Starting phenix.real_space_refine
on Sat May 10 00:28:14 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8otd_17175/05_2025/8otd_17175.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8otd_17175/05_2025/8otd_17175.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.6
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8otd_17175/05_2025/8otd_17175.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8otd_17175/05_2025/8otd_17175.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8otd_17175/05_2025/8otd_17175.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8otd_17175/05_2025/8otd_17175.cif"
  }
  resolution = 2.6
  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=   0.002
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      28      5.16       5
     C    2772      2.51       5
     N     692      2.21       5
     O     848      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 48 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 4340
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 1085
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 135, 1085
          Classifications: {'peptide': 135}
          Link IDs: {'PTRANS': 2, 'TRANS': 132}
  Restraints were copied for chains:
    C, B, D
  Time building chain proxies: 3.08, per 1000 atoms: 0.71
  Number of scatterers: 4340
  At special positions: 0
  Unit cell: (100.528, 97.232, 37.08, 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      28     16.00
     O     848      8.00
     N     692      7.00
     C    2772      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=4, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 214 " - pdb=" SG  CYS A 253 " distance=2.07
    Simple disulfide: pdb=" SG  CYS C 214 " - pdb=" SG  CYS C 253 " distance=2.07
    Simple disulfide: pdb=" SG  CYS B 214 " - pdb=" SG  CYS B 253 " distance=2.07
    Simple disulfide: pdb=" SG  CYS D 214 " - pdb=" SG  CYS D 253 " distance=2.07

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.96
  Conformation dependent library (CDL) restraints added in 511.3 milliseconds
  

