Starting phenix.real_space_refine
on Wed Mar  4 16:41:59 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8ddj_27337/03_2026/8ddj_27337.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8ddj_27337/03_2026/8ddj_27337.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.1
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8ddj_27337/03_2026/8ddj_27337.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8ddj_27337/03_2026/8ddj_27337.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8ddj_27337/03_2026/8ddj_27337.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8ddj_27337/03_2026/8ddj_27337.cif"
  }
  resolution = 3.1
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.001
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      49      5.16       5
     C    9548      2.51       5
     N    2590      2.21       5
     O    2716      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 35 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 14903
  Number of models: 1
  Model: ""
    Number of chains: 7
    Chain: "A"
      Number of atoms: 2129
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 280, 2129
          Classifications: {'peptide': 280}
          Link IDs: {'PTRANS': 5, 'TRANS': 274}
    Chain: "B"
      Number of atoms: 2129
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 280, 2129
          Classifications: {'peptide': 280}
          Link IDs: {'PTRANS': 5, 'TRANS': 274}
    Chain: "C"
      Number of atoms: 2129
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 280, 2129
          Classifications: {'peptide': 280}
          Link IDs: {'PTRANS': 5, 'TRANS': 274}
    Chain: "D"
      Number of atoms: 2129
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 280, 2129
          Classifications: {'peptide': 280}
          Link IDs: {'PTRANS': 5, 'TRANS': 274}
    Chain: "E"
      Number of atoms: 2129
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 280, 2129
          Classifications: {'peptide': 280}
          Link IDs: {'PTRANS': 5, 'TRANS': 274}
    Chain: "F"
      Number of atoms: 2129
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 280, 2129
          Classifications: {'peptide': 280}
          Link IDs: {'PTRANS': 5, 'TRANS': 274}
    Chain: "G"
      Number of atoms: 2129
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 280, 2129
          Classifications: {'peptide': 280}
          Link IDs: {'PTRANS': 5, 'TRANS': 274}
  Time building chain proxies: 3.06, per 1000 atoms: 0.21
  Number of scatterers: 14903
  At special positions: 0
  Unit cell: (103.111, 103.111, 130.749, 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      49     16.00
     O    2716      8.00
     N    2590      7.00
     C    9548      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: 1.29
  Conformation dependent library (CDL) restraints added in 592.5 milliseconds
  

  3892 Ramachandran restraints generated.
    1946 Oldfield, 0 Emsley, 1946 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3612

  Finding SS restraints...
    Secondary structure from input PDB file:
      63 helices and 9 sheets defined
      57.0% alpha, 18.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.47
  Creating SS restraints...
    Processing helix  chain 'A' and resid 10 through 14
      removed outlier: 3.650A  pdb=" N   GLY A  14 " --> pdb=" O   ASN A  11 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 15 through 20
    Processing helix  chain 'A' and resid 20 through 59
      removed outlier: 3.538A  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 112
      removed outlier: 3.877A  pdb=" N   ILE A  97 " --> pdb=" O   THR A  93 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 112 through 128
      removed outlier: 3.618A  pdb=" N   MET A 126 " --> pdb=" O   VAL A 122 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 167 through 173
    Processing helix  chain 'A' and resid 197 through 211
    Processing helix  chain 'A' and resid 245 through 265
    Processing helix  chain 'B' and resid 10 through 14
      removed outlier: 3.665A  pdb=" N   GLY B  14 " --> pdb=" O   ASN B  11 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 15 through 20
    Processing helix  chain 'B' and resid 20 through 59
    Processing helix  chain 'B' and resid 62 through 90
    Processing helix  chain 'B' and resid 93 through 112
      removed outlier: 3.834A  pdb=" N   ILE B  97 " --> pdb=" O   THR B  93 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 112 through 128
    Processing helix  chain 'B' and resid 167 through 173
      removed outlier: 3.509A  pdb=" N   ILE B 171 " --> pdb=" O   ASN B 167 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 197 through 211
    Processing helix  chain 'B' and resid 245 through 265
    Processing helix  chain 'C' and resid 10 through 14
      removed outlier: 3.708A  pdb=" N   GLY C  14 " --> pdb=" O   ASN C  11 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 15 through 20
    Processing helix  chain 'C' and resid 20 through 59
      removed outlier: 3.508A  pdb=" N   SER C  58 " --> pdb=" O   ARG C  54 " (cutoff:3.500A)
      removed outlier: 3.613A  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 94 through 112
    Processing helix  chain 'C' and resid 112 through 128
      removed outlier: 3.626A  pdb=" N   MET C 126 " --> pdb=" O   VAL C 122 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 167 through 173
    Processing helix  chain 'C' and resid 197 through 211
    Processing helix  chain 'C' and resid 245 through 265
    Processing helix  chain 'D' and resid 10 through 14
      removed outlier: 3.669A  pdb=" N   GLY D  14 " --> pdb=" O   ASN D  11 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 15 through 20
    Processing helix  chain 'D' and resid 20 through 59
      removed outlier: 3.609A  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 94 through 112
    Processing helix  chain 'D' and resid 112 through 128
    Processing helix  chain 'D' and resid 167 through 173
    Processing helix  chain 'D' and resid 197 through 211
    Processing helix  chain 'D' and resid 245 through 265
    Processing helix  chain 'E' and resid 10 through 14
      removed outlier: 3.741A  pdb=" N   GLY E  14 " --> pdb=" O   ASN E  11 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 15 through 20
    Processing helix  chain 'E' and resid 20 through 59
      removed outlier: 3.558A  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 112
    Processing helix  chain 'E' and resid 112 through 128
    Processing helix  chain 'E' and resid 167 through 173
    Processing helix  chain 'E' and resid 197 through 211
    Processing helix  chain 'E' and resid 245 through 265
    Processing helix  chain 'F' and resid 10 through 14
      removed outlier: 3.731A  pdb=" N   GLY F  14 " --> pdb=" O   ASN F  11 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 15 through 20
    Processing helix  chain 'F' and resid 20 through 59
    Processing helix  chain 'F' and resid 62 through 90
    Processing helix  chain 'F' and resid 93 through 112
    Processing helix  chain 'F' and resid 112 through 128
    Processing helix  chain 'F' and resid 167 through 173
    Processing helix  chain 'F' and resid 197 through 211
    Processing helix  chain 'F' and resid 245 through 265
    Processing helix  chain 'G' and resid 10 through 14
      removed outlier: 3.656A  pdb=" N   GLY G  14 " --> pdb=" O   ASN G  11 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 15 through 20
    Processing helix  chain 'G' and resid 20 through 59
    Processing helix  chain 'G' and resid 62 through 90
    Processing helix  chain 'G' and resid 93 through 112
      removed outlier: 3.833A  pdb=" N   ILE G  97 " --> pdb=" O   THR G  93 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 112 through 128
    Processing helix  chain 'G' and resid 167 through 173
    Processing helix  chain 'G' and resid 197 through 211
    Processing helix  chain 'G' and resid 245 through 265
    Processing sheet with id=AA1, first strand: chain 'A' and resid 135 through 137
      removed outlier: 6.849A  pdb=" N   THR A 154 " --> pdb=" O   LEU A 146 " (cutoff:3.500A)
      removed outlier: 5.073A  pdb=" N   VAL A 148 " --> pdb=" O   SER A 152 " (cutoff:3.500A)
      removed outlier: 6.641A  pdb=" N   SER A 152 " --> pdb=" O   VAL A 148 " (cutoff:3.500A)
      removed outlier: 7.027A  pdb=" N   THR G 154 " --> pdb=" O   LEU G 146 " (cutoff:3.500A)
      removed outlier: 5.214A  pdb=" N   VAL G 148 " --> pdb=" O   SER G 152 " (cutoff:3.500A)
      removed outlier: 6.677A  pdb=" N   SER G 152 " --> pdb=" O   VAL G 148 " (cutoff:3.500A)
      removed outlier: 7.053A  pdb=" N   THR F 154 " --> pdb=" O   LEU F 146 " (cutoff:3.500A)
      removed outlier: 5.208A  pdb=" N   VAL F 148 " --> pdb=" O   SER F 152 " (cutoff:3.500A)
      removed outlier: 6.768A  pdb=" N   SER F 152 " --> pdb=" O   VAL F 148 " (cutoff:3.500A)
      removed outlier: 6.951A  pdb=" N   THR E 154 " --> pdb=" O   LEU E 146 " (cutoff:3.500A)
      removed outlier: 5.207A  pdb=" N   VAL E 148 " --> pdb=" O   SER E 152 " (cutoff:3.500A)
      removed outlier: 6.735A  pdb=" N   SER E 152 " --> pdb=" O   VAL E 148 " (cutoff:3.500A)
      removed outlier: 3.610A  pdb=" N   ILE E 162 " --> pdb=" O   ASN D 177 " (cutoff:3.500A)
      removed outlier: 7.063A  pdb=" N   THR D 154 " --> pdb=" O   LEU D 146 " (cutoff:3.500A)
      removed outlier: 5.135A  pdb=" N   VAL D 148 " --> pdb=" O   SER D 152 " (cutoff:3.500A)
      removed outlier: 6.611A  pdb=" N   SER D 152 " --> pdb=" O   VAL D 148 " (cutoff:3.500A)
      removed outlier: 6.887A  pdb=" N   THR C 154 " --> pdb=" O   LEU C 146 " (cutoff:3.500A)
      removed outlier: 5.045A  pdb=" N   VAL C 148 " --> pdb=" O   SER C 152 " (cutoff:3.500A)
      removed outlier: 6.612A  pdb=" N   SER C 152 " --> pdb=" O   VAL C 148 " (cutoff:3.500A)
      removed outlier: 6.956A  pdb=" N   THR B 154 " --> pdb=" O   LEU B 146 " (cutoff:3.500A)
      removed outlier: 5.111A  pdb=" N   VAL B 148 " --> pdb=" O   SER B 152 " (cutoff:3.500A)
      removed outlier: 6.606A  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: 7.251A  pdb=" N   ASN A 234 " --> pdb=" O   ASN A 226 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 272 through 279
      removed outlier: 8.359A  pdb=" N   MET B 273 " --> pdb=" O   GLN A 272 " (cutoff:3.500A)
      removed outlier: 5.877A  pdb=" N   ASP A 274 " --> pdb=" O   MET B 273 " (cutoff:3.500A)
      removed outlier: 6.819A  pdb=" N   VAL B 275 " --> pdb=" O   ASP A 274 " (cutoff:3.500A)
      removed outlier: 5.898A  pdb=" N   ASN A 276 " --> pdb=" O   VAL B 275 " (cutoff:3.500A)
      removed outlier: 7.438A  pdb=" N   PHE B 277 " --> pdb=" O   ASN A 276 " (cutoff:3.500A)
      removed outlier: 7.496A  pdb=" N   LYS A 278 " --> pdb=" O   PHE B 277 " (cutoff:3.500A)
      removed outlier: 9.303A  pdb=" N   ARG B 279 " --> pdb=" O   LYS A 278 " (cutoff:3.500A)
      removed outlier: 8.575A  pdb=" N   MET C 273 " --> pdb=" O   GLN B 272 " (cutoff:3.500A)
      removed outlier: 5.972A  pdb=" N   ASP B 274 " --> pdb=" O   MET C 273 " (cutoff:3.500A)
      removed outlier: 6.967A  pdb=" N   VAL C 275 " --> pdb=" O   ASP B 274 " (cutoff:3.500A)
      removed outlier: 5.976A  pdb=" N   ASN B 276 " --> pdb=" O   VAL C 275 " (cutoff:3.500A)
      removed outlier: 7.433A  pdb=" N   PHE C 277 " --> pdb=" O   ASN B 276 " (cutoff:3.500A)
      removed outlier: 7.578A  pdb=" N   LYS B 278 " --> pdb=" O   PHE C 277 " (cutoff:3.500A)
      removed outlier: 9.343A  pdb=" N   ARG C 279 " --> pdb=" O   LYS B 278 " (cutoff:3.500A)
      removed outlier: 8.530A  pdb=" N   MET D 273 " --> pdb=" O   GLN C 272 " (cutoff:3.500A)
      removed outlier: 5.788A  pdb=" N   ASP C 274 " --> pdb=" O   MET D 273 " (cutoff:3.500A)
      removed outlier: 7.079A  pdb=" N   VAL D 275 " --> pdb=" O   ASP C 274 " (cutoff:3.500A)
      removed outlier: 5.954A  pdb=" N   ASN C 276 " --> pdb=" O   VAL D 275 " (cutoff:3.500A)
      removed outlier: 7.274A  pdb=" N   PHE D 277 " --> pdb=" O   ASN C 276 " (cutoff:3.500A)
      removed outlier: 7.413A  pdb=" N   LYS C 278 " --> pdb=" O   PHE D 277 " (cutoff:3.500A)
      removed outlier: 9.250A  pdb=" N   ARG D 279 " --> pdb=" O   LYS C 278 " (cutoff:3.500A)
      removed outlier: 8.564A  pdb=" N   MET E 273 " --> pdb=" O   GLN D 272 " (cutoff:3.500A)
      removed outlier: 6.471A  pdb=" N   ASP D 274 " --> pdb=" O   MET E 273 " (cutoff:3.500A)
      removed outlier: 7.490A  pdb=" N   VAL E 275 " --> pdb=" O   ASP D 274 " (cutoff:3.500A)
      removed outlier: 6.203A  pdb=" N   ASN D 276 " --> pdb=" O   VAL E 275 " (cutoff:3.500A)
      removed outlier: 7.670A  pdb=" N   PHE E 277 " --> pdb=" O   ASN D 276 " (cutoff:3.500A)
      removed outlier: 7.750A  pdb=" N   LYS D 278 " --> pdb=" O   PHE E 277 " (cutoff:3.500A)
      removed outlier: 9.438A  pdb=" N   ARG E 279 " --> pdb=" O   LYS D 278 " (cutoff:3.500A)
      removed outlier: 7.911A  pdb=" N   MET F 273 " --> pdb=" O   GLN E 272 " (cutoff:3.500A)
      removed outlier: 5.744A  pdb=" N   ASP E 274 " --> pdb=" O   MET F 273 " (cutoff:3.500A)
      removed outlier: 6.897A  pdb=" N   VAL F 275 " --> pdb=" O   ASP E 274 " (cutoff:3.500A)
      removed outlier: 5.911A  pdb=" N   ASN E 276 " --> pdb=" O   VAL F 275 " (cutoff:3.500A)
      removed outlier: 7.461A  pdb=" N   PHE F 277 " --> pdb=" O   ASN E 276 " (cutoff:3.500A)
      removed outlier: 7.549A  pdb=" N   LYS E 278 " --> pdb=" O   PHE F 277 " (cutoff:3.500A)
      removed outlier: 9.342A  pdb=" N   ARG F 279 " --> pdb=" O   LYS E 278 " (cutoff:3.500A)
      removed outlier: 8.510A  pdb=" N   MET G 273 " --> pdb=" O   GLN F 272 " (cutoff:3.500A)
      removed outlier: 6.082A  pdb=" N   ASP F 274 " --> pdb=" O   MET G 273 " (cutoff:3.500A)
      removed outlier: 6.809A  pdb=" N   VAL G 275 " --> pdb=" O   ASP F 274 " (cutoff:3.500A)
      removed outlier: 5.807A  pdb=" N   ASN F 276 " --> pdb=" O   VAL G 275 " (cutoff:3.500A)
      removed outlier: 7.114A  pdb=" N   PHE G 277 " --> pdb=" O   ASN F 276 " (cutoff:3.500A)
      removed outlier: 7.356A  pdb=" N   LYS F 278 " --> pdb=" O   PHE G 277 " (cutoff:3.500A)
      removed outlier: 9.254A  pdb=" N   ARG G 279 " --> pdb=" O   LYS F 278 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 183 through 192
      removed outlier: 7.310A  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: 7.327A  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: 7.286A  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: 7.237A  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: 7.218A  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: 7.159A  pdb=" N   ASN G 234 " --> pdb=" O   ASN G 226 " (cutoff:3.500A)

