Starting phenix.real_space_refine
on Wed Mar 12 16:57:17 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8uy0_42791/03_2025/8uy0_42791.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8uy0_42791/03_2025/8uy0_42791.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.2
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8uy0_42791/03_2025/8uy0_42791.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8uy0_42791/03_2025/8uy0_42791.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8uy0_42791/03_2025/8uy0_42791.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8uy0_42791/03_2025/8uy0_42791.cif"
  }
  resolution = 3.2
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.085
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      58      5.16       5
     C    5157      2.51       5
     N    1410      2.21       5
     O    1496      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 7 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 8121
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 2308
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 295, 2308
          Classifications: {'peptide': 295}
          Link IDs: {'PTRANS': 13, 'TRANS': 281}
          Chain breaks: 1
    Chain: "N"
      Number of atoms: 961
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 126, 961
          Classifications: {'peptide': 126}
          Link IDs: {'PTRANS': 5, 'TRANS': 120}
    Chain: "X"
      Number of atoms: 1818
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 216, 1818
          Classifications: {'peptide': 216}
          Link IDs: {'PTRANS': 5, 'TRANS': 210}
          Chain breaks: 4
    Chain: "Y"
      Number of atoms: 2594
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 338, 2594
          Classifications: {'peptide': 338}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 5, 'TRANS': 332}
          Unresolved non-hydrogen bonds: 6
          Unresolved non-hydrogen angles: 7
          Unresolved non-hydrogen dihedrals: 5
          Planarities with less than four sites: {'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 5
    Chain: "Z"
      Number of atoms: 429
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 56, 429
          Classifications: {'peptide': 56}
          Link IDs: {'PTRANS': 4, 'TRANS': 51}
    Chain: "A"
      Number of atoms: 11
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 11
          Unusual residues: {'0WU': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 5.37, per 1000 atoms: 0.66
  Number of scatterers: 8121
  At special positions: 0
  Unit cell: (93.74, 101.48, 132.44, 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      58     16.00
     O    1496      8.00
     N    1410      7.00
     C    5157      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  96 " - pdb=" SG  CYS A 178 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 168 " - pdb=" SG  CYS A 188 " 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=0, symmetry=0
  Time building additional restraints: 1.81
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  2022 Ramachandran restraints generated.
    1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1936