  1064 Ramachandran restraints generated.
    532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1040

  Finding SS restraints...
    Secondary structure from input PDB file:
      0 helices and 11 sheets defined
      0.0% alpha, 68.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.54
  Creating SS restraints...
    Processing sheet with id=AA1, first strand: chain 'C' and resid 124 through 126
      removed outlier: 6.034A  pdb=" N   TYR A 125 " --> pdb=" O   ILE B 126 " (cutoff:3.500A)
      removed outlier: 6.034A  pdb=" N   TYR B 125 " --> pdb=" O   ILE D 126 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'C' and resid 129 through 130
      removed outlier: 6.477A  pdb=" N   LYS A 129 " --> pdb=" O   SER B 130 " (cutoff:3.500A)
      removed outlier: 6.477A  pdb=" N   LYS B 129 " --> pdb=" O   SER D 130 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'C' and resid 133 through 134
      removed outlier: 6.868A  pdb=" N   VAL A 133 " --> pdb=" O   SER C 134 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'C' and resid 140 through 153
      removed outlier: 6.874A  pdb=" N   ILE C 146 " --> pdb=" O   ASN A 145 " (cutoff:3.500A)
      removed outlier: 6.957A  pdb=" N   THR A 147 " --> pdb=" O   ILE C 146 " (cutoff:3.500A)
      removed outlier: 6.990A  pdb=" N   ASN C 148 " --> pdb=" O   THR A 147 " (cutoff:3.500A)
      removed outlier: 6.971A  pdb=" N   THR A 149 " --> pdb=" O   ASN C 148 " (cutoff:3.500A)
      removed outlier: 6.964A  pdb=" N   LEU C 150 " --> pdb=" O   THR A 149 " (cutoff:3.500A)
      removed outlier: 6.994A  pdb=" N   ASN A 151 " --> pdb=" O   LEU C 150 " (cutoff:3.500A)
      removed outlier: 6.985A  pdb=" N   ILE C 152 " --> pdb=" O   ASN A 151 " (cutoff:3.500A)
      removed outlier: 6.916A  pdb=" N   THR A 153 " --> pdb=" O   ILE C 152 " (cutoff:3.500A)
      removed outlier: 6.744A  pdb=" N   ARG A 140 " --> pdb=" O   THR B 141 " (cutoff:3.500A)
      removed outlier: 7.882A  pdb=" N   TYR B 143 " --> pdb=" O   ARG A 140 " (cutoff:3.500A)
      removed outlier: 6.132A  pdb=" N   ILE A 142 " --> pdb=" O   TYR B 143 " (cutoff:3.500A)
      removed outlier: 7.592A  pdb=" N   ASN B 145 " --> pdb=" O   ILE A 142 " (cutoff:3.500A)
      removed outlier: 8.583A  pdb=" N   LEU A 144 " --> pdb=" O   ASN B 145 " (cutoff:3.500A)
      removed outlier: 7.866A  pdb=" N   THR B 147 " --> pdb=" O   LEU A 144 " (cutoff:3.500A)
      removed outlier: 9.204A  pdb=" N   ILE A 146 " --> pdb=" O   THR B 147 " (cutoff:3.500A)
      removed outlier: 10.021A  pdb=" N   THR B 149 " --> pdb=" O   ILE A 146 " (cutoff:3.500A)
      removed outlier: 9.017A  pdb=" N   ASN A 148 " --> pdb=" O   THR B 149 " (cutoff:3.500A)
      removed outlier: 10.210A  pdb=" N   ASN B 151 " --> pdb=" O   ASN A 148 " (cutoff:3.500A)
      removed outlier: 9.066A  pdb=" N   LEU A 150 " --> pdb=" O   ASN B 151 " (cutoff:3.500A)
      removed outlier: 10.067A  pdb=" N   THR B 153 " --> pdb=" O   LEU A 150 " (cutoff:3.500A)
      removed outlier: 9.314A  pdb=" N   ILE A 152 " --> pdb=" O   THR B 153 " (cutoff:3.500A)
      removed outlier: 6.743A  pdb=" N   ARG B 140 " --> pdb=" O   THR D 141 " (cutoff:3.500A)
      removed outlier: 7.881A  pdb=" N   TYR D 143 " --> pdb=" O   ARG B 140 " (cutoff:3.500A)
      removed outlier: 6.131A  pdb=" N   ILE B 142 " --> pdb=" O   TYR D 143 " (cutoff:3.500A)
      removed outlier: 7.591A  pdb=" N   ASN D 145 " --> pdb=" O   ILE B 142 " (cutoff:3.500A)
      removed outlier: 8.582A  pdb=" N   LEU B 144 " --> pdb=" O   ASN D 145 " (cutoff:3.500A)
      removed outlier: 7.866A  pdb=" N   THR D 147 " --> pdb=" O   LEU B 144 " (cutoff:3.500A)
      removed outlier: 9.205A  pdb=" N   ILE B 146 " --> pdb=" O   THR D 147 " (cutoff:3.500A)
      removed outlier: 10.021A  pdb=" N   THR D 149 " --> pdb=" O   ILE B 146 " (cutoff:3.500A)
      removed outlier: 9.017A  pdb=" N   ASN B 148 " --> pdb=" O   THR D 149 " (cutoff:3.500A)
      removed outlier: 10.209A  pdb=" N   ASN D 151 " --> pdb=" O   ASN B 148 " (cutoff:3.500A)
      removed outlier: 9.066A  pdb=" N   LEU B 150 " --> pdb=" O   ASN D 151 " (cutoff:3.500A)
      removed outlier: 10.067A  pdb=" N   THR D 153 " --> pdb=" O   LEU B 150 " (cutoff:3.500A)
      removed outlier: 9.314A  pdb=" N   ILE B 152 " --> pdb=" O   THR D 153 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'C' and resid 156 through 176
      removed outlier: 6.751A  pdb=" N   VAL A 162 " --> pdb=" O   GLU C 161 " (cutoff:3.500A)
      removed outlier: 6.948A  pdb=" N   GLU C 163 " --> pdb=" O   VAL A 162 " (cutoff:3.500A)
      removed outlier: 6.926A  pdb=" N   ASN A 164 " --> pdb=" O   GLU C 163 " (cutoff:3.500A)
      removed outlier: 6.958A  pdb=" N   ILE C 165 " --> pdb=" O   ASN A 164 " (cutoff:3.500A)
      removed outlier: 6.798A  pdb=" N   THR A 166 " --> pdb=" O   ILE C 165 " (cutoff:3.500A)
      removed outlier: 6.294A  pdb=" N   TYR A 157 " --> pdb=" O   TYR B 158 " (cutoff:3.500A)
      removed outlier: 7.445A  pdb=" N   VAL B 160 " --> pdb=" O   TYR A 157 " (cutoff:3.500A)
      removed outlier: 6.294A  pdb=" N   SER A 159 " --> pdb=" O   VAL B 160 " (cutoff:3.500A)
      removed outlier: 5.829A  pdb=" N   VAL B 162 " --> pdb=" O   SER A 159 " (cutoff:3.500A)
      removed outlier: 7.719A  pdb=" N   GLU A 161 " --> pdb=" O   VAL B 162 " (cutoff:3.500A)
      removed outlier: 9.726A  pdb=" N   ASN B 164 " --> pdb=" O   GLU A 161 " (cutoff:3.500A)
      removed outlier: 9.346A  pdb=" N   GLU A 163 " --> pdb=" O   ASN B 164 " (cutoff:3.500A)
      removed outlier: 10.000A  pdb=" N   THR B 166 " --> pdb=" O   GLU A 163 " (cutoff:3.500A)
      removed outlier: 6.167A  pdb=" N   ILE A 165 " --> pdb=" O   THR B 166 " (cutoff:3.500A)
      removed outlier: 8.460A  pdb=" N   GLN B 168 " --> pdb=" O   ILE A 165 " (cutoff:3.500A)
      removed outlier: 6.597A  pdb=" N   ALA A 167 " --> pdb=" O   GLN B 168 " (cutoff:3.500A)
      removed outlier: 8.365A  pdb=" N   GLN B 170 " --> pdb=" O   ALA A 167 " (cutoff:3.500A)
      removed outlier: 6.549A  pdb=" N   VAL A 169 " --> pdb=" O   GLN B 170 " (cutoff:3.500A)
      removed outlier: 7.777A  pdb=" N   SER B 172 " --> pdb=" O   VAL A 169 " (cutoff:3.500A)
      removed outlier: 6.411A  pdb=" N   PHE A 171 " --> pdb=" O   SER B 172 " (cutoff:3.500A)
      removed outlier: 8.447A  pdb=" N   THR B 174 " --> pdb=" O   PHE A 171 " (cutoff:3.500A)
      removed outlier: 6.704A  pdb=" N   LYS A 173 " --> pdb=" O   THR B 174 " (cutoff:3.500A)
      removed outlier: 8.200A  pdb=" N   ILE B 176 " --> pdb=" O   LYS A 173 " (cutoff:3.500A)
      removed outlier: 6.825A  pdb=" N   VAL A 175 " --> pdb=" O   ILE B 176 " (cutoff:3.500A)
      removed outlier: 6.294A  pdb=" N   TYR B 157 " --> pdb=" O   TYR D 158 " (cutoff:3.500A)
      removed outlier: 7.444A  pdb=" N   VAL D 160 " --> pdb=" O   TYR B 157 " (cutoff:3.500A)
      removed outlier: 6.294A  pdb=" N   SER B 159 " --> pdb=" O   VAL D 160 " (cutoff:3.500A)
      removed outlier: 5.829A  pdb=" N   VAL D 162 " --> pdb=" O   SER B 159 " (cutoff:3.500A)
      removed outlier: 7.719A  pdb=" N   GLU B 161 " --> pdb=" O   VAL D 162 " (cutoff:3.500A)
      removed outlier: 9.726A  pdb=" N   ASN D 164 " --> pdb=" O   GLU B 161 " (cutoff:3.500A)
      removed outlier: 9.346A  pdb=" N   GLU B 163 " --> pdb=" O   ASN D 164 " (cutoff:3.500A)
      removed outlier: 10.000A  pdb=" N   THR D 166 " --> pdb=" O   GLU B 163 " (cutoff:3.500A)
      removed outlier: 6.167A  pdb=" N   ILE B 165 " --> pdb=" O   THR D 166 " (cutoff:3.500A)
      removed outlier: 8.460A  pdb=" N   GLN D 168 " --> pdb=" O   ILE B 165 " (cutoff:3.500A)
      removed outlier: 6.596A  pdb=" N   ALA B 167 " --> pdb=" O   GLN D 168 " (cutoff:3.500A)
      removed outlier: 8.365A  pdb=" N   GLN D 170 " --> pdb=" O   ALA B 167 " (cutoff:3.500A)
      removed outlier: 6.549A  pdb=" N   VAL B 169 " --> pdb=" O   GLN D 170 " (cutoff:3.500A)
      removed outlier: 7.777A  pdb=" N   SER D 172 " --> pdb=" O   VAL B 169 " (cutoff:3.500A)
      removed outlier: 6.411A  pdb=" N   PHE B 171 " --> pdb=" O   SER D 172 " (cutoff:3.500A)
      removed outlier: 8.448A  pdb=" N   THR D 174 " --> pdb=" O   PHE B 171 " (cutoff:3.500A)
      removed outlier: 6.705A  pdb=" N   LYS B 173 " --> pdb=" O   THR D 174 " (cutoff:3.500A)
      removed outlier: 8.200A  pdb=" N   ILE D 176 " --> pdb=" O   LYS B 173 " (cutoff:3.500A)
      removed outlier: 6.825A  pdb=" N   VAL B 175 " --> pdb=" O   ILE D 176 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'C' and resid 180 through 187
      removed outlier: 8.672A  pdb=" N   ARG A 180 " --> pdb=" O   LEU C 181 " (cutoff:3.500A)
      removed outlier: 9.797A  pdb=" N   ASN C 183 " --> pdb=" O   ARG A 180 " (cutoff:3.500A)
      removed outlier: 5.912A  pdb=" N   ASN A 182 " --> pdb=" O   ASN C 183 " (cutoff:3.500A)
      removed outlier: 8.384A  pdb=" N   SER C 185 " --> pdb=" O   ASN A 182 " (cutoff:3.500A)
      removed outlier: 6.459A  pdb=" N   ILE A 184 " --> pdb=" O   SER C 185 " (cutoff:3.500A)
      removed outlier: 7.585A  pdb=" N   ILE C 187 " --> pdb=" O   ILE A 184 " (cutoff:3.500A)
      removed outlier: 6.245A  pdb=" N   ILE A 186 " --> pdb=" O   ILE C 187 " (cutoff:3.500A)
      removed outlier: 6.873A  pdb=" N   LEU A 181 " --> pdb=" O   ARG B 180 " (cutoff:3.500A)
      removed outlier: 6.905A  pdb=" N   ASN B 182 " --> pdb=" O   LEU A 181 " (cutoff:3.500A)
      removed outlier: 6.811A  pdb=" N   ASN A 183 " --> pdb=" O   ASN B 182 " (cutoff:3.500A)
      removed outlier: 6.873A  pdb=" N   LEU B 181 " --> pdb=" O   ARG D 180 " (cutoff:3.500A)
      removed outlier: 6.904A  pdb=" N   ASN D 182 " --> pdb=" O   LEU B 181 " (cutoff:3.500A)
      removed outlier: 6.811A  pdb=" N   ASN B 183 " --> pdb=" O   ASN D 182 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'C' and resid 192 through 198
      removed outlier: 5.862A  pdb=" N   LYS A 193 " --> pdb=" O   GLN C 194 " (cutoff:3.500A)
      removed outlier: 8.599A  pdb=" N   ASP C 196 " --> pdb=" O   LYS A 193 " (cutoff:3.500A)
      removed outlier: 6.540A  pdb=" N   ILE A 195 " --> pdb=" O   ASP C 196 " (cutoff:3.500A)
      removed outlier: 7.792A  pdb=" N   THR C 198 " --> pdb=" O   ILE A 195 " (cutoff:3.500A)
      removed outlier: 6.376A  pdb=" N   TYR A 197 " --> pdb=" O   THR C 198 " (cutoff:3.500A)
      removed outlier: 6.923A  pdb=" N   LYS B 193 " --> pdb=" O   MET A 192 " (cutoff:3.500A)
      removed outlier: 6.844A  pdb=" N   GLN A 194 " --> pdb=" O   LYS B 193 " (cutoff:3.500A)
      removed outlier: 6.923A  pdb=" N   LYS D 193 " --> pdb=" O   MET B 192 " (cutoff:3.500A)
      removed outlier: 6.844A  pdb=" N   GLN B 194 " --> pdb=" O   LYS D 193 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'C' and resid 201 through 206
      removed outlier: 6.552A  pdb=" N   THR A 201 " --> pdb=" O   VAL C 202 " (cutoff:3.500A)
      removed outlier: 8.040A  pdb=" N   ALA C 204 " --> pdb=" O   THR A 201 " (cutoff:3.500A)
      removed outlier: 6.161A  pdb=" N   ILE A 203 " --> pdb=" O   ALA C 204 " (cutoff:3.500A)
      removed outlier: 7.770A  pdb=" N   GLU C 206 " --> pdb=" O   ILE A 203 " (cutoff:3.500A)
      removed outlier: 6.195A  pdb=" N   GLU A 205 " --> pdb=" O   GLU C 206 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'C' and resid 209 through 219
      removed outlier: 6.838A  pdb=" N   THR C 215 " --> pdb=" O   CYS A 214 " (cutoff:3.500A)
      removed outlier: 6.885A  pdb=" N   LEU A 216 " --> pdb=" O   THR C 215 " (cutoff:3.500A)
      removed outlier: 6.929A  pdb=" N   ILE C 217 " --> pdb=" O   LEU A 216 " (cutoff:3.500A)
      removed outlier: 6.954A  pdb=" N   SER A 218 " --> pdb=" O   ILE C 217 " (cutoff:3.500A)
      removed outlier: 6.974A  pdb=" N   ILE C 219 " --> pdb=" O   SER A 218 " (cutoff:3.500A)
      removed outlier: 6.313A  pdb=" N   TYR A 209 " --> pdb=" O   MET B 210 " (cutoff:3.500A)
      removed outlier: 7.863A  pdb=" N   ASP B 212 " --> pdb=" O   TYR A 209 " (cutoff:3.500A)
      removed outlier: 6.293A  pdb=" N   TYR A 211 " --> pdb=" O   ASP B 212 " (cutoff:3.500A)
      removed outlier: 8.049A  pdb=" N   CYS B 214 " --> pdb=" O   TYR A 211 " (cutoff:3.500A)
      removed outlier: 8.472A  pdb=" N   PHE A 213 " --> pdb=" O   CYS B 214 " (cutoff:3.500A)
      removed outlier: 7.533A  pdb=" N   LEU B 216 " --> pdb=" O   PHE A 213 " (cutoff:3.500A)
      removed outlier: 8.980A  pdb=" N   THR A 215 " --> pdb=" O   LEU B 216 " (cutoff:3.500A)
      removed outlier: 9.711A  pdb=" N   SER B 218 " --> pdb=" O   THR A 215 " (cutoff:3.500A)
      removed outlier: 8.824A  pdb=" N   ILE A 217 " --> pdb=" O   SER B 218 " (cutoff:3.500A)
      removed outlier: 6.314A  pdb=" N   TYR B 209 " --> pdb=" O   MET D 210 " (cutoff:3.500A)
      removed outlier: 7.863A  pdb=" N   ASP D 212 " --> pdb=" O   TYR B 209 " (cutoff:3.500A)
      removed outlier: 6.293A  pdb=" N   TYR B 211 " --> pdb=" O   ASP D 212 " (cutoff:3.500A)
      removed outlier: 8.049A  pdb=" N   CYS D 214 " --> pdb=" O   TYR B 211 " (cutoff:3.500A)
      removed outlier: 8.472A  pdb=" N   PHE B 213 " --> pdb=" O   CYS D 214 " (cutoff:3.500A)
      removed outlier: 7.533A  pdb=" N   LEU D 216 " --> pdb=" O   PHE B 213 " (cutoff:3.500A)
      removed outlier: 8.980A  pdb=" N   THR B 215 " --> pdb=" O   LEU D 216 " (cutoff:3.500A)
      removed outlier: 9.711A  pdb=" N   SER D 218 " --> pdb=" O   THR B 215 " (cutoff:3.500A)
      removed outlier: 8.824A  pdb=" N   ILE B 217 " --> pdb=" O   SER D 218 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'C' and resid 222 through 230
      removed outlier: 6.224A  pdb=" N   ASN A 223 " --> pdb=" O   ILE C 224 " (cutoff:3.500A)
      removed outlier: 7.612A  pdb=" N   LEU C 226 " --> pdb=" O   ASN A 223 " (cutoff:3.500A)
      removed outlier: 6.263A  pdb=" N   VAL A 225 " --> pdb=" O   LEU C 226 " (cutoff:3.500A)
      removed outlier: 7.828A  pdb=" N   MET C 228 " --> pdb=" O   VAL A 225 " (cutoff:3.500A)
      removed outlier: 6.222A  pdb=" N   MET A 227 " --> pdb=" O   MET C 228 " (cutoff:3.500A)
      removed outlier: 6.209A  pdb=" N   VAL C 230 " --> pdb=" O   MET A 227 " (cutoff:3.500A)
      removed outlier: 7.689A  pdb=" N   GLN A 229 " --> pdb=" O   VAL C 230 " (cutoff:3.500A)
      removed outlier: 6.780A  pdb=" N   ASN B 223 " --> pdb=" O   HIS A 222 " (cutoff:3.500A)
      removed outlier: 6.865A  pdb=" N   VAL A 230 " --> pdb=" O   GLN B 229 " (cutoff:3.500A)
      removed outlier: 6.780A  pdb=" N   ASN D 223 " --> pdb=" O   HIS B 222 " (cutoff:3.500A)
      removed outlier: 6.865A  pdb=" N   VAL B 230 " --> pdb=" O   GLN D 229 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'C' and resid 233 through 252
      removed outlier: 6.672A  pdb=" N   THR A 233 " --> pdb=" O   THR C 234 " (cutoff:3.500A)
      removed outlier: 8.188A  pdb=" N   TYR C 236 " --> pdb=" O   THR A 233 " (cutoff:3.500A)
      removed outlier: 6.552A  pdb=" N   THR A 235 " --> pdb=" O   TYR C 236 " (cutoff:3.500A)
      removed outlier: 7.926A  pdb=" N   GLY C 238 " --> pdb=" O   THR A 235 " (cutoff:3.500A)
      removed outlier: 5.970A  pdb=" N   PHE A 237 " --> pdb=" O   GLY C 238 " (cutoff:3.500A)
      removed outlier: 7.533A  pdb=" N   SER C 240 " --> pdb=" O   PHE A 237 " (cutoff:3.500A)
      removed outlier: 6.336A  pdb=" N   HIS A 239 " --> pdb=" O   SER C 240 " (cutoff:3.500A)
      removed outlier: 8.437A  pdb=" N   GLN C 242 " --> pdb=" O   HIS A 239 " (cutoff:3.500A)
      removed outlier: 6.401A  pdb=" N   GLU A 241 " --> pdb=" O   GLN C 242 " (cutoff:3.500A)
      removed outlier: 8.202A  pdb=" N   SER C 244 " --> pdb=" O   GLU A 241 " (cutoff:3.500A)
      removed outlier: 6.344A  pdb=" N   ILE A 243 " --> pdb=" O   SER C 244 " (cutoff:3.500A)
      removed outlier: 8.312A  pdb=" N   GLU C 246 " --> pdb=" O   ILE A 243 " (cutoff:3.500A)
      removed outlier: 6.558A  pdb=" N   GLN A 245 " --> pdb=" O   GLU C 246 " (cutoff:3.500A)
      removed outlier: 7.644A  pdb=" N   TYR C 248 " --> pdb=" O   GLN A 245 " (cutoff:3.500A)
      removed outlier: 6.217A  pdb=" N   ARG A 247 " --> pdb=" O   TYR C 248 " (cutoff:3.500A)
      removed outlier: 7.993A  pdb=" N   TYR C 250 " --> pdb=" O   ARG A 247 " (cutoff:3.500A)
      removed outlier: 8.753A  pdb=" N   GLN A 249 " --> pdb=" O   TYR C 250 " (cutoff:3.500A)
      removed outlier: 7.128A  pdb=" N   ASP C 252 " --> pdb=" O   GLN A 249 " (cutoff:3.500A)
      removed outlier: 9.152A  pdb=" N   VAL A 251 " --> pdb=" O   ASP C 252 " (cutoff:3.500A)
      removed outlier: 6.946A  pdb=" N   VAL B 251 " --> pdb=" O   TYR A 250 " (cutoff:3.500A)
      removed outlier: 6.924A  pdb=" N   ASP A 252 " --> pdb=" O   VAL B 251 " (cutoff:3.500A)
      removed outlier: 6.946A  pdb=" N   VAL D 251 " --> pdb=" O   TYR B 250 " (cutoff:3.500A)
      removed outlier: 6.924A  pdb=" N   ASP B 252 " --> pdb=" O   VAL D 251 " (cutoff:3.500A)

