Starting phenix.real_space_refine
on Fri Jun 13 10:59:40 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8ddj_27337/06_2025/8ddj_27337.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8ddj_27337/06_2025/8ddj_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_27337/06_2025/8ddj_27337.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8ddj_27337/06_2025/8ddj_27337.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8ddj_27337/06_2025/8ddj_27337.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8ddj_27337/06_2025/8ddj_27337.cif"
  }
  resolution = 3.1
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.001
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): 0.05s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 8.85, per 1000 atoms: 0.59
  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: 3.50
  Conformation dependent library (CDL) restraints added in 1.9 seconds
  

  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: 1.61
  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: 5.19

  Time building geometry restraints manager: 4.16 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: 0.02
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:                  0.000
  Normalize map: mean=0, sd=1:             1.130
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.550
  Check model and map are aligned:         0.100
  Set scattering table:                    0.130
  Process input model:                     35.110
  Find NCS groups from input model:        0.600
  Set up NCS constraints:                  0.070
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.910
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   40.610
-------------------------------------------------------------------------------
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 : 8.70
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.06 (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
 TRP   0.009   0.001   TRP D 251 
 PHE   0.040   0.002   PHE F  80 
 TYR   0.014   0.001   TYR F 135 
 ARG   0.002   0.000   ARG G  46 

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

*********************** 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  : 1.547 
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: 0.8874 (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: 0.9076 (tm-30) cc_final: 0.8616 (tm-30)
REVERT: E  227 GLU cc_start: 0.8363 (pp20) cc_final: 0.8098 (pp20)
REVERT: F  134 GLU cc_start: 0.7961 (tt0) cc_final: 0.7412 (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: 0.8064 (pp20)
REVERT: G  134 GLU cc_start: 0.8008 (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: 0.8126 (pp20)
REVERT: G  255 GLU cc_start: 0.9226 (tt0) cc_final: 0.8983 (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: 0.2451
  time to fit residues: 120.5397
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  : 1.588 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 196
   random chunks:
   chunk 165 optimal weight:    0.9980
   chunk 148 optimal weight:    7.9990
   chunk 82 optimal weight:    0.9990
   chunk 50 optimal weight:    0.9980
   chunk 100 optimal weight:    6.9990
   chunk 79 optimal weight:    2.9990
   chunk 153 optimal weight:    6.9990
   chunk 59 optimal weight:   20.0000
   chunk 93 optimal weight:    9.9990
   chunk 114 optimal weight:   20.0000
   chunk 177 optimal weight:    9.9990
   overall best weight:    2.5986

-------------------------------------------------------------------------------
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 = 0.3566 r_free = 0.3566 target = 0.109430 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2926 r_free = 0.2926 target = 0.070542 restraints weight = 34268.759|
|-----------------------------------------------------------------------------|
r_work (start): 0.2790 rms_B_bonded: 3.48
r_work: 0.2637 rms_B_bonded: 4.18 restraints_weight: 0.5000
r_work (final): 0.2637
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8376
moved from start:          0.1259

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.044  15092  Z= 0.238
  Angle     :  0.602   7.932  20482  Z= 0.317
  Chirality :  0.045   0.185   2513
  Planarity :  0.003   0.022   2604
  Dihedral  :  4.195  17.386   2121
  Min Nonbonded Distance : 2.519

Molprobity Statistics.
  All-atom Clashscore : 6.73
  Ramachandran Plot:
    Outliers :  0.36 %
    Allowed  :  5.14 %
    Favored  : 94.50 %
  Rotamer:
    Outliers :  1.01 %
    Allowed  : 10.57 %
    Favored  : 88.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.08 (0.19), residues: 1946
  helix:  2.72 (0.16), residues: 1043
  sheet:  1.14 (0.30), residues: 273
  loop : -0.91 (0.25), residues: 630

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP G  16 
 PHE   0.028   0.002   PHE F  80 
 TYR   0.007   0.001   TYR E 135 
 ARG   0.002   0.000   ARG C 156 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04274 ( 1069)
  hydrogen bonds       : angle       4.52210 ( 3105)
  covalent geometry    : bond        0.00532 (15092)
  covalent geometry    : angle       0.60239 (20482)

*********************** 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
  312 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 296
  time to evaluate  : 1.749 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  134 GLU cc_start: 0.8404 (tt0) cc_final: 0.8032 (tt0)
REVERT: A  149 GLN cc_start: 0.9036 (mm110) cc_final: 0.8783 (mm-40)
REVERT: A  203 GLN cc_start: 0.9286 (tm-30) cc_final: 0.8927 (tm-30)
REVERT: A  220 GLU cc_start: 0.8665 (pp20) cc_final: 0.8389 (pp20)
REVERT: A  227 GLU cc_start: 0.9074 (pp20) cc_final: 0.8607 (pp20)
REVERT: B   47 MET cc_start: 0.8798 (mmp) cc_final: 0.8551 (mmm)
REVERT: B  112 GLN cc_start: 0.9229 (tm-30) cc_final: 0.8922 (tm-30)
REVERT: B  134 GLU cc_start: 0.8775 (tt0) cc_final: 0.7931 (tt0)
REVERT: B  203 GLN cc_start: 0.9243 (tm-30) cc_final: 0.8870 (tm-30)
REVERT: B  260 GLU cc_start: 0.9144 (mp0) cc_final: 0.8631 (mp0)
REVERT: C   56 MET cc_start: 0.8880 (ttm) cc_final: 0.8646 (ttm)
REVERT: C  112 GLN cc_start: 0.9193 (tp40) cc_final: 0.8992 (tp40)
REVERT: C  134 GLU cc_start: 0.8445 (tt0) cc_final: 0.8130 (tt0)
REVERT: C  149 GLN cc_start: 0.9358 (mm110) cc_final: 0.9025 (mm110)
REVERT: C  181 GLU cc_start: 0.9527 (mm-30) cc_final: 0.9108 (mm-30)
REVERT: C  203 GLN cc_start: 0.9365 (tm-30) cc_final: 0.8966 (tm-30)
REVERT: C  220 GLU cc_start: 0.8717 (pp20) cc_final: 0.8412 (pp20)
REVERT: D  203 GLN cc_start: 0.9335 (tm-30) cc_final: 0.8954 (tm-30)
REVERT: D  220 GLU cc_start: 0.8786 (pp20) cc_final: 0.8450 (pp20)
REVERT: D  255 GLU cc_start: 0.9584 (tt0) cc_final: 0.9111 (tm-30)
REVERT: E   55 LEU cc_start: 0.9247 (tt) cc_final: 0.8962 (mm)
REVERT: E  149 GLN cc_start: 0.9377 (mm110) cc_final: 0.9009 (mm110)
REVERT: E  203 GLN cc_start: 0.9296 (tm-30) cc_final: 0.8931 (tm-30)
REVERT: E  220 GLU cc_start: 0.8719 (pp20) cc_final: 0.8491 (pp20)
REVERT: E  260 GLU cc_start: 0.9566 (mm-30) cc_final: 0.9350 (mm-30)
REVERT: F  126 MET cc_start: 0.9443 (ppp) cc_final: 0.9201 (tmm)
REVERT: F  134 GLU cc_start: 0.8422 (tt0) cc_final: 0.8081 (tt0)
REVERT: F  203 GLN cc_start: 0.9265 (tm-30) cc_final: 0.8943 (tm-30)
REVERT: F  220 GLU cc_start: 0.8802 (pp20) cc_final: 0.8511 (pp20)
REVERT: F  227 GLU cc_start: 0.9106 (pp20) cc_final: 0.8686 (pp20)
REVERT: G   47 MET cc_start: 0.8661 (mmm) cc_final: 0.8414 (mmm)
REVERT: G  134 GLU cc_start: 0.8569 (tt0) cc_final: 0.8079 (tt0)
REVERT: G  149 GLN cc_start: 0.9076 (mm110) cc_final: 0.8824 (mm-40)
REVERT: G  220 GLU cc_start: 0.8759 (pp20) cc_final: 0.8517 (pp20)
REVERT: G  227 GLU cc_start: 0.9166 (pp20) cc_final: 0.8618 (pp20)
  outliers start: 16
  outliers final: 11
  residues processed: 299
  average time/residue: 0.2452
  time to fit residues: 110.3543
Evaluate side-chains
  285 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 274
  time to evaluate  : 1.723 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  154 THR
Chi-restraints excluded: chain B residue   69 LEU
Chi-restraints excluded: chain C residue  122 VAL
Chi-restraints excluded: chain C residue  138 LEU
Chi-restraints excluded: chain E residue   73 VAL
Chi-restraints excluded: chain E residue  153 THR
Chi-restraints excluded: chain F residue  153 THR
Chi-restraints excluded: chain G residue   23 LEU
Chi-restraints excluded: chain G residue   69 LEU
Chi-restraints excluded: chain G residue  122 VAL
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 70 optimal weight:    0.9980
   chunk 104 optimal weight:    0.0370
   chunk 129 optimal weight:    1.9990
   chunk 179 optimal weight:    1.9990
   chunk 25 optimal weight:    0.9980
   chunk 109 optimal weight:    1.9990
   chunk 122 optimal weight:   10.0000
   chunk 135 optimal weight:    1.9990
   chunk 98 optimal weight:    1.9990
   chunk 50 optimal weight:    2.9990
   chunk 33 optimal weight:    0.7980
   overall best weight:    0.9660