  Finding SS restraints...
    Secondary structure from input PDB file:
      28 helices and 11 sheets defined
      42.8% alpha, 20.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.87
  Creating SS restraints...
    Processing helix  chain 'A' and resid 19 through 21
      No H-bonds generated for 'chain 'A' and resid 19 through 21'
    Processing helix  chain 'A' and resid 22 through 50
      removed outlier: 3.714A  pdb=" N   LEU A  26 " --> pdb=" O   LEU A  22 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 56 through 87
      Proline residue:  A  78  - end of helix
      removed outlier: 3.620A  pdb=" N   LEU A  81 " --> pdb=" O   VAL A  77 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 92 through 127
      removed outlier: 3.848A  pdb=" N   ALA A 115 " --> pdb=" O   CYS A 111 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 130 through 135
    Processing helix  chain 'A' and resid 136 through 164
      removed outlier: 3.574A  pdb=" N   CYS A 140 " --> pdb=" O   ASN A 136 " (cutoff:3.500A)
      removed outlier: 3.628A  pdb=" N   SER A 164 " --> pdb=" O   VAL A 160 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 179 through 185
      removed outlier: 3.605A  pdb=" N   LYS A 185 " --> pdb=" O   PRO A 181 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 191 through 226
      removed outlier: 4.682A  pdb=" N   ILE A 208 " --> pdb=" O   LEU A 204 " (cutoff:3.500A)
      Proline residue:  A 209  - end of helix
    Processing helix  chain 'A' and resid 232 through 259
      removed outlier: 3.546A  pdb=" N   ALA A 236 " --> pdb=" O   GLY A 232 " (cutoff:3.500A)
      removed outlier: 3.731A  pdb=" N   VAL A 246 " --> pdb=" O   SER A 242 " (cutoff:3.500A)
      removed outlier: 3.652A  pdb=" N   ALA A 254 " --> pdb=" O   PHE A 250 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 266 through 279
      removed outlier: 3.545A  pdb=" N   ASP A 270 " --> pdb=" O   SER A 266 " (cutoff:3.500A)
      removed outlier: 4.263A  pdb=" N   VAL A 272 " --> pdb=" O   GLU A 268 " (cutoff:3.500A)
      removed outlier: 3.795A  pdb=" N   TYR A 277 " --> pdb=" O   VAL A 273 " (cutoff:3.500A)
      removed outlier: 3.582A  pdb=" N   ILE A 279 " --> pdb=" O   LEU A 275 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 279 through 290
      removed outlier: 3.755A  pdb=" N   MET A 283 " --> pdb=" O   ILE A 279 " (cutoff:3.500A)
      Proline residue:  A 286  - end of helix
    Processing helix  chain 'A' and resid 293 through 305
    Processing helix  chain 'N' and resid 28 through 32
      removed outlier: 3.988A  pdb=" N   ASN N  31 " --> pdb=" O   THR N  28 " (cutoff:3.500A)
      removed outlier: 3.547A  pdb=" N   TYR N  32 " --> pdb=" O   PHE N  29 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'N' and resid 28 through 32'
    Processing helix  chain 'N' and resid 87 through 91
      removed outlier: 4.269A  pdb=" N   THR N  91 " --> pdb=" O   PRO N  88 " (cutoff:3.500A)
    Processing helix  chain 'X' and resid 15 through 40
      removed outlier: 3.991A  pdb=" N   GLN X  35 " --> pdb=" O   GLN X  31 " (cutoff:3.500A)
      removed outlier: 4.011A  pdb=" N   VAL X  36 " --> pdb=" O   LYS X  32 " (cutoff:3.500A)
      removed outlier: 3.993A  pdb=" N   THR X  40 " --> pdb=" O   VAL X  36 " (cutoff:3.500A)
    Processing helix  chain 'X' and resid 52 through 60
      removed outlier: 4.172A  pdb=" N   MET X  60 " --> pdb=" O   ILE X  56 " (cutoff:3.500A)
    Processing helix  chain 'X' and resid 235 through 239
      removed outlier: 3.642A  pdb=" N   ASN X 239 " --> pdb=" O   GLN X 236 " (cutoff:3.500A)
    Processing helix  chain 'X' and resid 265 through 278
      removed outlier: 3.579A  pdb=" N   ALA X 269 " --> pdb=" O   ARG X 265 " (cutoff:3.500A)
    Processing helix  chain 'X' and resid 293 through 303
    Processing helix  chain 'X' and resid 307 through 311
    Processing helix  chain 'X' and resid 312 through 318
