Starting phenix.real_space_refine
on Mon Jun  9 00:32:26 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8f7s_28909/06_2025/8f7s_28909.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8f7s_28909/06_2025/8f7s_28909.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.0
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8f7s_28909/06_2025/8f7s_28909.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8f7s_28909/06_2025/8f7s_28909.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8f7s_28909/06_2025/8f7s_28909.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8f7s_28909/06_2025/8f7s_28909.cif"
  }
  resolution = 3.0
  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=   0.006
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      84      5.16       5
     C    6523      2.51       5
     N    1617      2.21       5
     O    1751      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 28 residue(s): 0.06s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib"
  Total number of atoms: 9975
  Number of models: 1
  Model: ""
    Number of chains: 14
    Chain: "R"
      Number of atoms: 2268
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 289, 2268
          Classifications: {'peptide': 289}
          Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 276}
    Chain: "P"
      Number of atoms: 12
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 12
          Classifications: {'peptide': 1}
    Chain: "P"
      Number of atoms: 43
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 6, 43
          Classifications: {'peptide': 6}
          Modifications used: {'PEPT-D': 1}
          Link IDs: {'TRANS': 5}
    Chain: "P"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {'NH2': 1}
          Classifications: {'undetermined': 1}
    Chain: "A"
      Number of atoms: 1783
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 221, 1783
          Classifications: {'peptide': 221}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 218}
          Chain breaks: 2
    Chain: "B"
      Number of atoms: 2601
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 338, 2601
          Classifications: {'peptide': 338}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 5, 'TRANS': 332}
    Chain: "C"
      Number of atoms: 438
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 57, 438
          Classifications: {'peptide': 57}
          Link IDs: {'PTRANS': 4, 'TRANS': 52}
    Chain: "D"
      Number of atoms: 2268
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 289, 2268
          Classifications: {'peptide': 289}
          Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 276}
    Chain: "Q"
      Number of atoms: 12
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 12
          Classifications: {'peptide': 1}
    Chain: "Q"
      Number of atoms: 43
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 6, 43
          Classifications: {'peptide': 6}
          Modifications used: {'PEPT-D': 1}
          Link IDs: {'TRANS': 5}
    Chain: "Q"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {'NH2': 1}
          Classifications: {'undetermined': 1}
    Chain: "F"
      Number of atoms: 149
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 19, 149
          Classifications: {'peptide': 19}
          Modifications used: {'COO': 1}
          Link IDs: {'TRANS': 18}
    Chain: "R"
      Number of atoms: 182
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 9, 182
          Unusual residues: {'CLR': 2, 'PLM': 7}
          Classifications: {'undetermined': 9}
          Link IDs: {None: 8}
    Chain: "D"
      Number of atoms: 174
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 8, 174
          Unusual residues: {'CLR': 3, 'PLM': 5}
          Classifications: {'undetermined': 8}
          Link IDs: {None: 7}
  Time building chain proxies: 6.63, per 1000 atoms: 0.66
  Number of scatterers: 9975
  At special positions: 0
  Unit cell: (143.64, 118.44, 105, 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      84     16.00
     O    1751      8.00
     N    1617      7.00
     C    6523      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS R 121 " - pdb=" SG  CYS R 198 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D 121 " - pdb=" SG  CYS D 198 " distance=2.03

  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=2, symmetry=0
  Links applied
    TRANS
      " DAL P   2 " - " TYR P   1 "
      " DAL Q   2 " - " TYR Q   1 "
  Number of additional bonds: simple=2, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 2.60
  Conformation dependent library (CDL) restraints added in 1.2 seconds
  

  2406 Ramachandran restraints generated.
    1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
    Skipped
      Input residue name is d-peptide
        pdb=" CB  DAL P   2 "
        pdb=" CB  DAL Q   2 "
  Number of C-beta restraints generated:  2332

