Starting phenix.real_space_refine
on Wed Mar  4 00:59:47 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7wut_32841/03_2026/7wut_32841.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7wut_32841/03_2026/7wut_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_2026/7wut_32841.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7wut_32841/03_2026/7wut_32841.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7wut_32841/03_2026/7wut_32841.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7wut_32841/03_2026/7wut_32841.cif"
  }
  resolution = 3.5
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
-------------------------------------------------------------------------------
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): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/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, 'PHE:plan': 3, 'TRP:plan': 2, 'GLU:plan': 2, 'ASP:plan': 1, 'ASN:plan1': 1}
          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, 'PHE:plan': 3, 'TRP:plan': 2, 'GLU:plan': 2, 'ASP:plan': 1, 'ASN:plan1': 1}
          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, 'PHE:plan': 3, 'TRP:plan': 2, 'GLU:plan': 2, 'ASP:plan': 1, 'ASN:plan1': 1}
          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, 'PHE:plan': 3, 'TRP:plan': 2, 'GLU:plan': 2, 'ASP:plan': 1, 'ASN:plan1': 1}
          Unresolved non-hydrogen planarities: 76
  Time building chain proxies: 2.33, per 1000 atoms: 0.24
  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: 0.74
  Conformation dependent library (CDL) restraints added in 417.1 milliseconds
  

  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: 0.37
  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: 1.49

  Time building geometry restraints manager: 1.05 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: 0.02
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'C'
  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:             0.260
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.020
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.130
  Check model and map are aligned:         0.030
  Set scattering table:                    0.020
  Process input model:                     9.320
  Find NCS groups from input model:        0.080
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.430
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   11.310
-------------------------------------------------------------------------------
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   9984  Z= 0.144
  Angle     :  0.832  10.516  13560  Z= 0.417
  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 : 13.87
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  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
 ARG   0.006   0.000   ARG A 294 
 TYR   0.006   0.001   TYR D 256 
 PHE   0.005   0.001   PHE A 217 
 TRP   0.021   0.002   TRP D 225 
 HIS   0.004   0.001   HIS A 254 

Details of bonding type rmsd
  covalent geometry    : bond        0.00294 ( 9964)
  covalent geometry    : angle       0.83254 (13520)
  SS BOND              : bond        0.00152 (   20)
  SS BOND              : angle       0.56574 (   40)
  hydrogen bonds       : bond        0.28396 (  213)
  hydrogen bonds       : angle      11.01054 (  492)

*********************** 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  : 0.471 
Fit side-chains
REVERT: A   86 LEU cc_start: 0.8738 (pp) cc_final: 0.8495 (tp)
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: 0.0710
  time to fit residues: 8.5647
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  : 0.378 
-------------------------------------------------------------------------------
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 108 optimal weight:    0.0770
   chunk 49 optimal weight:    2.9990
   chunk 97 optimal weight:    6.9990
   chunk 113 optimal weight:    5.9990
   chunk 53 optimal weight:    5.9990
   chunk 5 optimal weight:    0.0570
   chunk 33 optimal weight:    7.9990
   chunk 123 optimal weight:    9.9990
   chunk 65 optimal weight:    1.9990
   chunk 62 optimal weight:   30.0000
   chunk 51 optimal weight:    0.9980
   overall best weight:    1.2260

-------------------------------------------------------------------------------
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 = 0.4318 r_free = 0.4318 target = 0.116182 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3830 r_free = 0.3830 target = 0.078177 restraints weight = 33871.193|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3877 r_free = 0.3877 target = 0.081301 restraints weight = 17626.023|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3909 r_free = 0.3909 target = 0.083405 restraints weight = 12100.398|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.3929 r_free = 0.3929 target = 0.084826 restraints weight = 9540.604|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3942 r_free = 0.3942 target = 0.085735 restraints weight = 8198.668|
|-----------------------------------------------------------------------------|
r_work (final): 0.3885
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7750
moved from start:          0.1007

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   9984  Z= 0.146
  Angle     :  0.791  10.147  13560  Z= 0.406
  Chirality :  0.046   0.189   1480
  Planarity :  0.004   0.029   1740
  Dihedral  :  5.130  35.678   1342
  Min Nonbonded Distance : 2.585

Molprobity Statistics.
  All-atom Clashscore : 11.61
  Ramachandran Plot:
    Outliers :  0.32 %
    Allowed  : 13.94 %
    Favored  : 85.74 %
  Rotamer:
    Outliers :  2.34 %
    Allowed  : 29.59 %
    Favored  : 68.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.50 %
    Cis-general     : 5.03 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.62 (0.25), residues: 1248
  helix:  0.38 (0.48), residues: 128
  sheet: -0.59 (0.58), residues: 88
  loop : -1.44 (0.21), residues: 1032

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 294 
 TYR   0.015   0.001   TYR A 323 
 PHE   0.007   0.001   PHE D 217 
 TRP   0.016   0.001   TRP A 225 
 HIS   0.004   0.001   HIS D  77 

Details of bonding type rmsd
  covalent geometry    : bond        0.00300 ( 9964)
  covalent geometry    : angle       0.79213 (13520)
  SS BOND              : bond        0.00226 (   20)
  SS BOND              : angle       0.43778 (   40)
  hydrogen bonds       : bond        0.05046 (  213)
  hydrogen bonds       : angle       7.77919 (  492)

*********************** 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
  103 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 79
  time to evaluate  : 0.373 
Fit side-chains
REVERT: A   42 LEU cc_start: 0.9541 (tt) cc_final: 0.9069 (mp)
REVERT: A  190 ASP cc_start: 0.9042 (OUTLIER) cc_final: 0.8647 (p0)
REVERT: B  190 ASP cc_start: 0.9037 (OUTLIER) cc_final: 0.8632 (p0)
REVERT: C  190 ASP cc_start: 0.9048 (OUTLIER) cc_final: 0.8655 (p0)
REVERT: D  190 ASP cc_start: 0.9039 (OUTLIER) cc_final: 0.8648 (p0)
  outliers start: 24
  outliers final: 11
  residues processed: 96
  average time/residue: 0.0685
  time to fit residues: 10.7142
Evaluate side-chains
  96 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 81
  time to evaluate  : 0.519 
-------------------------------------------------------------------------------
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  329 CYS
Chi-restraints excluded: chain B residue  113 TYR
Chi-restraints excluded: chain B residue  190 ASP
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  190 ASP
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  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 101 optimal weight:    9.9990
   chunk 106 optimal weight:   10.0000
   chunk 10 optimal weight:   50.0000
   chunk 27 optimal weight:   20.0000
   chunk 115 optimal weight:    0.4980
   chunk 104 optimal weight:   20.0000
   chunk 78 optimal weight:   10.0000
   chunk 89 optimal weight:   20.0000
   chunk 108 optimal weight:    7.9990
   chunk 61 optimal weight:    0.8980
   chunk 30 optimal weight:    3.9990
   overall best weight:    4.6786

