Starting phenix.real_space_refine
on Wed Aug  5 19:29:05 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/13hs_77073/08_2026/13hs_77073.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/13hs_77073/08_2026/13hs_77073.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/13hs_77073/08_2026/13hs_77073.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/13hs_77073/08_2026/13hs_77073.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/13hs_77073/08_2026/13hs_77073.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/13hs_77073/08_2026/13hs_77073.cif"
  }
  resolution = 3.7
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.044
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       8      5.16       5
     C    6880      2.51       5
     N    2088      2.21       5
     O    2064      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 11040
  Number of models: 1
  Model: ""
    Number of chains: 8
    Chain: "A"
      Number of atoms: 1380
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 178, 1380
          Classifications: {'peptide': 178}
          Link IDs: {'PTRANS': 12, 'TRANS': 165}
    Chain: "B"
      Number of atoms: 1380
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 178, 1380
          Classifications: {'peptide': 178}
          Link IDs: {'PTRANS': 12, 'TRANS': 165}
    Chain: "C"
      Number of atoms: 1380
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 178, 1380
          Classifications: {'peptide': 178}
          Link IDs: {'PTRANS': 12, 'TRANS': 165}
    Chain: "D"
      Number of atoms: 1380
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 178, 1380
          Classifications: {'peptide': 178}
          Link IDs: {'PTRANS': 12, 'TRANS': 165}
    Chain: "E"
      Number of atoms: 1380
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 178, 1380
          Classifications: {'peptide': 178}
          Link IDs: {'PTRANS': 12, 'TRANS': 165}
    Chain: "F"
      Number of atoms: 1380
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 178, 1380
          Classifications: {'peptide': 178}
          Link IDs: {'PTRANS': 12, 'TRANS': 165}
    Chain: "G"
      Number of atoms: 1380
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 178, 1380
          Classifications: {'peptide': 178}
          Link IDs: {'PTRANS': 12, 'TRANS': 165}
    Chain: "H"
      Number of atoms: 1380
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 178, 1380
          Classifications: {'peptide': 178}
          Link IDs: {'PTRANS': 12, 'TRANS': 165}
  Time building chain proxies: 2.16, per 1000 atoms: 0.20
  Number of scatterers: 11040
  At special positions: 0
  Unit cell: (80.142, 123.462, 121.296, 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       8     16.00
     O    2064      8.00
     N    2088      7.00
     C    6880      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: 0.78
  Conformation dependent library (CDL) restraints added in 292.9 milliseconds
  

