Starting phenix.real_space_refine
on Wed Mar  4 13:09:16 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7onl_12997/03_2026/7onl_12997.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7onl_12997/03_2026/7onl_12997.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.9
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7onl_12997/03_2026/7onl_12997.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7onl_12997/03_2026/7onl_12997.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7onl_12997/03_2026/7onl_12997.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7onl_12997/03_2026/7onl_12997.cif"
  }
  resolution = 3.9
  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=   0.007
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    8932      2.51       5
     N    2436      2.21       5
     O    2513      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  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: 13923
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 1989
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 261, 1989
          Classifications: {'peptide': 261}
          Link IDs: {'PTRANS': 5, 'TRANS': 255}
  Restraints were copied for chains:
    B, C, D, E, F, G
  Time building chain proxies: 1.78, per 1000 atoms: 0.13
  Number of scatterers: 13923
  At special positions: 0
  Unit cell: (98.9055, 96.7785, 142.509, 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    2513      8.00
     N    2436      7.00
     C    8932      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: 0.95
  Conformation dependent library (CDL) restraints added in 645.0 milliseconds
  

  3626 Ramachandran restraints generated.
    1813 Oldfield, 0 Emsley, 1813 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3374

  Finding SS restraints...
    Secondary structure from input PDB file:
      42 helices and 9 sheets defined
      55.9% alpha, 19.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.37
  Creating SS restraints...
    Processing helix  chain 'A' and resid 22 through 59
      removed outlier: 3.502A  pdb=" N   ARG A  59 " --> pdb=" O   LEU A  55 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 62 through 90
    Processing helix  chain 'A' and resid 93 through 128
      removed outlier: 4.729A  pdb=" N   GLY A 113 " --> pdb=" O   LEU A 109 " (cutoff:3.500A)
      removed outlier: 5.014A  pdb=" N   SER A 114 " --> pdb=" O   ALA A 110 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 167 through 172
    Processing helix  chain 'A' and resid 197 through 212
      removed outlier: 3.564A  pdb=" N   GLU A 212 " --> pdb=" O   ILE A 208 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 245 through 265
    Processing helix  chain 'B' and resid 22 through 59
      removed outlier: 3.502A  pdb=" N   ARG B  59 " --> pdb=" O   LEU B  55 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 62 through 90
    Processing helix  chain 'B' and resid 93 through 128
      removed outlier: 4.730A  pdb=" N   GLY B 113 " --> pdb=" O   LEU B 109 " (cutoff:3.500A)
      removed outlier: 5.014A  pdb=" N   SER B 114 " --> pdb=" O   ALA B 110 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 167 through 172
    Processing helix  chain 'B' and resid 197 through 212
      removed outlier: 3.564A  pdb=" N   GLU B 212 " --> pdb=" O   ILE B 208 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 245 through 265
    Processing helix  chain 'C' and resid 22 through 59
      removed outlier: 3.503A  pdb=" N   ARG C  59 " --> pdb=" O   LEU C  55 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 62 through 90
    Processing helix  chain 'C' and resid 93 through 128
      removed outlier: 4.729A  pdb=" N   GLY C 113 " --> pdb=" O   LEU C 109 " (cutoff:3.500A)
      removed outlier: 5.014A  pdb=" N   SER C 114 " --> pdb=" O   ALA C 110 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 167 through 172
    Processing helix  chain 'C' and resid 197 through 212
      removed outlier: 3.563A  pdb=" N   GLU C 212 " --> pdb=" O   ILE C 208 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 245 through 265
    Processing helix  chain 'D' and resid 22 through 59
      removed outlier: 3.502A  pdb=" N   ARG D  59 " --> pdb=" O   LEU D  55 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 62 through 90
    Processing helix  chain 'D' and resid 93 through 128
      removed outlier: 4.729A  pdb=" N   GLY D 113 " --> pdb=" O   LEU D 109 " (cutoff:3.500A)
      removed outlier: 5.014A  pdb=" N   SER D 114 " --> pdb=" O   ALA D 110 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 167 through 172
    Processing helix  chain 'D' and resid 197 through 212
      removed outlier: 3.564A  pdb=" N   GLU D 212 " --> pdb=" O   ILE D 208 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 245 through 265
    Processing helix  chain 'E' and resid 22 through 59
      removed outlier: 3.502A  pdb=" N   ARG E  59 " --> pdb=" O   LEU E  55 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 62 through 90
    Processing helix  chain 'E' and resid 93 through 128
      removed outlier: 4.729A  pdb=" N   GLY E 113 " --> pdb=" O   LEU E 109 " (cutoff:3.500A)
      removed outlier: 5.013A  pdb=" N   SER E 114 " --> pdb=" O   ALA E 110 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 167 through 172
    Processing helix  chain 'E' and resid 197 through 212
      removed outlier: 3.563A  pdb=" N   GLU E 212 " --> pdb=" O   ILE E 208 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 245 through 265
    Processing helix  chain 'F' and resid 22 through 59
      removed outlier: 3.502A  pdb=" N   ARG F  59 " --> pdb=" O   LEU F  55 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 62 through 90
    Processing helix  chain 'F' and resid 93 through 128
      removed outlier: 4.729A  pdb=" N   GLY F 113 " --> pdb=" O   LEU F 109 " (cutoff:3.500A)
      removed outlier: 5.014A  pdb=" N   SER F 114 " --> pdb=" O   ALA F 110 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 167 through 172
    Processing helix  chain 'F' and resid 197 through 212
      removed outlier: 3.563A  pdb=" N   GLU F 212 " --> pdb=" O   ILE F 208 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 245 through 265
    Processing helix  chain 'G' and resid 22 through 59
      removed outlier: 3.503A  pdb=" N   ARG G  59 " --> pdb=" O   LEU G  55 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 62 through 90
    Processing helix  chain 'G' and resid 93 through 128
      removed outlier: 4.728A  pdb=" N   GLY G 113 " --> pdb=" O   LEU G 109 " (cutoff:3.500A)
      removed outlier: 5.013A  pdb=" N   SER G 114 " --> pdb=" O   ALA G 110 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 167 through 172
    Processing helix  chain 'G' and resid 197 through 212
      removed outlier: 3.563A  pdb=" N   GLU G 212 " --> pdb=" O   ILE G 208 " (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 138
      removed outlier: 3.842A  pdb=" N   VAL A 141 " --> pdb=" O   LEU A 138 " (cutoff:3.500A)
      removed outlier: 6.932A  pdb=" N   THR A 154 " --> pdb=" O   LEU A 146 " (cutoff:3.500A)
      removed outlier: 5.587A  pdb=" N   VAL A 148 " --> pdb=" O   SER A 152 " (cutoff:3.500A)
      removed outlier: 6.975A  pdb=" N   SER A 152 " --> pdb=" O   VAL A 148 " (cutoff:3.500A)
      removed outlier: 3.842A  pdb=" N   VAL G 141 " --> pdb=" O   LEU G 138 " (cutoff:3.500A)
      removed outlier: 6.932A  pdb=" N   THR G 154 " --> pdb=" O   LEU G 146 " (cutoff:3.500A)
      removed outlier: 5.587A  pdb=" N   VAL G 148 " --> pdb=" O   SER G 152 " (cutoff:3.500A)
      removed outlier: 6.975A  pdb=" N   SER G 152 " --> pdb=" O   VAL G 148 " (cutoff:3.500A)
      removed outlier: 3.842A  pdb=" N   VAL F 141 " --> pdb=" O   LEU F 138 " (cutoff:3.500A)
      removed outlier: 6.931A  pdb=" N   THR F 154 " --> pdb=" O   LEU F 146 " (cutoff:3.500A)
      removed outlier: 5.587A  pdb=" N   VAL F 148 " --> pdb=" O   SER F 152 " (cutoff:3.500A)
      removed outlier: 6.975A  pdb=" N   SER F 152 " --> pdb=" O   VAL F 148 " (cutoff:3.500A)
      removed outlier: 3.843A  pdb=" N   VAL E 141 " --> pdb=" O   LEU E 138 " (cutoff:3.500A)
      removed outlier: 6.931A  pdb=" N   THR E 154 " --> pdb=" O   LEU E 146 " (cutoff:3.500A)
      removed outlier: 5.587A  pdb=" N   VAL E 148 " --> pdb=" O   SER E 152 " (cutoff:3.500A)
      removed outlier: 6.975A  pdb=" N   SER E 152 " --> pdb=" O   VAL E 148 " (cutoff:3.500A)
      removed outlier: 3.842A  pdb=" N   VAL D 141 " --> pdb=" O   LEU D 138 " (cutoff:3.500A)
      removed outlier: 6.931A  pdb=" N   THR D 154 " --> pdb=" O   LEU D 146 " (cutoff:3.500A)
      removed outlier: 5.588A  pdb=" N   VAL D 148 " --> pdb=" O   SER D 152 " (cutoff:3.500A)
      removed outlier: 6.975A  pdb=" N   SER D 152 " --> pdb=" O   VAL D 148 " (cutoff:3.500A)
      removed outlier: 3.842A  pdb=" N   VAL C 141 " --> pdb=" O   LEU C 138 " (cutoff:3.500A)
      removed outlier: 6.932A  pdb=" N   THR C 154 " --> pdb=" O   LEU C 146 " (cutoff:3.500A)
      removed outlier: 5.587A  pdb=" N   VAL C 148 " --> pdb=" O   SER C 152 " (cutoff:3.500A)
      removed outlier: 6.974A  pdb=" N   SER C 152 " --> pdb=" O   VAL C 148 " (cutoff:3.500A)
      removed outlier: 3.842A  pdb=" N   VAL B 141 " --> pdb=" O   LEU B 138 " (cutoff:3.500A)
      removed outlier: 6.932A  pdb=" N   THR B 154 " --> pdb=" O   LEU B 146 " (cutoff:3.500A)
      removed outlier: 5.588A  pdb=" N   VAL B 148 " --> pdb=" O   SER B 152 " (cutoff:3.500A)
      removed outlier: 6.974A  pdb=" N   SER B 152 " --> pdb=" O   VAL B 148 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 183 through 192
      removed outlier: 7.035A  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 276
      removed outlier: 8.093A  pdb=" N   MET B 273 " --> pdb=" O   GLN A 272 " (cutoff:3.500A)
      removed outlier: 5.612A  pdb=" N   ASP A 274 " --> pdb=" O   MET B 273 " (cutoff:3.500A)
      removed outlier: 7.186A  pdb=" N   VAL B 275 " --> pdb=" O   ASP A 274 " (cutoff:3.500A)
      removed outlier: 6.394A  pdb=" N   ASN A 276 " --> pdb=" O   VAL B 275 " (cutoff:3.500A)
      removed outlier: 7.459A  pdb=" N   PHE B 277 " --> pdb=" O   ASN A 276 " (cutoff:3.500A)
      removed outlier: 8.223A  pdb=" N   MET C 273 " --> pdb=" O   GLN B 272 " (cutoff:3.500A)
      removed outlier: 5.671A  pdb=" N   ASP B 274 " --> pdb=" O   MET C 273 " (cutoff:3.500A)
      removed outlier: 6.985A  pdb=" N   VAL C 275 " --> pdb=" O   ASP B 274 " (cutoff:3.500A)
      removed outlier: 6.047A  pdb=" N   ASN B 276 " --> pdb=" O   VAL C 275 " (cutoff:3.500A)
      removed outlier: 6.864A  pdb=" N   PHE C 277 " --> pdb=" O   ASN B 276 " (cutoff:3.500A)
      removed outlier: 6.692A  pdb=" N   LYS B 278 " --> pdb=" O   PHE C 277 " (cutoff:3.500A)
      removed outlier: 8.266A  pdb=" N   MET D 273 " --> pdb=" O   GLN C 272 " (cutoff:3.500A)
      removed outlier: 5.737A  pdb=" N   ASP C 274 " --> pdb=" O   MET D 273 " (cutoff:3.500A)
      removed outlier: 7.147A  pdb=" N   VAL D 275 " --> pdb=" O   ASP C 274 " (cutoff:3.500A)
      removed outlier: 6.254A  pdb=" N   ASN C 276 " --> pdb=" O   VAL D 275 " (cutoff:3.500A)
      removed outlier: 8.210A  pdb=" N   MET E 273 " --> pdb=" O   GLN D 272 " (cutoff:3.500A)
      removed outlier: 5.689A  pdb=" N   ASP D 274 " --> pdb=" O   MET E 273 " (cutoff:3.500A)
      removed outlier: 7.164A  pdb=" N   VAL E 275 " --> pdb=" O   ASP D 274 " (cutoff:3.500A)
      removed outlier: 6.295A  pdb=" N   ASN D 276 " --> pdb=" O   VAL E 275 " (cutoff:3.500A)
      removed outlier: 7.241A  pdb=" N   PHE E 277 " --> pdb=" O   ASN D 276 " (cutoff:3.500A)
      removed outlier: 8.212A  pdb=" N   MET F 273 " --> pdb=" O   GLN E 272 " (cutoff:3.500A)
      removed outlier: 5.688A  pdb=" N   ASP E 274 " --> pdb=" O   MET F 273 " (cutoff:3.500A)
      removed outlier: 7.133A  pdb=" N   VAL F 275 " --> pdb=" O   ASP E 274 " (cutoff:3.500A)
      removed outlier: 6.258A  pdb=" N   ASN E 276 " --> pdb=" O   VAL F 275 " (cutoff:3.500A)
      removed outlier: 7.189A  pdb=" N   PHE F 277 " --> pdb=" O   ASN E 276 " (cutoff:3.500A)
      removed outlier: 7.002A  pdb=" N   LYS E 278 " --> pdb=" O   PHE F 277 " (cutoff:3.500A)
      removed outlier: 8.342A  pdb=" N   MET G 273 " --> pdb=" O   GLN F 272 " (cutoff:3.500A)
      removed outlier: 5.805A  pdb=" N   ASP F 274 " --> pdb=" O   MET G 273 " (cutoff:3.500A)
      removed outlier: 7.167A  pdb=" N   VAL G 275 " --> pdb=" O   ASP F 274 " (cutoff:3.500A)
      removed outlier: 6.244A  pdb=" N   ASN F 276 " --> pdb=" O   VAL G 275 " (cutoff:3.500A)
      removed outlier: 7.075A  pdb=" N   PHE G 277 " --> pdb=" O   ASN F 276 " (cutoff:3.500A)
      removed outlier: 6.901A  pdb=" N   LYS F 278 " --> pdb=" O   PHE G 277 " (cutoff:3.500A)
      removed outlier: 3.514A  pdb=" N   VAL A 275 " --> pdb=" O   ASN G 276 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 183 through 192
      removed outlier: 7.036A  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: 7.035A  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: 7.035A  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: 7.035A  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: 7.035A  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: 7.035A  pdb=" N   ASN G 234 " --> pdb=" O   ASN G 226 " (cutoff:3.500A)

