Starting phenix.real_space_refine
on Mon Jul 28 01:59:53 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6ysl_10899/07_2025/6ysl_10899.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6ysl_10899/07_2025/6ysl_10899.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.5
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6ysl_10899/07_2025/6ysl_10899.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6ysl_10899/07_2025/6ysl_10899.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6ysl_10899/07_2025/6ysl_10899.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6ysl_10899/07_2025/6ysl_10899.cif"
  }
  resolution = 3.5
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.003
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      40      5.16       5
     C    6595      2.51       5
     N    1646      2.21       5
     O    1847      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 13 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 10128
  Number of models: 1
  Model: ""
    Number of chains: 7
    Chain: "G"
      Number of atoms: 1939
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 254, 1939
          Classifications: {'peptide': 254}
          Link IDs: {'PTRANS': 8, 'TRANS': 245}
    Chain: "A"
      Number of atoms: 208
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 26, 208
          Classifications: {'peptide': 26}
          Link IDs: {'PTRANS': 1, 'TRANS': 24}
    Chain: "B"
      Number of atoms: 201
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 25, 201
          Classifications: {'peptide': 25}
          Link IDs: {'PTRANS': 1, 'TRANS': 23}
    Chain: "F"
      Number of atoms: 1939
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 254, 1939
          Classifications: {'peptide': 254}
          Link IDs: {'PTRANS': 8, 'TRANS': 245}
    Chain: "E"
      Number of atoms: 1947
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 255, 1947
          Classifications: {'peptide': 255}
          Link IDs: {'PTRANS': 8, 'TRANS': 246}
    Chain: "D"
      Number of atoms: 1947
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 255, 1947
          Classifications: {'peptide': 255}
          Link IDs: {'PTRANS': 8, 'TRANS': 246}
    Chain: "C"
      Number of atoms: 1947
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 255, 1947
          Classifications: {'peptide': 255}
          Link IDs: {'PTRANS': 8, 'TRANS': 246}
  Time building chain proxies: 6.85, per 1000 atoms: 0.68
  Number of scatterers: 10128
  At special positions: 0
  Unit cell: (96.996, 110.97, 94.53, 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      40     16.00
     O    1847      8.00
     N    1646      7.00
     C    6595      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: 2.54
  Conformation dependent library (CDL) restraints added in 1.8 seconds
  

  2620 Ramachandran restraints generated.
    1310 Oldfield, 0 Emsley, 1310 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2478

  Finding SS restraints...
    Secondary structure from input PDB file:
      67 helices and 0 sheets defined
      75.4% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.99
  Creating SS restraints...
    Processing helix  chain 'G' and resid 3 through 24
      removed outlier: 4.157A  pdb=" N   ILE G   7 " --> pdb=" O   LYS G   3 " (cutoff:3.500A)
      removed outlier: 3.654A  pdb=" N   LYS G  23 " --> pdb=" O   GLY G  19 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 39 through 51
    Processing helix  chain 'G' and resid 58 through 64
    Processing helix  chain 'G' and resid 74 through 79
      removed outlier: 4.163A  pdb=" N   ILE G  79 " --> pdb=" O   ILE G  75 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 84 through 93
      removed outlier: 3.509A  pdb=" N   ARG G  90 " --> pdb=" O   ALA G  86 " (cutoff:3.500A)
      removed outlier: 4.293A  pdb=" N   GLU G  92 " --> pdb=" O   LEU G  88 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 106 through 117
      removed outlier: 3.682A  pdb=" N   LYS G 110 " --> pdb=" O   ASP G 106 " (cutoff:3.500A)
      removed outlier: 3.582A  pdb=" N   GLY G 112 " --> pdb=" O   PHE G 108 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 122 through 170
      removed outlier: 4.078A  pdb=" N   ARG G 126 " --> pdb=" O   ALA G 122 " (cutoff:3.500A)
      removed outlier: 3.511A  pdb=" N   ILE G 128 " --> pdb=" O   PHE G 124 " (cutoff:3.500A)
      removed outlier: 4.184A  pdb=" N   ILE G 146 " --> pdb=" O   ALA G 142 " (cutoff:3.500A)
      removed outlier: 4.220A  pdb=" N   PHE G 147 " --> pdb=" O   GLY G 143 " (cutoff:3.500A)
      Proline residue:  G 155  - end of helix
    Processing helix  chain 'G' and resid 177 through 199
      removed outlier: 3.609A  pdb=" N   HIS G 181 " --> pdb=" O   ASP G 177 " (cutoff:3.500A)
      removed outlier: 6.054A  pdb=" N   ILE G 183 " --> pdb=" O   LEU G 179 " (cutoff:3.500A)
      removed outlier: 4.258A  pdb=" N   ALA G 189 " --> pdb=" O   ALA G 185 " (cutoff:3.500A)
      removed outlier: 4.115A  pdb=" N   THR G 190 " --> pdb=" O   ALA G 186 " (cutoff:3.500A)
      removed outlier: 4.362A  pdb=" N   GLY G 197 " --> pdb=" O   GLY G 193 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 200 through 232
      removed outlier: 3.879A  pdb=" N   MET G 222 " --> pdb=" O   LEU G 218 " (cutoff:3.500A)
      removed outlier: 3.627A  pdb=" N   ILE G 223 " --> pdb=" O   ARG G 219 " (cutoff:3.500A)
      removed outlier: 4.200A  pdb=" N   GLU G 224 " --> pdb=" O   GLU G 220 " (cutoff:3.500A)
      removed outlier: 3.659A  pdb=" N   GLY G 225 " --> pdb=" O   VAL G 221 " (cutoff:3.500A)
      removed outlier: 3.604A  pdb=" N   VAL G 229 " --> pdb=" O   GLY G 225 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 238 through 243
    Processing helix  chain 'G' and resid 247 through 252
      removed outlier: 3.765A  pdb=" N   LEU G 252 " --> pdb=" O   ALA G 248 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 18 through 37
      removed outlier: 3.697A  pdb=" N   TYR A  22 " --> pdb=" O   TRP A  18 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 18 through 37
    Processing helix  chain 'F' and resid 5 through 22
      removed outlier: 3.748A  pdb=" N   LEU F  11 " --> pdb=" O   ILE F   7 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 35 through 51
      removed outlier: 4.288A  pdb=" N   ILE F  39 " --> pdb=" O   ALA F  35 " (cutoff:3.500A)
      removed outlier: 3.751A  pdb=" N   ILE F  44 " --> pdb=" O   ILE F  40 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 58 through 66
      removed outlier: 3.540A  pdb=" N   LEU F  62 " --> pdb=" O   LYS F  58 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 74 through 77
    Processing helix  chain 'F' and resid 78 through 92
      removed outlier: 4.886A  pdb=" N   GLU F  84 " --> pdb=" O   PRO F  80 " (cutoff:3.500A)
      removed outlier: 3.677A  pdb=" N   TRP F  85 " --> pdb=" O   MET F  81 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 96 through 100
      removed outlier: 3.738A  pdb=" N   SER F 100 " --> pdb=" O   LEU F  97 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 109 through 114
    Processing helix  chain 'F' and resid 115 through 118
    Processing helix  chain 'F' and resid 124 through 171
      removed outlier: 3.639A  pdb=" N   GLY F 143 " --> pdb=" O   ARG F 139 " (cutoff:3.500A)
      Proline residue:  F 155  - end of helix
    Processing helix  chain 'F' and resid 179 through 196
      removed outlier: 5.268A  pdb=" N   ALA F 185 " --> pdb=" O   HIS F 181 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 200 through 232
      removed outlier: 3.509A  pdb=" N   LEU F 230 " --> pdb=" O   VAL F 226 " (cutoff:3.500A)
      removed outlier: 4.061A  pdb=" N   GLU F 231 " --> pdb=" O   LEU F 227 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 236 through 240
      removed outlier: 3.554A  pdb=" N   GLN F 240 " --> pdb=" O   VAL F 237 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 4 through 24
      removed outlier: 4.068A  pdb=" N   LEU E  22 " --> pdb=" O   VAL E  18 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 36 through 51
      removed outlier: 3.560A  pdb=" N   ILE E  40 " --> pdb=" O   ILE E  36 " (cutoff:3.500A)
      removed outlier: 3.758A  pdb=" N   ILE E  44 " --> pdb=" O   ILE E  40 " (cutoff:3.500A)
      removed outlier: 3.627A  pdb=" N   ALA E  50 " --> pdb=" O   ALA E  46 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 58 through 64
    Processing helix  chain 'E' and resid 74 through 78
    Processing helix  chain 'E' and resid 84 through 89
    Processing helix  chain 'E' and resid 97 through 102
      removed outlier: 3.734A  pdb=" N   ILE E 101 " --> pdb=" O   LEU E  97 " (cutoff:3.500A)
      removed outlier: 4.068A  pdb=" N   GLU E 102 " --> pdb=" O   GLU E  98 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'E' and resid 97 through 102'
    Processing helix  chain 'E' and resid 109 through 119
      removed outlier: 4.505A  pdb=" N   MET E 115 " --> pdb=" O   ASN E 111 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 123 through 172
      removed outlier: 3.946A  pdb=" N   ILE E 146 " --> pdb=" O   ALA E 142 " (cutoff:3.500A)
      removed outlier: 4.158A  pdb=" N   PHE E 147 " --> pdb=" O   GLY E 143 " (cutoff:3.500A)
      Proline residue:  E 155  - end of helix
      removed outlier: 3.839A  pdb=" N   ILE E 164 " --> pdb=" O   LEU E 160 " (cutoff:3.500A)
      removed outlier: 4.083A  pdb=" N   HIS E 172 " --> pdb=" O   ALA E 168 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 177 through 199
      removed outlier: 3.757A  pdb=" N   HIS E 181 " --> pdb=" O   ASP E 177 " (cutoff:3.500A)
      removed outlier: 4.693A  pdb=" N   ALA E 189 " --> pdb=" O   ALA E 185 " (cutoff:3.500A)
      removed outlier: 4.535A  pdb=" N   THR E 190 " --> pdb=" O   ALA E 186 " (cutoff:3.500A)
      removed outlier: 3.592A  pdb=" N   LEU E 191 " --> pdb=" O   PHE E 187 " (cutoff:3.500A)
      removed outlier: 3.607A  pdb=" N   GLY E 197 " --> pdb=" O   GLY E 193 " (cutoff:3.500A)
      removed outlier: 3.545A  pdb=" N   VAL E 199 " --> pdb=" O   PHE E 195 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 200 through 230
    Processing helix  chain 'E' and resid 234 through 242
    Processing helix  chain 'E' and resid 243 through 246
      removed outlier: 3.678A  pdb=" N   LEU E 246 " --> pdb=" O   LEU E 243 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'E' and resid 243 through 246'
    Processing helix  chain 'E' and resid 248 through 254
      removed outlier: 3.671A  pdb=" N   LEU E 252 " --> pdb=" O   ALA E 248 " (cutoff:3.500A)
      removed outlier: 3.811A  pdb=" N   LYS E 253 " --> pdb=" O   LYS E 249 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 4 through 23
      removed outlier: 4.074A  pdb=" N   GLY D   8 " --> pdb=" O   THR D   4 " (cutoff:3.500A)
      removed outlier: 3.789A  pdb=" N   GLY D  19 " --> pdb=" O   ALA D  15 " (cutoff:3.500A)
      removed outlier: 3.767A  pdb=" N   LYS D  23 " --> pdb=" O   GLY D  19 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 32 through 51
      removed outlier: 3.707A  pdb=" N   ILE D  36 " --> pdb=" O   ASN D  32 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 59 through 66
      removed outlier: 3.854A  pdb=" N   VAL D  65 " --> pdb=" O   THR D  61 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 74 through 79
      removed outlier: 3.580A  pdb=" N   ILE D  79 " --> pdb=" O   GLU D  76 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 84 through 91
      removed outlier: 3.668A  pdb=" N   LEU D  88 " --> pdb=" O   GLU D  84 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 108 through 118
    Processing helix  chain 'D' and resid 125 through 170
      removed outlier: 3.891A  pdb=" N   MET D 129 " --> pdb=" O   ILE D 125 " (cutoff:3.500A)
      removed outlier: 4.429A  pdb=" N   ILE D 146 " --> pdb=" O   ALA D 142 " (cutoff:3.500A)
      removed outlier: 4.854A  pdb=" N   PHE D 147 " --> pdb=" O   GLY D 143 " (cutoff:3.500A)
      removed outlier: 3.823A  pdb=" N   THR D 148 " --> pdb=" O   ALA D 144 " (cutoff:3.500A)
      Proline residue:  D 155  - end of helix
    Processing helix  chain 'D' and resid 181 through 199
      removed outlier: 3.791A  pdb=" N   ALA D 186 " --> pdb=" O   ALA D 182 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 200 through 230
    Processing helix  chain 'D' and resid 235 through 242
      removed outlier: 4.086A  pdb=" N   GLN D 240 " --> pdb=" O   LYS D 236 " (cutoff:3.500A)
      removed outlier: 3.717A  pdb=" N   LEU D 242 " --> pdb=" O   ILE D 238 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 243 through 245
      No H-bonds generated for 'chain 'D' and resid 243 through 245'
    Processing helix  chain 'D' and resid 249 through 254
      removed outlier: 4.333A  pdb=" N   LYS D 253 " --> pdb=" O   LYS D 249 " (cutoff:3.500A)
      removed outlier: 3.901A  pdb=" N   PHE D 254 " --> pdb=" O   ASP D 250 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'D' and resid 249 through 254'
    Processing helix  chain 'C' and resid 4 through 21
    Processing helix  chain 'C' and resid 27 through 31
      removed outlier: 3.815A  pdb=" N   LEU C  30 " --> pdb=" O   PHE C  27 " (cutoff:3.500A)
      removed outlier: 4.034A  pdb=" N   ALA C  31 " --> pdb=" O   SER C  28 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 27 through 31'
    Processing helix  chain 'C' and resid 34 through 51
    Processing helix  chain 'C' and resid 55 through 57
      No H-bonds generated for 'chain 'C' and resid 55 through 57'
    Processing helix  chain 'C' and resid 58 through 66
    Processing helix  chain 'C' and resid 74 through 76
      No H-bonds generated for 'chain 'C' and resid 74 through 76'
    Processing helix  chain 'C' and resid 77 through 82
    Processing helix  chain 'C' and resid 84 through 92
      removed outlier: 3.675A  pdb=" N   GLU C  92 " --> pdb=" O   LEU C  88 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 96 through 101
      removed outlier: 4.264A  pdb=" N   SER C 100 " --> pdb=" O   LEU C  97 " (cutoff:3.500A)
      removed outlier: 3.690A  pdb=" N   ILE C 101 " --> pdb=" O   GLU C  98 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 108 through 118
    Processing helix  chain 'C' and resid 123 through 171
      removed outlier: 4.005A  pdb=" N   ILE C 146 " --> pdb=" O   ALA C 142 " (cutoff:3.500A)
      removed outlier: 4.139A  pdb=" N   PHE C 147 " --> pdb=" O   GLY C 143 " (cutoff:3.500A)
      Proline residue:  C 155  - end of helix
    Processing helix  chain 'C' and resid 177 through 186
      removed outlier: 3.626A  pdb=" N   ALA C 182 " --> pdb=" O   GLU C 178 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 187 through 199
      removed outlier: 3.695A  pdb=" N   LEU C 191 " --> pdb=" O   PHE C 187 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 200 through 230
    Processing helix  chain 'C' and resid 237 through 243
    Processing helix  chain 'C' and resid 244 through 246
      No H-bonds generated for 'chain 'C' and resid 244 through 246'
    Processing helix  chain 'C' and resid 247 through 252