  Finding SS restraints...
    Secondary structure from input PDB file:
      39 helices and 10 sheets defined
      59.3% alpha, 14.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.99
  Creating SS restraints...
    Processing helix  chain 'R' and resid 45 through 77
    Processing helix  chain 'R' and resid 82 through 100
    Processing helix  chain 'R' and resid 101 through 112
      removed outlier: 3.699A  pdb=" N   GLN R 105 " --> pdb=" O   THR R 101 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 117 through 152
    Processing helix  chain 'R' and resid 152 through 160
      removed outlier: 3.564A  pdb=" N   LEU R 157 " --> pdb=" O   PRO R 153 " (cutoff:3.500A)
      removed outlier: 4.178A  pdb=" N   ASP R 158 " --> pdb=" O   VAL R 154 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 161 through 186
      removed outlier: 3.750A  pdb=" N   SER R 177 " --> pdb=" O   TRP R 173 " (cutoff:3.500A)
      removed outlier: 3.906A  pdb=" N   GLY R 178 " --> pdb=" O   VAL R 174 " (cutoff:3.500A)
      removed outlier: 3.875A  pdb=" N   VAL R 179 " --> pdb=" O   LEU R 175 " (cutoff:3.500A)
      Proline residue:  R 182  - end of helix
    Processing helix  chain 'R' and resid 205 through 241
      removed outlier: 4.943A  pdb=" N   VAL R 224 " --> pdb=" O   PHE R 220 " (cutoff:3.500A)
      Proline residue:  R 225  - end of helix
      removed outlier: 3.715A  pdb=" N   ARG R 241 " --> pdb=" O   LEU R 237 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 242 through 247
      removed outlier: 6.084A  pdb=" N   LEU R 245 " --> pdb=" O   SER R 242 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 249 through 287
      removed outlier: 4.212A  pdb=" N   VAL R 266 " --> pdb=" O   MET R 262 " (cutoff:3.500A)
      removed outlier: 4.072A  pdb=" N   VAL R 267 " --> pdb=" O   VAL R 263 " (cutoff:3.500A)
      Proline residue:  R 276  - end of helix
    Processing helix  chain 'R' and resid 293 through 322
      removed outlier: 3.524A  pdb=" N   VAL R 297 " --> pdb=" O   ASP R 293 " (cutoff:3.500A)
      removed outlier: 3.789A  pdb=" N   ASN R 314 " --> pdb=" O   ASN R 310 " (cutoff:3.500A)
      Proline residue:  R 315  - end of helix
    Processing helix  chain 'R' and resid 322 through 333
    Processing helix  chain 'P' and resid 2 through 7
      removed outlier: 3.755A  pdb=" N   VAL P   6 " --> pdb=" O   DAL P   2 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 6 through 32
      removed outlier: 4.018A  pdb=" N   ARG A  32 " --> pdb=" O   GLU A  28 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 45 through 55
    Processing helix  chain 'A' and resid 207 through 212
      removed outlier: 4.292A  pdb=" N   TRP A 211 " --> pdb=" O   GLU A 207 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 213 through 217
      removed outlier: 4.384A  pdb=" N   GLY A 217 " --> pdb=" O   CYS A 214 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 228 through 231
      removed outlier: 3.628A  pdb=" N   ASP A 231 " --> pdb=" O   SER A 228 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 228 through 231'
    Processing helix  chain 'A' and resid 241 through 255
    Processing helix  chain 'A' and resid 256 through 260
      removed outlier: 3.840A  pdb=" N   THR A 260 " --> pdb=" O   LYS A 257 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 270 through 281
      removed outlier: 3.525A  pdb=" N   GLU A 276 " --> pdb=" O   ASP A 272 " (cutoff:3.500A)
      removed outlier: 3.799A  pdb=" N   LYS A 279 " --> pdb=" O   GLU A 275 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 295 through 309
      removed outlier: 3.555A  pdb=" N   CYS A 305 " --> pdb=" O   ALA A 301 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 330 through 352
    Processing helix  chain 'B' and resid 9 through 31
    Processing helix  chain 'B' and resid 34 through 39
    Processing helix  chain 'B' and resid 40 through 42
      No H-bonds generated for 'chain 'B' and resid 40 through 42'
    Processing helix  chain 'C' and resid 8 through 24
      removed outlier: 3.528A  pdb=" N   LYS C  14 " --> pdb=" O   ALA C  10 " (cutoff:3.500A)
      removed outlier: 3.593A  pdb=" N   GLU C  22 " --> pdb=" O   GLN C  18 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 29 through 44
      removed outlier: 3.540A  pdb=" N   ALA C  33 " --> pdb=" O   LYS C  29 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 46 through 77
    Processing helix  chain 'D' and resid 82 through 100
    Processing helix  chain 'D' and resid 101 through 112
      removed outlier: 3.706A  pdb=" N   GLN D 105 " --> pdb=" O   THR D 101 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 117 through 152
    Processing helix  chain 'D' and resid 152 through 160
      removed outlier: 3.539A  pdb=" N   LEU D 157 " --> pdb=" O   PRO D 153 " (cutoff:3.500A)
      removed outlier: 4.195A  pdb=" N   ASP D 158 " --> pdb=" O   VAL D 154 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 161 through 186
      removed outlier: 3.540A  pdb=" N   GLY D 178 " --> pdb=" O   VAL D 174 " (cutoff:3.500A)
      removed outlier: 3.595A  pdb=" N   VAL D 179 " --> pdb=" O   LEU D 175 " (cutoff:3.500A)
      Proline residue:  D 182  - end of helix
    Processing helix  chain 'D' and resid 205 through 241
      removed outlier: 4.893A  pdb=" N   VAL D 224 " --> pdb=" O   PHE D 220 " (cutoff:3.500A)
      Proline residue:  D 225  - end of helix
      removed outlier: 3.716A  pdb=" N   ARG D 241 " --> pdb=" O   LEU D 237 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 249 through 287
      removed outlier: 4.257A  pdb=" N   VAL D 266 " --> pdb=" O   MET D 262 " (cutoff:3.500A)
      removed outlier: 4.119A  pdb=" N   VAL D 267 " --> pdb=" O   VAL D 263 " (cutoff:3.500A)
      Proline residue:  D 276  - end of helix
    Processing helix  chain 'D' and resid 293 through 322
      removed outlier: 3.739A  pdb=" N   VAL D 297 " --> pdb=" O   ASP D 293 " (cutoff:3.500A)
      removed outlier: 4.077A  pdb=" N   ASN D 314 " --> pdb=" O   ASN D 310 " (cutoff:3.500A)
      Proline residue:  D 315  - end of helix
    Processing helix  chain 'D' and resid 322 through 333
      removed outlier: 3.617A  pdb=" N   PHE D 329 " --> pdb=" O   PHE D 325 " (cutoff:3.500A)
    Processing helix  chain 'Q' and resid 2 through 7
      removed outlier: 3.727A  pdb=" N   VAL Q   6 " --> pdb=" O   DAL Q   2 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 337 through 352
    Processing sheet with id=AA1, first strand: chain 'R' and resid 187 through 192
      removed outlier: 3.575A  pdb=" N   MET R 199 " --> pdb=" O   VAL R 188 " (cutoff:3.500A)
      removed outlier: 3.741A  pdb=" N   ARG R 190 " --> pdb=" O   VAL R 197 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 185 through 190
      removed outlier: 6.256A  pdb=" N   VAL A  34 " --> pdb=" O   LYS A 197 " (cutoff:3.500A)
      removed outlier: 7.665A  pdb=" N   PHE A 199 " --> pdb=" O   VAL A  34 " (cutoff:3.500A)
      removed outlier: 6.854A  pdb=" N   LEU A  36 " --> pdb=" O   PHE A 199 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 51 through 56
      removed outlier: 5.172A  pdb=" N   THR B  52 " --> pdb=" O   ASN B 345 " (cutoff:3.500A)
      removed outlier: 6.438A  pdb=" N   ASN B 345 " --> pdb=" O   THR B  52 " (cutoff:3.500A)
      removed outlier: 3.959A  pdb=" N   ARG B  54 " --> pdb=" O   ILE B 343 " (cutoff:3.500A)
      removed outlier: 3.558A  pdb=" N   LEU B 341 " --> pdb=" O   LEU B  56 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 63 through 68
      removed outlier: 3.624A  pdb=" N   ALA B  65 " --> pdb=" O   ALA B  78 " (cutoff:3.500A)
      removed outlier: 3.835A  pdb=" N   LYS B  83 " --> pdb=" O   SER B  79 " (cutoff:3.500A)
      removed outlier: 6.593A  pdb=" N   ASP B  88 " --> pdb=" O   LYS B  94 " (cutoff:3.500A)
      removed outlier: 6.027A  pdb=" N   LYS B  94 " --> pdb=" O   ASP B  88 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 107 through 110
      removed outlier: 6.225A  pdb=" N   ASN B 130 " --> pdb=" O   VAL B 140 " (cutoff:3.500A)
      removed outlier: 5.982A  pdb=" N   VAL B 140 " --> pdb=" O   ASN B 130 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 151 through 156
      removed outlier: 3.578A  pdb=" N   CYS B 153 " --> pdb=" O   SER B 165 " (cutoff:3.500A)
      removed outlier: 3.602A  pdb=" N   THR B 183 " --> pdb=" O   LEU B 173 " (cutoff:3.500A)
      removed outlier: 7.375A  pdb=" N   ASP B 175 " --> pdb=" O   GLN B 181 " (cutoff:3.500A)
      removed outlier: 6.433A  pdb=" N   GLN B 181 " --> pdb=" O   ASP B 175 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 192 through 197
      removed outlier: 7.096A  pdb=" N   GLY B 207 " --> pdb=" O   MET B 193 " (cutoff:3.500A)
      removed outlier: 4.635A  pdb=" N   LEU B 195 " --> pdb=" O   VAL B 205 " (cutoff:3.500A)
      removed outlier: 7.019A  pdb=" N   VAL B 205 " --> pdb=" O   LEU B 195 " (cutoff:3.500A)
      removed outlier: 5.873A  pdb=" N   LEU B 197 " --> pdb=" O   LEU B 203 " (cutoff:3.500A)
      removed outlier: 8.186A  pdb=" N   LEU B 203 " --> pdb=" O   LEU B 197 " (cutoff:3.500A)
      removed outlier: 3.933A  pdb=" N   GLN B 225 " --> pdb=" O   LEU B 215 " (cutoff:3.500A)
      removed outlier: 6.933A  pdb=" N   ASP B 217 " --> pdb=" O   CYS B 223 " (cutoff:3.500A)
      removed outlier: 6.464A  pdb=" N   CYS B 223 " --> pdb=" O   ASP B 217 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 234 through 239
      removed outlier: 3.770A  pdb=" N   MET B 267 " --> pdb=" O   LEU B 257 " (cutoff:3.500A)
      removed outlier: 6.213A  pdb=" N   ASP B 259 " --> pdb=" O   GLU B 265 " (cutoff:3.500A)
      removed outlier: 5.962A  pdb=" N   GLU B 265 " --> pdb=" O   ASP B 259 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 278 through 283
      removed outlier: 3.909A  pdb=" N   SER B 280 " --> pdb=" O   GLY B 293 " (cutoff:3.500A)
      removed outlier: 6.191A  pdb=" N   ASP B 303 " --> pdb=" O   ARG B 309 " (cutoff:3.500A)
      removed outlier: 6.200A  pdb=" N   ARG B 309 " --> pdb=" O   ASP B 303 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'D' and resid 187 through 192
      removed outlier: 3.534A  pdb=" N   MET D 199 " --> pdb=" O   VAL D 188 " (cutoff:3.500A)
      removed outlier: 3.625A  pdb=" N   ARG D 190 " --> pdb=" O   VAL D 197 " (cutoff:3.500A)

    617 hydrogen bonds defined for protein.
    1806 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.89

  Time building geometry restraints manager: 2.81 seconds

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

  Histogram of bond lengths:
        1.23 -     1.35: 3058
        1.35 -     1.46: 2175
        1.46 -     1.58: 4811
        1.58 -     1.70: 0
        1.70 -     1.82: 121
  Bond restraints: 10165
  Sorted by residual:
  bond pdb=" CA  ALA R 275 "
       pdb=" C   ALA R 275 "
    ideal  model  delta    sigma   weight residual
    1.521  1.544 -0.023 1.14e-02 7.69e+03 4.01e+00
  bond pdb=" C   ALA D 275 "
       pdb=" N   PRO D 276 "
    ideal  model  delta    sigma   weight residual
    1.336  1.359 -0.023 1.20e-02 6.94e+03 3.82e+00
  bond pdb=" C   VAL R 224 "
       pdb=" N   PRO R 225 "
    ideal  model  delta    sigma   weight residual
    1.335  1.361 -0.026 1.36e-02 5.41e+03 3.59e+00
  bond pdb=" C   ALA R 275 "
       pdb=" N   PRO R 276 "
    ideal  model  delta    sigma   weight residual
    1.335  1.361 -0.026 1.36e-02 5.41e+03 3.55e+00
  bond pdb=" N   GLU D 112 "
       pdb=" CA  GLU D 112 "
    ideal  model  delta    sigma   weight residual
    1.459  1.483 -0.024 1.32e-02 5.74e+03 3.41e+00
  ... (remaining 10160 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.60: 12882
        1.60 -     3.21: 696
        3.21 -     4.81: 116
        4.81 -     6.42: 36
        6.42 -     8.02: 11
  Bond angle restraints: 13741
  Sorted by residual:
  angle pdb=" N   LEU R 102 "
        pdb=" CA  LEU R 102 "
        pdb=" C   LEU R 102 "
      ideal   model   delta    sigma   weight residual
     113.16  118.79   -5.63 1.42e+00 4.96e-01 1.57e+01
  angle pdb=" N   LEU D 102 "
        pdb=" CA  LEU D 102 "
        pdb=" C   LEU D 102 "
      ideal   model   delta    sigma   weight residual
     113.16  118.74   -5.58 1.42e+00 4.96e-01 1.54e+01
  angle pdb=" C   ILE B  86 "
        pdb=" N   TRP B  87 "
        pdb=" CA  TRP B  87 "
      ideal   model   delta    sigma   weight residual
     121.32  129.21   -7.89 2.10e+00 2.27e-01 1.41e+01
  angle pdb=" N   GLU R 112 "
        pdb=" CA  GLU R 112 "
        pdb=" C   GLU R 112 "
      ideal   model   delta    sigma   weight residual
     113.56  108.52    5.04 1.39e+00 5.18e-01 1.32e+01
  angle pdb=" N   GLU D 112 "
        pdb=" CA  GLU D 112 "
        pdb=" C   GLU D 112 "
      ideal   model   delta    sigma   weight residual
     113.56  108.58    4.98 1.39e+00 5.18e-01 1.29e+01
  ... (remaining 13736 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    11.84: 5888
       11.84 -    23.68: 368
       23.68 -    35.52: 68
       35.52 -    47.36: 17
       47.36 -    59.20: 11
  Dihedral angle restraints: 6352
    sinusoidal: 2764
      harmonic: 3588
  Sorted by residual:
  dihedral pdb=" CA  THR B 254 "
           pdb=" C   THR B 254 "
           pdb=" N   CYS B 255 "
           pdb=" CA  CYS B 255 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.89   17.11     0      5.00e+00 4.00e-02 1.17e+01
  dihedral pdb=" CA  PHE B 156 "
           pdb=" C   PHE B 156 "
           pdb=" N   LEU B 157 "
           pdb=" CA  LEU B 157 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  164.95   15.05     0      5.00e+00 4.00e-02 9.06e+00
  dihedral pdb=" CA  TRP B 302 "
           pdb=" C   TRP B 302 "
           pdb=" N   ASP B 303 "
           pdb=" CA  ASP B 303 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  165.13   14.87     0      5.00e+00 4.00e-02 8.85e+00
  ... (remaining 6349 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.082: 1444
       0.082 -    0.164: 142
       0.164 -    0.246: 17
       0.246 -    0.328: 7
       0.328 -    0.410: 5
  Chirality restraints: 1615
  Sorted by residual:
  chirality pdb=" C14 CLR R 401 "
            pdb=" C13 CLR R 401 "
            pdb=" C15 CLR R 401 "
            pdb=" C8  CLR R 401 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.32   -2.73    0.41 2.00e-01 2.50e+01 4.21e+00
  chirality pdb=" C14 CLR D 403 "
            pdb=" C13 CLR D 403 "
            pdb=" C15 CLR D 403 "
            pdb=" C8  CLR D 403 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.32   -2.72    0.41 2.00e-01 2.50e+01 4.14e+00
  chirality pdb=" C14 CLR D 404 "
            pdb=" C13 CLR D 404 "
            pdb=" C15 CLR D 404 "
            pdb=" C8  CLR D 404 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.32   -2.71    0.40 2.00e-01 2.50e+01 3.94e+00
  ... (remaining 1612 not shown)