    102 hydrogen bonds defined for protein.
    306 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.05

  Time building geometry restraints manager: 1.14 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: 1058
        1.34 -     1.46: 1274
        1.46 -     1.58: 2032
        1.58 -     1.70: 0
        1.70 -     1.82: 48
  Bond restraints: 4412
  Sorted by residual:
  bond pdb=" CG  HIS B 239 "
       pdb=" CD2 HIS B 239 "
    ideal  model  delta    sigma   weight residual
    1.354  1.327  0.027 1.10e-02 8.26e+03 6.20e+00
  bond pdb=" CG  HIS C 239 "
       pdb=" CD2 HIS C 239 "
    ideal  model  delta    sigma   weight residual
    1.354  1.327  0.027 1.10e-02 8.26e+03 6.03e+00
  bond pdb=" CG  HIS D 239 "
       pdb=" CD2 HIS D 239 "
    ideal  model  delta    sigma   weight residual
    1.354  1.327  0.027 1.10e-02 8.26e+03 5.97e+00
  bond pdb=" CG  HIS A 239 "
       pdb=" CD2 HIS A 239 "
    ideal  model  delta    sigma   weight residual
    1.354  1.327  0.027 1.10e-02 8.26e+03 5.85e+00
  bond pdb=" CA  SER B 218 "
       pdb=" CB  SER B 218 "
    ideal  model  delta    sigma   weight residual
    1.530  1.497  0.034 1.50e-02 4.44e+03 5.06e+00
  ... (remaining 4407 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.56: 4616
        1.56 -     3.11: 1091
        3.11 -     4.67: 213
        4.67 -     6.22: 60
        6.22 -     7.78: 16
  Bond angle restraints: 5996
  Sorted by residual:
  angle pdb=" C   ASP B 136 "
        pdb=" CA  ASP B 136 "
        pdb=" CB  ASP B 136 "
      ideal   model   delta    sigma   weight residual
     109.84  117.62   -7.78 1.63e+00 3.76e-01 2.28e+01
  angle pdb=" C   ASP A 136 "
        pdb=" CA  ASP A 136 "
        pdb=" CB  ASP A 136 "
      ideal   model   delta    sigma   weight residual
     109.84  117.61   -7.77 1.63e+00 3.76e-01 2.27e+01
  angle pdb=" C   ASP D 136 "
        pdb=" CA  ASP D 136 "
        pdb=" CB  ASP D 136 "
      ideal   model   delta    sigma   weight residual
     109.84  117.58   -7.74 1.63e+00 3.76e-01 2.26e+01
  angle pdb=" C   ASP C 136 "
        pdb=" CA  ASP C 136 "
        pdb=" CB  ASP C 136 "
      ideal   model   delta    sigma   weight residual
     109.84  117.58   -7.74 1.63e+00 3.76e-01 2.25e+01
  angle pdb=" N   GLU D 246 "
        pdb=" CA  GLU D 246 "
        pdb=" C   GLU D 246 "
      ideal   model   delta    sigma   weight residual
     108.76  116.05   -7.29 1.58e+00 4.01e-01 2.13e+01
  ... (remaining 5991 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    14.88: 2256
       14.88 -    29.77: 280
       29.77 -    44.65: 60
       44.65 -    59.54: 48
       59.54 -    74.42: 16
  Dihedral angle restraints: 2660
    sinusoidal: 1036
      harmonic: 1624
  Sorted by residual:
  dihedral pdb=" CA  THR C 231 "
           pdb=" C   THR C 231 "
           pdb=" N   VAL C 232 "
           pdb=" CA  VAL C 232 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  156.11   23.89     0      5.00e+00 4.00e-02 2.28e+01
  dihedral pdb=" CA  THR A 231 "
           pdb=" C   THR A 231 "
           pdb=" N   VAL A 232 "
           pdb=" CA  VAL A 232 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  156.13   23.87     0      5.00e+00 4.00e-02 2.28e+01
  dihedral pdb=" CA  THR D 231 "
           pdb=" C   THR D 231 "
           pdb=" N   VAL D 232 "
           pdb=" CA  VAL D 232 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  156.15   23.85     0      5.00e+00 4.00e-02 2.27e+01
  ... (remaining 2657 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.066: 338
       0.066 -    0.133: 270
       0.133 -    0.199: 93
       0.199 -    0.265: 7
       0.265 -    0.331: 12
  Chirality restraints: 720
  Sorted by residual:
  chirality pdb=" CA  LYS B 124 "
            pdb=" N   LYS B 124 "
            pdb=" C   LYS B 124 "
            pdb=" CB  LYS B 124 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.18    0.33 2.00e-01 2.50e+01 2.74e+00
  chirality pdb=" CA  LYS D 124 "
            pdb=" N   LYS D 124 "
            pdb=" C   LYS D 124 "
            pdb=" CB  LYS D 124 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.18    0.33 2.00e-01 2.50e+01 2.74e+00
  chirality pdb=" CA  LYS A 124 "
            pdb=" N   LYS A 124 "
            pdb=" C   LYS A 124 "
            pdb=" CB  LYS A 124 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.18    0.33 2.00e-01 2.50e+01 2.73e+00
  ... (remaining 717 not shown)

