Starting phenix.real_space_refine
on Sat Jun 14 23:38:32 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8wm8_37645/06_2025/8wm8_37645.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8wm8_37645/06_2025/8wm8_37645.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.54
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8wm8_37645/06_2025/8wm8_37645.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8wm8_37645/06_2025/8wm8_37645.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8wm8_37645/06_2025/8wm8_37645.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8wm8_37645/06_2025/8wm8_37645.cif"
  }
  resolution = 3.54
  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=   0.001 sd=   0.073
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: 5
    Type Number    sf(0)   Gaussians
     S      25      5.16       5
     C    5396      2.51       5
     N    1374      2.21       5
     O    1459      1.98       5
     H    8522      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 23 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib"
  Total number of atoms: 16776
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "D"
      Number of atoms: 4116
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 259, 4116
          Classifications: {'peptide': 259}
          Link IDs: {'PTRANS': 17, 'TRANS': 241}
    Chain: "B"
      Number of atoms: 4198
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 265, 4198
          Classifications: {'peptide': 265}
          Link IDs: {'PTRANS': 17, 'TRANS': 247}
    Chain: "A"
      Number of atoms: 4170
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 263, 4170
          Classifications: {'peptide': 263}
          Link IDs: {'PTRANS': 17, 'TRANS': 245}
    Chain: "C"
      Number of atoms: 4288
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 268, 4288
          Classifications: {'peptide': 268}
          Link IDs: {'PTRANS': 11, 'TRANS': 256}
    Chain: "A"
      Number of atoms: 4
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 4
          Unusual residues: {'NO3': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 7.82, per 1000 atoms: 0.47
  Number of scatterers: 16776
  At special positions: 0
  Unit cell: (81.32, 118.77, 95.23, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      25     16.00
     O    1459      8.00
     N    1374      7.00
     C    5396      6.00
     H    8522      1.00
    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: 4.00
  Conformation dependent library (CDL) restraints added in 1.3 seconds
  