-------------------------------------------------------------------------------
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 = 0.3586 r_free = 0.3586 target = 0.108611 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.2954 r_free = 0.2954 target = 0.070263 restraints weight = 34937.179|
|-----------------------------------------------------------------------------|
r_work (start): 0.2843 rms_B_bonded: 3.39
r_work: 0.2692 rms_B_bonded: 4.16 restraints_weight: 0.5000
r_work (final): 0.2692
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8376
moved from start:          0.1473

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031  15092  Z= 0.129
  Angle     :  0.559   8.472  20482  Z= 0.287
  Chirality :  0.044   0.191   2513
  Planarity :  0.003   0.021   2604
  Dihedral  :  4.083  17.035   2121
  Min Nonbonded Distance : 2.561

Molprobity Statistics.
  All-atom Clashscore : 6.17
  Ramachandran Plot:
    Outliers :  0.36 %
    Allowed  :  5.09 %
    Favored  : 94.55 %
  Rotamer:
    Outliers :  1.13 %
    Allowed  : 14.73 %
    Favored  : 84.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.99 (0.19), residues: 1946
  helix:  2.62 (0.16), residues: 1064
  sheet:  1.14 (0.31), residues: 259
  loop : -1.00 (0.24), residues: 623

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP G  16 
 PHE   0.022   0.001   PHE G  80 
 TYR   0.005   0.001   TYR D 135 
 ARG   0.002   0.000   ARG F 180 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03853 ( 1069)
  hydrogen bonds       : angle       4.26279 ( 3105)
  covalent geometry    : bond        0.00269 (15092)
  covalent geometry    : angle       0.55918 (20482)

*********************** 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
  297 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 279
  time to evaluate  : 1.620 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  134 GLU cc_start: 0.8368 (tt0) cc_final: 0.7917 (tt0)
REVERT: A  149 GLN cc_start: 0.9075 (mm110) cc_final: 0.8783 (mm-40)
REVERT: A  203 GLN cc_start: 0.9294 (tm-30) cc_final: 0.8865 (tm-30)
REVERT: A  220 GLU cc_start: 0.8709 (pp20) cc_final: 0.8389 (pp20)
REVERT: A  227 GLU cc_start: 0.9039 (pp20) cc_final: 0.8581 (pp20)
REVERT: B   47 MET cc_start: 0.8747 (mmp) cc_final: 0.8479 (mmm)
REVERT: B  112 GLN cc_start: 0.9247 (tm-30) cc_final: 0.8969 (tm-30)
REVERT: B  134 GLU cc_start: 0.8851 (tt0) cc_final: 0.8470 (tt0)
REVERT: B  203 GLN cc_start: 0.9237 (tm-30) cc_final: 0.8856 (tm-30)
REVERT: B  278 LYS cc_start: 0.9199 (mtmm) cc_final: 0.8897 (mttp)
REVERT: C  134 GLU cc_start: 0.8563 (tt0) cc_final: 0.8138 (tt0)
REVERT: C  149 GLN cc_start: 0.9387 (mm110) cc_final: 0.9069 (mm110)
REVERT: C  176 ILE cc_start: 0.9388 (mm) cc_final: 0.9186 (mm)
REVERT: C  181 GLU cc_start: 0.9514 (mm-30) cc_final: 0.9057 (mm-30)
REVERT: C  203 GLN cc_start: 0.9360 (tm-30) cc_final: 0.8930 (tm-30)
REVERT: C  220 GLU cc_start: 0.8772 (pp20) cc_final: 0.8457 (pp20)
REVERT: D  203 GLN cc_start: 0.9328 (tm-30) cc_final: 0.8918 (tm-30)
REVERT: D  220 GLU cc_start: 0.8810 (pp20) cc_final: 0.8476 (pp20)
REVERT: D  255 GLU cc_start: 0.9565 (tt0) cc_final: 0.9071 (tm-30)
REVERT: D  260 GLU cc_start: 0.9067 (mp0) cc_final: 0.8690 (mp0)
REVERT: D  273 MET cc_start: 0.8626 (OUTLIER) cc_final: 0.8233 (ptm)
REVERT: E   47 MET cc_start: 0.8725 (mmm) cc_final: 0.8375 (mmm)
REVERT: E   55 LEU cc_start: 0.9250 (tt) cc_final: 0.8990 (mm)
REVERT: E  149 GLN cc_start: 0.9405 (mm110) cc_final: 0.9031 (mm110)
REVERT: E  203 GLN cc_start: 0.9314 (tm-30) cc_final: 0.8951 (tm-30)
REVERT: E  220 GLU cc_start: 0.8753 (pp20) cc_final: 0.8483 (pp20)
REVERT: F  134 GLU cc_start: 0.8479 (tt0) cc_final: 0.8109 (tt0)
REVERT: F  203 GLN cc_start: 0.9264 (tm-30) cc_final: 0.8901 (tm-30)
REVERT: F  220 GLU cc_start: 0.8858 (pp20) cc_final: 0.8543 (pp20)
REVERT: F  227 GLU cc_start: 0.9138 (pp20) cc_final: 0.8705 (pp20)
REVERT: G   47 MET cc_start: 0.8646 (mmm) cc_final: 0.8360 (mmm)
REVERT: G  134 GLU cc_start: 0.8526 (tt0) cc_final: 0.7779 (tt0)
REVERT: G  149 GLN cc_start: 0.9065 (mm110) cc_final: 0.8758 (mm-40)
REVERT: G  220 GLU cc_start: 0.8810 (pp20) cc_final: 0.8548 (pp20)
REVERT: G  227 GLU cc_start: 0.9148 (pp20) cc_final: 0.8607 (pp20)
REVERT: G  255 GLU cc_start: 0.9543 (tt0) cc_final: 0.9033 (tm-30)
REVERT: G  260 GLU cc_start: 0.9181 (mp0) cc_final: 0.8520 (mp0)
  outliers start: 18
  outliers final: 10
  residues processed: 285
  average time/residue: 0.2549
  time to fit residues: 109.1012
Evaluate side-chains
  273 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 262
  time to evaluate  : 1.773 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  126 MET
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  138 LEU
Chi-restraints excluded: chain D residue  111 LEU
Chi-restraints excluded: chain D residue  273 MET
Chi-restraints excluded: chain E residue   73 VAL
Chi-restraints excluded: chain F residue   73 VAL
Chi-restraints excluded: chain G residue   23 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 196
   random chunks:
   chunk 124 optimal weight:    0.6980
   chunk 132 optimal weight:    0.0570
   chunk 26 optimal weight:    0.8980
   chunk 69 optimal weight:    6.9990
   chunk 165 optimal weight:    2.9990
   chunk 59 optimal weight:    9.9990
   chunk 36 optimal weight:    0.9990
   chunk 82 optimal weight:    3.9990
   chunk 78 optimal weight:    0.0970
   chunk 74 optimal weight:    5.9990
   chunk 166 optimal weight:    2.9990
   overall best weight:    0.5498

-------------------------------------------------------------------------------
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 = 0.3595 r_free = 0.3595 target = 0.108974 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.2952 r_free = 0.2952 target = 0.070338 restraints weight = 35111.894|
|-----------------------------------------------------------------------------|
r_work (start): 0.2841 rms_B_bonded: 3.33
r_work: 0.2692 rms_B_bonded: 4.12 restraints_weight: 0.5000
r_work (final): 0.2692
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8333
moved from start:          0.1690

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031  15092  Z= 0.109
  Angle     :  0.534   9.525  20482  Z= 0.272
  Chirality :  0.043   0.177   2513
  Planarity :  0.002   0.024   2604
  Dihedral  :  3.935  17.530   2121
  Min Nonbonded Distance : 2.515

Molprobity Statistics.
  All-atom Clashscore : 5.65
  Ramachandran Plot:
    Outliers :  0.36 %
    Allowed  :  5.19 %
    Favored  : 94.45 %
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.10 (0.19), residues: 1946
  helix:  2.73 (0.16), residues: 1064
  sheet:  0.85 (0.30), residues: 294
  loop : -0.91 (0.25), residues: 588

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP G  16 
 PHE   0.023   0.001   PHE F  80 
 TYR   0.004   0.001   TYR B 194 
 ARG   0.002   0.000   ARG D 180 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03562 ( 1069)
  hydrogen bonds       : angle       4.02445 ( 3105)
  covalent geometry    : bond        0.00217 (15092)
  covalent geometry    : angle       0.53419 (20482)