      removed outlier: 3.536A  pdb=" N   TYR X 318 " --> pdb=" O   PHE X 315 " (cutoff:3.500A)
    Processing helix  chain 'X' and resid 332 through 351
      removed outlier: 4.041A  pdb=" N   ARG X 336 " --> pdb=" O   PRO X 332 " (cutoff:3.500A)
      removed outlier: 4.063A  pdb=" N   ALA X 337 " --> pdb=" O   ARG X 333 " (cutoff:3.500A)
      removed outlier: 3.910A  pdb=" N   ARG X 342 " --> pdb=" O   LYS X 338 " (cutoff:3.500A)
      removed outlier: 3.564A  pdb=" N   GLU X 344 " --> pdb=" O   PHE X 340 " (cutoff:3.500A)
      removed outlier: 4.070A  pdb=" N   PHE X 345 " --> pdb=" O   ILE X 341 " (cutoff:3.500A)
    Processing helix  chain 'X' and resid 370 through 391
    Processing helix  chain 'Y' and resid 4 through 26
    Processing helix  chain 'Y' and resid 29 through 35
      removed outlier: 3.563A  pdb=" N   ILE Y  33 " --> pdb=" O   THR Y  29 " (cutoff:3.500A)
    Processing helix  chain 'Z' and resid 8 through 24
      removed outlier: 4.140A  pdb=" N   ASN Z  24 " --> pdb=" O   LYS Z  20 " (cutoff:3.500A)
    Processing helix  chain 'Z' and resid 29 through 44
      removed outlier: 3.850A  pdb=" N   ALA Z  33 " --> pdb=" O   LYS Z  29 " (cutoff:3.500A)
    Processing helix  chain 'Z' and resid 45 through 48
      removed outlier: 3.887A  pdb=" N   ASP Z  48 " --> pdb=" O   ALA Z  45 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'Z' and resid 45 through 48'
    Processing sheet with id=AA1, first strand: chain 'A' and resid 90 through 91
      removed outlier: 6.637A  pdb=" N   ILE A  12 " --> pdb=" O   ILE A 173 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'N' and resid 3 through 7
      removed outlier: 3.536A  pdb=" N   THR N  69 " --> pdb=" O   GLN N  82 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'N' and resid 58 through 60
      removed outlier: 6.914A  pdb=" N   TRP N  36 " --> pdb=" O   VAL N  48 " (cutoff:3.500A)
      removed outlier: 4.625A  pdb=" N   ASP N  50 " --> pdb=" O   MET N  34 " (cutoff:3.500A)
      removed outlier: 6.882A  pdb=" N   MET N  34 " --> pdb=" O   ASP N  50 " (cutoff:3.500A)
      removed outlier: 3.846A  pdb=" N   ASN N  35 " --> pdb=" O   ALA N  97 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'X' and resid 207 through 214
      removed outlier: 4.881A  pdb=" N   VAL X 224 " --> pdb=" O   LEU X  45 " (cutoff:3.500A)
      removed outlier: 7.278A  pdb=" N   ARG X  42 " --> pdb=" O   ALA X 243 " (cutoff:3.500A)
      removed outlier: 8.101A  pdb=" N   ILE X 245 " --> pdb=" O   ARG X  42 " (cutoff:3.500A)
      removed outlier: 6.383A  pdb=" N   LEU X  44 " --> pdb=" O   ILE X 245 " (cutoff:3.500A)
      removed outlier: 7.738A  pdb=" N   VAL X 247 " --> pdb=" O   LEU X  44 " (cutoff:3.500A)
      removed outlier: 6.973A  pdb=" N   LEU X  46 " --> pdb=" O   VAL X 247 " (cutoff:3.500A)
      removed outlier: 8.672A  pdb=" N   ASP X 249 " --> pdb=" O   LEU X  46 " (cutoff:3.500A)
      removed outlier: 6.258A  pdb=" N   ILE X 244 " --> pdb=" O   ILE X 288 " (cutoff:3.500A)
      removed outlier: 7.283A  pdb=" N   PHE X 290 " --> pdb=" O   ILE X 244 " (cutoff:3.500A)
      removed outlier: 6.216A  pdb=" N   PHE X 246 " --> pdb=" O   PHE X 290 " (cutoff:3.500A)
      removed outlier: 7.009A  pdb=" N   ASN X 292 " --> pdb=" O   PHE X 246 " (cutoff:3.500A)
      removed outlier: 6.546A  pdb=" N   VAL X 248 " --> pdb=" O   ASN X 292 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'Y' and resid 47 through 51
      removed outlier: 3.566A  pdb=" N   ARG Y  49 " --> pdb=" O   ILE Y 338 " (cutoff:3.500A)
      removed outlier: 4.154A  pdb=" N   CYS Y 317 " --> pdb=" O   GLY Y 330 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'Y' and resid 58 through 63
      removed outlier: 4.373A  pdb=" N   ALA Y  60 " --> pdb=" O   ALA Y  73 " (cutoff:3.500A)
      removed outlier: 4.052A  pdb=" N   LEU Y  70 " --> pdb=" O   TRP Y  82 " (cutoff:3.500A)
      removed outlier: 3.629A  pdb=" N   LYS Y  78 " --> pdb=" O   SER Y  74 " (cutoff:3.500A)
