Starting phenix.real_space_refine
on Wed Mar  4 14:23:44 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6pwo_20509/03_2026/6pwo_20509.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6pwo_20509/03_2026/6pwo_20509.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.4
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/6pwo_20509/03_2026/6pwo_20509.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6pwo_20509/03_2026/6pwo_20509.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/6pwo_20509/03_2026/6pwo_20509.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6pwo_20509/03_2026/6pwo_20509.map"
  }
  resolution = 3.4
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.002
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      42      5.16       5
     C    9142      2.51       5
     N    2478      2.21       5
     O    2555      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 14 residue(s): 0.02s

  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: 14217
  Number of models: 1
  Model: ""
    Number of chains: 7
    Chain: "A"
      Number of atoms: 2031
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 266, 2031
          Classifications: {'peptide': 266}
          Link IDs: {'PTRANS': 5, 'TRANS': 260}
    Chain: "B"
      Number of atoms: 2031
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 266, 2031
          Classifications: {'peptide': 266}
          Link IDs: {'PTRANS': 5, 'TRANS': 260}
    Chain: "C"
      Number of atoms: 2031
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 266, 2031
          Classifications: {'peptide': 266}
          Link IDs: {'PTRANS': 5, 'TRANS': 260}
    Chain: "D"
      Number of atoms: 2031
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 266, 2031
          Classifications: {'peptide': 266}
          Link IDs: {'PTRANS': 5, 'TRANS': 260}
    Chain: "E"
      Number of atoms: 2031
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 266, 2031
          Classifications: {'peptide': 266}
          Link IDs: {'PTRANS': 5, 'TRANS': 260}
    Chain: "F"
      Number of atoms: 2031
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 266, 2031
          Classifications: {'peptide': 266}
          Link IDs: {'PTRANS': 5, 'TRANS': 260}
    Chain: "G"
      Number of atoms: 2031
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 266, 2031
          Classifications: {'peptide': 266}
          Link IDs: {'PTRANS': 5, 'TRANS': 260}
  Time building chain proxies: 2.84, per 1000 atoms: 0.20
  Number of scatterers: 14217
  At special positions: 0
  Unit cell: (97.888, 100.016, 146.832, 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      42     16.00
     O    2555      8.00
     N    2478      7.00
     C    9142      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.94
  Conformation dependent library (CDL) restraints added in 685.1 milliseconds
  

  3696 Ramachandran restraints generated.
    1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3444

  Finding SS restraints...
    Secondary structure from input PDB file:
      49 helices and 9 sheets defined
      56.1% alpha, 19.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.45
  Creating SS restraints...
    Processing helix  chain 'A' and resid 15 through 20
      removed outlier: 3.698A  pdb=" N   ALA A  19 " --> pdb=" O   SER A  15 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 20 through 57
    Processing helix  chain 'A' and resid 65 through 90
    Processing helix  chain 'A' and resid 93 through 128
      removed outlier: 4.438A  pdb=" N   GLY A 113 " --> pdb=" O   LEU A 109 " (cutoff:3.500A)
      removed outlier: 5.100A  pdb=" N   SER A 114 " --> pdb=" O   ALA A 110 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 167 through 173
      removed outlier: 3.855A  pdb=" N   ALA A 172 " --> pdb=" O   GLY A 168 " (cutoff:3.500A)
      removed outlier: 3.613A  pdb=" N   GLY A 173 " --> pdb=" O   LYS A 169 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 197 through 212
      removed outlier: 3.644A  pdb=" N   VAL A 201 " --> pdb=" O   ASP A 197 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 245 through 265
    Processing helix  chain 'B' and resid 16 through 20
    Processing helix  chain 'B' and resid 20 through 57
    Processing helix  chain 'B' and resid 65 through 90
    Processing helix  chain 'B' and resid 93 through 128
      removed outlier: 4.438A  pdb=" N   GLY B 113 " --> pdb=" O   LEU B 109 " (cutoff:3.500A)
      removed outlier: 5.099A  pdb=" N   SER B 114 " --> pdb=" O   ALA B 110 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 167 through 173
      removed outlier: 3.855A  pdb=" N   ALA B 172 " --> pdb=" O   GLY B 168 " (cutoff:3.500A)
      removed outlier: 3.612A  pdb=" N   GLY B 173 " --> pdb=" O   LYS B 169 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 197 through 212
      removed outlier: 3.644A  pdb=" N   VAL B 201 " --> pdb=" O   ASP B 197 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 245 through 265
    Processing helix  chain 'C' and resid 16 through 20
    Processing helix  chain 'C' and resid 20 through 57
    Processing helix  chain 'C' and resid 65 through 90
    Processing helix  chain 'C' and resid 93 through 128
      removed outlier: 4.438A  pdb=" N   GLY C 113 " --> pdb=" O   LEU C 109 " (cutoff:3.500A)
      removed outlier: 5.099A  pdb=" N   SER C 114 " --> pdb=" O   ALA C 110 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 167 through 173
      removed outlier: 3.855A  pdb=" N   ALA C 172 " --> pdb=" O   GLY C 168 " (cutoff:3.500A)
      removed outlier: 3.612A  pdb=" N   GLY C 173 " --> pdb=" O   LYS C 169 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 197 through 212
      removed outlier: 3.644A  pdb=" N   VAL C 201 " --> pdb=" O   ASP C 197 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 245 through 265
    Processing helix  chain 'D' and resid 16 through 20
    Processing helix  chain 'D' and resid 20 through 57
    Processing helix  chain 'D' and resid 65 through 90
    Processing helix  chain 'D' and resid 93 through 128
      removed outlier: 4.438A  pdb=" N   GLY D 113 " --> pdb=" O   LEU D 109 " (cutoff:3.500A)
      removed outlier: 5.100A  pdb=" N   SER D 114 " --> pdb=" O   ALA D 110 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 167 through 173
      removed outlier: 3.855A  pdb=" N   ALA D 172 " --> pdb=" O   GLY D 168 " (cutoff:3.500A)
      removed outlier: 3.613A  pdb=" N   GLY D 173 " --> pdb=" O   LYS D 169 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 197 through 212
      removed outlier: 3.645A  pdb=" N   VAL D 201 " --> pdb=" O   ASP D 197 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 245 through 265
    Processing helix  chain 'E' and resid 16 through 20
    Processing helix  chain 'E' and resid 20 through 57
    Processing helix  chain 'E' and resid 65 through 90
    Processing helix  chain 'E' and resid 93 through 128
      removed outlier: 4.438A  pdb=" N   GLY E 113 " --> pdb=" O   LEU E 109 " (cutoff:3.500A)
      removed outlier: 5.099A  pdb=" N   SER E 114 " --> pdb=" O   ALA E 110 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 167 through 173
      removed outlier: 3.855A  pdb=" N   ALA E 172 " --> pdb=" O   GLY E 168 " (cutoff:3.500A)
      removed outlier: 3.612A  pdb=" N   GLY E 173 " --> pdb=" O   LYS E 169 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 197 through 212
      removed outlier: 3.644A  pdb=" N   VAL E 201 " --> pdb=" O   ASP E 197 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 245 through 265
    Processing helix  chain 'F' and resid 16 through 20
    Processing helix  chain 'F' and resid 20 through 57
    Processing helix  chain 'F' and resid 65 through 90
    Processing helix  chain 'F' and resid 93 through 128
      removed outlier: 4.438A  pdb=" N   GLY F 113 " --> pdb=" O   LEU F 109 " (cutoff:3.500A)
      removed outlier: 5.100A  pdb=" N   SER F 114 " --> pdb=" O   ALA F 110 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 167 through 173
      removed outlier: 3.854A  pdb=" N   ALA F 172 " --> pdb=" O   GLY F 168 " (cutoff:3.500A)
      removed outlier: 3.613A  pdb=" N   GLY F 173 " --> pdb=" O   LYS F 169 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 197 through 212
      removed outlier: 3.644A  pdb=" N   VAL F 201 " --> pdb=" O   ASP F 197 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 245 through 265
    Processing helix  chain 'G' and resid 16 through 20
    Processing helix  chain 'G' and resid 20 through 57
    Processing helix  chain 'G' and resid 65 through 90
    Processing helix  chain 'G' and resid 93 through 128
      removed outlier: 4.438A  pdb=" N   GLY G 113 " --> pdb=" O   LEU G 109 " (cutoff:3.500A)
      removed outlier: 5.099A  pdb=" N   SER G 114 " --> pdb=" O   ALA G 110 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 167 through 173
      removed outlier: 3.854A  pdb=" N   ALA G 172 " --> pdb=" O   GLY G 168 " (cutoff:3.500A)
      removed outlier: 3.612A  pdb=" N   GLY G 173 " --> pdb=" O   LYS G 169 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 197 through 212
      removed outlier: 3.644A  pdb=" N   VAL G 201 " --> pdb=" O   ASP G 197 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 245 through 265
    Processing sheet with id=AA1, first strand: chain 'A' and resid 135 through 137
      removed outlier: 7.360A  pdb=" N   THR A 154 " --> pdb=" O   LEU A 146 " (cutoff:3.500A)
      removed outlier: 5.690A  pdb=" N   VAL A 148 " --> pdb=" O   SER A 152 " (cutoff:3.500A)
      removed outlier: 7.341A  pdb=" N   SER A 152 " --> pdb=" O   VAL A 148 " (cutoff:3.500A)
      removed outlier: 4.048A  pdb=" N   ILE A 162 " --> pdb=" O   ASN B 177 " (cutoff:3.500A)
      removed outlier: 7.359A  pdb=" N   THR B 154 " --> pdb=" O   LEU B 146 " (cutoff:3.500A)
      removed outlier: 5.690A  pdb=" N   VAL B 148 " --> pdb=" O   SER B 152 " (cutoff:3.500A)
      removed outlier: 7.341A  pdb=" N   SER B 152 " --> pdb=" O   VAL B 148 " (cutoff:3.500A)
      removed outlier: 4.132A  pdb=" N   ILE B 162 " --> pdb=" O   ASN C 177 " (cutoff:3.500A)
      removed outlier: 7.360A  pdb=" N   THR C 154 " --> pdb=" O   LEU C 146 " (cutoff:3.500A)
      removed outlier: 5.690A  pdb=" N   VAL C 148 " --> pdb=" O   SER C 152 " (cutoff:3.500A)
      removed outlier: 7.341A  pdb=" N   SER C 152 " --> pdb=" O   VAL C 148 " (cutoff:3.500A)
      removed outlier: 3.961A  pdb=" N   ILE C 162 " --> pdb=" O   ASN D 177 " (cutoff:3.500A)
      removed outlier: 7.360A  pdb=" N   THR D 154 " --> pdb=" O   LEU D 146 " (cutoff:3.500A)
      removed outlier: 5.690A  pdb=" N   VAL D 148 " --> pdb=" O   SER D 152 " (cutoff:3.500A)
      removed outlier: 7.341A  pdb=" N   SER D 152 " --> pdb=" O   VAL D 148 " (cutoff:3.500A)
      removed outlier: 4.027A  pdb=" N   ILE D 162 " --> pdb=" O   ASN E 177 " (cutoff:3.500A)
      removed outlier: 7.360A  pdb=" N   THR E 154 " --> pdb=" O   LEU E 146 " (cutoff:3.500A)
      removed outlier: 5.690A  pdb=" N   VAL E 148 " --> pdb=" O   SER E 152 " (cutoff:3.500A)
      removed outlier: 7.341A  pdb=" N   SER E 152 " --> pdb=" O   VAL E 148 " (cutoff:3.500A)
      removed outlier: 4.102A  pdb=" N   ILE E 162 " --> pdb=" O   ASN F 177 " (cutoff:3.500A)
      removed outlier: 7.360A  pdb=" N   THR F 154 " --> pdb=" O   LEU F 146 " (cutoff:3.500A)
      removed outlier: 5.690A  pdb=" N   VAL F 148 " --> pdb=" O   SER F 152 " (cutoff:3.500A)
      removed outlier: 7.341A  pdb=" N   SER F 152 " --> pdb=" O   VAL F 148 " (cutoff:3.500A)
      removed outlier: 4.024A  pdb=" N   ILE F 162 " --> pdb=" O   ASN G 177 " (cutoff:3.500A)
      removed outlier: 7.359A  pdb=" N   THR G 154 " --> pdb=" O   LEU G 146 " (cutoff:3.500A)
      removed outlier: 5.690A  pdb=" N   VAL G 148 " --> pdb=" O   SER G 152 " (cutoff:3.500A)
      removed outlier: 7.341A  pdb=" N   SER G 152 " --> pdb=" O   VAL G 148 " (cutoff:3.500A)
      removed outlier: 4.041A  pdb=" N   ILE G 162 " --> pdb=" O   ASN A 177 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 183 through 192
      removed outlier: 7.461A  pdb=" N   ASN A 234 " --> pdb=" O   ASN A 226 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 272 through 279
      removed outlier: 3.586A  pdb=" N   LYS B 278 " --> pdb=" O   VAL A 275 " (cutoff:3.500A)
      removed outlier: 3.511A  pdb=" N   PHE A 277 " --> pdb=" O   LYS B 278 " (cutoff:3.500A)
      removed outlier: 6.439A  pdb=" N   MET B 273 " --> pdb=" O   ASN C 276 " (cutoff:3.500A)
      removed outlier: 7.917A  pdb=" N   LYS C 278 " --> pdb=" O   MET B 273 " (cutoff:3.500A)
      removed outlier: 6.111A  pdb=" N   VAL B 275 " --> pdb=" O   LYS C 278 " (cutoff:3.500A)
      removed outlier: 6.521A  pdb=" N   MET C 273 " --> pdb=" O   ASN D 276 " (cutoff:3.500A)
      removed outlier: 8.014A  pdb=" N   LYS D 278 " --> pdb=" O   MET C 273 " (cutoff:3.500A)
      removed outlier: 6.229A  pdb=" N   VAL C 275 " --> pdb=" O   LYS D 278 " (cutoff:3.500A)
      removed outlier: 6.555A  pdb=" N   MET D 273 " --> pdb=" O   ASN E 276 " (cutoff:3.500A)
      removed outlier: 8.046A  pdb=" N   LYS E 278 " --> pdb=" O   MET D 273 " (cutoff:3.500A)
      removed outlier: 6.226A  pdb=" N   VAL D 275 " --> pdb=" O   LYS E 278 " (cutoff:3.500A)
      removed outlier: 6.446A  pdb=" N   MET E 273 " --> pdb=" O   ASN F 276 " (cutoff:3.500A)
      removed outlier: 7.923A  pdb=" N   LYS F 278 " --> pdb=" O   MET E 273 " (cutoff:3.500A)
      removed outlier: 6.119A  pdb=" N   VAL E 275 " --> pdb=" O   LYS F 278 " (cutoff:3.500A)
      removed outlier: 6.519A  pdb=" N   MET F 273 " --> pdb=" O   ASN G 276 " (cutoff:3.500A)
      removed outlier: 8.014A  pdb=" N   LYS G 278 " --> pdb=" O   MET F 273 " (cutoff:3.500A)
      removed outlier: 6.231A  pdb=" N   VAL F 275 " --> pdb=" O   LYS G 278 " (cutoff:3.500A)
      removed outlier: 3.651A  pdb=" N   LYS A 278 " --> pdb=" O   VAL G 275 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 183 through 192
      removed outlier: 7.462A  pdb=" N   ASN B 234 " --> pdb=" O   ASN B 226 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'C' and resid 183 through 192
      removed outlier: 7.461A  pdb=" N   ASN C 234 " --> pdb=" O   ASN C 226 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'D' and resid 183 through 192
      removed outlier: 7.462A  pdb=" N   ASN D 234 " --> pdb=" O   ASN D 226 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'E' and resid 183 through 192
      removed outlier: 7.462A  pdb=" N   ASN E 234 " --> pdb=" O   ASN E 226 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'F' and resid 183 through 192
      removed outlier: 7.462A  pdb=" N   ASN F 234 " --> pdb=" O   ASN F 226 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'G' and resid 183 through 192
      removed outlier: 7.461A  pdb=" N   ASN G 234 " --> pdb=" O   ASN G 226 " (cutoff:3.500A)