*********************** 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
  316 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 282
  time to evaluate  : 1.714 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  134 GLU cc_start: 0.8328 (tt0) cc_final: 0.7894 (tt0)
REVERT: A  149 GLN cc_start: 0.9143 (mm110) cc_final: 0.8795 (mm-40)
REVERT: A  203 GLN cc_start: 0.9300 (tm-30) cc_final: 0.8844 (tm-30)
REVERT: A  210 GLN cc_start: 0.9486 (mm110) cc_final: 0.9186 (mm-40)
REVERT: A  220 GLU cc_start: 0.8711 (pp20) cc_final: 0.8380 (pp20)
REVERT: A  227 GLU cc_start: 0.9055 (pp20) cc_final: 0.8640 (pp20)
REVERT: B   47 MET cc_start: 0.8716 (mmp) cc_final: 0.8456 (mmm)
REVERT: B   74 ARG cc_start: 0.7357 (ttp-110) cc_final: 0.7082 (ttm170)
REVERT: B  134 GLU cc_start: 0.8805 (tt0) cc_final: 0.8558 (tt0)
REVERT: B  157 THR cc_start: 0.9558 (OUTLIER) cc_final: 0.9119 (p)
REVERT: B  203 GLN cc_start: 0.9246 (tm-30) cc_final: 0.8839 (tm-30)
REVERT: B  278 LYS cc_start: 0.9214 (mtmm) cc_final: 0.8635 (mttm)
REVERT: C   47 MET cc_start: 0.8679 (mmm) cc_final: 0.8310 (mmm)
REVERT: C  134 GLU cc_start: 0.8529 (tt0) cc_final: 0.8072 (tt0)
REVERT: C  149 GLN cc_start: 0.9391 (mm110) cc_final: 0.9050 (mm110)
REVERT: C  181 GLU cc_start: 0.9491 (mm-30) cc_final: 0.9106 (mm-30)
REVERT: C  203 GLN cc_start: 0.9360 (tm-30) cc_final: 0.8892 (tm-30)
REVERT: C  220 GLU cc_start: 0.8814 (pp20) cc_final: 0.8476 (pp20)
REVERT: D  181 GLU cc_start: 0.9549 (mm-30) cc_final: 0.9082 (mm-30)
REVERT: D  203 GLN cc_start: 0.9325 (tm-30) cc_final: 0.8907 (tm-30)
REVERT: D  220 GLU cc_start: 0.8876 (pp20) cc_final: 0.8510 (pp20)
REVERT: E   47 MET cc_start: 0.8544 (mmm) cc_final: 0.8186 (mmm)
REVERT: E   55 LEU cc_start: 0.9241 (tt) cc_final: 0.8976 (mm)
REVERT: E  149 GLN cc_start: 0.9401 (mm110) cc_final: 0.9032 (mm110)
REVERT: E  203 GLN cc_start: 0.9356 (tm-30) cc_final: 0.8949 (tm-30)
REVERT: E  220 GLU cc_start: 0.8786 (pp20) cc_final: 0.8491 (pp20)
REVERT: E  227 GLU cc_start: 0.9079 (pp20) cc_final: 0.8676 (pp20)
REVERT: F  134 GLU cc_start: 0.8389 (tt0) cc_final: 0.8007 (tp30)
REVERT: F  203 GLN cc_start: 0.9265 (tm-30) cc_final: 0.8856 (tm-30)
REVERT: F  220 GLU cc_start: 0.8883 (pp20) cc_final: 0.8532 (pp20)
REVERT: F  227 GLU cc_start: 0.9122 (pp20) cc_final: 0.8711 (pp20)
REVERT: F  274 ASP cc_start: 0.8987 (OUTLIER) cc_final: 0.8523 (t0)
REVERT: G   47 MET cc_start: 0.8664 (mmm) cc_final: 0.8374 (mmm)
REVERT: G  134 GLU cc_start: 0.8543 (tt0) cc_final: 0.7699 (tt0)
REVERT: G  149 GLN cc_start: 0.9133 (mm110) cc_final: 0.8768 (mm-40)
REVERT: G  220 GLU cc_start: 0.8787 (pp20) cc_final: 0.8432 (pp20)
REVERT: G  222 THR cc_start: 0.9527 (m) cc_final: 0.9254 (p)
REVERT: G  227 GLU cc_start: 0.9143 (pp20) cc_final: 0.8603 (pp20)
REVERT: G  255 GLU cc_start: 0.9548 (tt0) cc_final: 0.9032 (tm-30)
  outliers start: 34
  outliers final: 13
  residues processed: 301
  average time/residue: 0.2480
  time to fit residues: 111.6781
Evaluate side-chains
  284 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 269
  time to evaluate  : 1.557 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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 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  118 LEU
Chi-restraints excluded: chain F residue  126 MET
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 17 optimal weight:    5.9990
   chunk 43 optimal weight:    7.9990
   chunk 139 optimal weight:    2.9990
   chunk 140 optimal weight:   40.0000
   chunk 109 optimal weight:    3.9990
   chunk 137 optimal weight:    1.9990
   chunk 27 optimal weight:    3.9990
   chunk 142 optimal weight:   20.0000
   chunk 1 optimal weight:   20.0000
   chunk 124 optimal weight:    0.5980
   chunk 186 optimal weight:    3.9990
   overall best weight:    2.7188

-------------------------------------------------------------------------------
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 = 0.3544 r_free = 0.3544 target = 0.106112 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.2891 r_free = 0.2891 target = 0.069218 restraints weight = 36807.843|
|-----------------------------------------------------------------------------|
r_work (start): 0.2786 rms_B_bonded: 3.20
r_work: 0.2637 rms_B_bonded: 4.08 restraints_weight: 0.5000
r_work (final): 0.2637
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8378
moved from start:          0.1833

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.068  15092  Z= 0.248
  Angle     :  0.581   8.027  20482  Z= 0.302
  Chirality :  0.044   0.186   2513
  Planarity :  0.003   0.024   2604
  Dihedral  :  4.077  20.596   2121
  Min Nonbonded Distance : 2.454

Molprobity Statistics.
  All-atom Clashscore : 6.37
  Ramachandran Plot:
    Outliers :  0.36 %
    Allowed  :  4.98 %
    Favored  : 94.66 %
  Rotamer:
    Outliers :  2.01 %
    Allowed  : 15.98 %
    Favored  : 82.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.13 (0.20), residues: 1946
  helix:  2.71 (0.16), residues: 1071
  sheet:  0.80 (0.29), residues: 308
  loop : -0.87 (0.26), residues: 567

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP G  16 
 PHE   0.026   0.002   PHE F  80 
 TYR   0.005   0.001   TYR C 194 
 ARG   0.004   0.000   ARG G 256 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03643 ( 1069)
  hydrogen bonds       : angle       4.03492 ( 3105)
  covalent geometry    : bond        0.00549 (15092)
  covalent geometry    : angle       0.58079 (20482)