  Planarity restraints: 744
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR C 248 "    0.073 2.00e-02 2.50e+03   3.84e-02 2.95e+01
        pdb=" CG  TYR C 248 "   -0.067 2.00e-02 2.50e+03
        pdb=" CD1 TYR C 248 "   -0.022 2.00e-02 2.50e+03
        pdb=" CD2 TYR C 248 "   -0.029 2.00e-02 2.50e+03
        pdb=" CE1 TYR C 248 "    0.004 2.00e-02 2.50e+03
        pdb=" CE2 TYR C 248 "    0.009 2.00e-02 2.50e+03
        pdb=" CZ  TYR C 248 "    0.011 2.00e-02 2.50e+03
        pdb=" OH  TYR C 248 "    0.021 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR A 248 "    0.073 2.00e-02 2.50e+03   3.83e-02 2.94e+01
        pdb=" CG  TYR A 248 "   -0.067 2.00e-02 2.50e+03
        pdb=" CD1 TYR A 248 "   -0.022 2.00e-02 2.50e+03
        pdb=" CD2 TYR A 248 "   -0.029 2.00e-02 2.50e+03
        pdb=" CE1 TYR A 248 "    0.004 2.00e-02 2.50e+03
        pdb=" CE2 TYR A 248 "    0.009 2.00e-02 2.50e+03
        pdb=" CZ  TYR A 248 "    0.011 2.00e-02 2.50e+03
        pdb=" OH  TYR A 248 "    0.021 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR B 248 "    0.073 2.00e-02 2.50e+03   3.82e-02 2.92e+01
        pdb=" CG  TYR B 248 "   -0.067 2.00e-02 2.50e+03
        pdb=" CD1 TYR B 248 "   -0.022 2.00e-02 2.50e+03
        pdb=" CD2 TYR B 248 "   -0.029 2.00e-02 2.50e+03
        pdb=" CE1 TYR B 248 "    0.005 2.00e-02 2.50e+03
        pdb=" CE2 TYR B 248 "    0.009 2.00e-02 2.50e+03
        pdb=" CZ  TYR B 248 "    0.011 2.00e-02 2.50e+03
        pdb=" OH  TYR B 248 "    0.020 2.00e-02 2.50e+03
  ... (remaining 741 not shown)

  Histogram of nonbonded interaction distances:
        2.48 -     2.96: 1994
        2.96 -     3.45: 4022
        3.45 -     3.93: 7646
        3.93 -     4.42: 8118
        4.42 -     4.90: 15622
  Nonbonded interactions: 37402
  Sorted by model distance:
  nonbonded pdb=" NZ  LYS D 129 "
            pdb=" OD2 ASP D 136 "
     model   vdw
     2.478 3.120
  nonbonded pdb=" NZ  LYS A 129 "
            pdb=" OD2 ASP A 136 "
     model   vdw
     2.478 3.120
  nonbonded pdb=" NZ  LYS B 129 "
            pdb=" OD2 ASP B 136 "
     model   vdw
     2.478 3.120
  nonbonded pdb=" NZ  LYS C 129 "
            pdb=" OD2 ASP C 136 "
     model   vdw
     2.478 3.120
  nonbonded pdb=" OG  SER C 134 "
            pdb=" OD1 ASP C 136 "
     model   vdw
     2.504 3.040
  ... (remaining 37397 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: 0.03
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'C'
  selection = chain 'B'
  selection = chain 'D'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             5.360
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.180
  Check model and map are aligned:         0.030
  Set scattering table:                    0.050
  Process input model:                     14.030
  Find NCS groups from input model:        0.080
  Set up NCS constraints:                  0.010
  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:10.430
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   30.180
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8442
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      :  0.008   0.044   4416  Z= 0.527
  Angle     :  1.482   7.777   6004  Z= 0.939
  Chirality :  0.099   0.331    720
  Planarity :  0.015   0.168    744
  Dihedral  : 16.818  74.422   1608
  Min Nonbonded Distance : 2.478

Molprobity Statistics.
  All-atom Clashscore : 4.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.27 %
    Favored  : 91.73 %
  Rotamer:
    Outliers :  4.76 %
    Allowed  :  5.56 %
    Favored  : 89.68 %
  Cbeta Deviations :  0.77 %
  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: -3.89 (0.27), residues: 532
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.96 (0.21), residues: 532

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.007   0.004   HIS C 239 
 PHE   0.017   0.006   PHE B 171 
 TYR   0.073   0.008   TYR C 248 
 ARG   0.026   0.005   ARG A 247 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.12583 (  102)
  hydrogen bonds       : angle       7.20449 (  306)
  SS BOND              : bond        0.04303 (    4)
  SS BOND              : angle       1.54531 (    8)
  covalent geometry    : bond        0.00805 ( 4412)
  covalent geometry    : angle       1.48187 ( 5996)

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

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

  1064 Ramachandran restraints generated.
    532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1064 Ramachandran restraints generated.
    532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  175 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 151
  time to evaluate  : 0.472 
Fit side-chains
REVERT: A  178 LYS cc_start: 0.8086 (pttt) cc_final: 0.7376 (tttt)
REVERT: B  172 SER cc_start: 0.8563 (t) cc_final: 0.8212 (m)
REVERT: B  178 LYS cc_start: 0.8070 (pttt) cc_final: 0.7326 (tttt)
REVERT: B  207 MET cc_start: 0.8322 (mtt) cc_final: 0.8079 (mtm)
REVERT: C  145 ASN cc_start: 0.7983 (m-40) cc_final: 0.7709 (m-40)
REVERT: C  178 LYS cc_start: 0.8235 (pttt) cc_final: 0.7533 (tttt)
REVERT: C  247 ARG cc_start: 0.8300 (ttp80) cc_final: 0.6725 (ttp80)
REVERT: D  172 SER cc_start: 0.8571 (t) cc_final: 0.8214 (m)
REVERT: D  178 LYS cc_start: 0.8213 (pttt) cc_final: 0.7463 (tttt)
  outliers start: 24
  outliers final: 0
  residues processed: 159
  average time/residue: 1.1038
  time to fit residues: 181.7480
Evaluate side-chains
  104 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 104
  time to evaluate  : 0.536 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 43 optimal weight:    3.9990
   chunk 39 optimal weight:    4.9990
   chunk 21 optimal weight:    7.9990
   chunk 13 optimal weight:    2.9990
   chunk 26 optimal weight:    0.0370
   chunk 40 optimal weight:    2.9990
   chunk 15 optimal weight:   10.0000
   chunk 24 optimal weight:    5.9990
   chunk 30 optimal weight:    2.9990
   chunk 47 optimal weight:    7.9990
   chunk 14 optimal weight:    1.9990
   overall best weight:    2.2066

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

Flipped N/Q/H residues before XYZ refinement:
A 138 GLN
A 145 ASN
A 151 ASN
A 170 GLN
A 182 ASN
A 242 GLN
B 145 ASN
B 151 ASN
B 156 ASN
B 170 GLN
B 182 ASN
B 239 HIS
B 242 GLN
C 151 ASN
C 170 GLN
C 182 ASN
C 242 GLN
D 151 ASN
D 170 GLN
D 182 ASN
D 239 HIS
D 242 GLN

Total number of N/Q/H flips: 22

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4275 r_free = 0.4275 target = 0.137180 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4119 r_free = 0.4119 target = 0.121569 restraints weight = 5069.158|
|-----------------------------------------------------------------------------|
r_work (start): 0.4130 rms_B_bonded: 1.75
r_work: 0.4002 rms_B_bonded: 2.04 restraints_weight: 0.5000
r_work: 0.3888 rms_B_bonded: 3.53 restraints_weight: 0.2500
r_work (final): 0.3888
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8427
moved from start:          0.2728

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.026   4416  Z= 0.167
  Angle     :  0.668   7.196   6004  Z= 0.369
  Chirality :  0.053   0.142    720
  Planarity :  0.003   0.028    744
  Dihedral  :  6.488  20.787    596
  Min Nonbonded Distance : 2.572

Molprobity Statistics.
  All-atom Clashscore : 8.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.95 %
    Favored  : 96.05 %
  Rotamer:
    Outliers :  2.58 %
    Allowed  : 17.26 %
    Favored  : 80.16 %
  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: -3.36 (0.30), residues: 532
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.55 (0.23), residues: 532

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.009   0.002   HIS C 239 
 PHE   0.012   0.002   PHE B 213 
 TYR   0.022   0.002   TYR C 143 
 ARG   0.001   0.000   ARG D 247 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03164 (  102)
  hydrogen bonds       : angle       5.41662 (  306)
  SS BOND              : bond        0.00408 (    4)
  SS BOND              : angle       0.78810 (    8)
  covalent geometry    : bond        0.00384 ( 4412)
  covalent geometry    : angle       0.66768 ( 5996)

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

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

  1064 Ramachandran restraints generated.
    532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1064 Ramachandran restraints generated.
    532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 117
  time to evaluate  : 0.560 
Fit side-chains
REVERT: A  178 LYS cc_start: 0.7644 (pttt) cc_final: 0.6907 (ttmt)
REVERT: A  207 MET cc_start: 0.8207 (mtp) cc_final: 0.7812 (mtt)
REVERT: B  129 LYS cc_start: 0.7862 (pttt) cc_final: 0.7591 (pttp)
REVERT: B  178 LYS cc_start: 0.7709 (pttt) cc_final: 0.6984 (ttpt)
REVERT: C  178 LYS cc_start: 0.7828 (pttt) cc_final: 0.7013 (ttmt)
REVERT: C  207 MET cc_start: 0.8486 (mtp) cc_final: 0.8133 (mtt)
REVERT: D  172 SER cc_start: 0.8626 (t) cc_final: 0.8263 (m)
REVERT: D  178 LYS cc_start: 0.7853 (pttt) cc_final: 0.7250 (tttt)
  outliers start: 13
  outliers final: 4
  residues processed: 125
  average time/residue: 1.3725
  time to fit residues: 176.6699
Evaluate side-chains
  103 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 99
  time to evaluate  : 0.481 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  153 THR
Chi-restraints excluded: chain B residue  153 THR
Chi-restraints excluded: chain C residue  153 THR
Chi-restraints excluded: chain C residue  185 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 1 optimal weight:    9.9990
   chunk 35 optimal weight:    7.9990
   chunk 24 optimal weight:    8.9990
   chunk 26 optimal weight:    0.7980
   chunk 13 optimal weight:    6.9990
   chunk 19 optimal weight:   10.0000
   chunk 22 optimal weight:    7.9990
   chunk 23 optimal weight:    8.9990
   chunk 25 optimal weight:    0.9980
   chunk 43 optimal weight:    0.0270
   chunk 32 optimal weight:    5.9990
   overall best weight:    2.9642

