Starting phenix.real_space_refine
on Thu Jul 31 21:26:24 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7onl_12997/07_2025/7onl_12997.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7onl_12997/07_2025/7onl_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_12997/07_2025/7onl_12997.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7onl_12997/07_2025/7onl_12997.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7onl_12997/07_2025/7onl_12997.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7onl_12997/07_2025/7onl_12997.cif"
  }
  resolution = 3.9
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 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-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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:
    C, B, E, D, G, F
  Time building chain proxies: 5.23, per 1000 atoms: 0.38
  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: 3.13
  Conformation dependent library (CDL) restraints added in 1.8 seconds
  

  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: 1.34
  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: 4.38

  Time building geometry restraints manager: 3.75 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: 0.13
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'C'
  selection = chain 'B'
  selection = chain 'E'
  selection = chain 'D'
  selection = chain 'G'
  selection = chain 'F'
}

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:             1.490
  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:          0.480
  Check model and map are aligned:         0.090
  Set scattering table:                    0.120
  Process input model:                     29.170
  Find NCS groups from input model:        0.300
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.920
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   34.620
-------------------------------------------------------------------------------
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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.97 (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
 TRP   0.004   0.001   TRP E 240 
 PHE   0.006   0.001   PHE C  68 
 TYR   0.005   0.001   TYR E 135 
 ARG   0.002   0.000   ARG C 184 

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

*********************** 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  : 1.225 
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: 0.8127 (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: 0.2463
  time to fit residues: 146.2370
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  : 1.438 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 182
   random chunks:
   chunk 153 optimal weight:    0.0170
   chunk 137 optimal weight:    9.9990
   chunk 76 optimal weight:    6.9990
   chunk 47 optimal weight:    1.9990
   chunk 93 optimal weight:    3.9990
   chunk 73 optimal weight:    1.9990
   chunk 142 optimal weight:    7.9990
   chunk 55 optimal weight:    6.9990
   chunk 86 optimal weight:    9.9990
   chunk 106 optimal weight:    9.9990
   chunk 165 optimal weight:    0.9980
   overall best weight:    1.8024

-------------------------------------------------------------------------------
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 = 0.3670 r_free = 0.3670 target = 0.140885 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3239 r_free = 0.3239 target = 0.109936 restraints weight = 23240.180|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3279 r_free = 0.3279 target = 0.112659 restraints weight = 13216.274|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3304 r_free = 0.3304 target = 0.114486 restraints weight = 8630.587|
|-----------------------------------------------------------------------------|
r_work (final): 0.3293
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7929
moved from start:          0.1537

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045  14098  Z= 0.163
  Angle     :  0.553   6.191  19117  Z= 0.296
  Chirality :  0.041   0.146   2345
  Planarity :  0.004   0.072   2429
  Dihedral  :  3.814  13.213   1988
  Min Nonbonded Distance : 2.614

Molprobity Statistics.
  All-atom Clashscore : 8.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.38 %
    Favored  : 98.62 %
  Rotamer:
    Outliers :  3.32 %
    Allowed  : 10.02 %
    Favored  : 86.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.73 (0.20), residues: 1813
  helix:  3.07 (0.16), residues: 1001
  sheet:  0.77 (0.31), residues: 259
  loop : -0.09 (0.27), residues: 553

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP D 240 
 PHE   0.021   0.002   PHE B 127 
 TYR   0.005   0.001   TYR A  27 
 ARG   0.007   0.000   ARG G 259 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04247 ( 1046)
  hydrogen bonds       : angle       4.11253 ( 3054)
  covalent geometry    : bond        0.00378 (14098)
  covalent geometry    : angle       0.55343 (19117)

*********************** 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
  332 residues out of total 1477 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 283
  time to evaluate  : 1.558 
Fit side-chains
   revert: symmetry clash
REVERT: A   43 ILE cc_start: 0.8327 (mm) cc_final: 0.7964 (pt)
REVERT: A  131 ARG cc_start: 0.7170 (ptp-170) cc_final: 0.6807 (ptm-80)
REVERT: A  134 GLU cc_start: 0.7178 (tt0) cc_final: 0.6971 (tt0)
REVERT: B   86 LEU cc_start: 0.8401 (tp) cc_final: 0.8092 (tp)
REVERT: B  134 GLU cc_start: 0.7273 (tt0) cc_final: 0.6939 (tt0)
REVERT: B  161 LYS cc_start: 0.8733 (mtmm) cc_final: 0.8401 (mtmm)
REVERT: B  197 ASP cc_start: 0.7864 (t70) cc_final: 0.7636 (t70)
REVERT: B  272 GLN cc_start: 0.8371 (tt0) cc_final: 0.7470 (tt0)
REVERT: C  134 GLU cc_start: 0.7250 (tt0) cc_final: 0.6868 (tt0)
REVERT: C  220 GLU cc_start: 0.7584 (pp20) cc_final: 0.7329 (pp20)
REVERT: C  221 MET cc_start: 0.7416 (ptt) cc_final: 0.7108 (ptt)
REVERT: C  272 GLN cc_start: 0.8160 (tt0) cc_final: 0.7569 (tt0)
REVERT: D  135 TYR cc_start: 0.8034 (t80) cc_final: 0.7794 (t80)
REVERT: D  149 GLN cc_start: 0.7875 (mp10) cc_final: 0.7429 (mp10)
REVERT: D  272 GLN cc_start: 0.8120 (tt0) cc_final: 0.7688 (tt0)
REVERT: D  273 MET cc_start: 0.8553 (OUTLIER) cc_final: 0.8332 (ttm)
REVERT: E  134 GLU cc_start: 0.7156 (tt0) cc_final: 0.6842 (tt0)
REVERT: E  135 TYR cc_start: 0.8066 (t80) cc_final: 0.7800 (t80)
REVERT: E  272 GLN cc_start: 0.8120 (tt0) cc_final: 0.7559 (tt0)
REVERT: F  131 ARG cc_start: 0.7248 (ptp-170) cc_final: 0.6868 (ptm-80)
REVERT: F  134 GLU cc_start: 0.7153 (tt0) cc_final: 0.6730 (tt0)
REVERT: F  149 GLN cc_start: 0.8045 (mp10) cc_final: 0.7299 (mp10)
REVERT: F  272 GLN cc_start: 0.8189 (tt0) cc_final: 0.7173 (tt0)
REVERT: F  273 MET cc_start: 0.8845 (OUTLIER) cc_final: 0.8644 (ttm)
REVERT: G  134 GLU cc_start: 0.6883 (tt0) cc_final: 0.6634 (tt0)
REVERT: G  135 TYR cc_start: 0.7939 (t80) cc_final: 0.7717 (t80)
REVERT: G  197 ASP cc_start: 0.7443 (t70) cc_final: 0.7183 (t70)
  outliers start: 49
  outliers final: 17
  residues processed: 309
  average time/residue: 0.2602
  time to fit residues: 122.6458
Evaluate side-chains
  265 residues out of total 1477 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 246
  time to evaluate  : 1.461 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  171 ILE
Chi-restraints excluded: chain A residue  257 ILE
Chi-restraints excluded: chain B residue   42 LEU
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   42 LEU
Chi-restraints excluded: chain D residue  273 MET
Chi-restraints excluded: chain E residue  122 VAL
Chi-restraints excluded: chain E residue  171 ILE
Chi-restraints excluded: chain E residue  206 THR
Chi-restraints excluded: chain E residue  233 ILE
Chi-restraints excluded: chain F residue  100 LEU
Chi-restraints excluded: chain F residue  206 THR
Chi-restraints excluded: chain F residue  273 MET
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 1 optimal weight:    9.9990
   chunk 143 optimal weight:    7.9990
   chunk 41 optimal weight:    0.8980
   chunk 116 optimal weight:    3.9990
   chunk 48 optimal weight:    7.9990
   chunk 173 optimal weight:    0.4980
   chunk 75 optimal weight:    0.8980
   chunk 30 optimal weight:    5.9990
   chunk 50 optimal weight:    0.9990
   chunk 150 optimal weight:    1.9990
   chunk 46 optimal weight:    5.9990
   overall best weight:    1.0584