  2094 Ramachandran restraints generated.
    1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1948

  Finding SS restraints...
    Secondary structure from input PDB file:
      52 helices and 4 sheets defined
      56.6% alpha, 5.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.19
  Creating SS restraints...
    Processing helix  chain 'D' and resid 62 through 71
    Processing helix  chain 'D' and resid 83 through 86
    Processing helix  chain 'D' and resid 100 through 104
      removed outlier: 3.852A  pdb=" N   CYS D 103 " --> pdb=" O   GLN D 100 " (cutoff:3.500A)
      removed outlier: 4.607A  pdb=" N   LEU D 104 " --> pdb=" O   ASN D 101 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'D' and resid 100 through 104'
    Processing helix  chain 'D' and resid 109 through 119
      removed outlier: 4.008A  pdb=" N   ALA D 117 " --> pdb=" O   ASN D 113 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 126 through 140
      removed outlier: 3.710A  pdb=" N   ALA D 132 " --> pdb=" O   ALA D 128 " (cutoff:3.500A)
      removed outlier: 4.184A  pdb=" N   ARG D 135 " --> pdb=" O   ARG D 131 " (cutoff:3.500A)
      removed outlier: 3.536A  pdb=" N   MET D 140 " --> pdb=" O   GLU D 136 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 155 through 170
      removed outlier: 3.663A  pdb=" N   GLN D 160 " --> pdb=" O   GLY D 156 " (cutoff:3.500A)
      removed outlier: 4.413A  pdb=" N   ARG D 161 " --> pdb=" O   GLY D 157 " (cutoff:3.500A)
      removed outlier: 4.041A  pdb=" N   VAL D 162 " --> pdb=" O   MET D 158 " (cutoff:3.500A)
      removed outlier: 4.058A  pdb=" N   ILE D 170 " --> pdb=" O   ARG D 166 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 185 through 204
      removed outlier: 3.548A  pdb=" N   GLU D 191 " --> pdb=" O   ILE D 187 " (cutoff:3.500A)
      removed outlier: 3.817A  pdb=" N   GLN D 193 " --> pdb=" O   LYS D 189 " (cutoff:3.500A)
      removed outlier: 4.081A  pdb=" N   GLU D 194 " --> pdb=" O   GLU D 190 " (cutoff:3.500A)
      removed outlier: 3.501A  pdb=" N   GLU D 195 " --> pdb=" O   GLU D 191 " (cutoff:3.500A)
      removed outlier: 3.999A  pdb=" N   GLN D 198 " --> pdb=" O   GLU D 194 " (cutoff:3.500A)
      removed outlier: 4.349A  pdb=" N   ILE D 199 " --> pdb=" O   GLU D 195 " (cutoff:3.500A)
      removed outlier: 3.531A  pdb=" N   HIS D 203 " --> pdb=" O   ILE D 199 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 216 through 221
    Processing helix  chain 'D' and resid 256 through 271
      removed outlier: 3.769A  pdb=" N   ASP D 260 " --> pdb=" O   PRO D 256 " (cutoff:3.500A)
      removed outlier: 3.509A  pdb=" N   ASN D 271 " --> pdb=" O   ASP D 267 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 15 through 23
      removed outlier: 3.643A  pdb=" N   ASN B  19 " --> pdb=" O   GLN B  15 " (cutoff:3.500A)
      removed outlier: 3.922A  pdb=" N   PHE B  21 " --> pdb=" O   ALA B  17 " (cutoff:3.500A)
      removed outlier: 4.119A  pdb=" N   TRP B  23 " --> pdb=" O   ASN B  19 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 26 through 44
      removed outlier: 3.553A  pdb=" N   LEU B  30 " --> pdb=" O   VAL B  26 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 55 through 60
    Processing helix  chain 'B' and resid 61 through 67
      removed outlier: 3.686A  pdb=" N   PHE B  65 " --> pdb=" O   THR B  61 " (cutoff:3.500A)
      removed outlier: 3.539A  pdb=" N   ILE B  66 " --> pdb=" O   TRP B  62 " (cutoff:3.500A)
      removed outlier: 3.797A  pdb=" N   ILE B  67 " --> pdb=" O   ASP B  63 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 61 through 67'
    Processing helix  chain 'B' and resid 80 through 94
      removed outlier: 3.832A  pdb=" N   SER B  87 " --> pdb=" O   GLN B  83 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 95 through 111
      removed outlier: 3.823A  pdb=" N   ILE B 103 " --> pdb=" O   ALA B  99 " (cutoff:3.500A)
      removed outlier: 3.565A  pdb=" N   ILE B 104 " --> pdb=" O   ILE B 100 " (cutoff:3.500A)
      removed outlier: 4.012A  pdb=" N   LEU B 105 " --> pdb=" O   ALA B 101 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 112 through 129
      removed outlier: 4.034A  pdb=" N   ALA B 118 " --> pdb=" O   LEU B 114 " (cutoff:3.500A)
      Proline residue:  B 121  - end of helix
      removed outlier: 4.340A  pdb=" N   VAL B 125 " --> pdb=" O   PRO B 121 " (cutoff:3.500A)
      removed outlier: 4.169A  pdb=" N   LEU B 126 " --> pdb=" O   ILE B 122 " (cutoff:3.500A)
      removed outlier: 3.986A  pdb=" N   THR B 128 " --> pdb=" O   GLN B 124 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 130 through 133
    Processing helix  chain 'B' and resid 134 through 142
    Processing helix  chain 'B' and resid 145 through 155
      removed outlier: 3.664A  pdb=" N   ILE B 150 " --> pdb=" O   ASN B 146 " (cutoff:3.500A)
      removed outlier: 4.893A  pdb=" N   PHE B 151 " --> pdb=" O   PRO B 147 " (cutoff:3.500A)
      removed outlier: 3.677A  pdb=" N   ILE B 153 " --> pdb=" O   ALA B 149 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 158 through 171
      removed outlier: 3.871A  pdb=" N   ASN B 164 " --> pdb=" O   PRO B 160 " (cutoff:3.500A)
      removed outlier: 3.537A  pdb=" N   THR B 166 " --> pdb=" O   LEU B 162 " (cutoff:3.500A)
      removed outlier: 4.496A  pdb=" N   VAL B 167 " --> pdb=" O   LEU B 163 " (cutoff:3.500A)
      removed outlier: 3.826A  pdb=" N   GLY B 168 " --> pdb=" O   ASN B 164 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 173 through 183
      removed outlier: 3.620A  pdb=" N   ILE B 177 " --> pdb=" O   PRO B 173 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 187 through 195
    Processing helix  chain 'B' and resid 195 through 208
      Proline residue:  B 201  - end of helix
    Processing helix  chain 'B' and resid 208 through 219
      removed outlier: 3.804A  pdb=" N   GLY B 212 " --> pdb=" O   ARG B 208 " (cutoff:3.500A)
      removed outlier: 3.750A  pdb=" N   LEU B 213 " --> pdb=" O   ILE B 209 " (cutoff:3.500A)
      removed outlier: 3.905A  pdb=" N   SER B 214 " --> pdb=" O   GLY B 210 " (cutoff:3.500A)
      removed outlier: 3.622A  pdb=" N   ALA B 217 " --> pdb=" O   LEU B 213 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 235 through 240
      removed outlier: 3.610A  pdb=" N   ASN B 239 " --> pdb=" O   TRP B 235 " (cutoff:3.500A)
      removed outlier: 4.090A  pdb=" N   THR B 240 " --> pdb=" O   ASP B 236 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 235 through 240'
    Processing helix  chain 'B' and resid 244 through 275
      removed outlier: 3.950A  pdb=" N   GLU B 248 " --> pdb=" O   THR B 244 " (cutoff:3.500A)
      removed outlier: 4.031A  pdb=" N   ILE B 249 " --> pdb=" O   ASN B 245 " (cutoff:3.500A)
      removed outlier: 4.007A  pdb=" N   ILE B 250 " --> pdb=" O   LEU B 246 " (cutoff:3.500A)
      removed outlier: 3.725A  pdb=" N   LEU B 253 " --> pdb=" O   ILE B 249 " (cutoff:3.500A)
      removed outlier: 3.632A  pdb=" N   VAL B 267 " --> pdb=" O   LEU B 263 " (cutoff:3.500A)
      removed outlier: 4.108A  pdb=" N   GLY B 268 " --> pdb=" O   ASP B 264 " (cutoff:3.500A)
      removed outlier: 3.647A  pdb=" N   LYS B 273 " --> pdb=" O   PHE B 269 " (cutoff:3.500A)
      removed outlier: 3.700A  pdb=" N   VAL B 274 " --> pdb=" O   VAL B 270 " (cutoff:3.500A)
      removed outlier: 3.651A  pdb=" N   VAL B 275 " --> pdb=" O   ALA B 271 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 21 through 25
    Processing helix  chain 'A' and resid 26 through 44
    Processing helix  chain 'A' and resid 53 through 60
    Processing helix  chain 'A' and resid 83 through 88
    Processing helix  chain 'A' and resid 89 through 94
    Processing helix  chain 'A' and resid 96 through 109
      removed outlier: 3.530A  pdb=" N   GLY A 102 " --> pdb=" O   ALA A  98 " (cutoff:3.500A)
      removed outlier: 3.914A  pdb=" N   ILE A 104 " --> pdb=" O   ILE A 100 " (cutoff:3.500A)
      removed outlier: 4.356A  pdb=" N   LEU A 105 " --> pdb=" O   ALA A 101 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 130 through 133
    Processing helix  chain 'A' and resid 134 through 143
    Processing helix  chain 'A' and resid 144 through 157
    Processing helix  chain 'A' and resid 158 through 171
      removed outlier: 4.024A  pdb=" N   ASN A 164 " --> pdb=" O   PRO A 160 " (cutoff:3.500A)
      removed outlier: 3.873A  pdb=" N   VAL A 167 " --> pdb=" O   LEU A 163 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 173 through 182
      removed outlier: 3.549A  pdb=" N   ILE A 177 " --> pdb=" O   PRO A 173 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 187 through 192
    Processing helix  chain 'A' and resid 199 through 214
      removed outlier: 3.569A  pdb=" N   THR A 205 " --> pdb=" O   PRO A 201 " (cutoff:3.500A)
      removed outlier: 4.120A  pdb=" N   ILE A 209 " --> pdb=" O   THR A 205 " (cutoff:3.500A)
      removed outlier: 4.658A  pdb=" N   GLY A 212 " --> pdb=" O   ARG A 208 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 214 through 221
    Processing helix  chain 'A' and resid 221 through 226
      removed outlier: 3.736A  pdb=" N   VAL A 225 " --> pdb=" O   ALA A 221 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 246 through 256
      removed outlier: 3.562A  pdb=" N   LEU A 251 " --> pdb=" O   SER A 247 " (cutoff:3.500A)
      removed outlier: 3.870A  pdb=" N   ALA A 252 " --> pdb=" O   GLU A 248 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 263 through 275
      removed outlier: 3.697A  pdb=" N   VAL A 267 " --> pdb=" O   LEU A 263 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 48 through 57
      removed outlier: 3.534A  pdb=" N   ILE C  55 " --> pdb=" O   LEU C  51 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 67 through 71
    Processing helix  chain 'C' and resid 94 through 105
      removed outlier: 3.507A  pdb=" N   VAL C  99 " --> pdb=" O   VAL C  95 " (cutoff:3.500A)
      removed outlier: 3.626A  pdb=" N   ALA C 100 " --> pdb=" O   ARG C  96 " (cutoff:3.500A)
      removed outlier: 3.804A  pdb=" N   ALA C 102 " --> pdb=" O   ASN C  98 " (cutoff:3.500A)
      removed outlier: 3.959A  pdb=" N   GLU C 105 " --> pdb=" O   LEU C 101 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 111 through 123
      removed outlier: 3.745A  pdb=" N   ALA C 117 " --> pdb=" O   GLY C 113 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 142 through 155
      removed outlier: 3.805A  pdb=" N   ARG C 146 " --> pdb=" O   GLY C 142 " (cutoff:3.500A)
      removed outlier: 3.668A  pdb=" N   VAL C 147 " --> pdb=" O   MET C 143 " (cutoff:3.500A)
      removed outlier: 4.033A  pdb=" N   ALA C 148 " --> pdb=" O   LYS C 144 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 172 through 186
      removed outlier: 3.825A  pdb=" N   GLU C 179 " --> pdb=" O   GLY C 175 " (cutoff:3.500A)
      removed outlier: 4.252A  pdb=" N   GLN C 180 " --> pdb=" O   SER C 176 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 198 through 203
      removed outlier: 3.837A  pdb=" N   ALA C 202 " --> pdb=" O   ASP C 198 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 233 through 238
      removed outlier: 3.831A  pdb=" N   VAL C 238 " --> pdb=" O   ARG C 234 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 240 through 269
      removed outlier: 4.187A  pdb=" N   TYR C 244 " --> pdb=" O   HIS C 240 " (cutoff:3.500A)
      removed outlier: 3.816A  pdb=" N   ASN C 245 " --> pdb=" O   PRO C 241 " (cutoff:3.500A)
      removed outlier: 3.533A  pdb=" N   GLU C 249 " --> pdb=" O   ASN C 245 " (cutoff:3.500A)
      removed outlier: 3.598A  pdb=" N   ALA C 268 " --> pdb=" O   GLN C 264 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'D' and resid 37 through 47
      removed outlier: 6.433A  pdb=" N   LYS D  28 " --> pdb=" O   VAL D  39 " (cutoff:3.500A)
      removed outlier: 4.877A  pdb=" N   ASP D  41 " --> pdb=" O   VAL D  26 " (cutoff:3.500A)
      removed outlier: 6.615A  pdb=" N   VAL D  26 " --> pdb=" O   ASP D  41 " (cutoff:3.500A)
      removed outlier: 6.811A  pdb=" N   ILE D  43 " --> pdb=" O   GLU D  24 " (cutoff:3.500A)
      removed outlier: 4.359A  pdb=" N   GLU D  24 " --> pdb=" O   ILE D  43 " (cutoff:3.500A)
      removed outlier: 6.988A  pdb=" N   LEU D  45 " --> pdb=" O   VAL D  22 " (cutoff:3.500A)
      removed outlier: 4.996A  pdb=" N   VAL D  22 " --> pdb=" O   LEU D  45 " (cutoff:3.500A)
      removed outlier: 4.688A  pdb=" N   GLU D  24 " --> pdb=" O   VAL D  80 " (cutoff:3.500A)
      removed outlier: 4.653A  pdb=" N   VAL D  80 " --> pdb=" O   GLU D  24 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'D' and resid 97 through 98
      removed outlier: 3.518A  pdb=" N   LEU D 208 " --> pdb=" O   LEU D 175 " (cutoff:3.500A)
      removed outlier: 8.093A  pdb=" N   VAL D 225 " --> pdb=" O   PHE D  52 " (cutoff:3.500A)
      removed outlier: 6.365A  pdb=" N   CYS D  54 " --> pdb=" O   VAL D 225 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'C' and resid 23 through 25
      removed outlier: 6.529A  pdb=" N   ARG C  12 " --> pdb=" O   ALA C  24 " (cutoff:3.500A)
      removed outlier: 5.868A  pdb=" N   HIS C   9 " --> pdb=" O   GLY C  65 " (cutoff:3.500A)
      removed outlier: 4.357A  pdb=" N   GLY C  65 " --> pdb=" O   HIS C   9 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'C' and resid 161 through 162
      removed outlier: 7.129A  pdb=" N   LEU C 162 " --> pdb=" O   VAL C 195 " (cutoff:3.500A)
      removed outlier: 5.673A  pdb=" N   SER C  39 " --> pdb=" O   VAL C 210 " (cutoff:3.500A)