    1069 hydrogen bonds defined for protein.
    3105 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.29

  Time building geometry restraints manager: 1.69 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

  Histogram of bond lengths:
        1.22 -     1.34: 4990
        1.34 -     1.46: 3023
        1.46 -     1.58: 6981
        1.58 -     1.70: 0
        1.70 -     1.82: 98
  Bond restraints: 15092
  Sorted by residual:
  bond pdb=" CA  ARG D 128 "
       pdb=" CB  ARG D 128 "
    ideal  model  delta    sigma   weight residual
    1.525  1.538 -0.013 8.30e-03 1.45e+04 2.41e+00
  bond pdb=" CA  VAL B  91 "
       pdb=" C   VAL B  91 "
    ideal  model  delta    sigma   weight residual
    1.523  1.537 -0.014 1.27e-02 6.20e+03 1.23e+00
  bond pdb=" CA  VAL A  91 "
       pdb=" C   VAL A  91 "
    ideal  model  delta    sigma   weight residual
    1.523  1.537 -0.014 1.27e-02 6.20e+03 1.16e+00
  bond pdb=" CA  VAL E  91 "
       pdb=" C   VAL E  91 "
    ideal  model  delta    sigma   weight residual
    1.523  1.537 -0.014 1.31e-02 5.83e+03 1.15e+00
  bond pdb=" CA  VAL D  91 "
       pdb=" C   VAL D  91 "
    ideal  model  delta    sigma   weight residual
    1.523  1.537 -0.014 1.27e-02 6.20e+03 1.13e+00
  ... (remaining 15087 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.25: 20184
        2.25 -     4.49: 258
        4.49 -     6.74: 34
        6.74 -     8.98: 4
        8.98 -    11.23: 2
  Bond angle restraints: 20482
  Sorted by residual:
  angle pdb=" CB  MET B 273 "
        pdb=" CG  MET B 273 "
        pdb=" SD  MET B 273 "
      ideal   model   delta    sigma   weight residual
     112.70  101.47   11.23 3.00e+00 1.11e-01 1.40e+01
  angle pdb=" C   VAL C  91 "
        pdb=" N   GLN C  92 "
        pdb=" CA  GLN C  92 "
      ideal   model   delta    sigma   weight residual
     121.54  128.47   -6.93 1.91e+00 2.74e-01 1.31e+01
  angle pdb=" C   VAL D  91 "
        pdb=" N   GLN D  92 "
        pdb=" CA  GLN D  92 "
      ideal   model   delta    sigma   weight residual
     121.54  128.02   -6.48 1.91e+00 2.74e-01 1.15e+01
  angle pdb=" C   VAL G  91 "
        pdb=" N   GLN G  92 "
        pdb=" CA  GLN G  92 "
      ideal   model   delta    sigma   weight residual
     121.54  127.71   -6.17 1.91e+00 2.74e-01 1.04e+01
  angle pdb=" C   GLN D 112 "
        pdb=" N   GLY D 113 "
        pdb=" CA  GLY D 113 "
      ideal   model   delta    sigma   weight residual
     119.98  123.49   -3.51 1.11e+00 8.12e-01 1.00e+01
  ... (remaining 20477 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.92: 8231
       16.92 -    33.84: 663
       33.84 -    50.75: 123
       50.75 -    67.67: 19
       67.67 -    84.59: 15
  Dihedral angle restraints: 9051
    sinusoidal: 3444
      harmonic: 5607
  Sorted by residual:
  dihedral pdb=" CA  LEU D 111 "
           pdb=" C   LEU D 111 "
           pdb=" N   GLN D 112 "
           pdb=" CA  GLN D 112 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -157.57  -22.43     0      5.00e+00 4.00e-02 2.01e+01
  dihedral pdb=" CA  PHE F 277 "
           pdb=" C   PHE F 277 "
           pdb=" N   LYS F 278 "
           pdb=" CA  LYS F 278 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.34   19.66     0      5.00e+00 4.00e-02 1.55e+01
  dihedral pdb=" CG  ARG B 279 "
           pdb=" CD  ARG B 279 "
           pdb=" NE  ARG B 279 "
           pdb=" CZ  ARG B 279 "
      ideal   model   delta sinusoidal    sigma   weight residual
     180.00  135.44   44.56     2      1.50e+01 4.44e-03 1.05e+01
  ... (remaining 9048 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.039: 1772
       0.039 -    0.078: 522
       0.078 -    0.117: 182
       0.117 -    0.156: 30
       0.156 -    0.195: 7
  Chirality restraints: 2513
  Sorted by residual:
  chirality pdb=" CB  VAL C   6 "
            pdb=" CA  VAL C   6 "
            pdb=" CG1 VAL C   6 "
            pdb=" CG2 VAL C   6 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.43   -0.20 2.00e-01 2.50e+01 9.52e-01
  chirality pdb=" CA  ILE B 176 "
            pdb=" N   ILE B 176 "
            pdb=" C   ILE B 176 "
            pdb=" CB  ILE B 176 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.60   -0.16 2.00e-01 2.50e+01 6.55e-01
  chirality pdb=" CA  GLU B 260 "
            pdb=" N   GLU B 260 "
            pdb=" C   GLU B 260 "
            pdb=" CB  GLU B 260 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.35    0.16 2.00e-01 2.50e+01 6.34e-01
  ... (remaining 2510 not shown)

  Planarity restraints: 2604
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE F  80 "   -0.013 2.00e-02 2.50e+03   1.75e-02 5.35e+00
        pdb=" CG  PHE F  80 "    0.040 2.00e-02 2.50e+03
        pdb=" CD1 PHE F  80 "   -0.014 2.00e-02 2.50e+03
        pdb=" CD2 PHE F  80 "   -0.014 2.00e-02 2.50e+03
        pdb=" CE1 PHE F  80 "   -0.000 2.00e-02 2.50e+03
        pdb=" CE2 PHE F  80 "   -0.000 2.00e-02 2.50e+03
        pdb=" CZ  PHE F  80 "    0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE G  80 "   -0.011 2.00e-02 2.50e+03   1.44e-02 3.62e+00
        pdb=" CG  PHE G  80 "    0.033 2.00e-02 2.50e+03
        pdb=" CD1 PHE G  80 "   -0.011 2.00e-02 2.50e+03
        pdb=" CD2 PHE G  80 "   -0.011 2.00e-02 2.50e+03
        pdb=" CE1 PHE G  80 "    0.000 2.00e-02 2.50e+03
        pdb=" CE2 PHE G  80 "   -0.000 2.00e-02 2.50e+03
        pdb=" CZ  PHE G  80 "    0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ARG B 256 "   -0.009 2.00e-02 2.50e+03   1.89e-02 3.58e+00
        pdb=" C   ARG B 256 "    0.033 2.00e-02 2.50e+03
        pdb=" O   ARG B 256 "   -0.012 2.00e-02 2.50e+03
        pdb=" N   ILE B 257 "   -0.011 2.00e-02 2.50e+03
  ... (remaining 2601 not shown)

  Histogram of nonbonded interaction distances:
        2.24 -     2.77: 2583
        2.77 -     3.30: 15346
        3.30 -     3.83: 24928
        3.83 -     4.37: 27298
        4.37 -     4.90: 48610
  Nonbonded interactions: 118765
  Sorted by model distance:
  nonbonded pdb=" NZ  LYS A 169 "
            pdb=" OD1 ASN G 174 "
     model   vdw
     2.236 3.120
  nonbonded pdb=" OD1 ASN B 174 "
            pdb=" NZ  LYS C 169 "
     model   vdw
     2.236 3.120
  nonbonded pdb=" OE2 GLU C 255 "
            pdb=" NE  ARG C 259 "
     model   vdw
     2.242 3.120
  nonbonded pdb=" OE2 GLU D 220 "
            pdb=" NE1 TRP D 240 "
     model   vdw
     2.246 3.120
  nonbonded pdb=" OE2 GLU C 220 "
            pdb=" NE1 TRP C 240 "
     model   vdw
     2.254 3.120
  ... (remaining 118760 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 individual isotropic
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:                  0.010
  Normalize map: mean=0, sd=1:             1.180
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.200
  Check model and map are aligned:         0.050
  Set scattering table:                    0.040
  Process input model:                     13.130
  Find NCS groups from input model:        0.190
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.240
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   16.080
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8090
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029  15092  Z= 0.144
  Angle     :  0.625  11.228  20482  Z= 0.341
  Chirality :  0.044   0.195   2513
  Planarity :  0.002   0.026   2604
  Dihedral  : 13.091  84.591   5439
  Min Nonbonded Distance : 2.236

Molprobity Statistics.
  All-atom Clashscore : 8.67
  Ramachandran Plot:
    Outliers :  0.36 %
    Allowed  :  4.52 %
    Favored  : 95.12 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.38 %
    Favored  : 99.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.06 (0.19), residues: 1946
  helix:  2.80 (0.16), residues: 1022
  sheet:  1.35 (0.32), residues: 245
  loop : -0.98 (0.23), residues: 679

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG G  46 
 TYR   0.014   0.001   TYR F 135 
 PHE   0.040   0.002   PHE F  80 
 TRP   0.009   0.001   TRP D 251 

Details of bonding type rmsd
  covalent geometry    : bond        0.00291 (15092)
  covalent geometry    : angle       0.62513 (20482)
  hydrogen bonds       : bond        0.14148 ( 1069)
  hydrogen bonds       : angle       5.55168 ( 3105)