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3679 r_free = 0.3679 target = 0.141367 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3250 r_free = 0.3250 target = 0.110719 restraints weight = 23466.969|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3291 r_free = 0.3291 target = 0.113464 restraints weight = 13389.959|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3318 r_free = 0.3318 target = 0.115294 restraints weight = 8747.900|
|-----------------------------------------------------------------------------|
r_work (final): 0.3296
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7910
moved from start:          0.1863

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= 0.127
  Angle     :  0.508   7.207  19117  Z= 0.274
  Chirality :  0.041   0.141   2345
  Planarity :  0.003   0.040   2429
  Dihedral  :  3.750  14.356   1988
  Min Nonbonded Distance : 2.615

Molprobity Statistics.
  All-atom Clashscore : 7.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.43 %
    Favored  : 98.57 %
  Rotamer:
    Outliers :  2.78 %
    Allowed  : 11.37 %
    Favored  : 85.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.71 (0.20), residues: 1813
  helix:  3.03 (0.16), residues: 1001
  sheet:  1.82 (0.31), residues: 224
  loop : -0.49 (0.26), residues: 588

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.000   TRP D 240 
 PHE   0.013   0.001   PHE G  80 
 TYR   0.004   0.001   TYR C 135 
 ARG   0.003   0.000   ARG C 259 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03838 ( 1046)
  hydrogen bonds       : angle       3.96724 ( 3054)
  covalent geometry    : bond        0.00282 (14098)
  covalent geometry    : angle       0.50836 (19117)

*********************** 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
  307 residues out of total 1477 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 266
  time to evaluate  : 1.393 
Fit side-chains
   revert: symmetry clash
REVERT: A   43 ILE cc_start: 0.8234 (mm) cc_final: 0.7896 (pt)
REVERT: A  131 ARG cc_start: 0.7193 (ptp-170) cc_final: 0.6835 (ptm-80)
REVERT: A  134 GLU cc_start: 0.7083 (tt0) cc_final: 0.6864 (tt0)
REVERT: A  150 ILE cc_start: 0.8304 (mm) cc_final: 0.7991 (tp)
REVERT: A  273 MET cc_start: 0.7687 (ptm) cc_final: 0.7291 (ptm)
REVERT: B   86 LEU cc_start: 0.8408 (tp) cc_final: 0.8091 (tp)
REVERT: B  134 GLU cc_start: 0.7261 (tt0) cc_final: 0.6967 (tt0)
REVERT: B  161 LYS cc_start: 0.8695 (mtmm) cc_final: 0.8356 (mtmm)
REVERT: B  272 GLN cc_start: 0.8251 (tt0) cc_final: 0.7309 (tt0)
REVERT: C  134 GLU cc_start: 0.7189 (tt0) cc_final: 0.6816 (tt0)
REVERT: C  220 GLU cc_start: 0.7604 (pp20) cc_final: 0.7343 (pp20)
REVERT: C  272 GLN cc_start: 0.8120 (tt0) cc_final: 0.7590 (tt0)
REVERT: D  149 GLN cc_start: 0.7883 (mp10) cc_final: 0.7334 (mp10)
REVERT: D  272 GLN cc_start: 0.7874 (tt0) cc_final: 0.7631 (tt0)
REVERT: D  273 MET cc_start: 0.8372 (OUTLIER) cc_final: 0.8096 (ptm)
REVERT: E  134 GLU cc_start: 0.7125 (tt0) cc_final: 0.6886 (tt0)
REVERT: E  135 TYR cc_start: 0.8000 (t80) cc_final: 0.7685 (t80)
REVERT: E  272 GLN cc_start: 0.8130 (tt0) cc_final: 0.7687 (tt0)
REVERT: F  131 ARG cc_start: 0.7179 (ptp-170) cc_final: 0.6770 (ptm-80)
REVERT: F  134 GLU cc_start: 0.7191 (tt0) cc_final: 0.6729 (tt0)
REVERT: F  272 GLN cc_start: 0.8089 (tt0) cc_final: 0.7166 (tt0)
REVERT: F  273 MET cc_start: 0.8900 (OUTLIER) cc_final: 0.8446 (ttm)
REVERT: G  134 GLU cc_start: 0.6864 (tt0) cc_final: 0.6567 (tt0)
REVERT: G  135 TYR cc_start: 0.7920 (t80) cc_final: 0.7670 (t80)
  outliers start: 41
  outliers final: 21
  residues processed: 287
  average time/residue: 0.2536
  time to fit residues: 110.9896
Evaluate side-chains
  262 residues out of total 1477 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 239
  time to evaluate  : 1.904 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  122 VAL
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   97 ILE
Chi-restraints excluded: chain C residue  122 VAL
Chi-restraints excluded: chain C residue  206 THR
Chi-restraints excluded: chain D residue  257 ILE
Chi-restraints excluded: chain D residue  273 MET
Chi-restraints excluded: chain E residue  126 MET
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  122 VAL
Chi-restraints excluded: chain F residue  218 ASP
Chi-restraints excluded: chain F residue  273 MET
Chi-restraints excluded: chain G residue   97 ILE
Chi-restraints excluded: chain G residue  157 THR
Chi-restraints excluded: chain G residue  171 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 182
   random chunks:
   chunk 125 optimal weight:    5.9990
   chunk 165 optimal weight:    6.9990
   chunk 129 optimal weight:    2.9990
   chunk 42 optimal weight:    1.9990
   chunk 94 optimal weight:    0.9980
   chunk 150 optimal weight:    0.6980
   chunk 71 optimal weight:    2.9990
   chunk 24 optimal weight:    0.9980
   chunk 139 optimal weight:    2.9990
   chunk 181 optimal weight:    2.9990
   chunk 77 optimal weight:    0.0670
   overall best weight:    0.9520

-------------------------------------------------------------------------------
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 = 0.3684 r_free = 0.3684 target = 0.141798 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3259 r_free = 0.3259 target = 0.111339 restraints weight = 23282.986|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3299 r_free = 0.3299 target = 0.114044 restraints weight = 13446.970|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3321 r_free = 0.3321 target = 0.115635 restraints weight = 8821.242|
|-----------------------------------------------------------------------------|
r_work (final): 0.3331
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7921
moved from start:          0.2022