    318 hydrogen bonds defined for protein.
    927 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 5.64

  Time building geometry restraints manager: 4.93 seconds

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

  Histogram of bond lengths:
        0.84 -     1.03: 8514
        1.03 -     1.23: 9
        1.23 -     1.42: 3400
        1.42 -     1.62: 4997
        1.62 -     1.81: 42
  Bond restraints: 16962
  Sorted by residual:
  bond pdb=" N   NO3 A 301 "
       pdb=" O3  NO3 A 301 "
    ideal  model  delta    sigma   weight residual
    1.237  1.264 -0.027 2.00e-02 2.50e+03 1.84e+00
  bond pdb=" N   NO3 A 301 "
       pdb=" O2  NO3 A 301 "
    ideal  model  delta    sigma   weight residual
    1.237  1.264 -0.027 2.00e-02 2.50e+03 1.80e+00
  bond pdb=" N   NO3 A 301 "
       pdb=" O1  NO3 A 301 "
    ideal  model  delta    sigma   weight residual
    1.237  1.263 -0.026 2.00e-02 2.50e+03 1.73e+00
  bond pdb=" C   ILE B 209 "
       pdb=" O   ILE B 209 "
    ideal  model  delta    sigma   weight residual
    1.241  1.228  0.013 1.19e-02 7.06e+03 1.28e+00
  bond pdb=" C   GLY D  35 "
       pdb=" N   PRO D  36 "
    ideal  model  delta    sigma   weight residual
    1.333  1.343 -0.010 1.01e-02 9.80e+03 9.72e-01
  ... (remaining 16957 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.19: 29168
        1.19 -     2.38: 1571
        2.38 -     3.56: 100
        3.56 -     4.75: 33
        4.75 -     5.94: 6
  Bond angle restraints: 30878
  Sorted by residual:
  angle pdb=" N   SER A  96 "
        pdb=" CA  SER A  96 "
        pdb=" C   SER A  96 "
      ideal   model   delta    sigma   weight residual
     113.41  107.47    5.94 1.22e+00 6.72e-01 2.37e+01
  angle pdb=" N   ASN A 117 "
        pdb=" CA  ASN A 117 "
        pdb=" C   ASN A 117 "
      ideal   model   delta    sigma   weight residual
     114.62  109.17    5.45 1.14e+00 7.69e-01 2.28e+01
  angle pdb=" N   VAL C 106 "
        pdb=" CA  VAL C 106 "
        pdb=" C   VAL C 106 "
      ideal   model   delta    sigma   weight residual
     111.62  108.23    3.39 7.90e-01 1.60e+00 1.84e+01
  angle pdb=" N   ASP D 178 "
        pdb=" CA  ASP D 178 "
        pdb=" C   ASP D 178 "
      ideal   model   delta    sigma   weight residual
     110.41  106.28    4.13 1.23e+00 6.61e-01 1.13e+01
  angle pdb=" CA  ASN A 117 "
        pdb=" C   ASN A 117 "
        pdb=" N   ALA A 118 "
      ideal   model   delta    sigma   weight residual
     119.71  116.30    3.41 1.17e+00 7.31e-01 8.47e+00
  ... (remaining 30873 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.96: 7061
       17.96 -    35.92: 570
       35.92 -    53.88: 221
       53.88 -    71.84: 37
       71.84 -    89.80: 16
  Dihedral angle restraints: 7905
    sinusoidal: 4361
      harmonic: 3544
  Sorted by residual:
  dihedral pdb=" CA  TRP A 235 "
           pdb=" C   TRP A 235 "
           pdb=" N   ASP A 236 "
           pdb=" CA  ASP A 236 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  155.45   24.55     0      5.00e+00 4.00e-02 2.41e+01
  dihedral pdb=" CA  SER A 157 "
           pdb=" C   SER A 157 "
           pdb=" N   ILE A 158 "
           pdb=" CA  ILE A 158 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.86   22.14     0      5.00e+00 4.00e-02 1.96e+01
  dihedral pdb=" CA  TRP A  23 "
           pdb=" C   TRP A  23 "
           pdb=" N   LYS A  24 "
           pdb=" CA  LYS A  24 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.16   19.84     0      5.00e+00 4.00e-02 1.58e+01
  ... (remaining 7902 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.030: 851
       0.030 -    0.059: 303
       0.059 -    0.089: 118
       0.089 -    0.118: 62
       0.118 -    0.148: 13
  Chirality restraints: 1347
  Sorted by residual:
  chirality pdb=" CA  ILE B 172 "
            pdb=" N   ILE B 172 "
            pdb=" C   ILE B 172 "
            pdb=" CB  ILE B 172 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.58   -0.15 2.00e-01 2.50e+01 5.46e-01
  chirality pdb=" CA  ILE A 172 "
            pdb=" N   ILE A 172 "
            pdb=" C   ILE A 172 "
            pdb=" CB  ILE A 172 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.58   -0.14 2.00e-01 2.50e+01 5.24e-01
  chirality pdb=" CA  ILE D 241 "
            pdb=" N   ILE D 241 "
            pdb=" C   ILE D 241 "
            pdb=" CB  ILE D 241 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 4.62e-01
  ... (remaining 1344 not shown)