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

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

  3892 Ramachandran restraints generated.
    1946 Oldfield, 0 Emsley, 1946 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3892 Ramachandran restraints generated.
    1946 Oldfield, 0 Emsley, 1946 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  331 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 331
  time to evaluate  : 0.458 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  134 GLU cc_start: 0.8068 (tt0) cc_final: 0.7725 (tt0)
REVERT: A  203 GLN cc_start: 0.8966 (tm-30) cc_final: 0.8631 (tm-30)
REVERT: A  227 GLU cc_start: 0.8369 (pp20) cc_final: 0.8061 (pp20)
REVERT: B   47 MET cc_start: 0.8977 (mmp) cc_final: 0.8711 (mmm)
REVERT: B  112 GLN cc_start: 0.9160 (tm-30) cc_final: 0.8875 (tm-30)
REVERT: B  134 GLU cc_start: 0.8372 (tt0) cc_final: 0.7604 (tt0)
REVERT: B  176 ILE cc_start: 0.8843 (mm) cc_final: 0.8616 (mm)
REVERT: B  203 GLN cc_start: 0.8932 (tm-30) cc_final: 0.8598 (tm-30)
REVERT: B  260 GLU cc_start: 0.8762 (mp0) cc_final: 0.8194 (mp0)
REVERT: B  278 LYS cc_start: 0.9020 (mtmm) cc_final: 0.8729 (mtmm)
REVERT: C   56 MET cc_start: 0.8937 (ttm) cc_final: 0.8711 (ttm)
REVERT: C  112 GLN cc_start: 0.9285 (tp40) cc_final: 0.9069 (tp40)
REVERT: C  134 GLU cc_start: 0.8193 (tt0) cc_final: 0.7892 (tt0)
REVERT: C  149 GLN cc_start: 0.9056 (mm110) cc_final: 0.8783 (mm110)
REVERT: C  181 GLU cc_start: 0.9284 (mm-30) cc_final: 0.8955 (mm-30)
REVERT: C  203 GLN cc_start: 0.9090 (tm-30) cc_final: 0.8585 (tm-30)
REVERT: C  227 GLU cc_start: 0.8327 (pp20) cc_final: 0.8025 (pp20)
REVERT: C  260 GLU cc_start: 0.8675 (mp0) cc_final: 0.8069 (mp0)
REVERT: C  274 ASP cc_start: 0.7741 (t0) cc_final: 0.7419 (t0)
REVERT: D  112 GLN cc_start: 0.8393 (mp10) cc_final: 0.8191 (mp10)
REVERT: D  203 GLN cc_start: 0.9137 (tm-30) cc_final: 0.8688 (tm-30)
REVERT: D  260 GLU cc_start: 0.8692 (mp0) cc_final: 0.8035 (mp0)
REVERT: E  131 ARG cc_start: 0.8850 (ptt-90) cc_final: 0.8604 (ptp90)
REVERT: E  134 GLU cc_start: 0.7880 (pt0) cc_final: 0.7384 (pt0)
REVERT: E  149 GLN cc_start: 0.9189 (mm110) cc_final: 0.8847 (mm110)
REVERT: E  203 GLN cc_start: 0.9075 (tm-30) cc_final: 0.8616 (tm-30)
REVERT: E  227 GLU cc_start: 0.8363 (pp20) cc_final: 0.8099 (pp20)
REVERT: F  134 GLU cc_start: 0.7961 (tt0) cc_final: 0.7411 (tt0)
REVERT: F  203 GLN cc_start: 0.8978 (tm-30) cc_final: 0.8652 (tm-30)
REVERT: F  227 GLU cc_start: 0.8399 (pp20) cc_final: 0.8063 (pp20)
REVERT: G  134 GLU cc_start: 0.8007 (tt0) cc_final: 0.7678 (tt0)
REVERT: G  203 GLN cc_start: 0.8913 (tm-30) cc_final: 0.8608 (tm-30)
REVERT: G  227 GLU cc_start: 0.8497 (pp20) cc_final: 0.8127 (pp20)
REVERT: G  255 GLU cc_start: 0.9227 (tt0) cc_final: 0.8984 (tt0)
REVERT: G  260 GLU cc_start: 0.8733 (mp0) cc_final: 0.7998 (mp0)
  outliers start: 0
  outliers final: 0
  residues processed: 331
  average time/residue: 0.1092
  time to fit residues: 54.8606
Evaluate side-chains
  273 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 273
  time to evaluate  : 0.595 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 196
   random chunks:
   chunk 98 optimal weight:    0.9990
   chunk 194 optimal weight:    1.9990
   chunk 107 optimal weight:    0.3980
   chunk 10 optimal weight:    5.9990
   chunk 66 optimal weight:   10.0000
   chunk 130 optimal weight:    3.9990
   chunk 124 optimal weight:    0.6980
   chunk 103 optimal weight:    2.9990
   chunk 77 optimal weight:    0.3980
   chunk 122 optimal weight:    6.9990
   chunk 91 optimal weight:    5.9990
   overall best weight:    0.8984

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

Flipped N/Q/H residues before XYZ refinement:
B 149 GLN
D 149 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3600 r_free = 0.3600 target = 0.109522 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.2977 r_free = 0.2977 target = 0.071237 restraints weight = 35036.655|
|-----------------------------------------------------------------------------|
r_work (start): 0.2855 rms_B_bonded: 3.42
r_work: 0.2698 rms_B_bonded: 4.13 restraints_weight: 0.5000
r_work (final): 0.2698
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8344
moved from start:          0.1156

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  15092  Z= 0.135
  Angle     :  0.580   8.275  20482  Z= 0.301
  Chirality :  0.044   0.184   2513
  Planarity :  0.003   0.021   2604
  Dihedral  :  4.080  16.801   2121
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 6.57
  Ramachandran Plot:
    Outliers :  0.36 %
    Allowed  :  4.93 %
    Favored  : 94.71 %
  Rotamer:
    Outliers :  0.69 %
    Allowed  : 10.45 %
    Favored  : 88.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.08 (0.19), residues: 1946
  helix:  2.75 (0.16), residues: 1043
  sheet:  1.06 (0.31), residues: 259
  loop : -0.88 (0.24), residues: 644

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 180 
 TYR   0.006   0.001   TYR B 194 
 PHE   0.029   0.001   PHE F  80 
 TRP   0.009   0.001   TRP G  16 

Details of bonding type rmsd
  covalent geometry    : bond        0.00283 (15092)
  covalent geometry    : angle       0.58001 (20482)
  hydrogen bonds       : bond        0.04248 ( 1069)
  hydrogen bonds       : angle       4.51828 ( 3105)

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

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

  3892 Ramachandran restraints generated.
    1946 Oldfield, 0 Emsley, 1946 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3892 Ramachandran restraints generated.
    1946 Oldfield, 0 Emsley, 1946 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  311 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 300
  time to evaluate  : 0.503 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  134 GLU cc_start: 0.8517 (tt0) cc_final: 0.8258 (tt0)
REVERT: A  149 GLN cc_start: 0.9018 (mm110) cc_final: 0.8782 (mm-40)
REVERT: A  203 GLN cc_start: 0.9265 (tm-30) cc_final: 0.8884 (tm-30)
REVERT: A  220 GLU cc_start: 0.8639 (pp20) cc_final: 0.8367 (pp20)
REVERT: A  227 GLU cc_start: 0.9020 (pp20) cc_final: 0.8535 (pp20)
REVERT: B   47 MET cc_start: 0.8778 (mmp) cc_final: 0.8546 (mmm)
REVERT: B  112 GLN cc_start: 0.9222 (tm-30) cc_final: 0.8934 (tm-30)
REVERT: B  134 GLU cc_start: 0.8855 (tt0) cc_final: 0.8032 (tt0)
REVERT: B  203 GLN cc_start: 0.9204 (tm-30) cc_final: 0.8821 (tm-30)
REVERT: B  260 GLU cc_start: 0.9129 (mp0) cc_final: 0.8612 (mp0)
REVERT: C   56 MET cc_start: 0.8828 (ttm) cc_final: 0.8603 (ttm)
REVERT: C  112 GLN cc_start: 0.9152 (tp40) cc_final: 0.8947 (tp40)
REVERT: C  134 GLU cc_start: 0.8571 (tt0) cc_final: 0.8307 (tt0)
REVERT: C  149 GLN cc_start: 0.9335 (mm110) cc_final: 0.9017 (mm110)
REVERT: C  181 GLU cc_start: 0.9488 (mm-30) cc_final: 0.9156 (mm-30)
REVERT: C  203 GLN cc_start: 0.9357 (tm-30) cc_final: 0.8883 (tm-30)
REVERT: C  220 GLU cc_start: 0.8703 (pp20) cc_final: 0.8415 (pp20)
REVERT: D  203 GLN cc_start: 0.9328 (tm-30) cc_final: 0.8875 (tm-30)
REVERT: D  220 GLU cc_start: 0.8767 (pp20) cc_final: 0.8448 (pp20)
REVERT: D  255 GLU cc_start: 0.9574 (tt0) cc_final: 0.9108 (tm-30)
REVERT: E   55 LEU cc_start: 0.9228 (tt) cc_final: 0.8972 (mm)
REVERT: E  149 GLN cc_start: 0.9371 (mm110) cc_final: 0.9019 (mm110)
REVERT: E  169 LYS cc_start: 0.9392 (ttpp) cc_final: 0.9123 (ttpt)
REVERT: E  203 GLN cc_start: 0.9291 (tm-30) cc_final: 0.8848 (tm-30)
REVERT: E  220 GLU cc_start: 0.8708 (pp20) cc_final: 0.8500 (pp20)
REVERT: E  260 GLU cc_start: 0.9556 (mm-30) cc_final: 0.9338 (mm-30)
REVERT: F  126 MET cc_start: 0.9441 (ppp) cc_final: 0.9191 (tmm)
REVERT: F  134 GLU cc_start: 0.8389 (tt0) cc_final: 0.8024 (tt0)
REVERT: F  203 GLN cc_start: 0.9241 (tm-30) cc_final: 0.8899 (tm-30)
REVERT: F  220 GLU cc_start: 0.8815 (pp20) cc_final: 0.8526 (pp20)
REVERT: F  227 GLU cc_start: 0.9117 (pp20) cc_final: 0.8695 (pp20)
REVERT: G   47 MET cc_start: 0.8741 (mmm) cc_final: 0.8509 (mmm)
REVERT: G  134 GLU cc_start: 0.8580 (tt0) cc_final: 0.8079 (tt0)
REVERT: G  149 GLN cc_start: 0.9064 (mm110) cc_final: 0.8804 (mm-40)
REVERT: G  220 GLU cc_start: 0.8783 (pp20) cc_final: 0.8565 (pp20)
REVERT: G  227 GLU cc_start: 0.9115 (pp20) cc_final: 0.8542 (pp20)
  outliers start: 11
  outliers final: 6
  residues processed: 302
  average time/residue: 0.1146
  time to fit residues: 52.6993
Evaluate side-chains
  278 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 272
  time to evaluate  : 0.509 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   69 LEU
Chi-restraints excluded: chain C residue  122 VAL
Chi-restraints excluded: chain E residue   73 VAL
Chi-restraints excluded: chain G residue   23 LEU
Chi-restraints excluded: chain G residue   69 LEU
Chi-restraints excluded: chain G residue  153 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 196
   random chunks:
   chunk 179 optimal weight:    4.9990
   chunk 94 optimal weight:    1.9990
   chunk 85 optimal weight:    0.7980
   chunk 0 optimal weight:   50.0000
   chunk 2 optimal weight:   10.0000
   chunk 10 optimal weight:    9.9990
   chunk 96 optimal weight:    0.5980
   chunk 148 optimal weight:    4.9990
   chunk 130 optimal weight:    1.9990
   chunk 98 optimal weight:    5.9990
   chunk 178 optimal weight:    5.9990
   overall best weight:    2.0786

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

Flipped N/Q/H residues before XYZ refinement:
B 149 GLN
** D 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 149 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3567 r_free = 0.3567 target = 0.107732 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.2928 r_free = 0.2928 target = 0.069161 restraints weight = 35265.435|
|-----------------------------------------------------------------------------|
r_work (start): 0.2798 rms_B_bonded: 3.39
r_work: 0.2640 rms_B_bonded: 4.09 restraints_weight: 0.5000
r_work (final): 0.2640
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8375
moved from start:          0.1480

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036  15092  Z= 0.197
  Angle     :  0.564   8.062  20482  Z= 0.294
  Chirality :  0.044   0.201   2513
  Planarity :  0.003   0.021   2604
  Dihedral  :  4.108  16.813   2121
  Min Nonbonded Distance : 2.547

Molprobity Statistics.
  All-atom Clashscore : 6.07
  Ramachandran Plot:
    Outliers :  0.36 %
    Allowed  :  5.04 %
    Favored  : 94.60 %
  Rotamer:
    Outliers :  1.95 %
    Allowed  : 13.66 %
    Favored  : 84.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.00 (0.19), residues: 1946
  helix:  2.65 (0.16), residues: 1064
  sheet:  0.71 (0.28), residues: 308
  loop : -0.95 (0.26), residues: 574

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG D 185 
 TYR   0.009   0.001   TYR E 135 
 PHE   0.023   0.002   PHE G  80 
 TRP   0.007   0.001   TRP G  16 

Details of bonding type rmsd
  covalent geometry    : bond        0.00434 (15092)
  covalent geometry    : angle       0.56420 (20482)
  hydrogen bonds       : bond        0.03871 ( 1069)
  hydrogen bonds       : angle       4.28793 ( 3105)

