Starting phenix.real_space_refine
on Thu Sep 26 19:02:24 2024 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7onl_12997/09_2024/7onl_12997.cif
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7onl_12997/09_2024/7onl_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7onl_12997/09_2024/7onl_12997.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7onl_12997/09_2024/7onl_12997.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7onl_12997/09_2024/7onl_12997.cif"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7onl_12997/09_2024/7onl_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-5461/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: 5.11, per 1000 atoms: 0.37
  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: 3.56
  Conformation dependent library (CDL) restraints added in 1.9 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: 1.50
  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: 4.02

  Time building geometry restraints manager: 4.14 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: 0.00
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'C'
  selection = chain 'D'
  selection = chain 'E'
  selection = chain 'F'
  selection = chain 'G'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.080
  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:          0.520
  Check model and map are aligned:         0.100
  Set scattering table:                    0.130
  Process input model:                     28.540
  Find NCS groups from input model:        0.430
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.730
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   33.570
-------------------------------------------------------------------------------
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= 0.156
  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 

*********************** 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 fitting.
    rotamer outliers: 6
    poor density    : 397
  time to evaluate  : 1.597 
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: 0.2299
  time to fit residues: 136.2294
Evaluate side-chains
  270 residues out of total 1477 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 270
  time to evaluate  : 1.495 
-------------------------------------------------------------------------------
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
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7933
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= 0.250
  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 

*********************** 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 fitting.
    rotamer outliers: 49
    poor density    : 283
  time to evaluate  : 1.520 
Fit side-chains
   revert: symmetry clash
REVERT: A   43 ILE cc_start: 0.8367 (mm) cc_final: 0.7986 (pt)
REVERT: A  131 ARG cc_start: 0.7115 (ptp-170) cc_final: 0.6910 (ptm-80)
REVERT: B   86 LEU cc_start: 0.8493 (tp) cc_final: 0.8227 (tp)
REVERT: B  134 GLU cc_start: 0.7165 (tt0) cc_final: 0.6903 (tt0)
REVERT: B  161 LYS cc_start: 0.8672 (mtmm) cc_final: 0.8371 (mtmm)
REVERT: B  197 ASP cc_start: 0.7618 (t70) cc_final: 0.7327 (t70)
REVERT: B  272 GLN cc_start: 0.8323 (tt0) cc_final: 0.7498 (tt0)
REVERT: C  134 GLU cc_start: 0.7142 (tt0) cc_final: 0.6828 (tt0)
REVERT: C  221 MET cc_start: 0.7284 (ptt) cc_final: 0.7013 (ptt)
REVERT: C  272 GLN cc_start: 0.8130 (tt0) cc_final: 0.7577 (tt0)
REVERT: D  135 TYR cc_start: 0.7977 (t80) cc_final: 0.7752 (t80)
REVERT: D  149 GLN cc_start: 0.7813 (mp10) cc_final: 0.7439 (mp10)
REVERT: D  272 GLN cc_start: 0.8080 (tt0) cc_final: 0.7685 (tt0)
REVERT: D  273 MET cc_start: 0.8521 (OUTLIER) cc_final: 0.8307 (ttm)
REVERT: E  134 GLU cc_start: 0.7034 (tt0) cc_final: 0.6777 (tt0)
REVERT: E  135 TYR cc_start: 0.8009 (t80) cc_final: 0.7762 (t80)
REVERT: E  272 GLN cc_start: 0.8090 (tt0) cc_final: 0.7579 (tt0)
REVERT: F  134 GLU cc_start: 0.6966 (tt0) cc_final: 0.6650 (tt0)
REVERT: F  149 GLN cc_start: 0.7975 (mp10) cc_final: 0.7306 (mp10)
REVERT: F  272 GLN cc_start: 0.8137 (tt0) cc_final: 0.7203 (tt0)
REVERT: G  134 GLU cc_start: 0.6708 (tt0) cc_final: 0.6507 (tt0)
REVERT: G  135 TYR cc_start: 0.7890 (t80) cc_final: 0.7680 (t80)
REVERT: G  197 ASP cc_start: 0.7159 (t70) cc_final: 0.6824 (t70)
  outliers start: 49
  outliers final: 17
  residues processed: 309
  average time/residue: 0.2117
  time to fit residues: 99.0479
Evaluate side-chains
  263 residues out of total 1477 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 18
    poor density    : 245
  time to evaluate  : 1.393 
-------------------------------------------------------------------------------
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 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 91 optimal weight:    6.9990
   chunk 51 optimal weight:    4.9990
   chunk 137 optimal weight:    8.9990
   chunk 112 optimal weight:    2.9990
   chunk 45 optimal weight:    0.6980
   chunk 165 optimal weight:    1.9990
   chunk 178 optimal weight:    6.9990
   chunk 147 optimal weight:    5.9990
   chunk 164 optimal weight:    1.9990
   chunk 56 optimal weight:   10.0000
   chunk 132 optimal weight:    9.9990
   overall best weight:    2.5388

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

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7971
moved from start:          0.2013

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.048  14098  Z= 0.300
  Angle     :  0.558   7.201  19117  Z= 0.299
  Chirality :  0.042   0.141   2345
  Planarity :  0.003   0.033   2429
  Dihedral  :  3.954  12.604   1988
  Min Nonbonded Distance : 2.519

Molprobity Statistics.
  All-atom Clashscore : 8.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.21 %
    Favored  : 98.79 %
  Rotamer:
    Outliers :  3.39 %
    Allowed  : 10.77 %
    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:  2.57 (0.19), residues: 1813
  helix:  2.92 (0.16), residues: 1001
  sheet:  1.83 (0.31), residues: 224
  loop : -0.62 (0.25), residues: 588

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP D 240 
 PHE   0.013   0.002   PHE G  80 
 TYR   0.006   0.001   TYR C 135 
 ARG   0.006   0.000   ARG B  74 