-------------------------------------------------------------------------------
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 = 0.4227 r_free = 0.4227 target = 0.112907 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3760 r_free = 0.3760 target = 0.075633 restraints weight = 33871.427|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3804 r_free = 0.3804 target = 0.078549 restraints weight = 17871.884|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3832 r_free = 0.3832 target = 0.080446 restraints weight = 12326.840|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3851 r_free = 0.3851 target = 0.081708 restraints weight = 9788.524|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 41)----------------|
| r_work = 0.3864 r_free = 0.3864 target = 0.082567 restraints weight = 8488.085|
|-----------------------------------------------------------------------------|
r_work (final): 0.3800
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7872
moved from start:          0.1506

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.041   9984  Z= 0.246
  Angle     :  0.850   9.920  13560  Z= 0.438
  Chirality :  0.048   0.174   1480
  Planarity :  0.004   0.030   1740
  Dihedral  :  5.509  33.874   1342
  Min Nonbonded Distance : 2.554

Molprobity Statistics.
  All-atom Clashscore : 15.77
  Ramachandran Plot:
    Outliers :  0.32 %
    Allowed  : 13.78 %
    Favored  : 85.90 %
  Rotamer:
    Outliers :  6.05 %
    Allowed  : 28.12 %
    Favored  : 65.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.50 %
    Cis-general     : 5.03 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.83 (0.24), residues: 1248
  helix:  0.29 (0.46), residues: 144
  sheet: -1.24 (0.55), residues: 100
  loop : -1.58 (0.20), residues: 1004

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 294 
 TYR   0.009   0.001   TYR A 323 
 PHE   0.012   0.001   PHE C 217 
 TRP   0.016   0.002   TRP B 225 
 HIS   0.004   0.001   HIS C 195 

Details of bonding type rmsd
  covalent geometry    : bond        0.00520 ( 9964)
  covalent geometry    : angle       0.85042 (13520)
  SS BOND              : bond        0.00420 (   20)
  SS BOND              : angle       0.67199 (   40)
  hydrogen bonds       : bond        0.04606 (  213)
  hydrogen bonds       : angle       7.56390 (  492)

*********************** 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
  146 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 62
    poor density    : 84
  time to evaluate  : 0.388 
Fit side-chains
REVERT: A  195 HIS cc_start: 0.8745 (OUTLIER) cc_final: 0.8191 (m90)
REVERT: A  221 LYS cc_start: 0.7230 (OUTLIER) cc_final: 0.7013 (ptpt)
REVERT: A  242 ILE cc_start: 0.9313 (OUTLIER) cc_final: 0.8981 (mm)
REVERT: A  323 TYR cc_start: 0.7238 (m-80) cc_final: 0.6327 (m-80)
REVERT: B  184 MET cc_start: 0.7811 (mmm) cc_final: 0.7493 (mtp)
REVERT: B  190 ASP cc_start: 0.9108 (OUTLIER) cc_final: 0.8678 (p0)
REVERT: B  195 HIS cc_start: 0.8713 (OUTLIER) cc_final: 0.8175 (m90)
REVERT: B  227 LYS cc_start: 0.9168 (OUTLIER) cc_final: 0.8861 (mmmt)
REVERT: B  241 MET cc_start: 0.8678 (mmm) cc_final: 0.8287 (mtt)
REVERT: B  242 ILE cc_start: 0.9315 (OUTLIER) cc_final: 0.8972 (mm)
REVERT: B  323 TYR cc_start: 0.7231 (m-80) cc_final: 0.6253 (m-80)
REVERT: C  195 HIS cc_start: 0.8750 (OUTLIER) cc_final: 0.8196 (m90)
REVERT: C  242 ILE cc_start: 0.9321 (OUTLIER) cc_final: 0.8977 (mm)
REVERT: C  323 TYR cc_start: 0.7249 (m-80) cc_final: 0.6336 (m-80)
REVERT: D  195 HIS cc_start: 0.8730 (OUTLIER) cc_final: 0.8245 (m90)
REVERT: D  227 LYS cc_start: 0.9218 (OUTLIER) cc_final: 0.8913 (mmmt)
REVERT: D  242 ILE cc_start: 0.9301 (OUTLIER) cc_final: 0.8959 (mm)
REVERT: D  323 TYR cc_start: 0.7235 (m-80) cc_final: 0.6314 (m-80)
  outliers start: 62
  outliers final: 21
  residues processed: 128
  average time/residue: 0.0779
  time to fit residues: 15.2969
Evaluate side-chains
  114 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 81
  time to evaluate  : 0.388 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  113 TYR
Chi-restraints excluded: chain A residue  194 VAL
Chi-restraints excluded: chain A residue  195 HIS
Chi-restraints excluded: chain A residue  221 LYS
Chi-restraints excluded: chain A residue  232 TRP
Chi-restraints excluded: chain A residue  242 ILE
Chi-restraints excluded: chain A residue  264 THR
Chi-restraints excluded: chain A residue  273 LEU
Chi-restraints excluded: chain A residue  329 CYS
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  232 TRP
Chi-restraints excluded: chain B residue  242 ILE
Chi-restraints excluded: chain B residue  273 LEU
Chi-restraints excluded: chain B residue  329 CYS
Chi-restraints excluded: chain B residue  333 MET
Chi-restraints excluded: chain C residue  194 VAL
Chi-restraints excluded: chain C residue  195 HIS
Chi-restraints excluded: chain C residue  232 TRP
Chi-restraints excluded: chain C residue  242 ILE
Chi-restraints excluded: chain C residue  273 LEU
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  194 VAL
Chi-restraints excluded: chain D residue  195 HIS
Chi-restraints excluded: chain D residue  227 LYS
Chi-restraints excluded: chain D residue  232 TRP
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 74 optimal weight:    0.2980
   chunk 82 optimal weight:    0.9980
   chunk 16 optimal weight:   10.0000
   chunk 108 optimal weight:    7.9990
   chunk 64 optimal weight:    0.0570
   chunk 110 optimal weight:    4.9990
   chunk 103 optimal weight:   40.0000
   chunk 25 optimal weight:    9.9990
   chunk 35 optimal weight:    7.9990
   chunk 66 optimal weight:    0.9990
   chunk 53 optimal weight:    0.6980
   overall best weight:    0.6100