  2816 Ramachandran restraints generated.
    1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2688

  Finding SS restraints...
    Secondary structure from input PDB file:
      27 helices and 18 sheets defined
      30.5% alpha, 35.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.30
  Creating SS restraints...
    Processing helix  chain 'A' and resid 94 through 111
    Processing helix  chain 'A' and resid 140 through 144
      removed outlier: 3.593A  pdb=" N   GLY A 143 " --> pdb=" O   TYR A 140 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 180 through 207
      removed outlier: 3.990A  pdb=" N   SER A 185 " --> pdb=" O   ALA A 181 " (cutoff:3.500A)
      removed outlier: 3.955A  pdb=" N   ALA A 186 " --> pdb=" O   ALA A 182 " (cutoff:3.500A)
      removed outlier: 3.537A  pdb=" N   THR A 193 " --> pdb=" O   LYS A 189 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 94 through 111
      removed outlier: 3.921A  pdb=" N   PHE B 107 " --> pdb=" O   LEU B 103 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 140 through 144
    Processing helix  chain 'B' and resid 179 through 207
      removed outlier: 4.660A  pdb=" N   ALA B 196 " --> pdb=" O   ASP B 192 " (cutoff:3.500A)
      removed outlier: 4.654A  pdb=" N   GLN B 197 " --> pdb=" O   THR B 193 " (cutoff:3.500A)
      removed outlier: 3.535A  pdb=" N   VAL B 198 " --> pdb=" O   LEU B 194 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 66 through 70
      removed outlier: 3.598A  pdb=" N   GLU C  70 " --> pdb=" O   LEU C  67 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 94 through 111
    Processing helix  chain 'C' and resid 141 through 144
    Processing helix  chain 'C' and resid 179 through 208
      removed outlier: 3.505A  pdb=" N   VAL C 183 " --> pdb=" O   LYS C 179 " (cutoff:3.500A)
      removed outlier: 3.988A  pdb=" N   ALA C 196 " --> pdb=" O   ASP C 192 " (cutoff:3.500A)
      removed outlier: 3.695A  pdb=" N   GLN C 197 " --> pdb=" O   THR C 193 " (cutoff:3.500A)
      removed outlier: 3.923A  pdb=" N   ASP C 200 " --> pdb=" O   ALA C 196 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 94 through 111
      removed outlier: 3.505A  pdb=" N   ASP D 110 " --> pdb=" O   ALA D 106 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 140 through 144
    Processing helix  chain 'D' and resid 179 through 209
      removed outlier: 3.920A  pdb=" N   ALA D 196 " --> pdb=" O   ASP D 192 " (cutoff:3.500A)
      removed outlier: 3.736A  pdb=" N   GLN D 197 " --> pdb=" O   THR D 193 " (cutoff:3.500A)
      removed outlier: 3.714A  pdb=" N   ARG D 204 " --> pdb=" O   ASP D 200 " (cutoff:3.500A)
      removed outlier: 3.601A  pdb=" N   SER D 207 " --> pdb=" O   LEU D 203 " (cutoff:3.500A)
      removed outlier: 3.834A  pdb=" N   GLN D 209 " --> pdb=" O   GLN D 205 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 94 through 111
    Processing helix  chain 'E' and resid 140 through 144
    Processing helix  chain 'E' and resid 179 through 208
      removed outlier: 3.662A  pdb=" N   VAL E 183 " --> pdb=" O   LYS E 179 " (cutoff:3.500A)
      removed outlier: 4.009A  pdb=" N   ALA E 196 " --> pdb=" O   ASP E 192 " (cutoff:3.500A)
      removed outlier: 3.711A  pdb=" N   GLN E 197 " --> pdb=" O   THR E 193 " (cutoff:3.500A)
      removed outlier: 3.640A  pdb=" N   SER E 207 " --> pdb=" O   LEU E 203 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 94 through 111
    Processing helix  chain 'F' and resid 141 through 144
    Processing helix  chain 'F' and resid 179 through 209
      removed outlier: 3.905A  pdb=" N   ALA F 196 " --> pdb=" O   ASP F 192 " (cutoff:3.500A)
      removed outlier: 3.707A  pdb=" N   GLN F 197 " --> pdb=" O   THR F 193 " (cutoff:3.500A)
      removed outlier: 3.691A  pdb=" N   GLN F 209 " --> pdb=" O   GLN F 205 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 66 through 71
      removed outlier: 3.844A  pdb=" N   SER G  71 " --> pdb=" O   LEU G  67 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 94 through 111
    Processing helix  chain 'G' and resid 140 through 144
      removed outlier: 3.567A  pdb=" N   GLY G 143 " --> pdb=" O   TYR G 140 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 180 through 207
      removed outlier: 4.047A  pdb=" N   SER G 185 " --> pdb=" O   ALA G 181 " (cutoff:3.500A)
      removed outlier: 3.999A  pdb=" N   ALA G 186 " --> pdb=" O   ALA G 182 " (cutoff:3.500A)
      removed outlier: 3.558A  pdb=" N   THR G 193 " --> pdb=" O   LYS G 189 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 66 through 71
      removed outlier: 3.815A  pdb=" N   SER H  71 " --> pdb=" O   LEU H  67 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 94 through 111
    Processing helix  chain 'H' and resid 140 through 144
      removed outlier: 3.625A  pdb=" N   GLY H 143 " --> pdb=" O   TYR H 140 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 180 through 207
      removed outlier: 4.120A  pdb=" N   SER H 185 " --> pdb=" O   ALA H 181 " (cutoff:3.500A)
      removed outlier: 3.972A  pdb=" N   ALA H 186 " --> pdb=" O   ALA H 182 " (cutoff:3.500A)
      removed outlier: 3.580A  pdb=" N   THR H 193 " --> pdb=" O   LYS H 189 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 36 through 38
      removed outlier: 5.978A  pdb=" N   GLN A  36 " --> pdb=" O   ARG A  90 " (cutoff:3.500A)
      removed outlier: 5.972A  pdb=" N   ILE A  74 " --> pdb=" O   TYR A  86 " (cutoff:3.500A)
      removed outlier: 8.819A  pdb=" N   ARG A  73 " --> pdb=" O   PHE A 136 " (cutoff:3.500A)
      removed outlier: 9.177A  pdb=" N   THR A 138 " --> pdb=" O   ARG A  73 " (cutoff:3.500A)
      removed outlier: 7.373A  pdb=" N   ALA A  75 " --> pdb=" O   THR A 138 " (cutoff:3.500A)
      removed outlier: 6.535A  pdb=" N   ARG A  59 " --> pdb=" O   LEU A 129 " (cutoff:3.500A)
      removed outlier: 8.745A  pdb=" N   GLY A 131 " --> pdb=" O   ARG A  59 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 36 through 38
      removed outlier: 5.978A  pdb=" N   GLN A  36 " --> pdb=" O   ARG A  90 " (cutoff:3.500A)
      removed outlier: 5.972A  pdb=" N   ILE A  74 " --> pdb=" O   TYR A  86 " (cutoff:3.500A)
      removed outlier: 8.819A  pdb=" N   ARG A  73 " --> pdb=" O   PHE A 136 " (cutoff:3.500A)
      removed outlier: 9.177A  pdb=" N   THR A 138 " --> pdb=" O   ARG A  73 " (cutoff:3.500A)
      removed outlier: 7.373A  pdb=" N   ALA A  75 " --> pdb=" O   THR A 138 " (cutoff:3.500A)
      removed outlier: 5.808A  pdb=" N   ARG A 150 " --> pdb=" O   ARG A 134 " (cutoff:3.500A)
      removed outlier: 3.846A  pdb=" N   PHE A 136 " --> pdb=" O   LEU A 148 " (cutoff:3.500A)
      removed outlier: 6.925A  pdb=" N   LEU A 148 " --> pdb=" O   PHE A 136 " (cutoff:3.500A)
      removed outlier: 4.740A  pdb=" N   THR A 138 " --> pdb=" O   SER A 146 " (cutoff:3.500A)
      removed outlier: 6.265A  pdb=" N   SER A 146 " --> pdb=" O   THR A 138 " (cutoff:3.500A)
      removed outlier: 6.284A  pdb=" N   ALA A 147 " --> pdb=" O   SER A 172 " (cutoff:3.500A)
      removed outlier: 4.188A  pdb=" N   SER A 172 " --> pdb=" O   ALA A 147 " (cutoff:3.500A)
      removed outlier: 6.710A  pdb=" N   ILE A 149 " --> pdb=" O   GLU A 170 " (cutoff:3.500A)
      removed outlier: 4.273A  pdb=" N   GLU A 170 " --> pdb=" O   ILE A 149 " (cutoff:3.500A)
      removed outlier: 6.686A  pdb=" N   TYR A 151 " --> pdb=" O   ARG A 168 " (cutoff:3.500A)
      removed outlier: 4.715A  pdb=" N   ARG A 168 " --> pdb=" O   TYR A 151 " (cutoff:3.500A)
      removed outlier: 6.918A  pdb=" N   ALA A 153 " --> pdb=" O   SER A 166 " (cutoff:3.500A)
      removed outlier: 4.487A  pdb=" N   SER A 166 " --> pdb=" O   ALA A 153 " (cutoff:3.500A)
      removed outlier: 6.654A  pdb=" N   LEU A 155 " --> pdb=" O   VAL A 164 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 36 through 38
    Processing sheet with id=AA4, first strand: chain 'B' and resid 64 through 65
      removed outlier: 6.393A  pdb=" N   ARG B  64 " --> pdb=" O   LEU B 133 " (cutoff:3.500A)
      removed outlier: 7.784A  pdb=" N   ALA B 135 " --> pdb=" O   ARG B  64 " (cutoff:3.500A)
      removed outlier: 6.525A  pdb=" N   ARG B  59 " --> pdb=" O   LEU B 129 " (cutoff:3.500A)
      removed outlier: 8.954A  pdb=" N   GLY B 131 " --> pdb=" O   ARG B  59 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 64 through 65
      removed outlier: 6.393A  pdb=" N   ARG B  64 " --> pdb=" O   LEU B 133 " (cutoff:3.500A)
      removed outlier: 7.784A  pdb=" N   ALA B 135 " --> pdb=" O   ARG B  64 " (cutoff:3.500A)
      removed outlier: 6.276A  pdb=" N   ARG B 150 " --> pdb=" O   ARG B 134 " (cutoff:3.500A)
      removed outlier: 3.764A  pdb=" N   PHE B 136 " --> pdb=" O   LEU B 148 " (cutoff:3.500A)
      removed outlier: 6.372A  pdb=" N   LEU B 148 " --> pdb=" O   PHE B 136 " (cutoff:3.500A)
      removed outlier: 4.452A  pdb=" N   THR B 138 " --> pdb=" O   SER B 146 " (cutoff:3.500A)
      removed outlier: 6.485A  pdb=" N   SER B 146 " --> pdb=" O   THR B 138 " (cutoff:3.500A)
      removed outlier: 6.540A  pdb=" N   ARG B 157 " --> pdb=" O   VAL B 163 " (cutoff:3.500A)
      removed outlier: 6.123A  pdb=" N   VAL B 163 " --> pdb=" O   ARG B 157 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 75 through 76
    Processing sheet with id=AA7, first strand: chain 'C' and resid 36 through 38
    Processing sheet with id=AA8, first strand: chain 'C' and resid 116 through 118
      removed outlier: 6.380A  pdb=" N   LEU C  58 " --> pdb=" O   SER C 117 " (cutoff:3.500A)
      removed outlier: 6.651A  pdb=" N   ARG C  59 " --> pdb=" O   LEU C 129 " (cutoff:3.500A)
      removed outlier: 9.048A  pdb=" N   GLY C 131 " --> pdb=" O   ARG C  59 " (cutoff:3.500A)
      removed outlier: 5.140A  pdb=" N   LEU C 129 " --> pdb=" O   VAL C 156 " (cutoff:3.500A)
      removed outlier: 6.740A  pdb=" N   VAL C 156 " --> pdb=" O   LEU C 129 " (cutoff:3.500A)
      removed outlier: 5.445A  pdb=" N   GLY C 131 " --> pdb=" O   ARG C 154 " (cutoff:3.500A)
      removed outlier: 7.018A  pdb=" N   ARG C 154 " --> pdb=" O   GLY C 131 " (cutoff:3.500A)
      removed outlier: 5.312A  pdb=" N   LEU C 133 " --> pdb=" O   ASP C 152 " (cutoff:3.500A)
      removed outlier: 7.084A  pdb=" N   ASP C 152 " --> pdb=" O   LEU C 133 " (cutoff:3.500A)
      removed outlier: 3.889A  pdb=" N   ARG C 167 " --> pdb=" O   ALA C 153 " (cutoff:3.500A)
      removed outlier: 4.223A  pdb=" N   ALA C 165 " --> pdb=" O   LEU C 155 " (cutoff:3.500A)
      removed outlier: 6.344A  pdb=" N   ARG C 157 " --> pdb=" O   VAL C 163 " (cutoff:3.500A)
      removed outlier: 5.444A  pdb=" N   VAL C 163 " --> pdb=" O   ARG C 157 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'C' and resid 116 through 118
      removed outlier: 6.380A  pdb=" N   LEU C  58 " --> pdb=" O   SER C 117 " (cutoff:3.500A)
      removed outlier: 6.651A  pdb=" N   ARG C  59 " --> pdb=" O   LEU C 129 " (cutoff:3.500A)
      removed outlier: 9.048A  pdb=" N   GLY C 131 " --> pdb=" O   ARG C  59 " (cutoff:3.500A)
      removed outlier: 7.199A  pdb=" N   ALA C  75 " --> pdb=" O   THR C 138 " (cutoff:3.500A)
      removed outlier: 4.380A  pdb=" N   VAL D  37 " --> pdb=" O   ILE C  83 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'D' and resid 64 through 65
      removed outlier: 6.425A  pdb=" N   ARG D  64 " --> pdb=" O   LEU D 133 " (cutoff:3.500A)
      removed outlier: 7.786A  pdb=" N   ALA D 135 " --> pdb=" O   ARG D  64 " (cutoff:3.500A)
      removed outlier: 6.354A  pdb=" N   ARG D 150 " --> pdb=" O   ARG D 134 " (cutoff:3.500A)
      removed outlier: 3.913A  pdb=" N   PHE D 136 " --> pdb=" O   LEU D 148 " (cutoff:3.500A)
      removed outlier: 6.397A  pdb=" N   LEU D 148 " --> pdb=" O   PHE D 136 " (cutoff:3.500A)
      removed outlier: 4.446A  pdb=" N   THR D 138 " --> pdb=" O   SER D 146 " (cutoff:3.500A)
      removed outlier: 6.580A  pdb=" N   SER D 146 " --> pdb=" O   THR D 138 " (cutoff:3.500A)
      removed outlier: 3.746A  pdb=" N   ALA D 165 " --> pdb=" O   LEU D 155 " (cutoff:3.500A)
      removed outlier: 6.248A  pdb=" N   ARG D 157 " --> pdb=" O   VAL D 163 " (cutoff:3.500A)
      removed outlier: 5.566A  pdb=" N   VAL D 163 " --> pdb=" O   ARG D 157 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'D' and resid 116 through 118
      removed outlier: 6.366A  pdb=" N   LEU D  58 " --> pdb=" O   SER D 117 " (cutoff:3.500A)
      removed outlier: 7.214A  pdb=" N   ALA D  75 " --> pdb=" O   THR D 138 " (cutoff:3.500A)
      removed outlier: 4.387A  pdb=" N   VAL E  37 " --> pdb=" O   ILE D  83 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'E' and resid 117 through 118
      removed outlier: 6.774A  pdb=" N   ARG E 150 " --> pdb=" O   ARG E 134 " (cutoff:3.500A)
      removed outlier: 4.017A  pdb=" N   PHE E 136 " --> pdb=" O   LEU E 148 " (cutoff:3.500A)
      removed outlier: 6.597A  pdb=" N   LEU E 148 " --> pdb=" O   PHE E 136 " (cutoff:3.500A)
      removed outlier: 4.663A  pdb=" N   THR E 138 " --> pdb=" O   SER E 146 " (cutoff:3.500A)
      removed outlier: 6.539A  pdb=" N   SER E 146 " --> pdb=" O   THR E 138 " (cutoff:3.500A)
      removed outlier: 6.602A  pdb=" N   ALA E 147 " --> pdb=" O   SER E 172 " (cutoff:3.500A)
      removed outlier: 4.315A  pdb=" N   SER E 172 " --> pdb=" O   ALA E 147 " (cutoff:3.500A)
      removed outlier: 6.908A  pdb=" N   ILE E 149 " --> pdb=" O   GLU E 170 " (cutoff:3.500A)
      removed outlier: 4.517A  pdb=" N   GLU E 170 " --> pdb=" O   ILE E 149 " (cutoff:3.500A)
      removed outlier: 6.747A  pdb=" N   TYR E 151 " --> pdb=" O   ARG E 168 " (cutoff:3.500A)
      removed outlier: 4.854A  pdb=" N   ARG E 168 " --> pdb=" O   TYR E 151 " (cutoff:3.500A)
      removed outlier: 6.724A  pdb=" N   ALA E 153 " --> pdb=" O   SER E 166 " (cutoff:3.500A)
      removed outlier: 4.339A  pdb=" N   SER E 166 " --> pdb=" O   ALA E 153 " (cutoff:3.500A)
      removed outlier: 6.685A  pdb=" N   LEU E 155 " --> pdb=" O   VAL E 164 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'E' and resid 75 through 76
      removed outlier: 4.438A  pdb=" N   VAL F  37 " --> pdb=" O   ILE E  83 " (cutoff:3.500A)
      removed outlier: 5.634A  pdb=" N   ILE F  74 " --> pdb=" O   TYR F  86 " (cutoff:3.500A)
      removed outlier: 14.606A  pdb=" N   ARG F  73 " --> pdb=" O   ARG F 134 " (cutoff:3.500A)
      removed outlier: 9.423A  pdb=" N   PHE F 136 " --> pdb=" O   ARG F  73 " (cutoff:3.500A)
      removed outlier: 4.922A  pdb=" N   ALA F  75 " --> pdb=" O   PHE F 136 " (cutoff:3.500A)
      removed outlier: 6.674A  pdb=" N   ARG F  59 " --> pdb=" O   LEU F 129 " (cutoff:3.500A)
      removed outlier: 8.977A  pdb=" N   GLY F 131 " --> pdb=" O   ARG F  59 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'E' and resid 75 through 76
      removed outlier: 4.438A  pdb=" N   VAL F  37 " --> pdb=" O   ILE E  83 " (cutoff:3.500A)
      removed outlier: 5.634A  pdb=" N   ILE F  74 " --> pdb=" O   TYR F  86 " (cutoff:3.500A)
      removed outlier: 14.606A  pdb=" N   ARG F  73 " --> pdb=" O   ARG F 134 " (cutoff:3.500A)
      removed outlier: 9.423A  pdb=" N   PHE F 136 " --> pdb=" O   ARG F  73 " (cutoff:3.500A)
      removed outlier: 4.922A  pdb=" N   ALA F  75 " --> pdb=" O   PHE F 136 " (cutoff:3.500A)
      removed outlier: 6.446A  pdb=" N   ARG F 150 " --> pdb=" O   ARG F 134 " (cutoff:3.500A)
      removed outlier: 4.038A  pdb=" N   PHE F 136 " --> pdb=" O   LEU F 148 " (cutoff:3.500A)
      removed outlier: 6.638A  pdb=" N   LEU F 148 " --> pdb=" O   PHE F 136 " (cutoff:3.500A)
      removed outlier: 4.516A  pdb=" N   THR F 138 " --> pdb=" O   SER F 146 " (cutoff:3.500A)
      removed outlier: 6.623A  pdb=" N   SER F 146 " --> pdb=" O   THR F 138 " (cutoff:3.500A)
      removed outlier: 3.615A  pdb=" N   ALA F 165 " --> pdb=" O   LEU F 155 " (cutoff:3.500A)
      removed outlier: 6.541A  pdb=" N   ARG F 157 " --> pdb=" O   VAL F 163 " (cutoff:3.500A)
      removed outlier: 5.794A  pdb=" N   VAL F 163 " --> pdb=" O   ARG F 157 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'G' and resid 36 through 38
      removed outlier: 5.937A  pdb=" N   GLN G  36 " --> pdb=" O   ARG G  90 " (cutoff:3.500A)
      removed outlier: 5.994A  pdb=" N   ILE G  74 " --> pdb=" O   TYR G  86 " (cutoff:3.500A)
      removed outlier: 9.084A  pdb=" N   ARG G  73 " --> pdb=" O   PHE G 136 " (cutoff:3.500A)
      removed outlier: 9.348A  pdb=" N   THR G 138 " --> pdb=" O   ARG G  73 " (cutoff:3.500A)
      removed outlier: 7.457A  pdb=" N   ALA G  75 " --> pdb=" O   THR G 138 " (cutoff:3.500A)
      removed outlier: 6.619A  pdb=" N   ARG G  59 " --> pdb=" O   LEU G 129 " (cutoff:3.500A)
      removed outlier: 8.772A  pdb=" N   GLY G 131 " --> pdb=" O   ARG G  59 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'G' and resid 36 through 38
      removed outlier: 5.937A  pdb=" N   GLN G  36 " --> pdb=" O   ARG G  90 " (cutoff:3.500A)
      removed outlier: 5.994A  pdb=" N   ILE G  74 " --> pdb=" O   TYR G  86 " (cutoff:3.500A)
      removed outlier: 9.084A  pdb=" N   ARG G  73 " --> pdb=" O   PHE G 136 " (cutoff:3.500A)
      removed outlier: 9.348A  pdb=" N   THR G 138 " --> pdb=" O   ARG G  73 " (cutoff:3.500A)
      removed outlier: 7.457A  pdb=" N   ALA G  75 " --> pdb=" O   THR G 138 " (cutoff:3.500A)
      removed outlier: 5.510A  pdb=" N   LEU G 129 " --> pdb=" O   VAL G 156 " (cutoff:3.500A)
      removed outlier: 7.370A  pdb=" N   VAL G 156 " --> pdb=" O   LEU G 129 " (cutoff:3.500A)
      removed outlier: 5.105A  pdb=" N   GLY G 131 " --> pdb=" O   ARG G 154 " (cutoff:3.500A)
      removed outlier: 6.811A  pdb=" N   ARG G 154 " --> pdb=" O   GLY G 131 " (cutoff:3.500A)
      removed outlier: 5.653A  pdb=" N   LEU G 133 " --> pdb=" O   ASP G 152 " (cutoff:3.500A)
      removed outlier: 6.849A  pdb=" N   ASP G 152 " --> pdb=" O   LEU G 133 " (cutoff:3.500A)
      removed outlier: 3.551A  pdb=" N   ALA G 135 " --> pdb=" O   ARG G 150 " (cutoff:3.500A)
      removed outlier: 6.294A  pdb=" N   ALA G 147 " --> pdb=" O   SER G 172 " (cutoff:3.500A)
      removed outlier: 4.193A  pdb=" N   SER G 172 " --> pdb=" O   ALA G 147 " (cutoff:3.500A)
      removed outlier: 6.672A  pdb=" N   ILE G 149 " --> pdb=" O   GLU G 170 " (cutoff:3.500A)
      removed outlier: 4.243A  pdb=" N   GLU G 170 " --> pdb=" O   ILE G 149 " (cutoff:3.500A)
      removed outlier: 6.629A  pdb=" N   TYR G 151 " --> pdb=" O   ARG G 168 " (cutoff:3.500A)
      removed outlier: 4.595A  pdb=" N   ARG G 168 " --> pdb=" O   TYR G 151 " (cutoff:3.500A)
      removed outlier: 6.730A  pdb=" N   ALA G 153 " --> pdb=" O   SER G 166 " (cutoff:3.500A)
      removed outlier: 4.368A  pdb=" N   SER G 166 " --> pdb=" O   ALA G 153 " (cutoff:3.500A)
      removed outlier: 6.570A  pdb=" N   LEU G 155 " --> pdb=" O   VAL G 164 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'H' and resid 36 through 38
      removed outlier: 6.016A  pdb=" N   GLN H  36 " --> pdb=" O   ARG H  90 " (cutoff:3.500A)
      removed outlier: 5.861A  pdb=" N   ILE H  74 " --> pdb=" O   TYR H  86 " (cutoff:3.500A)
    Processing sheet with id=AB9, first strand: chain 'H' and resid 116 through 118
      removed outlier: 6.589A  pdb=" N   ARG H  59 " --> pdb=" O   LEU H 129 " (cutoff:3.500A)
      removed outlier: 8.773A  pdb=" N   GLY H 131 " --> pdb=" O   ARG H  59 " (cutoff:3.500A)
      removed outlier: 5.502A  pdb=" N   LEU H 129 " --> pdb=" O   VAL H 156 " (cutoff:3.500A)
      removed outlier: 7.315A  pdb=" N   VAL H 156 " --> pdb=" O   LEU H 129 " (cutoff:3.500A)
      removed outlier: 5.000A  pdb=" N   GLY H 131 " --> pdb=" O   ARG H 154 " (cutoff:3.500A)
      removed outlier: 6.701A  pdb=" N   ARG H 154 " --> pdb=" O   GLY H 131 " (cutoff:3.500A)
      removed outlier: 5.574A  pdb=" N   LEU H 133 " --> pdb=" O   ASP H 152 " (cutoff:3.500A)
      removed outlier: 6.794A  pdb=" N   ASP H 152 " --> pdb=" O   LEU H 133 " (cutoff:3.500A)
      removed outlier: 3.572A  pdb=" N   ALA H 135 " --> pdb=" O   ARG H 150 " (cutoff:3.500A)
      removed outlier: 6.397A  pdb=" N   ALA H 147 " --> pdb=" O   SER H 172 " (cutoff:3.500A)
      removed outlier: 4.253A  pdb=" N   SER H 172 " --> pdb=" O   ALA H 147 " (cutoff:3.500A)
      removed outlier: 6.661A  pdb=" N   ILE H 149 " --> pdb=" O   GLU H 170 " (cutoff:3.500A)
      removed outlier: 4.200A  pdb=" N   GLU H 170 " --> pdb=" O   ILE H 149 " (cutoff:3.500A)
      removed outlier: 6.580A  pdb=" N   TYR H 151 " --> pdb=" O   ARG H 168 " (cutoff:3.500A)
      removed outlier: 4.552A  pdb=" N   ARG H 168 " --> pdb=" O   TYR H 151 " (cutoff:3.500A)
      removed outlier: 6.710A  pdb=" N   ALA H 153 " --> pdb=" O   SER H 166 " (cutoff:3.500A)
      removed outlier: 4.350A  pdb=" N   SER H 166 " --> pdb=" O   ALA H 153 " (cutoff:3.500A)
      removed outlier: 6.594A  pdb=" N   LEU H 155 " --> pdb=" O   VAL H 164 " (cutoff:3.500A)