    1022 hydrogen bonds defined for protein.
    3003 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.51

  Time building geometry restraints manager: 1.33 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: 4725
        1.34 -     1.46: 2750
        1.46 -     1.58: 6847
        1.58 -     1.69: 0
        1.69 -     1.81: 84
  Bond restraints: 14406
  Sorted by residual:
  bond pdb=" N   ARG A  88 "
       pdb=" CA  ARG A  88 "
    ideal  model  delta    sigma   weight residual
    1.459  1.488 -0.029 1.21e-02 6.83e+03 5.89e+00
  bond pdb=" N   ARG C  88 "
       pdb=" CA  ARG C  88 "
    ideal  model  delta    sigma   weight residual
    1.459  1.488 -0.029 1.21e-02 6.83e+03 5.79e+00
  bond pdb=" N   ARG G  88 "
       pdb=" CA  ARG G  88 "
    ideal  model  delta    sigma   weight residual
    1.459  1.488 -0.029 1.21e-02 6.83e+03 5.68e+00
  bond pdb=" N   ARG D  88 "
       pdb=" CA  ARG D  88 "
    ideal  model  delta    sigma   weight residual
    1.459  1.488 -0.029 1.21e-02 6.83e+03 5.68e+00
  bond pdb=" N   ARG E  88 "
       pdb=" CA  ARG E  88 "
    ideal  model  delta    sigma   weight residual
    1.459  1.488 -0.029 1.21e-02 6.83e+03 5.66e+00
  ... (remaining 14401 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.47: 19069
        1.47 -     2.94: 391
        2.94 -     4.41: 70
        4.41 -     5.88: 8
        5.88 -     7.35: 13
  Bond angle restraints: 19551
  Sorted by residual:
  angle pdb=" C   LEU D 138 "
        pdb=" N   GLY D 139 "
        pdb=" CA  GLY D 139 "
      ideal   model   delta    sigma   weight residual
     121.41  128.76   -7.35 1.96e+00 2.60e-01 1.40e+01
  angle pdb=" C   LEU F 138 "
        pdb=" N   GLY F 139 "
        pdb=" CA  GLY F 139 "
      ideal   model   delta    sigma   weight residual
     121.41  128.75   -7.34 1.96e+00 2.60e-01 1.40e+01
  angle pdb=" C   LEU B 138 "
        pdb=" N   GLY B 139 "
        pdb=" CA  GLY B 139 "
      ideal   model   delta    sigma   weight residual
     121.41  128.75   -7.34 1.96e+00 2.60e-01 1.40e+01
  angle pdb=" C   LEU C 138 "
        pdb=" N   GLY C 139 "
        pdb=" CA  GLY C 139 "
      ideal   model   delta    sigma   weight residual
     121.41  128.74   -7.33 1.96e+00 2.60e-01 1.40e+01
  angle pdb=" C   LEU G 138 "
        pdb=" N   GLY G 139 "
        pdb=" CA  GLY G 139 "
      ideal   model   delta    sigma   weight residual
     121.41  128.73   -7.32 1.96e+00 2.60e-01 1.39e+01
  ... (remaining 19546 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.66: 7806
       17.66 -    35.32: 723
       35.32 -    52.98: 95
       52.98 -    70.64: 7
       70.64 -    88.30: 7
  Dihedral angle restraints: 8638
    sinusoidal: 3297
      harmonic: 5341
  Sorted by residual:
  dihedral pdb=" CA  ASN G 276 "
           pdb=" C   ASN G 276 "
           pdb=" N   PHE G 277 "
           pdb=" CA  PHE G 277 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -154.07  -25.93     0      5.00e+00 4.00e-02 2.69e+01
  dihedral pdb=" CA  ASN B 276 "
           pdb=" C   ASN B 276 "
           pdb=" N   PHE B 277 "
           pdb=" CA  PHE B 277 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -154.08  -25.92     0      5.00e+00 4.00e-02 2.69e+01
  dihedral pdb=" CA  ASN A 276 "
           pdb=" C   ASN A 276 "
           pdb=" N   PHE A 277 "
           pdb=" CA  PHE A 277 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -154.09  -25.91     0      5.00e+00 4.00e-02 2.68e+01
  ... (remaining 8635 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.042: 1763
       0.042 -    0.084: 452
       0.084 -    0.125: 151
       0.125 -    0.167: 16
       0.167 -    0.209: 19
  Chirality restraints: 2401
  Sorted by residual:
  chirality pdb=" CB  ILE E  61 "
            pdb=" CA  ILE E  61 "
            pdb=" CG1 ILE E  61 "
            pdb=" CG2 ILE E  61 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.44    0.21 2.00e-01 2.50e+01 1.09e+00
  chirality pdb=" CB  ILE C  61 "
            pdb=" CA  ILE C  61 "
            pdb=" CG1 ILE C  61 "
            pdb=" CG2 ILE C  61 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.44    0.21 2.00e-01 2.50e+01 1.08e+00
  chirality pdb=" CB  ILE B  61 "
            pdb=" CA  ILE B  61 "
            pdb=" CG1 ILE B  61 "
            pdb=" CG2 ILE B  61 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.44    0.21 2.00e-01 2.50e+01 1.05e+00
  ... (remaining 2398 not shown)

