues: 1004

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.047   0.002   TRP B 225 
 HIS   0.004   0.001   HIS B  77 
 PHE   0.008   0.001   PHE A 277 
 TYR   0.013   0.001   TYR A 323 
 ARG   0.003   0.000   ARG B 192 

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

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

  2496 Ramachandran restraints generated.
    1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2496 Ramachandran restraints generated.
    1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 78
  time to evaluate  : 1.204 
Fit side-chains
REVERT: A  136 ASP cc_start: 0.9058 (t0) cc_final: 0.8298 (t70)
REVERT: A  190 ASP cc_start: 0.8915 (OUTLIER) cc_final: 0.8601 (p0)
REVERT: A  242 ILE cc_start: 0.9316 (OUTLIER) cc_final: 0.9016 (mm)
REVERT: A  310 GLU cc_start: 0.8687 (OUTLIER) cc_final: 0.8430 (pp20)
REVERT: B  136 ASP cc_start: 0.9058 (t0) cc_final: 0.8311 (t70)
REVERT: B  190 ASP cc_start: 0.8911 (OUTLIER) cc_final: 0.8594 (p0)
REVERT: B  241 MET cc_start: 0.8393 (mtt) cc_final: 0.8095 (mtt)
REVERT: B  242 ILE cc_start: 0.9310 (OUTLIER) cc_final: 0.9001 (mm)
REVERT: B  310 GLU cc_start: 0.8702 (OUTLIER) cc_final: 0.8388 (pp20)
REVERT: B  323 TYR cc_start: 0.7250 (m-80) cc_final: 0.6941 (m-80)
REVERT: B  333 MET cc_start: 0.8209 (OUTLIER) cc_final: 0.7930 (ptp)
REVERT: C   26 HIS cc_start: 0.8019 (OUTLIER) cc_final: 0.7402 (t-90)
REVERT: C  136 ASP cc_start: 0.9029 (t0) cc_final: 0.8418 (t70)
REVERT: C  190 ASP cc_start: 0.8911 (OUTLIER) cc_final: 0.8599 (p0)
REVERT: C  242 ILE cc_start: 0.9319 (OUTLIER) cc_final: 0.9010 (mm)
REVERT: C  310 GLU cc_start: 0.8676 (OUTLIER) cc_final: 0.8425 (pp20)
REVERT: C  323 TYR cc_start: 0.7438 (m-80) cc_final: 0.6991 (m-80)
REVERT: C  333 MET cc_start: 0.7851 (OUTLIER) cc_final: 0.7580 (ptp)
REVERT: D  136 ASP cc_start: 0.9065 (t0) cc_final: 0.8305 (t70)
REVERT: D  190 ASP cc_start: 0.8926 (OUTLIER) cc_final: 0.8612 (p0)
REVERT: D  241 MET cc_start: 0.8526 (mtt) cc_final: 0.8120 (mtt)
REVERT: D  275 MET cc_start: 0.8853 (mmp) cc_final: 0.8483 (mmp)
REVERT: D  323 TYR cc_start: 0.7401 (m-80) cc_final: 0.6833 (m-80)
  outliers start: 39
  outliers final: 25
  residues processed: 109
  average time/residue: 0.1615
  time to fit residues: 27.8442
Evaluate side-chains
  115 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 77
  time to evaluate  : 1.105 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   72 THR
Chi-restraints excluded: chain A residue  190 ASP
Chi-restraints excluded: chain A residue  232 TRP
Chi-restraints excluded: chain A residue  242 ILE
Chi-restraints excluded: chain A residue  310 GLU
Chi-restraints excluded: chain A residue  329 CYS
Chi-restraints excluded: chain A residue  333 MET
Chi-restraints excluded: chain B residue   72 THR
Chi-restraints excluded: chain B residue  113 TYR
Chi-restraints excluded: chain B residue  188 ILE
Chi-restraints excluded: chain B residue  190 ASP
Chi-restraints excluded: chain B residue  195 HIS
Chi-restraints excluded: chain B residue  212 ILE
Chi-restraints excluded: chain B residue  232 TRP
Chi-restraints excluded: chain B residue  242 ILE
Chi-restraints excluded: chain B residue  310 GLU
Chi-restraints excluded: chain B residue  329 CYS
Chi-restraints excluded: chain B residue  333 MET
Chi-restraints excluded: chain C residue   26 HIS
Chi-restraints excluded: chain C residue   72 THR
Chi-restraints excluded: chain C residue   87 THR
Chi-restraints excluded: chain C residue  113 TYR
Chi-restraints excluded: chain C residue  190 ASP
Chi-restraints excluded: chain C residue  212 ILE
Chi-restraints excluded: chain C residue  232 TRP
Chi-restraints excluded: chain C residue  242 ILE
Chi-restraints excluded: chain C residue  283 THR
Chi-restraints excluded: chain C residue  310 GLU
Chi-restraints excluded: chain C residue  329 CYS
Chi-restraints excluded: chain C residue  333 MET
Chi-restraints excluded: chain D residue   72 THR
Chi-restraints excluded: chain D residue   87 THR
Chi-restraints excluded: chain D residue  113 TYR
Chi-restraints excluded: chain D residue  188 ILE
Chi-restraints excluded: chain D residue  190 ASP
Chi-restraints excluded: chain D residue  232 TRP
Chi-restraints excluded: chain D residue  329 CYS
Chi-restraints excluded: chain D residue  333 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 70 optimal weight:    0.0370
   chunk 26 optimal weight:   20.0000
   chunk 120 optimal weight:    9.9990
   chunk 7 optimal weight:   10.0000
   chunk 112 optimal weight:    7.9990
   chunk 13 optimal weight:   10.0000
   chunk 83 optimal weight:    8.9990
   chunk 110 optimal weight:    0.9980
   chunk 11 optimal weight:    8.9990
   chunk 97 optimal weight:    5.9990
   chunk 62 optimal weight:   20.0000
   overall best weight:    4.8064

-------------------------------------------------------------------------------
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 = 0.4240 r_free = 0.4240 target = 0.104298 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3727 r_free = 0.3727 target = 0.074248 restraints weight = 30633.342|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3771 r_free = 0.3771 target = 0.076950 restraints weight = 16654.290|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3804 r_free = 0.3804 target = 0.078762 restraints weight = 11542.476|
|-----------------------------------------------------------------------------|
r_work (final): 0.3769
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7841
moved from start:          0.2252

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.044   9964  Z= 0.363
  Angle     :  0.872  10.109  13520  Z= 0.443
  Chirality :  0.048   0.168   1480
  Planarity :  0.004   0.029   1740
  Dihedral  :  5.327  22.065   1340
  Min Nonbonded Distance : 2.546

Molprobity Statistics.
  All-atom Clashscore : 18.25
  Ramachandran Plot:
    Outliers :  0.32 %
    Allowed  : 14.18 %
    Favored  : 85.50 %
  Rotamer:
    Outliers :  4.10 %
    Allowed  : 30.96 %
    Favored  : 64.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.50 %
    Cis-general     : 5.03 %
    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: -1.71 (0.24), residues: 1248
  helix:  0.45 (0.50), residues: 132
  sheet: -0.40 (0.61), residues: 88
  loop : -1.57 (0.20), residues: 1028

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.075   0.003   TRP B 225 
 HIS   0.009   0.002   HIS B 195 
 PHE   0.016   0.002   PHE B 217 
 TYR   0.008   0.001   TYR A 323 
 ARG   0.003   0.000   ARG B 192 

===============================================================================
Job complete
usr+sys time: 2982.80 seconds
wall clock time: 52 minutes 53.33 seconds (3173.33 seconds total)