    467 hydrogen bonds defined for protein.
    1308 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: 1.64

  Time building geometry restraints manager: 1.05 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: 3881
        1.34 -     1.46: 1869
        1.46 -     1.57: 5498
        1.57 -     1.69: 0
        1.69 -     1.81: 16
  Bond restraints: 11264
  Sorted by residual:
  bond pdb=" C   ARG B  77 "
       pdb=" N   PRO B  78 "
    ideal  model  delta    sigma   weight residual
    1.335  1.315  0.020 1.30e-02 5.92e+03 2.40e+00
  bond pdb=" C   VAL E  76 "
       pdb=" N   ARG E  77 "
    ideal  model  delta    sigma   weight residual
    1.334  1.320  0.014 1.26e-02 6.30e+03 1.16e+00
  bond pdb=" CA  SER B 195 "
       pdb=" C   SER B 195 "
    ideal  model  delta    sigma   weight residual
    1.522  1.537 -0.014 1.36e-02 5.41e+03 1.12e+00
  bond pdb=" N   ARG E  77 "
       pdb=" CA  ARG E  77 "
    ideal  model  delta    sigma   weight residual
    1.462  1.453  0.010 1.07e-02 8.73e+03 8.28e-01
  bond pdb=" CB  TRP F  91 "
       pdb=" CG  TRP F  91 "
    ideal  model  delta    sigma   weight residual
    1.498  1.470  0.028 3.10e-02 1.04e+03 7.95e-01
  ... (remaining 11259 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.82: 14947
        1.82 -     3.64: 314
        3.64 -     5.46: 46
        5.46 -     7.28: 11
        7.28 -     9.10: 2
  Bond angle restraints: 15320
  Sorted by residual:
  angle pdb=" C   GLU E 139 "
        pdb=" N   TYR E 140 "
        pdb=" CA  TYR E 140 "
      ideal   model   delta    sigma   weight residual
     123.21  119.21    4.00 1.19e+00 7.06e-01 1.13e+01
  angle pdb=" N   SER B 195 "
        pdb=" CA  SER B 195 "
        pdb=" C   SER B 195 "
      ideal   model   delta    sigma   weight residual
     111.71  115.45   -3.74 1.15e+00 7.56e-01 1.06e+01
  angle pdb=" N   LEU B 194 "
        pdb=" CA  LEU B 194 "
        pdb=" C   LEU B 194 "
      ideal   model   delta    sigma   weight residual
     111.14  113.98   -2.84 1.08e+00 8.57e-01 6.91e+00
  angle pdb=" C   PHE E 136 "
        pdb=" N   GLN E 137 "
        pdb=" CA  GLN E 137 "
      ideal   model   delta    sigma   weight residual
     122.20  117.82    4.38 1.72e+00 3.38e-01 6.50e+00
  angle pdb=" C   ARG E 134 "
        pdb=" N   ALA E 135 "
        pdb=" CA  ALA E 135 "
      ideal   model   delta    sigma   weight residual
     122.29  118.41    3.88 1.65e+00 3.67e-01 5.54e+00
  ... (remaining 15315 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.85: 6544
       17.85 -    35.71: 269
       35.71 -    53.56: 68
       53.56 -    71.41: 28
       71.41 -    89.27: 3
  Dihedral angle restraints: 6912
    sinusoidal: 2776
      harmonic: 4136
  Sorted by residual:
  dihedral pdb=" CA  PHE C 136 "
           pdb=" C   PHE C 136 "
           pdb=" N   GLN C 137 "
           pdb=" CA  GLN C 137 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -160.70  -19.30     0      5.00e+00 4.00e-02 1.49e+01
  dihedral pdb=" CA  ARG F 157 "
           pdb=" C   ARG F 157 "
           pdb=" N   THR F 158 "
           pdb=" CA  THR F 158 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -160.83  -19.17     0      5.00e+00 4.00e-02 1.47e+01
  dihedral pdb=" CA  ASP E 152 "
           pdb=" C   ASP E 152 "
           pdb=" N   ALA E 153 "
           pdb=" CA  ALA E 153 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -160.93  -19.07     0      5.00e+00 4.00e-02 1.46e+01
  ... (remaining 6909 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.026: 946
       0.026 -    0.053: 461
       0.053 -    0.079: 152
       0.079 -    0.106: 109
       0.106 -    0.132: 28
  Chirality restraints: 1696
  Sorted by residual:
  chirality pdb=" CA  ARG B 134 "
            pdb=" N   ARG B 134 "
            pdb=" C   ARG B 134 "
            pdb=" CB  ARG B 134 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.38    0.13 2.00e-01 2.50e+01 4.35e-01
  chirality pdb=" CA  ILE G 149 "
            pdb=" N   ILE G 149 "
            pdb=" C   ILE G 149 "
            pdb=" CB  ILE G 149 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.04e-01
  chirality pdb=" CA  ILE H 149 "
            pdb=" N   ILE H 149 "
            pdb=" C   ILE H 149 "
            pdb=" CB  ILE H 149 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.00e-01
  ... (remaining 1693 not shown)