  Planarity restraints: 2471
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLY F  90 "    0.008 2.00e-02 2.50e+03   1.67e-02 2.79e+00
        pdb=" C   GLY F  90 "   -0.029 2.00e-02 2.50e+03
        pdb=" O   GLY F  90 "    0.011 2.00e-02 2.50e+03
        pdb=" N   VAL F  91 "    0.010 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLY D  90 "   -0.008 2.00e-02 2.50e+03   1.67e-02 2.79e+00
        pdb=" C   GLY D  90 "    0.029 2.00e-02 2.50e+03
        pdb=" O   GLY D  90 "   -0.011 2.00e-02 2.50e+03
        pdb=" N   VAL D  91 "   -0.010 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLY G  90 "    0.008 2.00e-02 2.50e+03   1.67e-02 2.78e+00
        pdb=" C   GLY G  90 "   -0.029 2.00e-02 2.50e+03
        pdb=" O   GLY G  90 "    0.011 2.00e-02 2.50e+03
        pdb=" N   VAL G  91 "    0.010 2.00e-02 2.50e+03
  ... (remaining 2468 not shown)

  Histogram of nonbonded interaction distances:
        2.41 -     2.91: 6203
        2.91 -     3.40: 15330
        3.40 -     3.90: 21746
        3.90 -     4.40: 23887
        4.40 -     4.90: 40510
  Nonbonded interactions: 107676
  Sorted by model distance:
  nonbonded pdb=" OD1 ASP E 197 "
            pdb=" N   ILE E 198 "
     model   vdw
     2.407 3.120
  nonbonded pdb=" OD1 ASP F 197 "
            pdb=" N   ILE F 198 "
     model   vdw
     2.407 3.120
  nonbonded pdb=" OD1 ASP B 197 "
            pdb=" N   ILE B 198 "
     model   vdw
     2.407 3.120
  nonbonded pdb=" OD1 ASP C 197 "
            pdb=" N   ILE C 198 "
     model   vdw
     2.407 3.120
  nonbonded pdb=" OD1 ASP D 197 "
            pdb=" N   ILE D 198 "
     model   vdw
     2.407 3.120
  ... (remaining 107671 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: 0.04
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'C'
  selection = chain 'D'
  selection = chain 'E'
  selection = chain 'F'
  selection = chain 'G'
}

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 individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.010
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.550
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.030
  Extract box with map and model:          0.190
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     12.730
  Find NCS groups from input model:        0.100
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.350
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   16.030
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8363
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      :  0.005   0.052  14406  Z= 0.262
  Angle     :  0.607   7.347  19551  Z= 0.363
  Chirality :  0.046   0.209   2401
  Planarity :  0.003   0.017   2471
  Dihedral  : 13.329  88.298   5194
  Min Nonbonded Distance : 2.407

Molprobity Statistics.
  All-atom Clashscore : 5.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.65 %
    Favored  : 97.35 %
  Rotamer:
    Outliers :  0.46 %
    Allowed  :  1.39 %
    Favored  : 98.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.76 (0.17), residues: 1848
  helix:  0.11 (0.14), residues: 966
  sheet: -0.00 (0.31), residues: 224
  loop : -1.51 (0.20), residues: 658

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG G 184 
 TYR   0.006   0.001   TYR E 250 
 PHE   0.012   0.002   PHE C 277 
 TRP   0.006   0.001   TRP A  16 

Details of bonding type rmsd
  covalent geometry    : bond        0.00532 (14406)
  covalent geometry    : angle       0.60737 (19551)
  hydrogen bonds       : bond        0.17898 ( 1022)
  hydrogen bonds       : angle       6.29489 ( 3003)

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

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

  3696 Ramachandran restraints generated.
    1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3696 Ramachandran restraints generated.
    1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  186 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 179
  time to evaluate  : 0.395 
Fit side-chains
REVERT: A   88 ARG cc_start: 0.8020 (OUTLIER) cc_final: 0.7457 (tpp-160)
REVERT: A  155 MET cc_start: 0.8812 (ptm) cc_final: 0.8566 (ptm)
REVERT: A  221 MET cc_start: 0.8451 (mtm) cc_final: 0.8207 (mtp)
REVERT: A  222 THR cc_start: 0.9241 (m) cc_final: 0.9026 (p)
REVERT: B   88 ARG cc_start: 0.8234 (OUTLIER) cc_final: 0.7764 (tpp-160)
REVERT: B  155 MET cc_start: 0.8883 (ptm) cc_final: 0.8413 (ptm)
REVERT: B  187 GLU cc_start: 0.8100 (tt0) cc_final: 0.7893 (tt0)
REVERT: C   88 ARG cc_start: 0.7918 (OUTLIER) cc_final: 0.7363 (tpp-160)
REVERT: D   88 ARG cc_start: 0.8127 (OUTLIER) cc_final: 0.7558 (tpp-160)
REVERT: E   88 ARG cc_start: 0.7641 (OUTLIER) cc_final: 0.7177 (tpp-160)
REVERT: E  227 GLU cc_start: 0.8240 (pt0) cc_final: 0.7986 (pm20)
REVERT: G   88 ARG cc_start: 0.8265 (OUTLIER) cc_final: 0.7760 (tpp-160)
  outliers start: 7
  outliers final: 1
  residues processed: 186
  average time/residue: 0.1240
  time to fit residues: 32.7514
Evaluate side-chains
  108 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 101
  time to evaluate  : 0.492 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   88 ARG
Chi-restraints excluded: chain B residue   88 ARG
Chi-restraints excluded: chain C residue   88 ARG
Chi-restraints excluded: chain D residue   88 ARG
Chi-restraints excluded: chain E residue   88 ARG
Chi-restraints excluded: chain F residue   88 ARG
Chi-restraints excluded: chain G residue   88 ARG
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 182
   random chunks:
   chunk 98 optimal weight:    5.9990
   chunk 107 optimal weight:    6.9990
   chunk 10 optimal weight:    3.9990
   chunk 66 optimal weight:    5.9990
   chunk 130 optimal weight:   40.0000
   chunk 124 optimal weight:    0.0980
   chunk 103 optimal weight:    7.9990
   chunk 77 optimal weight:    4.9990
   chunk 122 optimal weight:    5.9990
   chunk 91 optimal weight:    6.9990
   chunk 149 optimal weight:    3.9990
   overall best weight:    3.8188

-------------------------------------------------------------------------------
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 = 0.3396 r_free = 0.3396 target = 0.066159 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2904 r_free = 0.2904 target = 0.047273 restraints weight = 54202.450|
|-----------------------------------------------------------------------------|
r_work (start): 0.2836 rms_B_bonded: 3.76
r_work: 0.2673 rms_B_bonded: 4.59 restraints_weight: 0.5000
r_work (final): 0.2673
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8474
moved from start:          0.2612

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.032  14406  Z= 0.250
  Angle     :  0.592   6.036  19551  Z= 0.327
  Chirality :  0.043   0.134   2401
  Planarity :  0.003   0.027   2471
  Dihedral  :  5.084  51.994   2051
  Min Nonbonded Distance : 2.634

Molprobity Statistics.
  All-atom Clashscore : 4.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.79 %
    Favored  : 98.21 %
  Rotamer:
    Outliers :  0.79 %
    Allowed  : 10.52 %
    Favored  : 88.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.44 (0.19), residues: 1848
  helix:  1.91 (0.15), residues: 980
  sheet:  0.80 (0.29), residues: 273
  loop : -0.54 (0.25), residues: 595

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG F 180 
 TYR   0.005   0.001   TYR C 250 
 PHE   0.016   0.002   PHE C  80 
 TRP   0.007   0.001   TRP D 240 

Details of bonding type rmsd
  covalent geometry    : bond        0.00561 (14406)
  covalent geometry    : angle       0.59211 (19551)
  hydrogen bonds       : bond        0.05541 ( 1022)
  hydrogen bonds       : angle       4.48099 ( 3003)