    648 hydrogen bonds defined for protein.
    1917 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.61

  Time building geometry restraints manager: 3.01 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: 3055
        1.34 -     1.46: 1453
        1.46 -     1.57: 5705
        1.57 -     1.69: 0
        1.69 -     1.81: 80
  Bond restraints: 10293
  Sorted by residual:
  bond pdb=" C   ILE F  79 "
       pdb=" N   PRO F  80 "
    ideal  model  delta    sigma   weight residual
    1.334  1.383 -0.049 8.40e-03 1.42e+04 3.44e+01
  bond pdb=" C   ALA E 154 "
       pdb=" N   PRO E 155 "
    ideal  model  delta    sigma   weight residual
    1.336  1.373 -0.038 1.23e-02 6.61e+03 9.49e+00
  bond pdb=" C   VAL E  59 "
       pdb=" N   PRO E  60 "
    ideal  model  delta    sigma   weight residual
    1.336  1.372 -0.036 1.20e-02 6.94e+03 9.13e+00
  bond pdb=" N   GLU B  16 "
       pdb=" CA  GLU B  16 "
    ideal  model  delta    sigma   weight residual
    1.454  1.488 -0.034 1.31e-02 5.83e+03 6.66e+00
  bond pdb=" N   ASP A  15 "
       pdb=" CA  ASP A  15 "
    ideal  model  delta    sigma   weight residual
    1.459  1.488 -0.029 1.17e-02 7.31e+03 5.94e+00
  ... (remaining 10288 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.51: 13345
        2.51 -     5.02: 456
        5.02 -     7.54: 95
        7.54 -    10.05: 28
       10.05 -    12.56: 7
  Bond angle restraints: 13931
  Sorted by residual:
  angle pdb=" C   LEU C  78 "
        pdb=" N   ILE C  79 "
        pdb=" CA  ILE C  79 "
      ideal   model   delta    sigma   weight residual
     120.24  124.27   -4.03 6.30e-01 2.52e+00 4.09e+01
  angle pdb=" N   GLU E  84 "
        pdb=" CA  GLU E  84 "
        pdb=" C   GLU E  84 "
      ideal   model   delta    sigma   weight residual
     113.43  106.49    6.94 1.26e+00 6.30e-01 3.03e+01
  angle pdb=" N   ASN E  32 "
        pdb=" CA  ASN E  32 "
        pdb=" C   ASN E  32 "
      ideal   model   delta    sigma   weight residual
     109.81  120.95  -11.14 2.21e+00 2.05e-01 2.54e+01
  angle pdb=" C   GLU G 102 "
        pdb=" N   ASP G 103 "
        pdb=" CA  ASP G 103 "
      ideal   model   delta    sigma   weight residual
     121.54  131.14   -9.60 1.91e+00 2.74e-01 2.53e+01
  angle pdb=" C   VAL G 117 "
        pdb=" N   ASP G 118 "
        pdb=" CA  ASP G 118 "
      ideal   model   delta    sigma   weight residual
     121.54  130.75   -9.21 1.91e+00 2.74e-01 2.33e+01
  ... (remaining 13926 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.00: 5659
       15.00 -    30.00: 410
       30.00 -    45.00: 145
       45.00 -    60.00: 8
       60.00 -    75.00: 6
  Dihedral angle restraints: 6228
    sinusoidal: 2414
      harmonic: 3814
  Sorted by residual:
  dihedral pdb=" CA  ALA F 234 "
           pdb=" C   ALA F 234 "
           pdb=" N   PRO F 235 "
           pdb=" CA  PRO F 235 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -151.59  -28.41     0      5.00e+00 4.00e-02 3.23e+01
  dihedral pdb=" CA  HIS F 181 "
           pdb=" C   HIS F 181 "
           pdb=" N   ALA F 182 "
           pdb=" CA  ALA F 182 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  151.61   28.39     0      5.00e+00 4.00e-02 3.22e+01
  dihedral pdb=" CA  ASN G  32 "
           pdb=" C   ASN G  32 "
           pdb=" N   PRO G  33 "
           pdb=" CA  PRO G  33 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  153.62   26.38     0      5.00e+00 4.00e-02 2.78e+01
  ... (remaining 6225 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.060: 1227
       0.060 -    0.120: 370
       0.120 -    0.180: 85
       0.180 -    0.240: 11
       0.240 -    0.301: 1
  Chirality restraints: 1694
  Sorted by residual:
  chirality pdb=" CA  ASN E  32 "
            pdb=" N   ASN E  32 "
            pdb=" C   ASN E  32 "
            pdb=" CB  ASN E  32 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.21    0.30 2.00e-01 2.50e+01 2.26e+00
  chirality pdb=" CB  ILE D   7 "
            pdb=" CA  ILE D   7 "
            pdb=" CG1 ILE D   7 "
            pdb=" CG2 ILE D   7 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.41    0.24 2.00e-01 2.50e+01 1.42e+00
  chirality pdb=" CA  ASP G 118 "
            pdb=" N   ASP G 118 "
            pdb=" C   ASP G 118 "
            pdb=" CB  ASP G 118 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.29    0.22 2.00e-01 2.50e+01 1.18e+00
  ... (remaining 1691 not shown)