  Planarity restraints: 2056
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG D 154 "   -0.257 9.50e-02 1.11e+02   1.16e-01 1.07e+01
        pdb=" NE  ARG D 154 "    0.025 2.00e-02 2.50e+03
        pdb=" CZ  ARG D 154 "   -0.025 2.00e-02 2.50e+03
        pdb=" NH1 ARG D 154 "    0.012 2.00e-02 2.50e+03
        pdb=" NH2 ARG D 154 "   -0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU C  99 "    0.016 2.00e-02 2.50e+03   3.26e-02 1.06e+01
        pdb=" C   LEU C  99 "   -0.056 2.00e-02 2.50e+03
        pdb=" O   LEU C  99 "    0.021 2.00e-02 2.50e+03
        pdb=" N   ARG C 100 "    0.019 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG G 134 "    0.239 9.50e-02 1.11e+02   1.08e-01 9.21e+00
        pdb=" NE  ARG G 134 "   -0.023 2.00e-02 2.50e+03
        pdb=" CZ  ARG G 134 "    0.023 2.00e-02 2.50e+03
        pdb=" NH1 ARG G 134 "   -0.011 2.00e-02 2.50e+03
        pdb=" NH2 ARG G 134 "    0.000 2.00e-02 2.50e+03
  ... (remaining 2053 not shown)

  Histogram of nonbonded interaction distances:
        2.56 -     3.03: 6366
        3.03 -     3.50: 10338
        3.50 -     3.96: 16701
        3.96 -     4.43: 19666
        4.43 -     4.90: 31458
  Nonbonded interactions: 84529
  Sorted by model distance:
  nonbonded pdb=" O   HIS A  43 "
            pdb=" CA  ASN A  44 "
     model   vdw
     2.559 2.776
  nonbonded pdb=" O   HIS G  43 "
            pdb=" CA  ASN G  44 "
     model   vdw
     2.574 2.776
  nonbonded pdb=" CB  ARG A 204 "
            pdb=" NE  ARG A 204 "
     model   vdw
     2.587 2.816
  nonbonded pdb=" CB  ARG G 204 "
            pdb=" NE  ARG G 204 "
     model   vdw
     2.595 2.816
  nonbonded pdb=" O   LEU B 203 "
            pdb=" OG  SER B 207 "
     model   vdw
     2.599 3.040
  ... (remaining 84524 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: 0.01
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'C'
  selection = chain 'D'
  selection = chain 'E'
  selection = chain 'F'
  selection = chain 'G'
  selection = chain 'H'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.110
  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:          0.180
  Check model and map are aligned:         0.030
  Set scattering table:                    0.020
  Process input model:                     9.280
  Find NCS groups from input model:        0.190
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.020
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   11.860
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8198
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      :  0.004   0.050  11264  Z= 0.208
  Angle     :  0.669   9.095  15320  Z= 0.355
  Chirality :  0.041   0.132   1696
  Planarity :  0.010   0.116   2056
  Dihedral  : 12.051  89.266   4224
  Min Nonbonded Distance : 2.559

Molprobity Statistics.
  All-atom Clashscore : 2.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.99 %
    Favored  : 98.01 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.33 %
    Favored  : 97.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.73 (0.21), residues: 1408
  helix: -0.60 (0.24), residues: 392
  sheet:  0.20 (0.26), residues: 384
  loop : -0.72 (0.22), residues: 632

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.028   0.003   ARG D 154 
 TYR   0.017   0.002   TYR F 151 
 PHE   0.019   0.002   PHE E 136 
 TRP   0.017   0.001   TRP A  91 
 HIS   0.004   0.001   HIS F  43 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00435 /  0.21 (11264)
  covalent geometry    : angle       0.66854 /  0.36 (15320)
  hydrogen bonds       : bond        0.15474 / 10.71 (  450)
  hydrogen bonds       : angle       6.45498 /  4.52 ( 1308)

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

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

  2816 Ramachandran restraints generated.
    1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2816 Ramachandran restraints generated.
    1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  198 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 198
  time to evaluate  : 0.398 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   74 ILE cc_start: 0.8077 (mt) cc_final: 0.7004 (pt)
REVERT: A   86 TYR cc_start: 0.6984 (m-80) cc_final: 0.5848 (m-80)
REVERT: A  139 GLU cc_start: 0.9409 (mt-10) cc_final: 0.8974 (mp0)
REVERT: B   65 THR cc_start: 0.6692 (t) cc_final: 0.5540 (m)
REVERT: B  107 PHE cc_start: 0.9327 (m-80) cc_final: 0.8865 (m-80)
REVERT: B  129 LEU cc_start: 0.9477 (tp) cc_final: 0.9168 (tt)
REVERT: C  128 GLU cc_start: 0.9038 (tt0) cc_final: 0.8785 (tm-30)
REVERT: C  129 LEU cc_start: 0.9520 (tp) cc_final: 0.9169 (tt)
REVERT: D   90 ARG cc_start: 0.9210 (ptm160) cc_final: 0.8998 (ttp-110)
REVERT: D  128 GLU cc_start: 0.9056 (tt0) cc_final: 0.8598 (tm-30)
REVERT: E   64 ARG cc_start: 0.8781 (mmt180) cc_final: 0.8478 (mmm-85)
REVERT: F   39 LEU cc_start: 0.9211 (mt) cc_final: 0.8865 (pp)
REVERT: F  138 THR cc_start: 0.9240 (m) cc_final: 0.8855 (p)
REVERT: F  176 ASP cc_start: 0.8538 (t0) cc_final: 0.8306 (t0)
REVERT: G   60 ILE cc_start: 0.9192 (mt) cc_final: 0.8835 (mt)
REVERT: G  107 PHE cc_start: 0.9069 (m-80) cc_final: 0.8850 (m-80)
REVERT: G  128 GLU cc_start: 0.9245 (tt0) cc_final: 0.9006 (tm-30)
REVERT: G  179 LYS cc_start: 0.8791 (mttt) cc_final: 0.8367 (mmmt)
REVERT: H   60 ILE cc_start: 0.8912 (mt) cc_final: 0.8451 (mp)
  outliers start: 0
  outliers final: 0
  residues processed: 198
  average time/residue: 0.1281
  time to fit residues: 32.7154
Evaluate side-chains
  95 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 95
  time to evaluate  : 0.364 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 98 optimal weight:   10.0000
   chunk 107 optimal weight:    0.0270
   chunk 10 optimal weight:   20.0000
   chunk 66 optimal weight:    0.7980
   chunk 130 optimal weight:    3.9990
   chunk 124 optimal weight:   30.0000
   chunk 103 optimal weight:    0.0060
   chunk 77 optimal weight:    3.9990
   chunk 122 optimal weight:   20.0000
   chunk 91 optimal weight:    3.9990
   chunk 55 optimal weight:    3.9990
   overall best weight:    1.7658

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
D  33 GLN
E 108 GLN
G  33 GLN
H  44 ASN
H  87 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3441 r_free = 0.3441 target = 0.056747 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2939 r_free = 0.2939 target = 0.038883 restraints weight = 68034.876|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 22)----------------|
| r_work = 0.2970 r_free = 0.2970 target = 0.039943 restraints weight = 42568.830|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.2987 r_free = 0.2987 target = 0.040658 restraints weight = 30640.030|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3000 r_free = 0.3000 target = 0.041144 restraints weight = 23821.758|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3008 r_free = 0.3008 target = 0.041474 restraints weight = 20240.405|
|-----------------------------------------------------------------------------|
r_work (final): 0.2952
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8101
moved from start:          0.2302

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  11264  Z= 0.139
  Angle     :  0.635   8.676  15320  Z= 0.318
  Chirality :  0.042   0.171   1696
  Planarity :  0.006   0.155   2056
  Dihedral  :  4.397  18.865   1600
  Min Nonbonded Distance : 2.471

Molprobity Statistics.
  All-atom Clashscore : 7.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.42 %
    Favored  : 98.58 %
  Rotamer:
    Outliers :  1.03 %
    Allowed  :  8.02 %
    Favored  : 90.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.34 (0.21), residues: 1408
  helix:  1.45 (0.25), residues: 408
  sheet:  0.67 (0.28), residues: 304
  loop : -0.72 (0.21), residues: 696

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.019   0.000   ARG D  62 
 TYR   0.020   0.001   TYR A  38 
 PHE   0.017   0.001   PHE E 136 
 TRP   0.011   0.001   TRP B  91 
 HIS   0.002   0.001   HIS F  79 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00309 /  0.14 (11264)
  covalent geometry    : angle       0.63488 /  0.32 (15320)
  hydrogen bonds       : bond        0.04428 /  3.06 (  450)
  hydrogen bonds       : angle       4.86633 /  3.40 ( 1308)