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

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

  3696 Ramachandran restraints generated.
    1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3696 Ramachandran restraints generated.
    1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  134 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 122
  time to evaluate  : 0.540 
Fit side-chains
   revert: symmetry clash
REVERT: A  155 MET cc_start: 0.9267 (ptm) cc_final: 0.8993 (ptm)
REVERT: A  255 GLU cc_start: 0.9430 (tt0) cc_final: 0.9048 (tm-30)
REVERT: A  273 MET cc_start: 0.8169 (OUTLIER) cc_final: 0.7741 (ttm)
REVERT: B  155 MET cc_start: 0.9269 (ptm) cc_final: 0.8862 (ptm)
REVERT: B  203 GLN cc_start: 0.8749 (tp40) cc_final: 0.8406 (tp40)
REVERT: B  255 GLU cc_start: 0.9410 (tt0) cc_final: 0.9065 (tm-30)
REVERT: C  203 GLN cc_start: 0.8682 (tp40) cc_final: 0.8440 (tp40)
REVERT: C  255 GLU cc_start: 0.9446 (tt0) cc_final: 0.9119 (tm-30)
REVERT: D  155 MET cc_start: 0.9233 (ptm) cc_final: 0.8631 (ptm)
REVERT: D  255 GLU cc_start: 0.9438 (tt0) cc_final: 0.9008 (tm-30)
REVERT: D  273 MET cc_start: 0.8185 (ttm) cc_final: 0.7880 (ttp)
REVERT: E  227 GLU cc_start: 0.9268 (pt0) cc_final: 0.8814 (pm20)
REVERT: E  255 GLU cc_start: 0.9415 (tt0) cc_final: 0.8987 (tm-30)
REVERT: F  155 MET cc_start: 0.9261 (ptm) cc_final: 0.8978 (ptm)
REVERT: F  212 GLU cc_start: 0.8947 (tp30) cc_final: 0.8745 (tp30)
REVERT: F  255 GLU cc_start: 0.9408 (tt0) cc_final: 0.9060 (tm-30)
REVERT: F  273 MET cc_start: 0.7884 (ttp) cc_final: 0.7645 (ttp)
REVERT: G   56 MET cc_start: 0.4749 (OUTLIER) cc_final: 0.4509 (ptt)
REVERT: G  181 GLU cc_start: 0.9137 (tp30) cc_final: 0.8863 (tp30)
REVERT: G  255 GLU cc_start: 0.9462 (tt0) cc_final: 0.9019 (tm-30)
REVERT: G  260 GLU cc_start: 0.9485 (mm-30) cc_final: 0.9249 (mm-30)
REVERT: G  273 MET cc_start: 0.8069 (ttm) cc_final: 0.7727 (ttt)
  outliers start: 12
  outliers final: 1
  residues processed: 123
  average time/residue: 0.1000
  time to fit residues: 18.9750
Evaluate side-chains
  102 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 99
  time to evaluate  : 0.480 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  273 MET
Chi-restraints excluded: chain E residue   23 LEU
Chi-restraints excluded: chain G residue   56 MET
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 182
   random chunks:
   chunk 81 optimal weight:    9.9990
   chunk 57 optimal weight:   10.0000
   chunk 98 optimal weight:    0.9980
   chunk 129 optimal weight:    2.9990
   chunk 103 optimal weight:    4.9990
   chunk 51 optimal weight:    4.9990
   chunk 24 optimal weight:    1.9990
   chunk 48 optimal weight:    0.9990
   chunk 0 optimal weight:   50.0000
   chunk 125 optimal weight:    2.9990
   chunk 180 optimal weight:    0.9990
   overall best weight:    1.5988

-------------------------------------------------------------------------------
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 = 0.3428 r_free = 0.3428 target = 0.067505 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2945 r_free = 0.2945 target = 0.048651 restraints weight = 53398.074|
|-----------------------------------------------------------------------------|
r_work (start): 0.2880 rms_B_bonded: 3.82
r_work: 0.2721 rms_B_bonded: 4.66 restraints_weight: 0.5000
r_work (final): 0.2721
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8510
moved from start:          0.3167

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.022  14406  Z= 0.135
  Angle     :  0.496   8.020  19551  Z= 0.266
  Chirality :  0.040   0.119   2401
  Planarity :  0.003   0.020   2471
  Dihedral  :  4.384  16.207   2023
  Min Nonbonded Distance : 2.628

Molprobity Statistics.
  All-atom Clashscore : 4.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.52 %
    Favored  : 98.48 %
  Rotamer:
    Outliers :  0.86 %
    Allowed  : 13.36 %
    Favored  : 85.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.14 (0.19), residues: 1848
  helix:  2.43 (0.16), residues: 980
  sheet:  2.15 (0.32), residues: 224
  loop : -0.51 (0.22), residues: 644

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG F  88 
 TYR   0.004   0.001   TYR C 250 
 PHE   0.011   0.001   PHE D  80 
 TRP   0.004   0.001   TRP D  16 

Details of bonding type rmsd
  covalent geometry    : bond        0.00282 (14406)
  covalent geometry    : angle       0.49635 (19551)
  hydrogen bonds       : bond        0.04400 ( 1022)
  hydrogen bonds       : angle       3.93561 ( 3003)

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

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

  3696 Ramachandran restraints generated.
    1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3696 Ramachandran restraints generated.
    1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 113
  time to evaluate  : 0.546 
Fit side-chains
REVERT: A  203 GLN cc_start: 0.8797 (tp40) cc_final: 0.8315 (tm-30)
REVERT: A  255 GLU cc_start: 0.9411 (tt0) cc_final: 0.9056 (tm-30)
REVERT: A  260 GLU cc_start: 0.9530 (mm-30) cc_final: 0.9109 (mm-30)
REVERT: A  273 MET cc_start: 0.8487 (OUTLIER) cc_final: 0.8224 (ttp)
REVERT: B  203 GLN cc_start: 0.8698 (tp40) cc_final: 0.8394 (tp40)
REVERT: B  255 GLU cc_start: 0.9376 (tt0) cc_final: 0.9114 (tm-30)
REVERT: B  260 GLU cc_start: 0.9576 (mm-30) cc_final: 0.9373 (mm-30)
REVERT: C  134 GLU cc_start: 0.8214 (mt-10) cc_final: 0.7702 (tt0)
REVERT: C  255 GLU cc_start: 0.9442 (tt0) cc_final: 0.9029 (tm-30)
REVERT: D  155 MET cc_start: 0.9148 (ptm) cc_final: 0.8624 (ptm)
REVERT: D  203 GLN cc_start: 0.8778 (tp40) cc_final: 0.8558 (tp40)
REVERT: D  255 GLU cc_start: 0.9423 (tt0) cc_final: 0.9040 (tm-30)
REVERT: D  273 MET cc_start: 0.8475 (ttm) cc_final: 0.8241 (ttp)
REVERT: E  169 LYS cc_start: 0.9657 (ttpp) cc_final: 0.9308 (ttmt)
REVERT: E  203 GLN cc_start: 0.8657 (tp40) cc_final: 0.8255 (tp40)
REVERT: E  227 GLU cc_start: 0.9232 (pt0) cc_final: 0.8813 (pm20)
REVERT: E  255 GLU cc_start: 0.9441 (tt0) cc_final: 0.9126 (tm-30)
REVERT: F  155 MET cc_start: 0.9138 (ptm) cc_final: 0.8890 (ptm)
REVERT: G   56 MET cc_start: 0.4688 (OUTLIER) cc_final: 0.4421 (ptt)
REVERT: G  255 GLU cc_start: 0.9437 (tt0) cc_final: 0.9033 (tm-30)
REVERT: G  260 GLU cc_start: 0.9482 (mm-30) cc_final: 0.9236 (mm-30)
REVERT: G  273 MET cc_start: 0.8293 (ttm) cc_final: 0.7905 (ttp)
  outliers start: 13
  outliers final: 4
  residues processed: 122
  average time/residue: 0.1050
  time to fit residues: 19.5372
Evaluate side-chains
  109 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 103
  time to evaluate  : 0.512 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  273 MET
Chi-restraints excluded: chain C residue   23 LEU
Chi-restraints excluded: chain D residue  221 MET
Chi-restraints excluded: chain E residue  105 LEU
Chi-restraints excluded: chain F residue  170 ILE
Chi-restraints excluded: chain G residue   56 MET
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 182
   random chunks:
   chunk 69 optimal weight:    7.9990
   chunk 57 optimal weight:   10.0000
   chunk 130 optimal weight:   40.0000
   chunk 54 optimal weight:    5.9990
   chunk 77 optimal weight:    1.9990
   chunk 58 optimal weight:    8.9990
   chunk 127 optimal weight:    0.9980
   chunk 152 optimal weight:    1.9990
   chunk 170 optimal weight:    6.9990
   chunk 79 optimal weight:    6.9990
   chunk 129 optimal weight:    0.9990
   overall best weight:    2.3988

-------------------------------------------------------------------------------
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 = 0.3405 r_free = 0.3405 target = 0.066210 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2941 r_free = 0.2941 target = 0.048169 restraints weight = 53018.127|
|-----------------------------------------------------------------------------|
r_work (start): 0.2902 rms_B_bonded: 3.71
r_work: 0.2744 rms_B_bonded: 4.53 restraints_weight: 0.5000
r_work (final): 0.2744
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8561
moved from start:          0.3525

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.027  14406  Z= 0.165
  Angle     :  0.503   6.743  19551  Z= 0.268
  Chirality :  0.039   0.121   2401
  Planarity :  0.003   0.022   2471
  Dihedral  :  4.351  17.328   2023
  Min Nonbonded Distance : 2.625

Molprobity Statistics.
  All-atom Clashscore : 4.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.06 %
    Favored  : 97.94 %
  Rotamer:
    Outliers :  1.72 %
    Allowed  : 13.96 %
    Favored  : 84.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.40 (0.19), residues: 1848
  helix:  2.59 (0.16), residues: 987
  sheet:  2.44 (0.34), residues: 224
  loop : -0.40 (0.23), residues: 637