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  14098  Z= 0.120
  Angle     :  0.498   5.798  19117  Z= 0.266
  Chirality :  0.040   0.138   2345
  Planarity :  0.002   0.032   2429
  Dihedral  :  3.722  13.480   1988
  Min Nonbonded Distance : 2.612

Molprobity Statistics.
  All-atom Clashscore : 8.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.27 %
    Favored  : 98.73 %
  Rotamer:
    Outliers :  3.18 %
    Allowed  : 11.92 %
    Favored  : 84.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.71 (0.20), residues: 1813
  helix:  3.01 (0.16), residues: 1001
  sheet:  1.54 (0.29), residues: 259
  loop : -0.46 (0.26), residues: 553

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.000   TRP D 240 
 PHE   0.014   0.001   PHE E  80 
 TYR   0.005   0.001   TYR B 270 
 ARG   0.003   0.000   ARG B  74 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03666 ( 1046)
  hydrogen bonds       : angle       3.92948 ( 3054)
  covalent geometry    : bond        0.00269 (14098)
  covalent geometry    : angle       0.49783 (19117)

*********************** 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
  316 residues out of total 1477 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 269
  time to evaluate  : 1.602 
Fit side-chains
   revert: symmetry clash
REVERT: A   43 ILE cc_start: 0.8211 (mm) cc_final: 0.7870 (pt)
REVERT: A  131 ARG cc_start: 0.7163 (ptp-170) cc_final: 0.6893 (ptm-80)
REVERT: A  134 GLU cc_start: 0.7055 (tt0) cc_final: 0.6805 (tt0)
REVERT: A  150 ILE cc_start: 0.8285 (mm) cc_final: 0.7975 (tp)
REVERT: A  255 GLU cc_start: 0.8357 (tm-30) cc_final: 0.7921 (tm-30)
REVERT: B   86 LEU cc_start: 0.8426 (tp) cc_final: 0.8110 (tp)
REVERT: B  134 GLU cc_start: 0.7255 (tt0) cc_final: 0.6977 (tt0)
REVERT: B  161 LYS cc_start: 0.8665 (mtmm) cc_final: 0.8418 (mtmm)
REVERT: B  272 GLN cc_start: 0.8417 (tt0) cc_final: 0.7428 (tt0)
REVERT: C  134 GLU cc_start: 0.7125 (tt0) cc_final: 0.6763 (tt0)
REVERT: C  161 LYS cc_start: 0.8433 (OUTLIER) cc_final: 0.7826 (mtmm)
REVERT: C  203 GLN cc_start: 0.8603 (OUTLIER) cc_final: 0.8250 (tm130)
REVERT: C  220 GLU cc_start: 0.7573 (pp20) cc_final: 0.7295 (pp20)
REVERT: C  221 MET cc_start: 0.7365 (ptt) cc_final: 0.7162 (ptt)
REVERT: C  272 GLN cc_start: 0.8125 (tt0) cc_final: 0.7578 (tt0)
REVERT: D  149 GLN cc_start: 0.7857 (mp10) cc_final: 0.7346 (mp10)
REVERT: D  272 GLN cc_start: 0.7919 (tt0) cc_final: 0.7674 (tt0)
REVERT: D  273 MET cc_start: 0.8448 (OUTLIER) cc_final: 0.8124 (ptm)
REVERT: E  134 GLU cc_start: 0.7161 (tt0) cc_final: 0.6951 (tt0)
REVERT: E  135 TYR cc_start: 0.7981 (t80) cc_final: 0.7746 (t80)
REVERT: E  211 SER cc_start: 0.8510 (m) cc_final: 0.8291 (t)
REVERT: E  220 GLU cc_start: 0.7728 (pp20) cc_final: 0.7301 (pp20)
REVERT: E  272 GLN cc_start: 0.8011 (tt0) cc_final: 0.7602 (tt0)
REVERT: F  131 ARG cc_start: 0.7158 (ptp-170) cc_final: 0.6789 (ptm-80)
REVERT: F  134 GLU cc_start: 0.7336 (tt0) cc_final: 0.6905 (tt0)
REVERT: F  203 GLN cc_start: 0.8416 (OUTLIER) cc_final: 0.8057 (tm130)
REVERT: F  272 GLN cc_start: 0.8078 (tt0) cc_final: 0.7255 (tt0)
REVERT: F  273 MET cc_start: 0.8904 (OUTLIER) cc_final: 0.8282 (ttm)
REVERT: G  134 GLU cc_start: 0.6934 (tt0) cc_final: 0.6670 (tt0)
REVERT: G  135 TYR cc_start: 0.7933 (t80) cc_final: 0.7633 (t80)
REVERT: G  273 MET cc_start: 0.8680 (OUTLIER) cc_final: 0.8355 (ttm)
  outliers start: 47
  outliers final: 31
  residues processed: 299
  average time/residue: 0.2533
  time to fit residues: 115.5106
Evaluate side-chains
  280 residues out of total 1477 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 243
  time to evaluate  : 1.653 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  122 VAL
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   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 C residue   42 LEU
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  203 GLN
Chi-restraints excluded: chain C residue  206 THR
Chi-restraints excluded: chain C residue  252 ASP
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 D residue  273 MET
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  233 ILE
Chi-restraints excluded: chain E residue  273 MET
Chi-restraints excluded: chain F residue  100 LEU
Chi-restraints excluded: chain F residue  122 VAL
Chi-restraints excluded: chain F residue  197 ASP
Chi-restraints excluded: chain F residue  203 GLN
Chi-restraints excluded: chain F residue  273 MET
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  218 ASP
Chi-restraints excluded: chain G residue  257 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 110 optimal weight:    7.9990
   chunk 99 optimal weight:    5.9990
   chunk 155 optimal weight:    4.9990
   chunk 70 optimal weight:    0.9990
   chunk 41 optimal weight:    6.9990
   chunk 161 optimal weight:    9.9990
   chunk 165 optimal weight:    0.9990
   chunk 27 optimal weight:   10.0000
   chunk 43 optimal weight:    6.9990
   chunk 32 optimal weight:    6.9990
   chunk 156 optimal weight:    0.9990
   overall best weight:    2.7990

-------------------------------------------------------------------------------
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 = 0.3607 r_free = 0.3607 target = 0.134905 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3171 r_free = 0.3171 target = 0.104279 restraints weight = 23213.365|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3213 r_free = 0.3213 target = 0.107000 restraints weight = 13302.919|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3241 r_free = 0.3241 target = 0.108849 restraints weight = 8760.163|
|-----------------------------------------------------------------------------|
r_work (final): 0.3256
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7958
moved from start:          0.2258

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.046  14098  Z= 0.206
  Angle     :  0.567   9.664  19117  Z= 0.301
  Chirality :  0.042   0.140   2345
  Planarity :  0.003   0.021   2429
  Dihedral  :  3.924  12.306   1988
  Min Nonbonded Distance : 2.596

Molprobity Statistics.
  All-atom Clashscore : 8.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.27 %
    Favored  : 98.73 %
  Rotamer:
    Outliers :  4.33 %
    Allowed  : 12.53 %
    Favored  : 83.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.55 (0.19), residues: 1813
  helix:  2.88 (0.16), residues: 1008
  sheet:  1.53 (0.28), residues: 259
  loop : -0.61 (0.26), residues: 546