    1046 hydrogen bonds defined for protein.
    3054 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: 2.30

  Time building geometry restraints manager: 1.24 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: 4655
        1.34 -     1.46: 2538
        1.46 -     1.57: 6821
        1.57 -     1.69: 0
        1.69 -     1.81: 84
  Bond restraints: 14098
  Sorted by residual:
  bond pdb=" CA  ARG B 128 "
       pdb=" CB  ARG B 128 "
    ideal  model  delta    sigma   weight residual
    1.522  1.530 -0.008 7.00e-03 2.04e+04 1.36e+00
  bond pdb=" CA  ARG F 128 "
       pdb=" CB  ARG F 128 "
    ideal  model  delta    sigma   weight residual
    1.522  1.530 -0.008 7.00e-03 2.04e+04 1.34e+00
  bond pdb=" CA  ARG E 128 "
       pdb=" CB  ARG E 128 "
    ideal  model  delta    sigma   weight residual
    1.522  1.530 -0.008 7.00e-03 2.04e+04 1.29e+00
  bond pdb=" CA  ARG C 128 "
       pdb=" CB  ARG C 128 "
    ideal  model  delta    sigma   weight residual
    1.522  1.530 -0.008 7.00e-03 2.04e+04 1.23e+00
  bond pdb=" CA  ARG G 128 "
       pdb=" CB  ARG G 128 "
    ideal  model  delta    sigma   weight residual
    1.522  1.530 -0.008 7.00e-03 2.04e+04 1.20e+00
  ... (remaining 14093 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     0.91: 18492
        0.91 -     1.83: 568
        1.83 -     2.74: 28
        2.74 -     3.66: 15
        3.66 -     4.57: 14
  Bond angle restraints: 19117
  Sorted by residual:
  angle pdb=" C   ARG F 128 "
        pdb=" CA  ARG F 128 "
        pdb=" CB  ARG F 128 "
      ideal   model   delta    sigma   weight residual
     111.00  109.34    1.66 8.70e-01 1.32e+00 3.63e+00
  angle pdb=" C   ARG G 128 "
        pdb=" CA  ARG G 128 "
        pdb=" CB  ARG G 128 "
      ideal   model   delta    sigma   weight residual
     111.00  109.35    1.65 8.70e-01 1.32e+00 3.59e+00
  angle pdb=" C   ARG D 128 "
        pdb=" CA  ARG D 128 "
        pdb=" CB  ARG D 128 "
      ideal   model   delta    sigma   weight residual
     111.00  109.36    1.64 8.70e-01 1.32e+00 3.54e+00
  angle pdb=" C   ARG C 128 "
        pdb=" CA  ARG C 128 "
        pdb=" CB  ARG C 128 "
      ideal   model   delta    sigma   weight residual
     111.00  109.37    1.63 8.70e-01 1.32e+00 3.52e+00
  angle pdb=" C   ARG E 128 "
        pdb=" CA  ARG E 128 "
        pdb=" CB  ARG E 128 "
      ideal   model   delta    sigma   weight residual
     111.00  109.37    1.63 8.70e-01 1.32e+00 3.50e+00
  ... (remaining 19112 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -     8.34: 7296
        8.34 -    16.69: 789
       16.69 -    25.03: 238
       25.03 -    33.38: 119
       33.38 -    41.72: 42
  Dihedral angle restraints: 8484
    sinusoidal: 3248
      harmonic: 5236
  Sorted by residual:
  dihedral pdb=" N   LEU B  72 "
           pdb=" CA  LEU B  72 "
           pdb=" CB  LEU B  72 "
           pdb=" CG  LEU B  72 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00 -101.72   41.72     3      1.50e+01 4.44e-03 7.47e+00
  dihedral pdb=" N   LEU G  72 "
           pdb=" CA  LEU G  72 "
           pdb=" CB  LEU G  72 "
           pdb=" CG  LEU G  72 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00 -101.70   41.70     3      1.50e+01 4.44e-03 7.47e+00
  dihedral pdb=" N   LEU E  72 "
           pdb=" CA  LEU E  72 "
           pdb=" CB  LEU E  72 "
           pdb=" CG  LEU E  72 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00 -101.70   41.70     3      1.50e+01 4.44e-03 7.47e+00
  ... (remaining 8481 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.027: 1543
       0.027 -    0.055: 500
       0.055 -    0.082: 140
       0.082 -    0.109: 106
       0.109 -    0.137: 56
  Chirality restraints: 2345
  Sorted by residual:
  chirality pdb=" CA  ILE C 175 "
            pdb=" N   ILE C 175 "
            pdb=" C   ILE C 175 "
            pdb=" CB  ILE C 175 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 4.66e-01
  chirality pdb=" CA  ILE A 175 "
            pdb=" N   ILE A 175 "
            pdb=" C   ILE A 175 "
            pdb=" CB  ILE A 175 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 4.61e-01
  chirality pdb=" CA  ILE D 165 "
            pdb=" N   ILE D 165 "
            pdb=" C   ILE D 165 "
            pdb=" CB  ILE D 165 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 4.60e-01
  ... (remaining 2342 not shown)

  Planarity restraints: 2429
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU D 111 "    0.005 2.00e-02 2.50e+03   9.22e-03 8.49e-01
        pdb=" C   LEU D 111 "   -0.016 2.00e-02 2.50e+03
        pdb=" O   LEU D 111 "    0.006 2.00e-02 2.50e+03
        pdb=" N   GLN D 112 "    0.005 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU F 111 "    0.005 2.00e-02 2.50e+03   9.14e-03 8.35e-01
        pdb=" C   LEU F 111 "   -0.016 2.00e-02 2.50e+03
        pdb=" O   LEU F 111 "    0.006 2.00e-02 2.50e+03
        pdb=" N   GLN F 112 "    0.005 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU A 111 "    0.004 2.00e-02 2.50e+03   9.04e-03 8.16e-01
        pdb=" C   LEU A 111 "   -0.016 2.00e-02 2.50e+03
        pdb=" O   LEU A 111 "    0.006 2.00e-02 2.50e+03
        pdb=" N   GLN A 112 "    0.005 2.00e-02 2.50e+03
  ... (remaining 2426 not shown)

  Histogram of nonbonded interaction distances:
        2.18 -     2.72: 626
        2.72 -     3.27: 14169
        3.27 -     3.81: 22931
        3.81 -     4.36: 24538
        4.36 -     4.90: 45458
  Nonbonded interactions: 107722
  Sorted by model distance:
  nonbonded pdb=" OD1 ASP B 199 "
            pdb=" NH2 ARG C 259 "
     model   vdw
     2.180 3.120
  nonbonded pdb=" OD1 ASN B 174 "
            pdb=" NZ  LYS C 169 "
     model   vdw
     2.206 3.120
  nonbonded pdb=" OD1 ASN A 276 "
            pdb=" NE2 GLN B 272 "
     model   vdw
     2.214 3.120
  nonbonded pdb=" OD1 ASP D 199 "
            pdb=" NH2 ARG E 259 "
     model   vdw
     2.285 3.120
  nonbonded pdb=" O   ALA B  22 "
            pdb=" OG  SER B  26 "
     model   vdw
     2.292 3.040
  ... (remaining 107717 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 group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.050
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.200
  Check model and map are aligned:         0.040
  Set scattering table:                    0.040
  Process input model:                     11.740
  Find NCS groups from input model:        0.110
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.340
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   14.550
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7868
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      :  0.002   0.020  14098  Z= 0.121
  Angle     :  0.379   4.573  19117  Z= 0.224
  Chirality :  0.039   0.137   2345
  Planarity :  0.002   0.010   2429
  Dihedral  :  9.172  41.722   5110
  Min Nonbonded Distance : 2.180

Molprobity Statistics.
  All-atom Clashscore : 5.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.54 %
    Favored  : 98.46 %
  Rotamer:
    Outliers :  0.41 %
    Allowed  :  4.81 %
    Favored  : 94.79 %
  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:  2.97 (0.20), residues: 1813
  helix:  3.44 (0.15), residues: 1001
  sheet:  0.27 (0.27), residues: 308
  loop : -0.03 (0.29), residues: 504

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C 184 
 TYR   0.005   0.001   TYR E 135 
 PHE   0.006   0.001   PHE C  68 
 TRP   0.004   0.001   TRP E 240 

Details of bonding type rmsd
  covalent geometry    : bond        0.00235 (14098)
  covalent geometry    : angle       0.37940 (19117)
  hydrogen bonds       : bond        0.11370 ( 1046)
  hydrogen bonds       : angle       5.09322 ( 3054)