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

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

  2816 Ramachandran restraints generated.
    1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2816 Ramachandran restraints generated.
    1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 114
  time to evaluate  : 0.294 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   74 ILE cc_start: 0.7729 (mt) cc_final: 0.7206 (mp)
REVERT: A   86 TYR cc_start: 0.6905 (m-80) cc_final: 0.5967 (m-80)
REVERT: A  136 PHE cc_start: 0.7453 (t80) cc_final: 0.7128 (t80)
REVERT: A  139 GLU cc_start: 0.9413 (mt-10) cc_final: 0.9002 (mp0)
REVERT: B  107 PHE cc_start: 0.9513 (m-80) cc_final: 0.9169 (m-80)
REVERT: B  136 PHE cc_start: 0.9144 (t80) cc_final: 0.8503 (t80)
REVERT: C   70 GLU cc_start: 0.8974 (mm-30) cc_final: 0.8624 (mm-30)
REVERT: C  128 GLU cc_start: 0.9048 (tt0) cc_final: 0.8749 (tm-30)
REVERT: D  128 GLU cc_start: 0.9050 (tt0) cc_final: 0.8759 (tm-30)
REVERT: F  176 ASP cc_start: 0.8823 (t0) cc_final: 0.8618 (t0)
REVERT: G  103 LEU cc_start: 0.9847 (mt) cc_final: 0.9401 (tt)
REVERT: G  107 PHE cc_start: 0.9165 (m-80) cc_final: 0.8783 (m-80)
REVERT: G  128 GLU cc_start: 0.9187 (tt0) cc_final: 0.8962 (tm-30)
REVERT: G  179 LYS cc_start: 0.9093 (mttt) cc_final: 0.8668 (mmmt)
  outliers start: 12
  outliers final: 4
  residues processed: 119
  average time/residue: 0.1022
  time to fit residues: 16.3535
Evaluate side-chains
  83 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 79
  time to evaluate  : 0.256 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  122 ASN
Chi-restraints excluded: chain G residue  121 SER
Chi-restraints excluded: chain H residue   39 LEU
Chi-restraints excluded: chain H residue   68 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 6 optimal weight:   20.0000
   chunk 62 optimal weight:    8.9990
   chunk 18 optimal weight:    0.0370
   chunk 74 optimal weight:    8.9990
   chunk 28 optimal weight:   20.0000
   chunk 64 optimal weight:    5.9990
   chunk 110 optimal weight:    9.9990
   chunk 13 optimal weight:    7.9990
   chunk 27 optimal weight:    5.9990
   chunk 96 optimal weight:   10.0000
   chunk 53 optimal weight:    5.9990
   overall best weight:    5.2066

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  33 GLN
** G 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
G 173 GLN
H  33 GLN
H  87 GLN
H 122 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3361 r_free = 0.3361 target = 0.053194 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2843 r_free = 0.2843 target = 0.035625 restraints weight = 72792.105|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.2870 r_free = 0.2870 target = 0.036500 restraints weight = 46242.868|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.2888 r_free = 0.2888 target = 0.037135 restraints weight = 33168.274|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.2901 r_free = 0.2901 target = 0.037593 restraints weight = 26520.809|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.2908 r_free = 0.2908 target = 0.037832 restraints weight = 22611.734|
|-----------------------------------------------------------------------------|
r_work (final): 0.2856
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8301
moved from start:          0.3307

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.085  11264  Z= 0.300
  Angle     :  0.756  13.305  15320  Z= 0.375
  Chirality :  0.044   0.229   1696
  Planarity :  0.005   0.081   2056
  Dihedral  :  4.510  17.128   1600
  Min Nonbonded Distance : 2.213

Molprobity Statistics.
  All-atom Clashscore : 10.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.13 %
    Favored  : 97.87 %
  Rotamer:
    Outliers :  1.90 %
    Allowed  :  8.62 %
    Favored  : 89.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.48 (0.21), residues: 1408
  helix:  2.05 (0.25), residues: 408
  sheet:  0.24 (0.28), residues: 304
  loop : -0.69 (0.21), residues: 696

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG D  62 
 TYR   0.015   0.002   TYR A  38 
 PHE   0.019   0.002   PHE E 136 
 TRP   0.012   0.001   TRP G 201 
 HIS   0.006   0.002   HIS F  79 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00640 /  0.30 (11264)
  covalent geometry    : angle       0.75590 /  0.38 (15320)
  hydrogen bonds       : bond        0.04432 /  3.06 (  450)
  hydrogen bonds       : angle       5.02509 /  3.51 ( 1308)

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

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

  2816 Ramachandran restraints generated.
    1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2816 Ramachandran restraints generated.
    1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 80
  time to evaluate  : 0.407 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   74 ILE cc_start: 0.7703 (mt) cc_final: 0.7319 (mp)
REVERT: A   86 TYR cc_start: 0.6728 (m-80) cc_final: 0.5804 (m-80)
REVERT: A  137 GLN cc_start: 0.9047 (OUTLIER) cc_final: 0.8709 (pm20)
REVERT: B   70 GLU cc_start: 0.8610 (mm-30) cc_final: 0.8349 (mp0)
REVERT: B  107 PHE cc_start: 0.9522 (m-80) cc_final: 0.9083 (m-80)
REVERT: C  124 GLN cc_start: 0.9140 (OUTLIER) cc_final: 0.8637 (tm-30)
REVERT: C  128 GLU cc_start: 0.9077 (tt0) cc_final: 0.8834 (tm-30)
REVERT: C  161 LYS cc_start: 0.9554 (mmmm) cc_final: 0.9156 (mmtm)
REVERT: D   70 GLU cc_start: 0.8530 (mm-30) cc_final: 0.8177 (mp0)
REVERT: D  128 GLU cc_start: 0.9078 (tt0) cc_final: 0.8662 (tm-30)
REVERT: G  128 GLU cc_start: 0.9366 (tt0) cc_final: 0.9024 (tm-30)
REVERT: G  179 LYS cc_start: 0.9251 (mttt) cc_final: 0.8838 (mmmt)
REVERT: H   60 ILE cc_start: 0.8908 (mt) cc_final: 0.8685 (mp)
  outliers start: 22
  outliers final: 8
  residues processed: 94
  average time/residue: 0.1217
  time to fit residues: 15.8882
Evaluate side-chains
  77 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 67
  time to evaluate  : 0.406 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  137 GLN
Chi-restraints excluded: chain B residue  122 ASN
Chi-restraints excluded: chain B residue  176 ASP
Chi-restraints excluded: chain C residue  124 GLN
Chi-restraints excluded: chain F residue   83 ILE
Chi-restraints excluded: chain G residue   60 ILE
Chi-restraints excluded: chain G residue   76 VAL
Chi-restraints excluded: chain G residue  121 SER
Chi-restraints excluded: chain G residue  164 VAL
Chi-restraints excluded: chain H residue   68 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 50 optimal weight:    5.9990
   chunk 90 optimal weight:    3.9990
   chunk 116 optimal weight:   10.0000
   chunk 99 optimal weight:   10.0000
   chunk 124 optimal weight:   30.0000
   chunk 85 optimal weight:    0.0980
   chunk 69 optimal weight:    5.9990
   chunk 14 optimal weight:    3.9990
   chunk 63 optimal weight:    8.9990
   chunk 22 optimal weight:    4.9990
   chunk 44 optimal weight:    6.9990
   overall best weight:    3.8188

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
H 122 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3360 r_free = 0.3360 target = 0.053368 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2849 r_free = 0.2849 target = 0.035923 restraints weight = 72556.017|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.2883 r_free = 0.2883 target = 0.036862 restraints weight = 44961.378|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.2902 r_free = 0.2902 target = 0.037480 restraints weight = 32104.999|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.2914 r_free = 0.2914 target = 0.037952 restraints weight = 25883.197|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.2923 r_free = 0.2923 target = 0.038279 restraints weight = 21910.799|
|-----------------------------------------------------------------------------|
r_work (final): 0.2865
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8293
moved from start:          0.3734

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.059  11264  Z= 0.209
  Angle     :  0.629  12.809  15320  Z= 0.313
  Chirality :  0.042   0.152   1696
  Planarity :  0.004   0.050   2056
  Dihedral  :  4.237  16.489   1600
  Min Nonbonded Distance : 2.197

Molprobity Statistics.
  All-atom Clashscore : 9.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.70 %
    Favored  : 98.30 %
  Rotamer:
    Outliers :  1.64 %
    Allowed  : 10.09 %
    Favored  : 88.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.74 (0.22), residues: 1408
  helix:  2.60 (0.25), residues: 400
  sheet:  0.08 (0.29), residues: 304
  loop : -0.56 (0.22), residues: 704

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG D  62 
 TYR   0.012   0.001   TYR A  38 
 PHE   0.019   0.002   PHE G 136 
 TRP   0.015   0.001   TRP A  91 
 HIS   0.004   0.001   HIS F  79 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00446 /  0.21 (11264)
  covalent geometry    : angle       0.62949 /  0.31 (15320)
  hydrogen bonds       : bond        0.03898 /  2.70 (  450)
  hydrogen bonds       : angle       4.72306 /  3.31 ( 1308)

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

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

  2816 Ramachandran restraints generated.
    1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2816 Ramachandran restraints generated.
    1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  95 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 76
  time to evaluate  : 0.443 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   86 TYR cc_start: 0.6758 (m-80) cc_final: 0.5786 (m-80)
REVERT: A  139 GLU cc_start: 0.9500 (mt-10) cc_final: 0.9106 (mp0)
REVERT: B  107 PHE cc_start: 0.9555 (m-80) cc_final: 0.9089 (m-80)
REVERT: C   70 GLU cc_start: 0.9182 (mm-30) cc_final: 0.8739 (mm-30)
REVERT: C  128 GLU cc_start: 0.9131 (tt0) cc_final: 0.8841 (tm-30)
REVERT: C  161 LYS cc_start: 0.9532 (mmmm) cc_final: 0.9153 (mmtm)
REVERT: D  128 GLU cc_start: 0.9104 (tt0) cc_final: 0.8796 (tm-30)
REVERT: G  128 GLU cc_start: 0.9361 (tt0) cc_final: 0.9022 (tm-30)
REVERT: G  179 LYS cc_start: 0.9287 (mttt) cc_final: 0.8884 (mmmt)
  outliers start: 19
  outliers final: 8
  residues processed: 89
  average time/residue: 0.1268
  time to fit residues: 15.5145
Evaluate side-chains
  71 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 63
  time to evaluate  : 0.332 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  133 LEU
Chi-restraints excluded: chain B residue  104 MET
Chi-restraints excluded: chain B residue  122 ASN
Chi-restraints excluded: chain E residue   76 VAL
Chi-restraints excluded: chain F residue   83 ILE
Chi-restraints excluded: chain G residue   60 ILE
Chi-restraints excluded: chain G residue  121 SER
Chi-restraints excluded: chain H residue   68 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 27 optimal weight:    1.9990
   chunk 93 optimal weight:    9.9990
   chunk 32 optimal weight:   10.0000
   chunk 4 optimal weight:    4.9990
   chunk 16 optimal weight:   20.0000
   chunk 85 optimal weight:    3.9990
   chunk 115 optimal weight:   10.0000
   chunk 34 optimal weight:    9.9990
   chunk 40 optimal weight:    4.9990
   chunk 118 optimal weight:   10.0000
   chunk 87 optimal weight:    8.9990
   overall best weight:    4.9990