  Planarity restraints: 1736
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLY F 197 "    0.021 2.00e-02 2.50e+03   4.24e-02 1.79e+01
        pdb=" C   GLY F 197 "   -0.073 2.00e-02 2.50e+03
        pdb=" O   GLY F 197 "    0.027 2.00e-02 2.50e+03
        pdb=" N   TYR F 198 "    0.025 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE E 204 "   -0.012 2.00e-02 2.50e+03   1.89e-02 6.27e+00
        pdb=" CG  PHE E 204 "    0.043 2.00e-02 2.50e+03
        pdb=" CD1 PHE E 204 "   -0.015 2.00e-02 2.50e+03
        pdb=" CD2 PHE E 204 "   -0.017 2.00e-02 2.50e+03
        pdb=" CE1 PHE E 204 "   -0.000 2.00e-02 2.50e+03
        pdb=" CE2 PHE E 204 "    0.002 2.00e-02 2.50e+03
        pdb=" CZ  PHE E 204 "    0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE C 124 "   -0.023 2.00e-02 2.50e+03   1.82e-02 5.82e+00
        pdb=" CG  PHE C 124 "    0.041 2.00e-02 2.50e+03
        pdb=" CD1 PHE C 124 "   -0.005 2.00e-02 2.50e+03
        pdb=" CD2 PHE C 124 "   -0.000 2.00e-02 2.50e+03
        pdb=" CE1 PHE C 124 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE2 PHE C 124 "   -0.005 2.00e-02 2.50e+03
        pdb=" CZ  PHE C 124 "   -0.007 2.00e-02 2.50e+03
  ... (remaining 1733 not shown)

  Histogram of nonbonded interaction distances:
        2.23 -     2.77: 1761
        2.77 -     3.30: 10211
        3.30 -     3.83: 16641
        3.83 -     4.37: 19622
        4.37 -     4.90: 32248
  Nonbonded interactions: 80483
  Sorted by model distance:
  nonbonded pdb=" O   LEU E 192 "
            pdb=" OG1 THR E 196 "
     model   vdw
     2.232 3.040
  nonbonded pdb=" OE2 GLU B  16 "
            pdb=" OH  TYR C 198 "
     model   vdw
     2.234 3.040
  nonbonded pdb=" O   LEU F 192 "
            pdb=" OG1 THR F 196 "
     model   vdw
     2.235 3.040
  nonbonded pdb=" O   GLY F 180 "
            pdb=" OG  SER F 184 "
     model   vdw
     2.282 3.040
  nonbonded pdb=" O   ILE G  39 "
            pdb=" OG1 THR G  43 "
     model   vdw
     2.286 3.040
  ... (remaining 80478 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'A' and resid 15 through 39)
  selection = chain 'B'
}
ncs_group {
  reference = (chain 'C' and resid 3 through 256)
  selection = (chain 'D' and resid 3 through 256)
  selection = (chain 'E' and resid 3 through 256)
  selection = chain 'F'
  selection = chain 'G'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.050
  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:          0.390
  Check model and map are aligned:         0.060
  Set scattering table:                    0.100
  Process input model:                     25.940
  Find NCS groups from input model:        0.410
  Set up NCS constraints:                  0.040
  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:3.090
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   31.090
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7310
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.087  10293  Z= 0.280
  Angle     :  1.169  12.558  13931  Z= 0.607
  Chirality :  0.060   0.301   1694
  Planarity :  0.008   0.059   1736
  Dihedral  : 12.213  74.996   3750
  Min Nonbonded Distance : 2.232

Molprobity Statistics.
  All-atom Clashscore : 5.93
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  9.01 %
    Favored  : 90.92 %
  Rotamer:
    Outliers :  0.47 %
    Allowed  :  6.93 %
    Favored  : 92.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.73 (0.18), residues: 1310
  helix: -2.77 (0.13), residues: 942
  sheet:  None (None), residues: 0
  loop : -3.60 (0.28), residues: 368

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.030   0.003   TRP C 201 
 HIS   0.013   0.003   HIS C 202 
 PHE   0.043   0.003   PHE E 204 
 TYR   0.027   0.005   TYR G 153 
 ARG   0.004   0.001   ARG G 210 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.14638 (  648)
  hydrogen bonds       : angle       7.77303 ( 1917)
  covalent geometry    : bond        0.00606 (10293)
  covalent geometry    : angle       1.16896 (13931)

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

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

  2620 Ramachandran restraints generated.
    1310 Oldfield, 0 Emsley, 1310 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2620 Ramachandran restraints generated.
    1310 Oldfield, 0 Emsley, 1310 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  438 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 433
  time to evaluate  : 1.077 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: G   20 MET cc_start: 0.7364 (mmt) cc_final: 0.7094 (mmm)
REVERT: G   68 LYS cc_start: 0.7129 (ttmt) cc_final: 0.6445 (tppt)
REVERT: G  136 MET cc_start: 0.7955 (tmm) cc_final: 0.7527 (ttm)
REVERT: G  139 ARG cc_start: 0.7549 (ttm110) cc_final: 0.6695 (ttt-90)
REVERT: G  219 ARG cc_start: 0.8460 (mtp85) cc_final: 0.8153 (mtp85)
REVERT: G  221 VAL cc_start: 0.9235 (p) cc_final: 0.8962 (p)
REVERT: G  224 GLU cc_start: 0.8435 (mp0) cc_final: 0.8168 (mp0)
REVERT: B   20 VAL cc_start: 0.8659 (t) cc_final: 0.8352 (m)
REVERT: F   84 GLU cc_start: 0.6442 (pp20) cc_final: 0.6168 (pm20)
REVERT: F  125 ILE cc_start: 0.7587 (mm) cc_final: 0.7383 (tp)
REVERT: F  176 THR cc_start: 0.8083 (t) cc_final: 0.7857 (m)
REVERT: F  204 PHE cc_start: 0.7942 (m-10) cc_final: 0.7606 (m-80)
REVERT: F  219 ARG cc_start: 0.8276 (mtt-85) cc_final: 0.7443 (mtt-85)
REVERT: F  226 VAL cc_start: 0.9491 (p) cc_final: 0.9106 (m)
REVERT: F  241 LYS cc_start: 0.6419 (pttt) cc_final: 0.6150 (pttp)
REVERT: F  244 MET cc_start: 0.7025 (ptt) cc_final: 0.6799 (ptt)
REVERT: E   87 GLN cc_start: 0.6902 (tm-30) cc_final: 0.6691 (tm-30)
REVERT: E  129 MET cc_start: 0.8204 (tpp) cc_final: 0.7637 (mtp)
REVERT: E  134 GLU cc_start: 0.8315 (mm-30) cc_final: 0.8087 (mm-30)
REVERT: E  179 LEU cc_start: 0.7621 (tt) cc_final: 0.7276 (pp)
REVERT: E  217 LYS cc_start: 0.8736 (ttmm) cc_final: 0.8463 (tptt)
REVERT: D    6 LEU cc_start: 0.7847 (pt) cc_final: 0.7075 (tp)
REVERT: D   81 MET cc_start: 0.5785 (tpp) cc_final: 0.5569 (tmm)
REVERT: D   85 TRP cc_start: 0.6760 (p90) cc_final: 0.6407 (p90)
REVERT: D  181 HIS cc_start: 0.4848 (p90) cc_final: 0.3915 (m170)
REVERT: D  210 ARG cc_start: 0.8742 (mmt180) cc_final: 0.8011 (tmm160)
REVERT: D  244 MET cc_start: 0.6536 (mpt) cc_final: 0.5761 (mtp)
REVERT: C   72 GLN cc_start: 0.6937 (pp30) cc_final: 0.6672 (tt0)
REVERT: C   87 GLN cc_start: 0.6396 (mm-40) cc_final: 0.6100 (tp-100)
REVERT: C  127 ASP cc_start: 0.7381 (p0) cc_final: 0.6140 (p0)
REVERT: C  181 HIS cc_start: 0.6827 (t-170) cc_final: 0.6616 (t70)
REVERT: C  198 TYR cc_start: 0.6937 (m-10) cc_final: 0.6611 (m-80)
  outliers start: 5
  outliers final: 3
  residues processed: 437
  average time/residue: 0.2880
  time to fit residues: 170.2373
Evaluate side-chains
  263 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 260
  time to evaluate  : 1.160 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   15 ASP
Chi-restraints excluded: chain B residue   15 ASP
Chi-restraints excluded: chain B residue   16 GLU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 108 optimal weight:    0.6980
   chunk 97 optimal weight:    0.9980
   chunk 54 optimal weight:    1.9990
   chunk 33 optimal weight:    2.9990
   chunk 65 optimal weight:    5.9990
   chunk 52 optimal weight:    9.9990
   chunk 101 optimal weight:   10.0000
   chunk 39 optimal weight:    0.0010
   chunk 61 optimal weight:    7.9990
   chunk 75 optimal weight:    3.9990
   chunk 117 optimal weight:    5.9990
   overall best weight:    1.3390

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

Flipped N/Q/H residues before XYZ refinement:
G  87 GLN
G 140 HIS
G 172 HIS
** G 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 120 GLN
F 140 HIS
F 206 ASN
E 140 HIS
E 141 GLN
E 206 ASN
D 140 HIS
D 175 ASN
D 206 ASN
C  32 ASN
C  87 GLN
C 149 GLN
C 172 HIS
** C 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 16

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4455 r_free = 0.4455 target = 0.173172 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.4077 r_free = 0.4077 target = 0.142281 restraints weight = 17050.717|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.4110 r_free = 0.4110 target = 0.144847 restraints weight = 11141.408|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.4132 r_free = 0.4132 target = 0.146538 restraints weight = 8519.897|
|-----------------------------------------------------------------------------|
r_work (final): 0.4138
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7348
moved from start:          0.2777

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044  10293  Z= 0.167
  Angle     :  0.803   8.431  13931  Z= 0.406
  Chirality :  0.045   0.179   1694
  Planarity :  0.005   0.043   1736
  Dihedral  :  6.801  61.535   1383
  Min Nonbonded Distance : 2.284

Molprobity Statistics.
  All-atom Clashscore : 14.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.71 %
    Favored  : 92.29 %
  Rotamer:
    Outliers :  4.40 %
    Allowed  : 17.32 %
    Favored  : 78.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.98 (0.21), residues: 1310
  helix: -1.35 (0.16), residues: 945
  sheet:  None (None), residues: 0
  loop : -3.34 (0.30), residues: 365