  Planarity restraints: 1658
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE B 240 "    0.043 5.00e-02 4.00e+02   6.45e-02 6.66e+00
        pdb=" N   PRO B 241 "   -0.112 5.00e-02 4.00e+02
        pdb=" CA  PRO B 241 "    0.033 5.00e-02 4.00e+02
        pdb=" CD  PRO B 241 "    0.036 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ARG R 190 "   -0.037 5.00e-02 4.00e+02   5.63e-02 5.08e+00
        pdb=" N   PRO R 191 "    0.097 5.00e-02 4.00e+02
        pdb=" CA  PRO R 191 "   -0.030 5.00e-02 4.00e+02
        pdb=" CD  PRO R 191 "   -0.031 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ARG D 190 "    0.037 5.00e-02 4.00e+02   5.62e-02 5.05e+00
        pdb=" N   PRO D 191 "   -0.097 5.00e-02 4.00e+02
        pdb=" CA  PRO D 191 "    0.029 5.00e-02 4.00e+02
        pdb=" CD  PRO D 191 "    0.031 5.00e-02 4.00e+02
  ... (remaining 1655 not shown)

  Histogram of nonbonded interaction distances:
        2.29 -     2.81: 2323
        2.81 -     3.33: 9046
        3.33 -     3.86: 15653
        3.86 -     4.38: 17783
        4.38 -     4.90: 32025
  Nonbonded interactions: 76830
  Sorted by model distance:
  nonbonded pdb=" OG1 THR R  99 "
            pdb=" OG  SER R 312 "
     model   vdw
     2.290 3.040
  nonbonded pdb=" OH  TYR R 208 "
            pdb=" O   LEU D 237 "
     model   vdw
     2.292 3.040
  nonbonded pdb=" O   LEU R 237 "
            pdb=" OH  TYR D 208 "
     model   vdw
     2.305 3.040
  nonbonded pdb=" OE2 GLU B 265 "
            pdb=" OG1 THR B 268 "
     model   vdw
     2.312 3.040
  nonbonded pdb=" OD1 ASP A 251 "
            pdb=" ND2 ASN A 255 "
     model   vdw
     2.342 3.120
  ... (remaining 76825 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'D' and (resid 45 through 333 or resid 406 through 408))
  selection = (chain 'R' and (resid 45 through 333 or resid 406 through 408))
}
ncs_group {
  reference = chain 'P'
  selection = chain 'Q'
}

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:             1.180
  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:          0.410
  Check model and map are aligned:         0.080
  Set scattering table:                    0.090
  Process input model:                     25.260
  Find NCS groups from input model:        0.290
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:13.610
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   40.980
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7453
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045  10171  Z= 0.245
  Angle     :  0.867   8.024  13751  Z= 0.473
  Chirality :  0.059   0.410   1615
  Planarity :  0.006   0.065   1656
  Dihedral  :  8.474  59.200   4008
  Min Nonbonded Distance : 2.290

Molprobity Statistics.
  All-atom Clashscore : 3.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.58 %
    Favored  : 98.42 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.38 %
    Favored  : 99.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.71 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.29 (0.22), residues: 1203
  helix:  1.68 (0.16), residues: 677
  sheet:  1.03 (0.42), residues: 158
  loop : -0.75 (0.29), residues: 368

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP R 209 
 HIS   0.006   0.001   HIS C  44 
 PHE   0.029   0.002   PHE R 325 
 TYR   0.027   0.002   TYR D  87 
 ARG   0.008   0.001   ARG R 160 

Details of bonding type rmsd
  link_TRANS           : bond        0.00089 (    2)
  link_TRANS           : angle       0.20726 (    6)
  hydrogen bonds       : bond        0.11512 (  617)
  hydrogen bonds       : angle       5.39072 ( 1806)
  SS BOND              : bond        0.00213 (    2)
  SS BOND              : angle       2.23709 (    4)
  covalent geometry    : bond        0.00412 (10165)
  covalent geometry    : angle       0.86680 (13741)
  Misc. bond           : bond        0.04063 (    2)

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

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

  2406 Ramachandran restraints generated.
    1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2406 Ramachandran restraints generated.
    1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  258 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 258
  time to evaluate  : 1.270 
Fit side-chains
REVERT: R  190 ARG cc_start: 0.5956 (mtt180) cc_final: 0.5732 (mtt180)
REVERT: R  220 PHE cc_start: 0.8204 (m-80) cc_final: 0.8000 (m-80)
REVERT: A   22 ASN cc_start: 0.7411 (m-40) cc_final: 0.7192 (m-40)
REVERT: A  216 GLU cc_start: 0.7625 (tt0) cc_final: 0.7406 (tt0)
REVERT: A  251 ASP cc_start: 0.7559 (t0) cc_final: 0.7312 (t70)
REVERT: B   70 THR cc_start: 0.8076 (m) cc_final: 0.7732 (p)
REVERT: B  175 ASP cc_start: 0.7289 (t0) cc_final: 0.7086 (t70)
REVERT: B  217 ASP cc_start: 0.7542 (t0) cc_final: 0.7150 (t0)
REVERT: D  184 MET cc_start: 0.7860 (ttm) cc_final: 0.7643 (ttp)
  outliers start: 0
  outliers final: 1
  residues processed: 258
  average time/residue: 1.1673
  time to fit residues: 322.8932
Evaluate side-chains
  165 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 164
  time to evaluate  : 1.103 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  170 ILE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 98 optimal weight:    2.9990
   chunk 88 optimal weight:   10.0000
   chunk 49 optimal weight:    1.9990
   chunk 30 optimal weight:    3.9990
   chunk 59 optimal weight:    4.9990
   chunk 47 optimal weight:    0.6980
   chunk 91 optimal weight:    8.9990
   chunk 35 optimal weight:    4.9990
   chunk 55 optimal weight:    5.9990
   chunk 68 optimal weight:    0.7980
   chunk 106 optimal weight:    0.9990
   overall best weight:    1.4986

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

Flipped N/Q/H residues before XYZ refinement:
R 105 GLN
R 169 ASN
R 201 GLN
** R 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 188 HIS
A 269 ASN
A 306 GLN
B 181 GLN
C  44 HIS
D  67 ASN
D  85 ASN
D 169 ASN
D 314 ASN

Total number of N/Q/H flips: 12

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3956 r_free = 0.3956 target = 0.176128 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3542 r_free = 0.3542 target = 0.138037 restraints weight = 10957.215|
|-----------------------------------------------------------------------------|
r_work (start): 0.3551 rms_B_bonded: 1.85
r_work: 0.3326 rms_B_bonded: 3.11 restraints_weight: 0.5000
r_work: 0.3191 rms_B_bonded: 4.97 restraints_weight: 0.2500
r_work (final): 0.3191
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8044
moved from start:          0.2352

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050  10171  Z= 0.145
  Angle     :  0.555   7.686  13751  Z= 0.295
  Chirality :  0.040   0.146   1615
  Planarity :  0.005   0.051   1656
  Dihedral  :  7.186  55.693   1817
  Min Nonbonded Distance : 2.418

Molprobity Statistics.
  All-atom Clashscore : 3.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.16 %
    Favored  : 98.84 %
  Rotamer:
    Outliers :  2.75 %
    Allowed  :  9.94 %
    Favored  : 87.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.71 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.34 (0.23), residues: 1203
  helix:  2.76 (0.18), residues: 671
  sheet:  1.17 (0.42), residues: 164
  loop : -0.64 (0.30), residues: 368

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP B  87 
 HIS   0.005   0.001   HIS B 147 
 PHE   0.013   0.002   PHE A 189 
 TYR   0.015   0.002   TYR P   1 
 ARG   0.007   0.001   ARG B  47 