  Planarity restraints: 2447
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN A 112 "    0.030 5.00e-02 4.00e+02   4.61e-02 3.40e+00
        pdb=" N   PRO A 113 "   -0.080 5.00e-02 4.00e+02
        pdb=" CA  PRO A 113 "    0.024 5.00e-02 4.00e+02
        pdb=" CD  PRO A 113 "    0.026 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN B 146 "    0.030 5.00e-02 4.00e+02   4.49e-02 3.23e+00
        pdb=" N   PRO B 147 "   -0.078 5.00e-02 4.00e+02
        pdb=" CA  PRO B 147 "    0.023 5.00e-02 4.00e+02
        pdb=" CD  PRO B 147 "    0.025 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ARG D 245 "    0.026 5.00e-02 4.00e+02   3.90e-02 2.44e+00
        pdb=" N   PRO D 246 "   -0.068 5.00e-02 4.00e+02
        pdb=" CA  PRO D 246 "    0.020 5.00e-02 4.00e+02
        pdb=" CD  PRO D 246 "    0.022 5.00e-02 4.00e+02
  ... (remaining 2444 not shown)

  Histogram of nonbonded interaction distances:
        1.57 -     2.18: 795
        2.18 -     2.78: 34458
        2.78 -     3.39: 46449
        3.39 -     3.99: 59381
        3.99 -     4.60: 92618
  Nonbonded interactions: 233701
  Sorted by model distance:
  nonbonded pdb=" O   PRO A 160 "
            pdb="HD21 ASN A 164 "
     model   vdw
     1.572 2.450
  nonbonded pdb=" OD1 ASP D 267 "
            pdb="HD21 ASN D 271 "
     model   vdw
     1.592 2.450
  nonbonded pdb=" O   PHE D 219 "
            pdb="HH11 ARG D 247 "
     model   vdw
     1.614 2.450
  nonbonded pdb=" OD1 ASN D 263 "
            pdb=" HH  TYR C 244 "
     model   vdw
     1.650 2.450
  nonbonded pdb=" OD1 ASP C   8 "
            pdb=" HD1 HIS C   9 "
     model   vdw
     1.675 2.450
  ... (remaining 233696 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 277)
  selection = (chain 'B' and ((resid 15 and (name N or name CA or name C or name O or name CB  \ 
or name CG or name CD or name OE1 or name NE2 or name HA or name HB2 or name HB3 \ 
 or name HG2 or name HG3 or name HE21 or name HE22)) or resid 16 through 277))
}

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:             1.280
  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:             0.280
  Extract box with map and model:          0.670
  Check model and map are aligned:         0.140
  Set scattering table:                    0.160
  Process input model:                     35.590
  Find NCS groups from input model:        0.340
  Set up NCS constraints:                  0.050
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.870
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   41.380
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7547
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      :  0.002   0.044   8440  Z= 0.114
  Angle     :  0.581   5.941  11494  Z= 0.328
  Chirality :  0.040   0.148   1347
  Planarity :  0.004   0.046   1458
  Dihedral  : 14.853  89.805   3077
  Min Nonbonded Distance : 1.963

Molprobity Statistics.
  All-atom Clashscore : 8.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.26 %
    Favored  : 92.74 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.22 %
    Favored  : 99.78 %
  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: -2.51 (0.26), residues: 1047
  helix: -1.14 (0.24), residues: 517
  sheet: -2.40 (0.66), residues: 66
  loop : -2.07 (0.28), residues: 464

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 159 
 HIS   0.002   0.001   HIS C 240 
 PHE   0.015   0.001   PHE D  20 
 TYR   0.011   0.001   TYR D 102 
 ARG   0.004   0.000   ARG A 127 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.28261 (  318)
  hydrogen bonds       : angle       9.87400 (  927)
  covalent geometry    : bond        0.00238 ( 8440)
  covalent geometry    : angle       0.58135 (11494)

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

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

  2094 Ramachandran restraints generated.
    1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2094 Ramachandran restraints generated.
    1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  181 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 181
  time to evaluate  : 1.355 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  236 ASP cc_start: 0.7786 (t0) cc_final: 0.7582 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 181
  average time/residue: 0.3639
  time to fit residues: 96.4068
Evaluate side-chains
  150 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 150
  time to evaluate  : 1.206 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 86 optimal weight:    1.9990
   chunk 78 optimal weight:   10.0000
   chunk 43 optimal weight:    0.6980
   chunk 26 optimal weight:    0.0470
   chunk 52 optimal weight:    1.9990
   chunk 41 optimal weight:    1.9990
   chunk 80 optimal weight:    2.9990
   chunk 31 optimal weight:    4.9990
   chunk 49 optimal weight:    0.9980
   chunk 60 optimal weight:    2.9990
   chunk 93 optimal weight:    1.9990
   overall best weight:    1.1482

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

Flipped N/Q/H residues before XYZ refinement:
B 164 ASN
** A 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3789 r_free = 0.3789 target = 0.149811 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3386 r_free = 0.3386 target = 0.116355 restraints weight = 34750.750|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3466 r_free = 0.3466 target = 0.122506 restraints weight = 15534.145|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3514 r_free = 0.3514 target = 0.126334 restraints weight = 9473.739|
|-----------------------------------------------------------------------------|
r_work (final): 0.3499
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7366
moved from start:          0.1161

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   8440  Z= 0.171
  Angle     :  0.645   6.587  11494  Z= 0.337
  Chirality :  0.043   0.143   1347
  Planarity :  0.005   0.053   1458
  Dihedral  :  5.195  25.161   1122
  Min Nonbonded Distance : 2.348

Molprobity Statistics.
  All-atom Clashscore : 8.58
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  7.55 %
    Favored  : 92.36 %
  Rotamer:
    Outliers :  0.56 %
    Allowed  :  9.03 %
    Favored  : 90.41 %
  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: -2.63 (0.25), residues: 1047
  helix: -1.10 (0.22), residues: 527
  sheet: -2.70 (0.62), residues: 65
  loop : -2.31 (0.28), residues: 455

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A 159 
 HIS   0.006   0.001   HIS C 197 
 PHE   0.013   0.001   PHE A  95 
 TYR   0.018   0.002   TYR A 116 
 ARG   0.005   0.000   ARG C 129 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06266 (  318)
  hydrogen bonds       : angle       6.51182 (  927)
  covalent geometry    : bond        0.00382 ( 8440)
  covalent geometry    : angle       0.64474 (11494)