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP E 201 
 HIS   0.005   0.001   HIS F 202 
 PHE   0.041   0.003   PHE C 124 
 TYR   0.015   0.002   TYR D 153 
 ARG   0.004   0.001   ARG D 251 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04018 (  648)
  hydrogen bonds       : angle       5.24485 ( 1917)
  covalent geometry    : bond        0.00371 (10293)
  covalent geometry    : angle       0.80311 (13931)

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

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

  2620 Ramachandran restraints generated.
    1310 Oldfield, 0 Emsley, 1310 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2620 Ramachandran restraints generated.
    1310 Oldfield, 0 Emsley, 1310 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  332 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 285
  time to evaluate  : 1.245 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: G   68 LYS cc_start: 0.7189 (ttmt) cc_final: 0.6645 (mmtm)
REVERT: G  204 PHE cc_start: 0.7694 (m-10) cc_final: 0.7355 (m-80)
REVERT: G  221 VAL cc_start: 0.8988 (p) cc_final: 0.8738 (p)
REVERT: F  131 GLU cc_start: 0.7714 (mt-10) cc_final: 0.7220 (mp0)
REVERT: F  176 THR cc_start: 0.7991 (t) cc_final: 0.7790 (m)
REVERT: F  241 LYS cc_start: 0.6488 (pttt) cc_final: 0.6061 (pttp)
REVERT: E  103 ASP cc_start: 0.4816 (t70) cc_final: 0.4421 (t70)
REVERT: E  208 LEU cc_start: 0.7478 (OUTLIER) cc_final: 0.6327 (mt)
REVERT: D    6 LEU cc_start: 0.7626 (pt) cc_final: 0.7285 (tp)
REVERT: D  181 HIS cc_start: 0.4348 (p90) cc_final: 0.4131 (m90)
REVERT: D  210 ARG cc_start: 0.8376 (mmt180) cc_final: 0.8136 (tmm160)
REVERT: D  244 MET cc_start: 0.6221 (mpt) cc_final: 0.5355 (mtp)
REVERT: C  198 TYR cc_start: 0.6986 (m-10) cc_final: 0.6667 (m-80)
  outliers start: 47
  outliers final: 23
  residues processed: 316
  average time/residue: 0.1985
  time to fit residues: 89.0420
Evaluate side-chains
  265 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 241
  time to evaluate  : 1.063 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain G residue   71 LYS
Chi-restraints excluded: chain G residue  133 VAL
Chi-restraints excluded: chain G residue  192 LEU
Chi-restraints excluded: chain F residue   65 VAL
Chi-restraints excluded: chain F residue   75 ILE
Chi-restraints excluded: chain F residue  246 LEU
Chi-restraints excluded: chain E residue    4 THR
Chi-restraints excluded: chain E residue    9 ILE
Chi-restraints excluded: chain E residue   62 LEU
Chi-restraints excluded: chain E residue   75 ILE
Chi-restraints excluded: chain E residue  198 TYR
Chi-restraints excluded: chain E residue  199 VAL
Chi-restraints excluded: chain E residue  208 LEU
Chi-restraints excluded: chain D residue   17 SER
Chi-restraints excluded: chain D residue   69 GLU
Chi-restraints excluded: chain D residue  148 THR
Chi-restraints excluded: chain D residue  157 LEU
Chi-restraints excluded: chain D residue  172 HIS
Chi-restraints excluded: chain D residue  199 VAL
Chi-restraints excluded: chain D residue  206 ASN
Chi-restraints excluded: chain C residue    7 ILE
Chi-restraints excluded: chain C residue   28 SER
Chi-restraints excluded: chain C residue   63 PHE
Chi-restraints excluded: chain C residue  103 ASP
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 5 optimal weight:    4.9990
   chunk 71 optimal weight:    0.3980
   chunk 62 optimal weight:    1.9990
   chunk 36 optimal weight:    0.1980
   chunk 4 optimal weight:    3.9990
   chunk 38 optimal weight:    0.0570
   chunk 72 optimal weight:    0.9990
   chunk 99 optimal weight:    0.7980
   chunk 3 optimal weight:    0.3980
   chunk 14 optimal weight:    0.6980
   chunk 59 optimal weight:    0.0070
   overall best weight:    0.2116

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

Flipped N/Q/H residues before XYZ refinement:
** G 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 120 GLN
E 141 GLN
C 202 HIS
** C 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4490 r_free = 0.4490 target = 0.176511 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.4123 r_free = 0.4123 target = 0.146034 restraints weight = 17456.415|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.4158 r_free = 0.4158 target = 0.148747 restraints weight = 11147.920|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.4181 r_free = 0.4181 target = 0.150523 restraints weight = 8379.276|
|-----------------------------------------------------------------------------|
r_work (final): 0.4186
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7256
moved from start:          0.3422

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  10293  Z= 0.139
  Angle     :  0.770  13.125  13931  Z= 0.377
  Chirality :  0.043   0.274   1694
  Planarity :  0.005   0.045   1736
  Dihedral  :  5.699  26.633   1376
  Min Nonbonded Distance : 2.481

Molprobity Statistics.
  All-atom Clashscore : 12.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.63 %
    Favored  : 92.37 %
  Rotamer:
    Outliers :  3.93 %
    Allowed  : 20.41 %
    Favored  : 75.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.28 (0.22), residues: 1310
  helix: -0.81 (0.16), residues: 955
  sheet:  None (None), residues: 0
  loop : -3.24 (0.31), residues: 355

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP D  85 
 HIS   0.003   0.001   HIS G 202 
 PHE   0.030   0.002   PHE G 195 
 TYR   0.017   0.001   TYR C 153 
 ARG   0.006   0.000   ARG D 251 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03613 (  648)
  hydrogen bonds       : angle       4.79992 ( 1917)
  covalent geometry    : bond        0.00297 (10293)
  covalent geometry    : angle       0.76986 (13931)

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

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

  2620 Ramachandran restraints generated.
    1310 Oldfield, 0 Emsley, 1310 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2620 Ramachandran restraints generated.
    1310 Oldfield, 0 Emsley, 1310 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  329 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 287
  time to evaluate  : 1.072 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: G   68 LYS cc_start: 0.7215 (ttmt) cc_final: 0.6662 (mmtm)
REVERT: F  131 GLU cc_start: 0.7671 (mt-10) cc_final: 0.7303 (mt-10)
REVERT: F  204 PHE cc_start: 0.7847 (m-10) cc_final: 0.7501 (m-80)
REVERT: F  215 GLU cc_start: 0.7400 (tp30) cc_final: 0.7147 (tp30)
REVERT: F  241 LYS cc_start: 0.6367 (pttt) cc_final: 0.5991 (pttp)
REVERT: E  103 ASP cc_start: 0.4965 (t70) cc_final: 0.4537 (t70)
REVERT: E  208 LEU cc_start: 0.7394 (OUTLIER) cc_final: 0.6313 (mt)
REVERT: E  244 MET cc_start: 0.6222 (tpt) cc_final: 0.5991 (tpp)
REVERT: D    6 LEU cc_start: 0.7540 (pt) cc_final: 0.7180 (tp)
REVERT: D  210 ARG cc_start: 0.8407 (mmt180) cc_final: 0.8015 (tmm160)
REVERT: D  222 MET cc_start: 0.6757 (mtt) cc_final: 0.6549 (mtt)
REVERT: D  244 MET cc_start: 0.6159 (mpt) cc_final: 0.5506 (mtp)
REVERT: C   72 GLN cc_start: 0.6728 (pm20) cc_final: 0.6335 (pp30)
  outliers start: 42
  outliers final: 17
  residues processed: 321
  average time/residue: 0.1859
  time to fit residues: 87.2241
Evaluate side-chains
  265 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 247
  time to evaluate  : 1.032 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain G residue  192 LEU
Chi-restraints excluded: chain G residue  199 VAL
Chi-restraints excluded: chain A residue   15 ASP
Chi-restraints excluded: chain A residue   20 VAL
Chi-restraints excluded: chain F residue   65 VAL
Chi-restraints excluded: chain F residue  172 HIS
Chi-restraints excluded: chain F residue  246 LEU
Chi-restraints excluded: chain E residue    4 THR
Chi-restraints excluded: chain E residue    9 ILE
Chi-restraints excluded: chain E residue  198 TYR
Chi-restraints excluded: chain E residue  208 LEU
Chi-restraints excluded: chain D residue   25 VAL
Chi-restraints excluded: chain D residue   69 GLU
Chi-restraints excluded: chain D residue  172 HIS
Chi-restraints excluded: chain D residue  199 VAL
Chi-restraints excluded: chain C residue    7 ILE
Chi-restraints excluded: chain C residue   28 SER
Chi-restraints excluded: chain C residue   63 PHE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 28 optimal weight:    0.9980
   chunk 21 optimal weight:    1.9990
   chunk 106 optimal weight:   10.0000
   chunk 90 optimal weight:   10.0000
   chunk 51 optimal weight:    6.9990
   chunk 71 optimal weight:   20.0000
   chunk 78 optimal weight:    8.9990
   chunk 50 optimal weight:    2.9990
   chunk 76 optimal weight:    3.9990
   chunk 33 optimal weight:    2.9990
   chunk 70 optimal weight:    0.9990
   overall best weight:    1.9988

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

Flipped N/Q/H residues before XYZ refinement:
** G 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
G 240 GLN
F  72 GLN
F 206 ASN
E 141 GLN
** E 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  87 GLN
** C 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 214 GLN
C 240 GLN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4427 r_free = 0.4427 target = 0.171101 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.4049 r_free = 0.4049 target = 0.140313 restraints weight = 17345.066|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.4079 r_free = 0.4079 target = 0.142697 restraints weight = 11266.257|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.4103 r_free = 0.4103 target = 0.144460 restraints weight = 8611.489|
|-----------------------------------------------------------------------------|
r_work (final): 0.4110
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7383
moved from start:          0.3794

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045  10293  Z= 0.171
  Angle     :  0.785  12.060  13931  Z= 0.387
  Chirality :  0.046   0.201   1694
  Planarity :  0.004   0.040   1736
  Dihedral  :  5.527  26.884   1376
  Min Nonbonded Distance : 2.511

Molprobity Statistics.
  All-atom Clashscore : 13.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.40 %
    Favored  : 92.60 %
  Rotamer:
    Outliers :  3.93 %
    Allowed  : 22.38 %
    Favored  : 73.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.95 (0.23), residues: 1310
  helix: -0.55 (0.16), residues: 960
  sheet:  None (None), residues: 0
  loop : -3.20 (0.31), residues: 350

