Starting phenix.real_space_refine
on Thu Jul 31 09:33:42 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6vym_21464/07_2025/6vym_21464.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6vym_21464/07_2025/6vym_21464.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.7
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6vym_21464/07_2025/6vym_21464.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6vym_21464/07_2025/6vym_21464.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6vym_21464/07_2025/6vym_21464.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6vym_21464/07_2025/6vym_21464.cif"
  }
  resolution = 3.7
  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=   0.008
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      42      5.16       5
     C    8715      2.51       5
     N    2373      2.21       5
     O    2443      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 7 residue(s): 0.08s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 13573
  Number of models: 1
  Model: ""
    Number of chains: 7
    Chain: "A"
      Number of atoms: 1939
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 254, 1939
          Classifications: {'peptide': 254}
          Link IDs: {'PTRANS': 5, 'TRANS': 248}
    Chain: "B"
      Number of atoms: 1939
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 254, 1939
          Classifications: {'peptide': 254}
          Link IDs: {'PTRANS': 5, 'TRANS': 248}
    Chain: "C"
      Number of atoms: 1939
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 254, 1939
          Classifications: {'peptide': 254}
          Link IDs: {'PTRANS': 5, 'TRANS': 248}
    Chain: "D"
      Number of atoms: 1939
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 254, 1939
          Classifications: {'peptide': 254}
          Link IDs: {'PTRANS': 5, 'TRANS': 248}
    Chain: "E"
      Number of atoms: 1939
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 254, 1939
          Classifications: {'peptide': 254}
          Link IDs: {'PTRANS': 5, 'TRANS': 248}
    Chain: "F"
      Number of atoms: 1939
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 254, 1939
          Classifications: {'peptide': 254}
          Link IDs: {'PTRANS': 5, 'TRANS': 248}
    Chain: "G"
      Number of atoms: 1939
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 254, 1939
          Classifications: {'peptide': 254}
          Link IDs: {'PTRANS': 5, 'TRANS': 248}
  Time building chain proxies: 8.09, per 1000 atoms: 0.60
  Number of scatterers: 13573
  At special positions: 0
  Unit cell: (100, 99, 111, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      42     16.00
     O    2443      8.00
     N    2373      7.00
     C    8715      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: 3.02
  Conformation dependent library (CDL) restraints added in 1.8 seconds
  

  3528 Ramachandran restraints generated.
    1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3276

  Finding SS restraints...
    Secondary structure from input PDB file:
      42 helices and 9 sheets defined
      53.5% alpha, 18.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.65
  Creating SS restraints...
    Processing helix  chain 'A' and resid 28 through 60
    Processing helix  chain 'A' and resid 64 through 90
      removed outlier: 3.643A  pdb=" N   PHE A  68 " --> pdb=" O   THR A  64 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 94 through 127
      removed outlier: 4.037A  pdb=" N   VAL A  99 " --> pdb=" O   SER A  95 " (cutoff:3.500A)
      removed outlier: 4.708A  pdb=" N   GLY A 113 " --> pdb=" O   LEU A 109 " (cutoff:3.500A)
      removed outlier: 4.195A  pdb=" N   SER A 114 " --> pdb=" O   ALA A 110 " (cutoff:3.500A)
      removed outlier: 3.745A  pdb=" N   ASN A 117 " --> pdb=" O   GLY A 113 " (cutoff:3.500A)
      removed outlier: 4.789A  pdb=" N   LEU A 118 " --> pdb=" O   SER A 114 " (cutoff:3.500A)
      removed outlier: 3.573A  pdb=" N   LEU A 123 " --> pdb=" O   ALA A 119 " (cutoff:3.500A)
      removed outlier: 3.735A  pdb=" N   VAL A 125 " --> pdb=" O   GLY A 121 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 166 through 171
      removed outlier: 3.586A  pdb=" N   ILE A 170 " --> pdb=" O   PRO A 166 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 197 through 212
    Processing helix  chain 'A' and resid 245 through 264
      removed outlier: 3.651A  pdb=" N   LEU A 254 " --> pdb=" O   TYR A 250 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 28 through 60
    Processing helix  chain 'B' and resid 64 through 90
      removed outlier: 3.642A  pdb=" N   PHE B  68 " --> pdb=" O   THR B  64 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 94 through 127
      removed outlier: 4.036A  pdb=" N   VAL B  99 " --> pdb=" O   SER B  95 " (cutoff:3.500A)
      removed outlier: 4.708A  pdb=" N   GLY B 113 " --> pdb=" O   LEU B 109 " (cutoff:3.500A)
      removed outlier: 4.194A  pdb=" N   SER B 114 " --> pdb=" O   ALA B 110 " (cutoff:3.500A)
      removed outlier: 3.745A  pdb=" N   ASN B 117 " --> pdb=" O   GLY B 113 " (cutoff:3.500A)
      removed outlier: 4.788A  pdb=" N   LEU B 118 " --> pdb=" O   SER B 114 " (cutoff:3.500A)
      removed outlier: 3.572A  pdb=" N   LEU B 123 " --> pdb=" O   ALA B 119 " (cutoff:3.500A)
      removed outlier: 3.735A  pdb=" N   VAL B 125 " --> pdb=" O   GLY B 121 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 166 through 171
      removed outlier: 3.586A  pdb=" N   ILE B 170 " --> pdb=" O   PRO B 166 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 197 through 212
    Processing helix  chain 'B' and resid 245 through 264
      removed outlier: 3.651A  pdb=" N   LEU B 254 " --> pdb=" O   TYR B 250 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 28 through 60
    Processing helix  chain 'C' and resid 64 through 90
      removed outlier: 3.642A  pdb=" N   PHE C  68 " --> pdb=" O   THR C  64 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 94 through 127
      removed outlier: 4.036A  pdb=" N   VAL C  99 " --> pdb=" O   SER C  95 " (cutoff:3.500A)
      removed outlier: 4.708A  pdb=" N   GLY C 113 " --> pdb=" O   LEU C 109 " (cutoff:3.500A)
      removed outlier: 4.196A  pdb=" N   SER C 114 " --> pdb=" O   ALA C 110 " (cutoff:3.500A)
      removed outlier: 3.745A  pdb=" N   ASN C 117 " --> pdb=" O   GLY C 113 " (cutoff:3.500A)
      removed outlier: 4.789A  pdb=" N   LEU C 118 " --> pdb=" O   SER C 114 " (cutoff:3.500A)
      removed outlier: 3.572A  pdb=" N   LEU C 123 " --> pdb=" O   ALA C 119 " (cutoff:3.500A)
      removed outlier: 3.736A  pdb=" N   VAL C 125 " --> pdb=" O   GLY C 121 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 166 through 171
      removed outlier: 3.586A  pdb=" N   ILE C 170 " --> pdb=" O   PRO C 166 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 197 through 212
    Processing helix  chain 'C' and resid 245 through 264
      removed outlier: 3.652A  pdb=" N   LEU C 254 " --> pdb=" O   TYR C 250 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 28 through 60
    Processing helix  chain 'D' and resid 64 through 90
      removed outlier: 3.642A  pdb=" N   PHE D  68 " --> pdb=" O   THR D  64 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 94 through 127
      removed outlier: 4.036A  pdb=" N   VAL D  99 " --> pdb=" O   SER D  95 " (cutoff:3.500A)
      removed outlier: 4.707A  pdb=" N   GLY D 113 " --> pdb=" O   LEU D 109 " (cutoff:3.500A)
      removed outlier: 4.195A  pdb=" N   SER D 114 " --> pdb=" O   ALA D 110 " (cutoff:3.500A)
      removed outlier: 3.745A  pdb=" N   ASN D 117 " --> pdb=" O   GLY D 113 " (cutoff:3.500A)
      removed outlier: 4.788A  pdb=" N   LEU D 118 " --> pdb=" O   SER D 114 " (cutoff:3.500A)
      removed outlier: 3.572A  pdb=" N   LEU D 123 " --> pdb=" O   ALA D 119 " (cutoff:3.500A)
      removed outlier: 3.736A  pdb=" N   VAL D 125 " --> pdb=" O   GLY D 121 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 166 through 171
      removed outlier: 3.586A  pdb=" N   ILE D 170 " --> pdb=" O   PRO D 166 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 197 through 212
    Processing helix  chain 'D' and resid 245 through 264
      removed outlier: 3.651A  pdb=" N   LEU D 254 " --> pdb=" O   TYR D 250 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 28 through 60
    Processing helix  chain 'E' and resid 64 through 90
      removed outlier: 3.642A  pdb=" N   PHE E  68 " --> pdb=" O   THR E  64 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 94 through 127
      removed outlier: 4.036A  pdb=" N   VAL E  99 " --> pdb=" O   SER E  95 " (cutoff:3.500A)
      removed outlier: 4.708A  pdb=" N   GLY E 113 " --> pdb=" O   LEU E 109 " (cutoff:3.500A)
      removed outlier: 4.195A  pdb=" N   SER E 114 " --> pdb=" O   ALA E 110 " (cutoff:3.500A)
      removed outlier: 3.746A  pdb=" N   ASN E 117 " --> pdb=" O   GLY E 113 " (cutoff:3.500A)
      removed outlier: 4.789A  pdb=" N   LEU E 118 " --> pdb=" O   SER E 114 " (cutoff:3.500A)
      removed outlier: 3.571A  pdb=" N   LEU E 123 " --> pdb=" O   ALA E 119 " (cutoff:3.500A)
      removed outlier: 3.736A  pdb=" N   VAL E 125 " --> pdb=" O   GLY E 121 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 166 through 171
      removed outlier: 3.585A  pdb=" N   ILE E 170 " --> pdb=" O   PRO E 166 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 197 through 212
    Processing helix  chain 'E' and resid 245 through 264
      removed outlier: 3.652A  pdb=" N   LEU E 254 " --> pdb=" O   TYR E 250 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 28 through 60
    Processing helix  chain 'F' and resid 64 through 90
      removed outlier: 3.642A  pdb=" N   PHE F  68 " --> pdb=" O   THR F  64 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 94 through 127
      removed outlier: 4.037A  pdb=" N   VAL F  99 " --> pdb=" O   SER F  95 " (cutoff:3.500A)
      removed outlier: 4.708A  pdb=" N   GLY F 113 " --> pdb=" O   LEU F 109 " (cutoff:3.500A)
      removed outlier: 4.195A  pdb=" N   SER F 114 " --> pdb=" O   ALA F 110 " (cutoff:3.500A)
      removed outlier: 3.745A  pdb=" N   ASN F 117 " --> pdb=" O   GLY F 113 " (cutoff:3.500A)
      removed outlier: 4.788A  pdb=" N   LEU F 118 " --> pdb=" O   SER F 114 " (cutoff:3.500A)
      removed outlier: 3.573A  pdb=" N   LEU F 123 " --> pdb=" O   ALA F 119 " (cutoff:3.500A)
      removed outlier: 3.736A  pdb=" N   VAL F 125 " --> pdb=" O   GLY F 121 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 166 through 171
      removed outlier: 3.585A  pdb=" N   ILE F 170 " --> pdb=" O   PRO F 166 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 197 through 212
    Processing helix  chain 'F' and resid 245 through 264
      removed outlier: 3.651A  pdb=" N   LEU F 254 " --> pdb=" O   TYR F 250 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 28 through 60
    Processing helix  chain 'G' and resid 64 through 90
      removed outlier: 3.643A  pdb=" N   PHE G  68 " --> pdb=" O   THR G  64 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 94 through 127
      removed outlier: 4.035A  pdb=" N   VAL G  99 " --> pdb=" O   SER G  95 " (cutoff:3.500A)
      removed outlier: 4.708A  pdb=" N   GLY G 113 " --> pdb=" O   LEU G 109 " (cutoff:3.500A)
      removed outlier: 4.195A  pdb=" N   SER G 114 " --> pdb=" O   ALA G 110 " (cutoff:3.500A)
      removed outlier: 3.746A  pdb=" N   ASN G 117 " --> pdb=" O   GLY G 113 " (cutoff:3.500A)
      removed outlier: 4.790A  pdb=" N   LEU G 118 " --> pdb=" O   SER G 114 " (cutoff:3.500A)
      removed outlier: 3.572A  pdb=" N   LEU G 123 " --> pdb=" O   ALA G 119 " (cutoff:3.500A)
      removed outlier: 3.736A  pdb=" N   VAL G 125 " --> pdb=" O   GLY G 121 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 166 through 171
      removed outlier: 3.585A  pdb=" N   ILE G 170 " --> pdb=" O   PRO G 166 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 197 through 212
    Processing helix  chain 'G' and resid 245 through 264
      removed outlier: 3.651A  pdb=" N   LEU G 254 " --> pdb=" O   TYR G 250 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 135 through 138
      removed outlier: 5.133A  pdb=" N   VAL A 145 " --> pdb=" O   ARG A 156 " (cutoff:3.500A)
      removed outlier: 5.948A  pdb=" N   ARG A 156 " --> pdb=" O   VAL A 145 " (cutoff:3.500A)
      removed outlier: 3.519A  pdb=" N   VAL A 164 " --> pdb=" O   ILE G 175 " (cutoff:3.500A)
      removed outlier: 5.132A  pdb=" N   VAL G 145 " --> pdb=" O   ARG G 156 " (cutoff:3.500A)
      removed outlier: 5.947A  pdb=" N   ARG G 156 " --> pdb=" O   VAL G 145 " (cutoff:3.500A)
      removed outlier: 5.133A  pdb=" N   VAL F 145 " --> pdb=" O   ARG F 156 " (cutoff:3.500A)
      removed outlier: 5.948A  pdb=" N   ARG F 156 " --> pdb=" O   VAL F 145 " (cutoff:3.500A)
      removed outlier: 3.748A  pdb=" N   ILE F 162 " --> pdb=" O   ASN E 177 " (cutoff:3.500A)
      removed outlier: 3.861A  pdb=" N   VAL F 164 " --> pdb=" O   ILE E 175 " (cutoff:3.500A)
      removed outlier: 3.571A  pdb=" N   ILE E 175 " --> pdb=" O   VAL F 164 " (cutoff:3.500A)
      removed outlier: 5.133A  pdb=" N   VAL E 145 " --> pdb=" O   ARG E 156 " (cutoff:3.500A)
      removed outlier: 5.947A  pdb=" N   ARG E 156 " --> pdb=" O   VAL E 145 " (cutoff:3.500A)
      removed outlier: 5.133A  pdb=" N   VAL D 145 " --> pdb=" O   ARG D 156 " (cutoff:3.500A)
      removed outlier: 5.948A  pdb=" N   ARG D 156 " --> pdb=" O   VAL D 145 " (cutoff:3.500A)
      removed outlier: 3.690A  pdb=" N   ILE D 162 " --> pdb=" O   ASN C 177 " (cutoff:3.500A)
      removed outlier: 3.816A  pdb=" N   VAL D 164 " --> pdb=" O   ILE C 175 " (cutoff:3.500A)
      removed outlier: 5.132A  pdb=" N   VAL C 145 " --> pdb=" O   ARG C 156 " (cutoff:3.500A)
      removed outlier: 5.947A  pdb=" N   ARG C 156 " --> pdb=" O   VAL C 145 " (cutoff:3.500A)
      removed outlier: 3.578A  pdb=" N   ILE C 162 " --> pdb=" O   ASN B 177 " (cutoff:3.500A)
      removed outlier: 3.893A  pdb=" N   VAL C 164 " --> pdb=" O   ILE B 175 " (cutoff:3.500A)
      removed outlier: 5.133A  pdb=" N   VAL B 145 " --> pdb=" O   ARG B 156 " (cutoff:3.500A)
      removed outlier: 5.948A  pdb=" N   ARG B 156 " --> pdb=" O   VAL B 145 " (cutoff:3.500A)
      removed outlier: 3.854A  pdb=" N   ILE B 162 " --> pdb=" O   ASN A 177 " (cutoff:3.500A)
      removed outlier: 4.029A  pdb=" N   VAL B 164 " --> pdb=" O   ILE A 175 " (cutoff:3.500A)
      removed outlier: 3.634A  pdb=" N   ILE A 175 " --> pdb=" O   VAL B 164 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 183 through 192
      removed outlier: 7.286A  pdb=" N   ASN A 234 " --> pdb=" O   ASN A 226 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 272 through 276
      removed outlier: 6.809A  pdb=" N   MET A 273 " --> pdb=" O   ASN G 276 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 183 through 192
      removed outlier: 7.284A  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: 7.285A  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: 7.285A  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: 7.285A  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: 7.284A  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: 7.284A  pdb=" N   ASN G 234 " --> pdb=" O   ASN G 226 " (cutoff:3.500A)