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

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

  2094 Ramachandran restraints generated.
    1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2094 Ramachandran restraints generated.
    1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  167 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 162
  time to evaluate  : 1.374 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  176 TYR cc_start: 0.8106 (m-10) cc_final: 0.7452 (m-10)
REVERT: A  144 GLN cc_start: 0.6765 (mp-120) cc_final: 0.6549 (mp10)
REVERT: A  236 ASP cc_start: 0.8053 (t0) cc_final: 0.7766 (t0)
REVERT: C   75 GLU cc_start: 0.7681 (mm-30) cc_final: 0.7435 (mp0)
  outliers start: 5
  outliers final: 3
  residues processed: 164
  average time/residue: 0.3515
  time to fit residues: 84.8172
Evaluate side-chains
  156 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 153
  time to evaluate  : 1.225 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  181 PHE
Chi-restraints excluded: chain C residue   94 THR
Chi-restraints excluded: chain C residue  203 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 27 optimal weight:    1.9990
   chunk 74 optimal weight:    0.6980
   chunk 38 optimal weight:    0.9990
   chunk 44 optimal weight:    1.9990
   chunk 23 optimal weight:    0.7980
   chunk 33 optimal weight:    0.6980
   chunk 4 optimal weight:    3.9990
   chunk 73 optimal weight:    0.7980
   chunk 28 optimal weight:    0.5980
   chunk 62 optimal weight:    0.9980
   chunk 34 optimal weight:    0.9980
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3780 r_free = 0.3780 target = 0.149352 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3386 r_free = 0.3386 target = 0.116492 restraints weight = 34400.498|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3462 r_free = 0.3462 target = 0.122385 restraints weight = 15920.345|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3506 r_free = 0.3506 target = 0.126019 restraints weight = 9871.023|
|-----------------------------------------------------------------------------|
r_work (final): 0.3525
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7371
moved from start:          0.1430

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   8440  Z= 0.129
  Angle     :  0.593   6.267  11494  Z= 0.309
  Chirality :  0.042   0.148   1347
  Planarity :  0.005   0.056   1458
  Dihedral  :  5.126  25.212   1122
  Min Nonbonded Distance : 2.371

Molprobity Statistics.
  All-atom Clashscore : 7.63
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  7.07 %
    Favored  : 92.84 %
  Rotamer:
    Outliers :  0.45 %
    Allowed  : 10.81 %
    Favored  : 88.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.57 (0.25), residues: 1047
  helix: -1.06 (0.22), residues: 537
  sheet: -2.63 (0.63), residues: 60
  loop : -2.30 (0.28), residues: 450

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 159 
 HIS   0.005   0.001   HIS C 197 
 PHE   0.013   0.001   PHE A  95 
 TYR   0.011   0.001   TYR D 102 
 ARG   0.004   0.000   ARG C 129 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04746 (  318)
  hydrogen bonds       : angle       5.83489 (  927)
  covalent geometry    : bond        0.00295 ( 8440)
  covalent geometry    : angle       0.59264 (11494)

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

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

  2094 Ramachandran restraints generated.
    1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2094 Ramachandran restraints generated.
    1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  165 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 161
  time to evaluate  : 1.218 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: D  115 TYR cc_start: 0.8159 (t80) cc_final: 0.7956 (t80)
REVERT: A  144 GLN cc_start: 0.6725 (mp-120) cc_final: 0.6478 (mp10)
REVERT: A  236 ASP cc_start: 0.8008 (t0) cc_final: 0.7738 (t0)
REVERT: C   75 GLU cc_start: 0.7614 (mm-30) cc_final: 0.7393 (mp0)
  outliers start: 4
  outliers final: 4
  residues processed: 161
  average time/residue: 0.3454
  time to fit residues: 84.0670
Evaluate side-chains
  154 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 150
  time to evaluate  : 1.338 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  181 PHE
Chi-restraints excluded: chain A residue   44 CYS
Chi-restraints excluded: chain C residue   94 THR
Chi-restraints excluded: chain C residue  203 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 100 optimal weight:    3.9990
   chunk 96 optimal weight:    1.9990
   chunk 20 optimal weight:    2.9990
   chunk 99 optimal weight:    2.9990
   chunk 51 optimal weight:    0.3980
   chunk 0 optimal weight:    5.9990
   chunk 53 optimal weight:    2.9990
   chunk 2 optimal weight:    1.9990
   chunk 39 optimal weight:    0.9980
   chunk 52 optimal weight:    0.5980
   chunk 78 optimal weight:    9.9990
   overall best weight:    1.1984

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

Flipped N/Q/H residues before XYZ refinement:
** C 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3775 r_free = 0.3775 target = 0.148877 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3371 r_free = 0.3371 target = 0.115278 restraints weight = 34860.213|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3450 r_free = 0.3450 target = 0.121362 restraints weight = 15600.241|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3498 r_free = 0.3498 target = 0.125174 restraints weight = 9514.765|
|-----------------------------------------------------------------------------|
r_work (final): 0.3489
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7305
moved from start:          0.1683

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   8440  Z= 0.162
  Angle     :  0.600   6.718  11494  Z= 0.313
  Chirality :  0.042   0.145   1347
  Planarity :  0.005   0.057   1458
  Dihedral  :  5.191  25.605   1122
  Min Nonbonded Distance : 2.365

Molprobity Statistics.
  All-atom Clashscore : 8.23
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  7.83 %
    Favored  : 92.07 %
  Rotamer:
    Outliers :  0.67 %
    Allowed  : 12.93 %
    Favored  : 86.40 %
  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: -2.58 (0.25), residues: 1047
  helix: -1.02 (0.22), residues: 541
  sheet: -2.63 (0.59), residues: 70
  loop : -2.36 (0.29), residues: 436

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 159 
 HIS   0.007   0.001   HIS D 137 
 PHE   0.016   0.001   PHE A  95 
 TYR   0.012   0.001   TYR B 238 
 ARG   0.004   0.000   ARG C 129 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04133 (  318)
  hydrogen bonds       : angle       5.56022 (  927)
  covalent geometry    : bond        0.00375 ( 8440)
  covalent geometry    : angle       0.60029 (11494)

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

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

  2094 Ramachandran restraints generated.
    1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2094 Ramachandran restraints generated.
    1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  158 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 152
  time to evaluate  : 1.504 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D  115 TYR cc_start: 0.8121 (t80) cc_final: 0.7859 (t80)
REVERT: A  156 THR cc_start: 0.8728 (t) cc_final: 0.8511 (t)
REVERT: A  236 ASP cc_start: 0.8155 (t0) cc_final: 0.7896 (t0)
REVERT: C   75 GLU cc_start: 0.7676 (mm-30) cc_final: 0.7438 (mp0)
  outliers start: 6
  outliers final: 6
  residues processed: 154
  average time/residue: 0.3695
  time to fit residues: 86.6112
Evaluate side-chains
  152 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 146
  time to evaluate  : 1.396 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  181 PHE
Chi-restraints excluded: chain A residue   44 CYS
Chi-restraints excluded: chain C residue   67 THR
Chi-restraints excluded: chain C residue   94 THR
Chi-restraints excluded: chain C residue  103 VAL
Chi-restraints excluded: chain C residue  203 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 1 optimal weight:    4.9990
   chunk 6 optimal weight:    0.9990
   chunk 98 optimal weight:    4.9990
   chunk 97 optimal weight:    1.9990
   chunk 26 optimal weight:    0.8980
   chunk 25 optimal weight:    6.9990
   chunk 22 optimal weight:    2.9990
   chunk 14 optimal weight:    1.9990
   chunk 70 optimal weight:    0.8980
   chunk 89 optimal weight:    5.9990
   chunk 38 optimal weight:    0.8980
   overall best weight:    1.1384