*********************** 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
  310 residues out of total 1477 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 50
    poor density    : 260
  time to evaluate  : 1.662 
Fit side-chains
   revert: symmetry clash
REVERT: A   43 ILE cc_start: 0.8338 (mm) cc_final: 0.7924 (pt)
REVERT: A  150 ILE cc_start: 0.8309 (mm) cc_final: 0.8109 (tp)
REVERT: B   86 LEU cc_start: 0.8511 (tp) cc_final: 0.8234 (tp)
REVERT: B  134 GLU cc_start: 0.7139 (tt0) cc_final: 0.6865 (tt0)
REVERT: B  161 LYS cc_start: 0.8600 (mtmm) cc_final: 0.8281 (mtmm)
REVERT: B  272 GLN cc_start: 0.8330 (tt0) cc_final: 0.7396 (tt0)
REVERT: C  134 GLU cc_start: 0.7036 (tt0) cc_final: 0.6729 (tt0)
REVERT: C  272 GLN cc_start: 0.8124 (tt0) cc_final: 0.7605 (tt0)
REVERT: D  135 TYR cc_start: 0.7883 (t80) cc_final: 0.7670 (t80)
REVERT: D  272 GLN cc_start: 0.8033 (tt0) cc_final: 0.7813 (tt0)
REVERT: D  273 MET cc_start: 0.8437 (OUTLIER) cc_final: 0.8047 (ptm)
REVERT: E  135 TYR cc_start: 0.7925 (t80) cc_final: 0.7718 (t80)
REVERT: E  220 GLU cc_start: 0.7669 (pp20) cc_final: 0.7302 (pp20)
REVERT: E  272 GLN cc_start: 0.7986 (tt0) cc_final: 0.7560 (tt0)
REVERT: F  134 GLU cc_start: 0.7013 (tt0) cc_final: 0.6679 (tt0)
REVERT: F  272 GLN cc_start: 0.8064 (tt0) cc_final: 0.7183 (tt0)
REVERT: G  134 GLU cc_start: 0.6828 (tt0) cc_final: 0.6590 (tt0)
REVERT: G  220 GLU cc_start: 0.7492 (pp20) cc_final: 0.7249 (pp20)
REVERT: G  273 MET cc_start: 0.8741 (OUTLIER) cc_final: 0.8289 (ttm)
  outliers start: 50
  outliers final: 35
  residues processed: 289
  average time/residue: 0.2208
  time to fit residues: 97.0998
Evaluate side-chains
  272 residues out of total 1477 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 37
    poor density    : 235
  time to evaluate  : 1.525 
-------------------------------------------------------------------------------
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  208 ILE
Chi-restraints excluded: chain A residue  252 ASP
Chi-restraints excluded: chain A residue  257 ILE
Chi-restraints excluded: chain B residue   42 LEU
Chi-restraints excluded: chain B residue  122 VAL
Chi-restraints excluded: chain B residue  171 ILE
Chi-restraints excluded: chain B residue  206 THR
Chi-restraints excluded: chain B residue  252 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  206 THR
Chi-restraints excluded: chain C residue  208 ILE
Chi-restraints excluded: chain D residue   42 LEU
Chi-restraints excluded: chain D residue  161 LYS
Chi-restraints excluded: chain D residue  171 ILE
Chi-restraints excluded: chain D residue  257 ILE
Chi-restraints excluded: chain D residue  273 MET
Chi-restraints excluded: chain E residue   97 ILE
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  122 VAL
Chi-restraints excluded: chain F residue  171 ILE
Chi-restraints excluded: chain F residue  206 THR
Chi-restraints excluded: chain F residue  218 ASP
Chi-restraints excluded: chain G residue   97 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  233 ILE
Chi-restraints excluded: chain G residue  273 MET
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 182
   random chunks:
   chunk 163 optimal weight:    5.9990
   chunk 124 optimal weight:    2.9990
   chunk 85 optimal weight:    0.7980
   chunk 18 optimal weight:    3.9990
   chunk 79 optimal weight:   10.0000
   chunk 111 optimal weight:    2.9990
   chunk 166 optimal weight:    3.9990
   chunk 175 optimal weight:    1.9990
   chunk 86 optimal weight:    5.9990
   chunk 157 optimal weight:    4.9990
   chunk 47 optimal weight:    3.9990
   overall best weight:    2.5588

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

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7985
moved from start:          0.2275

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046  14098  Z= 0.297
  Angle     :  0.558  10.579  19117  Z= 0.297
  Chirality :  0.041   0.141   2345
  Planarity :  0.003   0.034   2429
  Dihedral  :  4.017  12.801   1988
  Min Nonbonded Distance : 2.578

Molprobity Statistics.
  All-atom Clashscore : 8.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.27 %
    Favored  : 98.73 %
  Rotamer:
    Outliers :  4.81 %
    Allowed  :  9.95 %
    Favored  : 85.24 %
  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:  2.80 (0.15), residues: 1008
  sheet:  1.90 (0.29), residues: 238
  loop : -0.93 (0.24), residues: 567

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP B 240 
 PHE   0.012   0.001   PHE F 178 
 TYR   0.007   0.001   TYR E 135 
 ARG   0.003   0.000   ARG G 184 