    911 hydrogen bonds defined for protein.
    2667 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 4.42

  Time building geometry restraints manager: 3.66 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: 4055
        1.34 -     1.45: 1891
        1.45 -     1.57: 7718
        1.57 -     1.69: 0
        1.69 -     1.81: 84
  Bond restraints: 13748
  Sorted by residual:
  bond pdb=" C   ILE F  39 "
       pdb=" N   VAL F  40 "
    ideal  model  delta    sigma   weight residual
    1.335  1.426 -0.091 1.09e-02 8.42e+03 6.95e+01
  bond pdb=" C   VAL F  40 "
       pdb=" N   GLY F  41 "
    ideal  model  delta    sigma   weight residual
    1.335  1.284  0.051 1.19e-02 7.06e+03 1.83e+01
  bond pdb=" C   PHE E 268 "
       pdb=" N   PRO E 269 "
    ideal  model  delta    sigma   weight residual
    1.333  1.314  0.019 1.20e-02 6.94e+03 2.62e+00
  bond pdb=" C   PHE D 268 "
       pdb=" N   PRO D 269 "
    ideal  model  delta    sigma   weight residual
    1.333  1.314  0.019 1.20e-02 6.94e+03 2.57e+00
  bond pdb=" C   PHE B 268 "
       pdb=" N   PRO B 269 "
    ideal  model  delta    sigma   weight residual
    1.333  1.314  0.019 1.20e-02 6.94e+03 2.46e+00
  ... (remaining 13743 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.34: 18127
        2.34 -     4.68: 469
        4.68 -     7.02: 25
        7.02 -     9.36: 13
        9.36 -    11.71: 7
  Bond angle restraints: 18641
  Sorted by residual:
  angle pdb=" O   ILE F  39 "
        pdb=" C   ILE F  39 "
        pdb=" N   VAL F  40 "
      ideal   model   delta    sigma   weight residual
     121.87  126.84   -4.97 9.70e-01 1.06e+00 2.63e+01
  angle pdb=" CA  ILE F  39 "
        pdb=" C   ILE F  39 "
        pdb=" N   VAL F  40 "
      ideal   model   delta    sigma   weight residual
     117.15  112.24    4.91 1.14e+00 7.69e-01 1.86e+01
  angle pdb=" N   GLY F  41 "
        pdb=" CA  GLY F  41 "
        pdb=" C   GLY F  41 "
      ideal   model   delta    sigma   weight residual
     113.86  108.62    5.24 1.50e+00 4.44e-01 1.22e+01
  angle pdb=" N   ILE F  39 "
        pdb=" CA  ILE F  39 "
        pdb=" C   ILE F  39 "
      ideal   model   delta    sigma   weight residual
     110.62  114.07   -3.45 1.02e+00 9.61e-01 1.14e+01
  angle pdb=" C   VAL F  40 "
        pdb=" N   GLY F  41 "
        pdb=" CA  GLY F  41 "
      ideal   model   delta    sigma   weight residual
     120.34  124.58   -4.24 1.26e+00 6.30e-01 1.13e+01
  ... (remaining 18636 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    11.53: 6650
       11.53 -    23.07: 1060
       23.07 -    34.60: 396
       34.60 -    46.13: 126
       46.13 -    57.66: 28
  Dihedral angle restraints: 8260
    sinusoidal: 3171
      harmonic: 5089
  Sorted by residual:
  dihedral pdb=" CA  PHE D 127 "
           pdb=" C   PHE D 127 "
           pdb=" N   ARG D 128 "
           pdb=" CA  ARG D 128 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -154.73  -25.27     0      5.00e+00 4.00e-02 2.56e+01
  dihedral pdb=" CA  PHE A 127 "
           pdb=" C   PHE A 127 "
           pdb=" N   ARG A 128 "
           pdb=" CA  ARG A 128 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -154.73  -25.27     0      5.00e+00 4.00e-02 2.55e+01
  dihedral pdb=" CA  PHE C 127 "
           pdb=" C   PHE C 127 "
           pdb=" N   ARG C 128 "
           pdb=" CA  ARG C 128 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -154.75  -25.25     0      5.00e+00 4.00e-02 2.55e+01
  ... (remaining 8257 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.086: 2011
       0.086 -    0.171: 243
       0.171 -    0.257: 17
       0.257 -    0.343: 4
       0.343 -    0.428: 7
  Chirality restraints: 2282
  Sorted by residual:
  chirality pdb=" CB  ILE D 176 "
            pdb=" CA  ILE D 176 "
            pdb=" CG1 ILE D 176 "
            pdb=" CG2 ILE D 176 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.22    0.43 2.00e-01 2.50e+01 4.59e+00
  chirality pdb=" CB  ILE E 176 "
            pdb=" CA  ILE E 176 "
            pdb=" CG1 ILE E 176 "
            pdb=" CG2 ILE E 176 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.22    0.43 2.00e-01 2.50e+01 4.57e+00
  chirality pdb=" CB  ILE B 176 "
            pdb=" CA  ILE B 176 "
            pdb=" CG1 ILE B 176 "
            pdb=" CG2 ILE B 176 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.22    0.43 2.00e-01 2.50e+01 4.57e+00
  ... (remaining 2279 not shown)

  Planarity restraints: 2366
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL F  40 "   -0.013 2.00e-02 2.50e+03   2.64e-02 6.97e+00
        pdb=" C   VAL F  40 "    0.046 2.00e-02 2.50e+03
        pdb=" O   VAL F  40 "   -0.017 2.00e-02 2.50e+03
        pdb=" N   GLY F  41 "   -0.016 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TYR C 270 "    0.031 5.00e-02 4.00e+02   4.74e-02 3.59e+00
        pdb=" N   PRO C 271 "   -0.082 5.00e-02 4.00e+02
        pdb=" CA  PRO C 271 "    0.024 5.00e-02 4.00e+02
        pdb=" CD  PRO C 271 "    0.027 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TYR E 270 "    0.031 5.00e-02 4.00e+02   4.74e-02 3.59e+00
        pdb=" N   PRO E 271 "   -0.082 5.00e-02 4.00e+02
        pdb=" CA  PRO E 271 "    0.024 5.00e-02 4.00e+02
        pdb=" CD  PRO E 271 "    0.027 5.00e-02 4.00e+02
  ... (remaining 2363 not shown)

  Histogram of nonbonded interaction distances:
        2.34 -     2.85: 4546
        2.85 -     3.36: 13032
        3.36 -     3.88: 22379
        3.88 -     4.39: 24500
        4.39 -     4.90: 43346
  Nonbonded interactions: 107803
  Sorted by model distance:
  nonbonded pdb=" O   SER A 179 "
            pdb=" OG  SER A 179 "
     model   vdw
     2.339 3.040
  nonbonded pdb=" O   SER G 179 "
            pdb=" OG  SER G 179 "
     model   vdw
     2.339 3.040
  nonbonded pdb=" O   SER E 179 "
            pdb=" OG  SER E 179 "
     model   vdw
     2.339 3.040
  nonbonded pdb=" O   SER B 179 "
            pdb=" OG  SER B 179 "
     model   vdw
     2.339 3.040
  nonbonded pdb=" O   SER C 179 "
            pdb=" OG  SER C 179 "
     model   vdw
     2.339 3.040
  ... (remaining 107798 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: 0.12
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'C'
  selection = chain 'B'
  selection = chain 'E'
  selection = chain 'D'
  selection = chain 'G'
  selection = chain 'F'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.650
  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:          0.530
  Check model and map are aligned:         0.110
  Set scattering table:                    0.140
  Process input model:                     33.070
  Find NCS groups from input model:        0.310
  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:             0.010
  Load rotamer database and sin/cos tables:3.000
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   37.900
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8077
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      :  0.006   0.091  13748  Z= 0.299
  Angle     :  0.876  11.706  18641  Z= 0.484
  Chirality :  0.059   0.428   2282
  Planarity :  0.006   0.047   2366
  Dihedral  : 14.085  57.663   4984
  Min Nonbonded Distance : 2.339

Molprobity Statistics.
  All-atom Clashscore : 6.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.14 %
    Favored  : 92.86 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  : 11.03 %
    Favored  : 88.97 %
  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: -4.56 (0.15), residues: 1764
  helix: -2.56 (0.12), residues: 896
  sheet: -3.05 (0.31), residues: 189
  loop : -3.48 (0.18), residues: 679

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.002   TRP E 240 
 PHE   0.010   0.003   PHE B 130 
 TYR   0.008   0.001   TYR B 194 
 ARG   0.002   0.000   ARG A 219 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.15862 (  911)
  hydrogen bonds       : angle       8.22214 ( 2667)
  covalent geometry    : bond        0.00641 (13748)
  covalent geometry    : angle       0.87580 (18641)