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.002   TRP D  85 
 HIS   0.005   0.001   HIS D 181 
 PHE   0.032   0.002   PHE E 195 
 TYR   0.015   0.002   TYR B  22 
 ARG   0.006   0.001   ARG D 251 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03652 (  648)
  hydrogen bonds       : angle       4.73902 ( 1917)
  covalent geometry    : bond        0.00404 (10293)
  covalent geometry    : angle       0.78502 (13931)

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

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

  2620 Ramachandran restraints generated.
    1310 Oldfield, 0 Emsley, 1310 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2620 Ramachandran restraints generated.
    1310 Oldfield, 0 Emsley, 1310 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  299 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 257
  time to evaluate  : 1.073 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: G   68 LYS cc_start: 0.7298 (ttmt) cc_final: 0.6693 (mmtm)
REVERT: G  129 MET cc_start: 0.6490 (mtp) cc_final: 0.6113 (mtt)
REVERT: F   20 MET cc_start: 0.5599 (tpt) cc_final: 0.4711 (tpt)
REVERT: F  131 GLU cc_start: 0.7742 (mt-10) cc_final: 0.7509 (mt-10)
REVERT: F  241 LYS cc_start: 0.6470 (pttt) cc_final: 0.6085 (pttp)
REVERT: E   61 THR cc_start: 0.7599 (p) cc_final: 0.7145 (m)
REVERT: E  103 ASP cc_start: 0.5418 (t70) cc_final: 0.4953 (t70)
REVERT: E  208 LEU cc_start: 0.7518 (OUTLIER) cc_final: 0.6810 (mt)
REVERT: E  244 MET cc_start: 0.6290 (tpt) cc_final: 0.6013 (tpp)
REVERT: D    6 LEU cc_start: 0.7624 (pt) cc_final: 0.7291 (tp)
REVERT: D  210 ARG cc_start: 0.8303 (mmt180) cc_final: 0.8074 (tmm160)
REVERT: D  244 MET cc_start: 0.6131 (mpt) cc_final: 0.5241 (mtp)
REVERT: C   72 GLN cc_start: 0.6620 (pm20) cc_final: 0.6132 (pp30)
  outliers start: 42
  outliers final: 29
  residues processed: 283
  average time/residue: 0.1886
  time to fit residues: 77.6851
Evaluate side-chains
  262 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 232
  time to evaluate  : 1.031 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain G residue    7 ILE
Chi-restraints excluded: chain G residue   25 VAL
Chi-restraints excluded: chain G residue  192 LEU
Chi-restraints excluded: chain G residue  200 LEU
Chi-restraints excluded: chain G residue  229 VAL
Chi-restraints excluded: chain A residue   15 ASP
Chi-restraints excluded: chain A residue   20 VAL
Chi-restraints excluded: chain A residue   28 LEU
Chi-restraints excluded: chain A residue   36 LEU
Chi-restraints excluded: chain F residue   65 VAL
Chi-restraints excluded: chain F residue   75 ILE
Chi-restraints excluded: chain F residue  170 LEU
Chi-restraints excluded: chain F residue  172 HIS
Chi-restraints excluded: chain F residue  246 LEU
Chi-restraints excluded: chain E residue    4 THR
Chi-restraints excluded: chain E residue  194 ILE
Chi-restraints excluded: chain E residue  198 TYR
Chi-restraints excluded: chain E residue  199 VAL
Chi-restraints excluded: chain E residue  208 LEU
Chi-restraints excluded: chain E residue  246 LEU
Chi-restraints excluded: chain D residue   69 GLU
Chi-restraints excluded: chain D residue  148 THR
Chi-restraints excluded: chain D residue  159 VAL
Chi-restraints excluded: chain D residue  172 HIS
Chi-restraints excluded: chain D residue  199 VAL
Chi-restraints excluded: chain C residue   28 SER
Chi-restraints excluded: chain C residue   30 LEU
Chi-restraints excluded: chain C residue   63 PHE
Chi-restraints excluded: chain C residue  103 ASP
Chi-restraints excluded: chain C residue  166 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 121 optimal weight:    6.9990
   chunk 116 optimal weight:    5.9990
   chunk 28 optimal weight:    0.9980
   chunk 37 optimal weight:    6.9990
   chunk 113 optimal weight:   20.0000
   chunk 98 optimal weight:    4.9990
   chunk 82 optimal weight:    3.9990
   chunk 69 optimal weight:    0.9980
   chunk 61 optimal weight:    6.9990
   chunk 68 optimal weight:    0.8980
   chunk 27 optimal weight:    0.9980
   overall best weight:    1.5782

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

Flipped N/Q/H residues before XYZ refinement:
** G 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 206 ASN
E 141 GLN
** E 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4429 r_free = 0.4429 target = 0.171767 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.4063 r_free = 0.4063 target = 0.141619 restraints weight = 17081.097|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.4096 r_free = 0.4096 target = 0.144224 restraints weight = 10831.253|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.4119 r_free = 0.4119 target = 0.146021 restraints weight = 8156.564|
|-----------------------------------------------------------------------------|
r_work (final): 0.4123
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7357
moved from start:          0.4072

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038  10293  Z= 0.153
  Angle     :  0.759  10.558  13931  Z= 0.371
  Chirality :  0.045   0.343   1694
  Planarity :  0.004   0.042   1736
  Dihedral  :  5.425  26.584   1376
  Min Nonbonded Distance : 2.470

Molprobity Statistics.
  All-atom Clashscore : 14.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.02 %
    Favored  : 92.98 %
  Rotamer:
    Outliers :  4.49 %
    Allowed  : 24.44 %
    Favored  : 71.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.75 (0.23), residues: 1310
  helix: -0.40 (0.16), residues: 965
  sheet:  None (None), residues: 0
  loop : -3.19 (0.31), residues: 345

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.002   TRP D  85 
 HIS   0.003   0.001   HIS F 172 
 PHE   0.028   0.002   PHE E 195 
 TYR   0.011   0.002   TYR D 153 
 ARG   0.007   0.000   ARG D 251 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03452 (  648)
  hydrogen bonds       : angle       4.62425 ( 1917)
  covalent geometry    : bond        0.00357 (10293)
  covalent geometry    : angle       0.75850 (13931)

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

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

  2620 Ramachandran restraints generated.
    1310 Oldfield, 0 Emsley, 1310 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2620 Ramachandran restraints generated.
    1310 Oldfield, 0 Emsley, 1310 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  309 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 261
  time to evaluate  : 1.162 
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: G   68 LYS cc_start: 0.7327 (ttmt) cc_final: 0.6765 (mmtm)
REVERT: G  129 MET cc_start: 0.6495 (mtp) cc_final: 0.6080 (mtt)
REVERT: F   20 MET cc_start: 0.5316 (tpt) cc_final: 0.4830 (tpt)
REVERT: F  131 GLU cc_start: 0.7724 (mt-10) cc_final: 0.7434 (mt-10)
REVERT: F  208 LEU cc_start: 0.7635 (OUTLIER) cc_final: 0.7363 (mm)
REVERT: F  241 LYS cc_start: 0.6462 (pttt) cc_final: 0.6072 (pttp)
REVERT: E   61 THR cc_start: 0.7572 (p) cc_final: 0.7262 (m)
REVERT: E   87 GLN cc_start: 0.6295 (tm-30) cc_final: 0.6038 (tm-30)
REVERT: E  208 LEU cc_start: 0.7511 (OUTLIER) cc_final: 0.6749 (mt)
REVERT: D    6 LEU cc_start: 0.7635 (OUTLIER) cc_final: 0.7270 (tp)
REVERT: D  210 ARG cc_start: 0.8288 (mmt180) cc_final: 0.8072 (tmm160)
  outliers start: 48
  outliers final: 27
  residues processed: 291
  average time/residue: 0.1924
  time to fit residues: 81.0920
Evaluate side-chains
  270 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 240
  time to evaluate  : 1.128 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain G residue    7 ILE
Chi-restraints excluded: chain G residue   25 VAL
Chi-restraints excluded: chain G residue   38 ILE
Chi-restraints excluded: chain G residue  166 LEU
Chi-restraints excluded: chain G residue  192 LEU
Chi-restraints excluded: chain G residue  229 VAL
Chi-restraints excluded: chain A residue   15 ASP
Chi-restraints excluded: chain A residue   20 VAL
Chi-restraints excluded: chain F residue   54 LYS
Chi-restraints excluded: chain F residue   65 VAL
Chi-restraints excluded: chain F residue   75 ILE
Chi-restraints excluded: chain F residue  170 LEU
Chi-restraints excluded: chain F residue  208 LEU
Chi-restraints excluded: chain F residue  237 VAL
Chi-restraints excluded: chain F residue  246 LEU
Chi-restraints excluded: chain E residue    4 THR
Chi-restraints excluded: chain E residue  199 VAL
Chi-restraints excluded: chain E residue  208 LEU
Chi-restraints excluded: chain E residue  227 LEU
Chi-restraints excluded: chain D residue    6 LEU
Chi-restraints excluded: chain D residue   25 VAL
Chi-restraints excluded: chain D residue   69 GLU
Chi-restraints excluded: chain D residue  148 THR
Chi-restraints excluded: chain D residue  159 VAL
Chi-restraints excluded: chain D residue  199 VAL
Chi-restraints excluded: chain C residue   28 SER
Chi-restraints excluded: chain C residue   30 LEU
Chi-restraints excluded: chain C residue   63 PHE
Chi-restraints excluded: chain C residue  103 ASP
Chi-restraints excluded: chain C residue  166 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 13 optimal weight:    0.9990
   chunk 87 optimal weight:    0.9980
   chunk 34 optimal weight:    0.5980
   chunk 49 optimal weight:    0.5980
   chunk 60 optimal weight:    1.9990
   chunk 19 optimal weight:    1.9990
   chunk 31 optimal weight:    0.7980
   chunk 97 optimal weight:    0.8980
   chunk 85 optimal weight:    0.9980
   chunk 103 optimal weight:   10.0000
   chunk 93 optimal weight:    0.9980
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
** G 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 206 ASN
E 141 GLN
** C 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4455 r_free = 0.4455 target = 0.173676 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.4084 r_free = 0.4084 target = 0.143330 restraints weight = 17216.543|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 47)----------------|
| r_work = 0.4118 r_free = 0.4118 target = 0.145977 restraints weight = 11099.814|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.4141 r_free = 0.4141 target = 0.147765 restraints weight = 8379.681|
|-----------------------------------------------------------------------------|
r_work (final): 0.4147
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7314
moved from start:          0.4296