*********************** 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
  325 residues out of total 1477 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 71
    poor density    : 254
  time to evaluate  : 1.527 
Fit side-chains
   revert: symmetry clash
REVERT: A   43 ILE cc_start: 0.8250 (mm) cc_final: 0.7901 (pt)
REVERT: A  150 ILE cc_start: 0.8347 (mm) cc_final: 0.8138 (tp)
REVERT: B   86 LEU cc_start: 0.8497 (tp) cc_final: 0.8226 (tp)
REVERT: B  134 GLU cc_start: 0.7113 (tt0) cc_final: 0.6897 (tt0)
REVERT: B  161 LYS cc_start: 0.8575 (mtmm) cc_final: 0.8287 (mtmm)
REVERT: B  272 GLN cc_start: 0.8280 (tt0) cc_final: 0.7400 (tt0)
REVERT: C  134 GLU cc_start: 0.7012 (tt0) cc_final: 0.6804 (tt0)
REVERT: C  161 LYS cc_start: 0.8455 (OUTLIER) cc_final: 0.7904 (mtmm)
REVERT: C  203 GLN cc_start: 0.8538 (OUTLIER) cc_final: 0.8325 (tm130)
REVERT: C  220 GLU cc_start: 0.7422 (pp20) cc_final: 0.7079 (pp20)
REVERT: C  272 GLN cc_start: 0.8126 (tt0) cc_final: 0.7618 (tt0)
REVERT: D  273 MET cc_start: 0.8643 (OUTLIER) cc_final: 0.8193 (ptm)
REVERT: E  203 GLN cc_start: 0.8526 (OUTLIER) cc_final: 0.8186 (tm130)
REVERT: E  220 GLU cc_start: 0.7697 (pp20) cc_final: 0.7330 (pp20)
REVERT: E  272 GLN cc_start: 0.7903 (tt0) cc_final: 0.7584 (tt0)
REVERT: F  134 GLU cc_start: 0.7099 (tt0) cc_final: 0.6709 (tt0)
REVERT: F  203 GLN cc_start: 0.8339 (OUTLIER) cc_final: 0.8071 (tm130)
REVERT: F  272 GLN cc_start: 0.8071 (tt0) cc_final: 0.7274 (tt0)
REVERT: G  134 GLU cc_start: 0.6829 (tt0) cc_final: 0.6586 (tt0)
REVERT: G  203 GLN cc_start: 0.8416 (OUTLIER) cc_final: 0.8006 (tm130)
REVERT: G  220 GLU cc_start: 0.7497 (pp20) cc_final: 0.7184 (pp20)
REVERT: G  273 MET cc_start: 0.8780 (OUTLIER) cc_final: 0.8351 (ttm)
  outliers start: 71
  outliers final: 37
  residues processed: 301
  average time/residue: 0.2139
  time to fit residues: 99.0228
Evaluate side-chains
  279 residues out of total 1477 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 44
    poor density    : 235
  time to evaluate  : 1.702 
-------------------------------------------------------------------------------
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  208 ILE
Chi-restraints excluded: chain A residue  252 ASP
Chi-restraints excluded: chain A residue  257 ILE
Chi-restraints excluded: chain B residue   42 LEU
Chi-restraints excluded: chain B residue  122 VAL
Chi-restraints excluded: chain B residue  123 LEU
Chi-restraints excluded: chain B residue  171 ILE
Chi-restraints excluded: chain B residue  206 THR
Chi-restraints excluded: chain C residue   42 LEU
Chi-restraints excluded: chain C residue   97 ILE
Chi-restraints excluded: chain C residue  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  252 ASP
Chi-restraints excluded: chain D residue   42 LEU
Chi-restraints excluded: chain D residue  161 LYS
Chi-restraints excluded: chain D residue  171 ILE
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  208 ILE
Chi-restraints excluded: chain E residue  233 ILE
Chi-restraints excluded: chain F residue  100 LEU
Chi-restraints excluded: chain F residue  122 VAL
Chi-restraints excluded: chain F residue  203 GLN
Chi-restraints excluded: chain F residue  206 THR
Chi-restraints excluded: chain G residue   43 ILE
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  218 ASP
Chi-restraints excluded: chain G residue  233 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 146 optimal weight:    0.9990
   chunk 99 optimal weight:    4.9990
   chunk 2 optimal weight:    5.9990
   chunk 130 optimal weight:    9.9990
   chunk 72 optimal weight:    4.9990
   chunk 150 optimal weight:    3.9990
   chunk 121 optimal weight:    6.9990
   chunk 0 optimal weight:   20.0000
   chunk 89 optimal weight:    4.9990
   chunk 157 optimal weight:    2.9990
   chunk 44 optimal weight:    0.9980
   overall best weight:    2.7988

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

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7997
moved from start:          0.2521

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.047  14098  Z= 0.320
  Angle     :  0.575   7.847  19117  Z= 0.308
  Chirality :  0.042   0.141   2345
  Planarity :  0.003   0.026   2429
  Dihedral  :  4.094  13.113   1988
  Min Nonbonded Distance : 2.579

Molprobity Statistics.
  All-atom Clashscore : 8.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.60 %
    Favored  : 98.40 %
  Rotamer:
    Outliers :  4.54 %
    Allowed  : 11.31 %
    Favored  : 84.16 %
  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:  2.24 (0.19), residues: 1813
  helix:  2.73 (0.15), residues: 1008
  sheet:  1.77 (0.28), residues: 238
  loop : -1.09 (0.24), residues: 567

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP B 240 
 PHE   0.014   0.002   PHE G 178 
 TYR   0.015   0.001   TYR B 270 
 ARG   0.004   0.000   ARG A 184 