*********************** 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
  297 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 265
  time to evaluate  : 1.557 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  134 GLU cc_start: 0.8202 (tt0) cc_final: 0.7721 (tt0)
REVERT: A  149 GLN cc_start: 0.9183 (mm110) cc_final: 0.8841 (mm-40)
REVERT: A  203 GLN cc_start: 0.9324 (tm-30) cc_final: 0.8899 (tm-30)
REVERT: A  220 GLU cc_start: 0.8732 (pp20) cc_final: 0.8381 (pp20)
REVERT: A  227 GLU cc_start: 0.9099 (pp20) cc_final: 0.8654 (pp20)
REVERT: B   47 MET cc_start: 0.8723 (mmp) cc_final: 0.8459 (mmm)
REVERT: B   56 MET cc_start: 0.8932 (mtp) cc_final: 0.8705 (mtm)
REVERT: B   69 LEU cc_start: 0.9277 (OUTLIER) cc_final: 0.9050 (pp)
REVERT: B   74 ARG cc_start: 0.7280 (ttp-110) cc_final: 0.7037 (ttm170)
REVERT: B  134 GLU cc_start: 0.8711 (tt0) cc_final: 0.8427 (tt0)
REVERT: B  157 THR cc_start: 0.9553 (OUTLIER) cc_final: 0.9068 (p)
REVERT: B  203 GLN cc_start: 0.9268 (tm-30) cc_final: 0.8876 (tm-30)
REVERT: C   47 MET cc_start: 0.8703 (mmm) cc_final: 0.8320 (mmm)
REVERT: C  134 GLU cc_start: 0.8483 (tt0) cc_final: 0.7983 (tt0)
REVERT: C  149 GLN cc_start: 0.9396 (mm110) cc_final: 0.9007 (mm110)
REVERT: C  181 GLU cc_start: 0.9540 (mm-30) cc_final: 0.9023 (mm-30)
REVERT: C  203 GLN cc_start: 0.9371 (tm-30) cc_final: 0.8905 (tm-30)
REVERT: C  220 GLU cc_start: 0.8842 (pp20) cc_final: 0.8478 (pp20)
REVERT: D  181 GLU cc_start: 0.9567 (mm-30) cc_final: 0.9079 (mm-30)
REVERT: D  203 GLN cc_start: 0.9343 (tm-30) cc_final: 0.8923 (tm-30)
REVERT: D  220 GLU cc_start: 0.8864 (pp20) cc_final: 0.8487 (pp20)
REVERT: D  255 GLU cc_start: 0.9566 (tt0) cc_final: 0.9112 (tm-30)
REVERT: D  260 GLU cc_start: 0.9476 (mm-30) cc_final: 0.8942 (mp0)
REVERT: E   47 MET cc_start: 0.8547 (mmm) cc_final: 0.8161 (mmm)
REVERT: E   55 LEU cc_start: 0.9257 (tt) cc_final: 0.8987 (mm)
REVERT: E  134 GLU cc_start: 0.8794 (pm20) cc_final: 0.8409 (pm20)
REVERT: E  149 GLN cc_start: 0.9398 (mm110) cc_final: 0.8980 (mm110)
REVERT: E  203 GLN cc_start: 0.9338 (tm-30) cc_final: 0.8963 (tm-30)
REVERT: E  220 GLU cc_start: 0.8833 (pp20) cc_final: 0.8608 (pp20)
REVERT: E  227 GLU cc_start: 0.9095 (pp20) cc_final: 0.8712 (pp20)
REVERT: F  134 GLU cc_start: 0.8388 (tt0) cc_final: 0.8033 (tt0)
REVERT: F  203 GLN cc_start: 0.9314 (tm-30) cc_final: 0.8923 (tm-30)
REVERT: F  220 GLU cc_start: 0.8853 (pp20) cc_final: 0.8490 (pp20)
REVERT: F  227 GLU cc_start: 0.9126 (pp20) cc_final: 0.8705 (pp20)
REVERT: F  270 TYR cc_start: 0.9439 (m-80) cc_final: 0.9178 (m-10)
REVERT: G   47 MET cc_start: 0.8592 (mmm) cc_final: 0.8274 (mmm)
REVERT: G  134 GLU cc_start: 0.8326 (tt0) cc_final: 0.7465 (tt0)
REVERT: G  149 GLN cc_start: 0.9158 (mm110) cc_final: 0.8769 (mm-40)
REVERT: G  220 GLU cc_start: 0.8737 (pp20) cc_final: 0.8446 (pp20)
REVERT: G  227 GLU cc_start: 0.9160 (pp20) cc_final: 0.8650 (pp20)
REVERT: G  255 GLU cc_start: 0.9563 (tt0) cc_final: 0.9045 (tm-30)
  outliers start: 32
  outliers final: 19
  residues processed: 276
  average time/residue: 0.2507
  time to fit residues: 102.6260
Evaluate side-chains
  279 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 258
  time to evaluate  : 1.711 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  126 MET
Chi-restraints excluded: chain A residue  153 THR
Chi-restraints excluded: chain A residue  155 MET
Chi-restraints excluded: chain A residue  255 GLU
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 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  126 MET
Chi-restraints excluded: chain G residue   73 VAL
Chi-restraints excluded: chain G residue  136 VAL
Chi-restraints excluded: chain G residue  153 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 196
   random chunks:
   chunk 153 optimal weight:    6.9990
   chunk 157 optimal weight:    0.9980
   chunk 188 optimal weight:    1.9990
   chunk 127 optimal weight:    2.9990
   chunk 62 optimal weight:    6.9990
   chunk 51 optimal weight:    2.9990
   chunk 102 optimal weight:    3.9990
   chunk 130 optimal weight:    2.9990
   chunk 33 optimal weight:    5.9990
   chunk 58 optimal weight:    2.9990
   chunk 55 optimal weight:    0.6980
   overall best weight:    1.9386

-------------------------------------------------------------------------------
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 = 0.3554 r_free = 0.3554 target = 0.107206 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2908 r_free = 0.2908 target = 0.069006 restraints weight = 35284.914|
|-----------------------------------------------------------------------------|
r_work (start): 0.2791 rms_B_bonded: 3.37
r_work: 0.2633 rms_B_bonded: 4.19 restraints_weight: 0.5000
r_work (final): 0.2633
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8378
moved from start:          0.1966

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050  15092  Z= 0.186
  Angle     :  0.576  11.634  20482  Z= 0.293
  Chirality :  0.044   0.274   2513
  Planarity :  0.002   0.023   2604
  Dihedral  :  4.187  25.335   2121
  Min Nonbonded Distance : 2.511

Molprobity Statistics.
  All-atom Clashscore : 5.91
  Ramachandran Plot:
    Outliers :  0.36 %
    Allowed  :  4.98 %
    Favored  : 94.66 %
  Rotamer:
    Outliers :  1.64 %
    Allowed  : 16.99 %
    Favored  : 81.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.11 (0.19), residues: 1946
  helix:  2.66 (0.16), residues: 1071
  sheet:  0.94 (0.30), residues: 294
  loop : -0.85 (0.26), residues: 581

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP G  16 
 PHE   0.021   0.002   PHE G  80 
 TYR   0.005   0.001   TYR B 194 
 ARG   0.002   0.000   ARG B 156 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03594 ( 1069)
  hydrogen bonds       : angle       3.96391 ( 3105)
  covalent geometry    : bond        0.00412 (15092)
  covalent geometry    : angle       0.57618 (20482)

*********************** 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
  285 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 259
  time to evaluate  : 1.646 
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  126 MET cc_start: 0.9392 (OUTLIER) cc_final: 0.9178 (tmm)
REVERT: A  134 GLU cc_start: 0.8161 (tt0) cc_final: 0.7633 (tt0)
REVERT: A  149 GLN cc_start: 0.9199 (mm110) cc_final: 0.8858 (mm-40)
REVERT: A  203 GLN cc_start: 0.9339 (tm-30) cc_final: 0.8904 (tm-30)
REVERT: A  220 GLU cc_start: 0.8738 (pp20) cc_final: 0.8387 (pp20)
REVERT: A  227 GLU cc_start: 0.9072 (pp20) cc_final: 0.8588 (pp20)
REVERT: B   47 MET cc_start: 0.8720 (mmp) cc_final: 0.8457 (mmm)
REVERT: B   56 MET cc_start: 0.8920 (mtp) cc_final: 0.8663 (mtm)
REVERT: B   69 LEU cc_start: 0.9301 (OUTLIER) cc_final: 0.9053 (pp)
REVERT: B   74 ARG cc_start: 0.7266 (ttp-110) cc_final: 0.7021 (ttm170)
REVERT: B  134 GLU cc_start: 0.8726 (tt0) cc_final: 0.8413 (tt0)
REVERT: B  157 THR cc_start: 0.9544 (OUTLIER) cc_final: 0.9199 (p)
REVERT: B  161 LYS cc_start: 0.9315 (OUTLIER) cc_final: 0.8834 (mmtm)
REVERT: B  203 GLN cc_start: 0.9293 (tm-30) cc_final: 0.8890 (tm-30)
REVERT: B  278 LYS cc_start: 0.9180 (mtmm) cc_final: 0.8918 (mttp)
REVERT: C   47 MET cc_start: 0.8704 (mmm) cc_final: 0.8330 (mmm)
REVERT: C   91 VAL cc_start: 0.7952 (OUTLIER) cc_final: 0.7674 (p)
REVERT: C  134 GLU cc_start: 0.8472 (tt0) cc_final: 0.7968 (tt0)
REVERT: C  149 GLN cc_start: 0.9399 (mm110) cc_final: 0.9153 (mm-40)
REVERT: C  181 GLU cc_start: 0.9565 (mm-30) cc_final: 0.9059 (mm-30)
REVERT: C  203 GLN cc_start: 0.9370 (tm-30) cc_final: 0.8893 (tm-30)
REVERT: C  220 GLU cc_start: 0.8861 (pp20) cc_final: 0.8508 (pp20)
REVERT: C  227 GLU cc_start: 0.9084 (pp20) cc_final: 0.8685 (pp20)
REVERT: D  134 GLU cc_start: 0.8731 (pm20) cc_final: 0.8527 (pm20)
REVERT: D  181 GLU cc_start: 0.9573 (mm-30) cc_final: 0.9170 (mm-30)
REVERT: D  203 GLN cc_start: 0.9352 (tm-30) cc_final: 0.8928 (tm-30)
REVERT: D  220 GLU cc_start: 0.8855 (pp20) cc_final: 0.8474 (pp20)
REVERT: D  255 GLU cc_start: 0.9574 (tt0) cc_final: 0.9115 (tm-30)
REVERT: D  260 GLU cc_start: 0.9521 (mm-30) cc_final: 0.8972 (mp0)
REVERT: E   47 MET cc_start: 0.8521 (mmm) cc_final: 0.8117 (mmm)
REVERT: E  134 GLU cc_start: 0.8696 (pm20) cc_final: 0.8469 (pm20)
REVERT: E  149 GLN cc_start: 0.9395 (mm110) cc_final: 0.9038 (mm-40)
REVERT: E  203 GLN cc_start: 0.9341 (tm-30) cc_final: 0.8930 (tm-30)
REVERT: E  220 GLU cc_start: 0.8827 (pp20) cc_final: 0.8587 (pp20)
REVERT: E  227 GLU cc_start: 0.9045 (pp20) cc_final: 0.8629 (pp20)
REVERT: F  134 GLU cc_start: 0.8336 (tt0) cc_final: 0.7920 (tt0)
REVERT: F  203 GLN cc_start: 0.9321 (tm-30) cc_final: 0.8921 (tm-30)
REVERT: F  220 GLU cc_start: 0.8837 (pp20) cc_final: 0.8469 (pp20)
REVERT: F  227 GLU cc_start: 0.9120 (pp20) cc_final: 0.8717 (pp20)
REVERT: F  270 TYR cc_start: 0.9429 (m-80) cc_final: 0.9179 (m-10)
REVERT: F  274 ASP cc_start: 0.8972 (OUTLIER) cc_final: 0.8485 (t0)
REVERT: G   47 MET cc_start: 0.8528 (mmm) cc_final: 0.8215 (mmm)
REVERT: G  134 GLU cc_start: 0.8254 (tt0) cc_final: 0.7331 (tt0)
REVERT: G  149 GLN cc_start: 0.9189 (mm110) cc_final: 0.8774 (mm110)
REVERT: G  203 GLN cc_start: 0.9230 (tm-30) cc_final: 0.8907 (tm-30)
REVERT: G  220 GLU cc_start: 0.8734 (pp20) cc_final: 0.8384 (pp20)
REVERT: G  222 THR cc_start: 0.9538 (m) cc_final: 0.9261 (p)
REVERT: G  227 GLU cc_start: 0.9162 (pp20) cc_final: 0.8677 (pp20)
REVERT: G  255 GLU cc_start: 0.9560 (tt0) cc_final: 0.9065 (tm-30)
  outliers start: 26
  outliers final: 17
  residues processed: 269
  average time/residue: 0.2592
  time to fit residues: 103.3946
Evaluate side-chains
  276 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 253
  time to evaluate  : 1.637 
-------------------------------------------------------------------------------
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    1 MET
Chi-restraints excluded: chain B residue   69 LEU
Chi-restraints excluded: chain B residue  105 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  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 E residue  154 THR
Chi-restraints excluded: chain F residue   73 VAL
Chi-restraints excluded: chain F residue  126 MET
Chi-restraints excluded: chain F residue  274 ASP
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 58 optimal weight:    6.9990
   chunk 9 optimal weight:    7.9990
   chunk 84 optimal weight:    8.9990
   chunk 54 optimal weight:    0.0070
   chunk 184 optimal weight:    1.9990
   chunk 85 optimal weight:   20.0000
   chunk 155 optimal weight:    0.9990
   chunk 40 optimal weight:    0.9990
   chunk 134 optimal weight:    0.9980
   chunk 94 optimal weight:    9.9990
   chunk 19 optimal weight:    1.9990
   overall best weight:    1.0004