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051  10293  Z= 0.139
  Angle     :  0.759  14.275  13931  Z= 0.370
  Chirality :  0.045   0.275   1694
  Planarity :  0.004   0.044   1736
  Dihedral  :  5.278  26.217   1376
  Min Nonbonded Distance : 2.478

Molprobity Statistics.
  All-atom Clashscore : 12.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.18 %
    Favored  : 92.82 %
  Rotamer:
    Outliers :  4.96 %
    Allowed  : 24.81 %
    Favored  : 70.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.40 (0.23), residues: 1310
  helix: -0.12 (0.17), residues: 938
  sheet:  None (None), residues: 0
  loop : -2.92 (0.31), residues: 372

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP D  85 
 HIS   0.004   0.001   HIS F 172 
 PHE   0.034   0.002   PHE E 195 
 TYR   0.014   0.002   TYR D 153 
 ARG   0.007   0.000   ARG D 251 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03366 (  648)
  hydrogen bonds       : angle       4.51867 ( 1917)
  covalent geometry    : bond        0.00313 (10293)
  covalent geometry    : angle       0.75910 (13931)

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

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

  2620 Ramachandran restraints generated.
    1310 Oldfield, 0 Emsley, 1310 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2620 Ramachandran restraints generated.
    1310 Oldfield, 0 Emsley, 1310 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  320 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 53
    poor density    : 267
  time to evaluate  : 1.072 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: G   68 LYS cc_start: 0.7247 (ttmt) cc_final: 0.6709 (mmtm)
REVERT: G  129 MET cc_start: 0.6550 (mtp) cc_final: 0.6154 (mtt)
REVERT: F   20 MET cc_start: 0.5199 (tpt) cc_final: 0.4935 (tpt)
REVERT: F  131 GLU cc_start: 0.7624 (mt-10) cc_final: 0.7322 (mt-10)
REVERT: F  208 LEU cc_start: 0.7623 (OUTLIER) cc_final: 0.7407 (mm)
REVERT: F  241 LYS cc_start: 0.6456 (pttt) cc_final: 0.6086 (pttp)
REVERT: E   61 THR cc_start: 0.7518 (p) cc_final: 0.7315 (m)
REVERT: E  192 LEU cc_start: 0.7703 (mm) cc_final: 0.7125 (tp)
REVERT: E  208 LEU cc_start: 0.7512 (OUTLIER) cc_final: 0.6388 (mt)
REVERT: E  244 MET cc_start: 0.6035 (tpt) cc_final: 0.5762 (tpp)
REVERT: D    6 LEU cc_start: 0.7610 (OUTLIER) cc_final: 0.7218 (tp)
REVERT: D   20 MET cc_start: 0.7191 (mmm) cc_final: 0.6609 (tpp)
REVERT: D  210 ARG cc_start: 0.8264 (mmt180) cc_final: 0.8055 (tmm160)
REVERT: C   72 GLN cc_start: 0.6681 (pm20) cc_final: 0.6147 (pp30)
REVERT: C   92 GLU cc_start: 0.6704 (OUTLIER) cc_final: 0.5328 (pp20)
  outliers start: 53
  outliers final: 28
  residues processed: 300
  average time/residue: 0.2611
  time to fit residues: 113.7457
Evaluate side-chains
  269 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 237
  time to evaluate  : 1.144 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain G residue    7 ILE
Chi-restraints excluded: chain G residue   25 VAL
Chi-restraints excluded: chain G residue   38 ILE
Chi-restraints excluded: chain G residue  166 LEU
Chi-restraints excluded: chain G residue  192 LEU
Chi-restraints excluded: chain G residue  200 LEU
Chi-restraints excluded: chain G residue  208 LEU
Chi-restraints excluded: chain G residue  227 LEU
Chi-restraints excluded: chain G residue  229 VAL
Chi-restraints excluded: chain A residue   15 ASP
Chi-restraints excluded: chain A residue   20 VAL
Chi-restraints excluded: chain A residue   28 LEU
Chi-restraints excluded: chain A residue   30 LEU
Chi-restraints excluded: chain F residue  170 LEU
Chi-restraints excluded: chain F residue  172 HIS
Chi-restraints excluded: chain F residue  208 LEU
Chi-restraints excluded: chain F residue  246 LEU
Chi-restraints excluded: chain E residue    4 THR
Chi-restraints excluded: chain E residue   62 LEU
Chi-restraints excluded: chain E residue  199 VAL
Chi-restraints excluded: chain E residue  208 LEU
Chi-restraints excluded: chain D residue    6 LEU
Chi-restraints excluded: chain D residue   25 VAL
Chi-restraints excluded: chain D residue   37 LEU
Chi-restraints excluded: chain D residue   69 GLU
Chi-restraints excluded: chain D residue  159 VAL
Chi-restraints excluded: chain D residue  199 VAL
Chi-restraints excluded: chain C residue   28 SER
Chi-restraints excluded: chain C residue   30 LEU
Chi-restraints excluded: chain C residue   63 PHE
Chi-restraints excluded: chain C residue   92 GLU
Chi-restraints excluded: chain C residue  166 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 101 optimal weight:    3.9990
   chunk 112 optimal weight:    4.9990
   chunk 128 optimal weight:    5.9990
   chunk 13 optimal weight:    5.9990
   chunk 55 optimal weight:    1.9990
   chunk 14 optimal weight:    0.7980
   chunk 31 optimal weight:    0.9990
   chunk 27 optimal weight:    0.3980
   chunk 81 optimal weight:    4.9990
   chunk 49 optimal weight:    5.9990
   chunk 17 optimal weight:    1.9990
   overall best weight:    1.2386

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

Flipped N/Q/H residues before XYZ refinement:
G 202 HIS
** G 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
G 240 GLN
** F 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 141 GLN
** E 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4443 r_free = 0.4443 target = 0.172784 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.4072 r_free = 0.4072 target = 0.142411 restraints weight = 17457.138|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.4106 r_free = 0.4106 target = 0.145073 restraints weight = 11177.690|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.4129 r_free = 0.4129 target = 0.146831 restraints weight = 8413.593|
|-----------------------------------------------------------------------------|
r_work (final): 0.4134
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7332
moved from start:          0.4506

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  10293  Z= 0.148
  Angle     :  0.781  14.700  13931  Z= 0.383
  Chirality :  0.046   0.286   1694
  Planarity :  0.004   0.042   1736
  Dihedral  :  5.218  25.999   1376
  Min Nonbonded Distance : 2.429

Molprobity Statistics.
  All-atom Clashscore : 13.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.79 %
    Favored  : 93.21 %
  Rotamer:
    Outliers :  4.31 %
    Allowed  : 26.59 %
    Favored  : 69.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.34 (0.23), residues: 1310
  helix: -0.08 (0.17), residues: 941
  sheet:  None (None), residues: 0
  loop : -2.91 (0.31), residues: 369

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP D  85 
 HIS   0.004   0.001   HIS E 202 
 PHE   0.025   0.002   PHE E 195 
 TYR   0.013   0.002   TYR C 198 
 ARG   0.007   0.000   ARG D 251 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03470 (  648)
  hydrogen bonds       : angle       4.58104 ( 1917)
  covalent geometry    : bond        0.00342 (10293)
  covalent geometry    : angle       0.78076 (13931)

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

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

  2620 Ramachandran restraints generated.
    1310 Oldfield, 0 Emsley, 1310 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2620 Ramachandran restraints generated.
    1310 Oldfield, 0 Emsley, 1310 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  303 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 257
  time to evaluate  : 2.848 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: G   68 LYS cc_start: 0.7352 (ttmt) cc_final: 0.6784 (mmtm)
REVERT: G  129 MET cc_start: 0.6588 (mtp) cc_final: 0.6335 (mtt)
REVERT: F  131 GLU cc_start: 0.7601 (mt-10) cc_final: 0.7323 (mt-10)
REVERT: F  208 LEU cc_start: 0.7476 (OUTLIER) cc_final: 0.7168 (mm)
REVERT: F  241 LYS cc_start: 0.6548 (pttt) cc_final: 0.6148 (pttp)
REVERT: E  192 LEU cc_start: 0.7678 (mm) cc_final: 0.7056 (tp)
REVERT: E  198 TYR cc_start: 0.6447 (OUTLIER) cc_final: 0.6195 (m-80)
REVERT: E  208 LEU cc_start: 0.7530 (OUTLIER) cc_final: 0.6773 (mt)
REVERT: D    6 LEU cc_start: 0.7563 (OUTLIER) cc_final: 0.7178 (tp)
REVERT: D   20 MET cc_start: 0.7137 (mmm) cc_final: 0.6553 (tpp)
REVERT: D  244 MET cc_start: 0.5179 (mpp) cc_final: 0.3982 (mtp)
REVERT: C   72 GLN cc_start: 0.6713 (pm20) cc_final: 0.6123 (pp30)
REVERT: C   92 GLU cc_start: 0.6644 (OUTLIER) cc_final: 0.5291 (pp20)
  outliers start: 46
  outliers final: 31
  residues processed: 288
  average time/residue: 0.2610
  time to fit residues: 110.7844
Evaluate side-chains
  275 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 239
  time to evaluate  : 1.573 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain G residue    7 ILE
Chi-restraints excluded: chain G residue   25 VAL
Chi-restraints excluded: chain G residue   38 ILE
Chi-restraints excluded: chain G residue  166 LEU
Chi-restraints excluded: chain G residue  200 LEU
Chi-restraints excluded: chain G residue  208 LEU
Chi-restraints excluded: chain G residue  229 VAL
Chi-restraints excluded: chain A residue   20 VAL
Chi-restraints excluded: chain B residue   32 LEU
Chi-restraints excluded: chain F residue   54 LYS
Chi-restraints excluded: chain F residue   75 ILE
Chi-restraints excluded: chain F residue  170 LEU
Chi-restraints excluded: chain F residue  172 HIS
Chi-restraints excluded: chain F residue  208 LEU
Chi-restraints excluded: chain F residue  237 VAL
Chi-restraints excluded: chain F residue  246 LEU
Chi-restraints excluded: chain E residue    4 THR
Chi-restraints excluded: chain E residue  163 VAL
Chi-restraints excluded: chain E residue  179 LEU
Chi-restraints excluded: chain E residue  198 TYR
Chi-restraints excluded: chain E residue  199 VAL
Chi-restraints excluded: chain E residue  208 LEU
Chi-restraints excluded: chain E residue  227 LEU
Chi-restraints excluded: chain D residue    6 LEU
Chi-restraints excluded: chain D residue   25 VAL
Chi-restraints excluded: chain D residue   37 LEU
Chi-restraints excluded: chain D residue   69 GLU
Chi-restraints excluded: chain D residue  148 THR
Chi-restraints excluded: chain D residue  159 VAL
Chi-restraints excluded: chain D residue  199 VAL
Chi-restraints excluded: chain C residue   28 SER
Chi-restraints excluded: chain C residue   30 LEU
Chi-restraints excluded: chain C residue   63 PHE
Chi-restraints excluded: chain C residue   92 GLU
Chi-restraints excluded: chain C residue  166 LEU
Chi-restraints excluded: chain C residue  202 HIS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 95 optimal weight:    5.9990
   chunk 53 optimal weight:    9.9990
   chunk 60 optimal weight:    3.9990
   chunk 72 optimal weight:    3.9990
   chunk 81 optimal weight:    9.9990
   chunk 110 optimal weight:    2.9990
   chunk 122 optimal weight:    0.9990
   chunk 128 optimal weight:    4.9990
   chunk 74 optimal weight:    0.9990
   chunk 32 optimal weight:    5.9990
   chunk 120 optimal weight:    3.9990
   overall best weight:    2.5990