Details of bonding type rmsd
  link_TRANS           : bond        0.00143 (    2)
  link_TRANS           : angle       0.42688 (    6)
  hydrogen bonds       : bond        0.04880 (  617)
  hydrogen bonds       : angle       4.19919 ( 1806)
  SS BOND              : bond        0.00023 (    2)
  SS BOND              : angle       1.26415 (    4)
  covalent geometry    : bond        0.00320 (10165)
  covalent geometry    : angle       0.55474 (13741)
  Misc. bond           : bond        0.00090 (    2)

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

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

  2406 Ramachandran restraints generated.
    1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2406 Ramachandran restraints generated.
    1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  180 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 151
  time to evaluate  : 1.141 
Fit side-chains
REVERT: R  113 THR cc_start: 0.8742 (t) cc_final: 0.8485 (t)
REVERT: A   22 ASN cc_start: 0.7826 (m-40) cc_final: 0.7416 (m-40)
REVERT: A   53 MET cc_start: 0.6816 (OUTLIER) cc_final: 0.6071 (mpt)
REVERT: A  240 MET cc_start: 0.4048 (ppp) cc_final: 0.3771 (pp-130)
REVERT: A  275 GLU cc_start: 0.7416 (tp30) cc_final: 0.6658 (tp30)
REVERT: B   47 ARG cc_start: 0.6806 (mmm-85) cc_final: 0.6279 (mmt90)
REVERT: B   70 THR cc_start: 0.8154 (m) cc_final: 0.7882 (p)
REVERT: B  175 ASP cc_start: 0.7920 (t0) cc_final: 0.7656 (t70)
REVERT: B  217 ASP cc_start: 0.8220 (t0) cc_final: 0.7875 (t0)
REVERT: D  130 TYR cc_start: 0.8800 (t80) cc_final: 0.8590 (t80)
  outliers start: 29
  outliers final: 11
  residues processed: 167
  average time/residue: 1.2204
  time to fit residues: 218.9562
Evaluate side-chains
  152 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 140
  time to evaluate  : 0.988 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  179 VAL
Chi-restraints excluded: chain R residue  206 SER
Chi-restraints excluded: chain R residue  302 LEU
Chi-restraints excluded: chain A residue   53 MET
Chi-restraints excluded: chain A residue  182 THR
Chi-restraints excluded: chain A residue  185 VAL
Chi-restraints excluded: chain A residue  190 THR
Chi-restraints excluded: chain A residue  225 VAL
Chi-restraints excluded: chain A residue  249 LEU
Chi-restraints excluded: chain A residue  324 THR
Chi-restraints excluded: chain B residue  103 SER
Chi-restraints excluded: chain B residue  151 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 9 optimal weight:    1.9990
   chunk 20 optimal weight:    8.9990
   chunk 82 optimal weight:    0.0870
   chunk 30 optimal weight:    2.9990
   chunk 5 optimal weight:    7.9990
   chunk 96 optimal weight:    0.8980
   chunk 14 optimal weight:    5.9990
   chunk 15 optimal weight:    0.8980
   chunk 103 optimal weight:   10.0000
   chunk 113 optimal weight:    6.9990
   chunk 84 optimal weight:   10.0000
   overall best weight:    1.3762

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

Flipped N/Q/H residues before XYZ refinement:
R 169 ASN
** R 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 188 HIS
A 306 GLN
B  37 GLN
B 345 ASN
D  67 ASN
D 105 GLN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3984 r_free = 0.3984 target = 0.178493 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3576 r_free = 0.3576 target = 0.140642 restraints weight = 10882.938|
|-----------------------------------------------------------------------------|
r_work (start): 0.3433 rms_B_bonded: 1.70
r_work: 0.3241 rms_B_bonded: 2.56 restraints_weight: 0.5000
r_work: 0.3107 rms_B_bonded: 3.99 restraints_weight: 0.2500
r_work (final): 0.3107
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7980
moved from start:          0.2913

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031  10171  Z= 0.128
  Angle     :  0.512   7.907  13751  Z= 0.273
  Chirality :  0.039   0.145   1615
  Planarity :  0.005   0.047   1656
  Dihedral  :  7.069  57.321   1815
  Min Nonbonded Distance : 2.302

Molprobity Statistics.
  All-atom Clashscore : 3.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.41 %
    Favored  : 98.59 %
  Rotamer:
    Outliers :  3.41 %
    Allowed  : 10.89 %
    Favored  : 85.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.71 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.51 (0.24), residues: 1203
  helix:  2.93 (0.19), residues: 671
  sheet:  1.30 (0.42), residues: 157
  loop : -0.63 (0.29), residues: 375

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP B  87 
 HIS   0.005   0.001   HIS B 147 
 PHE   0.016   0.001   PHE A 354 
 TYR   0.011   0.001   TYR P   1 
 ARG   0.005   0.001   ARG B  51 

Details of bonding type rmsd
  link_TRANS           : bond        0.00140 (    2)
  link_TRANS           : angle       0.22680 (    6)
  hydrogen bonds       : bond        0.04634 (  617)
  hydrogen bonds       : angle       4.05306 ( 1806)
  SS BOND              : bond        0.00060 (    2)
  SS BOND              : angle       0.81628 (    4)
  covalent geometry    : bond        0.00276 (10165)
  covalent geometry    : angle       0.51153 (13741)
  Misc. bond           : bond        0.00042 (    2)

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

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

  2406 Ramachandran restraints generated.
    1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2406 Ramachandran restraints generated.
    1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  183 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 147
  time to evaluate  : 1.062 
Fit side-chains
REVERT: R  111 MET cc_start: 0.8282 (OUTLIER) cc_final: 0.7124 (mpp)
REVERT: R  302 LEU cc_start: 0.8290 (OUTLIER) cc_final: 0.8050 (mp)
REVERT: A   17 LYS cc_start: 0.6914 (OUTLIER) cc_final: 0.6711 (mmtp)
REVERT: A   22 ASN cc_start: 0.7433 (m-40) cc_final: 0.7118 (m-40)
REVERT: A   53 MET cc_start: 0.6597 (OUTLIER) cc_final: 0.6081 (mpt)
REVERT: A  275 GLU cc_start: 0.7231 (tp30) cc_final: 0.6971 (tp30)
REVERT: A  306 GLN cc_start: 0.6662 (mm-40) cc_final: 0.6431 (mm110)
REVERT: B   83 LYS cc_start: 0.8304 (OUTLIER) cc_final: 0.8093 (mttp)
REVERT: B  175 ASP cc_start: 0.8069 (t0) cc_final: 0.7768 (t70)
REVERT: B  203 LEU cc_start: 0.8295 (OUTLIER) cc_final: 0.8022 (pp)
REVERT: B  217 ASP cc_start: 0.8207 (t0) cc_final: 0.7841 (t0)
REVERT: B  222 MET cc_start: 0.7265 (OUTLIER) cc_final: 0.6748 (ppp)
REVERT: D  130 TYR cc_start: 0.8653 (t80) cc_final: 0.8437 (t80)
REVERT: D  193 ASP cc_start: 0.6391 (t0) cc_final: 0.5851 (m-30)
REVERT: D  325 PHE cc_start: 0.6175 (t80) cc_final: 0.5951 (t80)
  outliers start: 36
  outliers final: 15
  residues processed: 165
  average time/residue: 1.1952
  time to fit residues: 211.7928
Evaluate side-chains
  156 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 134
  time to evaluate  : 1.077 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  111 MET
Chi-restraints excluded: chain R residue  302 LEU
Chi-restraints excluded: chain A residue   17 LYS
Chi-restraints excluded: chain A residue   53 MET
Chi-restraints excluded: chain A residue  182 THR
Chi-restraints excluded: chain A residue  185 VAL
Chi-restraints excluded: chain A residue  190 THR
Chi-restraints excluded: chain A residue  193 ASP
Chi-restraints excluded: chain A residue  225 VAL
Chi-restraints excluded: chain A residue  249 LEU
Chi-restraints excluded: chain A residue  324 THR
Chi-restraints excluded: chain B residue   83 LYS
Chi-restraints excluded: chain B residue  103 SER
Chi-restraints excluded: chain B residue  119 CYS
Chi-restraints excluded: chain B residue  151 LEU
Chi-restraints excluded: chain B residue  203 LEU
Chi-restraints excluded: chain B residue  222 MET
Chi-restraints excluded: chain B residue  332 VAL
Chi-restraints excluded: chain C residue   38 MET
Chi-restraints excluded: chain D residue  127 ILE
Chi-restraints excluded: chain D residue  143 CYS
Chi-restraints excluded: chain D residue  263 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 4 optimal weight:    4.9990
   chunk 13 optimal weight:    0.8980
   chunk 42 optimal weight:    5.9990
   chunk 27 optimal weight:    0.5980
   chunk 96 optimal weight:    0.9980
   chunk 75 optimal weight:    6.9990
   chunk 9 optimal weight:    0.9980
   chunk 93 optimal weight:    0.5980
   chunk 76 optimal weight:    0.9990
   chunk 70 optimal weight:    8.9990
   chunk 5 optimal weight:    7.9990
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
R 169 ASN
R 201 GLN
B 264 GLN
D  67 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3959 r_free = 0.3959 target = 0.176194 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3557 r_free = 0.3557 target = 0.138807 restraints weight = 10885.565|
|-----------------------------------------------------------------------------|
r_work (start): 0.3570 rms_B_bonded: 1.83
r_work: 0.3305 rms_B_bonded: 3.47 restraints_weight: 0.5000
r_work (final): 0.3305
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8007
moved from start:          0.3071