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP F 240 
 PHE   0.013   0.001   PHE G 178 
 TYR   0.012   0.001   TYR B 270 
 ARG   0.005   0.000   ARG B  74 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04018 ( 1046)
  hydrogen bonds       : angle       4.03949 ( 3054)
  covalent geometry    : bond        0.00479 (14098)
  covalent geometry    : angle       0.56657 (19117)

*********************** 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
  319 residues out of total 1477 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 64
    poor density    : 255
  time to evaluate  : 2.518 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   43 ILE cc_start: 0.8284 (mm) cc_final: 0.7872 (pt)
REVERT: A  131 ARG cc_start: 0.7089 (ptp-170) cc_final: 0.6875 (ptm-80)
REVERT: A  150 ILE cc_start: 0.8304 (mm) cc_final: 0.8047 (tp)
REVERT: A  255 GLU cc_start: 0.8373 (tm-30) cc_final: 0.7949 (tm-30)
REVERT: B   86 LEU cc_start: 0.8391 (tp) cc_final: 0.8081 (tp)
REVERT: B  134 GLU cc_start: 0.7274 (tt0) cc_final: 0.6940 (tt0)
REVERT: B  161 LYS cc_start: 0.8751 (mtmm) cc_final: 0.8443 (mtmm)
REVERT: B  272 GLN cc_start: 0.8348 (tt0) cc_final: 0.7467 (tt0)
REVERT: C  134 GLU cc_start: 0.7190 (tt0) cc_final: 0.6797 (tt0)
REVERT: C  203 GLN cc_start: 0.8699 (OUTLIER) cc_final: 0.8419 (tm130)
REVERT: C  220 GLU cc_start: 0.7659 (pp20) cc_final: 0.7336 (pp20)
REVERT: C  272 GLN cc_start: 0.8187 (tt0) cc_final: 0.7617 (tt0)
REVERT: D  203 GLN cc_start: 0.8446 (OUTLIER) cc_final: 0.8074 (tm130)
REVERT: D  272 GLN cc_start: 0.8159 (tt0) cc_final: 0.7543 (tt0)
REVERT: D  273 MET cc_start: 0.8686 (OUTLIER) cc_final: 0.8189 (ptm)
REVERT: E  134 GLU cc_start: 0.7189 (tt0) cc_final: 0.6957 (tt0)
REVERT: E  211 SER cc_start: 0.8550 (m) cc_final: 0.8310 (t)
REVERT: E  220 GLU cc_start: 0.7833 (pp20) cc_final: 0.7422 (pp20)
REVERT: E  272 GLN cc_start: 0.7972 (tt0) cc_final: 0.7563 (tt0)
REVERT: F  131 ARG cc_start: 0.7214 (ptp-170) cc_final: 0.6723 (ptm-80)
REVERT: F  134 GLU cc_start: 0.7236 (tt0) cc_final: 0.6768 (tt0)
REVERT: F  203 GLN cc_start: 0.8603 (OUTLIER) cc_final: 0.8282 (tm130)
REVERT: F  220 GLU cc_start: 0.7772 (pp20) cc_final: 0.7422 (pp20)
REVERT: F  272 GLN cc_start: 0.8226 (tt0) cc_final: 0.7315 (tt0)
REVERT: F  273 MET cc_start: 0.8894 (OUTLIER) cc_final: 0.8595 (ttm)
REVERT: G  134 GLU cc_start: 0.7089 (tt0) cc_final: 0.6770 (tt0)
REVERT: G  135 TYR cc_start: 0.7993 (t80) cc_final: 0.7781 (t80)
REVERT: G  203 GLN cc_start: 0.8583 (OUTLIER) cc_final: 0.8080 (tm130)
REVERT: G  220 GLU cc_start: 0.7706 (pp20) cc_final: 0.7432 (pp20)
REVERT: G  273 MET cc_start: 0.8828 (OUTLIER) cc_final: 0.8410 (ttm)
  outliers start: 64
  outliers final: 34
  residues processed: 299
  average time/residue: 0.2863
  time to fit residues: 133.4752
Evaluate side-chains
  283 residues out of total 1477 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 242
  time to evaluate  : 2.801 
-------------------------------------------------------------------------------
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  203 GLN
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  270 TYR
Chi-restraints excluded: chain C residue   42 LEU
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  203 GLN
Chi-restraints excluded: chain C residue  206 THR
Chi-restraints excluded: chain C residue  208 ILE
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  273 MET
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  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 F residue  206 THR
Chi-restraints excluded: chain F residue  273 MET
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  257 ILE
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 172 optimal weight:    1.9990
   chunk 9 optimal weight:    3.9990
   chunk 21 optimal weight:    1.9990
   chunk 46 optimal weight:    2.9990
   chunk 41 optimal weight:    4.9990
   chunk 66 optimal weight:    5.9990
   chunk 39 optimal weight:    1.9990
   chunk 127 optimal weight:    0.8980
   chunk 149 optimal weight:    9.9990
   chunk 126 optimal weight:    0.0270
   chunk 6 optimal weight:    0.8980
   overall best weight:    1.1642

-------------------------------------------------------------------------------
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
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 = 0.3622 r_free = 0.3622 target = 0.136216 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3194 r_free = 0.3194 target = 0.105923 restraints weight = 23265.251|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3236 r_free = 0.3236 target = 0.108722 restraints weight = 13092.828|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3261 r_free = 0.3261 target = 0.110415 restraints weight = 8486.315|
|-----------------------------------------------------------------------------|
r_work (final): 0.3276
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7925
moved from start:          0.2386

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.053  14098  Z= 0.134
  Angle     :  0.527   7.614  19117  Z= 0.282
  Chirality :  0.040   0.145   2345
  Planarity :  0.002   0.020   2429
  Dihedral  :  3.835  12.398   1988
  Min Nonbonded Distance : 2.590

Molprobity Statistics.
  All-atom Clashscore : 8.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.27 %
    Favored  : 98.73 %
  Rotamer:
    Outliers :  4.47 %
    Allowed  : 12.19 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.54 (0.19), residues: 1813
  helix:  2.87 (0.15), residues: 1008
  sheet:  1.49 (0.28), residues: 259
  loop : -0.61 (0.26), residues: 546

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.000   TRP B 240 
 PHE   0.011   0.001   PHE G 178 
 TYR   0.012   0.001   TYR B 270 
 ARG   0.004   0.000   ARG B  74 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03737 ( 1046)
  hydrogen bonds       : angle       4.01800 ( 3054)
  covalent geometry    : bond        0.00307 (14098)
  covalent geometry    : angle       0.52682 (19117)