-------------------------------------------------------------------------------
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 = 0.3581 r_free = 0.3581 target = 0.108024 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2934 r_free = 0.2934 target = 0.069817 restraints weight = 35706.491|
|-----------------------------------------------------------------------------|
r_work (start): 0.2816 rms_B_bonded: 3.39
r_work: 0.2660 rms_B_bonded: 4.24 restraints_weight: 0.5000
r_work (final): 0.2660
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8346
moved from start:          0.2068

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  15092  Z= 0.130
  Angle     :  0.561   9.409  20482  Z= 0.283
  Chirality :  0.044   0.253   2513
  Planarity :  0.002   0.023   2604
  Dihedral  :  4.081  19.178   2121
  Min Nonbonded Distance : 2.570

Molprobity Statistics.
  All-atom Clashscore : 5.84
  Ramachandran Plot:
    Outliers :  0.36 %
    Allowed  :  4.73 %
    Favored  : 94.91 %
  Rotamer:
    Outliers :  1.38 %
    Allowed  : 17.56 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.16 (0.20), residues: 1946
  helix:  2.70 (0.16), residues: 1071
  sheet:  0.95 (0.30), residues: 294
  loop : -0.80 (0.26), residues: 581

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP G  16 
 PHE   0.021   0.001   PHE G  80 
 TYR   0.008   0.001   TYR D 135 
 ARG   0.001   0.000   ARG E 180 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03483 ( 1069)
  hydrogen bonds       : angle       3.89715 ( 3105)
  covalent geometry    : bond        0.00276 (15092)
  covalent geometry    : angle       0.56116 (20482)

*********************** 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
  291 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 269
  time to evaluate  : 1.588 
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: A  134 GLU cc_start: 0.8181 (tt0) cc_final: 0.7634 (tt0)
REVERT: A  149 GLN cc_start: 0.9205 (mm110) cc_final: 0.8849 (mm-40)
REVERT: A  203 GLN cc_start: 0.9331 (tm-30) cc_final: 0.8874 (tm-30)
REVERT: A  220 GLU cc_start: 0.8747 (pp20) cc_final: 0.8431 (pp20)
REVERT: A  227 GLU cc_start: 0.9063 (pp20) cc_final: 0.8610 (pp20)
REVERT: B   47 MET cc_start: 0.8728 (mmp) cc_final: 0.8456 (mmm)
REVERT: B  134 GLU cc_start: 0.8750 (tt0) cc_final: 0.8449 (tt0)
REVERT: B  157 THR cc_start: 0.9568 (OUTLIER) cc_final: 0.9167 (p)
REVERT: B  169 LYS cc_start: 0.9262 (ttpp) cc_final: 0.9038 (ttpt)
REVERT: B  203 GLN cc_start: 0.9290 (tm-30) cc_final: 0.8882 (tm-30)
REVERT: B  212 GLU cc_start: 0.9139 (mm-30) cc_final: 0.8845 (tp30)
REVERT: B  278 LYS cc_start: 0.9205 (mtmm) cc_final: 0.8913 (mttp)
REVERT: C   47 MET cc_start: 0.8614 (mmm) cc_final: 0.8272 (mmm)
REVERT: C   91 VAL cc_start: 0.7831 (OUTLIER) cc_final: 0.7500 (p)
REVERT: C  134 GLU cc_start: 0.8568 (tt0) cc_final: 0.8079 (tt0)
REVERT: C  149 GLN cc_start: 0.9400 (mm110) cc_final: 0.9030 (mp10)
REVERT: C  157 THR cc_start: 0.9430 (OUTLIER) cc_final: 0.8911 (p)
REVERT: C  181 GLU cc_start: 0.9555 (mm-30) cc_final: 0.9065 (mm-30)
REVERT: C  203 GLN cc_start: 0.9369 (tm-30) cc_final: 0.8882 (tm-30)
REVERT: C  220 GLU cc_start: 0.8860 (pp20) cc_final: 0.8488 (pp20)
REVERT: C  227 GLU cc_start: 0.9070 (pp20) cc_final: 0.8677 (pp20)
REVERT: D  181 GLU cc_start: 0.9565 (mm-30) cc_final: 0.9243 (mm-30)
REVERT: D  203 GLN cc_start: 0.9343 (tm-30) cc_final: 0.8906 (tm-30)
REVERT: D  220 GLU cc_start: 0.8876 (pp20) cc_final: 0.8492 (pp20)
REVERT: D  260 GLU cc_start: 0.9535 (mm-30) cc_final: 0.9062 (mp0)
REVERT: E   47 MET cc_start: 0.8533 (mmm) cc_final: 0.8126 (mmm)
REVERT: E   55 LEU cc_start: 0.9237 (tt) cc_final: 0.8946 (mm)
REVERT: E  149 GLN cc_start: 0.9405 (mm110) cc_final: 0.9046 (mm-40)
REVERT: E  181 GLU cc_start: 0.9591 (mm-30) cc_final: 0.9227 (mm-30)
REVERT: E  203 GLN cc_start: 0.9373 (tm-30) cc_final: 0.8948 (tm-30)
REVERT: E  220 GLU cc_start: 0.8840 (pp20) cc_final: 0.8593 (pp20)
REVERT: E  227 GLU cc_start: 0.9040 (pp20) cc_final: 0.8597 (pp20)
REVERT: F  134 GLU cc_start: 0.8357 (tt0) cc_final: 0.7964 (tt0)
REVERT: F  149 GLN cc_start: 0.9202 (mm-40) cc_final: 0.8991 (mm-40)
REVERT: F  203 GLN cc_start: 0.9317 (tm-30) cc_final: 0.8909 (tm-30)
REVERT: F  220 GLU cc_start: 0.8847 (pp20) cc_final: 0.8485 (pp20)
REVERT: F  227 GLU cc_start: 0.9123 (pp20) cc_final: 0.8667 (pp20)
REVERT: F  270 TYR cc_start: 0.9409 (m-80) cc_final: 0.9142 (m-10)
REVERT: F  274 ASP cc_start: 0.8978 (OUTLIER) cc_final: 0.8274 (t0)
REVERT: F  278 LYS cc_start: 0.9111 (mtmm) cc_final: 0.8557 (mttm)
REVERT: G   47 MET cc_start: 0.8611 (mmm) cc_final: 0.8299 (mmm)
REVERT: G  134 GLU cc_start: 0.8288 (tt0) cc_final: 0.7335 (tt0)
REVERT: G  149 GLN cc_start: 0.9144 (mm110) cc_final: 0.8711 (mm110)
REVERT: G  220 GLU cc_start: 0.8769 (pp20) cc_final: 0.8393 (pp20)
REVERT: G  222 THR cc_start: 0.9531 (m) cc_final: 0.9256 (p)
REVERT: G  227 GLU cc_start: 0.9155 (pp20) cc_final: 0.8684 (pp20)
  outliers start: 22
  outliers final: 13
  residues processed: 279
  average time/residue: 0.2706
  time to fit residues: 113.4543
Evaluate side-chains
  272 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 255
  time to evaluate  : 1.719 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  274 ASP
Chi-restraints excluded: chain B residue    1 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 C residue   91 VAL
Chi-restraints excluded: chain C residue  138 LEU
Chi-restraints excluded: chain C residue  157 THR
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  274 ASP
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 57 optimal weight:   10.0000
   chunk 142 optimal weight:    9.9990
   chunk 42 optimal weight:    6.9990
   chunk 89 optimal weight:   10.0000
   chunk 29 optimal weight:   30.0000
   chunk 79 optimal weight:    4.9990
   chunk 56 optimal weight:   50.0000
   chunk 18 optimal weight:    5.9990
   chunk 118 optimal weight:    1.9990
   chunk 195 optimal weight:    0.9980
   chunk 165 optimal weight:    0.6980
   overall best weight:    2.9386