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

Flipped N/Q/H residues before XYZ refinement:
** G 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
G 240 GLN
** F 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 206 ASN
E 141 GLN
** E 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 202 HIS
** C 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4397 r_free = 0.4397 target = 0.168691 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.4014 r_free = 0.4014 target = 0.138014 restraints weight = 17394.882|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.4048 r_free = 0.4048 target = 0.140576 restraints weight = 11251.772|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.4070 r_free = 0.4070 target = 0.142241 restraints weight = 8545.834|
|-----------------------------------------------------------------------------|
r_work (final): 0.4078
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7427
moved from start:          0.4632

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.067  10293  Z= 0.198
  Angle     :  0.823  13.832  13931  Z= 0.410
  Chirality :  0.048   0.287   1694
  Planarity :  0.004   0.041   1736
  Dihedral  :  5.346  26.281   1376
  Min Nonbonded Distance : 2.414

Molprobity Statistics.
  All-atom Clashscore : 14.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.09 %
    Favored  : 91.91 %
  Rotamer:
    Outliers :  4.40 %
    Allowed  : 27.34 %
    Favored  : 68.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.45 (0.23), residues: 1310
  helix: -0.14 (0.17), residues: 946
  sheet:  None (None), residues: 0
  loop : -3.05 (0.30), residues: 364

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.027   0.003   TRP D  85 
 HIS   0.004   0.001   HIS E 202 
 PHE   0.021   0.002   PHE D 124 
 TYR   0.018   0.003   TYR D 153 
 ARG   0.007   0.001   ARG D 251 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03770 (  648)
  hydrogen bonds       : angle       4.78332 ( 1917)
  covalent geometry    : bond        0.00481 (10293)
  covalent geometry    : angle       0.82334 (13931)

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

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

  2620 Ramachandran restraints generated.
    1310 Oldfield, 0 Emsley, 1310 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2620 Ramachandran restraints generated.
    1310 Oldfield, 0 Emsley, 1310 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  288 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 241
  time to evaluate  : 1.377 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: G   68 LYS cc_start: 0.7360 (ttmt) cc_final: 0.6802 (mmtm)
REVERT: G  129 MET cc_start: 0.6546 (mtp) cc_final: 0.6281 (mtt)
REVERT: G  208 LEU cc_start: 0.7649 (OUTLIER) cc_final: 0.6327 (mp)
REVERT: F  208 LEU cc_start: 0.7516 (OUTLIER) cc_final: 0.7185 (mm)
REVERT: F  241 LYS cc_start: 0.6601 (pttt) cc_final: 0.6223 (pttp)
REVERT: E  192 LEU cc_start: 0.7766 (mm) cc_final: 0.7149 (tp)
REVERT: E  198 TYR cc_start: 0.6569 (OUTLIER) cc_final: 0.6096 (m-10)
REVERT: E  208 LEU cc_start: 0.7489 (OUTLIER) cc_final: 0.6766 (mt)
REVERT: D    6 LEU cc_start: 0.7627 (OUTLIER) cc_final: 0.7152 (tp)
REVERT: D   20 MET cc_start: 0.7247 (mmm) cc_final: 0.6617 (tpp)
REVERT: C   72 GLN cc_start: 0.6649 (pm20) cc_final: 0.5984 (pp30)
REVERT: C   92 GLU cc_start: 0.6826 (OUTLIER) cc_final: 0.5426 (pp20)
  outliers start: 47
  outliers final: 30
  residues processed: 271
  average time/residue: 0.1832
  time to fit residues: 72.9123
Evaluate side-chains
  263 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 227
  time to evaluate  : 1.180 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain G residue    7 ILE
Chi-restraints excluded: chain G residue   25 VAL
Chi-restraints excluded: chain G residue   38 ILE
Chi-restraints excluded: chain G residue  192 LEU
Chi-restraints excluded: chain G residue  200 LEU
Chi-restraints excluded: chain G residue  208 LEU
Chi-restraints excluded: chain G residue  229 VAL
Chi-restraints excluded: chain A residue   15 ASP
Chi-restraints excluded: chain A residue   20 VAL
Chi-restraints excluded: chain F residue   54 LYS
Chi-restraints excluded: chain F residue   75 ILE
Chi-restraints excluded: chain F residue  170 LEU
Chi-restraints excluded: chain F residue  172 HIS
Chi-restraints excluded: chain F residue  208 LEU
Chi-restraints excluded: chain F residue  237 VAL
Chi-restraints excluded: chain F residue  246 LEU
Chi-restraints excluded: chain E residue    4 THR
Chi-restraints excluded: chain E residue  198 TYR
Chi-restraints excluded: chain E residue  199 VAL
Chi-restraints excluded: chain E residue  208 LEU
Chi-restraints excluded: chain E residue  227 LEU
Chi-restraints excluded: chain E residue  246 LEU
Chi-restraints excluded: chain D residue    6 LEU
Chi-restraints excluded: chain D residue   25 VAL
Chi-restraints excluded: chain D residue   37 LEU
Chi-restraints excluded: chain D residue   69 GLU
Chi-restraints excluded: chain D residue   81 MET
Chi-restraints excluded: chain D residue  148 THR
Chi-restraints excluded: chain D residue  159 VAL
Chi-restraints excluded: chain D residue  199 VAL
Chi-restraints excluded: chain C residue   28 SER
Chi-restraints excluded: chain C residue   30 LEU
Chi-restraints excluded: chain C residue   63 PHE
Chi-restraints excluded: chain C residue   92 GLU
Chi-restraints excluded: chain C residue  103 ASP
Chi-restraints excluded: chain C residue  166 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 100 optimal weight:    0.7980
   chunk 9 optimal weight:    9.9990
   chunk 85 optimal weight:    0.9990
   chunk 45 optimal weight:    0.5980
   chunk 115 optimal weight:    5.9990
   chunk 51 optimal weight:    0.9980
   chunk 13 optimal weight:    3.9990
   chunk 12 optimal weight:    5.9990
   chunk 17 optimal weight:    5.9990
   chunk 38 optimal weight:    8.9990
   chunk 55 optimal weight:    2.9990
   overall best weight:    1.2784

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

Flipped N/Q/H residues before XYZ refinement:
** G 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
G 240 GLN
F 149 GLN
F 206 ASN
E 141 GLN
** E 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 206 ASN
** C 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4425 r_free = 0.4425 target = 0.171162 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.4047 r_free = 0.4047 target = 0.140445 restraints weight = 17249.492|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.4081 r_free = 0.4081 target = 0.143027 restraints weight = 11185.641|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.4102 r_free = 0.4102 target = 0.144685 restraints weight = 8514.703|
|-----------------------------------------------------------------------------|
r_work (final): 0.4111
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7374
moved from start:          0.4747

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.059  10293  Z= 0.158
  Angle     :  0.819  16.155  13931  Z= 0.404
  Chirality :  0.047   0.339   1694
  Planarity :  0.004   0.040   1736
  Dihedral  :  5.267  25.797   1376
  Min Nonbonded Distance : 2.426

Molprobity Statistics.
  All-atom Clashscore : 14.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.25 %
    Favored  : 92.75 %
  Rotamer:
    Outliers :  3.84 %
    Allowed  : 27.81 %
    Favored  : 68.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.32 (0.23), residues: 1310
  helix: -0.07 (0.17), residues: 960
  sheet:  None (None), residues: 0
  loop : -3.03 (0.31), residues: 350

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.033   0.002   TRP D 201 
 HIS   0.004   0.001   HIS F 172 
 PHE   0.028   0.002   PHE G 195 
 TYR   0.023   0.002   TYR A  22 
 ARG   0.007   0.001   ARG D 251 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03614 (  648)
  hydrogen bonds       : angle       4.78240 ( 1917)
  covalent geometry    : bond        0.00370 (10293)
  covalent geometry    : angle       0.81889 (13931)