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025  10171  Z= 0.104
  Angle     :  0.468   7.675  13751  Z= 0.249
  Chirality :  0.038   0.141   1615
  Planarity :  0.004   0.047   1656
  Dihedral  :  6.699  56.098   1815
  Min Nonbonded Distance : 2.366

Molprobity Statistics.
  All-atom Clashscore : 3.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.25 %
    Favored  : 98.75 %
  Rotamer:
    Outliers :  3.12 %
    Allowed  : 12.88 %
    Favored  : 84.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.71 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.64 (0.24), residues: 1203
  helix:  3.07 (0.19), residues: 672
  sheet:  1.31 (0.42), residues: 158
  loop : -0.63 (0.29), residues: 373

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP B  87 
 HIS   0.003   0.001   HIS B 147 
 PHE   0.017   0.001   PHE A 354 
 TYR   0.012   0.001   TYR P   1 
 ARG   0.006   0.000   ARG B  51 

Details of bonding type rmsd
  link_TRANS           : bond        0.00108 (    2)
  link_TRANS           : angle       0.19837 (    6)
  hydrogen bonds       : bond        0.04093 (  617)
  hydrogen bonds       : angle       3.92604 ( 1806)
  SS BOND              : bond        0.00078 (    2)
  SS BOND              : angle       0.61631 (    4)
  covalent geometry    : bond        0.00212 (10165)
  covalent geometry    : angle       0.46847 (13741)
  Misc. bond           : bond        0.00040 (    2)

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

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

  2406 Ramachandran restraints generated.
    1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2406 Ramachandran restraints generated.
    1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  172 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 139
  time to evaluate  : 1.079 
Fit side-chains
REVERT: R  302 LEU cc_start: 0.8315 (OUTLIER) cc_final: 0.8106 (mp)
REVERT: A   17 LYS cc_start: 0.6966 (OUTLIER) cc_final: 0.6762 (mmtp)
REVERT: A   22 ASN cc_start: 0.7530 (m-40) cc_final: 0.7212 (m-40)
REVERT: A  275 GLU cc_start: 0.7280 (tp30) cc_final: 0.6991 (tp30)
REVERT: B   47 ARG cc_start: 0.6496 (mmm-85) cc_final: 0.6096 (mmt90)
REVERT: B  175 ASP cc_start: 0.7991 (t0) cc_final: 0.7628 (t70)
REVERT: B  203 LEU cc_start: 0.8373 (OUTLIER) cc_final: 0.8035 (pp)
REVERT: B  217 ASP cc_start: 0.8083 (t0) cc_final: 0.7740 (t0)
REVERT: B  222 MET cc_start: 0.7260 (OUTLIER) cc_final: 0.6660 (ppp)
REVERT: D  193 ASP cc_start: 0.6404 (t0) cc_final: 0.6137 (m-30)
  outliers start: 33
  outliers final: 15
  residues processed: 154
  average time/residue: 1.2880
  time to fit residues: 212.8370
Evaluate side-chains
  154 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 135
  time to evaluate  : 1.117 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  167 LEU
Chi-restraints excluded: chain R residue  265 VAL
Chi-restraints excluded: chain R residue  302 LEU
Chi-restraints excluded: chain A residue   17 LYS
Chi-restraints excluded: chain A residue  182 THR
Chi-restraints excluded: chain A residue  185 VAL
Chi-restraints excluded: chain A residue  190 THR
Chi-restraints excluded: chain A residue  193 ASP
Chi-restraints excluded: chain A residue  225 VAL
Chi-restraints excluded: chain A residue  249 LEU
Chi-restraints excluded: chain A residue  324 THR
Chi-restraints excluded: chain B residue  103 SER
Chi-restraints excluded: chain B residue  119 CYS
Chi-restraints excluded: chain B residue  189 THR
Chi-restraints excluded: chain B residue  203 LEU
Chi-restraints excluded: chain B residue  222 MET
Chi-restraints excluded: chain B residue  284 SER
Chi-restraints excluded: chain C residue   38 MET
Chi-restraints excluded: chain D residue  263 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 5 optimal weight:    6.9990
   chunk 111 optimal weight:    0.5980
   chunk 19 optimal weight:    0.7980
   chunk 110 optimal weight:    3.9990
   chunk 13 optimal weight:    0.7980
   chunk 39 optimal weight:    6.9990
   chunk 85 optimal weight:    0.9980
   chunk 30 optimal weight:    0.3980
   chunk 37 optimal weight:    5.9990
   chunk 114 optimal weight:    5.9990
   chunk 56 optimal weight:    8.9990
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
R 169 ASN
R 201 GLN
** R 310 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 306 GLN
C  18 GLN
D  67 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3899 r_free = 0.3899 target = 0.171153 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3462 r_free = 0.3462 target = 0.131389 restraints weight = 10873.135|
|-----------------------------------------------------------------------------|
r_work (start): 0.3443 rms_B_bonded: 1.86
r_work: 0.3217 rms_B_bonded: 3.04 restraints_weight: 0.5000
r_work: 0.3080 rms_B_bonded: 4.81 restraints_weight: 0.2500
r_work (final): 0.3080
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8042
moved from start:          0.3199

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028  10171  Z= 0.099
  Angle     :  0.458   7.663  13751  Z= 0.241
  Chirality :  0.037   0.140   1615
  Planarity :  0.004   0.047   1656
  Dihedral  :  6.403  57.187   1815
  Min Nonbonded Distance : 2.330

Molprobity Statistics.
  All-atom Clashscore : 4.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.50 %
    Favored  : 98.50 %
  Rotamer:
    Outliers :  3.12 %
    Allowed  : 12.88 %
    Favored  : 84.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.71 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.69 (0.24), residues: 1203
  helix:  3.15 (0.19), residues: 672
  sheet:  1.08 (0.41), residues: 166
  loop : -0.62 (0.30), residues: 365

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP B  87 
 HIS   0.003   0.001   HIS B 147 
 PHE   0.014   0.001   PHE A 354 
 TYR   0.011   0.001   TYR P   1 
 ARG   0.007   0.000   ARG B  51 

Details of bonding type rmsd
  link_TRANS           : bond        0.00126 (    2)
  link_TRANS           : angle       0.17692 (    6)
  hydrogen bonds       : bond        0.03837 (  617)
  hydrogen bonds       : angle       3.85123 ( 1806)
  SS BOND              : bond        0.00091 (    2)
  SS BOND              : angle       0.54352 (    4)
  covalent geometry    : bond        0.00198 (10165)
  covalent geometry    : angle       0.45830 (13741)
  Misc. bond           : bond        0.00035 (    2)

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

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

  2406 Ramachandran restraints generated.
    1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2406 Ramachandran restraints generated.
    1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  173 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 140
  time to evaluate  : 1.117 
Fit side-chains
REVERT: R  189 THR cc_start: 0.8233 (OUTLIER) cc_final: 0.7996 (t)
REVERT: R  323 GLU cc_start: 0.6597 (OUTLIER) cc_final: 0.5832 (mp0)
REVERT: A   22 ASN cc_start: 0.7490 (m-40) cc_final: 0.7204 (m-40)
REVERT: A  275 GLU cc_start: 0.7217 (tp30) cc_final: 0.6928 (tp30)
REVERT: B   47 ARG cc_start: 0.6484 (mmm-85) cc_final: 0.6002 (mmt90)
REVERT: B  134 ARG cc_start: 0.6102 (ptp-170) cc_final: 0.5072 (tpt170)
REVERT: B  175 ASP cc_start: 0.8071 (t0) cc_final: 0.7746 (t70)
REVERT: B  217 ASP cc_start: 0.8212 (t0) cc_final: 0.7842 (t0)
REVERT: B  222 MET cc_start: 0.7270 (OUTLIER) cc_final: 0.6270 (ppp)
REVERT: C   21 MET cc_start: 0.5685 (mmm) cc_final: 0.4818 (ptm)
REVERT: D  193 ASP cc_start: 0.6374 (t0) cc_final: 0.6070 (m-30)
REVERT: D  245 LEU cc_start: 0.6938 (OUTLIER) cc_final: 0.6646 (tt)
  outliers start: 33
  outliers final: 19
  residues processed: 158
  average time/residue: 1.3249
  time to fit residues: 224.9897
Evaluate side-chains
  160 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 137
  time to evaluate  : 1.100 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  167 LEU
Chi-restraints excluded: chain R residue  189 THR
Chi-restraints excluded: chain R residue  323 GLU
Chi-restraints excluded: chain A residue  182 THR
Chi-restraints excluded: chain A residue  185 VAL
Chi-restraints excluded: chain A residue  190 THR
Chi-restraints excluded: chain A residue  193 ASP
Chi-restraints excluded: chain A residue  225 VAL
Chi-restraints excluded: chain A residue  249 LEU
Chi-restraints excluded: chain A residue  324 THR
Chi-restraints excluded: chain B residue  103 SER
Chi-restraints excluded: chain B residue  119 CYS
Chi-restraints excluded: chain B residue  151 LEU
Chi-restraints excluded: chain B residue  189 THR
Chi-restraints excluded: chain B residue  203 LEU
Chi-restraints excluded: chain B residue  222 MET
Chi-restraints excluded: chain B residue  266 LEU
Chi-restraints excluded: chain B residue  284 SER
Chi-restraints excluded: chain B residue  332 VAL
Chi-restraints excluded: chain C residue   38 MET
Chi-restraints excluded: chain D residue  127 ILE
Chi-restraints excluded: chain D residue  245 LEU
Chi-restraints excluded: chain D residue  263 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 54 optimal weight:    4.9990
   chunk 43 optimal weight:    0.9980
   chunk 30 optimal weight:    0.5980
   chunk 32 optimal weight:    4.9990
   chunk 108 optimal weight:    8.9990
   chunk 90 optimal weight:    0.9990
   chunk 72 optimal weight:    2.9990
   chunk 39 optimal weight:    5.9990
   chunk 98 optimal weight:    6.9990
   chunk 24 optimal weight:   10.0000
   chunk 80 optimal weight:    2.9990
   overall best weight:    1.7186