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

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

  3892 Ramachandran restraints generated.
    1946 Oldfield, 0 Emsley, 1946 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3892 Ramachandran restraints generated.
    1946 Oldfield, 0 Emsley, 1946 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  305 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 274
  time to evaluate  : 0.541 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   47 MET cc_start: 0.8676 (mmm) cc_final: 0.8472 (mmm)
REVERT: A  134 GLU cc_start: 0.8330 (tt0) cc_final: 0.7932 (tt0)
REVERT: A  149 GLN cc_start: 0.9124 (mm110) cc_final: 0.8834 (mm-40)
REVERT: A  203 GLN cc_start: 0.9323 (tm-30) cc_final: 0.8905 (tm-30)
REVERT: A  220 GLU cc_start: 0.8705 (pp20) cc_final: 0.8398 (pp20)
REVERT: A  227 GLU cc_start: 0.9050 (pp20) cc_final: 0.8591 (pp20)
REVERT: B   47 MET cc_start: 0.8748 (mmp) cc_final: 0.8486 (mmm)
REVERT: B  112 GLN cc_start: 0.9263 (tm-30) cc_final: 0.8983 (tm-30)
REVERT: B  134 GLU cc_start: 0.8749 (tt0) cc_final: 0.8334 (tt0)
REVERT: B  203 GLN cc_start: 0.9246 (tm-30) cc_final: 0.8872 (tm-30)
REVERT: B  260 GLU cc_start: 0.9162 (mp0) cc_final: 0.8627 (mp0)
REVERT: B  278 LYS cc_start: 0.9235 (mtmm) cc_final: 0.8952 (mttp)
REVERT: C   56 MET cc_start: 0.8945 (ttm) cc_final: 0.8730 (ttm)
REVERT: C  134 GLU cc_start: 0.8501 (tt0) cc_final: 0.8059 (tt0)
REVERT: C  149 GLN cc_start: 0.9389 (mm110) cc_final: 0.9068 (mm110)
REVERT: C  181 GLU cc_start: 0.9522 (mm-30) cc_final: 0.9041 (mm-30)
REVERT: C  203 GLN cc_start: 0.9365 (tm-30) cc_final: 0.8939 (tm-30)
REVERT: C  220 GLU cc_start: 0.8762 (pp20) cc_final: 0.8443 (pp20)
REVERT: D  203 GLN cc_start: 0.9338 (tm-30) cc_final: 0.8937 (tm-30)
REVERT: D  220 GLU cc_start: 0.8820 (pp20) cc_final: 0.8485 (pp20)
REVERT: D  255 GLU cc_start: 0.9577 (tt0) cc_final: 0.9054 (tm-30)
REVERT: D  260 GLU cc_start: 0.9073 (mp0) cc_final: 0.8735 (mp0)
REVERT: D  273 MET cc_start: 0.8773 (OUTLIER) cc_final: 0.8411 (ptm)
REVERT: E   55 LEU cc_start: 0.9243 (tt) cc_final: 0.8970 (mm)
REVERT: E  149 GLN cc_start: 0.9370 (mm110) cc_final: 0.9009 (mm110)
REVERT: E  203 GLN cc_start: 0.9327 (tm-30) cc_final: 0.8952 (tm-30)
REVERT: E  220 GLU cc_start: 0.8735 (pp20) cc_final: 0.8459 (pp20)
REVERT: F  134 GLU cc_start: 0.8451 (tt0) cc_final: 0.8106 (tt0)
REVERT: F  203 GLN cc_start: 0.9266 (tm-30) cc_final: 0.8892 (tm-30)
REVERT: F  220 GLU cc_start: 0.8853 (pp20) cc_final: 0.8541 (pp20)
REVERT: F  227 GLU cc_start: 0.9142 (pp20) cc_final: 0.8712 (pp20)
REVERT: G   47 MET cc_start: 0.8646 (mmm) cc_final: 0.8359 (mmm)
REVERT: G  134 GLU cc_start: 0.8430 (tt0) cc_final: 0.7654 (tt0)
REVERT: G  149 GLN cc_start: 0.9106 (mm110) cc_final: 0.8817 (mm-40)
REVERT: G  220 GLU cc_start: 0.8807 (pp20) cc_final: 0.8546 (pp20)
REVERT: G  227 GLU cc_start: 0.9156 (pp20) cc_final: 0.8609 (pp20)
REVERT: G  255 GLU cc_start: 0.9565 (tt0) cc_final: 0.9056 (tm-30)
REVERT: G  260 GLU cc_start: 0.9184 (mp0) cc_final: 0.8535 (mp0)
  outliers start: 31
  outliers final: 18
  residues processed: 285
  average time/residue: 0.1118
  time to fit residues: 48.6563
Evaluate side-chains
  282 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 263
  time to evaluate  : 0.509 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  153 THR
Chi-restraints excluded: chain A residue  154 THR
Chi-restraints excluded: chain A residue  155 MET
Chi-restraints excluded: chain B residue   69 LEU
Chi-restraints excluded: chain B residue  153 THR
Chi-restraints excluded: chain B residue  221 MET
Chi-restraints excluded: chain C residue  122 VAL
Chi-restraints excluded: chain C residue  138 LEU
Chi-restraints excluded: chain D residue  111 LEU
Chi-restraints excluded: chain D residue  153 THR
Chi-restraints excluded: chain D residue  273 MET
Chi-restraints excluded: chain E residue   73 VAL
Chi-restraints excluded: chain E residue  153 THR
Chi-restraints excluded: chain E residue  154 THR
Chi-restraints excluded: chain F residue   73 VAL
Chi-restraints excluded: chain F residue  111 LEU
Chi-restraints excluded: chain F residue  153 THR
Chi-restraints excluded: chain F residue  154 THR
Chi-restraints excluded: chain G residue  153 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 196
   random chunks:
   chunk 40 optimal weight:    0.4980
   chunk 187 optimal weight:    0.7980
   chunk 105 optimal weight:    0.9990
   chunk 44 optimal weight:    0.8980
   chunk 74 optimal weight:    4.9990
   chunk 53 optimal weight:    2.9990
   chunk 106 optimal weight:    0.1980
   chunk 47 optimal weight:    3.9990
   chunk 15 optimal weight:    0.5980
   chunk 189 optimal weight:    2.9990
   chunk 83 optimal weight:    3.9990
   overall best weight:    0.5980

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

Flipped N/Q/H residues before XYZ refinement:
B 149 GLN
F 149 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3589 r_free = 0.3589 target = 0.108674 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2965 r_free = 0.2965 target = 0.070883 restraints weight = 35252.184|
|-----------------------------------------------------------------------------|
r_work (start): 0.2842 rms_B_bonded: 3.32
r_work: 0.2694 rms_B_bonded: 4.08 restraints_weight: 0.5000
r_work (final): 0.2694
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8328
moved from start:          0.1684

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032  15092  Z= 0.110
  Angle     :  0.543   9.669  20482  Z= 0.276
  Chirality :  0.043   0.175   2513
  Planarity :  0.002   0.023   2604
  Dihedral  :  3.967  17.590   2121
  Min Nonbonded Distance : 2.578

Molprobity Statistics.
  All-atom Clashscore : 5.71
  Ramachandran Plot:
    Outliers :  0.36 %
    Allowed  :  5.24 %
    Favored  : 94.40 %
  Rotamer:
    Outliers :  2.14 %
    Allowed  : 15.36 %
    Favored  : 82.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.15 (0.19), residues: 1946
  helix:  2.76 (0.16), residues: 1064
  sheet:  0.86 (0.31), residues: 280
  loop : -0.81 (0.25), residues: 602

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG F 256 
 TYR   0.004   0.001   TYR D 270 
 PHE   0.023   0.001   PHE F  80 
 TRP   0.006   0.001   TRP G  16 

Details of bonding type rmsd
  covalent geometry    : bond        0.00222 (15092)
  covalent geometry    : angle       0.54255 (20482)
  hydrogen bonds       : bond        0.03580 ( 1069)
  hydrogen bonds       : angle       4.06993 ( 3105)

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

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

  3892 Ramachandran restraints generated.
    1946 Oldfield, 0 Emsley, 1946 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3892 Ramachandran restraints generated.
    1946 Oldfield, 0 Emsley, 1946 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  318 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 284
  time to evaluate  : 0.575 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   47 MET cc_start: 0.8687 (mmm) cc_final: 0.8475 (mmm)
REVERT: A  134 GLU cc_start: 0.8324 (tt0) cc_final: 0.7856 (tt0)
REVERT: A  149 GLN cc_start: 0.9155 (mm110) cc_final: 0.8833 (mm-40)
REVERT: A  203 GLN cc_start: 0.9294 (tm-30) cc_final: 0.8838 (tm-30)
REVERT: A  210 GLN cc_start: 0.9482 (mm110) cc_final: 0.9183 (mm-40)
REVERT: A  220 GLU cc_start: 0.8707 (pp20) cc_final: 0.8365 (pp20)
REVERT: A  227 GLU cc_start: 0.9042 (pp20) cc_final: 0.8629 (pp20)
REVERT: B   47 MET cc_start: 0.8704 (mmp) cc_final: 0.8435 (mmm)
REVERT: B  134 GLU cc_start: 0.8826 (tt0) cc_final: 0.8583 (tt0)
REVERT: B  157 THR cc_start: 0.9555 (OUTLIER) cc_final: 0.9120 (p)
REVERT: B  178 PHE cc_start: 0.9198 (m-10) cc_final: 0.8997 (m-10)
REVERT: B  203 GLN cc_start: 0.9242 (tm-30) cc_final: 0.8839 (tm-30)
REVERT: B  278 LYS cc_start: 0.9205 (mtmm) cc_final: 0.8707 (mttm)
REVERT: C   47 MET cc_start: 0.8669 (mmm) cc_final: 0.8295 (mmm)
REVERT: C   56 MET cc_start: 0.8899 (ttm) cc_final: 0.8683 (ttm)
REVERT: C  134 GLU cc_start: 0.8570 (tt0) cc_final: 0.8050 (tt0)
REVERT: C  149 GLN cc_start: 0.9387 (mm110) cc_final: 0.9043 (mm110)
REVERT: C  181 GLU cc_start: 0.9480 (mm-30) cc_final: 0.9054 (mm-30)
REVERT: C  203 GLN cc_start: 0.9361 (tm-30) cc_final: 0.8895 (tm-30)
REVERT: C  220 GLU cc_start: 0.8791 (pp20) cc_final: 0.8452 (pp20)
REVERT: D  181 GLU cc_start: 0.9553 (mm-30) cc_final: 0.9055 (mm-30)
REVERT: D  203 GLN cc_start: 0.9324 (tm-30) cc_final: 0.8907 (tm-30)
REVERT: D  220 GLU cc_start: 0.8874 (pp20) cc_final: 0.8510 (pp20)
REVERT: D  255 GLU cc_start: 0.9556 (tt0) cc_final: 0.9135 (tm-30)
REVERT: D  273 MET cc_start: 0.8774 (OUTLIER) cc_final: 0.8554 (ptm)
REVERT: E   55 LEU cc_start: 0.9239 (tt) cc_final: 0.8981 (mm)
REVERT: E  149 GLN cc_start: 0.9414 (mm110) cc_final: 0.8978 (mm110)
REVERT: E  203 GLN cc_start: 0.9354 (tm-30) cc_final: 0.8947 (tm-30)
REVERT: E  220 GLU cc_start: 0.8759 (pp20) cc_final: 0.8469 (pp20)
REVERT: F  134 GLU cc_start: 0.8443 (tt0) cc_final: 0.8032 (tp30)
REVERT: F  203 GLN cc_start: 0.9261 (tm-30) cc_final: 0.8852 (tm-30)
REVERT: F  220 GLU cc_start: 0.8863 (pp20) cc_final: 0.8511 (pp20)
REVERT: F  227 GLU cc_start: 0.9122 (pp20) cc_final: 0.8700 (pp20)
REVERT: F  270 TYR cc_start: 0.9419 (m-80) cc_final: 0.9110 (m-10)
REVERT: F  274 ASP cc_start: 0.9012 (OUTLIER) cc_final: 0.8514 (t0)
REVERT: G   47 MET cc_start: 0.8648 (mmm) cc_final: 0.8361 (mmm)
REVERT: G  134 GLU cc_start: 0.8490 (tt0) cc_final: 0.7621 (tt0)
REVERT: G  149 GLN cc_start: 0.9085 (mm110) cc_final: 0.8714 (mm-40)
REVERT: G  220 GLU cc_start: 0.8790 (pp20) cc_final: 0.8435 (pp20)
REVERT: G  222 THR cc_start: 0.9529 (m) cc_final: 0.9253 (p)
REVERT: G  227 GLU cc_start: 0.9114 (pp20) cc_final: 0.8554 (pp20)
REVERT: G  255 GLU cc_start: 0.9547 (tt0) cc_final: 0.9039 (tm-30)
  outliers start: 34
  outliers final: 14
  residues processed: 302
  average time/residue: 0.1123
  time to fit residues: 52.1312
Evaluate side-chains
  288 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 271
  time to evaluate  : 0.556 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  126 MET
Chi-restraints excluded: chain B residue   69 LEU
Chi-restraints excluded: chain B residue  153 THR
Chi-restraints excluded: chain B residue  157 THR
Chi-restraints excluded: chain B residue  221 MET
Chi-restraints excluded: chain C residue  138 LEU
Chi-restraints excluded: chain D residue  111 LEU
Chi-restraints excluded: chain D residue  171 ILE
Chi-restraints excluded: chain D residue  273 MET
Chi-restraints excluded: chain E residue   73 VAL
Chi-restraints excluded: chain E residue  138 LEU
Chi-restraints excluded: chain F residue   73 VAL
Chi-restraints excluded: chain F residue  126 MET
Chi-restraints excluded: chain F residue  138 LEU
Chi-restraints excluded: chain F residue  274 ASP
Chi-restraints excluded: chain G residue   23 LEU
Chi-restraints excluded: chain G residue   73 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 196
   random chunks:
   chunk 97 optimal weight:    0.9980
   chunk 91 optimal weight:    9.9990
   chunk 53 optimal weight:    2.9990
   chunk 68 optimal weight:    0.7980
   chunk 11 optimal weight:    8.9990
   chunk 79 optimal weight:    5.9990
   chunk 13 optimal weight:    1.9990
   chunk 40 optimal weight:    0.8980
   chunk 157 optimal weight:    0.6980
   chunk 145 optimal weight:    4.9990
   chunk 66 optimal weight:    9.9990
   overall best weight:    1.0782

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3581 r_free = 0.3581 target = 0.108537 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2950 r_free = 0.2950 target = 0.070494 restraints weight = 35334.218|
|-----------------------------------------------------------------------------|
r_work (start): 0.2821 rms_B_bonded: 3.38
r_work: 0.2665 rms_B_bonded: 4.16 restraints_weight: 0.5000
r_work (final): 0.2665
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8342
moved from start:          0.1851

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046  15092  Z= 0.134
  Angle     :  0.538   9.472  20482  Z= 0.277
  Chirality :  0.043   0.177   2513
  Planarity :  0.002   0.023   2604
  Dihedral  :  3.973  21.148   2121
  Min Nonbonded Distance : 2.514