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

Flipped N/Q/H residues before XYZ refinement:
A 138 GLN
A 145 ASN
A 151 ASN
B 138 GLN
B 151 ASN
C 168 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4226 r_free = 0.4226 target = 0.132452 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4078 r_free = 0.4078 target = 0.117055 restraints weight = 5179.254|
|-----------------------------------------------------------------------------|
r_work (start): 0.4082 rms_B_bonded: 1.70
r_work: 0.3954 rms_B_bonded: 1.99 restraints_weight: 0.5000
r_work: 0.3843 rms_B_bonded: 3.47 restraints_weight: 0.2500
r_work (final): 0.3843
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8465
moved from start:          0.3097

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.029   4416  Z= 0.203
  Angle     :  0.700   7.886   6004  Z= 0.379
  Chirality :  0.054   0.138    720
  Planarity :  0.003   0.026    744
  Dihedral  :  6.306  19.328    596
  Min Nonbonded Distance : 2.570

Molprobity Statistics.
  All-atom Clashscore : 9.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.76 %
    Favored  : 96.24 %
  Rotamer:
    Outliers :  4.17 %
    Allowed  : 17.86 %
    Favored  : 77.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -3.31 (0.30), residues: 532
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.51 (0.23), residues: 532

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.008   0.002   HIS C 239 
 PHE   0.023   0.002   PHE D 213 
 TYR   0.023   0.003   TYR A 248 
 ARG   0.002   0.001   ARG A 247 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02908 (  102)
  hydrogen bonds       : angle       5.14671 (  306)
  SS BOND              : bond        0.00533 (    4)
  SS BOND              : angle       0.78819 (    8)
  covalent geometry    : bond        0.00468 ( 4412)
  covalent geometry    : angle       0.69983 ( 5996)

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

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

  1064 Ramachandran restraints generated.
    532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1064 Ramachandran restraints generated.
    532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 106
  time to evaluate  : 0.530 
Fit side-chains
REVERT: A  124 LYS cc_start: 0.8636 (ptpp) cc_final: 0.8387 (ptpp)
REVERT: A  136 ASP cc_start: 0.8859 (p0) cc_final: 0.8528 (p0)
REVERT: A  145 ASN cc_start: 0.7994 (OUTLIER) cc_final: 0.7732 (m110)
REVERT: A  178 LYS cc_start: 0.7729 (pttt) cc_final: 0.7071 (tttt)
REVERT: A  192 MET cc_start: 0.7681 (mpp) cc_final: 0.7278 (mtp)
REVERT: A  207 MET cc_start: 0.8247 (mtp) cc_final: 0.7864 (mtt)
REVERT: B  122 ASP cc_start: 0.8813 (t70) cc_final: 0.8586 (t0)
REVERT: B  129 LYS cc_start: 0.7850 (OUTLIER) cc_final: 0.7586 (pttp)
REVERT: B  178 LYS cc_start: 0.7713 (pttt) cc_final: 0.7046 (tttt)
REVERT: C  178 LYS cc_start: 0.7918 (pttt) cc_final: 0.7080 (tttt)
REVERT: C  180 ARG cc_start: 0.7692 (mtp180) cc_final: 0.6763 (mtt180)
REVERT: C  207 MET cc_start: 0.8555 (mtp) cc_final: 0.8224 (mtt)
REVERT: C  246 GLU cc_start: 0.8674 (OUTLIER) cc_final: 0.7672 (pt0)
REVERT: D  172 SER cc_start: 0.8610 (t) cc_final: 0.8213 (m)
REVERT: D  178 LYS cc_start: 0.7867 (pttt) cc_final: 0.7255 (tttt)
REVERT: D  213 PHE cc_start: 0.8238 (t80) cc_final: 0.7860 (t80)
  outliers start: 21
  outliers final: 7
  residues processed: 124
  average time/residue: 1.3529
  time to fit residues: 172.7145
Evaluate side-chains
  105 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 95
  time to evaluate  : 0.511 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  145 ASN
Chi-restraints excluded: chain A residue  153 THR
Chi-restraints excluded: chain A residue  185 SER
Chi-restraints excluded: chain B residue  129 LYS
Chi-restraints excluded: chain B residue  149 THR
Chi-restraints excluded: chain B residue  253 CYS
Chi-restraints excluded: chain C residue  153 THR
Chi-restraints excluded: chain C residue  185 SER
Chi-restraints excluded: chain C residue  246 GLU
Chi-restraints excluded: chain D residue  149 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 24 optimal weight:    8.9990
   chunk 44 optimal weight:    5.9990
   chunk 42 optimal weight:    4.9990
   chunk 5 optimal weight:   10.0000
   chunk 36 optimal weight:    1.9990
   chunk 8 optimal weight:    9.9990
   chunk 35 optimal weight:    1.9990
   chunk 25 optimal weight:    0.9980
   chunk 27 optimal weight:    0.0020
   chunk 41 optimal weight:    0.1980
   chunk 19 optimal weight:    8.9990
   overall best weight:    1.0392

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

Flipped N/Q/H residues before XYZ refinement:
A 138 GLN
A 145 ASN
A 151 ASN
B 138 GLN
D 229 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4306 r_free = 0.4306 target = 0.139217 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4161 r_free = 0.4161 target = 0.124007 restraints weight = 5074.984|
|-----------------------------------------------------------------------------|
r_work (start): 0.4177 rms_B_bonded: 1.72
r_work: 0.4091 rms_B_bonded: 1.94 restraints_weight: 0.5000
r_work: 0.3993 rms_B_bonded: 3.35 restraints_weight: 0.2500
r_work (final): 0.3993
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8384
moved from start:          0.3501

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.016   4416  Z= 0.104
  Angle     :  0.602   8.276   6004  Z= 0.320
  Chirality :  0.051   0.130    720
  Planarity :  0.002   0.021    744
  Dihedral  :  5.626  18.313    596
  Min Nonbonded Distance : 2.555

Molprobity Statistics.
  All-atom Clashscore : 7.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.82 %
    Favored  : 97.18 %
  Rotamer:
    Outliers :  2.58 %
    Allowed  : 19.05 %
    Favored  : 78.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.11 (0.31), residues: 532
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.36 (0.24), residues: 532

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.007   0.002   HIS C 239 
 PHE   0.018   0.002   PHE D 213 
 TYR   0.017   0.002   TYR A 125 
 ARG   0.003   0.000   ARG A 247 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02270 (  102)
  hydrogen bonds       : angle       5.03265 (  306)
  SS BOND              : bond        0.00303 (    4)
  SS BOND              : angle       0.34577 (    8)
  covalent geometry    : bond        0.00230 ( 4412)
  covalent geometry    : angle       0.60247 ( 5996)

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

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

  1064 Ramachandran restraints generated.
    532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1064 Ramachandran restraints generated.
    532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 111
  time to evaluate  : 0.505 
Fit side-chains
   revert: symmetry clash
REVERT: A  149 THR cc_start: 0.8668 (OUTLIER) cc_final: 0.8460 (p)
REVERT: A  178 LYS cc_start: 0.7667 (pttt) cc_final: 0.7053 (ttmt)
REVERT: A  207 MET cc_start: 0.8145 (mtp) cc_final: 0.7770 (mtt)
REVERT: B  172 SER cc_start: 0.8599 (t) cc_final: 0.8150 (m)
REVERT: B  178 LYS cc_start: 0.7669 (pttt) cc_final: 0.7056 (tttt)
REVERT: C  178 LYS cc_start: 0.7779 (pttt) cc_final: 0.6934 (tttt)
REVERT: C  246 GLU cc_start: 0.8537 (OUTLIER) cc_final: 0.7534 (pt0)
REVERT: D  172 SER cc_start: 0.8598 (t) cc_final: 0.8233 (m)
REVERT: D  178 LYS cc_start: 0.7891 (pttt) cc_final: 0.7297 (tttt)
REVERT: D  213 PHE cc_start: 0.8141 (t80) cc_final: 0.7731 (t80)
  outliers start: 13
  outliers final: 4
  residues processed: 121
  average time/residue: 1.3377
  time to fit residues: 166.8567
Evaluate side-chains
  105 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 99
  time to evaluate  : 0.510 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  149 THR
Chi-restraints excluded: chain A residue  153 THR
Chi-restraints excluded: chain C residue  153 THR
Chi-restraints excluded: chain C residue  185 SER
Chi-restraints excluded: chain C residue  246 GLU
Chi-restraints excluded: chain D residue  253 CYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 9 optimal weight:    5.9990
   chunk 51 optimal weight:    2.9990
   chunk 48 optimal weight:    5.9990
   chunk 3 optimal weight:    2.9990
   chunk 18 optimal weight:    9.9990
   chunk 39 optimal weight:    0.7980
   chunk 21 optimal weight:    5.9990
   chunk 35 optimal weight:    0.9990
   chunk 14 optimal weight:   10.0000
   chunk 46 optimal weight:    8.9990
   chunk 42 optimal weight:    7.9990
   overall best weight:    2.7588