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

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

  3626 Ramachandran restraints generated.
    1813 Oldfield, 0 Emsley, 1813 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3626 Ramachandran restraints generated.
    1813 Oldfield, 0 Emsley, 1813 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  403 residues out of total 1477 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 397
  time to evaluate  : 0.309 
Fit side-chains
REVERT: A   43 ILE cc_start: 0.8326 (mm) cc_final: 0.7999 (pt)
REVERT: A  131 ARG cc_start: 0.7178 (ptp-170) cc_final: 0.6967 (ptm-80)
REVERT: A  203 GLN cc_start: 0.8128 (pp30) cc_final: 0.7672 (pp30)
REVERT: A  220 GLU cc_start: 0.7630 (pp20) cc_final: 0.7353 (pp20)
REVERT: A  272 GLN cc_start: 0.7864 (tt0) cc_final: 0.7640 (tt0)
REVERT: A  273 MET cc_start: 0.7755 (ptp) cc_final: 0.7328 (ptm)
REVERT: B   48 ILE cc_start: 0.7904 (tp) cc_final: 0.7653 (tp)
REVERT: B   86 LEU cc_start: 0.8513 (tp) cc_final: 0.8196 (tp)
REVERT: B  134 GLU cc_start: 0.7071 (tt0) cc_final: 0.6832 (tt0)
REVERT: B  197 ASP cc_start: 0.7704 (t70) cc_final: 0.7384 (t70)
REVERT: B  206 THR cc_start: 0.8791 (m) cc_final: 0.8587 (p)
REVERT: B  272 GLN cc_start: 0.8481 (tt0) cc_final: 0.7844 (tt0)
REVERT: C   48 ILE cc_start: 0.7801 (tp) cc_final: 0.7580 (tp)
REVERT: C  134 GLU cc_start: 0.7297 (tt0) cc_final: 0.6912 (tt0)
REVERT: C  255 GLU cc_start: 0.7948 (tm-30) cc_final: 0.7654 (tt0)
REVERT: C  272 GLN cc_start: 0.8072 (tt0) cc_final: 0.7568 (tt0)
REVERT: D  203 GLN cc_start: 0.8022 (pp30) cc_final: 0.7720 (pp30)
REVERT: D  220 GLU cc_start: 0.7495 (pp20) cc_final: 0.7241 (pp20)
REVERT: D  272 GLN cc_start: 0.7993 (tt0) cc_final: 0.7570 (tt0)
REVERT: E  135 TYR cc_start: 0.7958 (t80) cc_final: 0.7637 (t80)
REVERT: F   47 MET cc_start: 0.2489 (mmt) cc_final: 0.2254 (mmt)
REVERT: F  131 ARG cc_start: 0.7180 (ptp-170) cc_final: 0.6980 (ptm-80)
REVERT: F  197 ASP cc_start: 0.7180 (t70) cc_final: 0.6825 (t70)
REVERT: F  272 GLN cc_start: 0.8291 (tt0) cc_final: 0.7622 (tt0)
REVERT: G   47 MET cc_start: 0.2640 (mmt) cc_final: 0.2398 (mmt)
REVERT: G  134 GLU cc_start: 0.6834 (tt0) cc_final: 0.6539 (tt0)
REVERT: G  135 TYR cc_start: 0.7805 (t80) cc_final: 0.7546 (t80)
REVERT: G  197 ASP cc_start: 0.7083 (t70) cc_final: 0.6686 (t70)
REVERT: G  203 GLN cc_start: 0.7920 (pp30) cc_final: 0.7579 (pp30)
  outliers start: 6
  outliers final: 0
  residues processed: 403
  average time/residue: 0.1014
  time to fit residues: 61.4599
Evaluate side-chains
  270 residues out of total 1477 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 270
  time to evaluate  : 0.517 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 182
   random chunks:
   chunk 98 optimal weight:    2.9990
   chunk 107 optimal weight:    4.9990
   chunk 10 optimal weight:    1.9990
   chunk 66 optimal weight:    4.9990
   chunk 130 optimal weight:    2.9990
   chunk 124 optimal weight:    1.9990
   chunk 103 optimal weight:    0.6980
   chunk 77 optimal weight:    2.9990
   chunk 122 optimal weight:    0.3980
   chunk 91 optimal weight:    8.9990
   chunk 149 optimal weight:    0.3980
   overall best weight:    1.0984

-------------------------------------------------------------------------------
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 = 0.3687 r_free = 0.3687 target = 0.142238 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3259 r_free = 0.3259 target = 0.111310 restraints weight = 23327.904|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.3299 r_free = 0.3299 target = 0.114102 restraints weight = 13129.993|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3322 r_free = 0.3322 target = 0.115740 restraints weight = 8505.151|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3342 r_free = 0.3342 target = 0.117078 restraints weight = 6223.302|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3351 r_free = 0.3351 target = 0.117740 restraints weight = 4972.745|
|-----------------------------------------------------------------------------|
r_work (final): 0.3333
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7874
moved from start:          0.1489

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045  14098  Z= 0.137
  Angle     :  0.530   5.823  19117  Z= 0.285
  Chirality :  0.041   0.144   2345
  Planarity :  0.004   0.060   2429
  Dihedral  :  3.720  13.725   1988
  Min Nonbonded Distance : 2.615

Molprobity Statistics.
  All-atom Clashscore : 8.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.21 %
    Favored  : 98.79 %
  Rotamer:
    Outliers :  2.51 %
    Allowed  : 10.77 %
    Favored  : 86.73 %
  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:  2.77 (0.20), residues: 1813
  helix:  3.11 (0.15), residues: 1001
  sheet:  0.75 (0.31), residues: 259
  loop : -0.05 (0.27), residues: 553

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG G 259 
 TYR   0.005   0.001   TYR A  27 
 PHE   0.019   0.002   PHE B 127 
 TRP   0.002   0.000   TRP D 240 

Details of bonding type rmsd
  covalent geometry    : bond        0.00308 (14098)
  covalent geometry    : angle       0.52972 (19117)
  hydrogen bonds       : bond        0.04154 ( 1046)
  hydrogen bonds       : angle       4.08603 ( 3054)

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

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

  3626 Ramachandran restraints generated.
    1813 Oldfield, 0 Emsley, 1813 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3626 Ramachandran restraints generated.
    1813 Oldfield, 0 Emsley, 1813 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  320 residues out of total 1477 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 283
  time to evaluate  : 0.513 
Fit side-chains
   revert: symmetry clash
REVERT: A   43 ILE cc_start: 0.8345 (mm) cc_final: 0.7980 (pt)
REVERT: A  131 ARG cc_start: 0.7200 (ptp-170) cc_final: 0.6782 (ptm-80)
REVERT: A  134 GLU cc_start: 0.7199 (tt0) cc_final: 0.6958 (tt0)
REVERT: A  218 ASP cc_start: 0.8362 (OUTLIER) cc_final: 0.8138 (p0)
REVERT: B   86 LEU cc_start: 0.8382 (tp) cc_final: 0.8064 (tp)
REVERT: B  134 GLU cc_start: 0.7258 (tt0) cc_final: 0.6930 (tt0)
REVERT: B  161 LYS cc_start: 0.8698 (mtmm) cc_final: 0.8374 (mtmm)
REVERT: B  197 ASP cc_start: 0.7800 (t70) cc_final: 0.7560 (t70)
REVERT: B  272 GLN cc_start: 0.8319 (tt0) cc_final: 0.7259 (tt0)
REVERT: C  134 GLU cc_start: 0.7240 (tt0) cc_final: 0.6883 (tt0)
REVERT: C  220 GLU cc_start: 0.7585 (pp20) cc_final: 0.7346 (pp20)
REVERT: C  221 MET cc_start: 0.7365 (ptt) cc_final: 0.7045 (ptt)
REVERT: C  272 GLN cc_start: 0.8134 (tt0) cc_final: 0.7547 (tt0)
REVERT: D  149 GLN cc_start: 0.7836 (mp10) cc_final: 0.7318 (mp10)
REVERT: E  134 GLU cc_start: 0.7120 (tt0) cc_final: 0.6793 (tt0)
REVERT: E  135 TYR cc_start: 0.8040 (t80) cc_final: 0.7702 (t80)
REVERT: E  272 GLN cc_start: 0.8095 (tt0) cc_final: 0.7594 (tt0)
REVERT: F  131 ARG cc_start: 0.7205 (ptp-170) cc_final: 0.6861 (ptm-80)
REVERT: F  134 GLU cc_start: 0.7118 (tt0) cc_final: 0.6835 (tt0)
REVERT: F  149 GLN cc_start: 0.8063 (mp10) cc_final: 0.7398 (mp10)
REVERT: F  272 GLN cc_start: 0.8160 (tt0) cc_final: 0.7096 (tt0)
REVERT: G  134 GLU cc_start: 0.6831 (tt0) cc_final: 0.6562 (tt0)
REVERT: G  135 TYR cc_start: 0.7882 (t80) cc_final: 0.7671 (t80)
REVERT: G  197 ASP cc_start: 0.7326 (t70) cc_final: 0.7047 (t70)
  outliers start: 37
  outliers final: 10
  residues processed: 297
  average time/residue: 0.1055
  time to fit residues: 48.2745
Evaluate side-chains
  259 residues out of total 1477 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 248
  time to evaluate  : 0.386 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  218 ASP
Chi-restraints excluded: chain A residue  257 ILE
Chi-restraints excluded: chain B residue   42 LEU
Chi-restraints excluded: chain C residue   97 ILE
Chi-restraints excluded: chain D residue   42 LEU
Chi-restraints excluded: chain E residue  233 ILE
Chi-restraints excluded: chain F residue  100 LEU
Chi-restraints excluded: chain G residue   43 ILE
Chi-restraints excluded: chain G residue  157 THR
Chi-restraints excluded: chain G residue  218 ASP
Chi-restraints excluded: chain G residue  233 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 182
   random chunks:
   chunk 50 optimal weight:    0.9980
   chunk 127 optimal weight:    0.9980
   chunk 139 optimal weight:    0.9980
   chunk 146 optimal weight:    4.9990
   chunk 128 optimal weight:    2.9990
   chunk 72 optimal weight:    6.9990
   chunk 178 optimal weight:    5.9990
   chunk 155 optimal weight:    1.9990
   chunk 49 optimal weight:    0.8980
   chunk 16 optimal weight:    4.9990
   chunk 53 optimal weight:    0.7980
   overall best weight:    0.9380

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

Flipped N/Q/H residues before XYZ refinement:
A 272 GLN
E 203 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3681 r_free = 0.3681 target = 0.141582 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3264 r_free = 0.3264 target = 0.111652 restraints weight = 23604.591|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3298 r_free = 0.3298 target = 0.114071 restraints weight = 13569.361|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3325 r_free = 0.3325 target = 0.115863 restraints weight = 8977.244|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 43)----------------|
| r_work = 0.3341 r_free = 0.3341 target = 0.117032 restraints weight = 6590.714|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3349 r_free = 0.3349 target = 0.117639 restraints weight = 5316.412|
|-----------------------------------------------------------------------------|
r_work (final): 0.3351
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7879
moved from start:          0.1816

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  14098  Z= 0.121
  Angle     :  0.503   6.997  19117  Z= 0.270
  Chirality :  0.041   0.141   2345
  Planarity :  0.003   0.051   2429
  Dihedral  :  3.700  13.927   1988
  Min Nonbonded Distance : 2.615

Molprobity Statistics.
  All-atom Clashscore : 7.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.21 %
    Favored  : 98.79 %
  Rotamer:
    Outliers :  2.71 %
    Allowed  : 11.17 %
    Favored  : 86.12 %
  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:  2.78 (0.20), residues: 1813
  helix:  3.07 (0.16), residues: 1001
  sheet:  1.86 (0.30), residues: 224
  loop : -0.42 (0.26), residues: 588

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C 259 
 TYR   0.007   0.001   TYR B 270 
 PHE   0.012   0.001   PHE G 178 
 TRP   0.003   0.000   TRP D 240 

Details of bonding type rmsd
  covalent geometry    : bond        0.00269 (14098)
  covalent geometry    : angle       0.50341 (19117)
  hydrogen bonds       : bond        0.03795 ( 1046)
  hydrogen bonds       : angle       3.95903 ( 3054)