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

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

  3528 Ramachandran restraints generated.
    1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3528 Ramachandran restraints generated.
    1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  414 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 414
  time to evaluate  : 1.434 
Fit side-chains
   revert: symmetry clash
REVERT: A  138 LEU cc_start: 0.8682 (mp) cc_final: 0.8465 (mp)
REVERT: A  157 THR cc_start: 0.9412 (t) cc_final: 0.9146 (m)
REVERT: A  161 LYS cc_start: 0.9199 (mtmt) cc_final: 0.8934 (mtmm)
REVERT: A  200 GLN cc_start: 0.8726 (tt0) cc_final: 0.8518 (tt0)
REVERT: A  202 LYS cc_start: 0.8961 (mtpt) cc_final: 0.8758 (mtpp)
REVERT: A  273 MET cc_start: 0.8136 (ttm) cc_final: 0.7624 (ttm)
REVERT: B   47 MET cc_start: 0.4077 (ttt) cc_final: 0.3650 (mtt)
REVERT: B  111 LEU cc_start: 0.8787 (mp) cc_final: 0.8572 (mp)
REVERT: B  157 THR cc_start: 0.9256 (t) cc_final: 0.8932 (m)
REVERT: B  273 MET cc_start: 0.8068 (ttm) cc_final: 0.7540 (ttm)
REVERT: C   47 MET cc_start: 0.4280 (ttt) cc_final: 0.3934 (mtt)
REVERT: C  126 MET cc_start: 0.7484 (ttt) cc_final: 0.7194 (ttt)
REVERT: C  151 PHE cc_start: 0.8789 (m-80) cc_final: 0.8583 (m-80)
REVERT: C  200 GLN cc_start: 0.8681 (tt0) cc_final: 0.8372 (tt0)
REVERT: C  273 MET cc_start: 0.8253 (ttm) cc_final: 0.8014 (ttm)
REVERT: D   47 MET cc_start: 0.3559 (ttt) cc_final: 0.3088 (mtt)
REVERT: D  157 THR cc_start: 0.8945 (t) cc_final: 0.8728 (m)
REVERT: D  186 ASN cc_start: 0.8780 (m-40) cc_final: 0.8569 (m-40)
REVERT: D  190 ILE cc_start: 0.9565 (mp) cc_final: 0.9331 (mt)
REVERT: D  200 GLN cc_start: 0.8741 (tt0) cc_final: 0.8527 (tt0)
REVERT: D  203 GLN cc_start: 0.8316 (tp40) cc_final: 0.8094 (tp40)
REVERT: D  270 TYR cc_start: 0.9008 (m-80) cc_final: 0.8436 (m-80)
REVERT: D  273 MET cc_start: 0.7905 (ttm) cc_final: 0.7662 (ttm)
REVERT: E   47 MET cc_start: 0.3441 (ttt) cc_final: 0.3193 (ttt)
REVERT: E  138 LEU cc_start: 0.8503 (mp) cc_final: 0.8239 (mp)
REVERT: E  159 ASP cc_start: 0.8389 (p0) cc_final: 0.8126 (p0)
REVERT: E  161 LYS cc_start: 0.9122 (mtmt) cc_final: 0.8842 (mtmm)
REVERT: E  277 PHE cc_start: 0.7593 (m-10) cc_final: 0.7117 (m-10)
REVERT: F   47 MET cc_start: 0.4310 (ttt) cc_final: 0.3874 (mtt)
REVERT: F  115 LEU cc_start: 0.9121 (tt) cc_final: 0.8822 (tp)
REVERT: F  190 ILE cc_start: 0.9619 (mp) cc_final: 0.9373 (mt)
REVERT: F  200 GLN cc_start: 0.8926 (tt0) cc_final: 0.8671 (tt0)
REVERT: F  272 GLN cc_start: 0.8803 (mm-40) cc_final: 0.8507 (mm-40)
REVERT: G  273 MET cc_start: 0.7991 (ttm) cc_final: 0.7313 (ttm)
REVERT: G  274 ASP cc_start: 0.8146 (t0) cc_final: 0.7458 (t70)
  outliers start: 0
  outliers final: 0
  residues processed: 414
  average time/residue: 0.2500
  time to fit residues: 149.6333
Evaluate side-chains
  281 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 281
  time to evaluate  : 1.438 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 175
   random chunks:
   chunk 147 optimal weight:    0.7980
   chunk 132 optimal weight:    9.9990
   chunk 73 optimal weight:    2.9990
   chunk 45 optimal weight:    2.9990
   chunk 89 optimal weight:    0.7980
   chunk 70 optimal weight:    0.9980
   chunk 137 optimal weight:    0.0970
   chunk 53 optimal weight:    1.9990
   chunk 83 optimal weight:    6.9990
   chunk 102 optimal weight:    7.9990
   chunk 158 optimal weight:    1.9990
   overall best weight:    0.9380

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

Flipped N/Q/H residues before XYZ refinement:
A 112 GLN
A 167 ASN
B 167 ASN
C 167 ASN
D 167 ASN
E 167 ASN
F 167 ASN
G 112 GLN
G 167 ASN

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4039 r_free = 0.4039 target = 0.165734 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3389 r_free = 0.3389 target = 0.114881 restraints weight = 19064.164|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 48)----------------|
| r_work = 0.3450 r_free = 0.3450 target = 0.118974 restraints weight = 9787.882|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3489 r_free = 0.3489 target = 0.121640 restraints weight = 6529.328|
|-----------------------------------------------------------------------------|
r_work (final): 0.3063
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7930
moved from start:          0.2436

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028  13748  Z= 0.138
  Angle     :  0.581   8.417  18641  Z= 0.305
  Chirality :  0.046   0.306   2282
  Planarity :  0.004   0.034   2366
  Dihedral  :  5.296  23.451   1939
  Min Nonbonded Distance : 2.520

Molprobity Statistics.
  All-atom Clashscore : 9.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.50 %
    Favored  : 94.50 %
  Rotamer:
    Outliers :  2.98 %
    Allowed  : 15.88 %
    Favored  : 81.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.52 (0.17), residues: 1764
  helix: -0.50 (0.16), residues: 903
  sheet: -2.17 (0.29), residues: 238
  loop : -3.18 (0.19), residues: 623

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP E 240 
 PHE   0.017   0.001   PHE D 277 
 TYR   0.008   0.001   TYR G 135 
 ARG   0.006   0.000   ARG B 180 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04171 (  911)
  hydrogen bonds       : angle       5.15552 ( 2667)
  covalent geometry    : bond        0.00297 (13748)
  covalent geometry    : angle       0.58146 (18641)

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

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

  3528 Ramachandran restraints generated.
    1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3528 Ramachandran restraints generated.
    1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  371 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 328
  time to evaluate  : 1.565 
Fit side-chains
REVERT: A  161 LYS cc_start: 0.9080 (mtmt) cc_final: 0.8667 (mtmm)
REVERT: A  210 GLN cc_start: 0.8977 (mm-40) cc_final: 0.8533 (mm-40)
REVERT: A  273 MET cc_start: 0.8299 (ttm) cc_final: 0.7330 (ttm)
REVERT: B   47 MET cc_start: 0.3611 (ttt) cc_final: 0.3306 (mtt)
REVERT: B  273 MET cc_start: 0.8259 (ttm) cc_final: 0.7482 (ttm)
REVERT: C   47 MET cc_start: 0.4180 (ttt) cc_final: 0.3911 (mtt)
REVERT: C  126 MET cc_start: 0.7729 (ttt) cc_final: 0.7407 (ttt)
REVERT: C  127 PHE cc_start: 0.7024 (t80) cc_final: 0.6604 (t80)
REVERT: C  138 LEU cc_start: 0.8904 (mp) cc_final: 0.8582 (mp)
REVERT: C  150 ILE cc_start: 0.9138 (tp) cc_final: 0.8925 (tp)
REVERT: C  157 THR cc_start: 0.9425 (t) cc_final: 0.9141 (m)
REVERT: C  239 VAL cc_start: 0.9312 (OUTLIER) cc_final: 0.9088 (m)
REVERT: C  272 GLN cc_start: 0.9207 (mm-40) cc_final: 0.8872 (mm-40)
REVERT: C  273 MET cc_start: 0.8153 (ttm) cc_final: 0.7685 (ttm)
REVERT: C  274 ASP cc_start: 0.7987 (t0) cc_final: 0.7456 (t70)
REVERT: D   47 MET cc_start: 0.3108 (ttt) cc_final: 0.2708 (mtt)
REVERT: D  127 PHE cc_start: 0.7104 (t80) cc_final: 0.6737 (t80)
REVERT: D  151 PHE cc_start: 0.8865 (m-80) cc_final: 0.8548 (m-80)
REVERT: D  203 GLN cc_start: 0.8687 (tp40) cc_final: 0.8321 (tp40)
REVERT: D  270 TYR cc_start: 0.9086 (m-80) cc_final: 0.8606 (m-80)
REVERT: D  272 GLN cc_start: 0.9227 (mm-40) cc_final: 0.8778 (mm-40)
REVERT: D  273 MET cc_start: 0.7637 (ttm) cc_final: 0.7156 (ttm)
REVERT: D  277 PHE cc_start: 0.8205 (m-10) cc_final: 0.7891 (m-80)
REVERT: D  278 LYS cc_start: 0.8202 (mttp) cc_final: 0.7841 (mttp)
REVERT: E  161 LYS cc_start: 0.8986 (mtmt) cc_final: 0.8719 (mtmm)
REVERT: E  181 GLU cc_start: 0.8755 (tp30) cc_final: 0.8527 (tp30)
REVERT: E  273 MET cc_start: 0.7911 (OUTLIER) cc_final: 0.7577 (mtm)
REVERT: F   47 MET cc_start: 0.4083 (ttt) cc_final: 0.3709 (mtt)
REVERT: F  115 LEU cc_start: 0.8975 (OUTLIER) cc_final: 0.8632 (tt)
REVERT: F  134 GLU cc_start: 0.7630 (mt-10) cc_final: 0.7294 (mt-10)
REVERT: F  157 THR cc_start: 0.9236 (t) cc_final: 0.8977 (m)
REVERT: F  210 GLN cc_start: 0.9049 (tp40) cc_final: 0.8794 (mm110)
REVERT: F  272 GLN cc_start: 0.9013 (mm-40) cc_final: 0.8567 (mm-40)
REVERT: G  157 THR cc_start: 0.9339 (t) cc_final: 0.9042 (m)
REVERT: G  274 ASP cc_start: 0.8042 (t0) cc_final: 0.7622 (t70)
  outliers start: 43
  outliers final: 16
  residues processed: 355
  average time/residue: 0.2221
  time to fit residues: 120.2328
Evaluate side-chains
  282 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 263
  time to evaluate  : 2.018 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  176 ILE
Chi-restraints excluded: chain A residue  239 VAL
Chi-restraints excluded: chain B residue  109 LEU
Chi-restraints excluded: chain B residue  144 THR
Chi-restraints excluded: chain B residue  176 ILE
Chi-restraints excluded: chain C residue  144 THR
Chi-restraints excluded: chain C residue  176 ILE
Chi-restraints excluded: chain C residue  239 VAL
Chi-restraints excluded: chain D residue  141 VAL
Chi-restraints excluded: chain D residue  144 THR
Chi-restraints excluded: chain D residue  239 VAL
Chi-restraints excluded: chain E residue  176 ILE
Chi-restraints excluded: chain E residue  218 ASP
Chi-restraints excluded: chain E residue  273 MET
Chi-restraints excluded: chain F residue  115 LEU
Chi-restraints excluded: chain F residue  141 VAL
Chi-restraints excluded: chain F residue  239 VAL
Chi-restraints excluded: chain G residue  127 PHE
Chi-restraints excluded: chain G residue  176 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 175
   random chunks:
   chunk 143 optimal weight:    0.7980
   chunk 4 optimal weight:    9.9990
   chunk 104 optimal weight:    4.9990
   chunk 58 optimal weight:    7.9990
   chunk 52 optimal weight:    7.9990
   chunk 106 optimal weight:   10.0000
   chunk 42 optimal weight:    0.9980
   chunk 171 optimal weight:    0.9980
   chunk 30 optimal weight:    6.9990
   chunk 95 optimal weight:    2.9990
   chunk 118 optimal weight:    3.9990
   overall best weight:    1.9584

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3936 r_free = 0.3936 target = 0.157292 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3259 r_free = 0.3259 target = 0.106108 restraints weight = 18996.819|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 48)----------------|
| r_work = 0.3317 r_free = 0.3317 target = 0.109946 restraints weight = 9642.755|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3354 r_free = 0.3354 target = 0.112424 restraints weight = 6407.472|
|-----------------------------------------------------------------------------|
r_work (final): 0.3272
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8091
moved from start:          0.3124

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046  13748  Z= 0.190
  Angle     :  0.610   8.538  18641  Z= 0.319
  Chirality :  0.047   0.389   2282
  Planarity :  0.003   0.033   2366
  Dihedral  :  5.178  23.235   1939
  Min Nonbonded Distance : 2.531

Molprobity Statistics.
  All-atom Clashscore : 10.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.73 %
    Favored  : 94.27 %
  Rotamer:
    Outliers :  3.26 %
    Allowed  : 17.48 %
    Favored  : 79.26 %
  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: -1.71 (0.19), residues: 1764
  helix:  0.41 (0.17), residues: 896
  sheet: -2.21 (0.27), residues: 273
  loop : -2.98 (0.20), residues: 595

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP B 240 
 PHE   0.016   0.001   PHE E 178 
 TYR   0.008   0.001   TYR G 135 
 ARG   0.006   0.000   ARG D 256 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04063 (  911)
  hydrogen bonds       : angle       4.78335 ( 2667)
  covalent geometry    : bond        0.00429 (13748)
  covalent geometry    : angle       0.60981 (18641)