*********************** 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
  320 residues out of total 1477 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 66
    poor density    : 254
  time to evaluate  : 1.440 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   43 ILE cc_start: 0.8267 (mm) cc_final: 0.7860 (pt)
REVERT: A  150 ILE cc_start: 0.8255 (mm) cc_final: 0.7978 (tp)
REVERT: A  255 GLU cc_start: 0.8335 (tm-30) cc_final: 0.7857 (tm-30)
REVERT: B   86 LEU cc_start: 0.8410 (tp) cc_final: 0.8100 (tp)
REVERT: B  134 GLU cc_start: 0.7309 (tt0) cc_final: 0.6983 (tt0)
REVERT: B  272 GLN cc_start: 0.8335 (tt0) cc_final: 0.7494 (tt0)
REVERT: C  134 GLU cc_start: 0.7173 (tt0) cc_final: 0.6813 (tt0)
REVERT: C  161 LYS cc_start: 0.8448 (OUTLIER) cc_final: 0.7821 (mtmm)
REVERT: C  203 GLN cc_start: 0.8682 (OUTLIER) cc_final: 0.8479 (tm130)
REVERT: C  220 GLU cc_start: 0.7808 (pp20) cc_final: 0.7478 (pp20)
REVERT: C  272 GLN cc_start: 0.8170 (tt0) cc_final: 0.7586 (tt0)
REVERT: D  203 GLN cc_start: 0.8426 (OUTLIER) cc_final: 0.8102 (tm130)
REVERT: D  272 GLN cc_start: 0.8088 (tt0) cc_final: 0.7837 (tt0)
REVERT: D  273 MET cc_start: 0.8731 (OUTLIER) cc_final: 0.8217 (ptm)
REVERT: E  134 GLU cc_start: 0.7110 (tt0) cc_final: 0.6880 (tt0)
REVERT: E  203 GLN cc_start: 0.8581 (OUTLIER) cc_final: 0.8178 (tm130)
REVERT: E  220 GLU cc_start: 0.7847 (pp20) cc_final: 0.7466 (pp20)
REVERT: E  272 GLN cc_start: 0.7973 (tt0) cc_final: 0.7518 (tt0)
REVERT: F  131 ARG cc_start: 0.7218 (ptp-170) cc_final: 0.6736 (ptm-80)
REVERT: F  134 GLU cc_start: 0.7222 (tt0) cc_final: 0.6737 (tt0)
REVERT: F  203 GLN cc_start: 0.8494 (OUTLIER) cc_final: 0.8159 (tm130)
REVERT: F  220 GLU cc_start: 0.7789 (pp20) cc_final: 0.7481 (pp20)
REVERT: F  272 GLN cc_start: 0.8241 (tt0) cc_final: 0.7496 (tt0)
REVERT: F  273 MET cc_start: 0.8929 (OUTLIER) cc_final: 0.8266 (ttm)
REVERT: G  134 GLU cc_start: 0.7033 (tt0) cc_final: 0.6699 (tt0)
REVERT: G  203 GLN cc_start: 0.8506 (OUTLIER) cc_final: 0.8080 (tm130)
REVERT: G  272 GLN cc_start: 0.8204 (tt0) cc_final: 0.8000 (tt0)
REVERT: G  273 MET cc_start: 0.8734 (OUTLIER) cc_final: 0.8341 (ttm)
  outliers start: 66
  outliers final: 41
  residues processed: 297
  average time/residue: 0.2215
  time to fit residues: 100.8983
Evaluate side-chains
  287 residues out of total 1477 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 237
  time to evaluate  : 1.568 
-------------------------------------------------------------------------------
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  203 GLN
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  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  105 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 D residue  273 MET
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  273 MET
Chi-restraints excluded: chain G residue   43 ILE
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  218 ASP
Chi-restraints excluded: chain G residue  257 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 36 optimal weight:    1.9990
   chunk 180 optimal weight:    3.9990
   chunk 178 optimal weight:    7.9990
   chunk 21 optimal weight:    1.9990
   chunk 116 optimal weight:    5.9990
   chunk 172 optimal weight:    4.9990
   chunk 176 optimal weight:    0.3980
   chunk 170 optimal weight:    0.7980
   chunk 57 optimal weight:   10.0000
   chunk 91 optimal weight:    0.9990
   chunk 70 optimal weight:    1.9990
   overall best weight:    1.2386

-------------------------------------------------------------------------------
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 = 0.3628 r_free = 0.3628 target = 0.136577 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3199 r_free = 0.3199 target = 0.106295 restraints weight = 23269.345|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3242 r_free = 0.3242 target = 0.109091 restraints weight = 13072.678|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3270 r_free = 0.3270 target = 0.110957 restraints weight = 8470.066|
|-----------------------------------------------------------------------------|
r_work (final): 0.3284
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7924
moved from start:          0.2515

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= 0.135
  Angle     :  0.543   7.104  19117  Z= 0.289
  Chirality :  0.040   0.144   2345
  Planarity :  0.002   0.015   2429
  Dihedral  :  3.824  12.346   1988
  Min Nonbonded Distance : 2.600

Molprobity Statistics.
  All-atom Clashscore : 8.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.32 %
    Favored  : 98.68 %
  Rotamer:
    Outliers :  3.86 %
    Allowed  : 12.93 %
    Favored  : 83.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.52 (0.19), residues: 1813
  helix:  2.87 (0.15), residues: 1008
  sheet:  0.82 (0.28), residues: 294
  loop : -0.31 (0.27), residues: 511

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.002   0.001   TRP B 240 
 PHE   0.013   0.001   PHE D  80 
 TYR   0.011   0.001   TYR B 270 
 ARG   0.003   0.000   ARG B  74 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03715 ( 1046)
  hydrogen bonds       : angle       4.02515 ( 3054)
  covalent geometry    : bond        0.00310 (14098)
  covalent geometry    : angle       0.54333 (19117)