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

Flipped N/Q/H residues before XYZ refinement:
R 169 ASN
R 201 GLN
A 306 GLN
D  67 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3875 r_free = 0.3875 target = 0.168551 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3436 r_free = 0.3436 target = 0.129414 restraints weight = 10922.396|
|-----------------------------------------------------------------------------|
r_work (start): 0.3482 rms_B_bonded: 1.96
r_work: 0.3252 rms_B_bonded: 3.08 restraints_weight: 0.5000
r_work: 0.3115 rms_B_bonded: 4.87 restraints_weight: 0.2500
r_work (final): 0.3115
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8132
moved from start:          0.3527

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  10171  Z= 0.136
  Angle     :  0.517   8.402  13751  Z= 0.270
  Chirality :  0.039   0.144   1615
  Planarity :  0.004   0.049   1656
  Dihedral  :  6.984  52.857   1815
  Min Nonbonded Distance : 2.320

Molprobity Statistics.
  All-atom Clashscore : 3.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.50 %
    Favored  : 98.50 %
  Rotamer:
    Outliers :  2.94 %
    Allowed  : 13.26 %
    Favored  : 83.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.71 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.45 (0.24), residues: 1203
  helix:  2.96 (0.19), residues: 674
  sheet:  1.19 (0.41), residues: 157
  loop : -0.81 (0.29), residues: 372

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP B  87 
 HIS   0.004   0.001   HIS B 147 
 PHE   0.013   0.001   PHE A 354 
 TYR   0.017   0.001   TYR P   1 
 ARG   0.008   0.001   ARG B  51 

Details of bonding type rmsd
  link_TRANS           : bond        0.00219 (    2)
  link_TRANS           : angle       0.33308 (    6)
  hydrogen bonds       : bond        0.04645 (  617)
  hydrogen bonds       : angle       3.99587 ( 1806)
  SS BOND              : bond        0.00142 (    2)
  SS BOND              : angle       0.70092 (    4)
  covalent geometry    : bond        0.00310 (10165)
  covalent geometry    : angle       0.51689 (13741)
  Misc. bond           : bond        0.00056 (    2)

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

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

  2406 Ramachandran restraints generated.
    1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2406 Ramachandran restraints generated.
    1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  171 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 140
  time to evaluate  : 1.024 
Fit side-chains
REVERT: R  189 THR cc_start: 0.8287 (OUTLIER) cc_final: 0.8085 (t)
REVERT: A   22 ASN cc_start: 0.7518 (m-40) cc_final: 0.7249 (m-40)
REVERT: A  275 GLU cc_start: 0.7333 (tp30) cc_final: 0.7090 (tp30)
REVERT: B   47 ARG cc_start: 0.6535 (mmm-85) cc_final: 0.6021 (mmt90)
REVERT: B  134 ARG cc_start: 0.6359 (ptp-170) cc_final: 0.5404 (tpt170)
REVERT: B  175 ASP cc_start: 0.8205 (t0) cc_final: 0.7795 (t70)
REVERT: B  217 ASP cc_start: 0.8200 (t0) cc_final: 0.7846 (t0)
REVERT: B  313 LEU cc_start: 0.8047 (mp) cc_final: 0.7743 (mt)
REVERT: C   21 MET cc_start: 0.5667 (mmm) cc_final: 0.4941 (ptm)
REVERT: D  193 ASP cc_start: 0.6520 (t0) cc_final: 0.6260 (m-30)
REVERT: D  245 LEU cc_start: 0.7093 (OUTLIER) cc_final: 0.6824 (tt)
  outliers start: 31
  outliers final: 17
  residues processed: 159
  average time/residue: 1.2300
  time to fit residues: 209.9725
Evaluate side-chains
  160 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 141
  time to evaluate  : 1.034 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  167 LEU
Chi-restraints excluded: chain R residue  189 THR
Chi-restraints excluded: chain R residue  206 SER
Chi-restraints excluded: chain A residue  182 THR
Chi-restraints excluded: chain A residue  190 THR
Chi-restraints excluded: chain A residue  193 ASP
Chi-restraints excluded: chain A residue  225 VAL
Chi-restraints excluded: chain A residue  249 LEU
Chi-restraints excluded: chain B residue   70 THR
Chi-restraints excluded: chain B residue  103 SER
Chi-restraints excluded: chain B residue  119 CYS
Chi-restraints excluded: chain B residue  189 THR
Chi-restraints excluded: chain B residue  203 LEU
Chi-restraints excluded: chain B residue  284 SER
Chi-restraints excluded: chain B residue  332 VAL
Chi-restraints excluded: chain C residue   38 MET
Chi-restraints excluded: chain D residue  143 CYS
Chi-restraints excluded: chain D residue  245 LEU
Chi-restraints excluded: chain D residue  263 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 28 optimal weight:    2.9990
   chunk 61 optimal weight:    1.9990
   chunk 86 optimal weight:    6.9990
   chunk 108 optimal weight:    3.9990
   chunk 23 optimal weight:    0.7980
   chunk 71 optimal weight:    9.9990
   chunk 97 optimal weight:    0.8980
   chunk 46 optimal weight:    0.0030
   chunk 116 optimal weight:    2.9990
   chunk 35 optimal weight:    8.9990
   chunk 12 optimal weight:    0.9990
   overall best weight:    0.9394

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

Flipped N/Q/H residues before XYZ refinement:
R 201 GLN
A 306 GLN
A 331 ASN
D  67 ASN
D 278 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3940 r_free = 0.3940 target = 0.174467 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3517 r_free = 0.3517 target = 0.135735 restraints weight = 10897.923|
|-----------------------------------------------------------------------------|
r_work (start): 0.3478 rms_B_bonded: 1.78
r_work: 0.3286 rms_B_bonded: 2.76 restraints_weight: 0.5000
r_work: 0.3152 rms_B_bonded: 4.38 restraints_weight: 0.2500
r_work (final): 0.3152
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8072
moved from start:          0.3591

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032  10171  Z= 0.104
  Angle     :  0.474   7.993  13751  Z= 0.249
  Chirality :  0.038   0.143   1615
  Planarity :  0.004   0.047   1656
  Dihedral  :  6.669  54.791   1815
  Min Nonbonded Distance : 2.379

Molprobity Statistics.
  All-atom Clashscore : 3.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.41 %
    Favored  : 98.59 %
  Rotamer:
    Outliers :  2.37 %
    Allowed  : 13.64 %
    Favored  : 84.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.71 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.51 (0.24), residues: 1203
  helix:  3.05 (0.19), residues: 674
  sheet:  1.16 (0.41), residues: 157
  loop : -0.84 (0.29), residues: 372

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP B  87 
 HIS   0.003   0.001   HIS B 147 
 PHE   0.012   0.001   PHE A 354 
 TYR   0.012   0.001   TYR P   1 
 ARG   0.007   0.000   ARG B  51 

Details of bonding type rmsd
  link_TRANS           : bond        0.00148 (    2)
  link_TRANS           : angle       0.20661 (    6)
  hydrogen bonds       : bond        0.04028 (  617)
  hydrogen bonds       : angle       3.87888 ( 1806)
  SS BOND              : bond        0.00060 (    2)
  SS BOND              : angle       0.47638 (    4)
  covalent geometry    : bond        0.00215 (10165)
  covalent geometry    : angle       0.47441 (13741)
  Misc. bond           : bond        0.00034 (    2)

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

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

  2406 Ramachandran restraints generated.
    1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2406 Ramachandran restraints generated.
    1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  162 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 137
  time to evaluate  : 1.018 
Fit side-chains
REVERT: A   22 ASN cc_start: 0.7449 (m-40) cc_final: 0.7193 (m-40)
REVERT: A  275 GLU cc_start: 0.7305 (tp30) cc_final: 0.7096 (tp30)
REVERT: B   47 ARG cc_start: 0.6447 (mmm-85) cc_final: 0.5929 (mmt90)
REVERT: B  134 ARG cc_start: 0.6353 (ptp-170) cc_final: 0.5327 (tpt170)
REVERT: B  175 ASP cc_start: 0.8125 (t0) cc_final: 0.7738 (t70)
REVERT: B  217 ASP cc_start: 0.8138 (t0) cc_final: 0.7785 (t0)
REVERT: B  313 LEU cc_start: 0.7951 (mp) cc_final: 0.7682 (mt)
REVERT: C   21 MET cc_start: 0.5685 (mmm) cc_final: 0.4962 (ptm)
REVERT: D  193 ASP cc_start: 0.6434 (t0) cc_final: 0.6205 (m-30)
REVERT: D  241 ARG cc_start: 0.8070 (ptt-90) cc_final: 0.7833 (ptt-90)
  outliers start: 25
  outliers final: 19
  residues processed: 153
  average time/residue: 1.4730
  time to fit residues: 242.6228
Evaluate side-chains
  152 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 133
  time to evaluate  : 1.129 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  167 LEU
Chi-restraints excluded: chain R residue  197 VAL
Chi-restraints excluded: chain R residue  206 SER
Chi-restraints excluded: chain A residue   26 ASP
Chi-restraints excluded: chain A residue  182 THR
Chi-restraints excluded: chain A residue  190 THR
Chi-restraints excluded: chain A residue  193 ASP
Chi-restraints excluded: chain A residue  225 VAL
Chi-restraints excluded: chain A residue  249 LEU
Chi-restraints excluded: chain B residue   70 THR
Chi-restraints excluded: chain B residue  103 SER
Chi-restraints excluded: chain B residue  119 CYS
Chi-restraints excluded: chain B residue  189 THR
Chi-restraints excluded: chain B residue  203 LEU
Chi-restraints excluded: chain B residue  284 SER
Chi-restraints excluded: chain B residue  332 VAL
Chi-restraints excluded: chain C residue   38 MET
Chi-restraints excluded: chain D residue  263 VAL
Chi-restraints excluded: chain D residue  265 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 16 optimal weight:    2.9990
   chunk 34 optimal weight:    5.9990
   chunk 35 optimal weight:    9.9990
   chunk 69 optimal weight:    3.9990
   chunk 44 optimal weight:    0.5980
   chunk 50 optimal weight:    9.9990
   chunk 94 optimal weight:    3.9990
   chunk 62 optimal weight:    1.9990
   chunk 56 optimal weight:    7.9990
   chunk 22 optimal weight:    2.9990
   chunk 109 optimal weight:    1.9990
   overall best weight:    2.1188