      removed outlier: 3.696A  pdb=" N   HIS Y  91 " --> pdb=" O   ILE Y  81 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'Y' and resid 102 through 105
      removed outlier: 3.655A  pdb=" N   GLY Y 115 " --> pdb=" O   THR Y 102 " (cutoff:3.500A)
      removed outlier: 6.116A  pdb=" N   CYS Y 121 " --> pdb=" O   GLU Y 138 " (cutoff:3.500A)
      removed outlier: 4.232A  pdb=" N   GLU Y 138 " --> pdb=" O   CYS Y 121 " (cutoff:3.500A)
      removed outlier: 6.801A  pdb=" N   ILE Y 123 " --> pdb=" O   SER Y 136 " (cutoff:3.500A)
      removed outlier: 3.676A  pdb=" N   ARG Y 134 " --> pdb=" O   ASN Y 125 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'Y' and resid 146 through 151
      removed outlier: 6.915A  pdb=" N   SER Y 160 " --> pdb=" O   SER Y 147 " (cutoff:3.500A)
      removed outlier: 4.560A  pdb=" N   CYS Y 149 " --> pdb=" O   VAL Y 158 " (cutoff:3.500A)
      removed outlier: 6.883A  pdb=" N   VAL Y 158 " --> pdb=" O   CYS Y 149 " (cutoff:3.500A)
      removed outlier: 5.353A  pdb=" N   PHE Y 151 " --> pdb=" O   GLN Y 156 " (cutoff:3.500A)
      removed outlier: 7.790A  pdb=" N   GLN Y 156 " --> pdb=" O   PHE Y 151 " (cutoff:3.500A)
      removed outlier: 3.863A  pdb=" N   ILE Y 157 " --> pdb=" O   TRP Y 169 " (cutoff:3.500A)
      removed outlier: 3.903A  pdb=" N   THR Y 165 " --> pdb=" O   SER Y 161 " (cutoff:3.500A)
      removed outlier: 3.661A  pdb=" N   THR Y 178 " --> pdb=" O   LEU Y 168 " (cutoff:3.500A)
      removed outlier: 6.810A  pdb=" N   ASP Y 170 " --> pdb=" O   GLN Y 176 " (cutoff:3.500A)
      removed outlier: 6.588A  pdb=" N   GLN Y 176 " --> pdb=" O   ASP Y 170 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'Y' and resid 187 through 192
      removed outlier: 7.117A  pdb=" N   GLY Y 202 " --> pdb=" O   MET Y 188 " (cutoff:3.500A)
      removed outlier: 4.612A  pdb=" N   LEU Y 190 " --> pdb=" O   VAL Y 200 " (cutoff:3.500A)
      removed outlier: 6.937A  pdb=" N   VAL Y 200 " --> pdb=" O   LEU Y 190 " (cutoff:3.500A)
      removed outlier: 5.377A  pdb=" N   LEU Y 192 " --> pdb=" O   LEU Y 198 " (cutoff:3.500A)
      removed outlier: 7.461A  pdb=" N   LEU Y 198 " --> pdb=" O   LEU Y 192 " (cutoff:3.500A)
      removed outlier: 4.114A  pdb=" N   SER Y 207 " --> pdb=" O   ALA Y 203 " (cutoff:3.500A)
      removed outlier: 3.825A  pdb=" N   GLN Y 220 " --> pdb=" O   LEU Y 210 " (cutoff:3.500A)
      removed outlier: 7.148A  pdb=" N   ASP Y 212 " --> pdb=" O   CYS Y 218 " (cutoff:3.500A)
      removed outlier: 6.626A  pdb=" N   CYS Y 218 " --> pdb=" O   ASP Y 212 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'Y' and resid 229 through 234
      removed outlier: 6.966A  pdb=" N   GLY Y 244 " --> pdb=" O   ASN Y 230 " (cutoff:3.500A)
      removed outlier: 4.346A  pdb=" N   ILE Y 232 " --> pdb=" O   ALA Y 242 " (cutoff:3.500A)
      removed outlier: 6.780A  pdb=" N   ALA Y 242 " --> pdb=" O   ILE Y 232 " (cutoff:3.500A)
      removed outlier: 4.766A  pdb=" N   PHE Y 234 " --> pdb=" O   ALA Y 240 " (cutoff:3.500A)
      removed outlier: 7.067A  pdb=" N   ALA Y 240 " --> pdb=" O   PHE Y 234 " (cutoff:3.500A)
      removed outlier: 6.534A  pdb=" N   CYS Y 250 " --> pdb=" O   THR Y 263 " (cutoff:3.500A)
      removed outlier: 4.539A  pdb=" N   THR Y 263 " --> pdb=" O   CYS Y 250 " (cutoff:3.500A)
      removed outlier: 6.682A  pdb=" N   LEU Y 252 " --> pdb=" O   LEU Y 261 " (cutoff:3.500A)
      removed outlier: 3.911A  pdb=" N   GLN Y 259 " --> pdb=" O   ASP Y 254 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'Y' and resid 273 through 278
      removed outlier: 3.701A  pdb=" N   SER Y 275 " --> pdb=" O   GLY Y 288 " (cutoff:3.500A)
      removed outlier: 6.545A  pdb=" N   CYS Y 294 " --> pdb=" O   VAL Y 307 " (cutoff:3.500A)
      removed outlier: 4.555A  pdb=" N   VAL Y 307 " --> pdb=" O   CYS Y 294 " (cutoff:3.500A)
      removed outlier: 6.365A  pdb=" N   VAL Y 296 " --> pdb=" O   ALA Y 305 " (cutoff:3.500A)