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

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

  3626 Ramachandran restraints generated.
    1813 Oldfield, 0 Emsley, 1813 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3626 Ramachandran restraints generated.
    1813 Oldfield, 0 Emsley, 1813 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  309 residues out of total 1477 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 269
  time to evaluate  : 0.423 
Fit side-chains
   revert: symmetry clash
REVERT: A   43 ILE cc_start: 0.8257 (mm) cc_final: 0.7894 (pt)
REVERT: A   47 MET cc_start: 0.2892 (mmm) cc_final: 0.2575 (mmp)
REVERT: A  131 ARG cc_start: 0.7149 (ptp-170) cc_final: 0.6822 (ptm-80)
REVERT: A  134 GLU cc_start: 0.7015 (tt0) cc_final: 0.6794 (tt0)
REVERT: A  150 ILE cc_start: 0.8250 (mm) cc_final: 0.7946 (tp)
REVERT: A  272 GLN cc_start: 0.8223 (tt0) cc_final: 0.8020 (tt0)
REVERT: B   86 LEU cc_start: 0.8409 (tp) cc_final: 0.8088 (tp)
REVERT: B  134 GLU cc_start: 0.7208 (tt0) cc_final: 0.6951 (tt0)
REVERT: B  161 LYS cc_start: 0.8661 (mtmm) cc_final: 0.8439 (mtpt)
REVERT: B  272 GLN cc_start: 0.8307 (tt0) cc_final: 0.7316 (tt0)
REVERT: C  134 GLU cc_start: 0.7122 (tt0) cc_final: 0.6768 (tt0)
REVERT: C  220 GLU cc_start: 0.7578 (pp20) cc_final: 0.7336 (pp20)
REVERT: C  272 GLN cc_start: 0.8146 (tt0) cc_final: 0.7612 (tt0)
REVERT: D  149 GLN cc_start: 0.7835 (mp10) cc_final: 0.7228 (mp10)
REVERT: D  272 GLN cc_start: 0.7768 (tt0) cc_final: 0.7431 (tt0)
REVERT: E  135 TYR cc_start: 0.8035 (t80) cc_final: 0.7691 (t80)
REVERT: E  203 GLN cc_start: 0.8602 (OUTLIER) cc_final: 0.8158 (tm130)
REVERT: E  270 TYR cc_start: 0.8228 (m-80) cc_final: 0.7952 (m-80)
REVERT: E  272 GLN cc_start: 0.7952 (tt0) cc_final: 0.7454 (tt0)
REVERT: F  131 ARG cc_start: 0.7133 (ptp-170) cc_final: 0.6814 (ptm-80)
REVERT: F  134 GLU cc_start: 0.7090 (tt0) cc_final: 0.6730 (tt0)
REVERT: F  149 GLN cc_start: 0.7893 (mp10) cc_final: 0.7194 (mp10)
REVERT: F  272 GLN cc_start: 0.8034 (tt0) cc_final: 0.7148 (tt0)
REVERT: F  273 MET cc_start: 0.8518 (ttm) cc_final: 0.8292 (ttm)
REVERT: G  134 GLU cc_start: 0.6842 (tt0) cc_final: 0.6609 (tt0)
REVERT: G  135 TYR cc_start: 0.7935 (t80) cc_final: 0.7659 (t80)
REVERT: G  273 MET cc_start: 0.8654 (OUTLIER) cc_final: 0.8345 (ttm)
  outliers start: 40
  outliers final: 19
  residues processed: 290
  average time/residue: 0.0964
  time to fit residues: 43.0024
Evaluate side-chains
  262 residues out of total 1477 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 241
  time to evaluate  : 0.400 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  171 ILE
Chi-restraints excluded: chain A residue  252 ASP
Chi-restraints excluded: chain A residue  257 ILE
Chi-restraints excluded: chain B residue   42 LEU
Chi-restraints excluded: chain B residue  206 THR
Chi-restraints excluded: chain C residue   42 LEU
Chi-restraints excluded: chain C residue   97 ILE
Chi-restraints excluded: chain C residue  206 THR
Chi-restraints excluded: chain D residue  257 ILE
Chi-restraints excluded: chain E residue  122 VAL
Chi-restraints excluded: chain E residue  171 ILE
Chi-restraints excluded: chain E residue  203 GLN
Chi-restraints excluded: chain E residue  206 THR
Chi-restraints excluded: chain E residue  233 ILE
Chi-restraints excluded: chain E residue  273 MET
Chi-restraints excluded: chain F residue  100 LEU
Chi-restraints excluded: chain F residue  218 ASP
Chi-restraints excluded: chain G residue   97 ILE
Chi-restraints excluded: chain G residue  157 THR
Chi-restraints excluded: chain G residue  171 ILE
Chi-restraints excluded: chain G residue  273 MET
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 182
   random chunks:
   chunk 82 optimal weight:    4.9990
   chunk 68 optimal weight:    3.9990
   chunk 109 optimal weight:   10.0000
   chunk 152 optimal weight:    0.9990
   chunk 121 optimal weight:    6.9990
   chunk 105 optimal weight:    0.9990
   chunk 81 optimal weight:    0.9990
   chunk 6 optimal weight:    0.9990
   chunk 93 optimal weight:    7.9990
   chunk 125 optimal weight:    0.9980
   chunk 175 optimal weight:    0.1980
   overall best weight:    0.8386

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

Flipped N/Q/H residues before XYZ refinement:
A 203 GLN
C 203 GLN
E 203 GLN
F 203 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3650 r_free = 0.3650 target = 0.139380 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3237 r_free = 0.3237 target = 0.109404 restraints weight = 23420.819|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3277 r_free = 0.3277 target = 0.112168 restraints weight = 13042.231|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3302 r_free = 0.3302 target = 0.113970 restraints weight = 8392.198|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3317 r_free = 0.3317 target = 0.115019 restraints weight = 6079.662|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 49)----------------|
| r_work = 0.3331 r_free = 0.3331 target = 0.115956 restraints weight = 4881.237|
|-----------------------------------------------------------------------------|
r_work (final): 0.3355
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7860
moved from start:          0.1985

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  14098  Z= 0.117
  Angle     :  0.493   5.916  19117  Z= 0.265
  Chirality :  0.040   0.142   2345
  Planarity :  0.003   0.043   2429
  Dihedral  :  3.686  13.441   1988
  Min Nonbonded Distance : 2.600

Molprobity Statistics.
  All-atom Clashscore : 7.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.16 %
    Favored  : 98.84 %
  Rotamer:
    Outliers :  2.64 %
    Allowed  : 12.25 %
    Favored  : 85.10 %
  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:  2.77 (0.20), residues: 1813
  helix:  3.07 (0.16), residues: 1001
  sheet:  1.53 (0.29), residues: 259
  loop : -0.43 (0.26), residues: 553

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B  74 
 TYR   0.006   0.001   TYR E 135 
 PHE   0.013   0.001   PHE E  80 
 TRP   0.002   0.000   TRP D 240 

Details of bonding type rmsd
  covalent geometry    : bond        0.00258 (14098)
  covalent geometry    : angle       0.49349 (19117)
  hydrogen bonds       : bond        0.03631 ( 1046)
  hydrogen bonds       : angle       3.92107 ( 3054)

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

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

  3626 Ramachandran restraints generated.
    1813 Oldfield, 0 Emsley, 1813 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3626 Ramachandran restraints generated.
    1813 Oldfield, 0 Emsley, 1813 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  307 residues out of total 1477 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 268
  time to evaluate  : 0.593 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   43 ILE cc_start: 0.8286 (mm) cc_final: 0.7946 (pt)
REVERT: A  131 ARG cc_start: 0.7147 (ptp-170) cc_final: 0.6791 (ptm-80)
REVERT: A  134 GLU cc_start: 0.7016 (tt0) cc_final: 0.6785 (tt0)
REVERT: A  150 ILE cc_start: 0.8234 (mm) cc_final: 0.7925 (tp)
REVERT: A  255 GLU cc_start: 0.8327 (tm-30) cc_final: 0.7897 (tm-30)
REVERT: A  273 MET cc_start: 0.7658 (ptm) cc_final: 0.7304 (ptm)
REVERT: B   86 LEU cc_start: 0.8404 (tp) cc_final: 0.8084 (tp)
REVERT: B  134 GLU cc_start: 0.7228 (tt0) cc_final: 0.6927 (tt0)
REVERT: B  161 LYS cc_start: 0.8686 (mtmm) cc_final: 0.8423 (mtmm)
REVERT: B  272 GLN cc_start: 0.8389 (tt0) cc_final: 0.7500 (tt0)
REVERT: C  134 GLU cc_start: 0.7111 (tt0) cc_final: 0.6731 (tt0)
REVERT: C  203 GLN cc_start: 0.8603 (OUTLIER) cc_final: 0.8259 (tm130)
REVERT: C  220 GLU cc_start: 0.7600 (pp20) cc_final: 0.7302 (pp20)
REVERT: C  221 MET cc_start: 0.7376 (ptt) cc_final: 0.7144 (ptt)
REVERT: C  272 GLN cc_start: 0.8095 (tt0) cc_final: 0.7573 (tt0)
REVERT: D  149 GLN cc_start: 0.7834 (mp10) cc_final: 0.7218 (mp10)
REVERT: E  135 TYR cc_start: 0.8045 (t80) cc_final: 0.7735 (t80)
REVERT: E  203 GLN cc_start: 0.8521 (OUTLIER) cc_final: 0.8114 (tm130)
REVERT: E  211 SER cc_start: 0.8507 (m) cc_final: 0.8305 (t)
REVERT: E  220 GLU cc_start: 0.7767 (pp20) cc_final: 0.7331 (pp20)
REVERT: E  272 GLN cc_start: 0.7814 (tt0) cc_final: 0.7395 (tt0)
REVERT: F  131 ARG cc_start: 0.7156 (ptp-170) cc_final: 0.6795 (ptm-80)
REVERT: F  134 GLU cc_start: 0.7340 (tt0) cc_final: 0.6901 (tt0)
REVERT: F  203 GLN cc_start: 0.8411 (OUTLIER) cc_final: 0.8055 (tm130)
REVERT: F  272 GLN cc_start: 0.8044 (tt0) cc_final: 0.7115 (tt0)
REVERT: G  134 GLU cc_start: 0.6887 (tt0) cc_final: 0.6633 (tt0)
REVERT: G  135 TYR cc_start: 0.7980 (t80) cc_final: 0.7638 (t80)
  outliers start: 39
  outliers final: 25
  residues processed: 290
  average time/residue: 0.0975
  time to fit residues: 43.2102
Evaluate side-chains
  269 residues out of total 1477 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 241
  time to evaluate  : 0.363 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  171 ILE
Chi-restraints excluded: chain A residue  203 GLN
Chi-restraints excluded: chain A residue  252 ASP
Chi-restraints excluded: chain A residue  257 ILE
Chi-restraints excluded: chain B residue  122 VAL
Chi-restraints excluded: chain B residue  171 ILE
Chi-restraints excluded: chain B residue  197 ASP
Chi-restraints excluded: chain C residue   42 LEU
Chi-restraints excluded: chain C residue   97 ILE
Chi-restraints excluded: chain C residue  161 LYS
Chi-restraints excluded: chain C residue  203 GLN
Chi-restraints excluded: chain C residue  206 THR
Chi-restraints excluded: chain C residue  252 ASP
Chi-restraints excluded: chain D residue  257 ILE
Chi-restraints excluded: chain E residue  126 MET
Chi-restraints excluded: chain E residue  171 ILE
Chi-restraints excluded: chain E residue  203 GLN
Chi-restraints excluded: chain E residue  206 THR
Chi-restraints excluded: chain E residue  233 ILE
Chi-restraints excluded: chain E residue  257 ILE
Chi-restraints excluded: chain E residue  273 MET
Chi-restraints excluded: chain F residue  100 LEU
Chi-restraints excluded: chain F residue  197 ASP
Chi-restraints excluded: chain F residue  203 GLN
Chi-restraints excluded: chain G residue   97 ILE
Chi-restraints excluded: chain G residue  157 THR
Chi-restraints excluded: chain G residue  171 ILE
Chi-restraints excluded: chain G residue  273 MET
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 182
   random chunks:
   chunk 126 optimal weight:    7.9990
   chunk 56 optimal weight:    3.9990
   chunk 138 optimal weight:    6.9990
   chunk 25 optimal weight:    6.9990
   chunk 75 optimal weight:    1.9990
   chunk 26 optimal weight:    8.9990
   chunk 144 optimal weight:    1.9990
   chunk 128 optimal weight:    2.9990
   chunk 181 optimal weight:    0.9990
   chunk 157 optimal weight:    5.9990
   chunk 156 optimal weight:    5.9990
   overall best weight:    2.3990