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
E  36 GLN
** G 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3324 r_free = 0.3324 target = 0.051904 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2808 r_free = 0.2808 target = 0.034613 restraints weight = 75120.731|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.2834 r_free = 0.2834 target = 0.035471 restraints weight = 46761.251|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.2854 r_free = 0.2854 target = 0.036116 restraints weight = 33732.442|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 22)----------------|
| r_work = 0.2866 r_free = 0.2866 target = 0.036555 restraints weight = 26841.405|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.2875 r_free = 0.2875 target = 0.036871 restraints weight = 22998.259|
|-----------------------------------------------------------------------------|
r_work (final): 0.2824
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8378
moved from start:          0.4371

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.076  11264  Z= 0.280
  Angle     :  0.715  14.164  15320  Z= 0.353
  Chirality :  0.043   0.167   1696
  Planarity :  0.005   0.053   2056
  Dihedral  :  4.481  16.285   1600
  Min Nonbonded Distance : 2.412

Molprobity Statistics.
  All-atom Clashscore : 11.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.41 %
    Favored  : 97.59 %
  Rotamer:
    Outliers :  2.07 %
    Allowed  : 10.95 %
    Favored  : 86.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.55 (0.21), residues: 1408
  helix:  2.35 (0.24), residues: 400
  sheet:  0.13 (0.28), residues: 304
  loop : -0.70 (0.22), residues: 704

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG G 112 
 TYR   0.015   0.002   TYR G 151 
 PHE   0.016   0.002   PHE G 107 
 TRP   0.013   0.001   TRP B  91 
 HIS   0.006   0.002   HIS C  43 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00596 /  0.28 (11264)
  covalent geometry    : angle       0.71490 /  0.35 (15320)
  hydrogen bonds       : bond        0.04189 /  2.90 (  450)
  hydrogen bonds       : angle       5.04027 /  3.52 ( 1308)

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

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

  2816 Ramachandran restraints generated.
    1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2816 Ramachandran restraints generated.
    1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  91 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 67
  time to evaluate  : 0.415 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   74 ILE cc_start: 0.7457 (mp) cc_final: 0.7136 (mp)
REVERT: A   86 TYR cc_start: 0.6709 (m-80) cc_final: 0.5697 (m-80)
REVERT: A  137 GLN cc_start: 0.8990 (OUTLIER) cc_final: 0.8703 (pm20)
REVERT: A  139 GLU cc_start: 0.9543 (mt-10) cc_final: 0.9193 (mp0)
REVERT: B   70 GLU cc_start: 0.8651 (mm-30) cc_final: 0.8361 (mp0)
REVERT: B  107 PHE cc_start: 0.9559 (m-80) cc_final: 0.9091 (m-80)
REVERT: C   70 GLU cc_start: 0.9235 (mm-30) cc_final: 0.8813 (mm-30)
REVERT: C  124 GLN cc_start: 0.9165 (OUTLIER) cc_final: 0.8601 (tm-30)
REVERT: C  128 GLU cc_start: 0.9104 (tt0) cc_final: 0.8839 (tm-30)
REVERT: C  161 LYS cc_start: 0.9553 (mmmm) cc_final: 0.9179 (mmtm)
REVERT: D  128 GLU cc_start: 0.9069 (tt0) cc_final: 0.8721 (tp30)
REVERT: D  161 LYS cc_start: 0.9619 (mmmm) cc_final: 0.9304 (mmmm)
REVERT: E  101 ASP cc_start: 0.9421 (m-30) cc_final: 0.9127 (p0)
REVERT: G  128 GLU cc_start: 0.9439 (tt0) cc_final: 0.8982 (tm-30)
REVERT: G  179 LYS cc_start: 0.9303 (mttt) cc_final: 0.8902 (mmmt)
REVERT: G  203 LEU cc_start: 0.9452 (OUTLIER) cc_final: 0.9190 (mt)
REVERT: H  144 GLN cc_start: 0.8939 (mm-40) cc_final: 0.8544 (tp40)
  outliers start: 24
  outliers final: 10
  residues processed: 86
  average time/residue: 0.1177
  time to fit residues: 14.2698
Evaluate side-chains
  74 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 61
  time to evaluate  : 0.501 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  137 GLN
Chi-restraints excluded: chain B residue  104 MET
Chi-restraints excluded: chain B residue  122 ASN
Chi-restraints excluded: chain C residue  124 GLN
Chi-restraints excluded: chain E residue   76 VAL
Chi-restraints excluded: chain F residue   76 VAL
Chi-restraints excluded: chain F residue   83 ILE
Chi-restraints excluded: chain G residue   60 ILE
Chi-restraints excluded: chain G residue   76 VAL
Chi-restraints excluded: chain G residue  121 SER
Chi-restraints excluded: chain G residue  149 ILE
Chi-restraints excluded: chain G residue  203 LEU
Chi-restraints excluded: chain H residue   68 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 78 optimal weight:   10.0000
   chunk 41 optimal weight:    1.9990
   chunk 79 optimal weight:    3.9990
   chunk 102 optimal weight:    0.9990
   chunk 128 optimal weight:    6.9990
   chunk 65 optimal weight:    8.9990
   chunk 53 optimal weight:    1.9990
   chunk 33 optimal weight:    8.9990
   chunk 86 optimal weight:    0.0000
   chunk 119 optimal weight:   20.0000
   chunk 122 optimal weight:    0.9990
   overall best weight:    1.1992

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3369 r_free = 0.3369 target = 0.053842 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2861 r_free = 0.2861 target = 0.036712 restraints weight = 72763.828|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.2893 r_free = 0.2893 target = 0.037655 restraints weight = 45661.342|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.2912 r_free = 0.2912 target = 0.038329 restraints weight = 32658.472|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.2924 r_free = 0.2924 target = 0.038785 restraints weight = 25889.082|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.2933 r_free = 0.2933 target = 0.039053 restraints weight = 22089.076|
|-----------------------------------------------------------------------------|
r_work (final): 0.2875
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8304
moved from start:          0.4396

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.043  11264  Z= 0.105
  Angle     :  0.571  13.648  15320  Z= 0.279
  Chirality :  0.042   0.251   1696
  Planarity :  0.004   0.049   2056
  Dihedral  :  3.944  15.054   1600
  Min Nonbonded Distance : 2.415

Molprobity Statistics.
  All-atom Clashscore : 7.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.07 %
    Favored  : 98.93 %
  Rotamer:
    Outliers :  0.86 %
    Allowed  : 12.33 %
    Favored  : 86.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.02 (0.22), residues: 1408
  helix:  3.00 (0.25), residues: 400
  sheet:  0.06 (0.29), residues: 304
  loop : -0.40 (0.22), residues: 704

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG E 102 
 TYR   0.011   0.001   TYR F 151 
 PHE   0.017   0.001   PHE G 107 
 TRP   0.010   0.001   TRP B  91 
 HIS   0.002   0.000   HIS F  79 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00232 /  0.10 (11264)
  covalent geometry    : angle       0.57093 /  0.28 (15320)
  hydrogen bonds       : bond        0.03513 /  2.46 (  450)
  hydrogen bonds       : angle       4.46491 /  3.11 ( 1308)

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

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

  2816 Ramachandran restraints generated.
    1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2816 Ramachandran restraints generated.
    1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 87
  time to evaluate  : 0.487 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   74 ILE cc_start: 0.7403 (mt) cc_final: 0.7086 (mp)
REVERT: A   86 TYR cc_start: 0.6834 (m-80) cc_final: 0.5854 (m-80)
REVERT: A  129 LEU cc_start: 0.9187 (tt) cc_final: 0.8862 (tt)
REVERT: A  139 GLU cc_start: 0.9535 (mt-10) cc_final: 0.9125 (mp0)
REVERT: C   70 GLU cc_start: 0.9236 (mm-30) cc_final: 0.8723 (mm-30)
REVERT: C  128 GLU cc_start: 0.9089 (tt0) cc_final: 0.8836 (tm-30)
REVERT: C  161 LYS cc_start: 0.9536 (mmmm) cc_final: 0.9167 (mmtm)
REVERT: D   70 GLU cc_start: 0.8582 (mm-30) cc_final: 0.8328 (mm-30)
REVERT: D  128 GLU cc_start: 0.9105 (tt0) cc_final: 0.8857 (tm-30)
REVERT: D  161 LYS cc_start: 0.9610 (mmmm) cc_final: 0.9287 (mmmm)
REVERT: E   70 GLU cc_start: 0.9027 (mm-30) cc_final: 0.8772 (mm-30)
REVERT: G  107 PHE cc_start: 0.9026 (m-80) cc_final: 0.8708 (m-80)
REVERT: G  128 GLU cc_start: 0.9380 (tt0) cc_final: 0.9082 (tm-30)
REVERT: G  129 LEU cc_start: 0.9380 (OUTLIER) cc_final: 0.9032 (tp)
REVERT: G  151 TYR cc_start: 0.8904 (t80) cc_final: 0.8607 (t80)
REVERT: G  179 LYS cc_start: 0.9188 (mttt) cc_final: 0.8792 (mmmt)
REVERT: H  144 GLN cc_start: 0.8975 (mm-40) cc_final: 0.8575 (tp40)
  outliers start: 10
  outliers final: 3
  residues processed: 93
  average time/residue: 0.1319
  time to fit residues: 16.8884
Evaluate side-chains
  78 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 74
  time to evaluate  : 0.495 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  122 ASN
Chi-restraints excluded: chain G residue   60 ILE
Chi-restraints excluded: chain G residue  129 LEU
Chi-restraints excluded: chain H residue   68 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 115 optimal weight:    2.9990
   chunk 105 optimal weight:    0.0570
   chunk 113 optimal weight:    9.9990
   chunk 65 optimal weight:    0.6980
   chunk 10 optimal weight:   10.0000
   chunk 6 optimal weight:    5.9990
   chunk 56 optimal weight:    6.9990
   chunk 66 optimal weight:    0.9980
   chunk 49 optimal weight:    7.9990
   chunk 35 optimal weight:    0.8980
   chunk 75 optimal weight:    5.9990
   overall best weight:    1.1300