    404 hydrogen bonds defined for protein.
    1161 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: 2.18

  Time building geometry restraints manager: 2.05 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2652
        1.34 -     1.46: 1946
        1.46 -     1.59: 3596
        1.59 -     1.71: 0
        1.71 -     1.83: 82
  Bond restraints: 8276
  Sorted by residual:
  bond pdb=" C8  0WU A 401 "
       pdb=" C9  0WU A 401 "
    ideal  model  delta    sigma   weight residual
    1.331  1.529 -0.198 2.00e-02 2.50e+03 9.77e+01
  bond pdb=" C1  0WU A 401 "
       pdb=" C6  0WU A 401 "
    ideal  model  delta    sigma   weight residual
    1.509  1.391  0.118 2.00e-02 2.50e+03 3.50e+01
  bond pdb=" C2  0WU A 401 "
       pdb=" C7  0WU A 401 "
    ideal  model  delta    sigma   weight residual
    1.498  1.387  0.111 2.00e-02 2.50e+03 3.06e+01
  bond pdb=" C3  0WU A 401 "
       pdb=" C4  0WU A 401 "
    ideal  model  delta    sigma   weight residual
    1.492  1.387  0.105 2.00e-02 2.50e+03 2.74e+01
  bond pdb=" C1  0WU A 401 "
       pdb=" C2  0WU A 401 "
    ideal  model  delta    sigma   weight residual
    1.476  1.390  0.086 2.00e-02 2.50e+03 1.84e+01
  ... (remaining 8271 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.51: 10935
        1.51 -     3.02: 213
        3.02 -     4.53: 42
        4.53 -     6.04: 9
        6.04 -     7.55: 1
  Bond angle restraints: 11200
  Sorted by residual:
  angle pdb=" CA  VAL A 133 "
        pdb=" C   VAL A 133 "
        pdb=" O   VAL A 133 "
      ideal   model   delta    sigma   weight residual
     120.95  117.93    3.02 1.04e+00 9.25e-01 8.45e+00
  angle pdb=" CA  TYR A 131 "
        pdb=" C   TYR A 131 "
        pdb=" N   PRO A 132 "
      ideal   model   delta    sigma   weight residual
     118.44  122.93   -4.49 1.59e+00 3.96e-01 7.98e+00
  angle pdb=" CA  TYR A 131 "
        pdb=" C   TYR A 131 "
        pdb=" O   TYR A 131 "
      ideal   model   delta    sigma   weight residual
     120.16  116.34    3.82 1.37e+00 5.33e-01 7.79e+00
  angle pdb=" N   GLN Y  13 "
        pdb=" CA  GLN Y  13 "
        pdb=" CB  GLN Y  13 "
      ideal   model   delta    sigma   weight residual
     110.12  114.15   -4.03 1.47e+00 4.63e-01 7.50e+00
  angle pdb=" N   VAL A  77 "
        pdb=" CA  VAL A  77 "
        pdb=" C   VAL A  77 "
      ideal   model   delta    sigma   weight residual
     108.88  114.24   -5.36 2.16e+00 2.14e-01 6.16e+00
  ... (remaining 11195 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.96: 4485
       16.96 -    33.91: 392
       33.91 -    50.87: 70
       50.87 -    67.82: 9
       67.82 -    84.78: 13
  Dihedral angle restraints: 4969
    sinusoidal: 1974
      harmonic: 2995
  Sorted by residual:
  dihedral pdb=" CA  PHE Y 234 "
           pdb=" C   PHE Y 234 "
           pdb=" N   PHE Y 235 "
           pdb=" CA  PHE Y 235 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.86   18.14     0      5.00e+00 4.00e-02 1.32e+01
  dihedral pdb=" CA  VAL A  77 "
           pdb=" C   VAL A  77 "
           pdb=" N   PRO A  78 "
           pdb=" CA  PRO A  78 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -162.30  -17.70     0      5.00e+00 4.00e-02 1.25e+01
  dihedral pdb=" CA  LYS Y  89 "
           pdb=" C   LYS Y  89 "
           pdb=" N   VAL Y  90 "
           pdb=" CA  VAL Y  90 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -162.42  -17.58     0      5.00e+00 4.00e-02 1.24e+01
  ... (remaining 4966 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.045: 986
       0.045 -    0.090: 220
       0.090 -    0.136: 69
       0.136 -    0.181: 3
       0.181 -    0.226: 3
  Chirality restraints: 1281
  Sorted by residual:
  chirality pdb=" CA  TYR A 131 "
            pdb=" N   TYR A 131 "
            pdb=" C   TYR A 131 "
            pdb=" CB  TYR A 131 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.28    0.23 2.00e-01 2.50e+01 1.28e+00
  chirality pdb=" C5  0WU A 401 "
            pdb=" C4  0WU A 401 "
            pdb=" C6  0WU A 401 "
            pdb=" C8  0WU A 401 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.50   -2.72    0.21 2.00e-01 2.50e+01 1.13e+00
  chirality pdb=" CA  VAL A 133 "
            pdb=" N   VAL A 133 "
            pdb=" C   VAL A 133 "
            pdb=" CB  VAL A 133 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.63   -0.19 2.00e-01 2.50e+01 8.61e-01
  ... (remaining 1278 not shown)