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

Flipped N/Q/H residues before XYZ refinement:
A 138 GLN
A 151 ASN
B 138 GLN
C 168 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4230 r_free = 0.4230 target = 0.131332 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4075 r_free = 0.4075 target = 0.115910 restraints weight = 5274.221|
|-----------------------------------------------------------------------------|
r_work (start): 0.4079 rms_B_bonded: 1.76
r_work: 0.3992 rms_B_bonded: 1.94 restraints_weight: 0.5000
r_work: 0.3890 rms_B_bonded: 3.36 restraints_weight: 0.2500
r_work (final): 0.3890
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8449
moved from start:          0.3359

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.026   4416  Z= 0.193
  Angle     :  0.684   7.550   6004  Z= 0.367
  Chirality :  0.053   0.129    720
  Planarity :  0.003   0.021    744
  Dihedral  :  5.935  18.636    596
  Min Nonbonded Distance : 2.533

Molprobity Statistics.
  All-atom Clashscore : 8.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.76 %
    Favored  : 96.24 %
  Rotamer:
    Outliers :  3.77 %
    Allowed  : 19.64 %
    Favored  : 76.59 %
  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: -3.09 (0.31), residues: 532
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.35 (0.23), residues: 532

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.007   0.002   HIS C 239 
 PHE   0.019   0.002   PHE D 213 
 TYR   0.024   0.003   TYR A 248 
 ARG   0.002   0.000   ARG A 247 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02596 (  102)
  hydrogen bonds       : angle       4.96212 (  306)
  SS BOND              : bond        0.00376 (    4)
  SS BOND              : angle       0.49922 (    8)
  covalent geometry    : bond        0.00443 ( 4412)
  covalent geometry    : angle       0.68457 ( 5996)

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

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

  1064 Ramachandran restraints generated.
    532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1064 Ramachandran restraints generated.
    532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 102
  time to evaluate  : 0.471 
Fit side-chains
   revert: symmetry clash
REVERT: A  178 LYS cc_start: 0.7790 (pttt) cc_final: 0.7203 (tttt)
REVERT: A  192 MET cc_start: 0.7858 (mpp) cc_final: 0.7445 (mtp)
REVERT: A  207 MET cc_start: 0.8263 (mtp) cc_final: 0.7885 (mtt)
REVERT: B  122 ASP cc_start: 0.8769 (t70) cc_final: 0.8544 (t0)
REVERT: B  178 LYS cc_start: 0.7702 (pttt) cc_final: 0.7185 (tttt)
REVERT: B  183 ASN cc_start: 0.7999 (OUTLIER) cc_final: 0.7780 (m-40)
REVERT: C  138 GLN cc_start: 0.8762 (mt0) cc_final: 0.8521 (mt0)
REVERT: C  178 LYS cc_start: 0.7906 (pttt) cc_final: 0.7175 (tttt)
REVERT: C  180 ARG cc_start: 0.7639 (mtp180) cc_final: 0.6957 (mtt-85)
REVERT: C  246 GLU cc_start: 0.8705 (OUTLIER) cc_final: 0.7715 (pt0)
REVERT: D  172 SER cc_start: 0.8661 (t) cc_final: 0.8258 (m)
REVERT: D  178 LYS cc_start: 0.7883 (pttt) cc_final: 0.7305 (tttt)
REVERT: D  207 MET cc_start: 0.8533 (mtt) cc_final: 0.8316 (mtp)
REVERT: D  213 PHE cc_start: 0.8445 (t80) cc_final: 0.8134 (t80)
  outliers start: 19
  outliers final: 10
  residues processed: 118
  average time/residue: 1.3685
  time to fit residues: 166.3499
Evaluate side-chains
  107 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 95
  time to evaluate  : 0.506 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  134 SER
Chi-restraints excluded: chain A residue  149 THR
Chi-restraints excluded: chain A residue  153 THR
Chi-restraints excluded: chain A residue  253 CYS
Chi-restraints excluded: chain B residue  149 THR
Chi-restraints excluded: chain B residue  183 ASN
Chi-restraints excluded: chain B residue  253 CYS
Chi-restraints excluded: chain C residue  153 THR
Chi-restraints excluded: chain C residue  185 SER
Chi-restraints excluded: chain C residue  246 GLU
Chi-restraints excluded: chain D residue  149 THR
Chi-restraints excluded: chain D residue  253 CYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 29 optimal weight:    3.9990
   chunk 6 optimal weight:    9.9990
   chunk 40 optimal weight:    8.9990
   chunk 13 optimal weight:    4.9990
   chunk 17 optimal weight:    9.9990
   chunk 24 optimal weight:    3.9990
   chunk 1 optimal weight:   10.0000
   chunk 21 optimal weight:    9.9990
   chunk 38 optimal weight:    3.9990
   chunk 19 optimal weight:    2.9990
   chunk 34 optimal weight:    9.9990
   overall best weight:    3.9990

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

Flipped N/Q/H residues before XYZ refinement:
A 138 GLN
A 151 ASN
B 138 GLN
D 229 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4084 r_free = 0.4084 target = 0.114073 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3912 r_free = 0.3912 target = 0.098392 restraints weight = 5634.743|
|-----------------------------------------------------------------------------|
r_work (start): 0.3923 rms_B_bonded: 1.73
r_work: 0.3824 rms_B_bonded: 1.97 restraints_weight: 0.5000
r_work: 0.3728 rms_B_bonded: 3.32 restraints_weight: 0.2500
r_work (final): 0.3728
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8473
moved from start:          0.3353

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.032   4416  Z= 0.260
  Angle     :  0.738   7.640   6004  Z= 0.396
  Chirality :  0.055   0.131    720
  Planarity :  0.003   0.020    744
  Dihedral  :  6.176  19.201    596
  Min Nonbonded Distance : 2.519

Molprobity Statistics.
  All-atom Clashscore : 10.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.76 %
    Favored  : 96.24 %
  Rotamer:
    Outliers :  3.97 %
    Allowed  : 19.84 %
    Favored  : 76.19 %
  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: -3.12 (0.30), residues: 532
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.37 (0.23), residues: 532

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.007   0.002   HIS C 239 
 PHE   0.020   0.002   PHE D 213 
 TYR   0.029   0.003   TYR A 248 
 ARG   0.002   0.000   ARG D 180 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02858 (  102)
  hydrogen bonds       : angle       5.00212 (  306)
  SS BOND              : bond        0.00366 (    4)
  SS BOND              : angle       0.54637 (    8)
  covalent geometry    : bond        0.00596 ( 4412)
  covalent geometry    : angle       0.73817 ( 5996)

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

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

  1064 Ramachandran restraints generated.
    532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1064 Ramachandran restraints generated.
    532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 101
  time to evaluate  : 0.460 
Fit side-chains
   revert: symmetry clash
REVERT: A  178 LYS cc_start: 0.7839 (pttt) cc_final: 0.7206 (tttt)
REVERT: A  192 MET cc_start: 0.8017 (mpp) cc_final: 0.7599 (mtp)
REVERT: A  207 MET cc_start: 0.8341 (mtp) cc_final: 0.7967 (mtt)
REVERT: B  122 ASP cc_start: 0.8810 (t70) cc_final: 0.8584 (t0)
REVERT: B  178 LYS cc_start: 0.7672 (pttt) cc_final: 0.7117 (ttmt)
REVERT: B  183 ASN cc_start: 0.7968 (OUTLIER) cc_final: 0.7739 (m-40)
REVERT: C  178 LYS cc_start: 0.7886 (pttt) cc_final: 0.7129 (tttt)
REVERT: C  180 ARG cc_start: 0.7603 (mtp180) cc_final: 0.6873 (mtt-85)
REVERT: C  206 GLU cc_start: 0.7765 (mt-10) cc_final: 0.7563 (tt0)
REVERT: D  178 LYS cc_start: 0.7877 (pttt) cc_final: 0.7266 (tttt)
REVERT: D  213 PHE cc_start: 0.8469 (t80) cc_final: 0.8200 (t80)
  outliers start: 20
  outliers final: 12
  residues processed: 119
  average time/residue: 1.3069
  time to fit residues: 160.3710
Evaluate side-chains
  110 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 97
  time to evaluate  : 0.490 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  149 THR
Chi-restraints excluded: chain A residue  153 THR
Chi-restraints excluded: chain A residue  185 SER
Chi-restraints excluded: chain A residue  253 CYS
Chi-restraints excluded: chain B residue  149 THR
Chi-restraints excluded: chain B residue  183 ASN
Chi-restraints excluded: chain B residue  253 CYS
Chi-restraints excluded: chain C residue  136 ASP
Chi-restraints excluded: chain C residue  153 THR
Chi-restraints excluded: chain C residue  185 SER
Chi-restraints excluded: chain C residue  253 CYS
Chi-restraints excluded: chain D residue  149 THR
Chi-restraints excluded: chain D residue  253 CYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 34 optimal weight:    7.9990
   chunk 45 optimal weight:    9.9990
   chunk 48 optimal weight:    0.9990
   chunk 12 optimal weight:    6.9990
   chunk 31 optimal weight:   10.0000
   chunk 14 optimal weight:   10.0000
   chunk 9 optimal weight:    5.9990
   chunk 6 optimal weight:    9.9990
   chunk 3 optimal weight:    1.9990
   chunk 4 optimal weight:    5.9990
   chunk 13 optimal weight:    0.9980
   overall best weight:    3.1988

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

Flipped N/Q/H residues before XYZ refinement:
A 138 GLN
A 151 ASN
B 138 GLN
C 138 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4210 r_free = 0.4210 target = 0.129452 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4052 r_free = 0.4052 target = 0.114016 restraints weight = 5258.977|
|-----------------------------------------------------------------------------|
r_work (start): 0.4065 rms_B_bonded: 1.75
r_work: 0.3977 rms_B_bonded: 1.93 restraints_weight: 0.5000
r_work: 0.3875 rms_B_bonded: 3.35 restraints_weight: 0.2500
r_work (final): 0.3875
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8463
moved from start:          0.3423