-------------------------------------------------------------------------------
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 = 0.4316 r_free = 0.4316 target = 0.115471 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3850 r_free = 0.3850 target = 0.079733 restraints weight = 34126.400|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3898 r_free = 0.3898 target = 0.082970 restraints weight = 17306.223|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.3931 r_free = 0.3931 target = 0.085132 restraints weight = 11680.555|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3951 r_free = 0.3951 target = 0.086525 restraints weight = 9122.517|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3965 r_free = 0.3965 target = 0.087463 restraints weight = 7817.205|
|-----------------------------------------------------------------------------|
r_work (final): 0.3909
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7639
moved from start:          0.1533

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   9984  Z= 0.139
  Angle     :  0.813  10.350  13560  Z= 0.408
  Chirality :  0.046   0.173   1480
  Planarity :  0.004   0.029   1740
  Dihedral  :  5.053  23.112   1340
  Min Nonbonded Distance : 2.599

Molprobity Statistics.
  All-atom Clashscore : 10.23
  Ramachandran Plot:
    Outliers :  0.32 %
    Allowed  : 12.26 %
    Favored  : 87.42 %
  Rotamer:
    Outliers :  2.64 %
    Allowed  : 30.96 %
    Favored  : 66.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.50 %
    Cis-general     : 5.03 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.55 (0.25), residues: 1248
  helix:  0.38 (0.49), residues: 128
  sheet: -0.40 (0.55), residues: 84
  loop : -1.39 (0.21), residues: 1036

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 257 
 TYR   0.014   0.001   TYR A 323 
 PHE   0.011   0.001   PHE B 277 
 TRP   0.015   0.001   TRP B  28 
 HIS   0.004   0.001   HIS A  77 

Details of bonding type rmsd
  covalent geometry    : bond        0.00281 ( 9964)
  covalent geometry    : angle       0.81323 (13520)
  SS BOND              : bond        0.00155 (   20)
  SS BOND              : angle       0.73232 (   40)
  hydrogen bonds       : bond        0.03765 (  213)
  hydrogen bonds       : angle       6.98160 (  492)

*********************** 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
  117 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 90
  time to evaluate  : 0.314 
Fit side-chains
REVERT: A   42 LEU cc_start: 0.9552 (tt) cc_final: 0.9082 (mp)
REVERT: A  136 ASP cc_start: 0.9080 (t0) cc_final: 0.8348 (t70)
REVERT: A  183 LEU cc_start: 0.8813 (tp) cc_final: 0.8016 (pp)
REVERT: A  190 ASP cc_start: 0.9004 (OUTLIER) cc_final: 0.8633 (p0)
REVERT: A  241 MET cc_start: 0.7903 (mtp) cc_final: 0.7538 (mtt)
REVERT: A  323 TYR cc_start: 0.7342 (m-80) cc_final: 0.6867 (m-80)
REVERT: B  136 ASP cc_start: 0.9051 (t0) cc_final: 0.8506 (t70)
REVERT: B  190 ASP cc_start: 0.9035 (OUTLIER) cc_final: 0.8666 (p0)
REVERT: B  323 TYR cc_start: 0.7311 (m-80) cc_final: 0.6859 (m-80)
REVERT: C  190 ASP cc_start: 0.8981 (OUTLIER) cc_final: 0.8617 (p0)
REVERT: C  323 TYR cc_start: 0.7337 (m-80) cc_final: 0.6847 (m-80)
REVERT: C  333 MET cc_start: 0.8330 (OUTLIER) cc_final: 0.8092 (ptp)
REVERT: D  136 ASP cc_start: 0.9120 (t0) cc_final: 0.8354 (t70)
REVERT: D  190 ASP cc_start: 0.9001 (OUTLIER) cc_final: 0.8641 (p0)
REVERT: D  241 MET cc_start: 0.8365 (mtt) cc_final: 0.8140 (mtt)
REVERT: D  323 TYR cc_start: 0.7370 (m-80) cc_final: 0.6853 (m-80)
  outliers start: 27
  outliers final: 18
  residues processed: 110
  average time/residue: 0.0607
  time to fit residues: 10.9906
Evaluate side-chains
  104 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 81
  time to evaluate  : 0.352 
-------------------------------------------------------------------------------
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  329 CYS
Chi-restraints excluded: chain B residue   72 THR
Chi-restraints excluded: chain B residue  113 TYR
Chi-restraints excluded: chain B residue  190 ASP
Chi-restraints excluded: chain B residue  232 TRP
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  113 TYR
Chi-restraints excluded: chain C residue  190 ASP
Chi-restraints excluded: chain C residue  232 TRP
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  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=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 32 optimal weight:    6.9990
   chunk 63 optimal weight:   10.0000
   chunk 2 optimal weight:    0.0040
   chunk 20 optimal weight:    0.7980
   chunk 21 optimal weight:    0.9990
   chunk 102 optimal weight:   20.0000
   chunk 9 optimal weight:   30.0000
   chunk 64 optimal weight:    3.9990
   chunk 62 optimal weight:    7.9990
   chunk 80 optimal weight:   10.0000
   chunk 86 optimal weight:    9.9990
   overall best weight:    2.5598

-------------------------------------------------------------------------------
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 = 0.4276 r_free = 0.4276 target = 0.113537 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3792 r_free = 0.3792 target = 0.076611 restraints weight = 34169.148|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3837 r_free = 0.3837 target = 0.079721 restraints weight = 17739.443|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3868 r_free = 0.3868 target = 0.081783 restraints weight = 12180.445|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3888 r_free = 0.3888 target = 0.083145 restraints weight = 9640.032|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3901 r_free = 0.3901 target = 0.083979 restraints weight = 8320.063|
|-----------------------------------------------------------------------------|
r_work (final): 0.3856
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7705
moved from start:          0.1633

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   9984  Z= 0.168
  Angle     :  0.808  10.226  13560  Z= 0.406
  Chirality :  0.046   0.165   1480
  Planarity :  0.003   0.028   1740
  Dihedral  :  4.995  22.298   1340
  Min Nonbonded Distance : 2.581

Molprobity Statistics.
  All-atom Clashscore : 12.56
  Ramachandran Plot:
    Outliers :  0.32 %
    Allowed  : 13.38 %
    Favored  : 86.30 %
  Rotamer:
    Outliers :  3.61 %
    Allowed  : 31.05 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.56 (0.25), residues: 1248
  helix:  0.64 (0.53), residues: 128
  sheet: -1.20 (0.54), residues: 96
  loop : -1.36 (0.21), residues: 1024