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

Flipped N/Q/H residues before XYZ refinement:
C 203 GLN
D 203 GLN
E 203 GLN
F 203 GLN
G 203 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3620 r_free = 0.3620 target = 0.135904 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3190 r_free = 0.3190 target = 0.105572 restraints weight = 23084.678|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3232 r_free = 0.3232 target = 0.108291 restraints weight = 13101.696|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.3260 r_free = 0.3260 target = 0.110137 restraints weight = 8568.487|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3278 r_free = 0.3278 target = 0.111337 restraints weight = 6239.995|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3288 r_free = 0.3288 target = 0.112044 restraints weight = 4980.665|
|-----------------------------------------------------------------------------|
r_work (final): 0.3309
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7908
moved from start:          0.2156

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044  14098  Z= 0.182
  Angle     :  0.544   5.770  19117  Z= 0.291
  Chirality :  0.042   0.140   2345
  Planarity :  0.003   0.048   2429
  Dihedral  :  3.852  13.632   1988
  Min Nonbonded Distance : 2.599

Molprobity Statistics.
  All-atom Clashscore : 8.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.21 %
    Favored  : 98.79 %
  Rotamer:
    Outliers :  3.05 %
    Allowed  : 13.41 %
    Favored  : 83.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.65 (0.19), residues: 1813
  helix:  3.00 (0.16), residues: 1001
  sheet:  1.52 (0.28), residues: 259
  loop : -0.57 (0.26), residues: 553

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A  74 
 TYR   0.009   0.001   TYR E 135 
 PHE   0.013   0.001   PHE G 178 
 TRP   0.005   0.001   TRP F 240 

Details of bonding type rmsd
  covalent geometry    : bond        0.00423 (14098)
  covalent geometry    : angle       0.54442 (19117)
  hydrogen bonds       : bond        0.03909 ( 1046)
  hydrogen bonds       : angle       3.98766 ( 3054)

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

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

  3626 Ramachandran restraints generated.
    1813 Oldfield, 0 Emsley, 1813 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3626 Ramachandran restraints generated.
    1813 Oldfield, 0 Emsley, 1813 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  300 residues out of total 1477 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 255
  time to evaluate  : 0.394 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   43 ILE cc_start: 0.8339 (mm) cc_final: 0.7926 (pt)
REVERT: A  131 ARG cc_start: 0.7096 (ptp-170) cc_final: 0.6815 (ptm-80)
REVERT: A  150 ILE cc_start: 0.8265 (mm) cc_final: 0.8027 (tp)
REVERT: A  255 GLU cc_start: 0.8306 (tm-30) cc_final: 0.7855 (tm-30)
REVERT: B   86 LEU cc_start: 0.8411 (tp) cc_final: 0.8091 (tp)
REVERT: B  134 GLU cc_start: 0.7249 (tt0) cc_final: 0.6924 (tt0)
REVERT: B  161 LYS cc_start: 0.8720 (mtmm) cc_final: 0.8424 (mtmm)
REVERT: C  134 GLU cc_start: 0.7163 (tt0) cc_final: 0.6765 (tt0)
REVERT: C  203 GLN cc_start: 0.8671 (OUTLIER) cc_final: 0.8378 (tm130)
REVERT: C  220 GLU cc_start: 0.7662 (pp20) cc_final: 0.7337 (pp20)
REVERT: C  272 GLN cc_start: 0.8180 (tt0) cc_final: 0.7655 (tt0)
REVERT: D  149 GLN cc_start: 0.7916 (mp10) cc_final: 0.7300 (mp10)
REVERT: D  203 GLN cc_start: 0.8411 (OUTLIER) cc_final: 0.8040 (tm130)
REVERT: E  203 GLN cc_start: 0.8565 (OUTLIER) cc_final: 0.8214 (tm130)
REVERT: E  220 GLU cc_start: 0.7785 (pp20) cc_final: 0.7364 (pp20)
REVERT: E  221 MET cc_start: 0.7321 (ptt) cc_final: 0.7084 (ptt)
REVERT: E  272 GLN cc_start: 0.7895 (tt0) cc_final: 0.7465 (tt0)
REVERT: F  131 ARG cc_start: 0.7194 (ptp-170) cc_final: 0.6790 (ptm-80)
REVERT: F  134 GLU cc_start: 0.7253 (tt0) cc_final: 0.6781 (tt0)
REVERT: F  203 GLN cc_start: 0.8565 (OUTLIER) cc_final: 0.8253 (tm130)
REVERT: F  272 GLN cc_start: 0.8128 (tt0) cc_final: 0.7158 (tt0)
REVERT: G  134 GLU cc_start: 0.7003 (tt0) cc_final: 0.6685 (tt0)
REVERT: G  135 TYR cc_start: 0.7900 (t80) cc_final: 0.7613 (t80)
REVERT: G  203 GLN cc_start: 0.8579 (OUTLIER) cc_final: 0.8063 (tm130)
REVERT: G  273 MET cc_start: 0.8813 (OUTLIER) cc_final: 0.8224 (ttm)
  outliers start: 45
  outliers final: 26
  residues processed: 289
  average time/residue: 0.0900
  time to fit residues: 40.8864
Evaluate side-chains
  271 residues out of total 1477 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 239
  time to evaluate  : 0.486 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  122 VAL
Chi-restraints excluded: chain A residue  141 VAL
Chi-restraints excluded: chain A residue  171 ILE
Chi-restraints excluded: chain A residue  252 ASP
Chi-restraints excluded: chain A residue  257 ILE
Chi-restraints excluded: chain B residue   42 LEU
Chi-restraints excluded: chain B residue  122 VAL
Chi-restraints excluded: chain B residue  171 ILE
Chi-restraints excluded: chain B residue  206 THR
Chi-restraints excluded: chain C residue   42 LEU
Chi-restraints excluded: chain C residue   97 ILE
Chi-restraints excluded: chain C residue  161 LYS
Chi-restraints excluded: chain C residue  203 GLN
Chi-restraints excluded: chain C residue  206 THR
Chi-restraints excluded: chain C residue  257 ILE
Chi-restraints excluded: chain D residue   42 LEU
Chi-restraints excluded: chain D residue  203 GLN
Chi-restraints excluded: chain E residue  122 VAL
Chi-restraints excluded: chain E residue  126 MET
Chi-restraints excluded: chain E residue  171 ILE
Chi-restraints excluded: chain E residue  203 GLN
Chi-restraints excluded: chain E residue  206 THR
Chi-restraints excluded: chain E residue  208 ILE
Chi-restraints excluded: chain E residue  233 ILE
Chi-restraints excluded: chain E residue  273 MET
Chi-restraints excluded: chain F residue  100 LEU
Chi-restraints excluded: chain F residue  203 GLN
Chi-restraints excluded: chain F residue  206 THR
Chi-restraints excluded: chain G residue  157 THR
Chi-restraints excluded: chain G residue  171 ILE
Chi-restraints excluded: chain G residue  203 GLN
Chi-restraints excluded: chain G residue  273 MET
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 182
   random chunks:
   chunk 11 optimal weight:    6.9990
   chunk 120 optimal weight:    5.9990
   chunk 128 optimal weight:    2.9990
   chunk 31 optimal weight:    3.9990
   chunk 29 optimal weight:    0.9990
   chunk 90 optimal weight:    0.4980
   chunk 138 optimal weight:    4.9990
   chunk 28 optimal weight:    5.9990
   chunk 169 optimal weight:    2.9990
   chunk 7 optimal weight:    4.9990
   chunk 38 optimal weight:    7.9990
   overall best weight:    2.2988

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

Flipped N/Q/H residues before XYZ refinement:
A 207 ASN
C 203 GLN
D 203 GLN
F 203 GLN
G 203 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3616 r_free = 0.3616 target = 0.135564 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3182 r_free = 0.3182 target = 0.105002 restraints weight = 23211.456|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3225 r_free = 0.3225 target = 0.107750 restraints weight = 13286.422|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3252 r_free = 0.3252 target = 0.109592 restraints weight = 8745.392|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 58)----------------|
| r_work = 0.3271 r_free = 0.3271 target = 0.110804 restraints weight = 6419.461|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 45)----------------|
| r_work = 0.3282 r_free = 0.3282 target = 0.111545 restraints weight = 5138.556|
|-----------------------------------------------------------------------------|
r_work (final): 0.3300
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7923
moved from start:          0.2327

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.057  14098  Z= 0.180
  Angle     :  0.556   6.989  19117  Z= 0.296
  Chirality :  0.041   0.195   2345
  Planarity :  0.003   0.032   2429
  Dihedral  :  3.901  13.311   1988
  Min Nonbonded Distance : 2.597

Molprobity Statistics.
  All-atom Clashscore : 8.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.32 %
    Favored  : 98.68 %
  Rotamer:
    Outliers :  4.20 %
    Allowed  : 13.07 %
    Favored  : 82.74 %
  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: 1813
  helix:  2.85 (0.15), residues: 1008
  sheet:  1.46 (0.28), residues: 259
  loop : -0.65 (0.26), residues: 546

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A  74 
 TYR   0.012   0.001   TYR B 270 
 PHE   0.012   0.001   PHE G 178 
 TRP   0.005   0.001   TRP F 240 

Details of bonding type rmsd
  covalent geometry    : bond        0.00421 (14098)
  covalent geometry    : angle       0.55641 (19117)
  hydrogen bonds       : bond        0.03932 ( 1046)
  hydrogen bonds       : angle       4.02960 ( 3054)