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

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

  2620 Ramachandran restraints generated.
    1310 Oldfield, 0 Emsley, 1310 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2620 Ramachandran restraints generated.
    1310 Oldfield, 0 Emsley, 1310 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  282 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 241
  time to evaluate  : 1.217 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: G   68 LYS cc_start: 0.7275 (ttmt) cc_final: 0.6746 (mmtm)
REVERT: G  129 MET cc_start: 0.6512 (mtp) cc_final: 0.6243 (mtt)
REVERT: F  208 LEU cc_start: 0.7505 (OUTLIER) cc_final: 0.7212 (mm)
REVERT: F  241 LYS cc_start: 0.6500 (pttt) cc_final: 0.6106 (pttp)
REVERT: E  192 LEU cc_start: 0.7703 (mm) cc_final: 0.7199 (tp)
REVERT: E  198 TYR cc_start: 0.6603 (OUTLIER) cc_final: 0.6140 (m-10)
REVERT: E  208 LEU cc_start: 0.7562 (OUTLIER) cc_final: 0.6838 (mt)
REVERT: D    6 LEU cc_start: 0.7513 (OUTLIER) cc_final: 0.7291 (tp)
REVERT: D   20 MET cc_start: 0.7268 (mmm) cc_final: 0.6668 (tpp)
REVERT: C   92 GLU cc_start: 0.6724 (OUTLIER) cc_final: 0.5344 (pp20)
  outliers start: 41
  outliers final: 29
  residues processed: 267
  average time/residue: 0.1854
  time to fit residues: 72.6364
Evaluate side-chains
  263 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 229
  time to evaluate  : 1.032 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain G residue    7 ILE
Chi-restraints excluded: chain G residue   25 VAL
Chi-restraints excluded: chain G residue   38 ILE
Chi-restraints excluded: chain G residue  192 LEU
Chi-restraints excluded: chain G residue  200 LEU
Chi-restraints excluded: chain G residue  208 LEU
Chi-restraints excluded: chain G residue  229 VAL
Chi-restraints excluded: chain G residue  246 LEU
Chi-restraints excluded: chain A residue   20 VAL
Chi-restraints excluded: chain A residue   30 LEU
Chi-restraints excluded: chain B residue   32 LEU
Chi-restraints excluded: chain F residue   54 LYS
Chi-restraints excluded: chain F residue  170 LEU
Chi-restraints excluded: chain F residue  208 LEU
Chi-restraints excluded: chain F residue  237 VAL
Chi-restraints excluded: chain F residue  246 LEU
Chi-restraints excluded: chain E residue    4 THR
Chi-restraints excluded: chain E residue  163 VAL
Chi-restraints excluded: chain E residue  198 TYR
Chi-restraints excluded: chain E residue  199 VAL
Chi-restraints excluded: chain E residue  208 LEU
Chi-restraints excluded: chain E residue  227 LEU
Chi-restraints excluded: chain D residue    6 LEU
Chi-restraints excluded: chain D residue   25 VAL
Chi-restraints excluded: chain D residue   37 LEU
Chi-restraints excluded: chain D residue   69 GLU
Chi-restraints excluded: chain D residue  148 THR
Chi-restraints excluded: chain D residue  159 VAL
Chi-restraints excluded: chain D residue  199 VAL
Chi-restraints excluded: chain C residue   28 SER
Chi-restraints excluded: chain C residue   30 LEU
Chi-restraints excluded: chain C residue   63 PHE
Chi-restraints excluded: chain C residue   92 GLU
Chi-restraints excluded: chain C residue  166 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 120 optimal weight:    3.9990
   chunk 28 optimal weight:    0.8980
   chunk 128 optimal weight:    4.9990
   chunk 17 optimal weight:    6.9990
   chunk 99 optimal weight:    0.9980
   chunk 36 optimal weight:    0.0070
   chunk 90 optimal weight:    9.9990
   chunk 108 optimal weight:    3.9990
   chunk 85 optimal weight:    3.9990
   chunk 119 optimal weight:    0.7980
   chunk 43 optimal weight:    0.6980
   overall best weight:    0.6798

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

Flipped N/Q/H residues before XYZ refinement:
** G 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
G 240 GLN
F 120 GLN
F 172 HIS
** F 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 141 GLN
** E 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 206 ASN
** C 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 240 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4457 r_free = 0.4457 target = 0.173788 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.4084 r_free = 0.4084 target = 0.143460 restraints weight = 17352.282|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.4117 r_free = 0.4117 target = 0.146082 restraints weight = 11226.684|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.4140 r_free = 0.4140 target = 0.147827 restraints weight = 8515.088|
|-----------------------------------------------------------------------------|
r_work (final): 0.4147
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7314
moved from start:          0.4889

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049  10293  Z= 0.150
  Angle     :  0.830  16.062  13931  Z= 0.408
  Chirality :  0.048   0.333   1694
  Planarity :  0.004   0.042   1736
  Dihedral  :  5.146  25.556   1376
  Min Nonbonded Distance : 2.434

Molprobity Statistics.
  All-atom Clashscore : 13.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.18 %
    Favored  : 92.82 %
  Rotamer:
    Outliers :  3.56 %
    Allowed  : 28.65 %
    Favored  : 67.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.19 (0.23), residues: 1310
  helix:  0.01 (0.17), residues: 959
  sheet:  None (None), residues: 0
  loop : -2.91 (0.31), residues: 351

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.032   0.002   TRP D  85 
 HIS   0.004   0.001   HIS F 172 
 PHE   0.031   0.002   PHE G 195 
 TYR   0.054   0.002   TYR F 153 
 ARG   0.007   0.000   ARG D 251 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03562 (  648)
  hydrogen bonds       : angle       4.68964 ( 1917)
  covalent geometry    : bond        0.00339 (10293)
  covalent geometry    : angle       0.83022 (13931)

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

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

  2620 Ramachandran restraints generated.
    1310 Oldfield, 0 Emsley, 1310 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2620 Ramachandran restraints generated.
    1310 Oldfield, 0 Emsley, 1310 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  289 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 251
  time to evaluate  : 1.026 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: G   68 LYS cc_start: 0.7301 (ttmt) cc_final: 0.6774 (mmtm)
REVERT: G  129 MET cc_start: 0.6550 (mtp) cc_final: 0.6324 (mtt)
REVERT: F  208 LEU cc_start: 0.7475 (OUTLIER) cc_final: 0.7176 (mm)
REVERT: F  241 LYS cc_start: 0.6448 (pttt) cc_final: 0.6088 (pttp)
REVERT: E  192 LEU cc_start: 0.7649 (mm) cc_final: 0.7104 (tp)
REVERT: E  198 TYR cc_start: 0.6760 (OUTLIER) cc_final: 0.6165 (m-10)
REVERT: E  208 LEU cc_start: 0.7523 (OUTLIER) cc_final: 0.6805 (mt)
REVERT: D    6 LEU cc_start: 0.7516 (OUTLIER) cc_final: 0.7248 (tp)
REVERT: D  109 LEU cc_start: 0.6604 (OUTLIER) cc_final: 0.6356 (pt)
REVERT: C   92 GLU cc_start: 0.6683 (OUTLIER) cc_final: 0.5224 (pp20)
  outliers start: 38
  outliers final: 27
  residues processed: 274
  average time/residue: 0.1956
  time to fit residues: 79.3059
Evaluate side-chains
  276 residues out of total 1068 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 243
  time to evaluate  : 1.095 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain G residue    7 ILE
Chi-restraints excluded: chain G residue   25 VAL
Chi-restraints excluded: chain G residue   38 ILE
Chi-restraints excluded: chain G residue  192 LEU
Chi-restraints excluded: chain G residue  200 LEU
Chi-restraints excluded: chain G residue  208 LEU
Chi-restraints excluded: chain G residue  246 LEU
Chi-restraints excluded: chain A residue   20 VAL
Chi-restraints excluded: chain A residue   30 LEU
Chi-restraints excluded: chain B residue   32 LEU
Chi-restraints excluded: chain F residue   75 ILE
Chi-restraints excluded: chain F residue  170 LEU
Chi-restraints excluded: chain F residue  208 LEU
Chi-restraints excluded: chain F residue  246 LEU
Chi-restraints excluded: chain E residue    4 THR
Chi-restraints excluded: chain E residue  163 VAL
Chi-restraints excluded: chain E residue  198 TYR
Chi-restraints excluded: chain E residue  199 VAL
Chi-restraints excluded: chain E residue  208 LEU
Chi-restraints excluded: chain E residue  227 LEU
Chi-restraints excluded: chain D residue    6 LEU
Chi-restraints excluded: chain D residue   25 VAL
Chi-restraints excluded: chain D residue   37 LEU
Chi-restraints excluded: chain D residue   69 GLU
Chi-restraints excluded: chain D residue  109 LEU
Chi-restraints excluded: chain D residue  148 THR
Chi-restraints excluded: chain D residue  159 VAL
Chi-restraints excluded: chain D residue  199 VAL
Chi-restraints excluded: chain C residue   28 SER
Chi-restraints excluded: chain C residue   30 LEU
Chi-restraints excluded: chain C residue   63 PHE
Chi-restraints excluded: chain C residue   92 GLU
Chi-restraints excluded: chain C residue  166 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 72 optimal weight:    0.9980
   chunk 32 optimal weight:    1.9990
   chunk 47 optimal weight:    7.9990
   chunk 6 optimal weight:    0.0060
   chunk 52 optimal weight:    2.9990
   chunk 126 optimal weight:    3.9990
   chunk 108 optimal weight:    0.4980
   chunk 38 optimal weight:    0.0050
   chunk 42 optimal weight:    9.9990
   chunk 39 optimal weight:    0.0170
   chunk 54 optimal weight:    4.9990
   overall best weight:    0.3048

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

Flipped N/Q/H residues before XYZ refinement:
** G 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
G 240 GLN
F 120 GLN
** F 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 141 GLN
E 206 ASN
** C 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 214 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4485 r_free = 0.4485 target = 0.176257 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.4121 r_free = 0.4121 target = 0.146163 restraints weight = 17133.897|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.4154 r_free = 0.4154 target = 0.148845 restraints weight = 11083.201|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.4176 r_free = 0.4176 target = 0.150620 restraints weight = 8391.767|
|-----------------------------------------------------------------------------|
r_work (final): 0.4185
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7242
moved from start:          0.5112

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.059  10293  Z= 0.146
  Angle     :  0.832  16.127  13931  Z= 0.407
  Chirality :  0.047   0.309   1694
  Planarity :  0.004   0.045   1736
  Dihedral  :  5.032  25.621   1376
  Min Nonbonded Distance : 2.433

Molprobity Statistics.
  All-atom Clashscore : 14.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.02 %
    Favored  : 92.98 %
  Rotamer:
    Outliers :  3.00 %
    Allowed  : 29.87 %
    Favored  : 67.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.14 (0.23), residues: 1310
  helix:  0.06 (0.17), residues: 961
  sheet:  None (None), residues: 0
  loop : -2.97 (0.30), residues: 349

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.031   0.002   TRP D  85 
 HIS   0.002   0.000   HIS D 181 
 PHE   0.020   0.002   PHE D 124 
 TYR   0.017   0.002   TYR A  22 
 ARG   0.007   0.000   ARG D 251 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03461 (  648)
  hydrogen bonds       : angle       4.68261 ( 1917)
  covalent geometry    : bond        0.00324 (10293)
  covalent geometry    : angle       0.83210 (13931)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3797.77 seconds
wall clock time: 69 minutes 40.66 seconds (4180.66 seconds total)