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

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

  3528 Ramachandran restraints generated.
    1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3528 Ramachandran restraints generated.
    1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  318 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 271
  time to evaluate  : 1.581 
Fit side-chains
REVERT: A  112 GLN cc_start: 0.8814 (tm-30) cc_final: 0.8298 (tm-30)
REVERT: A  273 MET cc_start: 0.8180 (ttm) cc_final: 0.7342 (ttm)
REVERT: B   47 MET cc_start: 0.3686 (ttt) cc_final: 0.3423 (mtt)
REVERT: B  187 GLU cc_start: 0.7762 (tt0) cc_final: 0.7345 (tt0)
REVERT: B  212 GLU cc_start: 0.8195 (tm-30) cc_final: 0.7918 (tm-30)
REVERT: B  238 ARG cc_start: 0.8466 (mtt180) cc_final: 0.8084 (mtt-85)
REVERT: B  273 MET cc_start: 0.8266 (ttm) cc_final: 0.7543 (ttm)
REVERT: C   47 MET cc_start: 0.4221 (ttt) cc_final: 0.3937 (mtt)
REVERT: C  115 LEU cc_start: 0.9104 (OUTLIER) cc_final: 0.8889 (tt)
REVERT: C  126 MET cc_start: 0.7637 (ttt) cc_final: 0.7372 (ttt)
REVERT: C  127 PHE cc_start: 0.7018 (t80) cc_final: 0.6602 (t80)
REVERT: C  138 LEU cc_start: 0.9058 (mp) cc_final: 0.8773 (mp)
REVERT: C  150 ILE cc_start: 0.9142 (tp) cc_final: 0.8918 (tp)
REVERT: C  157 THR cc_start: 0.9504 (t) cc_final: 0.9256 (m)
REVERT: C  212 GLU cc_start: 0.8283 (tm-30) cc_final: 0.7928 (tm-30)
REVERT: C  272 GLN cc_start: 0.9151 (mm-40) cc_final: 0.8801 (mm-40)
REVERT: C  273 MET cc_start: 0.8120 (ttm) cc_final: 0.7797 (ttm)
REVERT: D   47 MET cc_start: 0.3186 (ttt) cc_final: 0.2746 (mtt)
REVERT: D  127 PHE cc_start: 0.7178 (t80) cc_final: 0.6792 (t80)
REVERT: D  187 GLU cc_start: 0.7624 (tp30) cc_final: 0.7390 (tp30)
REVERT: D  203 GLN cc_start: 0.8634 (tp40) cc_final: 0.8300 (tp40)
REVERT: D  212 GLU cc_start: 0.8293 (tm-30) cc_final: 0.7942 (tm-30)
REVERT: D  270 TYR cc_start: 0.9122 (m-80) cc_final: 0.8631 (m-80)
REVERT: E  126 MET cc_start: 0.7916 (ttt) cc_final: 0.7707 (ttt)
REVERT: E  134 GLU cc_start: 0.7600 (mt-10) cc_final: 0.7349 (mt-10)
REVERT: E  181 GLU cc_start: 0.8709 (tp30) cc_final: 0.8482 (tp30)
REVERT: E  273 MET cc_start: 0.8154 (mtm) cc_final: 0.7892 (mtp)
REVERT: F   47 MET cc_start: 0.4327 (ttt) cc_final: 0.3919 (mtt)
REVERT: F  115 LEU cc_start: 0.9124 (OUTLIER) cc_final: 0.8850 (tt)
REVERT: F  134 GLU cc_start: 0.7767 (mt-10) cc_final: 0.7532 (mt-10)
REVERT: F  149 GLN cc_start: 0.8443 (mt0) cc_final: 0.8177 (mm-40)
REVERT: F  157 THR cc_start: 0.9446 (t) cc_final: 0.9139 (m)
REVERT: F  212 GLU cc_start: 0.8181 (tm-30) cc_final: 0.7790 (tm-30)
REVERT: G  134 GLU cc_start: 0.7943 (pm20) cc_final: 0.7707 (pm20)
REVERT: G  157 THR cc_start: 0.9450 (t) cc_final: 0.9165 (m)
REVERT: G  273 MET cc_start: 0.7947 (ttm) cc_final: 0.7136 (ttm)
REVERT: G  274 ASP cc_start: 0.8095 (t0) cc_final: 0.7635 (t70)
  outliers start: 47
  outliers final: 24
  residues processed: 307
  average time/residue: 0.2053
  time to fit residues: 98.8062
Evaluate side-chains
  263 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 237
  time to evaluate  : 1.615 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  176 ILE
Chi-restraints excluded: chain B residue  109 LEU
Chi-restraints excluded: chain B residue  126 MET
Chi-restraints excluded: chain B residue  144 THR
Chi-restraints excluded: chain B residue  176 ILE
Chi-restraints excluded: chain B residue  223 VAL
Chi-restraints excluded: chain B residue  239 VAL
Chi-restraints excluded: chain C residue  115 LEU
Chi-restraints excluded: chain C residue  144 THR
Chi-restraints excluded: chain C residue  176 ILE
Chi-restraints excluded: chain C residue  223 VAL
Chi-restraints excluded: chain D residue  138 LEU
Chi-restraints excluded: chain D residue  144 THR
Chi-restraints excluded: chain D residue  223 VAL
Chi-restraints excluded: chain E residue  109 LEU
Chi-restraints excluded: chain E residue  176 ILE
Chi-restraints excluded: chain E residue  218 ASP
Chi-restraints excluded: chain E residue  225 LEU
Chi-restraints excluded: chain F residue  111 LEU
Chi-restraints excluded: chain F residue  115 LEU
Chi-restraints excluded: chain F residue  176 ILE
Chi-restraints excluded: chain F residue  223 VAL
Chi-restraints excluded: chain G residue  127 PHE
Chi-restraints excluded: chain G residue  152 SER
Chi-restraints excluded: chain G residue  176 ILE
Chi-restraints excluded: chain G residue  223 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 175
   random chunks:
   chunk 92 optimal weight:    1.9990
   chunk 59 optimal weight:    5.9990
   chunk 70 optimal weight:    3.9990
   chunk 125 optimal weight:   40.0000
   chunk 155 optimal weight:    6.9990
   chunk 73 optimal weight:    2.9990
   chunk 158 optimal weight:    0.8980
   chunk 169 optimal weight:    3.9990
   chunk 130 optimal weight:    5.9990
   chunk 147 optimal weight:    2.9990
   chunk 124 optimal weight:    5.9990
   overall best weight:    2.5788

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3861 r_free = 0.3861 target = 0.151374 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3177 r_free = 0.3177 target = 0.100770 restraints weight = 19034.125|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 48)----------------|
| r_work = 0.3231 r_free = 0.3231 target = 0.104205 restraints weight = 10137.332|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3266 r_free = 0.3266 target = 0.106476 restraints weight = 6905.699|
|-----------------------------------------------------------------------------|
r_work (final): 0.2945
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8075
moved from start:          0.3502

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.069  13748  Z= 0.234
  Angle     :  0.622   8.467  18641  Z= 0.326
  Chirality :  0.047   0.397   2282
  Planarity :  0.003   0.036   2366
  Dihedral  :  5.145  23.779   1939
  Min Nonbonded Distance : 2.526

Molprobity Statistics.
  All-atom Clashscore : 10.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.58 %
    Favored  : 93.42 %
  Rotamer:
    Outliers :  4.09 %
    Allowed  : 17.55 %
    Favored  : 78.36 %
  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: -1.31 (0.19), residues: 1764
  helix:  0.80 (0.17), residues: 896
  sheet: -1.87 (0.31), residues: 224
  loop : -2.98 (0.19), residues: 644

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP G 240 
 PHE   0.018   0.001   PHE D 277 
 TYR   0.010   0.001   TYR B 135 
 ARG   0.004   0.000   ARG D 256 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04066 (  911)
  hydrogen bonds       : angle       4.66163 ( 2667)
  covalent geometry    : bond        0.00533 (13748)
  covalent geometry    : angle       0.62242 (18641)

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

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

  3528 Ramachandran restraints generated.
    1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3528 Ramachandran restraints generated.
    1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  308 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 59
    poor density    : 249
  time to evaluate  : 1.503 
Fit side-chains
REVERT: A  112 GLN cc_start: 0.8859 (tm-30) cc_final: 0.8380 (tm-30)
REVERT: A  203 GLN cc_start: 0.8685 (tp40) cc_final: 0.8363 (tp40)
REVERT: A  212 GLU cc_start: 0.8663 (tp30) cc_final: 0.8087 (tm-30)
REVERT: A  272 GLN cc_start: 0.9247 (mm-40) cc_final: 0.8959 (mm-40)
REVERT: A  273 MET cc_start: 0.8191 (ttm) cc_final: 0.7254 (ttm)
REVERT: B   47 MET cc_start: 0.3620 (ttt) cc_final: 0.3364 (mtt)
REVERT: B  115 LEU cc_start: 0.9239 (OUTLIER) cc_final: 0.9009 (tt)
REVERT: B  187 GLU cc_start: 0.7837 (tt0) cc_final: 0.7301 (tt0)
REVERT: B  212 GLU cc_start: 0.8223 (tm-30) cc_final: 0.7997 (tm-30)
REVERT: B  238 ARG cc_start: 0.8528 (mtt180) cc_final: 0.8005 (mtt-85)
REVERT: B  273 MET cc_start: 0.8216 (ttm) cc_final: 0.7468 (ttm)
REVERT: C   47 MET cc_start: 0.4167 (ttt) cc_final: 0.3937 (mtt)
REVERT: C  112 GLN cc_start: 0.8193 (tt0) cc_final: 0.7954 (tm-30)
REVERT: C  126 MET cc_start: 0.8027 (ttt) cc_final: 0.7733 (ttt)
REVERT: C  138 LEU cc_start: 0.9062 (mp) cc_final: 0.8761 (mp)
REVERT: C  157 THR cc_start: 0.9478 (t) cc_final: 0.9249 (m)
REVERT: C  212 GLU cc_start: 0.8329 (tm-30) cc_final: 0.8124 (tm-30)
REVERT: C  273 MET cc_start: 0.8106 (ttm) cc_final: 0.7628 (ttm)
REVERT: C  274 ASP cc_start: 0.7953 (t0) cc_final: 0.7460 (t0)
REVERT: D   47 MET cc_start: 0.3293 (ttt) cc_final: 0.2860 (mtt)
REVERT: D  187 GLU cc_start: 0.7735 (tt0) cc_final: 0.7431 (tp30)
REVERT: D  212 GLU cc_start: 0.8237 (tm-30) cc_final: 0.7954 (tm-30)
REVERT: D  270 TYR cc_start: 0.9124 (m-80) cc_final: 0.8627 (m-80)
REVERT: D  272 GLN cc_start: 0.9305 (mm110) cc_final: 0.8897 (mm-40)
REVERT: E  134 GLU cc_start: 0.7786 (mt-10) cc_final: 0.7427 (mt-10)
REVERT: E  181 GLU cc_start: 0.8755 (tp30) cc_final: 0.8544 (tp30)
REVERT: E  212 GLU cc_start: 0.8464 (tm-30) cc_final: 0.8136 (tp30)
REVERT: F   47 MET cc_start: 0.4132 (ttt) cc_final: 0.3746 (mtt)
REVERT: F  115 LEU cc_start: 0.9238 (OUTLIER) cc_final: 0.8963 (tt)
REVERT: F  134 GLU cc_start: 0.7847 (mt-10) cc_final: 0.7521 (mt-10)
REVERT: F  149 GLN cc_start: 0.8505 (mt0) cc_final: 0.8233 (mt0)
REVERT: F  157 THR cc_start: 0.9445 (t) cc_final: 0.9212 (m)
REVERT: F  212 GLU cc_start: 0.8249 (tm-30) cc_final: 0.7940 (tm-30)
REVERT: G  134 GLU cc_start: 0.7942 (pm20) cc_final: 0.7629 (pm20)
REVERT: G  274 ASP cc_start: 0.7916 (t0) cc_final: 0.7372 (t70)
  outliers start: 59
  outliers final: 34
  residues processed: 293
  average time/residue: 0.2025
  time to fit residues: 94.6101
Evaluate side-chains
  268 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 232
  time to evaluate  : 1.918 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  144 THR
Chi-restraints excluded: chain A residue  176 ILE
Chi-restraints excluded: chain A residue  233 ILE
Chi-restraints excluded: chain B residue  109 LEU
Chi-restraints excluded: chain B residue  115 LEU
Chi-restraints excluded: chain B residue  144 THR
Chi-restraints excluded: chain B residue  176 ILE
Chi-restraints excluded: chain B residue  199 ASP
Chi-restraints excluded: chain B residue  223 VAL
Chi-restraints excluded: chain B residue  239 VAL
Chi-restraints excluded: chain C residue  144 THR
Chi-restraints excluded: chain C residue  149 GLN
Chi-restraints excluded: chain C residue  176 ILE
Chi-restraints excluded: chain C residue  223 VAL
Chi-restraints excluded: chain C residue  227 GLU
Chi-restraints excluded: chain D residue  138 LEU
Chi-restraints excluded: chain D residue  144 THR
Chi-restraints excluded: chain D residue  176 ILE
Chi-restraints excluded: chain D residue  199 ASP
Chi-restraints excluded: chain D residue  223 VAL
Chi-restraints excluded: chain E residue  127 PHE
Chi-restraints excluded: chain E residue  144 THR
Chi-restraints excluded: chain E residue  164 VAL
Chi-restraints excluded: chain E residue  176 ILE
Chi-restraints excluded: chain E residue  218 ASP
Chi-restraints excluded: chain E residue  225 LEU
Chi-restraints excluded: chain F residue  115 LEU
Chi-restraints excluded: chain F residue  144 THR
Chi-restraints excluded: chain F residue  176 ILE
Chi-restraints excluded: chain F residue  223 VAL
Chi-restraints excluded: chain F residue  233 ILE
Chi-restraints excluded: chain G residue  136 VAL
Chi-restraints excluded: chain G residue  144 THR
Chi-restraints excluded: chain G residue  152 SER
Chi-restraints excluded: chain G residue  176 ILE
Chi-restraints excluded: chain G residue  223 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 175
   random chunks:
   chunk 92 optimal weight:    0.7980
   chunk 156 optimal weight:   30.0000
   chunk 65 optimal weight:    2.9990
   chunk 158 optimal weight:    6.9990
   chunk 110 optimal weight:    0.1980
   chunk 113 optimal weight:    0.9990
   chunk 141 optimal weight:    1.9990
   chunk 102 optimal weight:    6.9990
   chunk 165 optimal weight:    3.9990
   chunk 28 optimal weight:    3.9990
   chunk 99 optimal weight:    2.9990
   overall best weight:    1.3986