  Planarity restraints: 1421
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLY A  40 "   -0.010 2.00e-02 2.50e+03   2.01e-02 4.05e+00
        pdb=" C   GLY A  40 "    0.035 2.00e-02 2.50e+03
        pdb=" O   GLY A  40 "   -0.013 2.00e-02 2.50e+03
        pdb=" N   ASN A  41 "   -0.012 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ALA A  37 "    0.010 2.00e-02 2.50e+03   1.98e-02 3.90e+00
        pdb=" C   ALA A  37 "   -0.034 2.00e-02 2.50e+03
        pdb=" O   ALA A  37 "    0.013 2.00e-02 2.50e+03
        pdb=" N   LEU A  38 "    0.011 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU A  39 "   -0.010 2.00e-02 2.50e+03   1.97e-02 3.88e+00
        pdb=" C   LEU A  39 "    0.034 2.00e-02 2.50e+03
        pdb=" O   LEU A  39 "   -0.013 2.00e-02 2.50e+03
        pdb=" N   GLY A  40 "   -0.011 2.00e-02 2.50e+03
  ... (remaining 1418 not shown)

  Histogram of nonbonded interaction distances:
        2.24 -     2.77: 1376
        2.77 -     3.30: 7247
        3.30 -     3.83: 12392
        3.83 -     4.37: 14006
        4.37 -     4.90: 26164
  Nonbonded interactions: 61185
  Sorted by model distance:
  nonbonded pdb=" OG1 THR Y 128 "
            pdb=" O   ASN Y 132 "
     model   vdw
     2.236 3.040
  nonbonded pdb=" OH  TYR X 318 "
            pdb=" OD2 ASP X 343 "
     model   vdw
     2.282 3.040
  nonbonded pdb=" OH  TYR A 103 "
            pdb=" OH  TYR A 277 "
     model   vdw
     2.310 3.040
  nonbonded pdb=" OG  SER Y 281 "
            pdb=" OD2 ASP Z  48 "
     model   vdw
     2.318 3.040
  nonbonded pdb=" O   SER N  52 "
            pdb=" NH1 ARG N  72 "
     model   vdw
     2.330 3.120
  ... (remaining 61180 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
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
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:             1.510
  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:          0.300
  Check model and map are aligned:         0.040
  Set scattering table:                    0.070
  Process input model:                     21.460
  Find NCS groups from input model:        0.080
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.910
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   26.410
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7010
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   0.198   8276  Z= 0.270
  Angle     :  0.549   7.545  11200  Z= 0.303
  Chirality :  0.042   0.226   1281
  Planarity :  0.003   0.028   1421
  Dihedral  : 13.386  84.781   3027
  Min Nonbonded Distance : 2.236

Molprobity Statistics.
  All-atom Clashscore : 4.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.88 %
    Favored  : 98.12 %
  Rotamer:
    Outliers :  0.11 %
    Allowed  :  0.00 %
    Favored  : 99.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.91 (0.27), residues: 1011
  helix:  1.92 (0.27), residues: 391
  sheet:  0.33 (0.34), residues: 228
  loop : -0.52 (0.30), residues: 392

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP Y 211 
 HIS   0.005   0.001   HIS X 357 
 PHE   0.011   0.001   PHE X 222 
 TYR   0.015   0.001   TYR A  72 
 ARG   0.003   0.000   ARG Y 197 

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

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

  2022 Ramachandran restraints generated.
    1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2022 Ramachandran restraints generated.
    1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  125 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 124
  time to evaluate  : 0.875 
Fit side-chains
REVERT: N    6 GLU cc_start: 0.7973 (mp0) cc_final: 0.7533 (mp0)
REVERT: Y  175 GLN cc_start: 0.7732 (pt0) cc_final: 0.7394 (pt0)
REVERT: Y  268 ASN cc_start: 0.6919 (t0) cc_final: 0.6685 (t0)
  outliers start: 1
  outliers final: 0
  residues processed: 124
  average time/residue: 0.2262
  time to fit residues: 37.1331
Evaluate side-chains
  98 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 98
  time to evaluate  : 0.817 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 84 optimal weight:    3.9990
   chunk 75 optimal weight:    7.9990
   chunk 42 optimal weight:    1.9990
   chunk 25 optimal weight:    2.9990
   chunk 51 optimal weight:    2.9990
   chunk 40 optimal weight:    2.9990
   chunk 78 optimal weight:    2.9990
   chunk 30 optimal weight:    0.0170
   chunk 47 optimal weight:    4.9990
   chunk 58 optimal weight:    1.9990
   chunk 90 optimal weight:    2.9990
   overall best weight:    2.0026

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

Flipped N/Q/H residues before XYZ refinement:
A  83 ASN
X 220 HIS
Y  88 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3820 r_free = 0.3820 target = 0.160232 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3301 r_free = 0.3301 target = 0.113671 restraints weight = 9910.459|
|-----------------------------------------------------------------------------|
r_work (start): 0.3316 rms_B_bonded: 3.17
r_work: 0.3173 rms_B_bonded: 3.68 restraints_weight: 0.5000
r_work (final): 0.3173
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7549
moved from start:          0.1406

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.044   8276  Z= 0.342
  Angle     :  0.640   8.671  11200  Z= 0.334
  Chirality :  0.045   0.156   1281
  Planarity :  0.004   0.037   1421
  Dihedral  :  4.253  17.821   1136
  Min Nonbonded Distance : 2.552

Molprobity Statistics.
  All-atom Clashscore : 3.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.77 %
    Favored  : 97.23 %
  Rotamer:
    Outliers :  1.69 %
    Allowed  :  8.56 %
    Favored  : 89.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.84 (0.26), residues: 1011
  helix:  1.96 (0.26), residues: 395
  sheet:  0.24 (0.35), residues: 219
  loop : -0.65 (0.29), residues: 397

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP N  47 
 HIS   0.010   0.001   HIS X 357 
 PHE   0.019   0.002   PHE Y 151 
 TYR   0.026   0.002   TYR A  72 
 ARG   0.005   0.001   ARG N 118 