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG F  88 
 TYR   0.007   0.001   TYR C 250 
 PHE   0.012   0.001   PHE G  80 
 TRP   0.006   0.001   TRP C  16 

Details of bonding type rmsd
  covalent geometry    : bond        0.00364 (14406)
  covalent geometry    : angle       0.50280 (19551)
  hydrogen bonds       : bond        0.04422 ( 1022)
  hydrogen bonds       : angle       3.84442 ( 3003)

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

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

  3696 Ramachandran restraints generated.
    1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3696 Ramachandran restraints generated.
    1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 110
  time to evaluate  : 0.559 
Fit side-chains
REVERT: A  255 GLU cc_start: 0.9372 (tt0) cc_final: 0.9062 (tm-30)
REVERT: A  260 GLU cc_start: 0.9511 (mm-30) cc_final: 0.9157 (mm-30)
REVERT: B  203 GLN cc_start: 0.8748 (tp40) cc_final: 0.8406 (tp40)
REVERT: B  255 GLU cc_start: 0.9353 (tt0) cc_final: 0.9083 (tm-30)
REVERT: C  134 GLU cc_start: 0.8334 (mt-10) cc_final: 0.7804 (tt0)
REVERT: C  181 GLU cc_start: 0.8918 (tp30) cc_final: 0.8444 (tp30)
REVERT: C  255 GLU cc_start: 0.9417 (tt0) cc_final: 0.9099 (tm-30)
REVERT: D  255 GLU cc_start: 0.9408 (tt0) cc_final: 0.9095 (tm-30)
REVERT: D  273 MET cc_start: 0.8566 (ttm) cc_final: 0.8297 (ttp)
REVERT: E  126 MET cc_start: 0.9424 (tmm) cc_final: 0.9210 (tmm)
REVERT: E  127 PHE cc_start: 0.8979 (OUTLIER) cc_final: 0.8751 (m-10)
REVERT: E  169 LYS cc_start: 0.9677 (ttpp) cc_final: 0.9409 (ttpt)
REVERT: E  203 GLN cc_start: 0.8759 (tp40) cc_final: 0.8373 (tp40)
REVERT: E  227 GLU cc_start: 0.9236 (pt0) cc_final: 0.8671 (pm20)
REVERT: E  255 GLU cc_start: 0.9409 (tt0) cc_final: 0.9151 (tm-30)
REVERT: F  155 MET cc_start: 0.9184 (ptm) cc_final: 0.8910 (ptm)
REVERT: F  255 GLU cc_start: 0.9328 (tt0) cc_final: 0.8991 (tm-30)
REVERT: F  273 MET cc_start: 0.8306 (ttp) cc_final: 0.8105 (ttp)
REVERT: G   56 MET cc_start: 0.4744 (OUTLIER) cc_final: 0.4337 (ptt)
REVERT: G  126 MET cc_start: 0.9435 (tmm) cc_final: 0.9111 (tmm)
REVERT: G  255 GLU cc_start: 0.9427 (tt0) cc_final: 0.9072 (tm-30)
  outliers start: 26
  outliers final: 10
  residues processed: 129
  average time/residue: 0.1024
  time to fit residues: 20.1427
Evaluate side-chains
  112 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 100
  time to evaluate  : 0.453 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   47 MET
Chi-restraints excluded: chain A residue  124 LEU
Chi-restraints excluded: chain B residue  170 ILE
Chi-restraints excluded: chain C residue   23 LEU
Chi-restraints excluded: chain C residue   47 MET
Chi-restraints excluded: chain C residue  170 ILE
Chi-restraints excluded: chain D residue  221 MET
Chi-restraints excluded: chain E residue   23 LEU
Chi-restraints excluded: chain E residue  127 PHE
Chi-restraints excluded: chain F residue  170 ILE
Chi-restraints excluded: chain G residue   56 MET
Chi-restraints excluded: chain G residue  170 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 182
   random chunks:
   chunk 65 optimal weight:    0.6980
   chunk 172 optimal weight:    6.9990
   chunk 158 optimal weight:    5.9990
   chunk 179 optimal weight:    3.9990
   chunk 42 optimal weight:    4.9990
   chunk 103 optimal weight:    3.9990
   chunk 68 optimal weight:    1.9990
   chunk 38 optimal weight:    0.9990
   chunk 4 optimal weight:   40.0000
   chunk 40 optimal weight:    3.9990
   chunk 140 optimal weight:    1.9990
   overall best weight:    1.9388

-------------------------------------------------------------------------------
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 = 0.3412 r_free = 0.3412 target = 0.066709 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2912 r_free = 0.2912 target = 0.047666 restraints weight = 54067.032|
|-----------------------------------------------------------------------------|
r_work (start): 0.2895 rms_B_bonded: 3.89
r_work: 0.2733 rms_B_bonded: 4.67 restraints_weight: 0.5000
r_work (final): 0.2733
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8606
moved from start:          0.3781

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029  14406  Z= 0.141
  Angle     :  0.497   9.133  19551  Z= 0.261
  Chirality :  0.039   0.120   2401
  Planarity :  0.002   0.020   2471
  Dihedral  :  4.258  16.546   2023
  Min Nonbonded Distance : 2.617

Molprobity Statistics.
  All-atom Clashscore : 4.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.95 %
    Favored  : 98.05 %
  Rotamer:
    Outliers :  2.78 %
    Allowed  : 13.03 %
    Favored  : 84.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.50 (0.19), residues: 1848
  helix:  2.71 (0.16), residues: 987
  sheet:  2.49 (0.34), residues: 224
  loop : -0.42 (0.23), residues: 637

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG F  88 
 TYR   0.006   0.001   TYR C 250 
 PHE   0.008   0.001   PHE G  80 
 TRP   0.005   0.001   TRP C  16 

Details of bonding type rmsd
  covalent geometry    : bond        0.00309 (14406)
  covalent geometry    : angle       0.49661 (19551)
  hydrogen bonds       : bond        0.04122 ( 1022)
  hydrogen bonds       : angle       3.74256 ( 3003)

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

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

  3696 Ramachandran restraints generated.
    1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3696 Ramachandran restraints generated.
    1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  144 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 102
  time to evaluate  : 0.521 
Fit side-chains
   revert: symmetry clash
REVERT: A  141 VAL cc_start: 0.8830 (OUTLIER) cc_final: 0.8562 (m)
REVERT: A  255 GLU cc_start: 0.9374 (tt0) cc_final: 0.9087 (tm-30)
REVERT: A  260 GLU cc_start: 0.9487 (mm-30) cc_final: 0.9131 (mm-30)
REVERT: B  126 MET cc_start: 0.9477 (tmm) cc_final: 0.9256 (tmm)
REVERT: B  181 GLU cc_start: 0.8889 (tp30) cc_final: 0.8269 (tp30)
REVERT: B  203 GLN cc_start: 0.8751 (tp40) cc_final: 0.8460 (tp40)
REVERT: B  255 GLU cc_start: 0.9351 (tt0) cc_final: 0.9084 (tm-30)
REVERT: C  181 GLU cc_start: 0.8938 (tp30) cc_final: 0.8433 (tp30)
REVERT: C  255 GLU cc_start: 0.9425 (tt0) cc_final: 0.9157 (tm-30)
REVERT: D  255 GLU cc_start: 0.9402 (tt0) cc_final: 0.9116 (tm-30)
REVERT: D  273 MET cc_start: 0.8578 (ttm) cc_final: 0.8341 (ttp)
REVERT: E  126 MET cc_start: 0.9429 (tmm) cc_final: 0.9135 (tmm)
REVERT: E  127 PHE cc_start: 0.9019 (OUTLIER) cc_final: 0.8691 (m-10)
REVERT: E  169 LYS cc_start: 0.9670 (ttpp) cc_final: 0.9420 (ttpt)
REVERT: E  203 GLN cc_start: 0.8764 (tp40) cc_final: 0.8345 (tp40)
REVERT: E  227 GLU cc_start: 0.9235 (pt0) cc_final: 0.8892 (pm20)
REVERT: E  255 GLU cc_start: 0.9403 (tt0) cc_final: 0.9171 (tm-30)
REVERT: F  141 VAL cc_start: 0.8726 (OUTLIER) cc_final: 0.8521 (m)
REVERT: F  181 GLU cc_start: 0.8802 (tp30) cc_final: 0.8422 (tp30)
REVERT: F  255 GLU cc_start: 0.9336 (tt0) cc_final: 0.9033 (tm-30)
REVERT: F  273 MET cc_start: 0.8447 (ttp) cc_final: 0.8050 (ttp)
REVERT: G   56 MET cc_start: 0.4663 (OUTLIER) cc_final: 0.4220 (ptt)
REVERT: G  141 VAL cc_start: 0.8836 (OUTLIER) cc_final: 0.8625 (m)
REVERT: G  255 GLU cc_start: 0.9437 (tt0) cc_final: 0.9103 (tm-30)
REVERT: G  273 MET cc_start: 0.8435 (ttm) cc_final: 0.8085 (ttt)
  outliers start: 42
  outliers final: 14
  residues processed: 138
  average time/residue: 0.0982
  time to fit residues: 21.1492
Evaluate side-chains
  118 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 99
  time to evaluate  : 0.481 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  124 LEU
Chi-restraints excluded: chain A residue  141 VAL
Chi-restraints excluded: chain B residue  124 LEU
Chi-restraints excluded: chain B residue  136 VAL
Chi-restraints excluded: chain C residue   23 LEU
Chi-restraints excluded: chain C residue   47 MET
Chi-restraints excluded: chain C residue  124 LEU
Chi-restraints excluded: chain C residue  141 VAL
Chi-restraints excluded: chain C residue  170 ILE
Chi-restraints excluded: chain D residue  136 VAL
Chi-restraints excluded: chain E residue  127 PHE
Chi-restraints excluded: chain E residue  136 VAL
Chi-restraints excluded: chain F residue  136 VAL
Chi-restraints excluded: chain F residue  141 VAL
Chi-restraints excluded: chain F residue  170 ILE
Chi-restraints excluded: chain G residue   56 MET
Chi-restraints excluded: chain G residue  124 LEU
Chi-restraints excluded: chain G residue  141 VAL
Chi-restraints excluded: chain G residue  170 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 182
   random chunks:
   chunk 24 optimal weight:    0.8980
   chunk 46 optimal weight:    0.0070
   chunk 168 optimal weight:    0.0000
   chunk 157 optimal weight:    5.9990
   chunk 102 optimal weight:    0.9990
   chunk 45 optimal weight:    0.9980
   chunk 161 optimal weight:    6.9990
   chunk 172 optimal weight:    0.7980
   chunk 30 optimal weight:    1.9990
   chunk 75 optimal weight:    0.7980
   chunk 34 optimal weight:    7.9990
   overall best weight:    0.5002