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3374 r_free = 0.3374 target = 0.054134 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2860 r_free = 0.2860 target = 0.036869 restraints weight = 72422.783|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.2893 r_free = 0.2893 target = 0.037850 restraints weight = 45598.210|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.2913 r_free = 0.2913 target = 0.038549 restraints weight = 32415.209|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.2926 r_free = 0.2926 target = 0.038967 restraints weight = 25698.165|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.2934 r_free = 0.2934 target = 0.039208 restraints weight = 22134.225|
|-----------------------------------------------------------------------------|
r_work (final): 0.2878
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8303
moved from start:          0.4512

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.042  11264  Z= 0.106
  Angle     :  0.582  14.821  15320  Z= 0.279
  Chirality :  0.044   0.522   1696
  Planarity :  0.004   0.067   2056
  Dihedral  :  3.746  17.539   1600
  Min Nonbonded Distance : 2.441

Molprobity Statistics.
  All-atom Clashscore : 6.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.63 %
    Favored  : 98.37 %
  Rotamer:
    Outliers :  0.78 %
    Allowed  : 13.10 %
    Favored  : 86.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.21 (0.22), residues: 1408
  helix:  3.09 (0.25), residues: 400
  sheet:  0.22 (0.29), residues: 304
  loop : -0.26 (0.22), residues: 704

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG E  59 
 TYR   0.009   0.001   TYR F 151 
 PHE   0.017   0.001   PHE H 136 
 TRP   0.009   0.001   TRP A  91 
 HIS   0.002   0.000   HIS F  79 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00237 /  0.11 (11264)
  covalent geometry    : angle       0.58241 /  0.28 (15320)
  hydrogen bonds       : bond        0.03325 /  2.34 (  450)
  hydrogen bonds       : angle       4.36264 /  3.04 ( 1308)

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

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

  2816 Ramachandran restraints generated.
    1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2816 Ramachandran restraints generated.
    1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  89 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 80
  time to evaluate  : 0.477 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   74 ILE cc_start: 0.7422 (mt) cc_final: 0.7111 (mp)
REVERT: A   86 TYR cc_start: 0.6988 (m-80) cc_final: 0.6088 (m-80)
REVERT: A  139 GLU cc_start: 0.9555 (mt-10) cc_final: 0.9168 (mp0)
REVERT: B   70 GLU cc_start: 0.8339 (mm-30) cc_final: 0.8078 (mp0)
REVERT: C   70 GLU cc_start: 0.9221 (mm-30) cc_final: 0.8702 (mm-30)
REVERT: C  101 ASP cc_start: 0.9425 (m-30) cc_final: 0.9193 (m-30)
REVERT: C  128 GLU cc_start: 0.9060 (tt0) cc_final: 0.8852 (tm-30)
REVERT: C  161 LYS cc_start: 0.9518 (mmmm) cc_final: 0.9150 (mmtm)
REVERT: D   70 GLU cc_start: 0.8625 (mm-30) cc_final: 0.8337 (mm-30)
REVERT: D  128 GLU cc_start: 0.9128 (tt0) cc_final: 0.8806 (tm-30)
REVERT: D  161 LYS cc_start: 0.9604 (mmmm) cc_final: 0.9269 (mmmm)
REVERT: D  179 LYS cc_start: 0.9121 (tppt) cc_final: 0.8902 (tppt)
REVERT: E   70 GLU cc_start: 0.9032 (mm-30) cc_final: 0.8745 (mm-30)
REVERT: E  124 GLN cc_start: 0.9200 (OUTLIER) cc_final: 0.8356 (tm-30)
REVERT: G  107 PHE cc_start: 0.9068 (m-80) cc_final: 0.8712 (m-80)
REVERT: G  128 GLU cc_start: 0.9374 (tt0) cc_final: 0.9070 (tm-30)
REVERT: G  129 LEU cc_start: 0.9372 (OUTLIER) cc_final: 0.8970 (tp)
REVERT: G  151 TYR cc_start: 0.8953 (t80) cc_final: 0.8615 (t80)
REVERT: G  179 LYS cc_start: 0.9159 (mttt) cc_final: 0.8778 (mmmt)
REVERT: H  144 GLN cc_start: 0.8960 (mm-40) cc_final: 0.8562 (tp40)
  outliers start: 9
  outliers final: 4
  residues processed: 86
  average time/residue: 0.1240
  time to fit residues: 14.6893
Evaluate side-chains
  82 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 76
  time to evaluate  : 0.268 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  122 ASN
Chi-restraints excluded: chain E residue  124 GLN
Chi-restraints excluded: chain G residue   60 ILE
Chi-restraints excluded: chain G residue  129 LEU
Chi-restraints excluded: chain H residue   68 VAL
Chi-restraints excluded: chain H residue  187 PHE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 78 optimal weight:    0.9990
   chunk 48 optimal weight:    0.9990
   chunk 60 optimal weight:    3.9990
   chunk 11 optimal weight:    5.9990
   chunk 41 optimal weight:    0.7980
   chunk 83 optimal weight:    0.9980
   chunk 104 optimal weight:    6.9990
   chunk 62 optimal weight:    5.9990
   chunk 35 optimal weight:    0.0050
   chunk 127 optimal weight:    8.9990
   chunk 55 optimal weight:    4.9990
   overall best weight:    0.7598

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
D 105 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3384 r_free = 0.3384 target = 0.054225 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.2877 r_free = 0.2877 target = 0.036759 restraints weight = 72613.895|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.2908 r_free = 0.2908 target = 0.037798 restraints weight = 44241.340|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.2926 r_free = 0.2926 target = 0.038499 restraints weight = 31696.297|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.2939 r_free = 0.2939 target = 0.038955 restraints weight = 25222.283|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.2947 r_free = 0.2947 target = 0.039243 restraints weight = 21565.746|
|-----------------------------------------------------------------------------|
r_work (final): 0.2894
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8294
moved from start:          0.4631

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.043  11264  Z= 0.093
  Angle     :  0.563  12.433  15320  Z= 0.269
  Chirality :  0.043   0.387   1696
  Planarity :  0.003   0.040   2056
  Dihedral  :  3.593  21.254   1600
  Min Nonbonded Distance : 2.503

Molprobity Statistics.
  All-atom Clashscore : 5.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.28 %
    Favored  : 98.72 %
  Rotamer:
    Outliers :  0.86 %
    Allowed  : 12.59 %
    Favored  : 86.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.37 (0.22), residues: 1408
  helix:  3.22 (0.25), residues: 400
  sheet:  0.36 (0.30), residues: 304
  loop : -0.18 (0.23), residues: 704

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG E  59 
 TYR   0.009   0.001   TYR F 151 
 PHE   0.014   0.001   PHE G 107 
 TRP   0.009   0.001   TRP A  91 
 HIS   0.001   0.000   HIS F  79 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00207 /  0.09 (11264)
  covalent geometry    : angle       0.56342 /  0.27 (15320)
  hydrogen bonds       : bond        0.03127 /  2.18 (  450)
  hydrogen bonds       : angle       4.25297 /  2.96 ( 1308)

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

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

  2816 Ramachandran restraints generated.
    1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2816 Ramachandran restraints generated.
    1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  92 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 82
  time to evaluate  : 0.384 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   74 ILE cc_start: 0.7322 (mt) cc_final: 0.7008 (mp)
REVERT: A   86 TYR cc_start: 0.7140 (m-80) cc_final: 0.6185 (m-80)
REVERT: A  139 GLU cc_start: 0.9557 (mt-10) cc_final: 0.9189 (mp0)
REVERT: C   70 GLU cc_start: 0.9223 (mm-30) cc_final: 0.8712 (mm-30)
REVERT: C  101 ASP cc_start: 0.9428 (m-30) cc_final: 0.9190 (m-30)
REVERT: C  128 GLU cc_start: 0.9093 (tt0) cc_final: 0.8876 (tm-30)
REVERT: C  129 LEU cc_start: 0.9578 (tp) cc_final: 0.9292 (tt)
REVERT: C  161 LYS cc_start: 0.9514 (mmmm) cc_final: 0.9151 (mmtm)
REVERT: D  161 LYS cc_start: 0.9593 (mmmm) cc_final: 0.9243 (mmmm)
REVERT: G  104 MET cc_start: 0.9055 (mmt) cc_final: 0.8786 (mmm)
REVERT: G  107 PHE cc_start: 0.9103 (m-80) cc_final: 0.8674 (m-80)
REVERT: G  128 GLU cc_start: 0.9363 (tt0) cc_final: 0.9063 (tm-30)
REVERT: G  129 LEU cc_start: 0.9369 (OUTLIER) cc_final: 0.8992 (tp)
REVERT: G  151 TYR cc_start: 0.8987 (t80) cc_final: 0.8680 (t80)
REVERT: G  179 LYS cc_start: 0.9131 (mttt) cc_final: 0.8767 (mmmt)
  outliers start: 10
  outliers final: 6
  residues processed: 89
  average time/residue: 0.1248
  time to fit residues: 15.3871
Evaluate side-chains
  82 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 75
  time to evaluate  : 0.439 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   67 LEU
Chi-restraints excluded: chain B residue  122 ASN
Chi-restraints excluded: chain G residue   60 ILE
Chi-restraints excluded: chain G residue  129 LEU
Chi-restraints excluded: chain G residue  164 VAL
Chi-restraints excluded: chain H residue   68 VAL
Chi-restraints excluded: chain H residue  187 PHE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 38 optimal weight:    2.9990
   chunk 131 optimal weight:    6.9990
   chunk 8 optimal weight:    8.9990
   chunk 93 optimal weight:    9.9990
   chunk 32 optimal weight:    9.9990
   chunk 73 optimal weight:    7.9990
   chunk 59 optimal weight:   10.0000
   chunk 54 optimal weight:    0.0170
   chunk 58 optimal weight:    0.9980
   chunk 109 optimal weight:    8.9990
   chunk 40 optimal weight:    7.9990
   overall best weight:    3.8024

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** G 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3343 r_free = 0.3343 target = 0.052617 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.2842 r_free = 0.2842 target = 0.035573 restraints weight = 73667.814|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.2869 r_free = 0.2869 target = 0.036540 restraints weight = 45098.075|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.2887 r_free = 0.2887 target = 0.037178 restraints weight = 32517.975|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.2899 r_free = 0.2899 target = 0.037608 restraints weight = 25901.526|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.2907 r_free = 0.2907 target = 0.037909 restraints weight = 22176.030|
|-----------------------------------------------------------------------------|
r_work (final): 0.2849
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8362
moved from start:          0.4836

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.061  11264  Z= 0.214
  Angle     :  0.675  11.904  15320  Z= 0.325
  Chirality :  0.043   0.371   1696
  Planarity :  0.004   0.045   2056
  Dihedral  :  3.885  17.163   1600
  Min Nonbonded Distance : 2.407