Molprobity Statistics.
  All-atom Clashscore : 5.88
  Ramachandran Plot:
    Outliers :  0.36 %
    Allowed  :  4.93 %
    Favored  : 94.71 %
  Rotamer:
    Outliers :  1.70 %
    Allowed  : 15.98 %
    Favored  : 82.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.19 (0.19), residues: 1946
  helix:  2.76 (0.16), residues: 1071
  sheet:  0.76 (0.30), residues: 294
  loop : -0.74 (0.26), residues: 581

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG G 256 
 TYR   0.006   0.001   TYR E  27 
 PHE   0.027   0.001   PHE F  80 
 TRP   0.005   0.001   TRP G  16 

Details of bonding type rmsd
  covalent geometry    : bond        0.00285 (15092)
  covalent geometry    : angle       0.53841 (20482)
  hydrogen bonds       : bond        0.03502 ( 1069)
  hydrogen bonds       : angle       3.95749 ( 3105)

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

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

  3892 Ramachandran restraints generated.
    1946 Oldfield, 0 Emsley, 1946 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3892 Ramachandran restraints generated.
    1946 Oldfield, 0 Emsley, 1946 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  305 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 278
  time to evaluate  : 0.588 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   47 MET cc_start: 0.8655 (mmm) cc_final: 0.8429 (mmm)
REVERT: A  134 GLU cc_start: 0.8256 (tt0) cc_final: 0.7817 (tt0)
REVERT: A  149 GLN cc_start: 0.9188 (mm110) cc_final: 0.8825 (mm-40)
REVERT: A  203 GLN cc_start: 0.9330 (tm-30) cc_final: 0.8873 (tm-30)
REVERT: A  210 GLN cc_start: 0.9425 (mm110) cc_final: 0.9207 (mm-40)
REVERT: A  220 GLU cc_start: 0.8730 (pp20) cc_final: 0.8381 (pp20)
REVERT: A  227 GLU cc_start: 0.9063 (pp20) cc_final: 0.8653 (pp20)
REVERT: B   47 MET cc_start: 0.8726 (mmp) cc_final: 0.8465 (mmm)
REVERT: B   74 ARG cc_start: 0.7349 (ttp-110) cc_final: 0.7096 (ttm170)
REVERT: B  134 GLU cc_start: 0.8741 (tt0) cc_final: 0.8459 (tt0)
REVERT: B  157 THR cc_start: 0.9522 (OUTLIER) cc_final: 0.9098 (p)
REVERT: B  161 LYS cc_start: 0.9283 (OUTLIER) cc_final: 0.8835 (mmtm)
REVERT: B  203 GLN cc_start: 0.9271 (tm-30) cc_final: 0.8865 (tm-30)
REVERT: B  278 LYS cc_start: 0.9235 (mtmm) cc_final: 0.8687 (mttm)
REVERT: C   47 MET cc_start: 0.8682 (mmm) cc_final: 0.8290 (mmm)
REVERT: C   56 MET cc_start: 0.8943 (ttm) cc_final: 0.8708 (ttm)
REVERT: C  134 GLU cc_start: 0.8577 (tt0) cc_final: 0.8020 (tt0)
REVERT: C  149 GLN cc_start: 0.9414 (mm110) cc_final: 0.9057 (mm110)
REVERT: C  181 GLU cc_start: 0.9498 (mm-30) cc_final: 0.9037 (mm-30)
REVERT: C  203 GLN cc_start: 0.9372 (tm-30) cc_final: 0.8902 (tm-30)
REVERT: C  220 GLU cc_start: 0.8848 (pp20) cc_final: 0.8521 (pp20)
REVERT: C  227 GLU cc_start: 0.9053 (pp20) cc_final: 0.8675 (pp20)
REVERT: D  181 GLU cc_start: 0.9534 (mm-30) cc_final: 0.9088 (mm-30)
REVERT: D  203 GLN cc_start: 0.9337 (tm-30) cc_final: 0.8915 (tm-30)
REVERT: D  220 GLU cc_start: 0.8894 (pp20) cc_final: 0.8514 (pp20)
REVERT: D  255 GLU cc_start: 0.9566 (tt0) cc_final: 0.9113 (tm-30)
REVERT: E   47 MET cc_start: 0.8711 (mmm) cc_final: 0.8325 (mmm)
REVERT: E   55 LEU cc_start: 0.9247 (tt) cc_final: 0.8957 (mm)
REVERT: E  134 GLU cc_start: 0.8402 (pt0) cc_final: 0.8180 (pm20)
REVERT: E  149 GLN cc_start: 0.9420 (mm110) cc_final: 0.9011 (mm110)
REVERT: E  169 LYS cc_start: 0.9383 (ttpp) cc_final: 0.9149 (ttpt)
REVERT: E  203 GLN cc_start: 0.9369 (tm-30) cc_final: 0.8958 (tm-30)
REVERT: E  220 GLU cc_start: 0.8778 (pp20) cc_final: 0.8495 (pp20)
REVERT: E  227 GLU cc_start: 0.9046 (pp20) cc_final: 0.8619 (pp20)
REVERT: F  134 GLU cc_start: 0.8452 (tt0) cc_final: 0.8094 (tt0)
REVERT: F  203 GLN cc_start: 0.9294 (tm-30) cc_final: 0.8900 (tm-30)
REVERT: F  220 GLU cc_start: 0.8877 (pp20) cc_final: 0.8526 (pp20)
REVERT: F  227 GLU cc_start: 0.9133 (pp20) cc_final: 0.8715 (pp20)
REVERT: F  270 TYR cc_start: 0.9438 (m-80) cc_final: 0.9166 (m-10)
REVERT: G   47 MET cc_start: 0.8615 (mmm) cc_final: 0.8305 (mmm)
REVERT: G  134 GLU cc_start: 0.8393 (tt0) cc_final: 0.7524 (tt0)
REVERT: G  149 GLN cc_start: 0.9185 (mm110) cc_final: 0.8798 (mm-40)
REVERT: G  220 GLU cc_start: 0.8785 (pp20) cc_final: 0.8432 (pp20)
REVERT: G  222 THR cc_start: 0.9543 (m) cc_final: 0.9278 (p)
REVERT: G  227 GLU cc_start: 0.9169 (pp20) cc_final: 0.8664 (pp20)
  outliers start: 27
  outliers final: 15
  residues processed: 290
  average time/residue: 0.1229
  time to fit residues: 53.6897
Evaluate side-chains
  279 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 262
  time to evaluate  : 0.562 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  126 MET
Chi-restraints excluded: chain A residue  155 MET
Chi-restraints excluded: chain A residue  274 ASP
Chi-restraints excluded: chain B residue   69 LEU
Chi-restraints excluded: chain B residue  153 THR
Chi-restraints excluded: chain B residue  157 THR
Chi-restraints excluded: chain B residue  161 LYS
Chi-restraints excluded: chain B residue  221 MET
Chi-restraints excluded: chain C residue  138 LEU
Chi-restraints excluded: chain D residue  111 LEU
Chi-restraints excluded: chain D residue  171 ILE
Chi-restraints excluded: chain E residue   73 VAL
Chi-restraints excluded: chain F residue   73 VAL
Chi-restraints excluded: chain F residue  126 MET
Chi-restraints excluded: chain G residue   23 LEU
Chi-restraints excluded: chain G residue   69 LEU
Chi-restraints excluded: chain G residue   73 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 196
   random chunks:
   chunk 95 optimal weight:    3.9990
   chunk 114 optimal weight:    6.9990
   chunk 119 optimal weight:   20.0000
   chunk 99 optimal weight:    2.9990
   chunk 55 optimal weight:    2.9990
   chunk 26 optimal weight:    2.9990
   chunk 35 optimal weight:    0.9990
   chunk 69 optimal weight:    7.9990
   chunk 195 optimal weight:    3.9990
   chunk 165 optimal weight:    1.9990
   chunk 117 optimal weight:    9.9990
   overall best weight:    2.3990

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

Flipped N/Q/H residues before XYZ refinement:
D 149 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3549 r_free = 0.3549 target = 0.106356 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2883 r_free = 0.2883 target = 0.068883 restraints weight = 36410.865|
|-----------------------------------------------------------------------------|
r_work (start): 0.2788 rms_B_bonded: 3.19
r_work: 0.2642 rms_B_bonded: 4.03 restraints_weight: 0.5000
r_work (final): 0.2642
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8375
moved from start:          0.1985

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.058  15092  Z= 0.221
  Angle     :  0.575  10.435  20482  Z= 0.297
  Chirality :  0.044   0.185   2513
  Planarity :  0.003   0.024   2604
  Dihedral  :  4.116  23.792   2121
  Min Nonbonded Distance : 2.533

Molprobity Statistics.
  All-atom Clashscore : 5.61
  Ramachandran Plot:
    Outliers :  0.36 %
    Allowed  :  5.09 %
    Favored  : 94.55 %
  Rotamer:
    Outliers :  1.95 %
    Allowed  : 16.36 %
    Favored  : 81.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.18 (0.19), residues: 1946
  helix:  2.71 (0.16), residues: 1071
  sheet:  0.95 (0.30), residues: 294
  loop : -0.79 (0.26), residues: 581

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG D 131 
 TYR   0.009   0.001   TYR E  27 
 PHE   0.023   0.002   PHE D  80 
 TRP   0.005   0.001   TRP G  16 

Details of bonding type rmsd
  covalent geometry    : bond        0.00492 (15092)
  covalent geometry    : angle       0.57470 (20482)
  hydrogen bonds       : bond        0.03580 ( 1069)
  hydrogen bonds       : angle       3.96106 ( 3105)

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

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

  3892 Ramachandran restraints generated.
    1946 Oldfield, 0 Emsley, 1946 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3892 Ramachandran restraints generated.
    1946 Oldfield, 0 Emsley, 1946 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  298 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 267
  time to evaluate  : 0.546 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   47 MET cc_start: 0.8643 (mmm) cc_final: 0.8417 (mmm)
REVERT: A  134 GLU cc_start: 0.8147 (tt0) cc_final: 0.7638 (tt0)
REVERT: A  149 GLN cc_start: 0.9201 (mm110) cc_final: 0.8847 (mm-40)
REVERT: A  203 GLN cc_start: 0.9330 (tm-30) cc_final: 0.8895 (tm-30)
REVERT: A  210 GLN cc_start: 0.9437 (mm110) cc_final: 0.9224 (mm-40)
REVERT: A  220 GLU cc_start: 0.8736 (pp20) cc_final: 0.8388 (pp20)
REVERT: A  227 GLU cc_start: 0.9069 (pp20) cc_final: 0.8615 (pp20)
REVERT: B   47 MET cc_start: 0.8724 (mmp) cc_final: 0.8460 (mmm)
REVERT: B   56 MET cc_start: 0.8906 (mtp) cc_final: 0.8684 (mtm)
REVERT: B   69 LEU cc_start: 0.9273 (OUTLIER) cc_final: 0.9045 (pp)
REVERT: B   74 ARG cc_start: 0.7243 (ttp-110) cc_final: 0.7009 (ttm170)
REVERT: B  134 GLU cc_start: 0.8648 (tt0) cc_final: 0.8322 (tt0)
REVERT: B  157 THR cc_start: 0.9489 (OUTLIER) cc_final: 0.9114 (p)
REVERT: B  161 LYS cc_start: 0.9300 (OUTLIER) cc_final: 0.8823 (mmtm)
REVERT: B  203 GLN cc_start: 0.9262 (tm-30) cc_final: 0.8859 (tm-30)
REVERT: C   47 MET cc_start: 0.8663 (mmm) cc_final: 0.8269 (mmm)
REVERT: C   56 MET cc_start: 0.8866 (ttm) cc_final: 0.8635 (ttm)
REVERT: C   91 VAL cc_start: 0.7752 (OUTLIER) cc_final: 0.7449 (p)
REVERT: C  134 GLU cc_start: 0.8439 (tt0) cc_final: 0.8082 (tt0)
REVERT: C  149 GLN cc_start: 0.9416 (mm110) cc_final: 0.8994 (mm110)
REVERT: C  181 GLU cc_start: 0.9554 (mm-30) cc_final: 0.9012 (mm-30)
REVERT: C  203 GLN cc_start: 0.9365 (tm-30) cc_final: 0.8887 (tm-30)
REVERT: C  220 GLU cc_start: 0.8844 (pp20) cc_final: 0.8506 (pp20)
REVERT: C  227 GLU cc_start: 0.9067 (pp20) cc_final: 0.8698 (pp20)
REVERT: D  181 GLU cc_start: 0.9564 (mm-30) cc_final: 0.9114 (mm-30)
REVERT: D  203 GLN cc_start: 0.9341 (tm-30) cc_final: 0.8913 (tm-30)
REVERT: D  220 GLU cc_start: 0.8857 (pp20) cc_final: 0.8480 (pp20)
REVERT: D  260 GLU cc_start: 0.9506 (mm-30) cc_final: 0.8898 (mp0)
REVERT: D  278 LYS cc_start: 0.9194 (mtmm) cc_final: 0.8986 (mtmm)
REVERT: E   47 MET cc_start: 0.8696 (mmm) cc_final: 0.8296 (mmm)
REVERT: E  149 GLN cc_start: 0.9412 (mm110) cc_final: 0.8948 (mm110)
REVERT: E  203 GLN cc_start: 0.9336 (tm-30) cc_final: 0.8952 (tm-30)
REVERT: E  220 GLU cc_start: 0.8807 (pp20) cc_final: 0.8577 (pp20)
REVERT: E  227 GLU cc_start: 0.9040 (pp20) cc_final: 0.8622 (pp20)
REVERT: F  134 GLU cc_start: 0.8290 (tt0) cc_final: 0.7901 (tt0)
REVERT: F  203 GLN cc_start: 0.9310 (tm-30) cc_final: 0.8905 (tm-30)
REVERT: F  220 GLU cc_start: 0.8834 (pp20) cc_final: 0.8454 (pp20)
REVERT: F  227 GLU cc_start: 0.9114 (pp20) cc_final: 0.8709 (pp20)
REVERT: F  270 TYR cc_start: 0.9436 (m-80) cc_final: 0.9195 (m-10)
REVERT: F  274 ASP cc_start: 0.9003 (OUTLIER) cc_final: 0.8505 (t0)
REVERT: G   47 MET cc_start: 0.8531 (mmm) cc_final: 0.8207 (mmm)
REVERT: G   88 ARG cc_start: 0.8246 (tpp-160) cc_final: 0.7622 (mmm160)
REVERT: G  134 GLU cc_start: 0.8218 (tt0) cc_final: 0.7305 (tt0)
REVERT: G  149 GLN cc_start: 0.9159 (mm110) cc_final: 0.8747 (mm110)
REVERT: G  203 GLN cc_start: 0.9221 (tm-30) cc_final: 0.8904 (tm-30)
REVERT: G  220 GLU cc_start: 0.8733 (pp20) cc_final: 0.8380 (pp20)
REVERT: G  222 THR cc_start: 0.9538 (m) cc_final: 0.9257 (p)
REVERT: G  227 GLU cc_start: 0.9147 (pp20) cc_final: 0.8666 (pp20)
  outliers start: 31
  outliers final: 18
  residues processed: 282
  average time/residue: 0.1188
  time to fit residues: 50.4222
Evaluate side-chains
  278 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 255
  time to evaluate  : 0.550 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  126 MET
Chi-restraints excluded: chain A residue  155 MET
Chi-restraints excluded: chain A residue  274 ASP
Chi-restraints excluded: chain B residue   69 LEU
Chi-restraints excluded: chain B residue  153 THR
Chi-restraints excluded: chain B residue  157 THR
Chi-restraints excluded: chain B residue  161 LYS
Chi-restraints excluded: chain B residue  221 MET
Chi-restraints excluded: chain C residue   91 VAL
Chi-restraints excluded: chain C residue  138 LEU
Chi-restraints excluded: chain D residue  111 LEU
Chi-restraints excluded: chain D residue  155 MET
Chi-restraints excluded: chain D residue  171 ILE
Chi-restraints excluded: chain E residue   73 VAL
Chi-restraints excluded: chain E residue  153 THR
Chi-restraints excluded: chain E residue  163 ILE
Chi-restraints excluded: chain F residue   73 VAL
Chi-restraints excluded: chain F residue  126 MET
Chi-restraints excluded: chain F residue  138 LEU
Chi-restraints excluded: chain F residue  274 ASP
Chi-restraints excluded: chain G residue   69 LEU
Chi-restraints excluded: chain G residue   73 VAL
Chi-restraints excluded: chain G residue  153 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 196
   random chunks:
   chunk 39 optimal weight:    2.9990
   chunk 15 optimal weight:    7.9990
   chunk 166 optimal weight:    0.9990
   chunk 18 optimal weight:    0.8980
   chunk 176 optimal weight:    7.9990
   chunk 1 optimal weight:    8.9990
   chunk 195 optimal weight:    3.9990
   chunk 119 optimal weight:    7.9990
   chunk 192 optimal weight:    0.9990
   chunk 46 optimal weight:    1.9990
   chunk 114 optimal weight:   30.0000
   overall best weight:    1.5788