-------------------------------------------------------------------------------
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 = 0.3457 r_free = 0.3457 target = 0.068476 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3005 r_free = 0.3005 target = 0.050490 restraints weight = 52756.073|
|-----------------------------------------------------------------------------|
r_work (start): 0.2966 rms_B_bonded: 3.83
r_work: 0.2800 rms_B_bonded: 4.63 restraints_weight: 0.5000
r_work (final): 0.2800
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8528
moved from start:          0.4085

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026  14406  Z= 0.100
  Angle     :  0.484   8.737  19551  Z= 0.250
  Chirality :  0.039   0.142   2401
  Planarity :  0.002   0.021   2471
  Dihedral  :  4.015  14.475   2023
  Min Nonbonded Distance : 2.649

Molprobity Statistics.
  All-atom Clashscore : 4.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.27 %
    Favored  : 97.73 %
  Rotamer:
    Outliers :  1.32 %
    Allowed  : 14.09 %
    Favored  : 84.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.57 (0.19), residues: 1848
  helix:  2.82 (0.16), residues: 987
  sheet:  2.48 (0.34), residues: 224
  loop : -0.46 (0.23), residues: 637

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG F  88 
 TYR   0.007   0.000   TYR G 250 
 PHE   0.009   0.001   PHE G  80 
 TRP   0.003   0.000   TRP A  16 

Details of bonding type rmsd
  covalent geometry    : bond        0.00196 (14406)
  covalent geometry    : angle       0.48374 (19551)
  hydrogen bonds       : bond        0.03505 ( 1022)
  hydrogen bonds       : angle       3.53498 ( 3003)

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

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

  3696 Ramachandran restraints generated.
    1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3696 Ramachandran restraints generated.
    1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 107
  time to evaluate  : 0.466 
Fit side-chains
   revert: symmetry clash
REVERT: A  203 GLN cc_start: 0.8788 (tp40) cc_final: 0.8301 (tm-30)
REVERT: A  255 GLU cc_start: 0.9388 (tt0) cc_final: 0.9049 (tm-30)
REVERT: A  260 GLU cc_start: 0.9477 (mm-30) cc_final: 0.9170 (mm-30)
REVERT: B  203 GLN cc_start: 0.8659 (tp40) cc_final: 0.8425 (tp40)
REVERT: B  255 GLU cc_start: 0.9350 (tt0) cc_final: 0.9119 (tm-30)
REVERT: C  181 GLU cc_start: 0.8919 (tp30) cc_final: 0.8381 (tp30)
REVERT: C  255 GLU cc_start: 0.9400 (tt0) cc_final: 0.9128 (tm-30)
REVERT: D  169 LYS cc_start: 0.9584 (tttm) cc_final: 0.9326 (tttt)
REVERT: D  255 GLU cc_start: 0.9384 (tt0) cc_final: 0.9103 (tm-30)
REVERT: D  260 GLU cc_start: 0.9539 (mm-30) cc_final: 0.9318 (mm-30)
REVERT: D  273 MET cc_start: 0.8668 (ttm) cc_final: 0.8457 (ttp)
REVERT: E  126 MET cc_start: 0.9397 (tmm) cc_final: 0.9115 (tmm)
REVERT: E  127 PHE cc_start: 0.8922 (OUTLIER) cc_final: 0.8633 (m-10)
REVERT: E  169 LYS cc_start: 0.9667 (ttpp) cc_final: 0.9405 (ttpt)
REVERT: E  203 GLN cc_start: 0.8670 (tp40) cc_final: 0.8426 (tm-30)
REVERT: E  227 GLU cc_start: 0.9236 (pt0) cc_final: 0.8868 (pm20)
REVERT: E  255 GLU cc_start: 0.9366 (tt0) cc_final: 0.9096 (tm-30)
REVERT: F  255 GLU cc_start: 0.9289 (tt0) cc_final: 0.8980 (tm-30)
REVERT: F  273 MET cc_start: 0.8438 (ttp) cc_final: 0.8128 (ttp)
REVERT: G  141 VAL cc_start: 0.8710 (OUTLIER) cc_final: 0.8457 (m)
REVERT: G  255 GLU cc_start: 0.9385 (tt0) cc_final: 0.9032 (tm-30)
REVERT: G  260 GLU cc_start: 0.9326 (mm-30) cc_final: 0.9087 (mm-30)
  outliers start: 20
  outliers final: 5
  residues processed: 123
  average time/residue: 0.0973
  time to fit residues: 18.6453
Evaluate side-chains
  109 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 102
  time to evaluate  : 0.493 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  124 LEU
Chi-restraints excluded: chain C residue  141 VAL
Chi-restraints excluded: chain E residue  124 LEU
Chi-restraints excluded: chain E residue  127 PHE
Chi-restraints excluded: chain F residue  221 MET
Chi-restraints excluded: chain G residue  141 VAL
Chi-restraints excluded: chain G residue  170 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 182
   random chunks:
   chunk 110 optimal weight:    9.9990
   chunk 66 optimal weight:    3.9990
   chunk 86 optimal weight:    5.9990
   chunk 61 optimal weight:   10.0000
   chunk 28 optimal weight:    6.9990
   chunk 169 optimal weight:    0.8980
   chunk 149 optimal weight:    3.9990
   chunk 174 optimal weight:    2.9990
   chunk 51 optimal weight:    6.9990
   chunk 0 optimal weight:   50.0000
   chunk 153 optimal weight:    1.9990
   overall best weight:    2.7788

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

Flipped N/Q/H residues before XYZ refinement:
G 203 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3402 r_free = 0.3402 target = 0.066066 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2927 r_free = 0.2927 target = 0.047815 restraints weight = 53238.790|
|-----------------------------------------------------------------------------|
r_work (start): 0.2891 rms_B_bonded: 3.71
r_work: 0.2732 rms_B_bonded: 4.50 restraints_weight: 0.5000
r_work (final): 0.2732
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8607
moved from start:          0.4085

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038  14406  Z= 0.181
  Angle     :  0.518   9.592  19551  Z= 0.273
  Chirality :  0.039   0.141   2401
  Planarity :  0.003   0.024   2471
  Dihedral  :  4.200  16.226   2023
  Min Nonbonded Distance : 2.642

Molprobity Statistics.
  All-atom Clashscore : 4.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.44 %
    Favored  : 97.56 %
  Rotamer:
    Outliers :  1.59 %
    Allowed  : 13.96 %
    Favored  : 84.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.56 (0.19), residues: 1848
  helix:  2.82 (0.16), residues: 987
  sheet:  2.45 (0.35), residues: 224
  loop : -0.49 (0.23), residues: 637

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG F  88 
 TYR   0.008   0.001   TYR C 250 
 PHE   0.010   0.001   PHE B 188 
 TRP   0.006   0.001   TRP E 240 

Details of bonding type rmsd
  covalent geometry    : bond        0.00406 (14406)
  covalent geometry    : angle       0.51826 (19551)
  hydrogen bonds       : bond        0.04162 ( 1022)
  hydrogen bonds       : angle       3.66964 ( 3003)