-------------------------------------------------------------------------------
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 = 0.3538 r_free = 0.3538 target = 0.105602 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2864 r_free = 0.2864 target = 0.068015 restraints weight = 36726.813|
|-----------------------------------------------------------------------------|
r_work (start): 0.2774 rms_B_bonded: 3.17
r_work: 0.2632 rms_B_bonded: 4.02 restraints_weight: 0.5000
r_work (final): 0.2632
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8392
moved from start:          0.2176

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.056  15092  Z= 0.263
  Angle     :  0.618   9.717  20482  Z= 0.316
  Chirality :  0.044   0.229   2513
  Planarity :  0.003   0.023   2604
  Dihedral  :  4.242  20.657   2121
  Min Nonbonded Distance : 2.459

Molprobity Statistics.
  All-atom Clashscore : 6.50
  Ramachandran Plot:
    Outliers :  0.36 %
    Allowed  :  5.14 %
    Favored  : 94.50 %
  Rotamer:
    Outliers :  1.95 %
    Allowed  : 17.56 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.11 (0.20), residues: 1946
  helix:  2.63 (0.16), residues: 1071
  sheet:  1.31 (0.33), residues: 259
  loop : -0.87 (0.25), residues: 616

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP G  16 
 PHE   0.024   0.002   PHE F  80 
 TYR   0.007   0.001   TYR B 194 
 ARG   0.003   0.000   ARG A 128 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03678 ( 1069)
  hydrogen bonds       : angle       4.00483 ( 3105)
  covalent geometry    : bond        0.00586 (15092)
  covalent geometry    : angle       0.61774 (20482)

*********************** 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
  283 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 252
  time to evaluate  : 1.508 
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: 0.8101 (tt0) cc_final: 0.7510 (tt0)
REVERT: A  149 GLN cc_start: 0.9166 (mm110) cc_final: 0.8822 (mm-40)
REVERT: A  203 GLN cc_start: 0.9356 (tm-30) cc_final: 0.8935 (tm-30)
REVERT: A  227 GLU cc_start: 0.9056 (pp20) cc_final: 0.8568 (pp20)
REVERT: B   47 MET cc_start: 0.8706 (mmp) cc_final: 0.8412 (mmm)
REVERT: B  134 GLU cc_start: 0.8601 (tt0) cc_final: 0.8275 (tt0)
REVERT: B  149 GLN cc_start: 0.9176 (mm-40) cc_final: 0.8965 (mm-40)
REVERT: B  161 LYS cc_start: 0.9333 (OUTLIER) cc_final: 0.9074 (mmmm)
REVERT: B  203 GLN cc_start: 0.9303 (tm-30) cc_final: 0.8893 (tm-30)
REVERT: C   47 MET cc_start: 0.8634 (mmm) cc_final: 0.8305 (mmm)
REVERT: C   91 VAL cc_start: 0.7738 (OUTLIER) cc_final: 0.7379 (p)
REVERT: C  134 GLU cc_start: 0.8467 (tt0) cc_final: 0.7946 (tt0)
REVERT: C  149 GLN cc_start: 0.9356 (mm110) cc_final: 0.9070 (mm-40)
REVERT: C  157 THR cc_start: 0.9451 (OUTLIER) cc_final: 0.9059 (p)
REVERT: C  181 GLU cc_start: 0.9585 (mm-30) cc_final: 0.9055 (mm-30)
REVERT: C  203 GLN cc_start: 0.9359 (tm-30) cc_final: 0.8871 (tm-30)
REVERT: C  220 GLU cc_start: 0.8834 (pp20) cc_final: 0.8423 (pp20)
REVERT: C  227 GLU cc_start: 0.9092 (pp20) cc_final: 0.8690 (pp20)
REVERT: D  181 GLU cc_start: 0.9572 (mm-30) cc_final: 0.9202 (mm-30)
REVERT: D  203 GLN cc_start: 0.9337 (tm-30) cc_final: 0.8894 (tm-30)
REVERT: D  220 GLU cc_start: 0.8906 (pp20) cc_final: 0.8532 (pp20)
REVERT: D  260 GLU cc_start: 0.9541 (mm-30) cc_final: 0.9058 (mp0)
REVERT: E   47 MET cc_start: 0.8541 (mmm) cc_final: 0.8114 (mmm)
REVERT: E  149 GLN cc_start: 0.9389 (mm110) cc_final: 0.9019 (mm-40)
REVERT: E  203 GLN cc_start: 0.9330 (tm-30) cc_final: 0.8900 (tm-30)
REVERT: E  220 GLU cc_start: 0.8852 (pp20) cc_final: 0.8609 (pp20)
REVERT: E  227 GLU cc_start: 0.9057 (pp20) cc_final: 0.8648 (pp20)
REVERT: F  134 GLU cc_start: 0.8265 (tt0) cc_final: 0.7863 (tt0)
REVERT: F  149 GLN cc_start: 0.9174 (mm-40) cc_final: 0.8949 (mm-40)
REVERT: F  203 GLN cc_start: 0.9308 (tm-30) cc_final: 0.8911 (tm-30)
REVERT: F  220 GLU cc_start: 0.8821 (pp20) cc_final: 0.8443 (pp20)
REVERT: F  227 GLU cc_start: 0.9113 (pp20) cc_final: 0.8718 (pp20)
REVERT: F  270 TYR cc_start: 0.9430 (m-80) cc_final: 0.9200 (m-10)
REVERT: F  274 ASP cc_start: 0.8968 (OUTLIER) cc_final: 0.8264 (t0)
REVERT: G   47 MET cc_start: 0.8518 (mmm) cc_final: 0.8179 (mmm)
REVERT: G  134 GLU cc_start: 0.8242 (tt0) cc_final: 0.7324 (tt0)
REVERT: G  149 GLN cc_start: 0.9212 (mm110) cc_final: 0.8801 (mm110)
REVERT: G  203 GLN cc_start: 0.9268 (tm-30) cc_final: 0.8997 (tm-30)
REVERT: G  220 GLU cc_start: 0.8776 (pp20) cc_final: 0.8485 (pp20)
REVERT: G  227 GLU cc_start: 0.9169 (pp20) cc_final: 0.8720 (pp20)
REVERT: G  255 GLU cc_start: 0.9563 (tt0) cc_final: 0.9060 (tm-30)
  outliers start: 31
  outliers final: 19
  residues processed: 267
  average time/residue: 0.3463
  time to fit residues: 137.4184
Evaluate side-chains
  266 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 243
  time to evaluate  : 3.131 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  155 MET
Chi-restraints excluded: chain A residue  255 GLU
Chi-restraints excluded: chain B residue    1 MET
Chi-restraints excluded: chain B residue   69 LEU
Chi-restraints excluded: chain B residue  153 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 C residue  157 THR
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 D residue  273 MET
Chi-restraints excluded: chain E residue   73 VAL
Chi-restraints excluded: chain E residue  138 LEU
Chi-restraints excluded: chain E residue  154 THR
Chi-restraints excluded: chain F residue   73 VAL
Chi-restraints excluded: chain F residue  126 MET
Chi-restraints excluded: chain F residue  136 VAL
Chi-restraints excluded: chain F residue  274 ASP
Chi-restraints excluded: chain G residue   73 VAL
Chi-restraints excluded: chain G residue  153 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 196
   random chunks:
   chunk 125 optimal weight:    0.9980
   chunk 137 optimal weight:    1.9990
   chunk 25 optimal weight:    0.6980
   chunk 28 optimal weight:   50.0000
   chunk 13 optimal weight:    0.6980
   chunk 92 optimal weight:    4.9990
   chunk 171 optimal weight:   10.0000
   chunk 36 optimal weight:   10.0000
   chunk 1 optimal weight:    8.9990
   chunk 162 optimal weight:    0.9990
   chunk 184 optimal weight:    0.8980
   overall best weight:    0.8582