*********************** 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
  301 residues out of total 1477 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 57
    poor density    : 244
  time to evaluate  : 1.675 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   43 ILE cc_start: 0.8307 (mm) cc_final: 0.7888 (pt)
REVERT: A  150 ILE cc_start: 0.8285 (mm) cc_final: 0.7988 (tp)
REVERT: A  255 GLU cc_start: 0.8355 (tm-30) cc_final: 0.7869 (tm-30)
REVERT: B   86 LEU cc_start: 0.8394 (tp) cc_final: 0.8069 (tp)
REVERT: B  134 GLU cc_start: 0.7224 (tt0) cc_final: 0.6910 (tt0)
REVERT: B  161 LYS cc_start: 0.8714 (mtmm) cc_final: 0.8449 (mtmm)
REVERT: B  272 GLN cc_start: 0.8361 (tt0) cc_final: 0.7538 (tt0)
REVERT: C  134 GLU cc_start: 0.7134 (tt0) cc_final: 0.6783 (tt0)
REVERT: C  161 LYS cc_start: 0.8464 (OUTLIER) cc_final: 0.7833 (mtmm)
REVERT: C  220 GLU cc_start: 0.7818 (pp20) cc_final: 0.7498 (pp20)
REVERT: C  272 GLN cc_start: 0.8221 (tt0) cc_final: 0.7616 (tt0)
REVERT: D  203 GLN cc_start: 0.8423 (OUTLIER) cc_final: 0.8096 (tm130)
REVERT: D  272 GLN cc_start: 0.8112 (tt0) cc_final: 0.7894 (tt0)
REVERT: D  273 MET cc_start: 0.8765 (OUTLIER) cc_final: 0.8272 (ptm)
REVERT: E  134 GLU cc_start: 0.7109 (tt0) cc_final: 0.6880 (tt0)
REVERT: E  203 GLN cc_start: 0.8507 (OUTLIER) cc_final: 0.8201 (tm130)
REVERT: E  220 GLU cc_start: 0.7929 (pp20) cc_final: 0.7555 (pp20)
REVERT: E  272 GLN cc_start: 0.7963 (tt0) cc_final: 0.7540 (tt0)
REVERT: F  131 ARG cc_start: 0.7237 (ptp-170) cc_final: 0.6749 (ptm-80)
REVERT: F  134 GLU cc_start: 0.7211 (tt0) cc_final: 0.6735 (tt0)
REVERT: F  149 GLN cc_start: 0.8204 (mp10) cc_final: 0.7867 (mp10)
REVERT: F  203 GLN cc_start: 0.8449 (OUTLIER) cc_final: 0.8126 (tm130)
REVERT: F  272 GLN cc_start: 0.8260 (tt0) cc_final: 0.7528 (tt0)
REVERT: F  273 MET cc_start: 0.8920 (OUTLIER) cc_final: 0.8478 (ttm)
REVERT: G  134 GLU cc_start: 0.6991 (tt0) cc_final: 0.6702 (tt0)
REVERT: G  203 GLN cc_start: 0.8512 (OUTLIER) cc_final: 0.8149 (tm130)
REVERT: G  273 MET cc_start: 0.8770 (OUTLIER) cc_final: 0.8364 (ttm)
  outliers start: 57
  outliers final: 38
  residues processed: 282
  average time/residue: 0.2546
  time to fit residues: 111.8579
Evaluate side-chains
  281 residues out of total 1477 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 235
  time to evaluate  : 2.473 
-------------------------------------------------------------------------------
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 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  122 VAL
Chi-restraints excluded: chain C residue  161 LYS
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 D residue  273 MET
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  273 MET
Chi-restraints excluded: chain G residue   43 ILE
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  218 ASP
Chi-restraints excluded: chain G residue  257 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 83 optimal weight:    4.9990
   chunk 154 optimal weight:    0.7980
   chunk 143 optimal weight:    4.9990
   chunk 168 optimal weight:    0.9980
   chunk 118 optimal weight:    0.9990
   chunk 131 optimal weight:   10.0000
   chunk 128 optimal weight:    0.6980
   chunk 106 optimal weight:    6.9990
   chunk 142 optimal weight:    5.9990
   chunk 58 optimal weight:    6.9990
   chunk 127 optimal weight:    0.7980
   overall best weight:    0.8582

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

Flipped N/Q/H residues before XYZ refinement:
A 207 ASN
C 203 GLN
D 203 GLN
E 203 GLN
G 149 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 = 0.3636 r_free = 0.3636 target = 0.137237 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3211 r_free = 0.3211 target = 0.107204 restraints weight = 23030.596|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3254 r_free = 0.3254 target = 0.109966 restraints weight = 13020.583|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3281 r_free = 0.3281 target = 0.111829 restraints weight = 8479.089|
|-----------------------------------------------------------------------------|
r_work (final): 0.3297
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7910
moved from start:          0.2596

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  14098  Z= 0.123
  Angle     :  0.554   7.388  19117  Z= 0.290
  Chirality :  0.040   0.142   2345
  Planarity :  0.002   0.015   2429
  Dihedral  :  3.800  13.656   1988
  Min Nonbonded Distance : 2.595

Molprobity Statistics.
  All-atom Clashscore : 8.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.16 %
    Favored  : 98.84 %
  Rotamer:
    Outliers :  3.11 %
    Allowed  : 13.27 %
    Favored  : 83.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.51 (0.19), residues: 1813
  helix:  2.85 (0.15), residues: 1008
  sheet:  0.85 (0.28), residues: 294
  loop : -0.32 (0.27), residues: 511

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.000   TRP A 251 
 PHE   0.011   0.001   PHE D  80 
 TYR   0.010   0.001   TYR B 270 
 ARG   0.003   0.000   ARG G 156 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03628 ( 1046)
  hydrogen bonds       : angle       4.02971 ( 3054)
  covalent geometry    : bond        0.00279 (14098)
  covalent geometry    : angle       0.55368 (19117)

*********************** 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
  292 residues out of total 1477 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 246
  time to evaluate  : 1.646 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   43 ILE cc_start: 0.8304 (mm) cc_final: 0.7890 (pt)
REVERT: A  150 ILE cc_start: 0.8291 (mm) cc_final: 0.8006 (tp)
REVERT: A  255 GLU cc_start: 0.8348 (tm-30) cc_final: 0.7891 (tm-30)
REVERT: B   86 LEU cc_start: 0.8399 (tp) cc_final: 0.8068 (tp)
REVERT: B  134 GLU cc_start: 0.7210 (tt0) cc_final: 0.6900 (tt0)
REVERT: B  149 GLN cc_start: 0.8349 (mp10) cc_final: 0.8108 (mp10)
REVERT: B  161 LYS cc_start: 0.8732 (mtmm) cc_final: 0.8422 (mtmm)
REVERT: B  272 GLN cc_start: 0.8358 (tt0) cc_final: 0.7600 (tt0)
REVERT: C  134 GLU cc_start: 0.7117 (tt0) cc_final: 0.6757 (tt0)
REVERT: C  149 GLN cc_start: 0.8041 (mp10) cc_final: 0.7786 (mp10)
REVERT: C  161 LYS cc_start: 0.8470 (OUTLIER) cc_final: 0.7826 (mtmm)
REVERT: C  203 GLN cc_start: 0.8603 (OUTLIER) cc_final: 0.8388 (tm130)
REVERT: C  220 GLU cc_start: 0.7923 (pp20) cc_final: 0.7606 (pp20)
REVERT: C  272 GLN cc_start: 0.8220 (tt0) cc_final: 0.7620 (tt0)
REVERT: D  149 GLN cc_start: 0.8300 (mp10) cc_final: 0.8043 (mp10)
REVERT: D  203 GLN cc_start: 0.8379 (OUTLIER) cc_final: 0.8066 (tm130)
REVERT: D  273 MET cc_start: 0.8787 (OUTLIER) cc_final: 0.8314 (ptm)
REVERT: E  134 GLU cc_start: 0.7114 (tt0) cc_final: 0.6904 (tt0)
REVERT: E  149 GLN cc_start: 0.8135 (mp10) cc_final: 0.7821 (mp10)
REVERT: E  220 GLU cc_start: 0.7798 (pp20) cc_final: 0.7505 (pp20)
REVERT: E  272 GLN cc_start: 0.7955 (tt0) cc_final: 0.7506 (tt0)
REVERT: F  131 ARG cc_start: 0.7228 (ptp-170) cc_final: 0.6747 (ptm-80)
REVERT: F  134 GLU cc_start: 0.7198 (tt0) cc_final: 0.6741 (tt0)
REVERT: F  272 GLN cc_start: 0.8274 (tt0) cc_final: 0.7539 (tt0)
REVERT: F  273 MET cc_start: 0.8896 (OUTLIER) cc_final: 0.8239 (ttm)
REVERT: G  134 GLU cc_start: 0.6991 (tt0) cc_final: 0.6704 (tt0)
REVERT: G  203 GLN cc_start: 0.8452 (OUTLIER) cc_final: 0.8063 (tm130)
REVERT: G  273 MET cc_start: 0.8769 (OUTLIER) cc_final: 0.8425 (ttm)
  outliers start: 46
  outliers final: 38
  residues processed: 279
  average time/residue: 0.2572
  time to fit residues: 110.4725
Evaluate side-chains
  276 residues out of total 1477 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 231
  time to evaluate  : 2.467 
-------------------------------------------------------------------------------
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  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 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  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  122 VAL
Chi-restraints excluded: chain C residue  161 LYS
Chi-restraints excluded: chain C residue  203 GLN
Chi-restraints excluded: chain C residue  252 ASP
Chi-restraints excluded: chain C residue  257 ILE
Chi-restraints excluded: chain D residue  105 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 D residue  273 MET
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  273 MET
Chi-restraints excluded: chain G residue   43 ILE
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  218 ASP
Chi-restraints excluded: chain G residue  257 ILE
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 108 optimal weight:   10.0000
   chunk 113 optimal weight:    4.9990
   chunk 126 optimal weight:    3.9990
   chunk 101 optimal weight:    1.9990
   chunk 41 optimal weight:    0.8980
   chunk 66 optimal weight:    0.8980
   chunk 79 optimal weight:    7.9990
   chunk 125 optimal weight:    2.9990
   chunk 60 optimal weight:    7.9990
   chunk 170 optimal weight:    0.9980
   chunk 176 optimal weight:    2.9990
   overall best weight:    1.5584