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

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

  3696 Ramachandran restraints generated.
    1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3696 Ramachandran restraints generated.
    1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 97
  time to evaluate  : 0.520 
Fit side-chains
   revert: symmetry clash
REVERT: A  255 GLU cc_start: 0.9383 (tt0) cc_final: 0.9114 (tm-30)
REVERT: A  260 GLU cc_start: 0.9474 (mm-30) cc_final: 0.9203 (mm-30)
REVERT: B  203 GLN cc_start: 0.8819 (tp40) cc_final: 0.8461 (tp40)
REVERT: B  255 GLU cc_start: 0.9352 (tt0) cc_final: 0.9113 (tm-30)
REVERT: C  181 GLU cc_start: 0.9000 (tp30) cc_final: 0.8457 (tp30)
REVERT: C  255 GLU cc_start: 0.9408 (tt0) cc_final: 0.9157 (tm-30)
REVERT: D  203 GLN cc_start: 0.8805 (tp40) cc_final: 0.8551 (tp40)
REVERT: D  255 GLU cc_start: 0.9406 (tt0) cc_final: 0.9152 (tm-30)
REVERT: E  126 MET cc_start: 0.9415 (tmm) cc_final: 0.8728 (tmm)
REVERT: E  127 PHE cc_start: 0.9016 (OUTLIER) cc_final: 0.8528 (m-10)
REVERT: E  169 LYS cc_start: 0.9689 (ttpp) cc_final: 0.9447 (ttpt)
REVERT: E  203 GLN cc_start: 0.8796 (tp40) cc_final: 0.8358 (tp40)
REVERT: E  255 GLU cc_start: 0.9376 (tt0) cc_final: 0.9165 (tm-30)
REVERT: E  273 MET cc_start: 0.8211 (ttm) cc_final: 0.7905 (ttp)
REVERT: F  181 GLU cc_start: 0.8774 (tp30) cc_final: 0.8411 (tp30)
REVERT: F  255 GLU cc_start: 0.9323 (tt0) cc_final: 0.9038 (tm-30)
REVERT: G  227 GLU cc_start: 0.8912 (pp20) cc_final: 0.8661 (pp20)
REVERT: G  255 GLU cc_start: 0.9415 (tt0) cc_final: 0.9090 (tm-30)
  outliers start: 24
  outliers final: 17
  residues processed: 117
  average time/residue: 0.0978
  time to fit residues: 17.7580
Evaluate side-chains
  113 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 95
  time to evaluate  : 0.508 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  124 LEU
Chi-restraints excluded: chain A residue  170 ILE
Chi-restraints excluded: chain B residue  124 LEU
Chi-restraints excluded: chain B residue  136 VAL
Chi-restraints excluded: chain B residue  170 ILE
Chi-restraints excluded: chain C residue  124 LEU
Chi-restraints excluded: chain C residue  141 VAL
Chi-restraints excluded: chain C residue  170 ILE
Chi-restraints excluded: chain D residue   23 LEU
Chi-restraints excluded: chain D residue  136 VAL
Chi-restraints excluded: chain E residue   23 LEU
Chi-restraints excluded: chain E residue  124 LEU
Chi-restraints excluded: chain E residue  127 PHE
Chi-restraints excluded: chain E residue  136 VAL
Chi-restraints excluded: chain F residue  136 VAL
Chi-restraints excluded: chain F residue  170 ILE
Chi-restraints excluded: chain F residue  221 MET
Chi-restraints excluded: chain G residue  170 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 182
   random chunks:
   chunk 152 optimal weight:    5.9990
   chunk 169 optimal weight:    0.0870
   chunk 146 optimal weight:    2.9990
   chunk 77 optimal weight:    3.9990
   chunk 118 optimal weight:    3.9990
   chunk 73 optimal weight:    3.9990
   chunk 65 optimal weight:    2.9990
   chunk 20 optimal weight:    2.9990
   chunk 52 optimal weight:   40.0000
   chunk 105 optimal weight:    8.9990
   chunk 135 optimal weight:    5.9990
   overall best weight:    2.6166

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

Flipped N/Q/H residues before XYZ refinement:
F 112 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3404 r_free = 0.3404 target = 0.066055 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2937 r_free = 0.2937 target = 0.048057 restraints weight = 53112.259|
|-----------------------------------------------------------------------------|
r_work (start): 0.2894 rms_B_bonded: 3.68
r_work: 0.2737 rms_B_bonded: 4.49 restraints_weight: 0.5000
r_work (final): 0.2737
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8566
moved from start:          0.4205

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030  14406  Z= 0.172
  Angle     :  0.526   9.674  19551  Z= 0.275
  Chirality :  0.039   0.126   2401
  Planarity :  0.003   0.022   2471
  Dihedral  :  4.257  15.891   2023
  Min Nonbonded Distance : 2.648

Molprobity Statistics.
  All-atom Clashscore : 4.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.27 %
    Favored  : 97.73 %
  Rotamer:
    Outliers :  1.79 %
    Allowed  : 14.09 %
    Favored  : 84.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.54 (0.19), residues: 1848
  helix:  2.79 (0.16), residues: 987
  sheet:  2.49 (0.35), residues: 224
  loop : -0.49 (0.23), residues: 637

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG F  88 
 TYR   0.007   0.001   TYR C 250 
 PHE   0.011   0.001   PHE C 188 
 TRP   0.005   0.001   TRP E 240 

Details of bonding type rmsd
  covalent geometry    : bond        0.00386 (14406)
  covalent geometry    : angle       0.52646 (19551)
  hydrogen bonds       : bond        0.04104 ( 1022)
  hydrogen bonds       : angle       3.66766 ( 3003)

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

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

  3696 Ramachandran restraints generated.
    1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3696 Ramachandran restraints generated.
    1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  123 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 96
  time to evaluate  : 0.396 
Fit side-chains
   revert: symmetry clash
REVERT: A  141 VAL cc_start: 0.8625 (OUTLIER) cc_final: 0.8348 (m)
REVERT: A  255 GLU cc_start: 0.9406 (tt0) cc_final: 0.9100 (tm-30)
REVERT: B  203 GLN cc_start: 0.8785 (tp40) cc_final: 0.8451 (tp40)
REVERT: B  255 GLU cc_start: 0.9382 (tt0) cc_final: 0.9111 (tm-30)
REVERT: C  181 GLU cc_start: 0.9051 (tp30) cc_final: 0.8441 (tp30)
REVERT: C  255 GLU cc_start: 0.9420 (tt0) cc_final: 0.9179 (tm-30)
REVERT: D  203 GLN cc_start: 0.8804 (tp40) cc_final: 0.8525 (tp40)
REVERT: D  255 GLU cc_start: 0.9427 (tt0) cc_final: 0.9141 (tm-30)
REVERT: E  126 MET cc_start: 0.9426 (tmm) cc_final: 0.8741 (tmm)
REVERT: E  127 PHE cc_start: 0.9014 (OUTLIER) cc_final: 0.8497 (m-10)
REVERT: E  169 LYS cc_start: 0.9700 (ttpp) cc_final: 0.9455 (ttpt)
REVERT: E  203 GLN cc_start: 0.8776 (tp40) cc_final: 0.8377 (tm-30)
REVERT: E  255 GLU cc_start: 0.9408 (tt0) cc_final: 0.9178 (tm-30)
REVERT: E  273 MET cc_start: 0.8341 (ttm) cc_final: 0.7994 (ttp)
REVERT: F  181 GLU cc_start: 0.8827 (tp30) cc_final: 0.8444 (tp30)
REVERT: F  255 GLU cc_start: 0.9348 (tt0) cc_final: 0.9091 (tm-30)
REVERT: G  227 GLU cc_start: 0.8956 (pp20) cc_final: 0.8627 (pp20)
REVERT: G  255 GLU cc_start: 0.9434 (tt0) cc_final: 0.9082 (tm-30)
  outliers start: 27
  outliers final: 20
  residues processed: 120
  average time/residue: 0.0951
  time to fit residues: 17.6610
Evaluate side-chains
  116 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 94
  time to evaluate  : 0.533 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  124 LEU
Chi-restraints excluded: chain A residue  141 VAL
Chi-restraints excluded: chain A residue  170 ILE
Chi-restraints excluded: chain B residue  124 LEU
Chi-restraints excluded: chain B residue  136 VAL
Chi-restraints excluded: chain B residue  170 ILE
Chi-restraints excluded: chain C residue   47 MET
Chi-restraints excluded: chain C residue  124 LEU
Chi-restraints excluded: chain C residue  127 PHE
Chi-restraints excluded: chain C residue  141 VAL
Chi-restraints excluded: chain C residue  170 ILE
Chi-restraints excluded: chain D residue   23 LEU
Chi-restraints excluded: chain D residue  136 VAL
Chi-restraints excluded: chain E residue   23 LEU
Chi-restraints excluded: chain E residue  124 LEU
Chi-restraints excluded: chain E residue  127 PHE
Chi-restraints excluded: chain E residue  136 VAL
Chi-restraints excluded: chain F residue  112 GLN
Chi-restraints excluded: chain F residue  170 ILE
Chi-restraints excluded: chain F residue  221 MET
Chi-restraints excluded: chain G residue   23 LEU
Chi-restraints excluded: chain G residue  170 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 182
   random chunks:
   chunk 172 optimal weight:    0.6980
   chunk 123 optimal weight:    1.9990
   chunk 47 optimal weight:    7.9990
   chunk 96 optimal weight:    6.9990
   chunk 178 optimal weight:    4.9990
   chunk 173 optimal weight:    4.9990
   chunk 0 optimal weight:   40.0000
   chunk 103 optimal weight:    3.9990
   chunk 33 optimal weight:    7.9990
   chunk 28 optimal weight:    5.9990
   chunk 175 optimal weight:    4.9990
   overall best weight:    3.3388

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

Flipped N/Q/H residues before XYZ refinement:
F 112 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3399 r_free = 0.3399 target = 0.064992 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2947 r_free = 0.2947 target = 0.047499 restraints weight = 54244.177|
|-----------------------------------------------------------------------------|
r_work (start): 0.2888 rms_B_bonded: 3.51
r_work: 0.2749 rms_B_bonded: 4.29 restraints_weight: 0.5000
r_work (final): 0.2749
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8671
moved from start:          0.4269

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.033  14406  Z= 0.210
  Angle     :  0.562   9.727  19551  Z= 0.294
  Chirality :  0.039   0.142   2401
  Planarity :  0.003   0.022   2471
  Dihedral  :  4.344  15.789   2023
  Min Nonbonded Distance : 2.439

Molprobity Statistics.
  All-atom Clashscore : 4.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.54 %
    Favored  : 97.46 %
  Rotamer:
    Outliers :  1.65 %
    Allowed  : 14.48 %
    Favored  : 83.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.50 (0.20), residues: 1848
  helix:  2.76 (0.16), residues: 987
  sheet:  2.47 (0.35), residues: 224
  loop : -0.52 (0.23), residues: 637

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG F  88 
 TYR   0.007   0.001   TYR C 250 
 PHE   0.010   0.001   PHE F 188 
 TRP   0.005   0.001   TRP E 240 

Details of bonding type rmsd
  covalent geometry    : bond        0.00477 (14406)
  covalent geometry    : angle       0.56195 (19551)
  hydrogen bonds       : bond        0.04354 ( 1022)
  hydrogen bonds       : angle       3.76431 ( 3003)