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

Flipped N/Q/H residues before XYZ refinement:

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3752 r_free = 0.3752 target = 0.147109 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3356 r_free = 0.3356 target = 0.113981 restraints weight = 35102.024|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 49)----------------|
| r_work = 0.3430 r_free = 0.3430 target = 0.119728 restraints weight = 16246.307|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3475 r_free = 0.3475 target = 0.123323 restraints weight = 10125.493|
|-----------------------------------------------------------------------------|
r_work (final): 0.3491
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7370
moved from start:          0.1798

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   8440  Z= 0.156
  Angle     :  0.596   6.453  11494  Z= 0.309
  Chirality :  0.042   0.151   1347
  Planarity :  0.005   0.057   1458
  Dihedral  :  5.210  26.071   1122
  Min Nonbonded Distance : 2.384

Molprobity Statistics.
  All-atom Clashscore : 7.99
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  7.45 %
    Favored  : 92.45 %
  Rotamer:
    Outliers :  0.78 %
    Allowed  : 14.83 %
    Favored  : 84.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -2.56 (0.25), residues: 1047
  helix: -0.98 (0.22), residues: 541
  sheet: -2.73 (0.58), residues: 71
  loop : -2.36 (0.29), residues: 435

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 159 
 HIS   0.003   0.001   HIS D 137 
 PHE   0.020   0.001   PHE A 154 
 TYR   0.012   0.001   TYR A 116 
 ARG   0.004   0.000   ARG C 234 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03767 (  318)
  hydrogen bonds       : angle       5.34686 (  927)
  covalent geometry    : bond        0.00361 ( 8440)
  covalent geometry    : angle       0.59553 (11494)

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

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

  2094 Ramachandran restraints generated.
    1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2094 Ramachandran restraints generated.
    1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  157 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 150
  time to evaluate  : 1.263 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D  115 TYR cc_start: 0.8148 (t80) cc_final: 0.7873 (t80)
REVERT: A  144 GLN cc_start: 0.6817 (mp-120) cc_final: 0.6559 (mp10)
REVERT: A  156 THR cc_start: 0.8793 (t) cc_final: 0.8572 (t)
REVERT: A  236 ASP cc_start: 0.8109 (t0) cc_final: 0.7873 (t0)
REVERT: C   75 GLU cc_start: 0.7661 (mm-30) cc_final: 0.7440 (mp0)
  outliers start: 7
  outliers final: 7
  residues processed: 152
  average time/residue: 0.3717
  time to fit residues: 84.2026
Evaluate side-chains
  153 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 146
  time to evaluate  : 1.425 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  181 PHE
Chi-restraints excluded: chain A residue   44 CYS
Chi-restraints excluded: chain A residue  132 LEU
Chi-restraints excluded: chain C residue   67 THR
Chi-restraints excluded: chain C residue   94 THR
Chi-restraints excluded: chain C residue  103 VAL
Chi-restraints excluded: chain C residue  203 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 50 optimal weight:    1.9990
   chunk 24 optimal weight:    1.9990
   chunk 15 optimal weight:    0.3980
   chunk 21 optimal weight:    0.8980
   chunk 70 optimal weight:    0.9990
   chunk 97 optimal weight:    3.9990
   chunk 65 optimal weight:    0.9990
   chunk 5 optimal weight:    2.9990
   chunk 73 optimal weight:    1.9990
   chunk 9 optimal weight:    1.9990
   chunk 51 optimal weight:    0.2980
   overall best weight:    0.7184

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

Flipped N/Q/H residues before XYZ refinement:

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3764 r_free = 0.3764 target = 0.148234 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3373 r_free = 0.3373 target = 0.115127 restraints weight = 34826.261|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3446 r_free = 0.3446 target = 0.120901 restraints weight = 16008.118|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.3492 r_free = 0.3492 target = 0.124541 restraints weight = 9951.690|
|-----------------------------------------------------------------------------|
r_work (final): 0.3524
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7374
moved from start:          0.1918

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   8440  Z= 0.121
  Angle     :  0.574   6.221  11494  Z= 0.296
  Chirality :  0.042   0.149   1347
  Planarity :  0.005   0.057   1458
  Dihedral  :  5.124  26.041   1122
  Min Nonbonded Distance : 2.392

Molprobity Statistics.
  All-atom Clashscore : 8.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.35 %
    Favored  : 92.65 %
  Rotamer:
    Outliers :  1.00 %
    Allowed  : 15.50 %
    Favored  : 83.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.40 (0.26), residues: 1047
  helix: -0.92 (0.22), residues: 540
  sheet: -2.66 (0.60), residues: 70
  loop : -2.18 (0.29), residues: 437

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 159 
 HIS   0.004   0.001   HIS D 137 
 PHE   0.018   0.001   PHE A 154 
 TYR   0.010   0.001   TYR B 238 
 ARG   0.005   0.000   ARG C 234 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03424 (  318)
  hydrogen bonds       : angle       5.12401 (  927)
  covalent geometry    : bond        0.00288 ( 8440)
  covalent geometry    : angle       0.57427 (11494)

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

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

  2094 Ramachandran restraints generated.
    1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2094 Ramachandran restraints generated.
    1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  163 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 154
  time to evaluate  : 1.436 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D  115 TYR cc_start: 0.8135 (t80) cc_final: 0.7899 (t80)
REVERT: A  144 GLN cc_start: 0.6742 (mp-120) cc_final: 0.6470 (mp10)
REVERT: A  236 ASP cc_start: 0.8055 (t0) cc_final: 0.7819 (t0)
REVERT: C   75 GLU cc_start: 0.7641 (mm-30) cc_final: 0.7436 (mp0)
  outliers start: 9
  outliers final: 9
  residues processed: 157
  average time/residue: 0.3485
  time to fit residues: 81.3050
Evaluate side-chains
  155 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 146
  time to evaluate  : 1.246 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  181 PHE
Chi-restraints excluded: chain A residue   42 LEU
Chi-restraints excluded: chain A residue   44 CYS
Chi-restraints excluded: chain A residue  132 LEU
Chi-restraints excluded: chain A residue  139 LEU
Chi-restraints excluded: chain C residue   67 THR
Chi-restraints excluded: chain C residue   94 THR
Chi-restraints excluded: chain C residue  103 VAL
Chi-restraints excluded: chain C residue  203 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 36 optimal weight:    0.9980
   chunk 55 optimal weight:    2.9990
   chunk 65 optimal weight:    0.9980
   chunk 73 optimal weight:    0.9980
   chunk 24 optimal weight:    1.9990
   chunk 64 optimal weight:    0.9980
   chunk 16 optimal weight:    4.9990
   chunk 56 optimal weight:    0.0570
   chunk 83 optimal weight:    4.9990
   chunk 85 optimal weight:    2.9990
   chunk 97 optimal weight:    1.9990
   overall best weight:    0.8098

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

Flipped N/Q/H residues before XYZ refinement:
** C 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3775 r_free = 0.3775 target = 0.149100 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3382 r_free = 0.3382 target = 0.115759 restraints weight = 34727.041|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 48)----------------|
| r_work = 0.3457 r_free = 0.3457 target = 0.121618 restraints weight = 16060.127|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3502 r_free = 0.3502 target = 0.125280 restraints weight = 10019.729|
|-----------------------------------------------------------------------------|
r_work (final): 0.3516
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7379
moved from start:          0.1997