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

Flipped N/Q/H residues before XYZ refinement:
B 149 GLN
E 149 GLN
E 200 GLN
F 210 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3948 r_free = 0.3948 target = 0.158060 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.3261 r_free = 0.3261 target = 0.106268 restraints weight = 19114.196|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 53)----------------|
| r_work = 0.3323 r_free = 0.3323 target = 0.110211 restraints weight = 9705.281|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 53)----------------|
| r_work = 0.3361 r_free = 0.3361 target = 0.112746 restraints weight = 6430.870|
|-----------------------------------------------------------------------------|
r_work (final): 0.3144
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8116
moved from start:          0.3677

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.068  13748  Z= 0.154
  Angle     :  0.579   8.997  18641  Z= 0.299
  Chirality :  0.046   0.382   2282
  Planarity :  0.003   0.034   2366
  Dihedral  :  4.944  21.216   1939
  Min Nonbonded Distance : 2.531

Molprobity Statistics.
  All-atom Clashscore : 9.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.07 %
    Favored  : 93.93 %
  Rotamer:
    Outliers :  2.91 %
    Allowed  : 20.32 %
    Favored  : 76.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.98 (0.19), residues: 1764
  helix:  1.09 (0.17), residues: 896
  sheet: -1.63 (0.31), residues: 224
  loop : -2.88 (0.19), residues: 644

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP D 240 
 PHE   0.014   0.001   PHE D 277 
 TYR   0.009   0.001   TYR B 135 
 ARG   0.003   0.000   ARG E 184 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03934 (  911)
  hydrogen bonds       : angle       4.48951 ( 2667)
  covalent geometry    : bond        0.00347 (13748)
  covalent geometry    : angle       0.57855 (18641)

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

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

  3528 Ramachandran restraints generated.
    1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3528 Ramachandran restraints generated.
    1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  305 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 263
  time to evaluate  : 1.447 
Fit side-chains
REVERT: A  112 GLN cc_start: 0.8837 (tm-30) cc_final: 0.8422 (tm-30)
REVERT: A  203 GLN cc_start: 0.8692 (tp40) cc_final: 0.8311 (tp40)
REVERT: A  212 GLU cc_start: 0.8525 (tp30) cc_final: 0.8131 (tm-30)
REVERT: A  216 LEU cc_start: 0.9420 (mt) cc_final: 0.9181 (mt)
REVERT: A  272 GLN cc_start: 0.9190 (mm-40) cc_final: 0.8880 (mm-40)
REVERT: A  273 MET cc_start: 0.8042 (ttm) cc_final: 0.7082 (ttm)
REVERT: B   47 MET cc_start: 0.3649 (ttt) cc_final: 0.3372 (mtt)
REVERT: B  273 MET cc_start: 0.8131 (ttm) cc_final: 0.7363 (ttm)
REVERT: C   47 MET cc_start: 0.4194 (ttt) cc_final: 0.3940 (mtt)
REVERT: C  126 MET cc_start: 0.7942 (ttt) cc_final: 0.7663 (ttt)
REVERT: C  138 LEU cc_start: 0.9115 (mp) cc_final: 0.8700 (mp)
REVERT: C  157 THR cc_start: 0.9490 (t) cc_final: 0.9178 (m)
REVERT: C  272 GLN cc_start: 0.9092 (mm-40) cc_final: 0.8836 (mm-40)
REVERT: C  273 MET cc_start: 0.8046 (ttm) cc_final: 0.7716 (ttm)
REVERT: D   47 MET cc_start: 0.3344 (ttt) cc_final: 0.2911 (mtt)
REVERT: D  115 LEU cc_start: 0.9274 (OUTLIER) cc_final: 0.8897 (tp)
REVERT: D  187 GLU cc_start: 0.7612 (tt0) cc_final: 0.7327 (tp30)
REVERT: D  203 GLN cc_start: 0.8580 (tp40) cc_final: 0.8348 (tp40)
REVERT: D  270 TYR cc_start: 0.9098 (m-80) cc_final: 0.8510 (m-80)
REVERT: D  272 GLN cc_start: 0.9190 (mm-40) cc_final: 0.8954 (mm-40)
REVERT: E   69 LEU cc_start: 0.8893 (mm) cc_final: 0.8621 (tp)
REVERT: E  150 ILE cc_start: 0.9383 (OUTLIER) cc_final: 0.9143 (tp)
REVERT: E  181 GLU cc_start: 0.8580 (tp30) cc_final: 0.8352 (tp30)
REVERT: E  212 GLU cc_start: 0.8420 (tm-30) cc_final: 0.8064 (tp30)
REVERT: F   47 MET cc_start: 0.4194 (ttt) cc_final: 0.3794 (mtt)
REVERT: F  112 GLN cc_start: 0.8678 (tm-30) cc_final: 0.8192 (tm-30)
REVERT: F  115 LEU cc_start: 0.9232 (OUTLIER) cc_final: 0.8958 (tt)
REVERT: F  134 GLU cc_start: 0.7676 (mt-10) cc_final: 0.7467 (mt-10)
REVERT: F  149 GLN cc_start: 0.8495 (mt0) cc_final: 0.8149 (mt0)
REVERT: F  157 THR cc_start: 0.9461 (t) cc_final: 0.9181 (m)
REVERT: G  112 GLN cc_start: 0.8675 (tm-30) cc_final: 0.8304 (tm-30)
REVERT: G  134 GLU cc_start: 0.7797 (pm20) cc_final: 0.7517 (pm20)
REVERT: G  272 GLN cc_start: 0.9018 (mm110) cc_final: 0.8762 (mm110)
REVERT: G  274 ASP cc_start: 0.8020 (t0) cc_final: 0.7498 (t70)
  outliers start: 42
  outliers final: 23
  residues processed: 295
  average time/residue: 0.2090
  time to fit residues: 95.0308
Evaluate side-chains
  268 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 242
  time to evaluate  : 1.493 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  144 THR
Chi-restraints excluded: chain A residue  176 ILE
Chi-restraints excluded: chain A residue  233 ILE
Chi-restraints excluded: chain B residue  109 LEU
Chi-restraints excluded: chain B residue  144 THR
Chi-restraints excluded: chain B residue  176 ILE
Chi-restraints excluded: chain B residue  223 VAL
Chi-restraints excluded: chain B residue  239 VAL
Chi-restraints excluded: chain C residue  144 THR
Chi-restraints excluded: chain C residue  149 GLN
Chi-restraints excluded: chain C residue  223 VAL
Chi-restraints excluded: chain D residue  115 LEU
Chi-restraints excluded: chain D residue  126 MET
Chi-restraints excluded: chain D residue  144 THR
Chi-restraints excluded: chain D residue  223 VAL
Chi-restraints excluded: chain E residue  127 PHE
Chi-restraints excluded: chain E residue  144 THR
Chi-restraints excluded: chain E residue  150 ILE
Chi-restraints excluded: chain E residue  176 ILE
Chi-restraints excluded: chain E residue  225 LEU
Chi-restraints excluded: chain F residue  115 LEU
Chi-restraints excluded: chain F residue  144 THR
Chi-restraints excluded: chain F residue  176 ILE
Chi-restraints excluded: chain F residue  223 VAL
Chi-restraints excluded: chain G residue  176 ILE
Chi-restraints excluded: chain G residue  223 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 175
   random chunks:
   chunk 27 optimal weight:   20.0000
   chunk 151 optimal weight:    8.9990
   chunk 47 optimal weight:    1.9990
   chunk 88 optimal weight:    2.9990
   chunk 150 optimal weight:    5.9990
   chunk 169 optimal weight:    2.9990
   chunk 170 optimal weight:    3.9990
   chunk 25 optimal weight:   40.0000
   chunk 10 optimal weight:    0.1980
   chunk 0 optimal weight:   40.0000
   chunk 55 optimal weight:    6.9990
   overall best weight:    2.4388

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

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3913 r_free = 0.3913 target = 0.155412 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3198 r_free = 0.3198 target = 0.102708 restraints weight = 19253.376|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 58)----------------|
| r_work = 0.3260 r_free = 0.3260 target = 0.106492 restraints weight = 10102.685|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 51)----------------|
| r_work = 0.3298 r_free = 0.3298 target = 0.108932 restraints weight = 6813.822|
|-----------------------------------------------------------------------------|
r_work (final): 0.2959
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8080
moved from start:          0.3849

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.074  13748  Z= 0.224
  Angle     :  0.624   7.425  18641  Z= 0.325
  Chirality :  0.046   0.389   2282
  Planarity :  0.003   0.035   2366
  Dihedral  :  5.037  22.946   1939
  Min Nonbonded Distance : 2.512

Molprobity Statistics.
  All-atom Clashscore : 10.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.80 %
    Favored  : 93.20 %
  Rotamer:
    Outliers :  3.68 %
    Allowed  : 21.08 %
    Favored  : 75.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.84 (0.19), residues: 1764
  helix:  1.19 (0.17), residues: 896
  sheet: -1.87 (0.31), residues: 210
  loop : -2.66 (0.20), residues: 658

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP G 240 
 PHE   0.012   0.001   PHE E 178 
 TYR   0.009   0.001   TYR D 135 
 ARG   0.006   0.000   ARG G 256 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03978 (  911)
  hydrogen bonds       : angle       4.53728 ( 2667)
  covalent geometry    : bond        0.00516 (13748)
  covalent geometry    : angle       0.62443 (18641)