*********************** 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
  317 residues out of total 1477 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 67
    poor density    : 250
  time to evaluate  : 1.682 
Fit side-chains
   revert: symmetry clash
REVERT: A   43 ILE cc_start: 0.8310 (mm) cc_final: 0.7890 (pt)
REVERT: B   86 LEU cc_start: 0.8488 (tp) cc_final: 0.8251 (tp)
REVERT: B  134 GLU cc_start: 0.7143 (tt0) cc_final: 0.6915 (tt0)
REVERT: B  161 LYS cc_start: 0.8533 (mtmm) cc_final: 0.8262 (mtmm)
REVERT: B  272 GLN cc_start: 0.8242 (tt0) cc_final: 0.7381 (tt0)
REVERT: C   72 LEU cc_start: 0.6494 (OUTLIER) cc_final: 0.6235 (tt)
REVERT: C  134 GLU cc_start: 0.7033 (tt0) cc_final: 0.6826 (tt0)
REVERT: C  161 LYS cc_start: 0.8466 (OUTLIER) cc_final: 0.7903 (mtmm)
REVERT: C  272 GLN cc_start: 0.8156 (tt0) cc_final: 0.7679 (tt0)
REVERT: D  273 MET cc_start: 0.8802 (OUTLIER) cc_final: 0.8136 (ptm)
REVERT: E  203 GLN cc_start: 0.8509 (OUTLIER) cc_final: 0.8244 (tm130)
REVERT: E  220 GLU cc_start: 0.7701 (pp20) cc_final: 0.7381 (pp20)
REVERT: E  272 GLN cc_start: 0.7888 (tt0) cc_final: 0.7540 (tt0)
REVERT: F  134 GLU cc_start: 0.7006 (tt0) cc_final: 0.6632 (tt0)
REVERT: F  272 GLN cc_start: 0.8067 (tt0) cc_final: 0.7326 (tt0)
REVERT: G  134 GLU cc_start: 0.6832 (tt0) cc_final: 0.6585 (tt0)
REVERT: G  203 GLN cc_start: 0.8459 (OUTLIER) cc_final: 0.8137 (tm130)
REVERT: G  220 GLU cc_start: 0.7543 (pp20) cc_final: 0.7238 (pp20)
REVERT: G  273 MET cc_start: 0.8918 (OUTLIER) cc_final: 0.8283 (ttm)
  outliers start: 67
  outliers final: 47
  residues processed: 291
  average time/residue: 0.2202
  time to fit residues: 97.8270
Evaluate side-chains
  286 residues out of total 1477 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 53
    poor density    : 233
  time to evaluate  : 1.495 
-------------------------------------------------------------------------------
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  203 GLN
Chi-restraints excluded: chain A residue  208 ILE
Chi-restraints excluded: chain A residue  252 ASP
Chi-restraints excluded: chain A residue  257 ILE
Chi-restraints excluded: chain B residue   42 LEU
Chi-restraints excluded: chain B residue  122 VAL
Chi-restraints excluded: chain B residue  123 LEU
Chi-restraints excluded: chain B residue  171 ILE
Chi-restraints excluded: chain B residue  206 THR
Chi-restraints excluded: chain B residue  252 ASP
Chi-restraints excluded: chain B residue  270 TYR
Chi-restraints excluded: chain C residue   42 LEU
Chi-restraints excluded: chain C residue   72 LEU
Chi-restraints excluded: chain C residue   83 ILE
Chi-restraints excluded: chain C residue   97 ILE
Chi-restraints excluded: chain C residue  122 VAL
Chi-restraints excluded: chain C residue  161 LYS
Chi-restraints excluded: chain C residue  171 ILE
Chi-restraints excluded: chain C residue  206 THR
Chi-restraints excluded: chain C residue  208 ILE
Chi-restraints excluded: chain C residue  252 ASP
Chi-restraints excluded: chain C residue  257 ILE
Chi-restraints excluded: chain D residue   42 LEU
Chi-restraints excluded: chain D residue  161 LYS
Chi-restraints excluded: chain D residue  171 ILE
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  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  105 LEU
Chi-restraints excluded: chain F residue  122 VAL
Chi-restraints excluded: chain F residue  206 THR
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  233 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 59 optimal weight:    4.9990
   chunk 158 optimal weight:    2.9990
   chunk 34 optimal weight:    0.9980
   chunk 103 optimal weight:    5.9990
   chunk 43 optimal weight:    5.9990
   chunk 176 optimal weight:    0.9980
   chunk 146 optimal weight:    0.0070
   chunk 81 optimal weight:    0.7980
   chunk 14 optimal weight:    1.9990
   chunk 58 optimal weight:    0.9980
   chunk 92 optimal weight:    2.9990
   overall best weight:    0.7598

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

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

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7951
moved from start:          0.2610

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= 0.179
  Angle     :  0.538   6.992  19117  Z= 0.285
  Chirality :  0.041   0.173   2345
  Planarity :  0.002   0.019   2429
  Dihedral  :  3.919  13.128   1988
  Min Nonbonded Distance : 2.589

Molprobity Statistics.
  All-atom Clashscore : 7.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.38 %
    Favored  : 98.62 %
  Rotamer:
    Outliers :  4.13 %
    Allowed  : 12.80 %
    Favored  : 83.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  2.38 (0.19), residues: 1813
  helix:  2.84 (0.15), residues: 1008
  sheet:  0.91 (0.29), residues: 259
  loop : -0.58 (0.26), residues: 546

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.000   TRP A 251 
 PHE   0.012   0.001   PHE D  80 
 TYR   0.012   0.001   TYR B 270 
 ARG   0.002   0.000   ARG D 259 