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 294 
 TYR   0.010   0.001   TYR C 323 
 PHE   0.010   0.001   PHE A 217 
 TRP   0.011   0.002   TRP B 225 
 HIS   0.004   0.001   HIS C 195 

Details of bonding type rmsd
  covalent geometry    : bond        0.00354 ( 9964)
  covalent geometry    : angle       0.80899 (13520)
  SS BOND              : bond        0.00305 (   20)
  SS BOND              : angle       0.51957 (   40)
  hydrogen bonds       : bond        0.03561 (  213)
  hydrogen bonds       : angle       6.92407 (  492)

*********************** 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
  119 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 82
  time to evaluate  : 0.321 
Fit side-chains
REVERT: A   42 LEU cc_start: 0.9587 (tt) cc_final: 0.9111 (mp)
REVERT: A  183 LEU cc_start: 0.8539 (tp) cc_final: 0.8150 (tp)
REVERT: A  190 ASP cc_start: 0.9052 (OUTLIER) cc_final: 0.8695 (p0)
REVERT: A  238 GLU cc_start: 0.8976 (OUTLIER) cc_final: 0.8759 (mt-10)
REVERT: B  190 ASP cc_start: 0.9046 (OUTLIER) cc_final: 0.8696 (p0)
REVERT: B  241 MET cc_start: 0.8372 (mmm) cc_final: 0.7781 (mtt)
REVERT: B  242 ILE cc_start: 0.9353 (OUTLIER) cc_final: 0.9038 (mm)
REVERT: B  323 TYR cc_start: 0.7330 (m-80) cc_final: 0.6459 (m-80)
REVERT: C   26 HIS cc_start: 0.8133 (OUTLIER) cc_final: 0.7540 (t-90)
REVERT: C  190 ASP cc_start: 0.9021 (OUTLIER) cc_final: 0.8667 (p0)
REVERT: C  241 MET cc_start: 0.8525 (mmm) cc_final: 0.7986 (mtt)
REVERT: C  242 ILE cc_start: 0.9360 (OUTLIER) cc_final: 0.9046 (mm)
REVERT: C  323 TYR cc_start: 0.7351 (m-80) cc_final: 0.6523 (m-80)
REVERT: C  333 MET cc_start: 0.8236 (OUTLIER) cc_final: 0.7955 (ptp)
REVERT: D  190 ASP cc_start: 0.9052 (OUTLIER) cc_final: 0.8683 (p0)
REVERT: D  323 TYR cc_start: 0.7353 (m-80) cc_final: 0.6518 (m-80)
  outliers start: 37
  outliers final: 21
  residues processed: 112
  average time/residue: 0.0675
  time to fit residues: 12.2027
Evaluate side-chains
  108 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 78
  time to evaluate  : 0.391 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   72 THR
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  329 CYS
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  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  232 TRP
Chi-restraints excluded: chain C residue  242 ILE
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  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 85 optimal weight:    4.9990
   chunk 86 optimal weight:    7.9990
   chunk 48 optimal weight:    4.9990
   chunk 93 optimal weight:    6.9990
   chunk 98 optimal weight:   10.0000
   chunk 84 optimal weight:    4.9990
   chunk 9 optimal weight:    8.9990
   chunk 51 optimal weight:    0.8980
   chunk 37 optimal weight:    8.9990
   chunk 79 optimal weight:    0.8980
   chunk 110 optimal weight:    6.9990
   overall best weight:    3.3586

-------------------------------------------------------------------------------
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 = 0.4255 r_free = 0.4255 target = 0.111559 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3745 r_free = 0.3745 target = 0.074850 restraints weight = 34856.836|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3792 r_free = 0.3792 target = 0.077921 restraints weight = 18460.549|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3822 r_free = 0.3822 target = 0.079959 restraints weight = 12854.397|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 43)----------------|
| r_work = 0.3843 r_free = 0.3843 target = 0.081285 restraints weight = 10284.274|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.3856 r_free = 0.3856 target = 0.082123 restraints weight = 8950.535|
|-----------------------------------------------------------------------------|
r_work (final): 0.3806
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7819
moved from start:          0.1789

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   9984  Z= 0.193
  Angle     :  0.824   9.975  13560  Z= 0.417
  Chirality :  0.046   0.164   1480
  Planarity :  0.004   0.028   1740
  Dihedral  :  5.202  22.080   1340
  Min Nonbonded Distance : 2.567

Molprobity Statistics.
  All-atom Clashscore : 14.30
  Ramachandran Plot:
    Outliers :  0.32 %
    Allowed  : 14.02 %
    Favored  : 85.66 %
  Rotamer:
    Outliers :  4.39 %
    Allowed  : 30.66 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.61 (0.25), residues: 1248
  helix:  0.66 (0.52), residues: 128
  sheet: -1.11 (0.55), residues: 96
  loop : -1.42 (0.20), residues: 1024

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 294 
 TYR   0.008   0.001   TYR C 323 
 PHE   0.012   0.001   PHE D 217 
 TRP   0.015   0.002   TRP B 225 
 HIS   0.005   0.001   HIS B 195 

Details of bonding type rmsd
  covalent geometry    : bond        0.00411 ( 9964)
  covalent geometry    : angle       0.82397 (13520)
  SS BOND              : bond        0.00322 (   20)
  SS BOND              : angle       0.70107 (   40)
  hydrogen bonds       : bond        0.03572 (  213)
  hydrogen bonds       : angle       6.95817 (  492)