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

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

  3626 Ramachandran restraints generated.
    1813 Oldfield, 0 Emsley, 1813 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3626 Ramachandran restraints generated.
    1813 Oldfield, 0 Emsley, 1813 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  307 residues out of total 1477 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 62
    poor density    : 245
  time to evaluate  : 0.512 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   43 ILE cc_start: 0.8314 (mm) cc_final: 0.7948 (pt)
REVERT: A  150 ILE cc_start: 0.8269 (mm) cc_final: 0.8032 (tp)
REVERT: A  255 GLU cc_start: 0.8328 (tm-30) cc_final: 0.7864 (tm-30)
REVERT: B   86 LEU cc_start: 0.8387 (tp) cc_final: 0.8071 (tp)
REVERT: B  134 GLU cc_start: 0.7237 (tt0) cc_final: 0.6907 (tt0)
REVERT: B  161 LYS cc_start: 0.8712 (mtmm) cc_final: 0.8397 (mtmm)
REVERT: B  272 GLN cc_start: 0.8410 (tt0) cc_final: 0.8085 (tt0)
REVERT: C  134 GLU cc_start: 0.7126 (tt0) cc_final: 0.6738 (tt0)
REVERT: C  220 GLU cc_start: 0.7795 (pp20) cc_final: 0.7461 (pp20)
REVERT: C  272 GLN cc_start: 0.8214 (tt0) cc_final: 0.7657 (tt0)
REVERT: D  135 TYR cc_start: 0.7922 (t80) cc_final: 0.7662 (t80)
REVERT: D  203 GLN cc_start: 0.8411 (OUTLIER) cc_final: 0.8102 (tm130)
REVERT: E  220 GLU cc_start: 0.7820 (pp20) cc_final: 0.7422 (pp20)
REVERT: E  272 GLN cc_start: 0.7874 (tt0) cc_final: 0.7445 (tt0)
REVERT: F  131 ARG cc_start: 0.7205 (ptp-170) cc_final: 0.6745 (ptm-80)
REVERT: F  134 GLU cc_start: 0.7152 (tt0) cc_final: 0.6681 (tt0)
REVERT: F  203 GLN cc_start: 0.8501 (OUTLIER) cc_final: 0.8194 (tm130)
REVERT: F  220 GLU cc_start: 0.7788 (pp20) cc_final: 0.7449 (pp20)
REVERT: F  272 GLN cc_start: 0.8132 (tt0) cc_final: 0.7211 (tt0)
REVERT: G  134 GLU cc_start: 0.6994 (tt0) cc_final: 0.6693 (tt0)
REVERT: G  135 TYR cc_start: 0.7970 (t80) cc_final: 0.7739 (t80)
REVERT: G  155 MET cc_start: 0.8569 (ttm) cc_final: 0.8338 (ptm)
REVERT: G  203 GLN cc_start: 0.8511 (OUTLIER) cc_final: 0.8116 (tm130)
REVERT: G  273 MET cc_start: 0.8893 (OUTLIER) cc_final: 0.8296 (ttm)
  outliers start: 62
  outliers final: 40
  residues processed: 289
  average time/residue: 0.0863
  time to fit residues: 39.2497
Evaluate side-chains
  283 residues out of total 1477 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 239
  time to evaluate  : 0.498 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   73 VAL
Chi-restraints excluded: chain A residue  122 VAL
Chi-restraints excluded: chain A residue  141 VAL
Chi-restraints excluded: chain A residue  171 ILE
Chi-restraints excluded: chain A residue  252 ASP
Chi-restraints excluded: chain A residue  257 ILE
Chi-restraints excluded: chain A residue  278 LYS
Chi-restraints excluded: chain B residue   42 LEU
Chi-restraints excluded: chain B residue  122 VAL
Chi-restraints excluded: chain B residue  171 ILE
Chi-restraints excluded: chain B residue  197 ASP
Chi-restraints excluded: chain B residue  206 THR
Chi-restraints excluded: chain B residue  252 ASP
Chi-restraints excluded: chain B residue  257 ILE
Chi-restraints excluded: chain B residue  270 TYR
Chi-restraints excluded: chain C residue   42 LEU
Chi-restraints excluded: chain C residue   83 ILE
Chi-restraints excluded: chain C residue   97 ILE
Chi-restraints excluded: chain C residue  122 VAL
Chi-restraints excluded: chain C residue  161 LYS
Chi-restraints excluded: chain C residue  206 THR
Chi-restraints excluded: chain C residue  208 ILE
Chi-restraints excluded: chain C residue  252 ASP
Chi-restraints excluded: chain C residue  257 ILE
Chi-restraints excluded: chain D residue   42 LEU
Chi-restraints excluded: chain D residue  203 GLN
Chi-restraints excluded: chain D residue  252 ASP
Chi-restraints excluded: chain D residue  257 ILE
Chi-restraints excluded: chain E residue  122 VAL
Chi-restraints excluded: chain E residue  126 MET
Chi-restraints excluded: chain E residue  171 ILE
Chi-restraints excluded: chain E residue  206 THR
Chi-restraints excluded: chain E residue  208 ILE
Chi-restraints excluded: chain E residue  233 ILE
Chi-restraints excluded: chain E residue  257 ILE
Chi-restraints excluded: chain F residue  100 LEU
Chi-restraints excluded: chain F residue  122 VAL
Chi-restraints excluded: chain F residue  203 GLN
Chi-restraints excluded: chain G residue  122 VAL
Chi-restraints excluded: chain G residue  157 THR
Chi-restraints excluded: chain G residue  171 ILE
Chi-restraints excluded: chain G residue  203 GLN
Chi-restraints excluded: chain G residue  208 ILE
Chi-restraints excluded: chain G residue  273 MET
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 182
   random chunks:
   chunk 56 optimal weight:    7.9990
   chunk 165 optimal weight:    4.9990
   chunk 116 optimal weight:    7.9990
   chunk 99 optimal weight:    3.9990
   chunk 176 optimal weight:    0.8980
   chunk 10 optimal weight:    0.9980
   chunk 167 optimal weight:    6.9990
   chunk 30 optimal weight:    2.9990
   chunk 158 optimal weight:    6.9990
   chunk 115 optimal weight:    7.9990
   chunk 118 optimal weight:    0.1980
   overall best weight:    1.8184

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

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

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3624 r_free = 0.3624 target = 0.136190 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3193 r_free = 0.3193 target = 0.105733 restraints weight = 23349.234|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3235 r_free = 0.3235 target = 0.108468 restraints weight = 13273.701|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3263 r_free = 0.3263 target = 0.110333 restraints weight = 8717.390|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3278 r_free = 0.3278 target = 0.111398 restraints weight = 6389.946|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 41)----------------|
| r_work = 0.3293 r_free = 0.3293 target = 0.112339 restraints weight = 5146.785|
|-----------------------------------------------------------------------------|
r_work (final): 0.3298
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7918
moved from start:          0.2473

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.057  14098  Z= 0.159
  Angle     :  0.557   7.745  19117  Z= 0.295
  Chirality :  0.041   0.213   2345
  Planarity :  0.003   0.042   2429
  Dihedral  :  3.890  12.988   1988
  Min Nonbonded Distance : 2.563

Molprobity Statistics.
  All-atom Clashscore : 8.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.38 %
    Favored  : 98.62 %
  Rotamer:
    Outliers :  3.79 %
    Allowed  : 13.13 %
    Favored  : 83.07 %
  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 (0.19), residues: 1813
  helix:  2.83 (0.15), residues: 1008
  sheet:  1.45 (0.28), residues: 259
  loop : -0.69 (0.25), residues: 546

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C  74 
 TYR   0.014   0.001   TYR B 270 
 PHE   0.011   0.001   PHE G 178 
 TRP   0.004   0.001   TRP B 240 

Details of bonding type rmsd
  covalent geometry    : bond        0.00371 (14098)
  covalent geometry    : angle       0.55726 (19117)
  hydrogen bonds       : bond        0.03876 ( 1046)
  hydrogen bonds       : angle       4.04245 ( 3054)

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

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

  3626 Ramachandran restraints generated.
    1813 Oldfield, 0 Emsley, 1813 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3626 Ramachandran restraints generated.
    1813 Oldfield, 0 Emsley, 1813 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  308 residues out of total 1477 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 56
    poor density    : 252
  time to evaluate  : 0.486 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   43 ILE cc_start: 0.8336 (mm) cc_final: 0.7942 (pt)
REVERT: A  150 ILE cc_start: 0.8258 (mm) cc_final: 0.8019 (tp)
REVERT: A  255 GLU cc_start: 0.8318 (tm-30) cc_final: 0.7842 (tm-30)
REVERT: B   86 LEU cc_start: 0.8385 (tp) cc_final: 0.8082 (tp)
REVERT: B  134 GLU cc_start: 0.7263 (tt0) cc_final: 0.6928 (tt0)
REVERT: B  272 GLN cc_start: 0.8330 (tt0) cc_final: 0.8062 (tt0)
REVERT: C  134 GLU cc_start: 0.7126 (tt0) cc_final: 0.6766 (tt0)
REVERT: C  203 GLN cc_start: 0.8517 (OUTLIER) cc_final: 0.8218 (tm130)
REVERT: C  220 GLU cc_start: 0.7820 (pp20) cc_final: 0.7506 (pp20)
REVERT: C  272 GLN cc_start: 0.8225 (tt0) cc_final: 0.7647 (tt0)
REVERT: D  203 GLN cc_start: 0.8375 (OUTLIER) cc_final: 0.8081 (tm130)
REVERT: E  203 GLN cc_start: 0.8503 (OUTLIER) cc_final: 0.8108 (tm130)
REVERT: E  220 GLU cc_start: 0.7896 (pp20) cc_final: 0.7571 (pp20)
REVERT: E  272 GLN cc_start: 0.7884 (tt0) cc_final: 0.7464 (tt0)
REVERT: F  131 ARG cc_start: 0.7181 (ptp-170) cc_final: 0.6764 (ptm-80)
REVERT: F  134 GLU cc_start: 0.7167 (tt0) cc_final: 0.6691 (tt0)
REVERT: F  203 GLN cc_start: 0.8481 (OUTLIER) cc_final: 0.8168 (tm130)
REVERT: F  272 GLN cc_start: 0.8128 (tt0) cc_final: 0.7235 (tt0)
REVERT: G  134 GLU cc_start: 0.6922 (tt0) cc_final: 0.6588 (tt0)
REVERT: G  135 TYR cc_start: 0.7971 (t80) cc_final: 0.7733 (t80)
REVERT: G  203 GLN cc_start: 0.8528 (OUTLIER) cc_final: 0.8127 (tm130)
  outliers start: 56
  outliers final: 39
  residues processed: 291
  average time/residue: 0.0911
  time to fit residues: 41.5723
Evaluate side-chains
  284 residues out of total 1477 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 240
  time to evaluate  : 0.473 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   73 VAL
Chi-restraints excluded: chain A residue  122 VAL
Chi-restraints excluded: chain A residue  141 VAL
Chi-restraints excluded: chain A residue  171 ILE
Chi-restraints excluded: chain A residue  252 ASP
Chi-restraints excluded: chain A residue  257 ILE
Chi-restraints excluded: chain A residue  270 TYR
Chi-restraints excluded: chain B residue   42 LEU
Chi-restraints excluded: chain B residue  122 VAL
Chi-restraints excluded: chain B residue  171 ILE
Chi-restraints excluded: chain B residue  197 ASP
Chi-restraints excluded: chain B residue  206 THR
Chi-restraints excluded: chain B residue  252 ASP
Chi-restraints excluded: chain B residue  257 ILE
Chi-restraints excluded: chain B residue  270 TYR
Chi-restraints excluded: chain C residue   42 LEU
Chi-restraints excluded: chain C residue   83 ILE
Chi-restraints excluded: chain C residue  122 VAL
Chi-restraints excluded: chain C residue  161 LYS
Chi-restraints excluded: chain C residue  203 GLN
Chi-restraints excluded: chain C residue  206 THR
Chi-restraints excluded: chain C residue  252 ASP
Chi-restraints excluded: chain C residue  257 ILE
Chi-restraints excluded: chain D residue   42 LEU
Chi-restraints excluded: chain D residue  203 GLN
Chi-restraints excluded: chain D residue  252 ASP
Chi-restraints excluded: chain D residue  257 ILE
Chi-restraints excluded: chain E residue  122 VAL
Chi-restraints excluded: chain E residue  126 MET
Chi-restraints excluded: chain E residue  171 ILE
Chi-restraints excluded: chain E residue  203 GLN
Chi-restraints excluded: chain E residue  206 THR
Chi-restraints excluded: chain E residue  233 ILE
Chi-restraints excluded: chain E residue  257 ILE
Chi-restraints excluded: chain F residue  100 LEU
Chi-restraints excluded: chain F residue  122 VAL
Chi-restraints excluded: chain F residue  203 GLN
Chi-restraints excluded: chain G residue  122 VAL
Chi-restraints excluded: chain G residue  157 THR
Chi-restraints excluded: chain G residue  171 ILE
Chi-restraints excluded: chain G residue  197 ASP
Chi-restraints excluded: chain G residue  203 GLN
Chi-restraints excluded: chain G residue  208 ILE
Chi-restraints excluded: chain G residue  273 MET
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 182
   random chunks:
   chunk 12 optimal weight:    0.9990
   chunk 71 optimal weight:    0.9980
   chunk 72 optimal weight:    2.9990
   chunk 8 optimal weight:    3.9990
   chunk 128 optimal weight:    0.9990
   chunk 15 optimal weight:    0.9980
   chunk 165 optimal weight:    5.9990
   chunk 170 optimal weight:    5.9990
   chunk 158 optimal weight:    4.9990
   chunk 87 optimal weight:    8.9990
   chunk 145 optimal weight:    0.8980
   overall best weight:    0.9784