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

Flipped N/Q/H residues before XYZ refinement:
A 306 GLN
D  67 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3859 r_free = 0.3859 target = 0.167271 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3405 r_free = 0.3405 target = 0.126683 restraints weight = 10983.910|
|-----------------------------------------------------------------------------|
r_work (start): 0.3350 rms_B_bonded: 1.92
r_work: 0.3110 rms_B_bonded: 3.32 restraints_weight: 0.5000
r_work (final): 0.3110
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8072
moved from start:          0.3859

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037  10171  Z= 0.155
  Angle     :  0.555   9.036  13751  Z= 0.289
  Chirality :  0.040   0.144   1615
  Planarity :  0.004   0.050   1656
  Dihedral  :  7.463  59.776   1815
  Min Nonbonded Distance : 2.316

Molprobity Statistics.
  All-atom Clashscore : 3.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.50 %
    Favored  : 98.50 %
  Rotamer:
    Outliers :  2.75 %
    Allowed  : 13.26 %
    Favored  : 84.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.71 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.22 (0.24), residues: 1203
  helix:  2.78 (0.19), residues: 674
  sheet:  1.09 (0.41), residues: 157
  loop : -0.93 (0.30), residues: 372

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP B  87 
 HIS   0.005   0.001   HIS B  67 
 PHE   0.012   0.002   PHE A 354 
 TYR   0.018   0.002   TYR P   1 
 ARG   0.006   0.001   ARG B  51 

Details of bonding type rmsd
  link_TRANS           : bond        0.00295 (    2)
  link_TRANS           : angle       0.35754 (    6)
  hydrogen bonds       : bond        0.04978 (  617)
  hydrogen bonds       : angle       4.11395 ( 1806)
  SS BOND              : bond        0.00224 (    2)
  SS BOND              : angle       0.68330 (    4)
  covalent geometry    : bond        0.00360 (10165)
  covalent geometry    : angle       0.55498 (13741)
  Misc. bond           : bond        0.00061 (    2)

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

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

  2406 Ramachandran restraints generated.
    1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2406 Ramachandran restraints generated.
    1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  161 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 132
  time to evaluate  : 1.095 
Fit side-chains
REVERT: R  323 GLU cc_start: 0.6651 (OUTLIER) cc_final: 0.5832 (mp0)
REVERT: A   22 ASN cc_start: 0.7518 (m-40) cc_final: 0.7231 (m-40)
REVERT: A  275 GLU cc_start: 0.7336 (tp30) cc_final: 0.7109 (tp30)
REVERT: B  134 ARG cc_start: 0.6552 (ptp-170) cc_final: 0.5629 (tpt170)
REVERT: B  175 ASP cc_start: 0.8115 (t0) cc_final: 0.7675 (t70)
REVERT: B  217 ASP cc_start: 0.8055 (t0) cc_final: 0.7689 (t0)
REVERT: B  239 PHE cc_start: 0.8888 (OUTLIER) cc_final: 0.8352 (m-80)
REVERT: B  313 LEU cc_start: 0.8026 (mp) cc_final: 0.7748 (mt)
REVERT: C   21 MET cc_start: 0.5693 (mmm) cc_final: 0.4912 (ptm)
REVERT: D  193 ASP cc_start: 0.6439 (t0) cc_final: 0.5741 (m-30)
  outliers start: 29
  outliers final: 21
  residues processed: 149
  average time/residue: 1.1794
  time to fit residues: 189.8950
Evaluate side-chains
  153 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 130
  time to evaluate  : 1.105 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  167 LEU
Chi-restraints excluded: chain R residue  197 VAL
Chi-restraints excluded: chain R residue  206 SER
Chi-restraints excluded: chain R residue  323 GLU
Chi-restraints excluded: chain A residue  182 THR
Chi-restraints excluded: chain A residue  190 THR
Chi-restraints excluded: chain A residue  193 ASP
Chi-restraints excluded: chain A residue  225 VAL
Chi-restraints excluded: chain A residue  248 LYS
Chi-restraints excluded: chain A residue  249 LEU
Chi-restraints excluded: chain B residue   70 THR
Chi-restraints excluded: chain B residue  103 SER
Chi-restraints excluded: chain B residue  119 CYS
Chi-restraints excluded: chain B residue  189 THR
Chi-restraints excluded: chain B residue  203 LEU
Chi-restraints excluded: chain B residue  239 PHE
Chi-restraints excluded: chain B residue  266 LEU
Chi-restraints excluded: chain B residue  284 SER
Chi-restraints excluded: chain B residue  332 VAL
Chi-restraints excluded: chain C residue   38 MET
Chi-restraints excluded: chain D residue  143 CYS
Chi-restraints excluded: chain D residue  263 VAL
Chi-restraints excluded: chain D residue  265 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 45 optimal weight:    0.9980
   chunk 75 optimal weight:    7.9990
   chunk 95 optimal weight:    4.9990
   chunk 55 optimal weight:    5.9990
   chunk 112 optimal weight:    0.0980
   chunk 64 optimal weight:    3.9990
   chunk 77 optimal weight:    0.8980
   chunk 93 optimal weight:    0.0770
   chunk 19 optimal weight:    8.9990
   chunk 14 optimal weight:    6.9990
   chunk 87 optimal weight:    4.9990
   overall best weight:    1.2140

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

Flipped N/Q/H residues before XYZ refinement:
A 306 GLN
D  67 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3846 r_free = 0.3846 target = 0.166426 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3402 r_free = 0.3402 target = 0.127040 restraints weight = 11038.290|
|-----------------------------------------------------------------------------|
r_work (start): 0.3388 rms_B_bonded: 1.85
r_work: 0.3170 rms_B_bonded: 2.88 restraints_weight: 0.5000
r_work: 0.3036 rms_B_bonded: 4.53 restraints_weight: 0.2500
r_work (final): 0.3036
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8111
moved from start:          0.3879

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  10171  Z= 0.116
  Angle     :  0.509   8.723  13751  Z= 0.265
  Chirality :  0.039   0.142   1615
  Planarity :  0.004   0.048   1656
  Dihedral  :  7.142  53.570   1815
  Min Nonbonded Distance : 2.368

Molprobity Statistics.
  All-atom Clashscore : 3.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.41 %
    Favored  : 98.59 %
  Rotamer:
    Outliers :  2.46 %
    Allowed  : 14.20 %
    Favored  : 83.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.71 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.34 (0.24), residues: 1203
  helix:  2.90 (0.19), residues: 674
  sheet:  1.15 (0.41), residues: 157
  loop : -0.92 (0.30), residues: 372

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP B  87 
 HIS   0.003   0.001   HIS B 147 
 PHE   0.011   0.001   PHE A 354 
 TYR   0.013   0.001   TYR P   1 
 ARG   0.007   0.001   ARG B  51 

Details of bonding type rmsd
  link_TRANS           : bond        0.00230 (    2)
  link_TRANS           : angle       0.25357 (    6)
  hydrogen bonds       : bond        0.04369 (  617)
  hydrogen bonds       : angle       3.99449 ( 1806)
  SS BOND              : bond        0.00098 (    2)
  SS BOND              : angle       0.57999 (    4)
  covalent geometry    : bond        0.00251 (10165)
  covalent geometry    : angle       0.50939 (13741)
  Misc. bond           : bond        0.00044 (    2)