*********************** 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
  315 residues out of total 1477 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 61
    poor density    : 254
  time to evaluate  : 1.575 
Fit side-chains
   revert: symmetry clash
REVERT: A   43 ILE cc_start: 0.8224 (mm) cc_final: 0.7873 (pt)
REVERT: A  169 LYS cc_start: 0.8012 (mmmt) cc_final: 0.7733 (mmmt)
REVERT: B   86 LEU cc_start: 0.8500 (tp) cc_final: 0.8223 (tp)
REVERT: B  134 GLU cc_start: 0.7131 (tt0) cc_final: 0.6896 (tt0)
REVERT: B  161 LYS cc_start: 0.8465 (mtmm) cc_final: 0.8217 (mtmm)
REVERT: B  272 GLN cc_start: 0.8273 (tt0) cc_final: 0.7375 (tt0)
REVERT: C  134 GLU cc_start: 0.6953 (tt0) cc_final: 0.6742 (tt0)
REVERT: C  161 LYS cc_start: 0.8441 (OUTLIER) cc_final: 0.7876 (mtmm)
REVERT: C  203 GLN cc_start: 0.8464 (OUTLIER) cc_final: 0.8155 (tm130)
REVERT: C  272 GLN cc_start: 0.8166 (tt0) cc_final: 0.7624 (tt0)
REVERT: D  203 GLN cc_start: 0.8212 (OUTLIER) cc_final: 0.7959 (tm130)
REVERT: D  273 MET cc_start: 0.8768 (OUTLIER) cc_final: 0.8224 (ptm)
REVERT: E  220 GLU cc_start: 0.7780 (pp20) cc_final: 0.7536 (pp20)
REVERT: E  272 GLN cc_start: 0.7837 (tt0) cc_final: 0.7483 (tt0)
REVERT: F  134 GLU cc_start: 0.7043 (tt0) cc_final: 0.6657 (tt0)
REVERT: F  203 GLN cc_start: 0.8310 (OUTLIER) cc_final: 0.8022 (tm130)
REVERT: F  272 GLN cc_start: 0.8022 (tt0) cc_final: 0.7235 (tt0)
REVERT: G  203 GLN cc_start: 0.8420 (OUTLIER) cc_final: 0.8122 (tm130)
REVERT: G  273 MET cc_start: 0.8856 (OUTLIER) cc_final: 0.8473 (ttm)
  outliers start: 61
  outliers final: 33
  residues processed: 288
  average time/residue: 0.2123
  time to fit residues: 93.5153
Evaluate side-chains
  277 residues out of total 1477 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 40
    poor density    : 237
  time to evaluate  : 1.536 
-------------------------------------------------------------------------------
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  203 GLN
Chi-restraints excluded: chain A residue  208 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  257 ILE
Chi-restraints excluded: chain B residue  270 TYR
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  252 ASP
Chi-restraints excluded: chain C residue  257 ILE
Chi-restraints excluded: chain D residue  161 LYS
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  126 MET
Chi-restraints excluded: chain E residue  203 GLN
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  105 LEU
Chi-restraints excluded: chain F residue  122 VAL
Chi-restraints excluded: chain F residue  126 MET
Chi-restraints excluded: chain F residue  203 GLN
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  218 ASP
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 169 optimal weight:    3.9990
   chunk 19 optimal weight:    2.9990
   chunk 100 optimal weight:    4.9990
   chunk 128 optimal weight:    1.9990
   chunk 99 optimal weight:    4.9990
   chunk 148 optimal weight:    0.9990
   chunk 98 optimal weight:    6.9990
   chunk 175 optimal weight:    2.9990
   chunk 109 optimal weight:    5.9990
   chunk 106 optimal weight:    3.9990
   chunk 80 optimal weight:    4.9990
   overall best weight:    2.5990

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

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

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7990
moved from start:          0.2717

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.063  14098  Z= 0.313
  Angle     :  0.592   7.659  19117  Z= 0.313
  Chirality :  0.042   0.144   2345
  Planarity :  0.003   0.020   2429
  Dihedral  :  4.060  12.777   1988
  Min Nonbonded Distance : 2.593

Molprobity Statistics.
  All-atom Clashscore : 8.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.49 %
    Favored  : 98.51 %
  Rotamer:
    Outliers :  3.99 %
    Allowed  : 13.34 %
    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:  2.23 (0.19), residues: 1813
  helix:  2.79 (0.15), residues: 1008
  sheet:  1.70 (0.28), residues: 238
  loop : -1.19 (0.24), residues: 567

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP B 240 
 PHE   0.012   0.001   PHE D 178 
 TYR   0.013   0.001   TYR B 270 
 ARG   0.003   0.000   ARG G 184 