-------------------------------------------------------------------------------
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 = 0.3580 r_free = 0.3580 target = 0.107957 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.2921 r_free = 0.2921 target = 0.070331 restraints weight = 36296.054|
|-----------------------------------------------------------------------------|
r_work (start): 0.2812 rms_B_bonded: 3.21
r_work: 0.2665 rms_B_bonded: 4.12 restraints_weight: 0.5000
r_work (final): 0.2665
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8342
moved from start:          0.2230

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  15092  Z= 0.128
  Angle     :  0.601  10.795  20482  Z= 0.297
  Chirality :  0.044   0.237   2513
  Planarity :  0.002   0.023   2604
  Dihedral  :  4.135  20.338   2121
  Min Nonbonded Distance : 2.490

Molprobity Statistics.
  All-atom Clashscore : 6.17
  Ramachandran Plot:
    Outliers :  0.36 %
    Allowed  :  4.78 %
    Favored  : 94.86 %
  Rotamer:
    Outliers :  1.38 %
    Allowed  : 18.88 %
    Favored  : 79.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.20 (0.20), residues: 1946
  helix:  2.66 (0.16), residues: 1071
  sheet:  1.01 (0.31), residues: 294
  loop : -0.66 (0.27), residues: 581

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP G  16 
 PHE   0.027   0.002   PHE B  80 
 TYR   0.004   0.001   TYR D 135 
 ARG   0.001   0.000   ARG E 180 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03537 ( 1069)
  hydrogen bonds       : angle       3.93137 ( 3105)
  covalent geometry    : bond        0.00273 (15092)
  covalent geometry    : angle       0.60053 (20482)

*********************** 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
  280 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 258
  time to evaluate  : 2.994 
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  134 GLU cc_start: 0.8139 (tt0) cc_final: 0.7517 (tt0)
REVERT: A  149 GLN cc_start: 0.9223 (mm110) cc_final: 0.8864 (mm-40)
REVERT: A  203 GLN cc_start: 0.9322 (tm-30) cc_final: 0.8862 (tm-30)
REVERT: A  227 GLU cc_start: 0.9058 (pp20) cc_final: 0.8608 (pp20)
REVERT: B   47 MET cc_start: 0.8711 (mmp) cc_final: 0.8413 (mmm)
REVERT: B  134 GLU cc_start: 0.8749 (tt0) cc_final: 0.8447 (tt0)
REVERT: B  149 GLN cc_start: 0.9237 (mm-40) cc_final: 0.9003 (mm-40)
REVERT: B  157 THR cc_start: 0.9565 (OUTLIER) cc_final: 0.9094 (p)
REVERT: B  203 GLN cc_start: 0.9276 (tm-30) cc_final: 0.8849 (tm-30)
REVERT: B  212 GLU cc_start: 0.9151 (mm-30) cc_final: 0.8854 (tp30)
REVERT: C   47 MET cc_start: 0.8613 (mmm) cc_final: 0.8281 (mmm)
REVERT: C   91 VAL cc_start: 0.7821 (OUTLIER) cc_final: 0.7497 (p)
REVERT: C  134 GLU cc_start: 0.8568 (tt0) cc_final: 0.8051 (tt0)
REVERT: C  149 GLN cc_start: 0.9349 (mm110) cc_final: 0.8870 (mp10)
REVERT: C  157 THR cc_start: 0.9463 (OUTLIER) cc_final: 0.9020 (p)
REVERT: C  181 GLU cc_start: 0.9546 (mm-30) cc_final: 0.9106 (mm-30)
REVERT: C  203 GLN cc_start: 0.9356 (tm-30) cc_final: 0.8856 (tm-30)
REVERT: C  220 GLU cc_start: 0.8848 (pp20) cc_final: 0.8489 (pp20)
REVERT: C  227 GLU cc_start: 0.9072 (pp20) cc_final: 0.8707 (pp20)
REVERT: C  255 GLU cc_start: 0.9459 (tm-30) cc_final: 0.9069 (tm-30)
REVERT: D  181 GLU cc_start: 0.9541 (mm-30) cc_final: 0.9229 (mm-30)
REVERT: D  203 GLN cc_start: 0.9324 (tm-30) cc_final: 0.8866 (tm-30)
REVERT: D  220 GLU cc_start: 0.8852 (pp20) cc_final: 0.8457 (pp20)
REVERT: D  260 GLU cc_start: 0.9516 (mm-30) cc_final: 0.9063 (mp0)
REVERT: E   47 MET cc_start: 0.8469 (mmm) cc_final: 0.8073 (mmm)
REVERT: E   55 LEU cc_start: 0.9227 (tt) cc_final: 0.8964 (mm)
REVERT: E  149 GLN cc_start: 0.9399 (mm110) cc_final: 0.9022 (mm-40)
REVERT: E  203 GLN cc_start: 0.9319 (tm-30) cc_final: 0.8873 (tm-30)
REVERT: E  220 GLU cc_start: 0.8828 (pp20) cc_final: 0.8583 (pp20)
REVERT: E  227 GLU cc_start: 0.9064 (pp20) cc_final: 0.8634 (pp20)
REVERT: F  134 GLU cc_start: 0.8327 (tt0) cc_final: 0.7896 (tt0)
REVERT: F  149 GLN cc_start: 0.9245 (mm-40) cc_final: 0.9015 (mm-40)
REVERT: F  203 GLN cc_start: 0.9311 (tm-30) cc_final: 0.8893 (tm-30)
REVERT: F  220 GLU cc_start: 0.8806 (pp20) cc_final: 0.8438 (pp20)
REVERT: F  227 GLU cc_start: 0.9119 (pp20) cc_final: 0.8699 (pp20)
REVERT: F  270 TYR cc_start: 0.9411 (m-80) cc_final: 0.9166 (m-10)
REVERT: F  274 ASP cc_start: 0.8972 (OUTLIER) cc_final: 0.8270 (t0)
REVERT: G   47 MET cc_start: 0.8545 (mmm) cc_final: 0.8197 (mmm)
REVERT: G  134 GLU cc_start: 0.8247 (tt0) cc_final: 0.7278 (tt0)
REVERT: G  149 GLN cc_start: 0.9196 (mm110) cc_final: 0.8760 (mm110)
REVERT: G  203 GLN cc_start: 0.9207 (tm-30) cc_final: 0.8906 (tm-30)
REVERT: G  220 GLU cc_start: 0.8751 (pp20) cc_final: 0.8377 (pp20)
REVERT: G  222 THR cc_start: 0.9538 (m) cc_final: 0.9264 (p)
REVERT: G  227 GLU cc_start: 0.9154 (pp20) cc_final: 0.8666 (pp20)
  outliers start: 22
  outliers final: 14
  residues processed: 268
  average time/residue: 0.3177
  time to fit residues: 129.7428
Evaluate side-chains
  272 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 254
  time to evaluate  : 2.170 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  274 ASP
Chi-restraints excluded: chain B residue    1 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 C residue   91 VAL
Chi-restraints excluded: chain C residue  115 LEU
Chi-restraints excluded: chain C residue  138 LEU
Chi-restraints excluded: chain C residue  157 THR
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  274 ASP
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 80 optimal weight:    4.9990
   chunk 44 optimal weight:    3.9990
   chunk 126 optimal weight:    6.9990
   chunk 116 optimal weight:    5.9990
   chunk 73 optimal weight:    0.0870
   chunk 75 optimal weight:    5.9990
   chunk 33 optimal weight:    3.9990
   chunk 169 optimal weight:    6.9990
   chunk 193 optimal weight:    0.7980
   chunk 48 optimal weight:    0.7980
   chunk 68 optimal weight:    1.9990
   overall best weight:    1.5362

-------------------------------------------------------------------------------
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 = 0.3572 r_free = 0.3572 target = 0.107439 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.2915 r_free = 0.2915 target = 0.068843 restraints weight = 35986.557|
|-----------------------------------------------------------------------------|
r_work (start): 0.2796 rms_B_bonded: 3.32
r_work: 0.2645 rms_B_bonded: 4.22 restraints_weight: 0.5000
r_work (final): 0.2645
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8370
moved from start:          0.2298