*********************** 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
  126 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 81
  time to evaluate  : 0.327 
Fit side-chains
REVERT: A   42 LEU cc_start: 0.9614 (tt) cc_final: 0.9151 (mp)
REVERT: A  190 ASP cc_start: 0.9042 (OUTLIER) cc_final: 0.8691 (p0)
REVERT: A  242 ILE cc_start: 0.9313 (OUTLIER) cc_final: 0.8970 (mm)
REVERT: B  225 TRP cc_start: 0.7997 (t-100) cc_final: 0.7786 (t-100)
REVERT: B  238 GLU cc_start: 0.8908 (OUTLIER) cc_final: 0.8675 (mt-10)
REVERT: B  242 ILE cc_start: 0.9353 (OUTLIER) cc_final: 0.9032 (mm)
REVERT: B  323 TYR cc_start: 0.7296 (m-80) cc_final: 0.6507 (m-80)
REVERT: B  333 MET cc_start: 0.7970 (OUTLIER) cc_final: 0.7571 (ptp)
REVERT: C  190 ASP cc_start: 0.9017 (OUTLIER) cc_final: 0.8700 (p0)
REVERT: C  227 LYS cc_start: 0.9158 (OUTLIER) cc_final: 0.8891 (mmmm)
REVERT: C  242 ILE cc_start: 0.9356 (OUTLIER) cc_final: 0.9038 (mm)
REVERT: C  323 TYR cc_start: 0.7304 (m-80) cc_final: 0.6549 (m-80)
REVERT: C  333 MET cc_start: 0.7848 (OUTLIER) cc_final: 0.7557 (ptp)
REVERT: D  190 ASP cc_start: 0.9037 (OUTLIER) cc_final: 0.8672 (p0)
REVERT: D  242 ILE cc_start: 0.9349 (OUTLIER) cc_final: 0.9024 (mm)
REVERT: D  323 TYR cc_start: 0.7345 (m-80) cc_final: 0.6560 (m-80)
  outliers start: 45
  outliers final: 21
  residues processed: 119
  average time/residue: 0.0706
  time to fit residues: 13.3617
Evaluate side-chains
  108 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 76
  time to evaluate  : 0.384 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   72 THR
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  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  232 TRP
Chi-restraints excluded: chain B residue  238 GLU
Chi-restraints excluded: chain B residue  242 ILE
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  188 ILE
Chi-restraints excluded: chain C residue  190 ASP
Chi-restraints excluded: chain C residue  227 LYS
Chi-restraints excluded: chain C residue  232 TRP
Chi-restraints excluded: chain C residue  242 ILE
Chi-restraints excluded: chain C residue  329 CYS
Chi-restraints excluded: chain C residue  333 MET
Chi-restraints excluded: chain D residue   57 ILE
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  232 TRP
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=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 61 optimal weight:    9.9990
   chunk 44 optimal weight:   20.0000
   chunk 24 optimal weight:    0.9980
   chunk 77 optimal weight:    9.9990
   chunk 43 optimal weight:    2.9990
   chunk 66 optimal weight:    0.0000
   chunk 63 optimal weight:   20.0000
   chunk 72 optimal weight:   20.0000
   chunk 121 optimal weight:    1.9990
   chunk 22 optimal weight:    0.3980
   chunk 69 optimal weight:   10.0000
   overall best weight:    1.2788

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

Flipped N/Q/H residues before XYZ refinement:
C  50 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4314 r_free = 0.4314 target = 0.114809 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3816 r_free = 0.3816 target = 0.077463 restraints weight = 34066.255|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3863 r_free = 0.3863 target = 0.080827 restraints weight = 17888.845|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3894 r_free = 0.3894 target = 0.082998 restraints weight = 12259.433|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3915 r_free = 0.3915 target = 0.084447 restraints weight = 9698.716|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3928 r_free = 0.3928 target = 0.085354 restraints weight = 8385.651|
|-----------------------------------------------------------------------------|
r_work (final): 0.3883
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7750
moved from start:          0.1889

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   9984  Z= 0.139
  Angle     :  0.807  10.232  13560  Z= 0.402
  Chirality :  0.046   0.167   1480
  Planarity :  0.003   0.027   1740
  Dihedral  :  4.995  22.767   1340
  Min Nonbonded Distance : 2.600

Molprobity Statistics.
  All-atom Clashscore : 11.29
  Ramachandran Plot:
    Outliers :  0.32 %
    Allowed  : 13.46 %
    Favored  : 86.22 %
  Rotamer:
    Outliers :  3.12 %
    Allowed  : 30.66 %
    Favored  : 66.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.50 %
    Cis-general     : 5.03 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.59 (0.25), residues: 1248
  helix:  0.24 (0.51), residues: 132
  sheet: -0.98 (0.46), residues: 112
  loop : -1.35 (0.21), residues: 1004

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A  62 
 TYR   0.012   0.001   TYR B 323 
 PHE   0.009   0.001   PHE A 277 
 TRP   0.017   0.001   TRP B 225 
 HIS   0.002   0.000   HIS A  77 

Details of bonding type rmsd
  covalent geometry    : bond        0.00293 ( 9964)
  covalent geometry    : angle       0.80731 (13520)
  SS BOND              : bond        0.00191 (   20)
  SS BOND              : angle       0.73000 (   40)
  hydrogen bonds       : bond        0.03305 (  213)
  hydrogen bonds       : angle       6.73575 (  492)

*********************** 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
  114 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 82
  time to evaluate  : 0.288 
Fit side-chains
REVERT: A   66 LEU cc_start: 0.9296 (mm) cc_final: 0.9003 (pp)
REVERT: A  136 ASP cc_start: 0.9078 (t0) cc_final: 0.8177 (t70)
REVERT: A  190 ASP cc_start: 0.8995 (OUTLIER) cc_final: 0.8662 (p0)
REVERT: B   66 LEU cc_start: 0.9269 (mm) cc_final: 0.9001 (pp)
REVERT: B  136 ASP cc_start: 0.9110 (t0) cc_final: 0.8346 (t70)
REVERT: B  190 ASP cc_start: 0.9005 (OUTLIER) cc_final: 0.8671 (p0)
REVERT: B  241 MET cc_start: 0.8134 (mtp) cc_final: 0.7907 (mtt)
REVERT: B  242 ILE cc_start: 0.9320 (OUTLIER) cc_final: 0.9014 (mm)
REVERT: B  323 TYR cc_start: 0.7303 (m-80) cc_final: 0.6541 (m-80)
REVERT: B  333 MET cc_start: 0.7921 (OUTLIER) cc_final: 0.7580 (ptp)
REVERT: C  136 ASP cc_start: 0.9044 (t0) cc_final: 0.8471 (t70)
REVERT: C  190 ASP cc_start: 0.8961 (OUTLIER) cc_final: 0.8642 (p0)
REVERT: C  242 ILE cc_start: 0.9328 (OUTLIER) cc_final: 0.9000 (mm)
REVERT: C  275 MET cc_start: 0.8820 (mmp) cc_final: 0.8339 (mmt)
REVERT: C  323 TYR cc_start: 0.7625 (m-80) cc_final: 0.7104 (m-80)
REVERT: C  333 MET cc_start: 0.7889 (OUTLIER) cc_final: 0.7615 (ptp)
REVERT: D  136 ASP cc_start: 0.9087 (t0) cc_final: 0.8319 (t70)
REVERT: D  190 ASP cc_start: 0.8995 (OUTLIER) cc_final: 0.8668 (p0)
REVERT: D  275 MET cc_start: 0.8826 (mmp) cc_final: 0.8335 (mmt)
REVERT: D  323 TYR cc_start: 0.7665 (m-80) cc_final: 0.7120 (m-80)
  outliers start: 32
  outliers final: 21
  residues processed: 107
  average time/residue: 0.0686
  time to fit residues: 11.9717
Evaluate side-chains
  111 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 82
  time to evaluate  : 0.383 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   72 THR
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  329 CYS
Chi-restraints excluded: chain B residue   57 ILE
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  232 TRP
Chi-restraints excluded: chain B residue  242 ILE
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  113 TYR
Chi-restraints excluded: chain C residue  188 ILE
Chi-restraints excluded: chain C residue  190 ASP
Chi-restraints excluded: chain C residue  232 TRP
Chi-restraints excluded: chain C residue  242 ILE
Chi-restraints excluded: chain C residue  329 CYS
Chi-restraints excluded: chain C residue  333 MET
Chi-restraints excluded: chain D residue   57 ILE
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  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 53 optimal weight:    2.9990
   chunk 27 optimal weight:   20.0000
   chunk 122 optimal weight:    7.9990
   chunk 109 optimal weight:    8.9990
   chunk 10 optimal weight:   30.0000
   chunk 6 optimal weight:    0.9980
   chunk 34 optimal weight:    4.9990
   chunk 38 optimal weight:    9.9990
   chunk 42 optimal weight:    5.9990
   chunk 49 optimal weight:    0.7980
   chunk 71 optimal weight:   10.0000
   overall best weight:    3.1586