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   8440  Z= 0.127
  Angle     :  0.575   6.240  11494  Z= 0.297
  Chirality :  0.041   0.149   1347
  Planarity :  0.005   0.057   1458
  Dihedral  :  5.105  25.686   1122
  Min Nonbonded Distance : 2.380

Molprobity Statistics.
  All-atom Clashscore : 8.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.35 %
    Favored  : 92.65 %
  Rotamer:
    Outliers :  1.23 %
    Allowed  : 15.50 %
    Favored  : 83.28 %
  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: -2.31 (0.26), residues: 1047
  helix: -0.81 (0.23), residues: 539
  sheet: -2.69 (0.59), residues: 71
  loop : -2.17 (0.29), residues: 437

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 159 
 HIS   0.003   0.001   HIS C 122 
 PHE   0.018   0.001   PHE A 154 
 TYR   0.009   0.001   TYR B 238 
 ARG   0.003   0.000   ARG C 234 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03297 (  318)
  hydrogen bonds       : angle       5.04920 (  927)
  covalent geometry    : bond        0.00302 ( 8440)
  covalent geometry    : angle       0.57523 (11494)

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

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

  2094 Ramachandran restraints generated.
    1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2094 Ramachandran restraints generated.
    1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  162 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 151
  time to evaluate  : 1.338 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D  115 TYR cc_start: 0.8134 (t80) cc_final: 0.7899 (t80)
REVERT: A  144 GLN cc_start: 0.6798 (mp-120) cc_final: 0.6535 (mp10)
REVERT: A  236 ASP cc_start: 0.8076 (t0) cc_final: 0.7797 (t0)
REVERT: C   75 GLU cc_start: 0.7621 (mm-30) cc_final: 0.7419 (mp0)
  outliers start: 11
  outliers final: 11
  residues processed: 155
  average time/residue: 0.3374
  time to fit residues: 77.4312
Evaluate side-chains
  159 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 148
  time to evaluate  : 1.152 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   51 GLU
Chi-restraints excluded: chain D residue  181 PHE
Chi-restraints excluded: chain A residue   42 LEU
Chi-restraints excluded: chain A residue   44 CYS
Chi-restraints excluded: chain A residue  132 LEU
Chi-restraints excluded: chain A residue  139 LEU
Chi-restraints excluded: chain A residue  158 ILE
Chi-restraints excluded: chain C residue   67 THR
Chi-restraints excluded: chain C residue   94 THR
Chi-restraints excluded: chain C residue  103 VAL
Chi-restraints excluded: chain C residue  203 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 40 optimal weight:    1.9990
   chunk 67 optimal weight:    1.9990
   chunk 72 optimal weight:    0.5980
   chunk 10 optimal weight:    2.9990
   chunk 43 optimal weight:    0.5980
   chunk 102 optimal weight:    0.4980
   chunk 17 optimal weight:    0.8980
   chunk 100 optimal weight:    2.9990
   chunk 74 optimal weight:    0.9990
   chunk 60 optimal weight:    0.8980
   chunk 55 optimal weight:    1.9990
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
** C 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3780 r_free = 0.3780 target = 0.149433 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3390 r_free = 0.3390 target = 0.116298 restraints weight = 34439.440|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 50)----------------|
| r_work = 0.3464 r_free = 0.3464 target = 0.122116 restraints weight = 15884.010|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 50)----------------|
| r_work = 0.3510 r_free = 0.3510 target = 0.125774 restraints weight = 9902.468|
|-----------------------------------------------------------------------------|
r_work (final): 0.3514
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7366
moved from start:          0.2083

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   8440  Z= 0.118
  Angle     :  0.572   6.728  11494  Z= 0.294
  Chirality :  0.042   0.148   1347
  Planarity :  0.005   0.058   1458
  Dihedral  :  5.064  25.634   1122
  Min Nonbonded Distance : 2.385

Molprobity Statistics.
  All-atom Clashscore : 7.87
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  7.07 %
    Favored  : 92.84 %
  Rotamer:
    Outliers :  1.23 %
    Allowed  : 15.83 %
    Favored  : 82.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.20 (0.26), residues: 1047
  helix: -0.70 (0.23), residues: 539
  sheet: -2.65 (0.60), residues: 71
  loop : -2.15 (0.29), residues: 437

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 159 
 HIS   0.003   0.001   HIS D 137 
 PHE   0.017   0.001   PHE A 154 
 TYR   0.009   0.001   TYR B 238 
 ARG   0.004   0.000   ARG C 234 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03196 (  318)
  hydrogen bonds       : angle       4.96382 (  927)
  covalent geometry    : bond        0.00282 ( 8440)
  covalent geometry    : angle       0.57226 (11494)

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

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

  2094 Ramachandran restraints generated.
    1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2094 Ramachandran restraints generated.
    1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  164 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 153
  time to evaluate  : 1.474 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D  115 TYR cc_start: 0.8119 (t80) cc_final: 0.7885 (t80)
REVERT: A  144 GLN cc_start: 0.6747 (mp-120) cc_final: 0.6486 (mp10)
REVERT: A  236 ASP cc_start: 0.8060 (t0) cc_final: 0.7771 (t0)
  outliers start: 11
  outliers final: 11
  residues processed: 157
  average time/residue: 0.3990
  time to fit residues: 94.8266
Evaluate side-chains
  157 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 146
  time to evaluate  : 2.156 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   51 GLU
Chi-restraints excluded: chain D residue  181 PHE
Chi-restraints excluded: chain A residue   42 LEU
Chi-restraints excluded: chain A residue   44 CYS
Chi-restraints excluded: chain A residue  132 LEU
Chi-restraints excluded: chain A residue  139 LEU
Chi-restraints excluded: chain A residue  158 ILE
Chi-restraints excluded: chain C residue   67 THR
Chi-restraints excluded: chain C residue   94 THR
Chi-restraints excluded: chain C residue  103 VAL
Chi-restraints excluded: chain C residue  203 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 5 optimal weight:    2.9990
   chunk 66 optimal weight:    0.5980
   chunk 100 optimal weight:    1.9990
   chunk 69 optimal weight:    0.6980
   chunk 53 optimal weight:    1.9990
   chunk 29 optimal weight:    2.9990
   chunk 39 optimal weight:    0.9980
   chunk 30 optimal weight:    0.8980
   chunk 90 optimal weight:    0.0980
   chunk 6 optimal weight:    0.9980
   chunk 34 optimal weight:    1.9990
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3784 r_free = 0.3784 target = 0.149718 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3395 r_free = 0.3395 target = 0.116787 restraints weight = 34665.717|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3469 r_free = 0.3469 target = 0.122583 restraints weight = 15921.035|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 50)----------------|
| r_work = 0.3515 r_free = 0.3515 target = 0.126224 restraints weight = 9860.639|
|-----------------------------------------------------------------------------|
r_work (final): 0.3529
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7360
moved from start:          0.2137

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   8440  Z= 0.116
  Angle     :  0.573   7.047  11494  Z= 0.295
  Chirality :  0.041   0.149   1347
  Planarity :  0.005   0.059   1458
  Dihedral  :  5.026  25.132   1122
  Min Nonbonded Distance : 2.371