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

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

  3528 Ramachandran restraints generated.
    1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3528 Ramachandran restraints generated.
    1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  303 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 53
    poor density    : 250
  time to evaluate  : 2.003 
Fit side-chains
REVERT: A  112 GLN cc_start: 0.8778 (tm-30) cc_final: 0.8396 (tm-30)
REVERT: A  212 GLU cc_start: 0.8680 (tp30) cc_final: 0.8124 (tm-30)
REVERT: A  272 GLN cc_start: 0.9264 (mm-40) cc_final: 0.8952 (mm-40)
REVERT: A  273 MET cc_start: 0.8044 (ttm) cc_final: 0.7629 (ttm)
REVERT: B   47 MET cc_start: 0.3607 (ttt) cc_final: 0.3366 (mtt)
REVERT: B  273 MET cc_start: 0.8173 (ttm) cc_final: 0.7390 (ttm)
REVERT: C   47 MET cc_start: 0.4133 (ttt) cc_final: 0.3881 (mtt)
REVERT: C  126 MET cc_start: 0.8008 (ttt) cc_final: 0.7712 (ttt)
REVERT: C  212 GLU cc_start: 0.8302 (tm-30) cc_final: 0.7961 (tp30)
REVERT: C  272 GLN cc_start: 0.9228 (mm-40) cc_final: 0.8897 (mm-40)
REVERT: C  273 MET cc_start: 0.8131 (ttm) cc_final: 0.7682 (ttm)
REVERT: D   47 MET cc_start: 0.3250 (ttt) cc_final: 0.2862 (mtt)
REVERT: D  115 LEU cc_start: 0.9261 (OUTLIER) cc_final: 0.8854 (tp)
REVERT: D  187 GLU cc_start: 0.7789 (tt0) cc_final: 0.7520 (tp30)
REVERT: D  203 GLN cc_start: 0.8735 (tp40) cc_final: 0.8461 (tp40)
REVERT: D  270 TYR cc_start: 0.9134 (m-80) cc_final: 0.8514 (m-80)
REVERT: E   69 LEU cc_start: 0.8976 (mm) cc_final: 0.8681 (tp)
REVERT: E  150 ILE cc_start: 0.9425 (OUTLIER) cc_final: 0.9166 (tp)
REVERT: E  181 GLU cc_start: 0.8704 (tp30) cc_final: 0.8481 (tp30)
REVERT: E  212 GLU cc_start: 0.8566 (tm-30) cc_final: 0.8298 (tp30)
REVERT: E  267 SER cc_start: 0.9099 (t) cc_final: 0.8754 (p)
REVERT: F   47 MET cc_start: 0.4201 (ttt) cc_final: 0.3840 (mtt)
REVERT: F  112 GLN cc_start: 0.8676 (tm-30) cc_final: 0.8210 (tm-30)
REVERT: F  115 LEU cc_start: 0.9244 (OUTLIER) cc_final: 0.8970 (tt)
REVERT: F  134 GLU cc_start: 0.7870 (mt-10) cc_final: 0.7488 (mt-10)
REVERT: F  149 GLN cc_start: 0.8579 (mt0) cc_final: 0.8172 (mt0)
REVERT: F  157 THR cc_start: 0.9423 (t) cc_final: 0.9156 (m)
REVERT: G  112 GLN cc_start: 0.8729 (tm-30) cc_final: 0.8377 (tm-30)
REVERT: G  138 LEU cc_start: 0.9171 (mt) cc_final: 0.8930 (mt)
REVERT: G  212 GLU cc_start: 0.8280 (tm-30) cc_final: 0.7952 (tm-30)
REVERT: G  272 GLN cc_start: 0.9107 (mm110) cc_final: 0.8735 (mm110)
REVERT: G  274 ASP cc_start: 0.7933 (t0) cc_final: 0.7333 (t70)
  outliers start: 53
  outliers final: 33
  residues processed: 291
  average time/residue: 0.2453
  time to fit residues: 110.8550
Evaluate side-chains
  274 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 238
  time to evaluate  : 1.582 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  144 THR
Chi-restraints excluded: chain A residue  176 ILE
Chi-restraints excluded: chain A residue  199 ASP
Chi-restraints excluded: chain A residue  227 GLU
Chi-restraints excluded: chain A residue  233 ILE
Chi-restraints excluded: chain B residue  109 LEU
Chi-restraints excluded: chain B residue  144 THR
Chi-restraints excluded: chain B residue  176 ILE
Chi-restraints excluded: chain B residue  223 VAL
Chi-restraints excluded: chain B residue  239 VAL
Chi-restraints excluded: chain C residue  144 THR
Chi-restraints excluded: chain C residue  149 GLN
Chi-restraints excluded: chain C residue  176 ILE
Chi-restraints excluded: chain C residue  223 VAL
Chi-restraints excluded: chain C residue  227 GLU
Chi-restraints excluded: chain D residue  115 LEU
Chi-restraints excluded: chain D residue  126 MET
Chi-restraints excluded: chain D residue  144 THR
Chi-restraints excluded: chain D residue  199 ASP
Chi-restraints excluded: chain D residue  223 VAL
Chi-restraints excluded: chain E residue  127 PHE
Chi-restraints excluded: chain E residue  144 THR
Chi-restraints excluded: chain E residue  150 ILE
Chi-restraints excluded: chain E residue  176 ILE
Chi-restraints excluded: chain E residue  187 GLU
Chi-restraints excluded: chain E residue  199 ASP
Chi-restraints excluded: chain E residue  225 LEU
Chi-restraints excluded: chain F residue  115 LEU
Chi-restraints excluded: chain F residue  124 LEU
Chi-restraints excluded: chain F residue  144 THR
Chi-restraints excluded: chain F residue  176 ILE
Chi-restraints excluded: chain F residue  223 VAL
Chi-restraints excluded: chain G residue  144 THR
Chi-restraints excluded: chain G residue  152 SER
Chi-restraints excluded: chain G residue  176 ILE
Chi-restraints excluded: chain G residue  223 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 175
   random chunks:
   chunk 147 optimal weight:    0.9990
   chunk 14 optimal weight:    1.9990
   chunk 30 optimal weight:   10.0000
   chunk 10 optimal weight:    1.9990
   chunk 89 optimal weight:    4.9990
   chunk 127 optimal weight:    7.9990
   chunk 78 optimal weight:   10.0000
   chunk 15 optimal weight:    0.9980
   chunk 150 optimal weight:   40.0000
   chunk 148 optimal weight:    1.9990
   chunk 67 optimal weight:    0.9980
   overall best weight:    1.3986

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3946 r_free = 0.3946 target = 0.157892 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3248 r_free = 0.3248 target = 0.105540 restraints weight = 19262.068|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3311 r_free = 0.3311 target = 0.109499 restraints weight = 9940.419|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 48)----------------|
| r_work = 0.3351 r_free = 0.3351 target = 0.112082 restraints weight = 6595.239|
|-----------------------------------------------------------------------------|
r_work (final): 0.3009
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8074
moved from start:          0.3986

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.059  13748  Z= 0.154
  Angle     :  0.597  10.097  18641  Z= 0.304
  Chirality :  0.046   0.489   2282
  Planarity :  0.003   0.034   2366
  Dihedral  :  4.891  20.880   1939
  Min Nonbonded Distance : 2.535

Molprobity Statistics.
  All-atom Clashscore : 9.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.18 %
    Favored  : 93.82 %
  Rotamer:
    Outliers :  3.26 %
    Allowed  : 21.98 %
    Favored  : 74.76 %
  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: -0.72 (0.19), residues: 1764
  helix:  1.28 (0.17), residues: 896
  sheet: -1.45 (0.32), residues: 224
  loop : -2.74 (0.20), residues: 644

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.000   TRP D 240 
 PHE   0.011   0.001   PHE E 178 
 TYR   0.010   0.001   TYR D 135 
 ARG   0.004   0.000   ARG G 259 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03915 (  911)
  hydrogen bonds       : angle       4.44629 ( 2667)
  covalent geometry    : bond        0.00353 (13748)
  covalent geometry    : angle       0.59705 (18641)

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

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

  3528 Ramachandran restraints generated.
    1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3528 Ramachandran restraints generated.
    1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  304 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 257
  time to evaluate  : 2.279 
Fit side-chains
REVERT: A  112 GLN cc_start: 0.8799 (tm-30) cc_final: 0.8452 (tm-30)
REVERT: A  212 GLU cc_start: 0.8624 (tp30) cc_final: 0.8283 (tm-30)
REVERT: A  273 MET cc_start: 0.8006 (ttm) cc_final: 0.7603 (ttm)
REVERT: B   47 MET cc_start: 0.3660 (ttt) cc_final: 0.3382 (mtt)
REVERT: B  112 GLN cc_start: 0.8742 (tm-30) cc_final: 0.8346 (tm-30)
REVERT: B  212 GLU cc_start: 0.8521 (tp30) cc_final: 0.8320 (tm-30)
REVERT: B  273 MET cc_start: 0.8163 (ttm) cc_final: 0.7407 (ttm)
REVERT: C   47 MET cc_start: 0.4138 (ttt) cc_final: 0.3880 (mtt)
REVERT: C  126 MET cc_start: 0.7987 (ttt) cc_final: 0.7703 (ttt)
REVERT: C  212 GLU cc_start: 0.8298 (tm-30) cc_final: 0.7953 (tp30)
REVERT: C  272 GLN cc_start: 0.9174 (mm-40) cc_final: 0.8878 (mm-40)
REVERT: C  273 MET cc_start: 0.8027 (ttm) cc_final: 0.7607 (ttm)
REVERT: D   47 MET cc_start: 0.3236 (ttt) cc_final: 0.2819 (mtt)
REVERT: D  112 GLN cc_start: 0.8365 (tt0) cc_final: 0.8087 (tm-30)
REVERT: D  115 LEU cc_start: 0.9277 (OUTLIER) cc_final: 0.8837 (tp)
REVERT: D  187 GLU cc_start: 0.7659 (tt0) cc_final: 0.7367 (tp30)
REVERT: D  203 GLN cc_start: 0.8700 (tp40) cc_final: 0.8388 (tp40)
REVERT: D  212 GLU cc_start: 0.8581 (tp30) cc_final: 0.7952 (tm-30)
REVERT: D  270 TYR cc_start: 0.9139 (m-80) cc_final: 0.8539 (m-80)
REVERT: E  150 ILE cc_start: 0.9377 (OUTLIER) cc_final: 0.9128 (tp)
REVERT: E  181 GLU cc_start: 0.8599 (tp30) cc_final: 0.8363 (tp30)
REVERT: E  212 GLU cc_start: 0.8525 (tm-30) cc_final: 0.8270 (tp30)
REVERT: E  267 SER cc_start: 0.9036 (t) cc_final: 0.8682 (p)
REVERT: F   47 MET cc_start: 0.4143 (ttt) cc_final: 0.3775 (mtt)
REVERT: F  112 GLN cc_start: 0.8726 (tm-30) cc_final: 0.8290 (tm-30)
REVERT: F  115 LEU cc_start: 0.9236 (OUTLIER) cc_final: 0.8969 (tt)
REVERT: F  134 GLU cc_start: 0.7775 (mt-10) cc_final: 0.7463 (mt-10)
REVERT: F  149 GLN cc_start: 0.8604 (mt0) cc_final: 0.8197 (mt0)
REVERT: F  157 THR cc_start: 0.9437 (t) cc_final: 0.9166 (m)
REVERT: F  212 GLU cc_start: 0.8622 (tp30) cc_final: 0.8158 (tm-30)
REVERT: G  112 GLN cc_start: 0.8781 (tm-30) cc_final: 0.8401 (tm-30)
REVERT: G  138 LEU cc_start: 0.9173 (mt) cc_final: 0.8956 (mt)
REVERT: G  272 GLN cc_start: 0.9072 (mm110) cc_final: 0.8732 (mm110)
  outliers start: 47
  outliers final: 31
  residues processed: 292
  average time/residue: 0.2273
  time to fit residues: 105.9495
Evaluate side-chains
  273 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 239
  time to evaluate  : 1.999 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  144 THR
Chi-restraints excluded: chain A residue  176 ILE
Chi-restraints excluded: chain A residue  199 ASP
Chi-restraints excluded: chain A residue  233 ILE
Chi-restraints excluded: chain B residue   95 SER
Chi-restraints excluded: chain B residue  109 LEU
Chi-restraints excluded: chain B residue  144 THR
Chi-restraints excluded: chain B residue  176 ILE
Chi-restraints excluded: chain B residue  223 VAL
Chi-restraints excluded: chain B residue  239 VAL
Chi-restraints excluded: chain C residue  109 LEU
Chi-restraints excluded: chain C residue  144 THR
Chi-restraints excluded: chain C residue  176 ILE
Chi-restraints excluded: chain C residue  223 VAL
Chi-restraints excluded: chain D residue  109 LEU
Chi-restraints excluded: chain D residue  115 LEU
Chi-restraints excluded: chain D residue  144 THR
Chi-restraints excluded: chain D residue  223 VAL
Chi-restraints excluded: chain E residue  127 PHE
Chi-restraints excluded: chain E residue  144 THR
Chi-restraints excluded: chain E residue  150 ILE
Chi-restraints excluded: chain E residue  164 VAL
Chi-restraints excluded: chain E residue  176 ILE
Chi-restraints excluded: chain E residue  187 GLU
Chi-restraints excluded: chain E residue  225 LEU
Chi-restraints excluded: chain F residue  115 LEU
Chi-restraints excluded: chain F residue  124 LEU
Chi-restraints excluded: chain F residue  144 THR
Chi-restraints excluded: chain F residue  176 ILE
Chi-restraints excluded: chain F residue  223 VAL
Chi-restraints excluded: chain G residue  144 THR
Chi-restraints excluded: chain G residue  152 SER
Chi-restraints excluded: chain G residue  176 ILE
Chi-restraints excluded: chain G residue  223 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 175
   random chunks:
   chunk 34 optimal weight:    0.9990
   chunk 102 optimal weight:   20.0000
   chunk 50 optimal weight:   40.0000
   chunk 68 optimal weight:    0.8980
   chunk 153 optimal weight:    5.9990
   chunk 27 optimal weight:   20.0000
   chunk 2 optimal weight:   20.0000
   chunk 83 optimal weight:    1.9990
   chunk 152 optimal weight:    7.9990
   chunk 7 optimal weight:    3.9990
   chunk 47 optimal weight:    2.9990
   overall best weight:    2.1788

-------------------------------------------------------------------------------
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 = 0.3925 r_free = 0.3925 target = 0.155993 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3214 r_free = 0.3214 target = 0.103306 restraints weight = 19371.884|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 47)----------------|
| r_work = 0.3275 r_free = 0.3275 target = 0.107182 restraints weight = 10020.470|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3315 r_free = 0.3315 target = 0.109635 restraints weight = 6722.599|
|-----------------------------------------------------------------------------|
r_work (final): 0.2967
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8105
moved from start:          0.4085