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

Flipped N/Q/H residues before XYZ refinement:
D 149 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3560 r_free = 0.3560 target = 0.107146 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2907 r_free = 0.2907 target = 0.068732 restraints weight = 35143.423|
|-----------------------------------------------------------------------------|
r_work (start): 0.2798 rms_B_bonded: 3.34
r_work: 0.2646 rms_B_bonded: 4.15 restraints_weight: 0.5000
r_work (final): 0.2646
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8363
moved from start:          0.2050

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046  15092  Z= 0.164
  Angle     :  0.565   8.809  20482  Z= 0.289
  Chirality :  0.044   0.277   2513
  Planarity :  0.002   0.024   2604
  Dihedral  :  4.087  21.515   2121
  Min Nonbonded Distance : 2.495

Molprobity Statistics.
  All-atom Clashscore : 5.97
  Ramachandran Plot:
    Outliers :  0.36 %
    Allowed  :  4.93 %
    Favored  : 94.71 %
  Rotamer:
    Outliers :  1.95 %
    Allowed  : 16.99 %
    Favored  : 81.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.20 (0.20), residues: 1946
  helix:  2.71 (0.16), residues: 1071
  sheet:  1.01 (0.30), residues: 294
  loop : -0.77 (0.26), residues: 581

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG E 131 
 TYR   0.009   0.001   TYR E  27 
 PHE   0.022   0.002   PHE F  80 
 TRP   0.006   0.001   TRP G  16 

Details of bonding type rmsd
  covalent geometry    : bond        0.00363 (15092)
  covalent geometry    : angle       0.56530 (20482)
  hydrogen bonds       : bond        0.03529 ( 1069)
  hydrogen bonds       : angle       3.91062 ( 3105)

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

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

  3892 Ramachandran restraints generated.
    1946 Oldfield, 0 Emsley, 1946 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3892 Ramachandran restraints generated.
    1946 Oldfield, 0 Emsley, 1946 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  298 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 267
  time to evaluate  : 0.796 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   47 MET cc_start: 0.8627 (mmm) cc_final: 0.8400 (mmm)
REVERT: A  126 MET cc_start: 0.9409 (OUTLIER) cc_final: 0.9192 (tmm)
REVERT: A  134 GLU cc_start: 0.8162 (tt0) cc_final: 0.7617 (tt0)
REVERT: A  149 GLN cc_start: 0.9228 (mm110) cc_final: 0.8832 (mm-40)
REVERT: A  203 GLN cc_start: 0.9334 (tm-30) cc_final: 0.8892 (tm-30)
REVERT: A  210 GLN cc_start: 0.9426 (mm110) cc_final: 0.9220 (mm-40)
REVERT: A  220 GLU cc_start: 0.8726 (pp20) cc_final: 0.8361 (pp20)
REVERT: A  227 GLU cc_start: 0.9066 (pp20) cc_final: 0.8622 (pp20)
REVERT: B   47 MET cc_start: 0.8718 (mmp) cc_final: 0.8450 (mmm)
REVERT: B  134 GLU cc_start: 0.8670 (tt0) cc_final: 0.8332 (tt0)
REVERT: B  157 THR cc_start: 0.9479 (OUTLIER) cc_final: 0.9063 (p)
REVERT: B  203 GLN cc_start: 0.9269 (tm-30) cc_final: 0.8856 (tm-30)
REVERT: B  278 LYS cc_start: 0.9045 (mtmm) cc_final: 0.8831 (mttp)
REVERT: C   47 MET cc_start: 0.8708 (mmm) cc_final: 0.8362 (mmm)
REVERT: C   56 MET cc_start: 0.8894 (ttm) cc_final: 0.8647 (ttm)
REVERT: C   91 VAL cc_start: 0.7826 (OUTLIER) cc_final: 0.7521 (p)
REVERT: C  134 GLU cc_start: 0.8495 (tt0) cc_final: 0.7850 (tt0)
REVERT: C  149 GLN cc_start: 0.9410 (mm110) cc_final: 0.9155 (mm-40)
REVERT: C  181 GLU cc_start: 0.9565 (mm-30) cc_final: 0.9032 (mm-30)
REVERT: C  203 GLN cc_start: 0.9367 (tm-30) cc_final: 0.8882 (tm-30)
REVERT: C  220 GLU cc_start: 0.8834 (pp20) cc_final: 0.8489 (pp20)
REVERT: C  227 GLU cc_start: 0.9050 (pp20) cc_final: 0.8661 (pp20)
REVERT: D  181 GLU cc_start: 0.9565 (mm-30) cc_final: 0.9158 (mm-30)
REVERT: D  203 GLN cc_start: 0.9346 (tm-30) cc_final: 0.8915 (tm-30)
REVERT: D  220 GLU cc_start: 0.8855 (pp20) cc_final: 0.8456 (pp20)
REVERT: D  260 GLU cc_start: 0.9524 (mm-30) cc_final: 0.8957 (mp0)
REVERT: D  278 LYS cc_start: 0.9260 (mtmm) cc_final: 0.9025 (mtmm)
REVERT: E   47 MET cc_start: 0.8676 (mmm) cc_final: 0.8277 (mmm)
REVERT: E  149 GLN cc_start: 0.9404 (mm110) cc_final: 0.9036 (mm-40)
REVERT: E  181 GLU cc_start: 0.9596 (mm-30) cc_final: 0.9194 (mm-30)
REVERT: E  203 GLN cc_start: 0.9337 (tm-30) cc_final: 0.8922 (tm-30)
REVERT: E  220 GLU cc_start: 0.8842 (pp20) cc_final: 0.8595 (pp20)
REVERT: E  227 GLU cc_start: 0.9002 (pp20) cc_final: 0.8572 (pp20)
REVERT: F  134 GLU cc_start: 0.8342 (tt0) cc_final: 0.7937 (tt0)
REVERT: F  203 GLN cc_start: 0.9312 (tm-30) cc_final: 0.8900 (tm-30)
REVERT: F  220 GLU cc_start: 0.8824 (pp20) cc_final: 0.8444 (pp20)
REVERT: F  227 GLU cc_start: 0.9121 (pp20) cc_final: 0.8684 (pp20)
REVERT: F  270 TYR cc_start: 0.9417 (m-80) cc_final: 0.9170 (m-10)
REVERT: F  274 ASP cc_start: 0.9028 (OUTLIER) cc_final: 0.8519 (t0)
REVERT: F  278 LYS cc_start: 0.9140 (mtmm) cc_final: 0.8837 (mttm)
REVERT: G   47 MET cc_start: 0.8531 (mmm) cc_final: 0.8227 (mmm)
REVERT: G  134 GLU cc_start: 0.8280 (tt0) cc_final: 0.7315 (tt0)
REVERT: G  149 GLN cc_start: 0.9188 (mm110) cc_final: 0.8764 (mm110)
REVERT: G  220 GLU cc_start: 0.8719 (pp20) cc_final: 0.8359 (pp20)
REVERT: G  222 THR cc_start: 0.9529 (m) cc_final: 0.9256 (p)
REVERT: G  227 GLU cc_start: 0.9139 (pp20) cc_final: 0.8659 (pp20)
  outliers start: 31
  outliers final: 16
  residues processed: 283
  average time/residue: 0.1155
  time to fit residues: 49.3299
Evaluate side-chains
  273 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 253
  time to evaluate  : 0.558 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  126 MET
Chi-restraints excluded: chain A residue  274 ASP
Chi-restraints excluded: chain B residue   69 LEU
Chi-restraints excluded: chain B residue  153 THR
Chi-restraints excluded: chain B residue  157 THR
Chi-restraints excluded: chain B residue  221 MET
Chi-restraints excluded: chain C residue   91 VAL
Chi-restraints excluded: chain C residue  138 LEU
Chi-restraints excluded: chain D residue  111 LEU
Chi-restraints excluded: chain D residue  155 MET
Chi-restraints excluded: chain D residue  171 ILE
Chi-restraints excluded: chain E residue   23 LEU
Chi-restraints excluded: chain E residue   73 VAL
Chi-restraints excluded: chain E residue  163 ILE
Chi-restraints excluded: chain F residue   73 VAL
Chi-restraints excluded: chain F residue  126 MET
Chi-restraints excluded: chain F residue  138 LEU
Chi-restraints excluded: chain F residue  274 ASP
Chi-restraints excluded: chain G residue   69 LEU
Chi-restraints excluded: chain G residue   73 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 196
   random chunks:
   chunk 187 optimal weight:    0.7980
   chunk 43 optimal weight:    0.9980
   chunk 162 optimal weight:    0.8980
   chunk 133 optimal weight:    0.0970
   chunk 3 optimal weight:   10.0000
   chunk 89 optimal weight:    7.9990
   chunk 76 optimal weight:    0.6980
   chunk 114 optimal weight:    6.9990
   chunk 51 optimal weight:    3.9990
   chunk 110 optimal weight:    0.9980
   chunk 121 optimal weight:    3.9990
   overall best weight:    0.6978

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

Flipped N/Q/H residues before XYZ refinement:
D 149 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3587 r_free = 0.3587 target = 0.108579 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.2946 r_free = 0.2946 target = 0.070291 restraints weight = 35561.927|
|-----------------------------------------------------------------------------|
r_work (start): 0.2826 rms_B_bonded: 3.33
r_work: 0.2678 rms_B_bonded: 4.17 restraints_weight: 0.5000
r_work (final): 0.2678
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8345
moved from start:          0.2215

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  15092  Z= 0.120
  Angle     :  0.573  10.078  20482  Z= 0.289
  Chirality :  0.044   0.270   2513
  Planarity :  0.002   0.023   2604
  Dihedral  :  4.041  19.547   2121
  Min Nonbonded Distance : 2.504

Molprobity Statistics.
  All-atom Clashscore : 5.84
  Ramachandran Plot:
    Outliers :  0.36 %
    Allowed  :  4.98 %
    Favored  : 94.66 %
  Rotamer:
    Outliers :  1.38 %
    Allowed  : 18.12 %
    Favored  : 80.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.20 (0.20), residues: 1946
  helix:  2.71 (0.16), residues: 1071
  sheet:  0.99 (0.31), residues: 294
  loop : -0.75 (0.26), residues: 581

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 180 
 TYR   0.009   0.001   TYR E  27 
 PHE   0.020   0.002   PHE G  80 
 TRP   0.006   0.001   TRP A  16 