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

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

  2406 Ramachandran restraints generated.
    1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2406 Ramachandran restraints generated.
    1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  161 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 135
  time to evaluate  : 1.291 
Fit side-chains
REVERT: R  321 LEU cc_start: 0.7124 (mp) cc_final: 0.6922 (mt)
REVERT: R  323 GLU cc_start: 0.6670 (OUTLIER) cc_final: 0.5837 (mp0)
REVERT: A   22 ASN cc_start: 0.7512 (m-40) cc_final: 0.7246 (m-40)
REVERT: B   47 ARG cc_start: 0.6396 (mmm-85) cc_final: 0.5873 (mmt90)
REVERT: B  134 ARG cc_start: 0.6542 (ptp-170) cc_final: 0.5490 (tpt170)
REVERT: B  175 ASP cc_start: 0.8156 (t0) cc_final: 0.7752 (t70)
REVERT: B  217 ASP cc_start: 0.8161 (t0) cc_final: 0.7813 (t0)
REVERT: B  313 LEU cc_start: 0.8093 (mp) cc_final: 0.7796 (mt)
REVERT: C   21 MET cc_start: 0.5679 (mmm) cc_final: 0.4896 (ptm)
REVERT: D  193 ASP cc_start: 0.6470 (t0) cc_final: 0.5752 (m-30)
  outliers start: 26
  outliers final: 18
  residues processed: 153
  average time/residue: 1.7285
  time to fit residues: 285.2948
Evaluate side-chains
  144 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 125
  time to evaluate  : 1.544 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  197 VAL
Chi-restraints excluded: chain R residue  206 SER
Chi-restraints excluded: chain R residue  323 GLU
Chi-restraints excluded: chain A residue  182 THR
Chi-restraints excluded: chain A residue  190 THR
Chi-restraints excluded: chain A residue  193 ASP
Chi-restraints excluded: chain A residue  225 VAL
Chi-restraints excluded: chain A residue  249 LEU
Chi-restraints excluded: chain B residue   70 THR
Chi-restraints excluded: chain B residue  103 SER
Chi-restraints excluded: chain B residue  119 CYS
Chi-restraints excluded: chain B residue  189 THR
Chi-restraints excluded: chain B residue  203 LEU
Chi-restraints excluded: chain B residue  228 THR
Chi-restraints excluded: chain B residue  284 SER
Chi-restraints excluded: chain B residue  332 VAL
Chi-restraints excluded: chain C residue   38 MET
Chi-restraints excluded: chain D residue  263 VAL
Chi-restraints excluded: chain D residue  265 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 4 optimal weight:    2.9990
   chunk 1 optimal weight:    3.9990
   chunk 40 optimal weight:    1.9990
   chunk 69 optimal weight:    1.9990
   chunk 45 optimal weight:   10.0000
   chunk 26 optimal weight:    2.9990
   chunk 58 optimal weight:    0.2980
   chunk 64 optimal weight:    0.7980
   chunk 22 optimal weight:    2.9990
   chunk 111 optimal weight:    0.9980
   chunk 77 optimal weight:    3.9990
   overall best weight:    1.2184

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

Flipped N/Q/H residues before XYZ refinement:
A 306 GLN
D  67 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3851 r_free = 0.3851 target = 0.166794 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3407 r_free = 0.3407 target = 0.127129 restraints weight = 11051.844|
|-----------------------------------------------------------------------------|
r_work (start): 0.3443 rms_B_bonded: 1.85
r_work: 0.3215 rms_B_bonded: 3.16 restraints_weight: 0.5000
r_work (final): 0.3215
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8039
moved from start:          0.3959

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  10171  Z= 0.117
  Angle     :  0.509   8.513  13751  Z= 0.265
  Chirality :  0.039   0.148   1615
  Planarity :  0.004   0.048   1656
  Dihedral  :  6.989  51.334   1815
  Min Nonbonded Distance : 2.378

Molprobity Statistics.
  All-atom Clashscore : 4.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.58 %
    Favored  : 98.42 %
  Rotamer:
    Outliers :  1.89 %
    Allowed  : 14.87 %
    Favored  : 83.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.71 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.34 (0.24), residues: 1203
  helix:  2.90 (0.19), residues: 674
  sheet:  1.16 (0.41), residues: 157
  loop : -0.92 (0.30), residues: 372

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP B  87 
 HIS   0.004   0.001   HIS B 147 
 PHE   0.011   0.001   PHE A 354 
 TYR   0.014   0.001   TYR P   1 
 ARG   0.007   0.000   ARG B  51 

Details of bonding type rmsd
  link_TRANS           : bond        0.00183 (    2)
  link_TRANS           : angle       0.24613 (    6)
  hydrogen bonds       : bond        0.04299 (  617)
  hydrogen bonds       : angle       3.98216 ( 1806)
  SS BOND              : bond        0.00158 (    2)
  SS BOND              : angle       0.76182 (    4)
  covalent geometry    : bond        0.00252 (10165)
  covalent geometry    : angle       0.50939 (13741)
  Misc. bond           : bond        0.00043 (    2)

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

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

  2406 Ramachandran restraints generated.
    1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2406 Ramachandran restraints generated.
    1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  142 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 122
  time to evaluate  : 0.989 
Fit side-chains
REVERT: R   81 LYS cc_start: 0.6518 (OUTLIER) cc_final: 0.6281 (ttpp)
REVERT: R  323 GLU cc_start: 0.6627 (OUTLIER) cc_final: 0.5813 (mp0)
REVERT: A   22 ASN cc_start: 0.7518 (m-40) cc_final: 0.7244 (m-40)
REVERT: A  305 CYS cc_start: 0.7482 (m) cc_final: 0.6507 (p)
REVERT: B   47 ARG cc_start: 0.6322 (mmm-85) cc_final: 0.5821 (mmt90)
REVERT: B  134 ARG cc_start: 0.6560 (ptp-170) cc_final: 0.5641 (tpt170)
REVERT: B  175 ASP cc_start: 0.8065 (t0) cc_final: 0.7646 (t70)
REVERT: B  217 ASP cc_start: 0.7984 (t0) cc_final: 0.7623 (t0)
REVERT: B  313 LEU cc_start: 0.7991 (mp) cc_final: 0.7746 (mt)
REVERT: C   21 MET cc_start: 0.5707 (mmm) cc_final: 0.4897 (ptm)
REVERT: D  193 ASP cc_start: 0.6530 (t0) cc_final: 0.6017 (m-30)
REVERT: D  245 LEU cc_start: 0.7202 (OUTLIER) cc_final: 0.6924 (tt)
  outliers start: 20
  outliers final: 17
  residues processed: 135
  average time/residue: 1.3266
  time to fit residues: 193.8459
Evaluate side-chains
  141 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 121
  time to evaluate  : 1.607 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   81 LYS
Chi-restraints excluded: chain R residue  197 VAL
Chi-restraints excluded: chain R residue  206 SER
Chi-restraints excluded: chain R residue  323 GLU
Chi-restraints excluded: chain A residue  182 THR
Chi-restraints excluded: chain A residue  190 THR
Chi-restraints excluded: chain A residue  193 ASP
Chi-restraints excluded: chain A residue  225 VAL
Chi-restraints excluded: chain A residue  249 LEU
Chi-restraints excluded: chain B residue   70 THR
Chi-restraints excluded: chain B residue  103 SER
Chi-restraints excluded: chain B residue  119 CYS
Chi-restraints excluded: chain B residue  189 THR
Chi-restraints excluded: chain B residue  203 LEU
Chi-restraints excluded: chain B residue  284 SER
Chi-restraints excluded: chain B residue  332 VAL
Chi-restraints excluded: chain C residue   38 MET
Chi-restraints excluded: chain D residue  245 LEU
Chi-restraints excluded: chain D residue  263 VAL
Chi-restraints excluded: chain D residue  265 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 14 optimal weight:    7.9990
   chunk 11 optimal weight:    1.9990
   chunk 29 optimal weight:    4.9990
   chunk 58 optimal weight:    1.9990
   chunk 91 optimal weight:    4.9990
   chunk 17 optimal weight:    2.9990
   chunk 69 optimal weight:    1.9990
   chunk 22 optimal weight:    0.9990
   chunk 96 optimal weight:    0.8980
   chunk 46 optimal weight:    0.9990
   chunk 61 optimal weight:    7.9990
   overall best weight:    1.3788

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

Flipped N/Q/H residues before XYZ refinement:
D  67 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3911 r_free = 0.3911 target = 0.172035 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3481 r_free = 0.3481 target = 0.133367 restraints weight = 10777.152|
|-----------------------------------------------------------------------------|
r_work (start): 0.3455 rms_B_bonded: 1.93
r_work: 0.3238 rms_B_bonded: 3.06 restraints_weight: 0.5000
r_work: 0.3104 rms_B_bonded: 4.86 restraints_weight: 0.2500
r_work (final): 0.3104
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8142
moved from start:          0.4048

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  10171  Z= 0.122
  Angle     :  0.519   8.514  13751  Z= 0.271
  Chirality :  0.039   0.146   1615
  Planarity :  0.004   0.048   1656
  Dihedral  :  7.079  53.773   1815
  Min Nonbonded Distance : 2.371

Molprobity Statistics.
  All-atom Clashscore : 3.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.33 %
    Favored  : 98.67 %
  Rotamer:
    Outliers :  1.99 %
    Allowed  : 14.77 %
    Favored  : 83.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.71 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.30 (0.24), residues: 1203
  helix:  2.86 (0.19), residues: 673
  sheet:  1.14 (0.40), residues: 157
  loop : -0.93 (0.30), residues: 373

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP B  87 
 HIS   0.004   0.001   HIS B 147 
 PHE   0.010   0.001   PHE A 354 
 TYR   0.016   0.001   TYR P   1 
 ARG   0.007   0.001   ARG B  51 

Details of bonding type rmsd
  link_TRANS           : bond        0.00226 (    2)
  link_TRANS           : angle       0.26017 (    6)
  hydrogen bonds       : bond        0.04427 (  617)
  hydrogen bonds       : angle       4.00341 ( 1806)
  SS BOND              : bond        0.00211 (    2)
  SS BOND              : angle       0.83804 (    4)
  covalent geometry    : bond        0.00269 (10165)
  covalent geometry    : angle       0.51902 (13741)
  Misc. bond           : bond        0.00048 (    2)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 8308.63 seconds
wall clock time: 146 minutes 42.12 seconds (8802.12 seconds total)