Molprobity Statistics.
  All-atom Clashscore : 8.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.63 %
    Favored  : 98.37 %
  Rotamer:
    Outliers :  1.03 %
    Allowed  : 12.67 %
    Favored  : 86.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.29 (0.22), residues: 1408
  helix:  3.12 (0.25), residues: 400
  sheet:  0.19 (0.29), residues: 304
  loop : -0.15 (0.23), residues: 704

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG G  73 
 TYR   0.010   0.001   TYR F  38 
 PHE   0.013   0.002   PHE G 136 
 TRP   0.011   0.001   TRP C 201 
 HIS   0.005   0.001   HIS F  43 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00462 /  0.21 (11264)
  covalent geometry    : angle       0.67540 /  0.33 (15320)
  hydrogen bonds       : bond        0.03514 /  2.43 (  450)
  hydrogen bonds       : angle       4.69369 /  3.25 ( 1308)

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

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

  2816 Ramachandran restraints generated.
    1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2816 Ramachandran restraints generated.
    1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  76 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 64
  time to evaluate  : 0.471 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   86 TYR cc_start: 0.7248 (m-80) cc_final: 0.6163 (m-80)
REVERT: A  139 GLU cc_start: 0.9582 (mt-10) cc_final: 0.9193 (mp0)
REVERT: B   70 GLU cc_start: 0.8635 (mp0) cc_final: 0.8327 (mp0)
REVERT: C   70 GLU cc_start: 0.9284 (mm-30) cc_final: 0.8780 (mm-30)
REVERT: C  101 ASP cc_start: 0.9447 (m-30) cc_final: 0.9227 (m-30)
REVERT: C  128 GLU cc_start: 0.9137 (tt0) cc_final: 0.8819 (tm-30)
REVERT: C  161 LYS cc_start: 0.9531 (mmmm) cc_final: 0.9166 (mmtm)
REVERT: D  128 GLU cc_start: 0.8091 (tp30) cc_final: 0.7745 (tp30)
REVERT: D  161 LYS cc_start: 0.9594 (mmmm) cc_final: 0.9269 (mmmm)
REVERT: E  124 GLN cc_start: 0.9285 (OUTLIER) cc_final: 0.8307 (tm-30)
REVERT: G  104 MET cc_start: 0.9132 (mmt) cc_final: 0.8836 (mmt)
REVERT: G  128 GLU cc_start: 0.9397 (tt0) cc_final: 0.9055 (tm-30)
REVERT: G  179 LYS cc_start: 0.9202 (mttt) cc_final: 0.8754 (mmmt)
REVERT: H  144 GLN cc_start: 0.8971 (mm-40) cc_final: 0.8565 (tp40)
  outliers start: 12
  outliers final: 7
  residues processed: 73
  average time/residue: 0.1159
  time to fit residues: 12.0644
Evaluate side-chains
  73 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 65
  time to evaluate  : 0.464 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  142 ASN
Chi-restraints excluded: chain B residue   67 LEU
Chi-restraints excluded: chain B residue  122 ASN
Chi-restraints excluded: chain E residue  124 GLN
Chi-restraints excluded: chain G residue   60 ILE
Chi-restraints excluded: chain G residue  129 LEU
Chi-restraints excluded: chain H residue   68 VAL
Chi-restraints excluded: chain H residue  203 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 35 optimal weight:    6.9990
   chunk 82 optimal weight:    0.0370
   chunk 30 optimal weight:    7.9990
   chunk 20 optimal weight:    0.0870
   chunk 11 optimal weight:    2.9990
   chunk 70 optimal weight:    9.9990
   chunk 88 optimal weight:   10.0000
   chunk 8 optimal weight:    9.9990
   chunk 81 optimal weight:    9.9990
   chunk 101 optimal weight:    2.9990
   chunk 121 optimal weight:    8.9990
   overall best weight:    2.6242

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** G 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3354 r_free = 0.3354 target = 0.053022 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2848 r_free = 0.2848 target = 0.036021 restraints weight = 73816.514|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.2878 r_free = 0.2878 target = 0.036953 restraints weight = 45701.709|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.2897 r_free = 0.2897 target = 0.037619 restraints weight = 32586.325|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.2911 r_free = 0.2911 target = 0.038079 restraints weight = 25780.894|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.2919 r_free = 0.2919 target = 0.038368 restraints weight = 21923.029|
|-----------------------------------------------------------------------------|
r_work (final): 0.2862
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8344
moved from start:          0.4962

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045  11264  Z= 0.155
  Angle     :  0.629  13.537  15320  Z= 0.300
  Chirality :  0.043   0.383   1696
  Planarity :  0.004   0.043   2056
  Dihedral  :  3.792  16.513   1600
  Min Nonbonded Distance : 2.436

Molprobity Statistics.
  All-atom Clashscore : 7.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.21 %
    Favored  : 98.79 %
  Rotamer:
    Outliers :  0.78 %
    Allowed  : 12.67 %
    Favored  : 86.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.31 (0.23), residues: 1408
  helix:  3.15 (0.25), residues: 400
  sheet:  0.24 (0.29), residues: 304
  loop : -0.16 (0.23), residues: 704

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG H 100 
 TYR   0.021   0.001   TYR G 151 
 PHE   0.011   0.001   PHE G 136 
 TRP   0.010   0.001   TRP B  91 
 HIS   0.003   0.001   HIS F  79 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00340 /  0.15 (11264)
  covalent geometry    : angle       0.62851 /  0.30 (15320)
  hydrogen bonds       : bond        0.03327 /  2.31 (  450)
  hydrogen bonds       : angle       4.56447 /  3.17 ( 1308)

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

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

  2816 Ramachandran restraints generated.
    1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2816 Ramachandran restraints generated.
    1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  77 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 68
  time to evaluate  : 0.451 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   86 TYR cc_start: 0.7071 (m-80) cc_final: 0.6225 (m-80)
REVERT: A  139 GLU cc_start: 0.9576 (mt-10) cc_final: 0.9194 (mp0)
REVERT: B   70 GLU cc_start: 0.8545 (mp0) cc_final: 0.8222 (mp0)
REVERT: C   70 GLU cc_start: 0.9298 (mm-30) cc_final: 0.8848 (mm-30)
REVERT: C  101 ASP cc_start: 0.9439 (m-30) cc_final: 0.9213 (m-30)
REVERT: C  128 GLU cc_start: 0.9097 (tt0) cc_final: 0.8820 (tm-30)
REVERT: C  161 LYS cc_start: 0.9534 (mmmm) cc_final: 0.9161 (mmtm)
REVERT: D  128 GLU cc_start: 0.8042 (tp30) cc_final: 0.7733 (tp30)
REVERT: D  161 LYS cc_start: 0.9597 (mmmm) cc_final: 0.9258 (mmmm)
REVERT: E  124 GLN cc_start: 0.9261 (OUTLIER) cc_final: 0.8323 (tm-30)
REVERT: G  104 MET cc_start: 0.9133 (mmt) cc_final: 0.8807 (mmt)
REVERT: G  107 PHE cc_start: 0.9035 (m-80) cc_final: 0.8563 (m-80)
REVERT: G  128 GLU cc_start: 0.9406 (tt0) cc_final: 0.9116 (tm-30)
REVERT: G  129 LEU cc_start: 0.9366 (OUTLIER) cc_final: 0.8942 (tp)
REVERT: G  151 TYR cc_start: 0.8908 (t80) cc_final: 0.8590 (t80)
REVERT: G  179 LYS cc_start: 0.9165 (mttt) cc_final: 0.8728 (mmmt)
REVERT: H  144 GLN cc_start: 0.9019 (mm-40) cc_final: 0.8613 (tp40)
  outliers start: 9
  outliers final: 6
  residues processed: 75
  average time/residue: 0.1224
  time to fit residues: 13.0096
Evaluate side-chains
  76 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 68
  time to evaluate  : 0.437 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   67 LEU
Chi-restraints excluded: chain B residue  122 ASN
Chi-restraints excluded: chain E residue  124 GLN
Chi-restraints excluded: chain G residue   60 ILE
Chi-restraints excluded: chain G residue  129 LEU
Chi-restraints excluded: chain G residue  164 VAL
Chi-restraints excluded: chain H residue   68 VAL
Chi-restraints excluded: chain H residue  203 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 66 optimal weight:    0.6980
   chunk 73 optimal weight:    0.9990
   chunk 88 optimal weight:    9.9990
   chunk 24 optimal weight:   10.0000
   chunk 75 optimal weight:    7.9990
   chunk 9 optimal weight:   20.0000
   chunk 79 optimal weight:    9.9990
   chunk 115 optimal weight:    7.9990
   chunk 77 optimal weight:    8.9990
   chunk 32 optimal weight:    9.9990
   chunk 12 optimal weight:    7.9990
   overall best weight:    5.1388

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
F 197 GLN
** G 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3317 r_free = 0.3317 target = 0.051685 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.2808 r_free = 0.2808 target = 0.034931 restraints weight = 76465.563|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.2837 r_free = 0.2837 target = 0.035883 restraints weight = 46483.627|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.2855 r_free = 0.2855 target = 0.036525 restraints weight = 33338.262|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 50)----------------|
| r_work = 0.2867 r_free = 0.2867 target = 0.036936 restraints weight = 26569.574|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.2875 r_free = 0.2875 target = 0.037208 restraints weight = 22720.111|
|-----------------------------------------------------------------------------|
r_work (final): 0.2823
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8403
moved from start:          0.5216

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.064  11264  Z= 0.273
  Angle     :  0.722  13.635  15320  Z= 0.350
  Chirality :  0.044   0.356   1696
  Planarity :  0.004   0.047   2056
  Dihedral  :  4.160  18.060   1600
  Min Nonbonded Distance : 2.435

Molprobity Statistics.
  All-atom Clashscore : 10.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.41 %
    Favored  : 97.59 %
  Rotamer:
    Outliers :  1.03 %
    Allowed  : 12.59 %
    Favored  : 86.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.06 (0.22), residues: 1408
  helix:  2.80 (0.25), residues: 400
  sheet:  0.40 (0.29), residues: 304
  loop : -0.38 (0.23), residues: 704

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG E  59 
 TYR   0.024   0.002   TYR G 151 
 PHE   0.014   0.002   PHE G 136 
 TRP   0.013   0.001   TRP B  91 
 HIS   0.006   0.002   HIS G  79 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00581 /  0.27 (11264)
  covalent geometry    : angle       0.72249 /  0.35 (15320)
  hydrogen bonds       : bond        0.03748 /  2.58 (  450)
  hydrogen bonds       : angle       4.92198 /  3.41 ( 1308)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1725.26 seconds
wall clock time: 30 minutes 27.38 seconds (1827.38 seconds total)