Details of bonding type rmsd
  covalent geometry    : bond        0.00253 (15092)
  covalent geometry    : angle       0.57350 (20482)
  hydrogen bonds       : bond        0.03470 ( 1069)
  hydrogen bonds       : angle       3.86275 ( 3105)

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

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

  3892 Ramachandran restraints generated.
    1946 Oldfield, 0 Emsley, 1946 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3892 Ramachandran restraints generated.
    1946 Oldfield, 0 Emsley, 1946 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  291 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 269
  time to evaluate  : 0.564 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   47 MET cc_start: 0.8585 (mmm) cc_final: 0.8359 (mmm)
REVERT: A  134 GLU cc_start: 0.8224 (tt0) cc_final: 0.7685 (tt0)
REVERT: A  149 GLN cc_start: 0.9278 (mm110) cc_final: 0.8869 (mm-40)
REVERT: A  203 GLN cc_start: 0.9321 (tm-30) cc_final: 0.8857 (tm-30)
REVERT: A  210 GLN cc_start: 0.9421 (mm110) cc_final: 0.9204 (mm-40)
REVERT: A  227 GLU cc_start: 0.9046 (pp20) cc_final: 0.8608 (pp20)
REVERT: B   47 MET cc_start: 0.8713 (mmp) cc_final: 0.8439 (mmm)
REVERT: B  134 GLU cc_start: 0.8680 (tt0) cc_final: 0.8374 (tt0)
REVERT: B  149 GLN cc_start: 0.9210 (mm-40) cc_final: 0.8997 (mm-40)
REVERT: B  161 LYS cc_start: 0.9323 (OUTLIER) cc_final: 0.9061 (mmmm)
REVERT: B  203 GLN cc_start: 0.9278 (tm-30) cc_final: 0.8866 (tm-30)
REVERT: B  212 GLU cc_start: 0.9121 (mm-30) cc_final: 0.8841 (tp30)
REVERT: B  278 LYS cc_start: 0.9092 (mtmm) cc_final: 0.8832 (mttp)
REVERT: C   47 MET cc_start: 0.8620 (mmm) cc_final: 0.8310 (mmm)
REVERT: C   56 MET cc_start: 0.8919 (ttm) cc_final: 0.8663 (ttm)
REVERT: C   91 VAL cc_start: 0.7711 (OUTLIER) cc_final: 0.7416 (p)
REVERT: C  134 GLU cc_start: 0.8556 (tt0) cc_final: 0.7953 (tt0)
REVERT: C  149 GLN cc_start: 0.9407 (mm110) cc_final: 0.9031 (mp10)
REVERT: C  181 GLU cc_start: 0.9546 (mm-30) cc_final: 0.9056 (mm-30)
REVERT: C  203 GLN cc_start: 0.9367 (tm-30) cc_final: 0.8874 (tm-30)
REVERT: C  220 GLU cc_start: 0.8836 (pp20) cc_final: 0.8502 (pp20)
REVERT: C  227 GLU cc_start: 0.9020 (pp20) cc_final: 0.8627 (pp20)
REVERT: C  255 GLU cc_start: 0.9470 (tm-30) cc_final: 0.9103 (tm-30)
REVERT: D  181 GLU cc_start: 0.9538 (mm-30) cc_final: 0.9199 (mm-30)
REVERT: D  203 GLN cc_start: 0.9326 (tm-30) cc_final: 0.8890 (tm-30)
REVERT: D  220 GLU cc_start: 0.8861 (pp20) cc_final: 0.8472 (pp20)
REVERT: E   47 MET cc_start: 0.8516 (mmm) cc_final: 0.8111 (mmm)
REVERT: E  149 GLN cc_start: 0.9407 (mm110) cc_final: 0.9036 (mm-40)
REVERT: E  181 GLU cc_start: 0.9567 (mm-30) cc_final: 0.9170 (mm-30)
REVERT: E  203 GLN cc_start: 0.9364 (tm-30) cc_final: 0.8930 (tm-30)
REVERT: E  220 GLU cc_start: 0.8846 (pp20) cc_final: 0.8594 (pp20)
REVERT: E  227 GLU cc_start: 0.8989 (pp20) cc_final: 0.8548 (pp20)
REVERT: F  134 GLU cc_start: 0.8378 (tt0) cc_final: 0.7993 (tt0)
REVERT: F  149 GLN cc_start: 0.9161 (mm-40) cc_final: 0.8958 (mm-40)
REVERT: F  203 GLN cc_start: 0.9302 (tm-30) cc_final: 0.8884 (tm-30)
REVERT: F  220 GLU cc_start: 0.8819 (pp20) cc_final: 0.8489 (pp20)
REVERT: F  227 GLU cc_start: 0.9123 (pp20) cc_final: 0.8680 (pp20)
REVERT: F  270 TYR cc_start: 0.9405 (m-80) cc_final: 0.9153 (m-10)
REVERT: F  274 ASP cc_start: 0.9049 (OUTLIER) cc_final: 0.8331 (t0)
REVERT: F  278 LYS cc_start: 0.9256 (mtmm) cc_final: 0.8931 (mttm)
REVERT: G   47 MET cc_start: 0.8610 (mmm) cc_final: 0.8305 (mmm)
REVERT: G  134 GLU cc_start: 0.8304 (tt0) cc_final: 0.7332 (tt0)
REVERT: G  149 GLN cc_start: 0.9154 (mm110) cc_final: 0.8713 (mm110)
REVERT: G  203 GLN cc_start: 0.9208 (tm-30) cc_final: 0.8933 (tm-30)
REVERT: G  220 GLU cc_start: 0.8762 (pp20) cc_final: 0.8389 (pp20)
REVERT: G  222 THR cc_start: 0.9525 (m) cc_final: 0.9260 (p)
REVERT: G  227 GLU cc_start: 0.9119 (pp20) cc_final: 0.8629 (pp20)
  outliers start: 22
  outliers final: 14
  residues processed: 277
  average time/residue: 0.1177
  time to fit residues: 49.4800
Evaluate side-chains
  278 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 261
  time to evaluate  : 0.527 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  274 ASP
Chi-restraints excluded: chain B residue   69 LEU
Chi-restraints excluded: chain B residue   82 LEU
Chi-restraints excluded: chain B residue  153 THR
Chi-restraints excluded: chain B residue  161 LYS
Chi-restraints excluded: chain C residue   91 VAL
Chi-restraints excluded: chain C residue  138 LEU
Chi-restraints excluded: chain D residue  111 LEU
Chi-restraints excluded: chain D residue  171 ILE
Chi-restraints excluded: chain E residue   23 LEU
Chi-restraints excluded: chain E residue   73 VAL
Chi-restraints excluded: chain E residue  163 ILE
Chi-restraints excluded: chain F residue   73 VAL
Chi-restraints excluded: chain F residue  126 MET
Chi-restraints excluded: chain F residue  138 LEU
Chi-restraints excluded: chain F residue  274 ASP
Chi-restraints excluded: chain G residue   69 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 196
   random chunks:
   chunk 179 optimal weight:    9.9990
   chunk 122 optimal weight:    6.9990
   chunk 21 optimal weight:    0.0570
   chunk 46 optimal weight:    0.8980
   chunk 133 optimal weight:    0.0470
   chunk 19 optimal weight:    0.0770
   chunk 53 optimal weight:    0.6980
   chunk 13 optimal weight:    0.9990
   chunk 152 optimal weight:    0.0670
   chunk 147 optimal weight:    9.9990
   chunk 194 optimal weight:    0.7980
   overall best weight:    0.1892

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3608 r_free = 0.3608 target = 0.109634 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.2979 r_free = 0.2979 target = 0.073008 restraints weight = 35913.001|
|-----------------------------------------------------------------------------|
r_work (start): 0.2873 rms_B_bonded: 3.22
r_work: 0.2719 rms_B_bonded: 3.98 restraints_weight: 0.5000
r_work (final): 0.2719
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8312
moved from start:          0.2323

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034  15092  Z= 0.112
  Angle     :  0.573   9.537  20482  Z= 0.287
  Chirality :  0.044   0.243   2513
  Planarity :  0.002   0.022   2604
  Dihedral  :  3.948  20.691   2121
  Min Nonbonded Distance : 2.532

Molprobity Statistics.
  All-atom Clashscore : 5.74
  Ramachandran Plot:
    Outliers :  0.36 %
    Allowed  :  5.14 %
    Favored  : 94.50 %
  Rotamer:
    Outliers :  1.51 %
    Allowed  : 18.00 %
    Favored  : 80.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.24 (0.20), residues: 1946
  helix:  2.72 (0.16), residues: 1071
  sheet:  0.94 (0.32), residues: 280
  loop : -0.62 (0.26), residues: 595

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG D 180 
 TYR   0.014   0.001   TYR E 135 
 PHE   0.025   0.001   PHE B  80 
 TRP   0.006   0.001   TRP G  16 

Details of bonding type rmsd
  covalent geometry    : bond        0.00226 (15092)
  covalent geometry    : angle       0.57313 (20482)
  hydrogen bonds       : bond        0.03378 ( 1069)
  hydrogen bonds       : angle       3.82112 ( 3105)

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

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

  3892 Ramachandran restraints generated.
    1946 Oldfield, 0 Emsley, 1946 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3892 Ramachandran restraints generated.
    1946 Oldfield, 0 Emsley, 1946 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  304 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 280
  time to evaluate  : 0.550 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   47 MET cc_start: 0.8622 (mmm) cc_final: 0.8376 (mmm)
REVERT: A  134 GLU cc_start: 0.8281 (tt0) cc_final: 0.7777 (tt0)
REVERT: A  149 GLN cc_start: 0.9280 (mm110) cc_final: 0.8868 (mm-40)
REVERT: A  161 LYS cc_start: 0.9323 (mmmm) cc_final: 0.9064 (mtpp)
REVERT: A  203 GLN cc_start: 0.9314 (tm-30) cc_final: 0.8835 (tm-30)
REVERT: A  210 GLN cc_start: 0.9406 (mm110) cc_final: 0.9191 (mm-40)
REVERT: A  227 GLU cc_start: 0.9005 (pp20) cc_final: 0.8602 (pp20)
REVERT: B   47 MET cc_start: 0.8765 (mmp) cc_final: 0.8478 (mmm)
REVERT: B   56 MET cc_start: 0.8933 (mtp) cc_final: 0.8652 (ttm)
REVERT: B  134 GLU cc_start: 0.8688 (tt0) cc_final: 0.8393 (tt0)
REVERT: B  149 GLN cc_start: 0.9284 (mm-40) cc_final: 0.9057 (mm-40)
REVERT: B  157 THR cc_start: 0.9425 (OUTLIER) cc_final: 0.8849 (p)
REVERT: B  161 LYS cc_start: 0.9331 (OUTLIER) cc_final: 0.8853 (mmmm)
REVERT: B  203 GLN cc_start: 0.9271 (tm-30) cc_final: 0.8851 (tm-30)
REVERT: B  212 GLU cc_start: 0.9106 (mm-30) cc_final: 0.8857 (tp30)
REVERT: B  278 LYS cc_start: 0.9138 (mtmm) cc_final: 0.8897 (mttp)
REVERT: C   47 MET cc_start: 0.8618 (mmm) cc_final: 0.8402 (mmm)
REVERT: C   56 MET cc_start: 0.8936 (ttm) cc_final: 0.8698 (ttm)
REVERT: C   91 VAL cc_start: 0.8056 (OUTLIER) cc_final: 0.7833 (p)
REVERT: C  134 GLU cc_start: 0.8595 (tt0) cc_final: 0.8056 (tt0)
REVERT: C  149 GLN cc_start: 0.9378 (mm110) cc_final: 0.8957 (mp10)
REVERT: C  181 GLU cc_start: 0.9520 (mm-30) cc_final: 0.9077 (mm-30)
REVERT: C  203 GLN cc_start: 0.9373 (tm-30) cc_final: 0.8889 (tm-30)
REVERT: C  220 GLU cc_start: 0.8836 (pp20) cc_final: 0.8551 (pp20)
REVERT: C  227 GLU cc_start: 0.9020 (pp20) cc_final: 0.8671 (pp20)
REVERT: C  255 GLU cc_start: 0.9466 (tm-30) cc_final: 0.9069 (tm-30)
REVERT: D  181 GLU cc_start: 0.9490 (mm-30) cc_final: 0.9266 (mm-30)
REVERT: D  203 GLN cc_start: 0.9318 (tm-30) cc_final: 0.8871 (tm-30)
REVERT: D  220 GLU cc_start: 0.8914 (pp20) cc_final: 0.8556 (pp20)
REVERT: D  260 GLU cc_start: 0.9516 (mm-30) cc_final: 0.8985 (mp0)
REVERT: E   47 MET cc_start: 0.8542 (mmm) cc_final: 0.8119 (mmm)
REVERT: E  149 GLN cc_start: 0.9440 (mm110) cc_final: 0.9072 (mm-40)
REVERT: E  181 GLU cc_start: 0.9504 (mm-30) cc_final: 0.9132 (mm-30)
REVERT: E  203 GLN cc_start: 0.9358 (tm-30) cc_final: 0.8921 (tm-30)
REVERT: E  220 GLU cc_start: 0.8854 (pp20) cc_final: 0.8598 (pp20)
REVERT: E  227 GLU cc_start: 0.8969 (pp20) cc_final: 0.8562 (pp20)
REVERT: F  134 GLU cc_start: 0.8455 (tt0) cc_final: 0.8050 (tt0)
REVERT: F  203 GLN cc_start: 0.9277 (tm-30) cc_final: 0.8817 (tm-30)
REVERT: F  220 GLU cc_start: 0.8845 (pp20) cc_final: 0.8520 (pp20)
REVERT: F  227 GLU cc_start: 0.9084 (pp20) cc_final: 0.8655 (pp20)
REVERT: F  270 TYR cc_start: 0.9401 (m-80) cc_final: 0.9140 (m-10)
REVERT: F  274 ASP cc_start: 0.9072 (OUTLIER) cc_final: 0.8358 (t0)
REVERT: G   47 MET cc_start: 0.8647 (mmm) cc_final: 0.8301 (mmm)
REVERT: G  134 GLU cc_start: 0.8373 (tt0) cc_final: 0.7449 (tt0)
REVERT: G  149 GLN cc_start: 0.9190 (mm110) cc_final: 0.8761 (mm110)
REVERT: G  203 GLN cc_start: 0.9195 (tm-30) cc_final: 0.8894 (tm-30)
REVERT: G  210 GLN cc_start: 0.9469 (mm110) cc_final: 0.9153 (mm-40)
REVERT: G  222 THR cc_start: 0.9525 (m) cc_final: 0.9303 (p)
REVERT: G  227 GLU cc_start: 0.9112 (pp20) cc_final: 0.8596 (pp20)
  outliers start: 24
  outliers final: 16
  residues processed: 291
  average time/residue: 0.1094
  time to fit residues: 48.4071
Evaluate side-chains
  281 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 261
  time to evaluate  : 0.583 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   89 VAL
Chi-restraints excluded: chain A residue  115 LEU
Chi-restraints excluded: chain A residue  155 MET
Chi-restraints excluded: chain B residue   69 LEU
Chi-restraints excluded: chain B residue   82 LEU
Chi-restraints excluded: chain B residue  157 THR
Chi-restraints excluded: chain B residue  161 LYS
Chi-restraints excluded: chain C residue   91 VAL
Chi-restraints excluded: chain C residue  115 LEU
Chi-restraints excluded: chain C residue  138 LEU
Chi-restraints excluded: chain D residue  111 LEU
Chi-restraints excluded: chain E residue   23 LEU
Chi-restraints excluded: chain E residue   73 VAL
Chi-restraints excluded: chain E residue  163 ILE
Chi-restraints excluded: chain F residue   73 VAL
Chi-restraints excluded: chain F residue  126 MET
Chi-restraints excluded: chain F residue  138 LEU
Chi-restraints excluded: chain F residue  274 ASP
Chi-restraints excluded: chain G residue   69 LEU
Chi-restraints excluded: chain G residue   73 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 196
   random chunks:
   chunk 191 optimal weight:    0.6980
   chunk 104 optimal weight:    1.9990
   chunk 158 optimal weight:    5.9990
   chunk 38 optimal weight:    6.9990
   chunk 77 optimal weight:    0.0770
   chunk 108 optimal weight:    4.9990
   chunk 101 optimal weight:    0.6980
   chunk 17 optimal weight:    0.9990
   chunk 8 optimal weight:    5.9990
   chunk 160 optimal weight:    0.6980
   chunk 34 optimal weight:    5.9990
   overall best weight:    0.6340