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

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

  2022 Ramachandran restraints generated.
    1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2022 Ramachandran restraints generated.
    1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 97
  time to evaluate  : 0.844 
Fit side-chains
   revert: symmetry clash
REVERT: A   91 ILE cc_start: 0.8177 (tt) cc_final: 0.7951 (tt)
REVERT: A   96 CYS cc_start: 0.4846 (OUTLIER) cc_final: 0.4575 (m)
REVERT: N    6 GLU cc_start: 0.8159 (mp0) cc_final: 0.7363 (mp0)
REVERT: Y   59 TYR cc_start: 0.8509 (OUTLIER) cc_final: 0.7280 (m-10)
REVERT: Y  175 GLN cc_start: 0.8130 (pt0) cc_final: 0.7772 (pt0)
REVERT: Y  186 ASP cc_start: 0.7882 (m-30) cc_final: 0.7628 (m-30)
REVERT: Y  267 ASP cc_start: 0.7617 (m-30) cc_final: 0.7402 (m-30)
REVERT: Y  268 ASN cc_start: 0.7146 (t0) cc_final: 0.6770 (t0)
REVERT: Y  303 ASP cc_start: 0.7524 (m-30) cc_final: 0.7015 (p0)
REVERT: Z   21 MET cc_start: 0.7268 (tmm) cc_final: 0.6626 (mtp)
REVERT: Z   42 GLU cc_start: 0.7277 (mm-30) cc_final: 0.7014 (mm-30)
  outliers start: 15
  outliers final: 8
  residues processed: 105
  average time/residue: 0.2200
  time to fit residues: 31.1313
Evaluate side-chains
  104 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 94
  time to evaluate  : 0.930 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   96 CYS
Chi-restraints excluded: chain A residue  221 LEU
Chi-restraints excluded: chain N residue   64 VAL
Chi-restraints excluded: chain X residue  209 GLU
Chi-restraints excluded: chain X residue  210 THR
Chi-restraints excluded: chain X residue  229 ASP
Chi-restraints excluded: chain Y residue   59 TYR
Chi-restraints excluded: chain Y residue  100 VAL
Chi-restraints excluded: chain Y residue  118 ASP
Chi-restraints excluded: chain Y residue  243 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 49 optimal weight:    0.8980
   chunk 55 optimal weight:    0.9990
   chunk 77 optimal weight:    0.6980
   chunk 40 optimal weight:    0.0070
   chunk 93 optimal weight:    3.9990
   chunk 78 optimal weight:    3.9990
   chunk 96 optimal weight:    4.9990
   chunk 83 optimal weight:    2.9990
   chunk 73 optimal weight:    0.8980
   chunk 46 optimal weight:    2.9990
   chunk 99 optimal weight:    7.9990
   overall best weight:    0.7000

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

Flipped N/Q/H residues before XYZ refinement:
A  83 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3868 r_free = 0.3868 target = 0.164879 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3367 r_free = 0.3367 target = 0.118764 restraints weight = 9945.733|
|-----------------------------------------------------------------------------|
r_work (start): 0.3392 rms_B_bonded: 3.11
r_work: 0.3252 rms_B_bonded: 3.64 restraints_weight: 0.5000
r_work (final): 0.3252
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7555
moved from start:          0.1405

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.041   8276  Z= 0.162
  Angle     :  0.507   7.655  11200  Z= 0.265
  Chirality :  0.040   0.143   1281
  Planarity :  0.003   0.034   1421
  Dihedral  :  3.898  18.242   1136
  Min Nonbonded Distance : 2.536

Molprobity Statistics.
  All-atom Clashscore : 3.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.58 %
    Favored  : 98.42 %
  Rotamer:
    Outliers :  1.24 %
    Allowed  : 11.15 %
    Favored  : 87.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.31 (0.26), residues: 1011
  helix:  2.60 (0.26), residues: 392
  sheet:  0.44 (0.35), residues: 220
  loop : -0.65 (0.29), residues: 399

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP N  47 
 HIS   0.005   0.001   HIS X 357 
 PHE   0.010   0.001   PHE X 212 
 TYR   0.014   0.001   TYR A  72 
 ARG   0.003   0.000   ARG Z  62 

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

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

  2022 Ramachandran restraints generated.
    1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2022 Ramachandran restraints generated.
    1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 95
  time to evaluate  : 0.862 
Fit side-chains
   revert: symmetry clash
REVERT: N    6 GLU cc_start: 0.8032 (mp0) cc_final: 0.7311 (mp0)
REVERT: Y   44 GLN cc_start: 0.7096 (mt0) cc_final: 0.6769 (mt0)
REVERT: Y   59 TYR cc_start: 0.8429 (OUTLIER) cc_final: 0.7260 (m-80)
REVERT: Y  175 GLN cc_start: 0.8066 (pt0) cc_final: 0.7747 (pt0)
REVERT: Y  268 ASN cc_start: 0.7155 (t0) cc_final: 0.6783 (t0)
  outliers start: 11
  outliers final: 7
  residues processed: 100
  average time/residue: 0.2306
  time to fit residues: 30.6052
Evaluate side-chains
  100 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 92
  time to evaluate  : 0.829 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   93 PHE
Chi-restraints excluded: chain N residue  105 ARG
Chi-restraints excluded: chain X residue  229 ASP
Chi-restraints excluded: chain Y residue   59 TYR
Chi-restraints excluded: chain Y residue  100 VAL
Chi-restraints excluded: chain Y residue  118 ASP
Chi-restraints excluded: chain Y residue  120 ILE
Chi-restraints excluded: chain Y residue  243 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 37 optimal weight:    3.9990
   chunk 35 optimal weight:    0.7980
   chunk 64 optimal weight:   10.0000
   chunk 25 optimal weight:    2.9990
   chunk 13 optimal weight:    3.9990
   chunk 63 optimal weight:    5.9990
   chunk 36 optimal weight:    0.6980
   chunk 6 optimal weight:    5.9990
   chunk 98 optimal weight:    5.9990
   chunk 29 optimal weight:    4.9990
   chunk 2 optimal weight:    1.9990
   overall best weight:    2.0986