-------------------------------------------------------------------------------
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 = 0.4283 r_free = 0.4283 target = 0.113525 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3779 r_free = 0.3779 target = 0.075479 restraints weight = 34471.932|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3827 r_free = 0.3827 target = 0.078647 restraints weight = 18076.485|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3858 r_free = 0.3858 target = 0.080706 restraints weight = 12418.651|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 42)----------------|
| r_work = 0.3877 r_free = 0.3877 target = 0.082038 restraints weight = 9873.947|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3890 r_free = 0.3890 target = 0.082886 restraints weight = 8540.136|
|-----------------------------------------------------------------------------|
r_work (final): 0.3833
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7821
moved from start:          0.1986

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   9984  Z= 0.188
  Angle     :  0.826  10.202  13560  Z= 0.414
  Chirality :  0.047   0.162   1480
  Planarity :  0.003   0.027   1740
  Dihedral  :  5.127  22.149   1340
  Min Nonbonded Distance : 2.569

Molprobity Statistics.
  All-atom Clashscore : 14.40
  Ramachandran Plot:
    Outliers :  0.32 %
    Allowed  : 13.54 %
    Favored  : 86.14 %
  Rotamer:
    Outliers :  3.71 %
    Allowed  : 30.96 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.61 (0.25), residues: 1248
  helix:  0.47 (0.52), residues: 132
  sheet: -1.29 (0.45), residues: 120
  loop : -1.37 (0.21), residues: 996

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 257 
 TYR   0.008   0.001   TYR C 323 
 PHE   0.011   0.001   PHE A 217 
 TRP   0.041   0.002   TRP B 225 
 HIS   0.003   0.001   HIS B 195 

Details of bonding type rmsd
  covalent geometry    : bond        0.00400 ( 9964)
  covalent geometry    : angle       0.82676 (13520)
  SS BOND              : bond        0.00322 (   20)
  SS BOND              : angle       0.69548 (   40)
  hydrogen bonds       : bond        0.03352 (  213)
  hydrogen bonds       : angle       6.79012 (  492)

*********************** 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
  122 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 84
  time to evaluate  : 0.336 
Fit side-chains
REVERT: A  190 ASP cc_start: 0.9048 (OUTLIER) cc_final: 0.8728 (p0)
REVERT: A  242 ILE cc_start: 0.9334 (OUTLIER) cc_final: 0.8992 (mm)
REVERT: B   66 LEU cc_start: 0.9308 (mm) cc_final: 0.9043 (pp)
REVERT: B  190 ASP cc_start: 0.9059 (OUTLIER) cc_final: 0.8734 (p0)
REVERT: B  242 ILE cc_start: 0.9354 (OUTLIER) cc_final: 0.9016 (mm)
REVERT: B  323 TYR cc_start: 0.7091 (m-80) cc_final: 0.6401 (m-80)
REVERT: B  333 MET cc_start: 0.7917 (OUTLIER) cc_final: 0.7525 (ptp)
REVERT: C   66 LEU cc_start: 0.9281 (mm) cc_final: 0.9016 (pp)
REVERT: C  190 ASP cc_start: 0.8991 (OUTLIER) cc_final: 0.8693 (p0)
REVERT: C  242 ILE cc_start: 0.9316 (OUTLIER) cc_final: 0.8972 (mm)
REVERT: C  333 MET cc_start: 0.7783 (OUTLIER) cc_final: 0.7424 (ptp)
REVERT: D   66 LEU cc_start: 0.9301 (mm) cc_final: 0.9027 (pp)
REVERT: D  136 ASP cc_start: 0.9073 (t0) cc_final: 0.8515 (t70)
REVERT: D  190 ASP cc_start: 0.9060 (OUTLIER) cc_final: 0.8756 (p0)
REVERT: D  242 ILE cc_start: 0.9329 (OUTLIER) cc_final: 0.8993 (mm)
REVERT: D  275 MET cc_start: 0.8890 (mmp) cc_final: 0.8649 (mmp)
  outliers start: 38
  outliers final: 23
  residues processed: 113
  average time/residue: 0.0622
  time to fit residues: 11.4323
Evaluate side-chains
  115 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 82
  time to evaluate  : 0.388 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   57 ILE
Chi-restraints excluded: chain A residue   72 THR
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  329 CYS
Chi-restraints excluded: chain B residue   57 ILE
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  329 CYS
Chi-restraints excluded: chain B residue  333 MET
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  232 TRP
Chi-restraints excluded: chain C residue  242 ILE
Chi-restraints excluded: chain C residue  329 CYS
Chi-restraints excluded: chain C residue  333 MET
Chi-restraints excluded: chain D residue   57 ILE
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  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 61 optimal weight:    9.9990
   chunk 91 optimal weight:    7.9990
   chunk 77 optimal weight:   10.0000
   chunk 89 optimal weight:   20.0000
   chunk 40 optimal weight:    6.9990
   chunk 69 optimal weight:    8.9990
   chunk 82 optimal weight:    1.9990
   chunk 103 optimal weight:    9.9990
   chunk 60 optimal weight:    2.9990
   chunk 75 optimal weight:    0.3980
   chunk 104 optimal weight:    0.7980
   overall best weight:    2.6386