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

Flipped N/Q/H residues before XYZ refinement:
A 203 GLN
A 207 ASN
D 203 GLN
E 203 GLN
F 203 GLN
G 203 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3629 r_free = 0.3629 target = 0.136616 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3202 r_free = 0.3202 target = 0.106378 restraints weight = 23295.501|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3244 r_free = 0.3244 target = 0.109123 restraints weight = 13271.926|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3272 r_free = 0.3272 target = 0.110989 restraints weight = 8684.116|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3286 r_free = 0.3286 target = 0.111993 restraints weight = 6333.675|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 40)----------------|
| r_work = 0.3301 r_free = 0.3301 target = 0.112945 restraints weight = 5133.526|
|-----------------------------------------------------------------------------|
r_work (final): 0.3315
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7898
moved from start:          0.2579

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047  14098  Z= 0.130
  Angle     :  0.563   8.552  19117  Z= 0.294
  Chirality :  0.041   0.228   2345
  Planarity :  0.002   0.027   2429
  Dihedral  :  3.837  13.182   1988
  Min Nonbonded Distance : 2.612

Molprobity Statistics.
  All-atom Clashscore : 8.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.38 %
    Favored  : 98.62 %
  Rotamer:
    Outliers :  3.45 %
    Allowed  : 13.20 %
    Favored  : 83.34 %
  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:  2.44 (0.19), residues: 1813
  helix:  2.83 (0.15), residues: 1008
  sheet:  0.76 (0.28), residues: 294
  loop : -0.38 (0.27), residues: 511

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG F 256 
 TYR   0.013   0.001   TYR B 270 
 PHE   0.012   0.001   PHE A 178 
 TRP   0.003   0.000   TRP A 251 

Details of bonding type rmsd
  covalent geometry    : bond        0.00298 (14098)
  covalent geometry    : angle       0.56282 (19117)
  hydrogen bonds       : bond        0.03727 ( 1046)
  hydrogen bonds       : angle       4.03359 ( 3054)

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

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

  3626 Ramachandran restraints generated.
    1813 Oldfield, 0 Emsley, 1813 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3626 Ramachandran restraints generated.
    1813 Oldfield, 0 Emsley, 1813 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  303 residues out of total 1477 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 51
    poor density    : 252
  time to evaluate  : 0.345 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   43 ILE cc_start: 0.8321 (mm) cc_final: 0.7933 (pt)
REVERT: A  150 ILE cc_start: 0.8243 (mm) cc_final: 0.7984 (tp)
REVERT: A  255 GLU cc_start: 0.8336 (tm-30) cc_final: 0.7857 (tm-30)
REVERT: B   86 LEU cc_start: 0.8372 (tp) cc_final: 0.8063 (tp)
REVERT: B  134 GLU cc_start: 0.7193 (tt0) cc_final: 0.6862 (tt0)
REVERT: B  272 GLN cc_start: 0.8288 (tt0) cc_final: 0.8028 (tt0)
REVERT: C  134 GLU cc_start: 0.7088 (tt0) cc_final: 0.6732 (tt0)
REVERT: C  149 GLN cc_start: 0.8024 (mp10) cc_final: 0.7773 (mp10)
REVERT: C  203 GLN cc_start: 0.8501 (OUTLIER) cc_final: 0.8203 (tm130)
REVERT: C  220 GLU cc_start: 0.7893 (pp20) cc_final: 0.7601 (pp20)
REVERT: D  203 GLN cc_start: 0.8429 (OUTLIER) cc_final: 0.8130 (tm130)
REVERT: E  220 GLU cc_start: 0.7940 (pp20) cc_final: 0.7600 (pp20)
REVERT: E  272 GLN cc_start: 0.7861 (tt0) cc_final: 0.7407 (tt0)
REVERT: F  131 ARG cc_start: 0.7175 (ptp-170) cc_final: 0.6752 (ptm-80)
REVERT: F  134 GLU cc_start: 0.7174 (tt0) cc_final: 0.6693 (tt0)
REVERT: F  149 GLN cc_start: 0.8232 (mp10) cc_final: 0.7899 (mp10)
REVERT: F  203 GLN cc_start: 0.8422 (OUTLIER) cc_final: 0.8161 (tm130)
REVERT: F  272 GLN cc_start: 0.8134 (tt0) cc_final: 0.7256 (tt0)
REVERT: G  134 GLU cc_start: 0.6946 (tt0) cc_final: 0.6649 (tt0)
REVERT: G  135 TYR cc_start: 0.7910 (t80) cc_final: 0.7667 (t80)
REVERT: G  203 GLN cc_start: 0.8556 (OUTLIER) cc_final: 0.8182 (tm130)
  outliers start: 51
  outliers final: 37
  residues processed: 286
  average time/residue: 0.0912
  time to fit residues: 40.9407
Evaluate side-chains
  279 residues out of total 1477 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 238
  time to evaluate  : 0.535 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  105 LEU
Chi-restraints excluded: chain A residue  122 VAL
Chi-restraints excluded: chain A residue  171 ILE
Chi-restraints excluded: chain A residue  252 ASP
Chi-restraints excluded: chain A residue  257 ILE
Chi-restraints excluded: chain B residue   42 LEU
Chi-restraints excluded: chain B residue  122 VAL
Chi-restraints excluded: chain B residue  171 ILE
Chi-restraints excluded: chain B residue  197 ASP
Chi-restraints excluded: chain B residue  257 ILE
Chi-restraints excluded: chain B residue  270 TYR
Chi-restraints excluded: chain C residue   42 LEU
Chi-restraints excluded: chain C residue   83 ILE
Chi-restraints excluded: chain C residue  122 VAL
Chi-restraints excluded: chain C residue  161 LYS
Chi-restraints excluded: chain C residue  203 GLN
Chi-restraints excluded: chain C residue  206 THR
Chi-restraints excluded: chain C residue  252 ASP
Chi-restraints excluded: chain C residue  257 ILE
Chi-restraints excluded: chain D residue   42 LEU
Chi-restraints excluded: chain D residue  109 LEU
Chi-restraints excluded: chain D residue  203 GLN
Chi-restraints excluded: chain D residue  252 ASP
Chi-restraints excluded: chain D residue  257 ILE
Chi-restraints excluded: chain E residue  122 VAL
Chi-restraints excluded: chain E residue  126 MET
Chi-restraints excluded: chain E residue  171 ILE
Chi-restraints excluded: chain E residue  203 GLN
Chi-restraints excluded: chain E residue  206 THR
Chi-restraints excluded: chain E residue  233 ILE
Chi-restraints excluded: chain E residue  257 ILE
Chi-restraints excluded: chain E residue  270 TYR
Chi-restraints excluded: chain F residue  100 LEU
Chi-restraints excluded: chain F residue  122 VAL
Chi-restraints excluded: chain F residue  203 GLN
Chi-restraints excluded: chain F residue  206 THR
Chi-restraints excluded: chain G residue  122 VAL
Chi-restraints excluded: chain G residue  157 THR
Chi-restraints excluded: chain G residue  197 ASP
Chi-restraints excluded: chain G residue  203 GLN
Chi-restraints excluded: chain G residue  273 MET
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 182
   random chunks:
   chunk 128 optimal weight:    0.8980
   chunk 154 optimal weight:    2.9990
   chunk 104 optimal weight:    6.9990
   chunk 105 optimal weight:    7.9990
   chunk 29 optimal weight:    3.9990
   chunk 113 optimal weight:    7.9990
   chunk 72 optimal weight:    5.9990
   chunk 101 optimal weight:    4.9990
   chunk 108 optimal weight:    4.9990
   chunk 3 optimal weight:    5.9990
   chunk 97 optimal weight:    3.9990
   overall best weight:    3.3788

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

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

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3586 r_free = 0.3586 target = 0.133199 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3153 r_free = 0.3153 target = 0.103034 restraints weight = 23569.625|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3196 r_free = 0.3196 target = 0.105757 restraints weight = 13560.514|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3224 r_free = 0.3224 target = 0.107611 restraints weight = 8934.500|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.3243 r_free = 0.3243 target = 0.108843 restraints weight = 6547.430|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 40)----------------|
| r_work = 0.3255 r_free = 0.3255 target = 0.109626 restraints weight = 5241.273|
|-----------------------------------------------------------------------------|
r_work (final): 0.3264
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7953
moved from start:          0.2740

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.056  14098  Z= 0.242
  Angle     :  0.640   9.703  19117  Z= 0.335
  Chirality :  0.043   0.222   2345
  Planarity :  0.004   0.039   2429
  Dihedral  :  4.065  12.918   1988
  Min Nonbonded Distance : 2.599

Molprobity Statistics.
  All-atom Clashscore : 9.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.60 %
    Favored  : 98.40 %
  Rotamer:
    Outliers :  3.32 %
    Allowed  : 13.74 %
    Favored  : 82.94 %
  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:  2.18 (0.19), residues: 1813
  helix:  2.67 (0.15), residues: 1008
  sheet:  1.42 (0.27), residues: 273
  loop : -1.07 (0.25), residues: 532

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG C 156 
 TYR   0.014   0.001   TYR B 270 
 PHE   0.014   0.002   PHE A 178 
 TRP   0.007   0.001   TRP G 240 

Details of bonding type rmsd
  covalent geometry    : bond        0.00572 (14098)
  covalent geometry    : angle       0.64019 (19117)
  hydrogen bonds       : bond        0.04201 ( 1046)
  hydrogen bonds       : angle       4.18025 ( 3054)