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

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

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3625 r_free = 0.3625 target = 0.136279 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3198 r_free = 0.3198 target = 0.106201 restraints weight = 23109.167|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3237 r_free = 0.3237 target = 0.108882 restraints weight = 13097.088|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3268 r_free = 0.3268 target = 0.110769 restraints weight = 8568.702|
|-----------------------------------------------------------------------------|
r_work (final): 0.3283
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7929
moved from start:          0.2676

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= 0.147
  Angle     :  0.580   7.697  19117  Z= 0.302
  Chirality :  0.041   0.243   2345
  Planarity :  0.003   0.018   2429
  Dihedral  :  3.841  13.722   1988
  Min Nonbonded Distance : 2.605

Molprobity Statistics.
  All-atom Clashscore : 8.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.54 %
    Favored  : 98.46 %
  Rotamer:
    Outliers :  3.52 %
    Allowed  : 13.54 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.45 (0.19), residues: 1813
  helix:  2.81 (0.15), residues: 1008
  sheet:  0.85 (0.28), residues: 294
  loop : -0.37 (0.26), residues: 511

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP B 240 
 PHE   0.011   0.001   PHE G 127 
 TYR   0.010   0.001   TYR E 270 
 ARG   0.003   0.000   ARG B  74 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03737 ( 1046)
  hydrogen bonds       : angle       4.07330 ( 3054)
  covalent geometry    : bond        0.00342 (14098)
  covalent geometry    : angle       0.58027 (19117)

*********************** 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
  289 residues out of total 1477 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 52
    poor density    : 237
  time to evaluate  : 1.886 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   43 ILE cc_start: 0.8302 (mm) cc_final: 0.7891 (pt)
REVERT: A  150 ILE cc_start: 0.8266 (mm) cc_final: 0.8023 (tp)
REVERT: A  255 GLU cc_start: 0.8351 (tm-30) cc_final: 0.7885 (tm-30)
REVERT: B   86 LEU cc_start: 0.8390 (tp) cc_final: 0.8080 (tp)
REVERT: B  134 GLU cc_start: 0.7198 (tt0) cc_final: 0.6879 (tt0)
REVERT: B  161 LYS cc_start: 0.8737 (mtmm) cc_final: 0.8437 (mtmm)
REVERT: B  272 GLN cc_start: 0.8373 (tt0) cc_final: 0.7761 (tt0)
REVERT: B  273 MET cc_start: 0.8419 (ttt) cc_final: 0.8137 (ttt)
REVERT: C  134 GLU cc_start: 0.7121 (tt0) cc_final: 0.6743 (tt0)
REVERT: C  161 LYS cc_start: 0.8491 (OUTLIER) cc_final: 0.7845 (mtmm)
REVERT: C  203 GLN cc_start: 0.8406 (OUTLIER) cc_final: 0.8180 (tm130)
REVERT: C  220 GLU cc_start: 0.7941 (pp20) cc_final: 0.7603 (pp20)
REVERT: C  272 GLN cc_start: 0.8165 (tt0) cc_final: 0.7566 (tt0)
REVERT: D  273 MET cc_start: 0.8823 (OUTLIER) cc_final: 0.8198 (ptm)
REVERT: E  203 GLN cc_start: 0.8483 (OUTLIER) cc_final: 0.8217 (tm130)
REVERT: E  220 GLU cc_start: 0.7833 (pp20) cc_final: 0.7555 (pp20)
REVERT: E  272 GLN cc_start: 0.7975 (tt0) cc_final: 0.7500 (tt0)
REVERT: F  131 ARG cc_start: 0.7202 (ptp-170) cc_final: 0.6753 (ptm-80)
REVERT: F  134 GLU cc_start: 0.7190 (tt0) cc_final: 0.6731 (tt0)
REVERT: F  149 GLN cc_start: 0.8221 (mp10) cc_final: 0.7894 (mp10)
REVERT: F  220 GLU cc_start: 0.7943 (pp20) cc_final: 0.7680 (pp20)
REVERT: F  272 GLN cc_start: 0.8302 (tt0) cc_final: 0.7571 (tt0)
REVERT: F  273 MET cc_start: 0.8913 (OUTLIER) cc_final: 0.8288 (ttm)
REVERT: G  134 GLU cc_start: 0.7001 (tt0) cc_final: 0.6718 (tt0)
REVERT: G  273 MET cc_start: 0.8825 (OUTLIER) cc_final: 0.8350 (ttm)
  outliers start: 52
  outliers final: 36
  residues processed: 271
  average time/residue: 0.2521
  time to fit residues: 106.1301
Evaluate side-chains
  277 residues out of total 1477 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 235
  time to evaluate  : 1.929 
-------------------------------------------------------------------------------
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  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 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  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  257 ILE
Chi-restraints excluded: chain D residue  105 LEU
Chi-restraints excluded: chain D residue  257 ILE
Chi-restraints excluded: chain D residue  273 MET
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  273 MET
Chi-restraints excluded: chain G residue   43 ILE
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  218 ASP
Chi-restraints excluded: chain G residue  257 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 120 optimal weight:    5.9990
   chunk 135 optimal weight:    5.9990
   chunk 142 optimal weight:    5.9990
   chunk 167 optimal weight:    5.9990
   chunk 154 optimal weight:    1.9990
   chunk 125 optimal weight:    0.6980
   chunk 62 optimal weight:    1.9990
   chunk 122 optimal weight:    3.9990
   chunk 81 optimal weight:    5.9990
   chunk 170 optimal weight:    5.9990
   chunk 96 optimal weight:    0.0570
   overall best weight:    1.7504