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3606 r_free = 0.3606 target = 0.109462 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.2978 r_free = 0.2978 target = 0.072849 restraints weight = 35894.903|
|-----------------------------------------------------------------------------|
r_work (start): 0.2876 rms_B_bonded: 3.22
r_work: 0.2717 rms_B_bonded: 4.03 restraints_weight: 0.5000
r_work (final): 0.2717
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8335
moved from start:          0.2435

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046  15092  Z= 0.120
  Angle     :  0.581   9.580  20482  Z= 0.293
  Chirality :  0.044   0.240   2513
  Planarity :  0.002   0.024   2604
  Dihedral  :  3.977  20.507   2121
  Min Nonbonded Distance : 2.466

Molprobity Statistics.
  All-atom Clashscore : 5.94
  Ramachandran Plot:
    Outliers :  0.36 %
    Allowed  :  5.09 %
    Favored  : 94.55 %
  Rotamer:
    Outliers :  1.38 %
    Allowed  : 17.94 %
    Favored  : 80.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.22 (0.20), residues: 1946
  helix:  2.71 (0.16), residues: 1071
  sheet:  1.27 (0.34), residues: 245
  loop : -0.70 (0.25), residues: 630

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 180 
 TYR   0.019   0.001   TYR G  27 
 PHE   0.029   0.002   PHE F  80 
 TRP   0.007   0.001   TRP G  16 

Details of bonding type rmsd
  covalent geometry    : bond        0.00256 (15092)
  covalent geometry    : angle       0.58104 (20482)
  hydrogen bonds       : bond        0.03361 ( 1069)
  hydrogen bonds       : angle       3.84328 ( 3105)

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

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

  3892 Ramachandran restraints generated.
    1946 Oldfield, 0 Emsley, 1946 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3892 Ramachandran restraints generated.
    1946 Oldfield, 0 Emsley, 1946 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  290 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 268
  time to evaluate  : 0.573 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   47 MET cc_start: 0.8606 (mmm) cc_final: 0.8372 (mmm)
REVERT: A  134 GLU cc_start: 0.8238 (tt0) cc_final: 0.7732 (tt0)
REVERT: A  149 GLN cc_start: 0.9242 (mm110) cc_final: 0.8824 (mm-40)
REVERT: A  161 LYS cc_start: 0.9337 (mmmm) cc_final: 0.9123 (mtpp)
REVERT: A  203 GLN cc_start: 0.9329 (tm-30) cc_final: 0.8855 (tm-30)
REVERT: A  210 GLN cc_start: 0.9405 (mm110) cc_final: 0.9189 (mm-40)
REVERT: A  227 GLU cc_start: 0.9015 (pp20) cc_final: 0.8636 (pp20)
REVERT: B   47 MET cc_start: 0.8746 (mmp) cc_final: 0.8467 (mmm)
REVERT: B   56 MET cc_start: 0.8919 (mtp) cc_final: 0.8643 (ttm)
REVERT: B  134 GLU cc_start: 0.8624 (tt0) cc_final: 0.8060 (tp30)
REVERT: B  149 GLN cc_start: 0.9301 (mm-40) cc_final: 0.9070 (mm-40)
REVERT: B  187 GLU cc_start: 0.9014 (tt0) cc_final: 0.8696 (tp30)
REVERT: B  203 GLN cc_start: 0.9272 (tm-30) cc_final: 0.8850 (tm-30)
REVERT: B  278 LYS cc_start: 0.9052 (mtmm) cc_final: 0.8669 (mttm)
REVERT: C   56 MET cc_start: 0.8947 (ttm) cc_final: 0.8743 (ttm)
REVERT: C   91 VAL cc_start: 0.7767 (OUTLIER) cc_final: 0.7554 (p)
REVERT: C  134 GLU cc_start: 0.8649 (tt0) cc_final: 0.8300 (tp30)
REVERT: C  149 GLN cc_start: 0.9380 (mm110) cc_final: 0.9014 (mp10)
REVERT: C  181 GLU cc_start: 0.9514 (mm-30) cc_final: 0.9076 (mm-30)
REVERT: C  203 GLN cc_start: 0.9373 (tm-30) cc_final: 0.8890 (tm-30)
REVERT: C  220 GLU cc_start: 0.8862 (pp20) cc_final: 0.8571 (pp20)
REVERT: C  227 GLU cc_start: 0.9033 (pp20) cc_final: 0.8683 (pp20)
REVERT: C  255 GLU cc_start: 0.9477 (tm-30) cc_final: 0.9082 (tm-30)
REVERT: D  181 GLU cc_start: 0.9481 (mm-30) cc_final: 0.9234 (mm-30)
REVERT: D  203 GLN cc_start: 0.9322 (tm-30) cc_final: 0.8878 (tm-30)
REVERT: D  220 GLU cc_start: 0.8908 (pp20) cc_final: 0.8558 (pp20)
REVERT: D  260 GLU cc_start: 0.9502 (mm-30) cc_final: 0.8972 (mp0)
REVERT: D  278 LYS cc_start: 0.9221 (mtmm) cc_final: 0.8806 (mttm)
REVERT: E   47 MET cc_start: 0.8509 (mmm) cc_final: 0.8088 (mmm)
REVERT: E  149 GLN cc_start: 0.9443 (mm110) cc_final: 0.9077 (mm-40)
REVERT: E  181 GLU cc_start: 0.9499 (mm-30) cc_final: 0.9132 (mm-30)
REVERT: E  203 GLN cc_start: 0.9350 (tm-30) cc_final: 0.8919 (tm-30)
REVERT: E  220 GLU cc_start: 0.8859 (pp20) cc_final: 0.8613 (pp20)
REVERT: E  227 GLU cc_start: 0.8982 (pp20) cc_final: 0.8580 (pp20)
REVERT: F  134 GLU cc_start: 0.8433 (tt0) cc_final: 0.8030 (tt0)
REVERT: F  203 GLN cc_start: 0.9296 (tm-30) cc_final: 0.8844 (tm-30)
REVERT: F  220 GLU cc_start: 0.8861 (pp20) cc_final: 0.8537 (pp20)
REVERT: F  227 GLU cc_start: 0.9102 (pp20) cc_final: 0.8699 (pp20)
REVERT: F  270 TYR cc_start: 0.9401 (m-80) cc_final: 0.9152 (m-10)
REVERT: F  274 ASP cc_start: 0.9056 (OUTLIER) cc_final: 0.8342 (t0)
REVERT: G   47 MET cc_start: 0.8641 (mmm) cc_final: 0.8306 (mmm)
REVERT: G  134 GLU cc_start: 0.8331 (tt0) cc_final: 0.7384 (tt0)
REVERT: G  149 GLN cc_start: 0.9203 (mm110) cc_final: 0.8767 (mm110)
REVERT: G  203 GLN cc_start: 0.9215 (tm-30) cc_final: 0.8911 (tm-30)
REVERT: G  210 GLN cc_start: 0.9473 (mm110) cc_final: 0.9168 (mm-40)
REVERT: G  222 THR cc_start: 0.9535 (m) cc_final: 0.9314 (p)
REVERT: G  227 GLU cc_start: 0.9096 (pp20) cc_final: 0.8585 (pp20)
  outliers start: 22
  outliers final: 16
  residues processed: 279
  average time/residue: 0.1151
  time to fit residues: 48.8735
Evaluate side-chains
  280 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 262
  time to evaluate  : 0.549 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   89 VAL
Chi-restraints excluded: chain A residue  115 LEU
Chi-restraints excluded: chain A residue  155 MET
Chi-restraints excluded: chain B residue   69 LEU
Chi-restraints excluded: chain B residue   82 LEU
Chi-restraints excluded: chain C residue   91 VAL
Chi-restraints excluded: chain C residue  115 LEU
Chi-restraints excluded: chain C residue  138 LEU
Chi-restraints excluded: chain D residue  111 LEU
Chi-restraints excluded: chain E residue   23 LEU
Chi-restraints excluded: chain E residue   73 VAL
Chi-restraints excluded: chain E residue  163 ILE
Chi-restraints excluded: chain F residue   73 VAL
Chi-restraints excluded: chain F residue  126 MET
Chi-restraints excluded: chain F residue  138 LEU
Chi-restraints excluded: chain F residue  274 ASP
Chi-restraints excluded: chain G residue   69 LEU
Chi-restraints excluded: chain G residue   73 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 196
   random chunks:
   chunk 193 optimal weight:    0.9980
   chunk 115 optimal weight:    5.9990
   chunk 150 optimal weight:    9.9990
   chunk 172 optimal weight:    6.9990
   chunk 74 optimal weight:    4.9990
   chunk 98 optimal weight:    3.9990
   chunk 122 optimal weight:    9.9990
   chunk 54 optimal weight:    0.9980
   chunk 136 optimal weight:    0.9990
   chunk 149 optimal weight:    5.9990
   chunk 73 optimal weight:    0.9990
   overall best weight:    1.5986

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3584 r_free = 0.3584 target = 0.108091 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.2957 r_free = 0.2957 target = 0.070656 restraints weight = 35491.375|
|-----------------------------------------------------------------------------|
r_work (start): 0.2829 rms_B_bonded: 3.28
r_work: 0.2670 rms_B_bonded: 4.13 restraints_weight: 0.5000
r_work (final): 0.2670
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8364
moved from start:          0.2448

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.068  15092  Z= 0.168
  Angle     :  0.603  15.519  20482  Z= 0.304
  Chirality :  0.044   0.235   2513
  Planarity :  0.002   0.024   2604
  Dihedral  :  4.035  20.983   2121
  Min Nonbonded Distance : 2.464

Molprobity Statistics.
  All-atom Clashscore : 6.34
  Ramachandran Plot:
    Outliers :  0.36 %
    Allowed  :  5.19 %
    Favored  : 94.45 %
  Rotamer:
    Outliers :  1.38 %
    Allowed  : 18.00 %
    Favored  : 80.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.24 (0.20), residues: 1946
  helix:  2.73 (0.16), residues: 1064
  sheet:  1.35 (0.34), residues: 245
  loop : -0.68 (0.25), residues: 637

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG G 259 
 TYR   0.016   0.001   TYR G  27 
 PHE   0.027   0.002   PHE F  80 
 TRP   0.007   0.001   TRP G  16 

Details of bonding type rmsd
  covalent geometry    : bond        0.00378 (15092)
  covalent geometry    : angle       0.60292 (20482)
  hydrogen bonds       : bond        0.03470 ( 1069)
  hydrogen bonds       : angle       3.87279 ( 3105)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3927.68 seconds
wall clock time: 67 minutes 47.35 seconds (4067.35 seconds total)