-------------------------------------------------------------------------------
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 = 0.4298 r_free = 0.4298 target = 0.114534 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3799 r_free = 0.3799 target = 0.076316 restraints weight = 34335.700|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3846 r_free = 0.3846 target = 0.079513 restraints weight = 17958.052|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3876 r_free = 0.3876 target = 0.081586 restraints weight = 12286.274|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3896 r_free = 0.3896 target = 0.082933 restraints weight = 9729.754|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3908 r_free = 0.3908 target = 0.083793 restraints weight = 8418.515|
|-----------------------------------------------------------------------------|
r_work (final): 0.3851
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7804
moved from start:          0.2032

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   9984  Z= 0.169
  Angle     :  0.823  10.041  13560  Z= 0.412
  Chirality :  0.046   0.164   1480
  Planarity :  0.003   0.027   1740
  Dihedral  :  5.113  22.535   1340
  Min Nonbonded Distance : 2.580

Molprobity Statistics.
  All-atom Clashscore : 13.50
  Ramachandran Plot:
    Outliers :  0.32 %
    Allowed  : 13.78 %
    Favored  : 85.90 %
  Rotamer:
    Outliers :  3.42 %
    Allowed  : 31.35 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.61 (0.25), residues: 1248
  helix:  0.46 (0.51), residues: 132
  sheet: -1.23 (0.46), residues: 120
  loop : -1.38 (0.21), residues: 996

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 257 
 TYR   0.010   0.001   TYR B 323 
 PHE   0.012   0.001   PHE A 277 
 TRP   0.041   0.002   TRP B 225 
 HIS   0.002   0.001   HIS C 261 

Details of bonding type rmsd
  covalent geometry    : bond        0.00362 ( 9964)
  covalent geometry    : angle       0.82373 (13520)
  SS BOND              : bond        0.00275 (   20)
  SS BOND              : angle       0.64142 (   40)
  hydrogen bonds       : bond        0.03292 (  213)
  hydrogen bonds       : angle       6.81217 (  492)

*********************** 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
  120 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 85
  time to evaluate  : 0.386 
Fit side-chains
REVERT: A  136 ASP cc_start: 0.9050 (t0) cc_final: 0.8092 (t70)
REVERT: A  190 ASP cc_start: 0.9031 (OUTLIER) cc_final: 0.8718 (p0)
REVERT: A  242 ILE cc_start: 0.9322 (OUTLIER) cc_final: 0.8979 (mm)
REVERT: A  275 MET cc_start: 0.8426 (mmp) cc_final: 0.8211 (mmp)
REVERT: B   66 LEU cc_start: 0.9298 (mm) cc_final: 0.9064 (pp)
REVERT: B  190 ASP cc_start: 0.9048 (OUTLIER) cc_final: 0.8740 (p0)
REVERT: B  238 GLU cc_start: 0.8892 (OUTLIER) cc_final: 0.8664 (mt-10)
REVERT: B  242 ILE cc_start: 0.9338 (OUTLIER) cc_final: 0.9018 (mm)
REVERT: B  323 TYR cc_start: 0.7372 (m-80) cc_final: 0.6957 (m-80)
REVERT: B  333 MET cc_start: 0.7883 (OUTLIER) cc_final: 0.7532 (ptp)
REVERT: C   26 HIS cc_start: 0.8125 (OUTLIER) cc_final: 0.7474 (t-90)
REVERT: C   66 LEU cc_start: 0.9302 (mm) cc_final: 0.9072 (pp)
REVERT: C  190 ASP cc_start: 0.8980 (OUTLIER) cc_final: 0.8676 (p0)
REVERT: C  242 ILE cc_start: 0.9348 (OUTLIER) cc_final: 0.9016 (mm)
REVERT: C  333 MET cc_start: 0.7691 (OUTLIER) cc_final: 0.7390 (ptp)
REVERT: D   66 LEU cc_start: 0.9314 (mm) cc_final: 0.9041 (pp)
REVERT: D  136 ASP cc_start: 0.9115 (t0) cc_final: 0.8597 (t70)
REVERT: D  190 ASP cc_start: 0.9012 (OUTLIER) cc_final: 0.8701 (p0)
  outliers start: 35
  outliers final: 23
  residues processed: 114
  average time/residue: 0.0656
  time to fit residues: 12.0820
Evaluate side-chains
  118 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 84
  time to evaluate  : 0.355 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   57 ILE
Chi-restraints excluded: chain A residue   72 THR
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  329 CYS
Chi-restraints excluded: chain B residue   57 ILE
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  238 GLU
Chi-restraints excluded: chain B residue  242 ILE
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  232 TRP
Chi-restraints excluded: chain C residue  242 ILE
Chi-restraints excluded: chain C residue  329 CYS
Chi-restraints excluded: chain C residue  333 MET
Chi-restraints excluded: chain D residue   57 ILE
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  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 36 optimal weight:    8.9990
   chunk 38 optimal weight:   10.0000
   chunk 52 optimal weight:    5.9990
   chunk 107 optimal weight:    9.9990
   chunk 106 optimal weight:    0.9990
   chunk 22 optimal weight:    0.8980
   chunk 81 optimal weight:   10.0000
   chunk 19 optimal weight:    2.9990
   chunk 80 optimal weight:    7.9990
   chunk 42 optimal weight:    0.4980
   chunk 98 optimal weight:   10.0000
   overall best weight:    2.2786

-------------------------------------------------------------------------------
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 = 0.4297 r_free = 0.4297 target = 0.114479 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3803 r_free = 0.3803 target = 0.076288 restraints weight = 34055.695|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3849 r_free = 0.3849 target = 0.079498 restraints weight = 17919.866|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3880 r_free = 0.3880 target = 0.081604 restraints weight = 12324.038|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3900 r_free = 0.3900 target = 0.082951 restraints weight = 9766.890|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 41)----------------|
| r_work = 0.3912 r_free = 0.3912 target = 0.083807 restraints weight = 8454.462|
|-----------------------------------------------------------------------------|
r_work (final): 0.3854
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7785
moved from start:          0.2068

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   9984  Z= 0.160
  Angle     :  0.824  10.268  13560  Z= 0.411
  Chirality :  0.046   0.164   1480
  Planarity :  0.003   0.027   1740
  Dihedral  :  5.065  22.730   1340
  Min Nonbonded Distance : 2.581