-------------------------------------------------------------------------------
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
G 203 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3619 r_free = 0.3619 target = 0.135894 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3192 r_free = 0.3192 target = 0.105881 restraints weight = 23108.269|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3235 r_free = 0.3235 target = 0.108636 restraints weight = 13152.974|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3259 r_free = 0.3259 target = 0.110294 restraints weight = 8623.324|
|-----------------------------------------------------------------------------|
r_work (final): 0.3271
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7939
moved from start:          0.2734

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042  14098  Z= 0.157
  Angle     :  0.604  10.423  19117  Z= 0.312
  Chirality :  0.042   0.314   2345
  Planarity :  0.003   0.016   2429
  Dihedral  :  3.880  13.883   1988
  Min Nonbonded Distance : 2.605

Molprobity Statistics.
  All-atom Clashscore : 8.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.65 %
    Favored  : 98.35 %
  Rotamer:
    Outliers :  3.18 %
    Allowed  : 14.15 %
    Favored  : 82.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.39 (0.19), residues: 1813
  helix:  2.77 (0.15), residues: 1008
  sheet:  0.81 (0.28), residues: 294
  loop : -0.42 (0.26), residues: 511

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP B 240 
 PHE   0.011   0.001   PHE G 127 
 TYR   0.011   0.001   TYR B 270 
 ARG   0.003   0.000   ARG B  74 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03813 ( 1046)
  hydrogen bonds       : angle       4.10896 ( 3054)
  covalent geometry    : bond        0.00366 (14098)
  covalent geometry    : angle       0.60375 (19117)

********************** 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
  290 residues out of total 1477 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 243
  time to evaluate  : 1.896 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   43 ILE cc_start: 0.8267 (mm) cc_final: 0.7860 (pt)
REVERT: A  150 ILE cc_start: 0.8238 (mm) cc_final: 0.7997 (tp)
REVERT: A  255 GLU cc_start: 0.8327 (tm-30) cc_final: 0.7855 (tm-30)
REVERT: B  134 GLU cc_start: 0.7175 (tt0) cc_final: 0.6865 (tt0)
REVERT: B  149 GLN cc_start: 0.8323 (mp10) cc_final: 0.8084 (mp10)
REVERT: B  220 GLU cc_start: 0.7735 (pp20) cc_final: 0.7523 (pp20)
REVERT: B  272 GLN cc_start: 0.8379 (tt0) cc_final: 0.7906 (tt0)
REVERT: C  134 GLU cc_start: 0.7096 (tt0) cc_final: 0.6721 (tt0)
REVERT: C  149 GLN cc_start: 0.8069 (mp10) cc_final: 0.7814 (mp10)
REVERT: C  161 LYS cc_start: 0.8489 (OUTLIER) cc_final: 0.7857 (mtmm)
REVERT: C  203 GLN cc_start: 0.8385 (OUTLIER) cc_final: 0.8161 (tm130)
REVERT: C  220 GLU cc_start: 0.7965 (pp20) cc_final: 0.7683 (pp20)
REVERT: C  272 GLN cc_start: 0.8167 (tt0) cc_final: 0.7578 (tt0)
REVERT: D  149 GLN cc_start: 0.8207 (mp10) cc_final: 0.7948 (mp10)
REVERT: D  273 MET cc_start: 0.8769 (OUTLIER) cc_final: 0.8135 (ptm)
REVERT: E  149 GLN cc_start: 0.8165 (mp10) cc_final: 0.7843 (mp10)
REVERT: E  203 GLN cc_start: 0.8557 (OUTLIER) cc_final: 0.8225 (tm130)
REVERT: E  272 GLN cc_start: 0.7929 (tt0) cc_final: 0.7488 (tt0)
REVERT: F  131 ARG cc_start: 0.7208 (ptp-170) cc_final: 0.6772 (ptm-80)
REVERT: F  134 GLU cc_start: 0.7173 (tt0) cc_final: 0.6722 (tt0)
REVERT: F  149 GLN cc_start: 0.8221 (mp10) cc_final: 0.7897 (mp10)
REVERT: F  272 GLN cc_start: 0.8286 (tt0) cc_final: 0.7553 (tt0)
REVERT: F  273 MET cc_start: 0.8909 (OUTLIER) cc_final: 0.8332 (ttm)
REVERT: G  134 GLU cc_start: 0.6992 (tt0) cc_final: 0.6715 (tt0)
REVERT: G  273 MET cc_start: 0.8854 (OUTLIER) cc_final: 0.8531 (ttm)
  outliers start: 47
  outliers final: 37
  residues processed: 275
  average time/residue: 0.2927
  time to fit residues: 122.1981
Evaluate side-chains
  279 residues out of total 1477 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 236
  time to evaluate  : 2.187 
-------------------------------------------------------------------------------
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  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 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  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  257 ILE
Chi-restraints excluded: chain D residue  105 LEU
Chi-restraints excluded: chain D residue  257 ILE
Chi-restraints excluded: chain D residue  273 MET
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  273 MET
Chi-restraints excluded: chain G residue   43 ILE
Chi-restraints excluded: chain G residue  122 VAL
Chi-restraints excluded: chain G residue  155 MET
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  218 ASP
Chi-restraints excluded: chain G residue  257 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 56 optimal weight:    0.3980
   chunk 15 optimal weight:    1.9990
   chunk 118 optimal weight:    0.9990
   chunk 62 optimal weight:    0.9990
   chunk 115 optimal weight:    6.9990
   chunk 13 optimal weight:    6.9990
   chunk 122 optimal weight:    0.9990
   chunk 65 optimal weight:    0.3980
   chunk 67 optimal weight:    1.9990
   chunk 152 optimal weight:    4.9990
   chunk 60 optimal weight:    5.9990
   overall best weight:    0.7586

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

Flipped N/Q/H residues before XYZ refinement:
C 203 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 = 0.3634 r_free = 0.3634 target = 0.137033 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3205 r_free = 0.3205 target = 0.106925 restraints weight = 23506.976|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3248 r_free = 0.3248 target = 0.109680 restraints weight = 13270.041|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3275 r_free = 0.3275 target = 0.111499 restraints weight = 8659.202|
|-----------------------------------------------------------------------------|
r_work (final): 0.3289
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7913
moved from start:          0.2809

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  14098  Z= 0.127
  Angle     :  0.594   9.791  19117  Z= 0.307
  Chirality :  0.042   0.285   2345
  Planarity :  0.002   0.016   2429
  Dihedral  :  3.834  14.629   1988
  Min Nonbonded Distance : 2.611

Molprobity Statistics.
  All-atom Clashscore : 8.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.21 %
    Favored  : 98.79 %
  Rotamer:
    Outliers :  2.71 %
    Allowed  : 14.90 %
    Favored  : 82.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.39 (0.19), residues: 1813
  helix:  2.79 (0.15), residues: 1008
  sheet:  0.93 (0.27), residues: 308
  loop : -0.60 (0.26), residues: 497

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.000   TRP E 251 
 PHE   0.011   0.001   PHE G 127 
 TYR   0.010   0.001   TYR B 270 
 ARG   0.002   0.000   ARG B  74 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03692 ( 1046)
  hydrogen bonds       : angle       4.10135 ( 3054)
  covalent geometry    : bond        0.00284 (14098)
  covalent geometry    : angle       0.59415 (19117)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4576.80 seconds
wall clock time: 87 minutes 8.56 seconds (5228.56 seconds total)