*********************** 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 fitting.
    rotamer outliers: 59
    poor density    : 242
  time to evaluate  : 1.570 
Fit side-chains
   revert: symmetry clash
REVERT: A   43 ILE cc_start: 0.8291 (mm) cc_final: 0.7866 (pt)
REVERT: B   86 LEU cc_start: 0.8495 (tp) cc_final: 0.8251 (tp)
REVERT: B  134 GLU cc_start: 0.7103 (tt0) cc_final: 0.6870 (tt0)
REVERT: B  161 LYS cc_start: 0.8517 (mtmm) cc_final: 0.8232 (mtmm)
REVERT: B  272 GLN cc_start: 0.8289 (tt0) cc_final: 0.7423 (tt0)
REVERT: C  134 GLU cc_start: 0.7007 (tt0) cc_final: 0.6791 (tt0)
REVERT: C  161 LYS cc_start: 0.8465 (OUTLIER) cc_final: 0.7900 (mtmm)
REVERT: C  203 GLN cc_start: 0.8489 (OUTLIER) cc_final: 0.8198 (tm130)
REVERT: C  220 GLU cc_start: 0.7544 (pp20) cc_final: 0.7343 (pp20)
REVERT: C  272 GLN cc_start: 0.8174 (tt0) cc_final: 0.7680 (tt0)
REVERT: D  273 MET cc_start: 0.8865 (OUTLIER) cc_final: 0.8354 (ptm)
REVERT: E  203 GLN cc_start: 0.8428 (OUTLIER) cc_final: 0.8174 (tm130)
REVERT: E  220 GLU cc_start: 0.7824 (pp20) cc_final: 0.7611 (pp20)
REVERT: E  272 GLN cc_start: 0.7929 (tt0) cc_final: 0.7600 (tt0)
REVERT: F  134 GLU cc_start: 0.7042 (tt0) cc_final: 0.6648 (tt0)
REVERT: F  272 GLN cc_start: 0.8096 (tt0) cc_final: 0.7405 (tt0)
REVERT: G  203 GLN cc_start: 0.8435 (OUTLIER) cc_final: 0.8176 (tm130)
  outliers start: 59
  outliers final: 38
  residues processed: 282
  average time/residue: 0.2145
  time to fit residues: 93.1152
Evaluate side-chains
  277 residues out of total 1477 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 43
    poor density    : 234
  time to evaluate  : 1.649 
-------------------------------------------------------------------------------
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  201 VAL
Chi-restraints excluded: chain A residue  203 GLN
Chi-restraints excluded: chain A residue  208 ILE
Chi-restraints excluded: chain A residue  252 ASP
Chi-restraints excluded: chain A residue  257 ILE
Chi-restraints excluded: chain A residue  270 TYR
Chi-restraints excluded: chain B residue   42 LEU
Chi-restraints excluded: chain B residue  122 VAL
Chi-restraints excluded: chain B residue  171 ILE
Chi-restraints excluded: chain B residue  206 THR
Chi-restraints excluded: chain B residue  270 TYR
Chi-restraints excluded: chain C residue   83 ILE
Chi-restraints excluded: chain C residue  122 VAL
Chi-restraints excluded: chain C residue  161 LYS
Chi-restraints excluded: chain C residue  203 GLN
Chi-restraints excluded: chain C residue  206 THR
Chi-restraints excluded: chain C residue  257 ILE
Chi-restraints excluded: chain D residue   42 LEU
Chi-restraints excluded: chain D residue  161 LYS
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  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  105 LEU
Chi-restraints excluded: chain F residue  122 VAL
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  273 MET
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 182
   random chunks:
   chunk 108 optimal weight:    0.0980
   chunk 70 optimal weight:    0.9990
   chunk 104 optimal weight:    4.9990
   chunk 52 optimal weight:    9.9990
   chunk 34 optimal weight:    3.9990
   chunk 33 optimal weight:    2.9990
   chunk 111 optimal weight:    9.9990
   chunk 119 optimal weight:    0.1980
   chunk 86 optimal weight:    1.9990
   chunk 16 optimal weight:    0.7980
   chunk 137 optimal weight:    0.0770
   overall best weight:    0.4340

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

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

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7934
moved from start:          0.2796

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= 0.180
  Angle     :  0.571   7.720  19117  Z= 0.299
  Chirality :  0.041   0.143   2345
  Planarity :  0.002   0.017   2429
  Dihedral  :  3.904  13.579   1988
  Min Nonbonded Distance : 2.607

Molprobity Statistics.
  All-atom Clashscore : 8.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.27 %
    Favored  : 98.73 %
  Rotamer:
    Outliers :  2.98 %
    Allowed  : 14.69 %
    Favored  : 82.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  2.38 (0.19), residues: 1813
  helix:  2.87 (0.15), residues: 1008
  sheet:  0.91 (0.29), residues: 259
  loop : -0.64 (0.26), residues: 546

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.000   TRP A 251 
 PHE   0.009   0.001   PHE F  80 
 TYR   0.011   0.001   TYR B 270 
 ARG   0.003   0.000   ARG B 156 

*********************** 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
  300 residues out of total 1477 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 44
    poor density    : 256
  time to evaluate  : 1.556 
Fit side-chains
   revert: symmetry clash
REVERT: A   43 ILE cc_start: 0.8288 (mm) cc_final: 0.7869 (pt)
REVERT: B  134 GLU cc_start: 0.7075 (tt0) cc_final: 0.6871 (tt0)
REVERT: B  161 LYS cc_start: 0.8407 (mtmm) cc_final: 0.8187 (mtmm)
REVERT: B  272 GLN cc_start: 0.8224 (tt0) cc_final: 0.7340 (tt0)
REVERT: C  149 GLN cc_start: 0.7915 (mp10) cc_final: 0.7693 (mp10)
REVERT: C  161 LYS cc_start: 0.8456 (OUTLIER) cc_final: 0.7877 (mtmm)
REVERT: C  203 GLN cc_start: 0.8460 (OUTLIER) cc_final: 0.8175 (tm130)
REVERT: C  272 GLN cc_start: 0.8151 (tt0) cc_final: 0.7663 (tt0)
REVERT: D  149 GLN cc_start: 0.8063 (mp10) cc_final: 0.7818 (mp10)
REVERT: D  273 MET cc_start: 0.8739 (OUTLIER) cc_final: 0.8203 (ptm)
REVERT: E  272 GLN cc_start: 0.7843 (tt0) cc_final: 0.7486 (tt0)
REVERT: F  134 GLU cc_start: 0.7035 (tt0) cc_final: 0.6701 (tt0)
REVERT: F  149 GLN cc_start: 0.8112 (mp10) cc_final: 0.7823 (mp10)
REVERT: F  272 GLN cc_start: 0.8083 (tt0) cc_final: 0.7367 (tt0)
REVERT: G  203 GLN cc_start: 0.8279 (OUTLIER) cc_final: 0.7977 (tt0)
REVERT: G  273 MET cc_start: 0.8972 (OUTLIER) cc_final: 0.8464 (ptm)
  outliers start: 44
  outliers final: 34
  residues processed: 286
  average time/residue: 0.2130
  time to fit residues: 92.9445
Evaluate side-chains
  285 residues out of total 1477 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 39
    poor density    : 246
  time to evaluate  : 1.614 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  105 LEU
Chi-restraints excluded: chain A residue  122 VAL
Chi-restraints excluded: chain A residue  171 ILE
Chi-restraints excluded: chain A residue  201 VAL
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  270 TYR
Chi-restraints excluded: chain B residue   42 LEU
Chi-restraints excluded: chain B residue  122 VAL
Chi-restraints excluded: chain B residue  171 ILE
Chi-restraints excluded: chain B residue  257 ILE
Chi-restraints excluded: chain B residue  270 TYR
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  161 LYS
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  126 MET
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  105 LEU
Chi-restraints excluded: chain F residue  122 VAL
Chi-restraints excluded: chain F residue  126 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  218 ASP
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 159 optimal weight:    6.9990
   chunk 168 optimal weight:    5.9990
   chunk 153 optimal weight:    0.5980
   chunk 163 optimal weight:    7.9990
   chunk 98 optimal weight:    0.9980
   chunk 71 optimal weight:    0.6980
   chunk 128 optimal weight:    0.9990
   chunk 50 optimal weight:    0.9990
   chunk 147 optimal weight:    5.9990
   chunk 154 optimal weight:    4.9990
   chunk 162 optimal weight:    0.8980
   overall best weight:    0.8382