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.067  13748  Z= 0.206
  Angle     :  0.632   8.758  18641  Z= 0.322
  Chirality :  0.048   0.473   2282
  Planarity :  0.003   0.033   2366
  Dihedral  :  4.974  21.655   1939
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 10.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.52 %
    Favored  : 93.48 %
  Rotamer:
    Outliers :  3.74 %
    Allowed  : 21.15 %
    Favored  : 75.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -0.69 (0.19), residues: 1764
  helix:  1.28 (0.16), residues: 896
  sheet: -1.75 (0.31), residues: 210
  loop : -2.55 (0.21), residues: 658

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP G 240 
 PHE   0.011   0.001   PHE E 178 
 TYR   0.011   0.001   TYR D 135 
 ARG   0.005   0.000   ARG G 256 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03950 (  911)
  hydrogen bonds       : angle       4.55731 ( 2667)
  covalent geometry    : bond        0.00472 (13748)
  covalent geometry    : angle       0.63235 (18641)

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

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

  3528 Ramachandran restraints generated.
    1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3528 Ramachandran restraints generated.
    1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  300 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 54
    poor density    : 246
  time to evaluate  : 1.644 
Fit side-chains
REVERT: A  112 GLN cc_start: 0.8841 (tm-30) cc_final: 0.8487 (tm-30)
REVERT: A  212 GLU cc_start: 0.8650 (tp30) cc_final: 0.8296 (tm-30)
REVERT: A  273 MET cc_start: 0.8021 (ttm) cc_final: 0.7647 (ttm)
REVERT: B   47 MET cc_start: 0.3695 (ttt) cc_final: 0.3439 (mtt)
REVERT: B  112 GLN cc_start: 0.8744 (tm-30) cc_final: 0.8359 (tm-30)
REVERT: B  212 GLU cc_start: 0.8605 (tp30) cc_final: 0.8266 (tm-30)
REVERT: B  273 MET cc_start: 0.8173 (ttm) cc_final: 0.7402 (ttm)
REVERT: C   47 MET cc_start: 0.4021 (ttt) cc_final: 0.3774 (mtt)
REVERT: C  112 GLN cc_start: 0.8694 (tm-30) cc_final: 0.8283 (tm-30)
REVERT: C  126 MET cc_start: 0.7889 (ttt) cc_final: 0.7637 (ttt)
REVERT: C  212 GLU cc_start: 0.8328 (tm-30) cc_final: 0.8064 (tm-30)
REVERT: C  272 GLN cc_start: 0.9174 (mm-40) cc_final: 0.8878 (mm-40)
REVERT: C  273 MET cc_start: 0.7806 (ttm) cc_final: 0.7393 (ttm)
REVERT: D   47 MET cc_start: 0.3242 (ttt) cc_final: 0.2844 (mtt)
REVERT: D  112 GLN cc_start: 0.8455 (tt0) cc_final: 0.8165 (tm-30)
REVERT: D  115 LEU cc_start: 0.9268 (OUTLIER) cc_final: 0.9026 (tp)
REVERT: D  187 GLU cc_start: 0.7747 (tt0) cc_final: 0.7485 (tp30)
REVERT: D  203 GLN cc_start: 0.8723 (tp40) cc_final: 0.8408 (tp40)
REVERT: D  212 GLU cc_start: 0.8643 (tp30) cc_final: 0.8057 (tm-30)
REVERT: D  270 TYR cc_start: 0.9121 (m-80) cc_final: 0.8525 (m-80)
REVERT: E   69 LEU cc_start: 0.8985 (mm) cc_final: 0.8699 (tp)
REVERT: E  150 ILE cc_start: 0.9390 (OUTLIER) cc_final: 0.9153 (tp)
REVERT: E  181 GLU cc_start: 0.8656 (tp30) cc_final: 0.8429 (tp30)
REVERT: E  212 GLU cc_start: 0.8576 (tm-30) cc_final: 0.8292 (tp30)
REVERT: E  267 SER cc_start: 0.9035 (t) cc_final: 0.8681 (p)
REVERT: F   47 MET cc_start: 0.4134 (ttt) cc_final: 0.3785 (mtt)
REVERT: F  112 GLN cc_start: 0.8747 (tm-30) cc_final: 0.8326 (tm-30)
REVERT: F  115 LEU cc_start: 0.9227 (OUTLIER) cc_final: 0.8965 (tt)
REVERT: F  134 GLU cc_start: 0.7831 (mt-10) cc_final: 0.7500 (mt-10)
REVERT: F  149 GLN cc_start: 0.8598 (mt0) cc_final: 0.8191 (mt0)
REVERT: F  157 THR cc_start: 0.9454 (t) cc_final: 0.9167 (m)
REVERT: F  212 GLU cc_start: 0.8626 (tp30) cc_final: 0.8169 (tm-30)
REVERT: F  272 GLN cc_start: 0.9313 (mm-40) cc_final: 0.8912 (mm110)
REVERT: F  274 ASP cc_start: 0.7996 (m-30) cc_final: 0.7694 (m-30)
REVERT: G  112 GLN cc_start: 0.8773 (tm-30) cc_final: 0.8394 (tm-30)
REVERT: G  212 GLU cc_start: 0.8606 (tp30) cc_final: 0.8214 (tm-30)
  outliers start: 54
  outliers final: 41
  residues processed: 288
  average time/residue: 0.2204
  time to fit residues: 101.1019
Evaluate side-chains
  282 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 238
  time to evaluate  : 1.513 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  144 THR
Chi-restraints excluded: chain A residue  176 ILE
Chi-restraints excluded: chain A residue  199 ASP
Chi-restraints excluded: chain A residue  233 ILE
Chi-restraints excluded: chain B residue   95 SER
Chi-restraints excluded: chain B residue  109 LEU
Chi-restraints excluded: chain B residue  138 LEU
Chi-restraints excluded: chain B residue  144 THR
Chi-restraints excluded: chain B residue  176 ILE
Chi-restraints excluded: chain B residue  218 ASP
Chi-restraints excluded: chain B residue  223 VAL
Chi-restraints excluded: chain B residue  239 VAL
Chi-restraints excluded: chain C residue  109 LEU
Chi-restraints excluded: chain C residue  144 THR
Chi-restraints excluded: chain C residue  176 ILE
Chi-restraints excluded: chain C residue  223 VAL
Chi-restraints excluded: chain D residue   95 SER
Chi-restraints excluded: chain D residue  109 LEU
Chi-restraints excluded: chain D residue  115 LEU
Chi-restraints excluded: chain D residue  144 THR
Chi-restraints excluded: chain D residue  199 ASP
Chi-restraints excluded: chain D residue  223 VAL
Chi-restraints excluded: chain E residue  127 PHE
Chi-restraints excluded: chain E residue  144 THR
Chi-restraints excluded: chain E residue  150 ILE
Chi-restraints excluded: chain E residue  164 VAL
Chi-restraints excluded: chain E residue  176 ILE
Chi-restraints excluded: chain E residue  187 GLU
Chi-restraints excluded: chain E residue  199 ASP
Chi-restraints excluded: chain E residue  223 VAL
Chi-restraints excluded: chain E residue  225 LEU
Chi-restraints excluded: chain F residue  115 LEU
Chi-restraints excluded: chain F residue  124 LEU
Chi-restraints excluded: chain F residue  138 LEU
Chi-restraints excluded: chain F residue  144 THR
Chi-restraints excluded: chain F residue  176 ILE
Chi-restraints excluded: chain F residue  223 VAL
Chi-restraints excluded: chain F residue  233 ILE
Chi-restraints excluded: chain G residue  124 LEU
Chi-restraints excluded: chain G residue  144 THR
Chi-restraints excluded: chain G residue  152 SER
Chi-restraints excluded: chain G residue  176 ILE
Chi-restraints excluded: chain G residue  223 VAL
Chi-restraints excluded: chain G residue  227 GLU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 175
   random chunks:
   chunk 122 optimal weight:    0.9990
   chunk 139 optimal weight:    2.9990
   chunk 31 optimal weight:    6.9990
   chunk 115 optimal weight:    1.9990
   chunk 146 optimal weight:    6.9990
   chunk 70 optimal weight:    0.7980
   chunk 81 optimal weight:   50.0000
   chunk 32 optimal weight:    5.9990
   chunk 27 optimal weight:   20.0000
   chunk 55 optimal weight:   10.0000
   chunk 5 optimal weight:    9.9990
   overall best weight:    2.5588

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

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3916 r_free = 0.3916 target = 0.155151 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3199 r_free = 0.3199 target = 0.102447 restraints weight = 19315.978|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 54)----------------|
| r_work = 0.3261 r_free = 0.3261 target = 0.106284 restraints weight = 10000.984|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3299 r_free = 0.3299 target = 0.108757 restraints weight = 6705.113|
|-----------------------------------------------------------------------------|
r_work (final): 0.2967
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8118
moved from start:          0.4161

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.053  13748  Z= 0.233
  Angle     :  0.661  10.375  18641  Z= 0.335
  Chirality :  0.049   0.482   2282
  Planarity :  0.003   0.034   2366
  Dihedral  :  5.018  22.262   1939
  Min Nonbonded Distance : 2.520

Molprobity Statistics.
  All-atom Clashscore : 10.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.58 %
    Favored  : 93.42 %
  Rotamer:
    Outliers :  3.47 %
    Allowed  : 22.26 %
    Favored  : 74.27 %
  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: -0.72 (0.19), residues: 1764
  helix:  1.25 (0.16), residues: 896
  sheet: -1.78 (0.31), residues: 210
  loop : -2.56 (0.21), residues: 658

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP G 240 
 PHE   0.012   0.001   PHE E 178 
 TYR   0.011   0.001   TYR D 135 
 ARG   0.005   0.000   ARG G 256 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03973 (  911)
  hydrogen bonds       : angle       4.61345 ( 2667)
  covalent geometry    : bond        0.00533 (13748)
  covalent geometry    : angle       0.66083 (18641)