Molprobity Statistics.
  All-atom Clashscore : 8.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.16 %
    Favored  : 92.84 %
  Rotamer:
    Outliers :  1.23 %
    Allowed  : 16.28 %
    Favored  : 82.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.10 (0.26), residues: 1047
  helix: -0.60 (0.23), residues: 541
  sheet: -2.61 (0.60), residues: 71
  loop : -2.13 (0.29), residues: 435

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 159 
 HIS   0.004   0.001   HIS D 137 
 PHE   0.017   0.001   PHE A 154 
 TYR   0.009   0.001   TYR B 176 
 ARG   0.005   0.000   ARG C 234 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03094 (  318)
  hydrogen bonds       : angle       4.89479 (  927)
  covalent geometry    : bond        0.00278 ( 8440)
  covalent geometry    : angle       0.57320 (11494)

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

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

  2094 Ramachandran restraints generated.
    1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2094 Ramachandran restraints generated.
    1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  159 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 148
  time to evaluate  : 1.659 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D  115 TYR cc_start: 0.8083 (t80) cc_final: 0.7875 (t80)
REVERT: A  144 GLN cc_start: 0.6777 (mp-120) cc_final: 0.6506 (mp10)
REVERT: A  236 ASP cc_start: 0.8062 (t0) cc_final: 0.7772 (t0)
  outliers start: 11
  outliers final: 10
  residues processed: 152
  average time/residue: 0.4269
  time to fit residues: 98.1398
Evaluate side-chains
  158 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 148
  time to evaluate  : 1.301 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   51 GLU
Chi-restraints excluded: chain D residue  181 PHE
Chi-restraints excluded: chain A residue   44 CYS
Chi-restraints excluded: chain A residue  132 LEU
Chi-restraints excluded: chain A residue  139 LEU
Chi-restraints excluded: chain A residue  158 ILE
Chi-restraints excluded: chain C residue   67 THR
Chi-restraints excluded: chain C residue   94 THR
Chi-restraints excluded: chain C residue  103 VAL
Chi-restraints excluded: chain C residue  203 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 30 optimal weight:    0.3980
   chunk 5 optimal weight:    2.9990
   chunk 4 optimal weight:    0.6980
   chunk 3 optimal weight:    0.6980
   chunk 38 optimal weight:    0.7980
   chunk 14 optimal weight:    2.9990
   chunk 23 optimal weight:    0.7980
   chunk 52 optimal weight:    0.5980
   chunk 57 optimal weight:    0.2980
   chunk 17 optimal weight:    0.9990
   chunk 21 optimal weight:    4.9990
   overall best weight:    0.5380

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

Flipped N/Q/H residues before XYZ refinement:
D 137 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3789 r_free = 0.3789 target = 0.150150 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3406 r_free = 0.3406 target = 0.117639 restraints weight = 34468.912|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3479 r_free = 0.3479 target = 0.123409 restraints weight = 15742.736|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.3525 r_free = 0.3525 target = 0.127059 restraints weight = 9737.300|
|-----------------------------------------------------------------------------|
r_work (final): 0.3530
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7361
moved from start:          0.2209

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   8440  Z= 0.108
  Angle     :  0.571   7.195  11494  Z= 0.293
  Chirality :  0.042   0.148   1347
  Planarity :  0.005   0.059   1458
  Dihedral  :  4.976  24.903   1122
  Min Nonbonded Distance : 2.358

Molprobity Statistics.
  All-atom Clashscore : 7.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.78 %
    Favored  : 93.22 %
  Rotamer:
    Outliers :  1.00 %
    Allowed  : 16.83 %
    Favored  : 82.16 %
  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: -1.97 (0.26), residues: 1047
  helix: -0.50 (0.23), residues: 553
  sheet: -2.52 (0.62), residues: 70
  loop : -2.11 (0.30), residues: 424

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 159 
 HIS   0.005   0.001   HIS D 137 
 PHE   0.017   0.001   PHE A 154 
 TYR   0.014   0.001   TYR D 102 
 ARG   0.006   0.000   ARG C 234 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02986 (  318)
  hydrogen bonds       : angle       4.82720 (  927)
  covalent geometry    : bond        0.00260 ( 8440)
  covalent geometry    : angle       0.57112 (11494)

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

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

  2094 Ramachandran restraints generated.
    1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2094 Ramachandran restraints generated.
    1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  160 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 151
  time to evaluate  : 1.696 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D  115 TYR cc_start: 0.8078 (t80) cc_final: 0.7873 (t80)
REVERT: A  144 GLN cc_start: 0.6710 (mp-120) cc_final: 0.6438 (mp10)
REVERT: A  236 ASP cc_start: 0.7973 (t0) cc_final: 0.7669 (t0)
  outliers start: 9
  outliers final: 9
  residues processed: 154
  average time/residue: 0.4214
  time to fit residues: 96.6173
Evaluate side-chains
  158 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 149
  time to evaluate  : 1.714 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   51 GLU
Chi-restraints excluded: chain D residue  181 PHE
Chi-restraints excluded: chain A residue   44 CYS
Chi-restraints excluded: chain A residue  132 LEU
Chi-restraints excluded: chain A residue  139 LEU
Chi-restraints excluded: chain A residue  158 ILE
Chi-restraints excluded: chain C residue   67 THR
Chi-restraints excluded: chain C residue  103 VAL
Chi-restraints excluded: chain C residue  203 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 70 optimal weight:    0.9980
   chunk 20 optimal weight:    2.9990
   chunk 81 optimal weight:    4.9990
   chunk 37 optimal weight:    0.9980
   chunk 50 optimal weight:    1.9990
   chunk 87 optimal weight:    0.4980
   chunk 48 optimal weight:    0.8980
   chunk 24 optimal weight:    2.9990
   chunk 16 optimal weight:    3.9990
   chunk 17 optimal weight:    0.8980
   chunk 100 optimal weight:    1.9990
   overall best weight:    0.8580

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

Flipped N/Q/H residues before XYZ refinement:

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3781 r_free = 0.3781 target = 0.149385 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3391 r_free = 0.3391 target = 0.116381 restraints weight = 34633.326|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3464 r_free = 0.3464 target = 0.122149 restraints weight = 15992.777|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3510 r_free = 0.3510 target = 0.125790 restraints weight = 9962.359|
|-----------------------------------------------------------------------------|
r_work (final): 0.3532
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7369
moved from start:          0.2223

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   8440  Z= 0.129
  Angle     :  0.581   7.153  11494  Z= 0.298
  Chirality :  0.042   0.147   1347
  Planarity :  0.005   0.059   1458
  Dihedral  :  4.989  24.444   1122
  Min Nonbonded Distance : 2.343

Molprobity Statistics.
  All-atom Clashscore : 7.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.35 %
    Favored  : 92.65 %
  Rotamer:
    Outliers :  1.00 %
    Allowed  : 16.83 %
    Favored  : 82.16 %
  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: -2.01 (0.26), residues: 1047
  helix: -0.52 (0.23), residues: 553
  sheet: -2.57 (0.60), residues: 71
  loop : -2.13 (0.30), residues: 423

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 159 
 HIS   0.003   0.001   HIS D 203 
 PHE   0.017   0.001   PHE A 154 
 TYR   0.011   0.001   TYR D 102 
 ARG   0.005   0.000   ARG C 234 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02991 (  318)
  hydrogen bonds       : angle       4.83584 (  927)
  covalent geometry    : bond        0.00308 ( 8440)
  covalent geometry    : angle       0.58106 (11494)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5481.20 seconds
wall clock time: 96 minutes 15.38 seconds (5775.38 seconds total)