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

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

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7937
moved from start:          0.2856

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043  14098  Z= 0.200
  Angle     :  0.603  11.168  19117  Z= 0.312
  Chirality :  0.042   0.298   2345
  Planarity :  0.003   0.019   2429
  Dihedral  :  3.905  13.759   1988
  Min Nonbonded Distance : 2.607

Molprobity Statistics.
  All-atom Clashscore : 8.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.54 %
    Favored  : 98.46 %
  Rotamer:
    Outliers :  3.52 %
    Allowed  : 15.10 %
    Favored  : 81.38 %
  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:  2.33 (0.19), residues: 1813
  helix:  2.83 (0.15), residues: 1008
  sheet:  0.90 (0.29), residues: 259
  loop : -0.66 (0.25), residues: 546

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP E 251 
 PHE   0.011   0.001   PHE D 127 
 TYR   0.022   0.001   TYR E 270 
 ARG   0.002   0.000   ARG D 259 

*********************** 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
  303 residues out of total 1477 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 52
    poor density    : 251
  time to evaluate  : 1.365 
Fit side-chains
   revert: symmetry clash
REVERT: A   43 ILE cc_start: 0.8293 (mm) cc_final: 0.7871 (pt)
REVERT: B   86 LEU cc_start: 0.8527 (tp) cc_final: 0.8286 (tp)
REVERT: B  134 GLU cc_start: 0.7050 (tt0) cc_final: 0.6846 (tt0)
REVERT: B  161 LYS cc_start: 0.8428 (mtmm) cc_final: 0.8183 (mtmm)
REVERT: B  272 GLN cc_start: 0.8201 (tt0) cc_final: 0.7488 (tt0)
REVERT: C  161 LYS cc_start: 0.8463 (OUTLIER) cc_final: 0.7890 (mtmm)
REVERT: C  203 GLN cc_start: 0.8470 (OUTLIER) cc_final: 0.8185 (tm130)
REVERT: C  272 GLN cc_start: 0.8162 (tt0) cc_final: 0.7664 (tt0)
REVERT: D  149 GLN cc_start: 0.8040 (mp10) cc_final: 0.7808 (mp10)
REVERT: D  273 MET cc_start: 0.8744 (OUTLIER) cc_final: 0.8231 (ptm)
REVERT: E  149 GLN cc_start: 0.8061 (mp10) cc_final: 0.7753 (mp10)
REVERT: E  272 GLN cc_start: 0.7868 (tt0) cc_final: 0.7487 (tt0)
REVERT: F  134 GLU cc_start: 0.6982 (tt0) cc_final: 0.6666 (tt0)
REVERT: F  149 GLN cc_start: 0.8139 (mp10) cc_final: 0.7868 (mp10)
REVERT: F  272 GLN cc_start: 0.8120 (tt0) cc_final: 0.7383 (tt0)
REVERT: G  203 GLN cc_start: 0.8373 (OUTLIER) cc_final: 0.8029 (tt0)
  outliers start: 52
  outliers final: 40
  residues processed: 282
  average time/residue: 0.2130
  time to fit residues: 92.2036
Evaluate side-chains
  289 residues out of total 1477 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 44
    poor density    : 245
  time to evaluate  : 1.467 
-------------------------------------------------------------------------------
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  208 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  273 MET
Chi-restraints excluded: chain A residue  278 LYS
Chi-restraints excluded: chain B residue  122 VAL
Chi-restraints excluded: chain B residue  171 ILE
Chi-restraints excluded: chain B residue  257 ILE
Chi-restraints excluded: chain B residue  270 TYR
Chi-restraints excluded: chain C residue   83 ILE
Chi-restraints excluded: chain C residue  122 VAL
Chi-restraints excluded: chain C residue  157 THR
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  161 LYS
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  126 MET
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 E residue  257 ILE
Chi-restraints excluded: chain E residue  270 TYR
Chi-restraints excluded: chain F residue  100 LEU
Chi-restraints excluded: chain F residue  105 LEU
Chi-restraints excluded: chain F residue  122 VAL
Chi-restraints excluded: chain F residue  126 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  199 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  273 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 182
   random chunks:
   chunk 107 optimal weight:    5.9990
   chunk 172 optimal weight:    5.9990
   chunk 105 optimal weight:   10.0000
   chunk 82 optimal weight:    3.9990
   chunk 120 optimal weight:    0.4980
   chunk 181 optimal weight:    0.7980
   chunk 166 optimal weight:    6.9990
   chunk 144 optimal weight:    0.8980
   chunk 14 optimal weight:    0.7980
   chunk 111 optimal weight:    8.9990
   chunk 88 optimal weight:    3.9990
   overall best weight:    1.3982

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7948
moved from start:          0.2926

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043  14098  Z= 0.230
  Angle     :  0.629   9.783  19117  Z= 0.325
  Chirality :  0.043   0.352   2345
  Planarity :  0.003   0.019   2429
  Dihedral  :  3.946  14.653   1988
  Min Nonbonded Distance : 2.595