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

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

  3528 Ramachandran restraints generated.
    1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3528 Ramachandran restraints generated.
    1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  291 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 241
  time to evaluate  : 1.548 
Fit side-chains
REVERT: A  112 GLN cc_start: 0.8839 (tm-30) cc_final: 0.8481 (tm-30)
REVERT: A  212 GLU cc_start: 0.8584 (tp30) cc_final: 0.8244 (tm-30)
REVERT: A  273 MET cc_start: 0.7982 (ttm) cc_final: 0.7096 (ttm)
REVERT: B   47 MET cc_start: 0.3857 (ttt) cc_final: 0.3644 (mtt)
REVERT: B  187 GLU cc_start: 0.7944 (tt0) cc_final: 0.7697 (tt0)
REVERT: B  212 GLU cc_start: 0.8669 (tp30) cc_final: 0.8314 (tm-30)
REVERT: B  273 MET cc_start: 0.8219 (ttm) cc_final: 0.7430 (ttm)
REVERT: C   47 MET cc_start: 0.4023 (ttt) cc_final: 0.3772 (mtt)
REVERT: C  112 GLN cc_start: 0.8849 (tm-30) cc_final: 0.8429 (tm-30)
REVERT: C  126 MET cc_start: 0.7936 (ttt) cc_final: 0.7699 (ttt)
REVERT: C  212 GLU cc_start: 0.8333 (tm-30) cc_final: 0.8097 (tm-30)
REVERT: C  272 GLN cc_start: 0.9178 (mm-40) cc_final: 0.8864 (mm-40)
REVERT: C  273 MET cc_start: 0.7917 (ttm) cc_final: 0.7508 (ttm)
REVERT: D   47 MET cc_start: 0.3319 (ttt) cc_final: 0.2928 (mtt)
REVERT: D  112 GLN cc_start: 0.8474 (tt0) cc_final: 0.8158 (tm-30)
REVERT: D  115 LEU cc_start: 0.9278 (OUTLIER) cc_final: 0.9008 (tp)
REVERT: D  134 GLU cc_start: 0.7657 (mt-10) cc_final: 0.7408 (pm20)
REVERT: D  187 GLU cc_start: 0.7751 (tt0) cc_final: 0.7478 (tp30)
REVERT: D  212 GLU cc_start: 0.8653 (tp30) cc_final: 0.8089 (tm-30)
REVERT: D  270 TYR cc_start: 0.9110 (m-80) cc_final: 0.8488 (m-80)
REVERT: E   69 LEU cc_start: 0.8981 (mm) cc_final: 0.8688 (tp)
REVERT: E  181 GLU cc_start: 0.8663 (tp30) cc_final: 0.8444 (tp30)
REVERT: E  212 GLU cc_start: 0.8568 (tm-30) cc_final: 0.8271 (tp30)
REVERT: E  267 SER cc_start: 0.9043 (t) cc_final: 0.8721 (p)
REVERT: F   47 MET cc_start: 0.4185 (ttt) cc_final: 0.3838 (mtt)
REVERT: F  112 GLN cc_start: 0.8748 (tm-30) cc_final: 0.8342 (tm-30)
REVERT: F  115 LEU cc_start: 0.9234 (OUTLIER) cc_final: 0.8984 (tt)
REVERT: F  134 GLU cc_start: 0.7867 (mt-10) cc_final: 0.7522 (mt-10)
REVERT: F  149 GLN cc_start: 0.8593 (mt0) cc_final: 0.8232 (mt0)
REVERT: F  157 THR cc_start: 0.9454 (t) cc_final: 0.9113 (m)
REVERT: F  212 GLU cc_start: 0.8659 (tp30) cc_final: 0.8168 (tm-30)
REVERT: F  272 GLN cc_start: 0.9254 (mm-40) cc_final: 0.8946 (mm110)
REVERT: F  273 MET cc_start: 0.8259 (mtm) cc_final: 0.7996 (ttm)
REVERT: G  112 GLN cc_start: 0.8860 (tm-30) cc_final: 0.8510 (tm-30)
REVERT: G  212 GLU cc_start: 0.8631 (tp30) cc_final: 0.8267 (tm-30)
  outliers start: 50
  outliers final: 41
  residues processed: 282
  average time/residue: 0.2088
  time to fit residues: 93.5083
Evaluate side-chains
  274 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 231
  time to evaluate  : 1.427 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  144 THR
Chi-restraints excluded: chain A residue  176 ILE
Chi-restraints excluded: chain A residue  199 ASP
Chi-restraints excluded: chain A residue  233 ILE
Chi-restraints excluded: chain B residue   95 SER
Chi-restraints excluded: chain B residue  109 LEU
Chi-restraints excluded: chain B residue  138 LEU
Chi-restraints excluded: chain B residue  144 THR
Chi-restraints excluded: chain B residue  176 ILE
Chi-restraints excluded: chain B residue  218 ASP
Chi-restraints excluded: chain B residue  223 VAL
Chi-restraints excluded: chain B residue  239 VAL
Chi-restraints excluded: chain C residue  144 THR
Chi-restraints excluded: chain C residue  176 ILE
Chi-restraints excluded: chain C residue  223 VAL
Chi-restraints excluded: chain D residue   56 MET
Chi-restraints excluded: chain D residue   95 SER
Chi-restraints excluded: chain D residue  115 LEU
Chi-restraints excluded: chain D residue  144 THR
Chi-restraints excluded: chain D residue  199 ASP
Chi-restraints excluded: chain D residue  223 VAL
Chi-restraints excluded: chain E residue  141 VAL
Chi-restraints excluded: chain E residue  144 THR
Chi-restraints excluded: chain E residue  164 VAL
Chi-restraints excluded: chain E residue  176 ILE
Chi-restraints excluded: chain E residue  187 GLU
Chi-restraints excluded: chain E residue  199 ASP
Chi-restraints excluded: chain E residue  223 VAL
Chi-restraints excluded: chain E residue  225 LEU
Chi-restraints excluded: chain F residue  115 LEU
Chi-restraints excluded: chain F residue  124 LEU
Chi-restraints excluded: chain F residue  138 LEU
Chi-restraints excluded: chain F residue  144 THR
Chi-restraints excluded: chain F residue  176 ILE
Chi-restraints excluded: chain F residue  199 ASP
Chi-restraints excluded: chain F residue  223 VAL
Chi-restraints excluded: chain F residue  233 ILE
Chi-restraints excluded: chain G residue  124 LEU
Chi-restraints excluded: chain G residue  144 THR
Chi-restraints excluded: chain G residue  152 SER
Chi-restraints excluded: chain G residue  176 ILE
Chi-restraints excluded: chain G residue  223 VAL
Chi-restraints excluded: chain G residue  227 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 175
   random chunks:
   chunk 61 optimal weight:    0.8980
   chunk 69 optimal weight:    3.9990
   chunk 147 optimal weight:    0.7980
   chunk 5 optimal weight:   20.0000
   chunk 8 optimal weight:    0.4980
   chunk 43 optimal weight:    2.9990
   chunk 25 optimal weight:   30.0000
   chunk 56 optimal weight:   20.0000
   chunk 125 optimal weight:   30.0000
   chunk 111 optimal weight:    0.7980
   chunk 85 optimal weight:    0.7980
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
B 149 GLN
** F 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
G 149 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3963 r_free = 0.3963 target = 0.159465 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3279 r_free = 0.3279 target = 0.107703 restraints weight = 19351.354|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 49)----------------|
| r_work = 0.3339 r_free = 0.3339 target = 0.111664 restraints weight = 9848.608|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 50)----------------|
| r_work = 0.3378 r_free = 0.3378 target = 0.114278 restraints weight = 6533.842|
|-----------------------------------------------------------------------------|
r_work (final): 0.3074
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8050
moved from start:          0.4306

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.066  13748  Z= 0.124
  Angle     :  0.626  11.266  18641  Z= 0.306
  Chirality :  0.047   0.459   2282
  Planarity :  0.003   0.032   2366
  Dihedral  :  4.785  18.784   1939
  Min Nonbonded Distance : 2.564

Molprobity Statistics.
  All-atom Clashscore : 8.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.07 %
    Favored  : 93.93 %
  Rotamer:
    Outliers :  2.43 %
    Allowed  : 23.58 %
    Favored  : 73.99 %
  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: -0.55 (0.19), residues: 1764
  helix:  1.37 (0.16), residues: 896
  sheet: -1.12 (0.32), residues: 224
  loop : -2.68 (0.21), residues: 644

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP C 251 
 PHE   0.010   0.001   PHE E 178 
 TYR   0.012   0.001   TYR D 135 
 ARG   0.005   0.000   ARG G 256 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03819 (  911)
  hydrogen bonds       : angle       4.41556 ( 2667)
  covalent geometry    : bond        0.00280 (13748)
  covalent geometry    : angle       0.62568 (18641)

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

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

  3528 Ramachandran restraints generated.
    1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3528 Ramachandran restraints generated.
    1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  305 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 270
  time to evaluate  : 1.448 
Fit side-chains
REVERT: A  212 GLU cc_start: 0.8612 (tp30) cc_final: 0.8353 (tm-30)
REVERT: A  216 LEU cc_start: 0.9405 (mt) cc_final: 0.9150 (mt)
REVERT: A  273 MET cc_start: 0.7963 (ttm) cc_final: 0.7579 (ttm)
REVERT: B   47 MET cc_start: 0.3897 (ttt) cc_final: 0.3660 (mtt)
REVERT: B  212 GLU cc_start: 0.8568 (tp30) cc_final: 0.8192 (tm-30)
REVERT: B  273 MET cc_start: 0.8152 (ttm) cc_final: 0.7422 (ttm)
REVERT: C   47 MET cc_start: 0.3990 (ttt) cc_final: 0.3710 (mtt)
REVERT: C  112 GLN cc_start: 0.8831 (tm-30) cc_final: 0.8451 (tm-30)
REVERT: C  115 LEU cc_start: 0.9168 (OUTLIER) cc_final: 0.8956 (tp)
REVERT: C  126 MET cc_start: 0.7792 (ttt) cc_final: 0.7569 (ttt)
REVERT: C  273 MET cc_start: 0.8060 (ttm) cc_final: 0.7640 (ttm)
REVERT: D   47 MET cc_start: 0.3342 (ttt) cc_final: 0.2946 (mtt)
REVERT: D  187 GLU cc_start: 0.7634 (tt0) cc_final: 0.7359 (tp30)
REVERT: D  203 GLN cc_start: 0.8677 (tp40) cc_final: 0.8362 (tp40)
REVERT: D  212 GLU cc_start: 0.8577 (tp30) cc_final: 0.8120 (tm-30)
REVERT: E   69 LEU cc_start: 0.8943 (mm) cc_final: 0.8636 (tp)
REVERT: E  181 GLU cc_start: 0.8507 (tp30) cc_final: 0.8283 (tp30)
REVERT: E  212 GLU cc_start: 0.8541 (tm-30) cc_final: 0.8110 (tp30)
REVERT: E  267 SER cc_start: 0.8884 (t) cc_final: 0.8579 (p)
REVERT: F   47 MET cc_start: 0.4008 (ttt) cc_final: 0.3637 (mtt)
REVERT: F  112 GLN cc_start: 0.8760 (tm-30) cc_final: 0.8360 (tm-30)
REVERT: F  115 LEU cc_start: 0.9183 (OUTLIER) cc_final: 0.8917 (tt)
REVERT: F  134 GLU cc_start: 0.7750 (mt-10) cc_final: 0.7448 (mt-10)
REVERT: F  149 GLN cc_start: 0.8611 (mt0) cc_final: 0.8227 (mt0)
REVERT: F  157 THR cc_start: 0.9422 (t) cc_final: 0.9176 (m)
REVERT: F  212 GLU cc_start: 0.8615 (tp30) cc_final: 0.8213 (tm-30)
REVERT: F  272 GLN cc_start: 0.9180 (mm-40) cc_final: 0.8915 (mm110)
REVERT: F  273 MET cc_start: 0.8218 (mtm) cc_final: 0.7874 (ttm)
REVERT: G  112 GLN cc_start: 0.8830 (tm-30) cc_final: 0.8497 (tm-30)
  outliers start: 35
  outliers final: 28
  residues processed: 299
  average time/residue: 0.2052
  time to fit residues: 96.1661
Evaluate side-chains
  281 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 251
  time to evaluate  : 1.418 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  176 ILE
Chi-restraints excluded: chain A residue  233 ILE
Chi-restraints excluded: chain B residue   95 SER
Chi-restraints excluded: chain B residue  109 LEU
Chi-restraints excluded: chain B residue  138 LEU
Chi-restraints excluded: chain B residue  144 THR
Chi-restraints excluded: chain B residue  176 ILE
Chi-restraints excluded: chain B residue  223 VAL
Chi-restraints excluded: chain B residue  239 VAL
Chi-restraints excluded: chain C residue  115 LEU
Chi-restraints excluded: chain C residue  144 THR
Chi-restraints excluded: chain C residue  176 ILE
Chi-restraints excluded: chain C residue  223 VAL
Chi-restraints excluded: chain D residue   56 MET
Chi-restraints excluded: chain D residue   95 SER
Chi-restraints excluded: chain D residue  144 THR
Chi-restraints excluded: chain D residue  170 ILE
Chi-restraints excluded: chain D residue  223 VAL
Chi-restraints excluded: chain E residue  144 THR
Chi-restraints excluded: chain E residue  176 ILE
Chi-restraints excluded: chain E residue  187 GLU
Chi-restraints excluded: chain E residue  223 VAL
Chi-restraints excluded: chain F residue  115 LEU
Chi-restraints excluded: chain F residue  124 LEU
Chi-restraints excluded: chain F residue  176 ILE
Chi-restraints excluded: chain F residue  223 VAL
Chi-restraints excluded: chain G residue  124 LEU
Chi-restraints excluded: chain G residue  176 ILE
Chi-restraints excluded: chain G residue  223 VAL
Chi-restraints excluded: chain G residue  227 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 175
   random chunks:
   chunk 74 optimal weight:    6.9990
   chunk 161 optimal weight:    1.9990
   chunk 163 optimal weight:    3.9990
   chunk 137 optimal weight:    0.9980
   chunk 157 optimal weight:    7.9990
   chunk 8 optimal weight:    0.7980
   chunk 35 optimal weight:    0.8980
   chunk 40 optimal weight:    0.7980
   chunk 125 optimal weight:   30.0000
   chunk 39 optimal weight:    0.7980
   chunk 41 optimal weight:    0.9990
   overall best weight:    0.8580

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

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3968 r_free = 0.3968 target = 0.159722 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3279 r_free = 0.3279 target = 0.107641 restraints weight = 19419.749|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 50)----------------|
| r_work = 0.3340 r_free = 0.3340 target = 0.111662 restraints weight = 9890.702|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 49)----------------|
| r_work = 0.3378 r_free = 0.3378 target = 0.114230 restraints weight = 6573.405|
|-----------------------------------------------------------------------------|
r_work (final): 0.3056
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8056
moved from start:          0.4419

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.056  13748  Z= 0.129
  Angle     :  0.629  11.193  18641  Z= 0.310
  Chirality :  0.047   0.449   2282
  Planarity :  0.003   0.032   2366
  Dihedral  :  4.721  18.548   1939
  Min Nonbonded Distance : 2.581

Molprobity Statistics.
  All-atom Clashscore : 8.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.07 %
    Favored  : 93.93 %
  Rotamer:
    Outliers :  2.36 %
    Allowed  : 24.34 %
    Favored  : 73.30 %
  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: -0.42 (0.19), residues: 1764
  helix:  1.46 (0.16), residues: 896
  sheet: -0.97 (0.32), residues: 224
  loop : -2.64 (0.21), residues: 644

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.000   TRP C 251 
 PHE   0.013   0.001   PHE B 178 
 TYR   0.012   0.001   TYR D 135 
 ARG   0.007   0.000   ARG F 256 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03813 (  911)
  hydrogen bonds       : angle       4.34759 ( 2667)
  covalent geometry    : bond        0.00287 (13748)
  covalent geometry    : angle       0.62902 (18641)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4532.89 seconds
wall clock time: 81 minutes 50.54 seconds (4910.54 seconds total)