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

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

  3626 Ramachandran restraints generated.
    1813 Oldfield, 0 Emsley, 1813 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3626 Ramachandran restraints generated.
    1813 Oldfield, 0 Emsley, 1813 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  296 residues out of total 1477 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 247
  time to evaluate  : 0.571 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   43 ILE cc_start: 0.8337 (mm) cc_final: 0.7942 (pt)
REVERT: A  255 GLU cc_start: 0.8327 (tm-30) cc_final: 0.7847 (tm-30)
REVERT: B   86 LEU cc_start: 0.8369 (tp) cc_final: 0.8147 (tp)
REVERT: B  134 GLU cc_start: 0.7236 (tt0) cc_final: 0.6892 (tt0)
REVERT: B  272 GLN cc_start: 0.8382 (tt0) cc_final: 0.8085 (tt0)
REVERT: C  134 GLU cc_start: 0.7121 (tt0) cc_final: 0.6813 (tt0)
REVERT: C  203 GLN cc_start: 0.8559 (OUTLIER) cc_final: 0.8265 (tm130)
REVERT: C  220 GLU cc_start: 0.7976 (pp20) cc_final: 0.7649 (pp20)
REVERT: C  272 GLN cc_start: 0.7838 (tt0) cc_final: 0.7338 (tt0)
REVERT: D  203 GLN cc_start: 0.8471 (OUTLIER) cc_final: 0.8208 (tm130)
REVERT: E  220 GLU cc_start: 0.7853 (pp20) cc_final: 0.7538 (pp20)
REVERT: E  272 GLN cc_start: 0.7828 (tt0) cc_final: 0.7424 (tt0)
REVERT: F  134 GLU cc_start: 0.7159 (tt0) cc_final: 0.6657 (tt0)
REVERT: F  203 GLN cc_start: 0.8512 (OUTLIER) cc_final: 0.8221 (tm130)
REVERT: F  272 GLN cc_start: 0.8041 (tt0) cc_final: 0.7300 (tt0)
REVERT: G  134 GLU cc_start: 0.6949 (tt0) cc_final: 0.6626 (tt0)
REVERT: G  135 TYR cc_start: 0.7914 (t80) cc_final: 0.7710 (t80)
REVERT: G  203 GLN cc_start: 0.8468 (OUTLIER) cc_final: 0.8086 (tm130)
  outliers start: 49
  outliers final: 38
  residues processed: 281
  average time/residue: 0.0935
  time to fit residues: 41.3975
Evaluate side-chains
  281 residues out of total 1477 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 239
  time to evaluate  : 0.518 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   73 VAL
Chi-restraints excluded: chain A residue  105 LEU
Chi-restraints excluded: chain A residue  122 VAL
Chi-restraints excluded: chain A residue  171 ILE
Chi-restraints excluded: chain A residue  252 ASP
Chi-restraints excluded: chain A residue  257 ILE
Chi-restraints excluded: chain B residue   42 LEU
Chi-restraints excluded: chain B residue  122 VAL
Chi-restraints excluded: chain B residue  171 ILE
Chi-restraints excluded: chain B residue  206 THR
Chi-restraints excluded: chain B residue  257 ILE
Chi-restraints excluded: chain B residue  270 TYR
Chi-restraints excluded: chain C residue   42 LEU
Chi-restraints excluded: chain C residue   83 ILE
Chi-restraints excluded: chain C residue  122 VAL
Chi-restraints excluded: chain C residue  161 LYS
Chi-restraints excluded: chain C residue  203 GLN
Chi-restraints excluded: chain C residue  206 THR
Chi-restraints excluded: chain C residue  257 ILE
Chi-restraints excluded: chain D residue   42 LEU
Chi-restraints excluded: chain D residue  109 LEU
Chi-restraints excluded: chain D residue  203 GLN
Chi-restraints excluded: chain D residue  252 ASP
Chi-restraints excluded: chain D residue  257 ILE
Chi-restraints excluded: chain E residue  122 VAL
Chi-restraints excluded: chain E residue  126 MET
Chi-restraints excluded: chain E residue  171 ILE
Chi-restraints excluded: chain E residue  203 GLN
Chi-restraints excluded: chain E residue  206 THR
Chi-restraints excluded: chain E residue  233 ILE
Chi-restraints excluded: chain E residue  257 ILE
Chi-restraints excluded: chain F residue  100 LEU
Chi-restraints excluded: chain F residue  122 VAL
Chi-restraints excluded: chain F residue  203 GLN
Chi-restraints excluded: chain F residue  206 THR
Chi-restraints excluded: chain G residue  122 VAL
Chi-restraints excluded: chain G residue  157 THR
Chi-restraints excluded: chain G residue  171 ILE
Chi-restraints excluded: chain G residue  197 ASP
Chi-restraints excluded: chain G residue  203 GLN
Chi-restraints excluded: chain G residue  208 ILE
Chi-restraints excluded: chain G residue  273 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 182
   random chunks:
   chunk 160 optimal weight:    0.3980
   chunk 86 optimal weight:    2.9990
   chunk 76 optimal weight:    1.9990
   chunk 84 optimal weight:    5.9990
   chunk 37 optimal weight:    6.9990
   chunk 19 optimal weight:    0.7980
   chunk 90 optimal weight:    0.8980
   chunk 101 optimal weight:    0.6980
   chunk 177 optimal weight:    1.9990
   chunk 94 optimal weight:    0.9980
   chunk 181 optimal weight:    2.9990
   overall best weight:    0.7580

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

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3622 r_free = 0.3622 target = 0.135994 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3197 r_free = 0.3197 target = 0.106026 restraints weight = 23213.410|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3239 r_free = 0.3239 target = 0.108758 restraints weight = 13097.554|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3267 r_free = 0.3267 target = 0.110606 restraints weight = 8559.061|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 21)----------------|
| r_work = 0.3282 r_free = 0.3282 target = 0.111690 restraints weight = 6251.932|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 45)----------------|
| r_work = 0.3297 r_free = 0.3297 target = 0.112630 restraints weight = 5026.317|
|-----------------------------------------------------------------------------|
r_work (final): 0.3309
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7893
moved from start:          0.2816

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043  14098  Z= 0.130
  Angle     :  0.595   8.483  19117  Z= 0.309
  Chirality :  0.041   0.188   2345
  Planarity :  0.003   0.022   2429
  Dihedral  :  3.899  13.380   1988
  Min Nonbonded Distance : 2.592

Molprobity Statistics.
  All-atom Clashscore : 8.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.38 %
    Favored  : 98.62 %
  Rotamer:
    Outliers :  2.51 %
    Allowed  : 14.69 %
    Favored  : 82.80 %
  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:  2.29 (0.19), residues: 1813
  helix:  2.74 (0.15), residues: 1008
  sheet:  0.67 (0.27), residues: 294
  loop : -0.51 (0.26), residues: 511

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG G  74 
 TYR   0.013   0.001   TYR B 270 
 PHE   0.012   0.001   PHE A 178 
 TRP   0.002   0.000   TRP A 251 

Details of bonding type rmsd
  covalent geometry    : bond        0.00294 (14098)
  covalent geometry    : angle       0.59546 (19117)
  hydrogen bonds       : bond        0.03785 ( 1046)
  hydrogen bonds       : angle       4.13156 ( 3054)

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

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

  3626 Ramachandran restraints generated.
    1813 Oldfield, 0 Emsley, 1813 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3626 Ramachandran restraints generated.
    1813 Oldfield, 0 Emsley, 1813 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  285 residues out of total 1477 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 248
  time to evaluate  : 0.504 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   43 ILE cc_start: 0.8325 (mm) cc_final: 0.7934 (pt)
REVERT: A  255 GLU cc_start: 0.8365 (tm-30) cc_final: 0.7897 (tm-30)
REVERT: B  134 GLU cc_start: 0.7165 (tt0) cc_final: 0.6799 (tt0)
REVERT: B  272 GLN cc_start: 0.8207 (tt0) cc_final: 0.7882 (tt0)
REVERT: C  134 GLU cc_start: 0.7093 (tt0) cc_final: 0.6732 (tt0)
REVERT: C  203 GLN cc_start: 0.8521 (OUTLIER) cc_final: 0.8217 (tm130)
REVERT: C  220 GLU cc_start: 0.7955 (pp20) cc_final: 0.7657 (pp20)
REVERT: C  272 GLN cc_start: 0.7941 (tt0) cc_final: 0.7355 (tt0)
REVERT: D  149 GLN cc_start: 0.8190 (mp10) cc_final: 0.7919 (mp10)
REVERT: E  149 GLN cc_start: 0.8146 (mp10) cc_final: 0.7800 (mp10)
REVERT: E  220 GLU cc_start: 0.7826 (pp20) cc_final: 0.7549 (pp20)
REVERT: E  272 GLN cc_start: 0.7772 (tt0) cc_final: 0.7299 (tt0)
REVERT: F  134 GLU cc_start: 0.7121 (tt0) cc_final: 0.6659 (tt0)
REVERT: F  149 GLN cc_start: 0.8226 (mp10) cc_final: 0.7904 (mp10)
REVERT: F  203 GLN cc_start: 0.8429 (OUTLIER) cc_final: 0.8186 (tm130)
REVERT: F  272 GLN cc_start: 0.8126 (tt0) cc_final: 0.7327 (tt0)
REVERT: G  134 GLU cc_start: 0.6968 (tt0) cc_final: 0.6711 (tt0)
REVERT: G  135 TYR cc_start: 0.7926 (t80) cc_final: 0.7714 (t80)
REVERT: G  203 GLN cc_start: 0.8540 (tm-30) cc_final: 0.8128 (tm-30)
  outliers start: 37
  outliers final: 32
  residues processed: 273
  average time/residue: 0.0927
  time to fit residues: 39.7632
Evaluate side-chains
  275 residues out of total 1477 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 241
  time to evaluate  : 0.555 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   73 VAL
Chi-restraints excluded: chain A residue  105 LEU
Chi-restraints excluded: chain A residue  171 ILE
Chi-restraints excluded: chain A residue  252 ASP
Chi-restraints excluded: chain A residue  257 ILE
Chi-restraints excluded: chain B residue   42 LEU
Chi-restraints excluded: chain B residue  122 VAL
Chi-restraints excluded: chain B residue  171 ILE
Chi-restraints excluded: chain B residue  257 ILE
Chi-restraints excluded: chain B residue  270 TYR
Chi-restraints excluded: chain C residue   42 LEU
Chi-restraints excluded: chain C residue   83 ILE
Chi-restraints excluded: chain C residue  122 VAL
Chi-restraints excluded: chain C residue  161 LYS
Chi-restraints excluded: chain C residue  203 GLN
Chi-restraints excluded: chain C residue  257 ILE
Chi-restraints excluded: chain D residue   42 LEU
Chi-restraints excluded: chain D residue  252 ASP
Chi-restraints excluded: chain D residue  257 ILE
Chi-restraints excluded: chain E residue  126 MET
Chi-restraints excluded: chain E residue  171 ILE
Chi-restraints excluded: chain E residue  203 GLN
Chi-restraints excluded: chain E residue  206 THR
Chi-restraints excluded: chain E residue  233 ILE
Chi-restraints excluded: chain E residue  257 ILE
Chi-restraints excluded: chain E residue  270 TYR
Chi-restraints excluded: chain F residue  100 LEU
Chi-restraints excluded: chain F residue  122 VAL
Chi-restraints excluded: chain F residue  203 GLN
Chi-restraints excluded: chain F residue  206 THR
Chi-restraints excluded: chain G residue  122 VAL
Chi-restraints excluded: chain G residue  157 THR
Chi-restraints excluded: chain G residue  197 ASP
Chi-restraints excluded: chain G residue  273 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 182
   random chunks:
   chunk 149 optimal weight:    0.9980
   chunk 115 optimal weight:    0.8980
   chunk 90 optimal weight:    7.9990
   chunk 101 optimal weight:    1.9990
   chunk 123 optimal weight:    0.3980
   chunk 117 optimal weight:    7.9990
   chunk 50 optimal weight:    1.9990
   chunk 104 optimal weight:   10.0000
   chunk 47 optimal weight:    5.9990
   chunk 174 optimal weight:    0.9980
   chunk 40 optimal weight:    2.9990
   overall best weight:    1.0582

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3629 r_free = 0.3629 target = 0.136466 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3203 r_free = 0.3203 target = 0.106487 restraints weight = 23146.991|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3245 r_free = 0.3245 target = 0.109180 restraints weight = 13180.831|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3272 r_free = 0.3272 target = 0.111018 restraints weight = 8650.832|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3287 r_free = 0.3287 target = 0.112033 restraints weight = 6327.000|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 40)----------------|
| r_work = 0.3301 r_free = 0.3301 target = 0.112951 restraints weight = 5116.571|
|-----------------------------------------------------------------------------|
r_work (final): 0.3291
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7892
moved from start:          0.2861

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043  14098  Z= 0.135
  Angle     :  0.598   8.297  19117  Z= 0.310
  Chirality :  0.041   0.217   2345
  Planarity :  0.003   0.020   2429
  Dihedral  :  3.873  12.954   1988
  Min Nonbonded Distance : 2.591

Molprobity Statistics.
  All-atom Clashscore : 8.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.71 %
    Favored  : 98.29 %
  Rotamer:
    Outliers :  2.64 %
    Allowed  : 15.17 %
    Favored  : 82.19 %
  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:  2.32 (0.19), residues: 1813
  helix:  2.78 (0.15), residues: 1008
  sheet:  0.65 (0.27), residues: 294
  loop : -0.51 (0.26), residues: 511

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  74 
 TYR   0.012   0.001   TYR B 270 
 PHE   0.011   0.001   PHE G 178 
 TRP   0.003   0.001   TRP E 251 

Details of bonding type rmsd
  covalent geometry    : bond        0.00311 (14098)
  covalent geometry    : angle       0.59779 (19117)
  hydrogen bonds       : bond        0.03779 ( 1046)
  hydrogen bonds       : angle       4.13539 ( 3054)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1966.29 seconds
wall clock time: 34 minutes 41.20 seconds (2081.20 seconds total)