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

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

  3696 Ramachandran restraints generated.
    1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3696 Ramachandran restraints generated.
    1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 93
  time to evaluate  : 0.574 
Fit side-chains
   revert: symmetry clash
REVERT: A  141 VAL cc_start: 0.8759 (OUTLIER) cc_final: 0.8496 (m)
REVERT: A  255 GLU cc_start: 0.9348 (tt0) cc_final: 0.9123 (tm-30)
REVERT: B  203 GLN cc_start: 0.8823 (tp40) cc_final: 0.8472 (tp40)
REVERT: C  181 GLU cc_start: 0.9055 (tp30) cc_final: 0.8517 (tp30)
REVERT: D  203 GLN cc_start: 0.8798 (tp40) cc_final: 0.8361 (tm-30)
REVERT: E  126 MET cc_start: 0.9390 (tmm) cc_final: 0.8797 (tmm)
REVERT: E  127 PHE cc_start: 0.9091 (OUTLIER) cc_final: 0.8544 (m-10)
REVERT: E  169 LYS cc_start: 0.9677 (ttpp) cc_final: 0.9454 (ttpt)
REVERT: E  255 GLU cc_start: 0.9360 (tt0) cc_final: 0.9154 (tm-30)
REVERT: E  273 MET cc_start: 0.8362 (ttm) cc_final: 0.8004 (ttp)
REVERT: G  227 GLU cc_start: 0.8911 (pp20) cc_final: 0.8592 (pp20)
REVERT: G  255 GLU cc_start: 0.9393 (tt0) cc_final: 0.9121 (tm-30)
  outliers start: 25
  outliers final: 21
  residues processed: 115
  average time/residue: 0.1064
  time to fit residues: 18.8625
Evaluate side-chains
  112 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 89
  time to evaluate  : 0.532 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  124 LEU
Chi-restraints excluded: chain A residue  141 VAL
Chi-restraints excluded: chain A residue  170 ILE
Chi-restraints excluded: chain B residue  136 VAL
Chi-restraints excluded: chain B residue  170 ILE
Chi-restraints excluded: chain C residue   23 LEU
Chi-restraints excluded: chain C residue   47 MET
Chi-restraints excluded: chain C residue  124 LEU
Chi-restraints excluded: chain C residue  127 PHE
Chi-restraints excluded: chain C residue  141 VAL
Chi-restraints excluded: chain C residue  170 ILE
Chi-restraints excluded: chain D residue   23 LEU
Chi-restraints excluded: chain D residue  136 VAL
Chi-restraints excluded: chain E residue   23 LEU
Chi-restraints excluded: chain E residue  124 LEU
Chi-restraints excluded: chain E residue  127 PHE
Chi-restraints excluded: chain E residue  136 VAL
Chi-restraints excluded: chain F residue  112 GLN
Chi-restraints excluded: chain F residue  170 ILE
Chi-restraints excluded: chain F residue  221 MET
Chi-restraints excluded: chain G residue   23 LEU
Chi-restraints excluded: chain G residue  136 VAL
Chi-restraints excluded: chain G residue  170 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 182
   random chunks:
   chunk 177 optimal weight:    0.8980
   chunk 5 optimal weight:    6.9990
   chunk 15 optimal weight:    0.0870
   chunk 11 optimal weight:    3.9990
   chunk 61 optimal weight:    9.9990
   chunk 101 optimal weight:    1.9990
   chunk 118 optimal weight:    5.9990
   chunk 164 optimal weight:    5.9990
   chunk 121 optimal weight:    5.9990
   chunk 62 optimal weight:    0.9980
   chunk 7 optimal weight:    0.0970
   overall best weight:    0.8158

-------------------------------------------------------------------------------
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 = 0.3446 r_free = 0.3446 target = 0.067784 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2995 r_free = 0.2995 target = 0.049913 restraints weight = 51583.667|
|-----------------------------------------------------------------------------|
r_work (start): 0.2937 rms_B_bonded: 3.75
r_work: 0.2778 rms_B_bonded: 4.53 restraints_weight: 0.5000
r_work (final): 0.2778
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8517
moved from start:          0.4453

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033  14406  Z= 0.111
  Angle     :  0.544  10.474  19551  Z= 0.281
  Chirality :  0.039   0.139   2401
  Planarity :  0.003   0.024   2471
  Dihedral  :  4.115  14.639   2023
  Min Nonbonded Distance : 2.460

Molprobity Statistics.
  All-atom Clashscore : 4.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.38 %
    Favored  : 97.62 %
  Rotamer:
    Outliers :  0.53 %
    Allowed  : 15.81 %
    Favored  : 83.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.45 (0.20), residues: 1848
  helix:  2.73 (0.16), residues: 1015
  sheet:  2.36 (0.34), residues: 224
  loop : -0.69 (0.23), residues: 609

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG F  88 
 TYR   0.009   0.000   TYR B 250 
 PHE   0.008   0.001   PHE G 127 
 TRP   0.002   0.000   TRP A  16 

Details of bonding type rmsd
  covalent geometry    : bond        0.00234 (14406)
  covalent geometry    : angle       0.54362 (19551)
  hydrogen bonds       : bond        0.03708 ( 1022)
  hydrogen bonds       : angle       3.53892 ( 3003)

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

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

  3696 Ramachandran restraints generated.
    1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3696 Ramachandran restraints generated.
    1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 92
  time to evaluate  : 0.543 
Fit side-chains
   revert: symmetry clash
REVERT: A  141 VAL cc_start: 0.8595 (OUTLIER) cc_final: 0.8325 (m)
REVERT: A  203 GLN cc_start: 0.8839 (tp40) cc_final: 0.8353 (tm-30)
REVERT: A  255 GLU cc_start: 0.9385 (tt0) cc_final: 0.9035 (tm-30)
REVERT: A  260 GLU cc_start: 0.9287 (mm-30) cc_final: 0.9080 (mm-30)
REVERT: B  203 GLN cc_start: 0.8692 (tp40) cc_final: 0.8445 (tp40)
REVERT: C  181 GLU cc_start: 0.9063 (tp30) cc_final: 0.8417 (tp30)
REVERT: D  203 GLN cc_start: 0.8742 (tp40) cc_final: 0.8457 (tm-30)
REVERT: D  260 GLU cc_start: 0.9525 (mm-30) cc_final: 0.9279 (mm-30)
REVERT: E  126 MET cc_start: 0.9424 (tmm) cc_final: 0.8706 (tmm)
REVERT: E  127 PHE cc_start: 0.8967 (OUTLIER) cc_final: 0.8425 (m-10)
REVERT: E  169 LYS cc_start: 0.9693 (ttpp) cc_final: 0.9441 (ttpt)
REVERT: E  203 GLN cc_start: 0.8693 (tp40) cc_final: 0.8447 (tm-30)
REVERT: E  255 GLU cc_start: 0.9390 (tt0) cc_final: 0.9113 (tm-30)
REVERT: E  273 MET cc_start: 0.8317 (ttm) cc_final: 0.7800 (ttp)
REVERT: G  227 GLU cc_start: 0.8981 (pp20) cc_final: 0.8608 (pp20)
REVERT: G  255 GLU cc_start: 0.9406 (tt0) cc_final: 0.9026 (tm-30)
  outliers start: 8
  outliers final: 4
  residues processed: 99
  average time/residue: 0.1045
  time to fit residues: 16.0274
Evaluate side-chains
  97 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 91
  time to evaluate  : 0.403 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  141 VAL
Chi-restraints excluded: chain C residue  127 PHE
Chi-restraints excluded: chain C residue  141 VAL
Chi-restraints excluded: chain E residue  124 LEU
Chi-restraints excluded: chain E residue  127 PHE
Chi-restraints excluded: chain G residue  170 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 182
   random chunks:
   chunk 170 optimal weight:    4.9990
   chunk 123 optimal weight:    0.8980
   chunk 61 optimal weight:    9.9990
   chunk 116 optimal weight:   10.0000
   chunk 12 optimal weight:    8.9990
   chunk 26 optimal weight:   40.0000
   chunk 173 optimal weight:    7.9990
   chunk 14 optimal weight:    0.6980
   chunk 55 optimal weight:   10.0000
   chunk 36 optimal weight:    3.9990
   chunk 81 optimal weight:   10.0000
   overall best weight:    3.7186

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

Flipped N/Q/H residues before XYZ refinement:
F 112 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3396 r_free = 0.3396 target = 0.065524 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2950 r_free = 0.2950 target = 0.047994 restraints weight = 52573.834|
|-----------------------------------------------------------------------------|
r_work (start): 0.2887 rms_B_bonded: 3.56
r_work: 0.2737 rms_B_bonded: 4.35 restraints_weight: 0.5000
r_work (final): 0.2737
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8616
moved from start:          0.4411

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.040  14406  Z= 0.233
  Angle     :  0.591   9.865  19551  Z= 0.311
  Chirality :  0.040   0.147   2401
  Planarity :  0.003   0.025   2471
  Dihedral  :  4.372  16.488   2023
  Min Nonbonded Distance : 2.456

Molprobity Statistics.
  All-atom Clashscore : 5.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.76 %
    Favored  : 97.24 %
  Rotamer:
    Outliers :  0.99 %
    Allowed  : 15.61 %
    Favored  : 83.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.41 (0.20), residues: 1848
  helix:  2.67 (0.16), residues: 1015
  sheet:  2.39 (0.34), residues: 224
  loop : -0.66 (0.23), residues: 609

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG E 156 
 TYR   0.008   0.001   TYR C 250 
 PHE   0.011   0.001   PHE G 188 
 TRP   0.006   0.001   TRP D 240 

Details of bonding type rmsd
  covalent geometry    : bond        0.00529 (14406)
  covalent geometry    : angle       0.59136 (19551)
  hydrogen bonds       : bond        0.04525 ( 1022)
  hydrogen bonds       : angle       3.81761 ( 3003)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2826.91 seconds
wall clock time: 49 minutes 3.79 seconds (2943.79 seconds total)