Molprobity Statistics.
  All-atom Clashscore : 8.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.65 %
    Favored  : 98.35 %
  Rotamer:
    Outliers :  3.32 %
    Allowed  : 15.91 %
    Favored  : 80.77 %
  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:  2.29 (0.19), residues: 1813
  helix:  2.79 (0.15), residues: 1008
  sheet:  0.92 (0.29), residues: 259
  loop : -0.68 (0.25), residues: 546

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP E 251 
 PHE   0.011   0.001   PHE D 127 
 TYR   0.019   0.001   TYR E 270 
 ARG   0.003   0.000   ARG G 156 

********************** 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
  298 residues out of total 1477 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 49
    poor density    : 249
  time to evaluate  : 1.494 
Fit side-chains
   revert: symmetry clash
REVERT: A   43 ILE cc_start: 0.8293 (mm) cc_final: 0.7880 (pt)
REVERT: B   86 LEU cc_start: 0.8514 (tp) cc_final: 0.8277 (tp)
REVERT: B  134 GLU cc_start: 0.7049 (tt0) cc_final: 0.6827 (tt0)
REVERT: B  161 LYS cc_start: 0.8450 (mtmm) cc_final: 0.8196 (mtmm)
REVERT: B  272 GLN cc_start: 0.8240 (tt0) cc_final: 0.7502 (tt0)
REVERT: C  161 LYS cc_start: 0.8464 (OUTLIER) cc_final: 0.7906 (mtmm)
REVERT: C  203 GLN cc_start: 0.8476 (OUTLIER) cc_final: 0.8193 (tm130)
REVERT: C  272 GLN cc_start: 0.8198 (tt0) cc_final: 0.7725 (tt0)
REVERT: D  149 GLN cc_start: 0.8080 (mp10) cc_final: 0.7862 (mp10)
REVERT: D  203 GLN cc_start: 0.8074 (OUTLIER) cc_final: 0.7851 (tm130)
REVERT: D  273 MET cc_start: 0.8795 (OUTLIER) cc_final: 0.8291 (ptm)
REVERT: E  149 GLN cc_start: 0.8052 (mp10) cc_final: 0.7770 (mp10)
REVERT: E  272 GLN cc_start: 0.7865 (tt0) cc_final: 0.7469 (tt0)
REVERT: F  134 GLU cc_start: 0.6984 (tt0) cc_final: 0.6673 (tt0)
REVERT: F  149 GLN cc_start: 0.8149 (mp10) cc_final: 0.7886 (mp10)
REVERT: F  272 GLN cc_start: 0.8107 (tt0) cc_final: 0.7335 (tt0)
REVERT: G  203 GLN cc_start: 0.8403 (OUTLIER) cc_final: 0.8126 (tm130)
  outliers start: 49
  outliers final: 39
  residues processed: 277
  average time/residue: 0.2090
  time to fit residues: 89.2279
Evaluate side-chains
  287 residues out of total 1477 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 44
    poor density    : 243
  time to evaluate  : 1.477 
-------------------------------------------------------------------------------
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  273 MET
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  257 ILE
Chi-restraints excluded: chain B residue  270 TYR
Chi-restraints excluded: chain C residue   83 ILE
Chi-restraints excluded: chain C residue  122 VAL
Chi-restraints excluded: chain C residue  157 THR
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  161 LYS
Chi-restraints excluded: chain D residue  203 GLN
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  171 ILE
Chi-restraints excluded: chain E residue  206 THR
Chi-restraints excluded: chain E residue  233 ILE
Chi-restraints excluded: chain E residue  257 ILE
Chi-restraints excluded: chain E residue  270 TYR
Chi-restraints excluded: chain F residue  100 LEU
Chi-restraints excluded: chain F residue  105 LEU
Chi-restraints excluded: chain F residue  122 VAL
Chi-restraints excluded: chain F residue  126 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  199 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  273 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 182
   random chunks:
   chunk 114 optimal weight:    2.9990
   chunk 153 optimal weight:    0.9980
   chunk 44 optimal weight:    0.0050
   chunk 133 optimal weight:    1.9990
   chunk 21 optimal weight:    0.6980
   chunk 40 optimal weight:    0.9980
   chunk 144 optimal weight:    1.9990
   chunk 60 optimal weight:   10.0000
   chunk 148 optimal weight:    2.9990
   chunk 18 optimal weight:    0.5980
   chunk 26 optimal weight:    0.0070
   overall best weight:    0.4612

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

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3638 r_free = 0.3638 target = 0.137353 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3218 r_free = 0.3218 target = 0.107676 restraints weight = 23207.671|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3260 r_free = 0.3260 target = 0.110423 restraints weight = 12976.583|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3288 r_free = 0.3288 target = 0.112249 restraints weight = 8416.456|
|-----------------------------------------------------------------------------|
r_work (final): 0.3298
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7897
moved from start:          0.2975

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  14098  Z= 0.187
  Angle     :  0.618  11.078  19117  Z= 0.317
  Chirality :  0.043   0.376   2345
  Planarity :  0.002   0.016   2429
  Dihedral  :  3.861  14.963   1988
  Min Nonbonded Distance : 2.611

Molprobity Statistics.
  All-atom Clashscore : 8.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.10 %
    Favored  : 98.90 %
  Rotamer:
    Outliers :  2.84 %
    Allowed  : 16.32 %
    Favored  : 80.84 %
  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:  2.29 (0.19), residues: 1813
  helix:  2.77 (0.15), residues: 1008
  sheet:  0.92 (0.29), residues: 259
  loop : -0.65 (0.26), residues: 546

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.000   TRP E 251 
 PHE   0.011   0.001   PHE D 127 
 TYR   0.015   0.001   TYR E 270 
 ARG   0.002   0.000   ARG D 259 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2689.46 seconds
wall clock time: 48 minutes 48.95 seconds (2928.95 seconds total)