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.038   4416  Z= 0.219
  Angle     :  0.722   7.850   6004  Z= 0.384
  Chirality :  0.054   0.129    720
  Planarity :  0.003   0.017    744
  Dihedral  :  6.047  18.771    596
  Min Nonbonded Distance : 2.517

Molprobity Statistics.
  All-atom Clashscore : 10.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.57 %
    Favored  : 96.43 %
  Rotamer:
    Outliers :  3.57 %
    Allowed  : 20.83 %
    Favored  : 75.60 %
  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: -3.13 (0.30), residues: 532
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.37 (0.23), residues: 532

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.007   0.002   HIS C 239 
 PHE   0.019   0.002   PHE D 213 
 TYR   0.025   0.003   TYR A 248 
 ARG   0.002   0.000   ARG D 180 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02730 (  102)
  hydrogen bonds       : angle       4.98559 (  306)
  SS BOND              : bond        0.00267 (    4)
  SS BOND              : angle       0.35276 (    8)
  covalent geometry    : bond        0.00505 ( 4412)
  covalent geometry    : angle       0.72281 ( 5996)

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

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

  1064 Ramachandran restraints generated.
    532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1064 Ramachandran restraints generated.
    532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 102
  time to evaluate  : 0.525 
Fit side-chains
   revert: symmetry clash
REVERT: A  145 ASN cc_start: 0.7761 (OUTLIER) cc_final: 0.7524 (m-40)
REVERT: A  178 LYS cc_start: 0.7796 (pttt) cc_final: 0.7151 (tttt)
REVERT: A  192 MET cc_start: 0.7856 (mpp) cc_final: 0.7353 (mtp)
REVERT: A  247 ARG cc_start: 0.8365 (ttm-80) cc_final: 0.8156 (ttm-80)
REVERT: B  122 ASP cc_start: 0.8794 (t70) cc_final: 0.8554 (t0)
REVERT: B  178 LYS cc_start: 0.7670 (pttt) cc_final: 0.7079 (ttmt)
REVERT: B  183 ASN cc_start: 0.7987 (OUTLIER) cc_final: 0.7776 (m-40)
REVERT: C  178 LYS cc_start: 0.7820 (pttt) cc_final: 0.7065 (tttt)
REVERT: C  180 ARG cc_start: 0.7647 (mtp180) cc_final: 0.6931 (mtt-85)
REVERT: C  206 GLU cc_start: 0.7695 (mt-10) cc_final: 0.7481 (tt0)
REVERT: D  178 LYS cc_start: 0.7902 (pttt) cc_final: 0.7269 (tttt)
REVERT: D  213 PHE cc_start: 0.8488 (t80) cc_final: 0.8186 (t80)
  outliers start: 18
  outliers final: 15
  residues processed: 118
  average time/residue: 1.4856
  time to fit residues: 180.2391
Evaluate side-chains
  113 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 96
  time to evaluate  : 0.520 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  134 SER
Chi-restraints excluded: chain A residue  145 ASN
Chi-restraints excluded: chain A residue  149 THR
Chi-restraints excluded: chain A residue  153 THR
Chi-restraints excluded: chain A residue  185 SER
Chi-restraints excluded: chain A residue  253 CYS
Chi-restraints excluded: chain B residue  136 ASP
Chi-restraints excluded: chain B residue  149 THR
Chi-restraints excluded: chain B residue  183 ASN
Chi-restraints excluded: chain B residue  208 SER
Chi-restraints excluded: chain B residue  253 CYS
Chi-restraints excluded: chain C residue  136 ASP
Chi-restraints excluded: chain C residue  153 THR
Chi-restraints excluded: chain C residue  185 SER
Chi-restraints excluded: chain C residue  253 CYS
Chi-restraints excluded: chain D residue  149 THR
Chi-restraints excluded: chain D residue  253 CYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 6 optimal weight:    9.9990
   chunk 29 optimal weight:    6.9990
   chunk 35 optimal weight:    0.5980
   chunk 2 optimal weight:    8.9990
   chunk 24 optimal weight:   10.0000
   chunk 27 optimal weight:    0.9980
   chunk 49 optimal weight:    7.9990
   chunk 17 optimal weight:    7.9990
   chunk 42 optimal weight:    3.9990
   chunk 19 optimal weight:    4.9990
   chunk 30 optimal weight:    0.6980
   overall best weight:    2.2584

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

Flipped N/Q/H residues before XYZ refinement:
A 138 GLN
A 151 ASN
B 138 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4236 r_free = 0.4236 target = 0.131927 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.4083 r_free = 0.4083 target = 0.116646 restraints weight = 5177.759|
|-----------------------------------------------------------------------------|
r_work (start): 0.4099 rms_B_bonded: 1.73
r_work: 0.4012 rms_B_bonded: 1.91 restraints_weight: 0.5000
r_work: 0.3912 rms_B_bonded: 3.32 restraints_weight: 0.2500
r_work (final): 0.3912
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8444
moved from start:          0.3531

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   4416  Z= 0.168
  Angle     :  0.691   8.055   6004  Z= 0.365
  Chirality :  0.053   0.129    720
  Planarity :  0.002   0.020    744
  Dihedral  :  5.865  18.211    596
  Min Nonbonded Distance : 2.515

Molprobity Statistics.
  All-atom Clashscore : 9.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.76 %
    Favored  : 96.24 %
  Rotamer:
    Outliers :  3.57 %
    Allowed  : 21.63 %
    Favored  : 74.80 %
  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: -3.12 (0.30), residues: 532
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.37 (0.23), residues: 532

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.007   0.002   HIS C 239 
 PHE   0.017   0.002   PHE D 213 
 TYR   0.020   0.002   TYR A 248 
 ARG   0.004   0.000   ARG D 247 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02559 (  102)
  hydrogen bonds       : angle       4.95283 (  306)
  SS BOND              : bond        0.00214 (    4)
  SS BOND              : angle       0.26715 (    8)
  covalent geometry    : bond        0.00387 ( 4412)
  covalent geometry    : angle       0.69092 ( 5996)

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

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

  1064 Ramachandran restraints generated.
    532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1064 Ramachandran restraints generated.
    532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 102
  time to evaluate  : 0.538 
Fit side-chains
   revert: symmetry clash
REVERT: A  178 LYS cc_start: 0.7803 (pttt) cc_final: 0.7154 (ttmt)
REVERT: A  192 MET cc_start: 0.7824 (mpp) cc_final: 0.7331 (mtp)
REVERT: A  207 MET cc_start: 0.8275 (mtp) cc_final: 0.7915 (mtt)
REVERT: B  122 ASP cc_start: 0.8780 (t70) cc_final: 0.8532 (t0)
REVERT: B  178 LYS cc_start: 0.7637 (pttt) cc_final: 0.7113 (ttmt)
REVERT: B  183 ASN cc_start: 0.7958 (OUTLIER) cc_final: 0.7718 (m-40)
REVERT: C  178 LYS cc_start: 0.7789 (pttt) cc_final: 0.7015 (tttt)
REVERT: C  180 ARG cc_start: 0.7644 (mtp180) cc_final: 0.6929 (mtt-85)
REVERT: C  206 GLU cc_start: 0.7689 (mt-10) cc_final: 0.7485 (tt0)
REVERT: D  178 LYS cc_start: 0.7913 (pttt) cc_final: 0.7296 (tttt)
REVERT: D  213 PHE cc_start: 0.8482 (t80) cc_final: 0.8192 (t80)
  outliers start: 18
  outliers final: 14
  residues processed: 119
  average time/residue: 1.2914
  time to fit residues: 158.5199
Evaluate side-chains
  114 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 99
  time to evaluate  : 0.482 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  134 SER
Chi-restraints excluded: chain A residue  149 THR
Chi-restraints excluded: chain A residue  153 THR
Chi-restraints excluded: chain A residue  185 SER
Chi-restraints excluded: chain A residue  253 CYS
Chi-restraints excluded: chain B residue  134 SER
Chi-restraints excluded: chain B residue  149 THR
Chi-restraints excluded: chain B residue  183 ASN
Chi-restraints excluded: chain B residue  208 SER
Chi-restraints excluded: chain B residue  253 CYS
Chi-restraints excluded: chain C residue  136 ASP
Chi-restraints excluded: chain C residue  153 THR
Chi-restraints excluded: chain C residue  185 SER
Chi-restraints excluded: chain D residue  149 THR
Chi-restraints excluded: chain D residue  253 CYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 1 optimal weight:   10.0000
   chunk 44 optimal weight:   10.0000
   chunk 15 optimal weight:    9.9990
   chunk 34 optimal weight:    8.9990
   chunk 48 optimal weight:    0.7980
   chunk 30 optimal weight:    9.9990
   chunk 49 optimal weight:    8.9990
   chunk 35 optimal weight:    4.9990
   chunk 4 optimal weight:    2.9990
   chunk 26 optimal weight:    0.9980
   chunk 31 optimal weight:    9.9990
   overall best weight:    3.7586

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

Flipped N/Q/H residues before XYZ refinement:
A 138 GLN
A 151 ASN
B 138 GLN
C 151 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4094 r_free = 0.4094 target = 0.114464 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3923 r_free = 0.3923 target = 0.098750 restraints weight = 5728.542|
|-----------------------------------------------------------------------------|
r_work (start): 0.3933 rms_B_bonded: 1.75
r_work: 0.3827 rms_B_bonded: 2.00 restraints_weight: 0.5000
r_work: 0.3728 rms_B_bonded: 3.37 restraints_weight: 0.2500
r_work (final): 0.3728
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8477
moved from start:          0.3473

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.045   4416  Z= 0.251
  Angle     :  0.753   8.056   6004  Z= 0.401
  Chirality :  0.055   0.132    720
  Planarity :  0.003   0.045    744
  Dihedral  :  6.106  18.391    596
  Min Nonbonded Distance : 2.508

Molprobity Statistics.
  All-atom Clashscore : 9.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.57 %
    Favored  : 96.43 %
  Rotamer:
    Outliers :  3.77 %
    Allowed  : 21.03 %
    Favored  : 75.20 %
  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: -3.16 (0.30), residues: 532
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.40 (0.23), residues: 532