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040  15092  Z= 0.163
  Angle     :  0.605  11.185  20482  Z= 0.301
  Chirality :  0.044   0.222   2513
  Planarity :  0.002   0.024   2604
  Dihedral  :  4.107  19.725   2121
  Min Nonbonded Distance : 2.490

Molprobity Statistics.
  All-atom Clashscore : 6.14
  Ramachandran Plot:
    Outliers :  0.36 %
    Allowed  :  4.78 %
    Favored  : 94.86 %
  Rotamer:
    Outliers :  1.57 %
    Allowed  : 19.13 %
    Favored  : 79.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.17 (0.20), residues: 1946
  helix:  2.64 (0.16), residues: 1071
  sheet:  1.31 (0.33), residues: 259
  loop : -0.75 (0.26), residues: 616

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP G  16 
 PHE   0.022   0.001   PHE G  80 
 TYR   0.004   0.001   TYR B 194 
 ARG   0.002   0.000   ARG C 180 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03539 ( 1069)
  hydrogen bonds       : angle       3.92609 ( 3105)
  covalent geometry    : bond        0.00362 (15092)
  covalent geometry    : angle       0.60515 (20482)

********************** 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
  278 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 253
  time to evaluate  : 1.763 
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: 0.8151 (tt0) cc_final: 0.7566 (tt0)
REVERT: A  149 GLN cc_start: 0.9222 (mm110) cc_final: 0.8876 (mm-40)
REVERT: A  203 GLN cc_start: 0.9341 (tm-30) cc_final: 0.8894 (tm-30)
REVERT: A  227 GLU cc_start: 0.9102 (pp20) cc_final: 0.8665 (pp20)
REVERT: B   47 MET cc_start: 0.8693 (mmp) cc_final: 0.8410 (mmm)
REVERT: B  134 GLU cc_start: 0.8739 (tt0) cc_final: 0.8432 (tt0)
REVERT: B  149 GLN cc_start: 0.9273 (mm-40) cc_final: 0.9035 (mm-40)
REVERT: B  157 THR cc_start: 0.9562 (OUTLIER) cc_final: 0.9105 (p)
REVERT: B  161 LYS cc_start: 0.9338 (OUTLIER) cc_final: 0.9135 (mmtp)
REVERT: B  203 GLN cc_start: 0.9296 (tm-30) cc_final: 0.8877 (tm-30)
REVERT: C   47 MET cc_start: 0.8603 (mmm) cc_final: 0.8283 (mmm)
REVERT: C   91 VAL cc_start: 0.7604 (OUTLIER) cc_final: 0.7291 (p)
REVERT: C  134 GLU cc_start: 0.8538 (tt0) cc_final: 0.8025 (tt0)
REVERT: C  149 GLN cc_start: 0.9373 (mm110) cc_final: 0.8910 (mp10)
REVERT: C  157 THR cc_start: 0.9441 (OUTLIER) cc_final: 0.8980 (p)
REVERT: C  181 GLU cc_start: 0.9550 (mm-30) cc_final: 0.9111 (mm-30)
REVERT: C  203 GLN cc_start: 0.9365 (tm-30) cc_final: 0.8871 (tm-30)
REVERT: C  220 GLU cc_start: 0.8875 (pp20) cc_final: 0.8506 (pp20)
REVERT: C  227 GLU cc_start: 0.9065 (pp20) cc_final: 0.8662 (pp20)
REVERT: C  255 GLU cc_start: 0.9463 (tm-30) cc_final: 0.9068 (tm-30)
REVERT: D  181 GLU cc_start: 0.9546 (mm-30) cc_final: 0.9218 (mm-30)
REVERT: D  203 GLN cc_start: 0.9344 (tm-30) cc_final: 0.8884 (tm-30)
REVERT: D  220 GLU cc_start: 0.8890 (pp20) cc_final: 0.8500 (pp20)
REVERT: D  260 GLU cc_start: 0.9524 (mm-30) cc_final: 0.9082 (mp0)
REVERT: D  278 LYS cc_start: 0.9151 (mtmm) cc_final: 0.8946 (mtmm)
REVERT: E   47 MET cc_start: 0.8437 (mmm) cc_final: 0.8070 (mmm)
REVERT: E  149 GLN cc_start: 0.9392 (mm110) cc_final: 0.9010 (mm-40)
REVERT: E  203 GLN cc_start: 0.9333 (tm-30) cc_final: 0.8892 (tm-30)
REVERT: E  220 GLU cc_start: 0.8855 (pp20) cc_final: 0.8613 (pp20)
REVERT: E  227 GLU cc_start: 0.9079 (pp20) cc_final: 0.8642 (pp20)
REVERT: F  134 GLU cc_start: 0.8324 (tt0) cc_final: 0.7928 (tt0)
REVERT: F  149 GLN cc_start: 0.9216 (mm-40) cc_final: 0.8978 (mm-40)
REVERT: F  181 GLU cc_start: 0.9597 (mm-30) cc_final: 0.9293 (mm-30)
REVERT: F  203 GLN cc_start: 0.9308 (tm-30) cc_final: 0.8905 (tm-30)
REVERT: F  220 GLU cc_start: 0.8826 (pp20) cc_final: 0.8456 (pp20)
REVERT: F  227 GLU cc_start: 0.9132 (pp20) cc_final: 0.8715 (pp20)
REVERT: F  270 TYR cc_start: 0.9411 (m-80) cc_final: 0.9166 (m-10)
REVERT: F  274 ASP cc_start: 0.8975 (OUTLIER) cc_final: 0.8286 (t0)
REVERT: G   47 MET cc_start: 0.8529 (mmm) cc_final: 0.8209 (mmm)
REVERT: G  134 GLU cc_start: 0.8316 (tt0) cc_final: 0.7386 (tt0)
REVERT: G  149 GLN cc_start: 0.9223 (mm110) cc_final: 0.8786 (mm110)
REVERT: G  203 GLN cc_start: 0.9239 (tm-30) cc_final: 0.8924 (tm-30)
REVERT: G  222 THR cc_start: 0.9550 (m) cc_final: 0.9276 (p)
REVERT: G  227 GLU cc_start: 0.9171 (pp20) cc_final: 0.8693 (pp20)
  outliers start: 25
  outliers final: 17
  residues processed: 266
  average time/residue: 0.2524
  time to fit residues: 100.5658
Evaluate side-chains
  270 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 248
  time to evaluate  : 1.774 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   89 VAL
Chi-restraints excluded: chain A residue  274 ASP
Chi-restraints excluded: chain B residue    1 MET
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  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 C residue  157 THR
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  105 LEU
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  274 ASP
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 95 optimal weight:    1.9990
   chunk 25 optimal weight:    1.9990
   chunk 174 optimal weight:   10.0000
   chunk 103 optimal weight:    2.9990
   chunk 52 optimal weight:    0.8980
   chunk 106 optimal weight:    4.9990
   chunk 180 optimal weight:    0.0050
   chunk 63 optimal weight:    0.9990
   chunk 94 optimal weight:    7.9990
   chunk 155 optimal weight:    6.9990
   chunk 139 optimal weight:    2.9990
   overall best weight:    1.1800

-------------------------------------------------------------------------------
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 = 0.3582 r_free = 0.3582 target = 0.107852 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.2924 r_free = 0.2924 target = 0.070422 restraints weight = 36419.201|
|-----------------------------------------------------------------------------|
r_work (start): 0.2822 rms_B_bonded: 3.21
r_work: 0.2678 rms_B_bonded: 4.06 restraints_weight: 0.5000
r_work (final): 0.2678
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8361
moved from start:          0.2363

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  15092  Z= 0.139
  Angle     :  0.598  10.736  20482  Z= 0.297
  Chirality :  0.044   0.216   2513
  Planarity :  0.002   0.023   2604
  Dihedral  :  4.064  21.938   2121
  Min Nonbonded Distance : 2.505

Molprobity Statistics.
  All-atom Clashscore : 6.20
  Ramachandran Plot:
    Outliers :  0.36 %
    Allowed  :  4.83 %
    Favored  : 94.81 %
  Rotamer:
    Outliers :  1.32 %
    Allowed  : 19.19 %
    Favored  : 79.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.17 (0.20), residues: 1946
  helix:  2.62 (0.16), residues: 1071
  sheet:  1.30 (0.33), residues: 259
  loop : -0.72 (0.26), residues: 616

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP G  16 
 PHE   0.025   0.002   PHE D  80 
 TYR   0.005   0.001   TYR C 135 
 ARG   0.001   0.000   ARG G 180 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03489 ( 1069)
  hydrogen bonds       : angle       3.88831 ( 3105)
  covalent geometry    : bond        0.00303 (15092)
  covalent geometry    : angle       0.59836 (20482)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 8419.93 seconds
wall clock time: 147 minutes 40.92 seconds (8860.92 seconds total)