Molprobity Statistics.
  All-atom Clashscore : 12.61
  Ramachandran Plot:
    Outliers :  0.32 %
    Allowed  : 14.18 %
    Favored  : 85.50 %
  Rotamer:
    Outliers :  3.32 %
    Allowed  : 31.74 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.62 (0.25), residues: 1248
  helix:  0.45 (0.51), residues: 132
  sheet: -1.29 (0.45), residues: 120
  loop : -1.37 (0.21), residues: 996

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 257 
 TYR   0.017   0.001   TYR A 323 
 PHE   0.012   0.001   PHE D 277 
 TRP   0.046   0.002   TRP B 225 
 HIS   0.002   0.001   HIS C 261 

Details of bonding type rmsd
  covalent geometry    : bond        0.00342 ( 9964)
  covalent geometry    : angle       0.82469 (13520)
  SS BOND              : bond        0.00254 (   20)
  SS BOND              : angle       0.60530 (   40)
  hydrogen bonds       : bond        0.03215 (  213)
  hydrogen bonds       : angle       6.77585 (  492)

********************** 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
  119 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 85
  time to evaluate  : 0.378 
Fit side-chains
REVERT: A  136 ASP cc_start: 0.9047 (t0) cc_final: 0.8159 (t70)
REVERT: A  190 ASP cc_start: 0.9014 (OUTLIER) cc_final: 0.8715 (p0)
REVERT: B   66 LEU cc_start: 0.9295 (mm) cc_final: 0.9059 (pp)
REVERT: B  190 ASP cc_start: 0.9034 (OUTLIER) cc_final: 0.8725 (p0)
REVERT: B  238 GLU cc_start: 0.8912 (OUTLIER) cc_final: 0.8676 (mt-10)
REVERT: B  242 ILE cc_start: 0.9340 (OUTLIER) cc_final: 0.9022 (mm)
REVERT: B  275 MET cc_start: 0.8911 (mmp) cc_final: 0.8560 (mmp)
REVERT: B  323 TYR cc_start: 0.7376 (m-80) cc_final: 0.6980 (m-80)
REVERT: B  333 MET cc_start: 0.7878 (OUTLIER) cc_final: 0.7539 (ptp)
REVERT: C   26 HIS cc_start: 0.8122 (OUTLIER) cc_final: 0.7475 (t-90)
REVERT: C   66 LEU cc_start: 0.9298 (mm) cc_final: 0.9075 (pp)
REVERT: C  190 ASP cc_start: 0.8965 (OUTLIER) cc_final: 0.8662 (p0)
REVERT: C  242 ILE cc_start: 0.9309 (OUTLIER) cc_final: 0.8956 (mm)
REVERT: D   66 LEU cc_start: 0.9310 (mm) cc_final: 0.9045 (pp)
REVERT: D  136 ASP cc_start: 0.9089 (t0) cc_final: 0.8348 (t70)
REVERT: D  190 ASP cc_start: 0.8995 (OUTLIER) cc_final: 0.8685 (p0)
REVERT: D  242 ILE cc_start: 0.9314 (OUTLIER) cc_final: 0.8993 (mm)
  outliers start: 34
  outliers final: 23
  residues processed: 113
  average time/residue: 0.0693
  time to fit residues: 12.6306
Evaluate side-chains
  117 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 84
  time to evaluate  : 0.309 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   57 ILE
Chi-restraints excluded: chain A residue   72 THR
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  329 CYS
Chi-restraints excluded: chain B residue   57 ILE
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  238 GLU
Chi-restraints excluded: chain B residue  242 ILE
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  232 TRP
Chi-restraints excluded: chain C residue  242 ILE
Chi-restraints excluded: chain C residue  329 CYS
Chi-restraints excluded: chain D residue   57 ILE
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  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 111 optimal weight:    0.9990
   chunk 4 optimal weight:    2.9990
   chunk 36 optimal weight:    8.9990
   chunk 53 optimal weight:    7.9990
   chunk 112 optimal weight:    6.9990
   chunk 29 optimal weight:    5.9990
   chunk 60 optimal weight:    1.9990
   chunk 121 optimal weight:    9.9990
   chunk 5 optimal weight:    5.9990
   chunk 1 optimal weight:    6.9990
   chunk 54 optimal weight:    6.9990
   overall best weight:    3.5990

-------------------------------------------------------------------------------
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 = 0.4273 r_free = 0.4273 target = 0.112843 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3763 r_free = 0.3763 target = 0.074813 restraints weight = 34562.648|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3811 r_free = 0.3811 target = 0.077891 restraints weight = 18206.827|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3842 r_free = 0.3842 target = 0.079957 restraints weight = 12481.512|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3862 r_free = 0.3862 target = 0.081293 restraints weight = 9920.819|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3868 r_free = 0.3868 target = 0.081972 restraints weight = 8596.561|
|-----------------------------------------------------------------------------|
r_work (final): 0.3811
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7830
moved from start:          0.2152

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045   9984  Z= 0.203
  Angle     :  0.844  10.072  13560  Z= 0.424
  Chirality :  0.047   0.163   1480
  Planarity :  0.004   0.026   1740
  Dihedral  :  5.248  22.247   1340
  Min Nonbonded Distance : 2.564

Molprobity Statistics.
  All-atom Clashscore : 15.56
  Ramachandran Plot:
    Outliers :  0.32 %
    Allowed  : 13.94 %
    Favored  : 85.74 %
  Rotamer:
    Outliers :  3.61 %
    Allowed  : 31.45 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.62 (0.25), residues: 1248
  helix:  0.50 (0.51), residues: 132
  sheet: -0.95 (0.56), residues: 96
  loop : -1.43 (0.20), residues: 1020

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 257 
 TYR   0.009   0.001   TYR B 323 
 PHE   0.015   0.002   PHE B 217 
 TRP   0.058   0.002   TRP A 225 
 HIS   0.003   0.001   HIS A 195 

Details of bonding type rmsd
  covalent geometry    : bond        0.00434 ( 9964)
  covalent geometry    : angle       0.84459 (13520)
  SS BOND              : bond        0.00359 (   20)
  SS BOND              : angle       0.64747 (   40)
  hydrogen bonds       : bond        0.03368 (  213)
  hydrogen bonds       : angle       6.94132 (  492)

===============================================================================
Job complete
usr+sys time: 1839.53 seconds
wall clock time: 32 minutes 32.70 seconds (1952.70 seconds total)