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.006   0.002   HIS C 239 
 PHE   0.019   0.002   PHE D 213 
 TYR   0.027   0.003   TYR A 248 
 ARG   0.008   0.001   ARG D 247 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02829 (  102)
  hydrogen bonds       : angle       4.94569 (  306)
  SS BOND              : bond        0.00189 (    4)
  SS BOND              : angle       0.34304 (    8)
  covalent geometry    : bond        0.00579 ( 4412)
  covalent geometry    : angle       0.75316 ( 5996)

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

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

  1064 Ramachandran restraints generated.
    532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1064 Ramachandran restraints generated.
    532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 98
  time to evaluate  : 0.529 
Fit side-chains
   revert: symmetry clash
REVERT: A  178 LYS cc_start: 0.7778 (pttt) cc_final: 0.7073 (tttt)
REVERT: A  192 MET cc_start: 0.7978 (mpp) cc_final: 0.7419 (mtp)
REVERT: A  207 MET cc_start: 0.8349 (mtp) cc_final: 0.8006 (mtt)
REVERT: B  122 ASP cc_start: 0.8816 (t70) cc_final: 0.8587 (t0)
REVERT: B  178 LYS cc_start: 0.7609 (pttt) cc_final: 0.7069 (ttmt)
REVERT: B  183 ASN cc_start: 0.7983 (OUTLIER) cc_final: 0.7761 (m-40)
REVERT: C  178 LYS cc_start: 0.7788 (pttt) cc_final: 0.7035 (tttt)
REVERT: C  180 ARG cc_start: 0.7607 (mtp180) cc_final: 0.6888 (mtt-85)
REVERT: D  178 LYS cc_start: 0.7874 (pttt) cc_final: 0.7270 (tttt)
REVERT: D  213 PHE cc_start: 0.8520 (t80) cc_final: 0.8253 (t80)
  outliers start: 19
  outliers final: 16
  residues processed: 116
  average time/residue: 1.1961
  time to fit residues: 143.4394
Evaluate side-chains
  116 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 99
  time to evaluate  : 0.543 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  134 SER
Chi-restraints excluded: chain A residue  149 THR
Chi-restraints excluded: chain A residue  153 THR
Chi-restraints excluded: chain A residue  183 ASN
Chi-restraints excluded: chain A residue  185 SER
Chi-restraints excluded: chain A residue  253 CYS
Chi-restraints excluded: chain B residue  134 SER
Chi-restraints excluded: chain B residue  149 THR
Chi-restraints excluded: chain B residue  183 ASN
Chi-restraints excluded: chain B residue  208 SER
Chi-restraints excluded: chain B residue  253 CYS
Chi-restraints excluded: chain C residue  136 ASP
Chi-restraints excluded: chain C residue  153 THR
Chi-restraints excluded: chain C residue  185 SER
Chi-restraints excluded: chain C residue  253 CYS
Chi-restraints excluded: chain D residue  149 THR
Chi-restraints excluded: chain D residue  253 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 20 optimal weight:    3.9990
   chunk 8 optimal weight:   10.0000
   chunk 40 optimal weight:    7.9990
   chunk 25 optimal weight:    0.8980
   chunk 13 optimal weight:    4.9990
   chunk 48 optimal weight:    0.9990
   chunk 51 optimal weight:    3.9990
   chunk 17 optimal weight:    6.9990
   chunk 2 optimal weight:    6.9990
   chunk 31 optimal weight:    9.9990
   chunk 29 optimal weight:    3.9990
   overall best weight:    2.7788

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

Flipped N/Q/H residues before XYZ refinement:
A 138 GLN
A 151 ASN
B 138 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4220 r_free = 0.4220 target = 0.130309 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4065 r_free = 0.4065 target = 0.115131 restraints weight = 5170.338|
|-----------------------------------------------------------------------------|
r_work (start): 0.4076 rms_B_bonded: 1.74
r_work: 0.3990 rms_B_bonded: 1.91 restraints_weight: 0.5000
r_work: 0.3891 rms_B_bonded: 3.30 restraints_weight: 0.2500
r_work (final): 0.3891
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8458
moved from start:          0.3549

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.039   4416  Z= 0.197
  Angle     :  0.720   8.137   6004  Z= 0.381
  Chirality :  0.053   0.129    720
  Planarity :  0.003   0.043    744
  Dihedral  :  5.955  18.394    596
  Min Nonbonded Distance : 2.508

Molprobity Statistics.
  All-atom Clashscore : 9.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.57 %
    Favored  : 96.43 %
  Rotamer:
    Outliers :  3.77 %
    Allowed  : 21.23 %
    Favored  : 75.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.15 (0.30), residues: 532
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.39 (0.23), residues: 532

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.007   0.002   HIS C 239 
 PHE   0.017   0.002   PHE D 213 
 TYR   0.022   0.002   TYR A 248 
 ARG   0.008   0.001   ARG D 247 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02647 (  102)
  hydrogen bonds       : angle       4.94027 (  306)
  SS BOND              : bond        0.00156 (    4)
  SS BOND              : angle       0.33035 (    8)
  covalent geometry    : bond        0.00454 ( 4412)
  covalent geometry    : angle       0.71991 ( 5996)

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

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

  1064 Ramachandran restraints generated.
    532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1064 Ramachandran restraints generated.
    532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 103
  time to evaluate  : 0.479 
Fit side-chains
   revert: symmetry clash
REVERT: A  145 ASN cc_start: 0.7738 (OUTLIER) cc_final: 0.7483 (m-40)
REVERT: A  178 LYS cc_start: 0.7765 (pttt) cc_final: 0.7101 (tttt)
REVERT: A  192 MET cc_start: 0.7838 (mpp) cc_final: 0.7354 (mtp)
REVERT: A  207 MET cc_start: 0.8304 (mtp) cc_final: 0.7948 (mtt)
REVERT: B  122 ASP cc_start: 0.8804 (t70) cc_final: 0.8559 (t0)
REVERT: B  178 LYS cc_start: 0.7605 (pttt) cc_final: 0.7082 (ttmt)
REVERT: B  183 ASN cc_start: 0.7978 (OUTLIER) cc_final: 0.7751 (m-40)
REVERT: C  178 LYS cc_start: 0.7810 (pttt) cc_final: 0.7063 (tttt)
REVERT: C  180 ARG cc_start: 0.7628 (mtp180) cc_final: 0.6914 (mtt-85)
REVERT: D  178 LYS cc_start: 0.7899 (pttt) cc_final: 0.7280 (tttt)
REVERT: D  213 PHE cc_start: 0.8510 (t80) cc_final: 0.8215 (t80)
  outliers start: 19
  outliers final: 15
  residues processed: 120
  average time/residue: 1.2762
  time to fit residues: 158.0663
Evaluate side-chains
  117 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 100
  time to evaluate  : 0.504 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  134 SER
Chi-restraints excluded: chain A residue  145 ASN
Chi-restraints excluded: chain A residue  149 THR
Chi-restraints excluded: chain A residue  153 THR
Chi-restraints excluded: chain A residue  183 ASN
Chi-restraints excluded: chain A residue  185 SER
Chi-restraints excluded: chain A residue  253 CYS
Chi-restraints excluded: chain B residue  134 SER
Chi-restraints excluded: chain B residue  149 THR
Chi-restraints excluded: chain B residue  183 ASN
Chi-restraints excluded: chain B residue  208 SER
Chi-restraints excluded: chain B residue  253 CYS
Chi-restraints excluded: chain C residue  153 THR
Chi-restraints excluded: chain C residue  185 SER
Chi-restraints excluded: chain C residue  253 CYS
Chi-restraints excluded: chain D residue  149 THR
Chi-restraints excluded: chain D residue  253 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 14 optimal weight:   10.0000
   chunk 34 optimal weight:    0.9990
   chunk 21 optimal weight:   10.0000
   chunk 10 optimal weight:    7.9990
   chunk 41 optimal weight:    8.9990
   chunk 35 optimal weight:    2.9990
   chunk 51 optimal weight:    7.9990
   chunk 45 optimal weight:   10.0000
   chunk 22 optimal weight:    3.9990
   chunk 18 optimal weight:   10.0000
   chunk 25 optimal weight:    0.9980
   overall best weight:    3.3988

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

Flipped N/Q/H residues before XYZ refinement:
A 138 GLN
A 151 ASN
B 138 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4202 r_free = 0.4202 target = 0.129015 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4042 r_free = 0.4042 target = 0.113619 restraints weight = 5272.542|
|-----------------------------------------------------------------------------|
r_work (start): 0.4057 rms_B_bonded: 1.75
r_work: 0.3934 rms_B_bonded: 2.04 restraints_weight: 0.5000
r_work: 0.3821 rms_B_bonded: 3.55 restraints_weight: 0.2500
r_work (final): 0.3821
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8484
moved from start:          0.3514

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.043   4416  Z= 0.233
  Angle     :  0.760   9.026   6004  Z= 0.399
  Chirality :  0.054   0.131    720
  Planarity :  0.003   0.044    744
  Dihedral  :  6.054  18.482    596
  Min Nonbonded Distance : 2.499

Molprobity Statistics.
  All-atom Clashscore : 9.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.95 %
    Favored  : 96.05 %
  Rotamer:
    Outliers :  3.77 %
    Allowed  : 21.83 %
    Favored  : 74.40 %
  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: -3.18 (0.30), residues: 532
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.42 (0.23), residues: 532

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.006   0.002   HIS C 239 
 PHE   0.018   0.002   PHE D 213 
 TYR   0.026   0.003   TYR A 248 
 ARG   0.009   0.001   ARG D 247 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02783 (  102)
  hydrogen bonds       : angle       4.95557 (  306)
  SS BOND              : bond        0.00153 (    4)
  SS BOND              : angle       0.38532 (    8)
  covalent geometry    : bond        0.00537 ( 4412)
  covalent geometry    : angle       0.76004 ( 5996)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4617.19 seconds
wall clock time: 80 minutes 40.63 seconds (4840.63 seconds total)