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

Flipped N/Q/H residues before XYZ refinement:
A  83 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3829 r_free = 0.3829 target = 0.161468 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3402 r_free = 0.3402 target = 0.121523 restraints weight = 9722.143|
|-----------------------------------------------------------------------------|
r_work (start): 0.3381 rms_B_bonded: 2.49
r_work: 0.3213 rms_B_bonded: 3.03 restraints_weight: 0.5000
r_work: 0.3057 rms_B_bonded: 4.84 restraints_weight: 0.2500
r_work (final): 0.3057
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7533
moved from start:          0.1879

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.037   8276  Z= 0.344
  Angle     :  0.620   8.305  11200  Z= 0.324
  Chirality :  0.044   0.151   1281
  Planarity :  0.004   0.037   1421
  Dihedral  :  4.288  17.905   1136
  Min Nonbonded Distance : 2.491

Molprobity Statistics.
  All-atom Clashscore : 3.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.87 %
    Favored  : 97.13 %
  Rotamer:
    Outliers :  2.25 %
    Allowed  : 12.50 %
    Favored  : 85.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.98 (0.26), residues: 1011
  helix:  2.30 (0.26), residues: 396
  sheet:  0.23 (0.35), residues: 219
  loop : -0.81 (0.29), residues: 396

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP N  47 
 HIS   0.009   0.001   HIS X 357 
 PHE   0.019   0.002   PHE Y 151 
 TYR   0.025   0.002   TYR A  72 
 ARG   0.005   0.001   ARG N 118 

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

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

  2022 Ramachandran restraints generated.
    1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2022 Ramachandran restraints generated.
    1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 93
  time to evaluate  : 0.938 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   96 CYS cc_start: 0.5118 (OUTLIER) cc_final: 0.4680 (m)
REVERT: Y   59 TYR cc_start: 0.8668 (OUTLIER) cc_final: 0.7330 (m-80)
REVERT: Y  175 GLN cc_start: 0.8136 (pt0) cc_final: 0.7755 (pt0)
REVERT: Y  186 ASP cc_start: 0.8092 (m-30) cc_final: 0.7790 (m-30)
REVERT: Y  220 GLN cc_start: 0.7481 (pt0) cc_final: 0.7074 (pt0)
REVERT: Y  267 ASP cc_start: 0.7629 (m-30) cc_final: 0.7316 (m-30)
REVERT: Y  268 ASN cc_start: 0.7092 (t0) cc_final: 0.6714 (t0)
REVERT: Y  303 ASP cc_start: 0.7651 (m-30) cc_final: 0.7084 (p0)
  outliers start: 20
  outliers final: 11
  residues processed: 104
  average time/residue: 0.2296
  time to fit residues: 32.0009
Evaluate side-chains
  105 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 92
  time to evaluate  : 0.826 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   93 PHE
Chi-restraints excluded: chain A residue   96 CYS
Chi-restraints excluded: chain N residue   64 VAL
Chi-restraints excluded: chain N residue  105 ARG
Chi-restraints excluded: chain X residue  209 GLU
Chi-restraints excluded: chain X residue  210 THR
Chi-restraints excluded: chain X residue  221 MET
Chi-restraints excluded: chain X residue  229 ASP
Chi-restraints excluded: chain Y residue   59 TYR
Chi-restraints excluded: chain Y residue  100 VAL
Chi-restraints excluded: chain Y residue  118 ASP
Chi-restraints excluded: chain Y residue  243 THR
Chi-restraints excluded: chain Z residue   17 GLU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 56 optimal weight:    4.9990
   chunk 62 optimal weight:    0.8980
   chunk 89 optimal weight:    0.4980
   chunk 31 optimal weight:    0.0370
   chunk 46 optimal weight:    4.9990
   chunk 24 optimal weight:    3.9990
   chunk 25 optimal weight:    3.9990
   chunk 51 optimal weight:    0.7980
   chunk 38 optimal weight:    0.9990
   chunk 14 optimal weight:    0.8980
   chunk 33 optimal weight:    0.6980
   overall best weight:    0.5858

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

Flipped N/Q/H residues before XYZ refinement:
Y 220 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3843 r_free = 0.3843 target = 0.162905 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3336 r_free = 0.3336 target = 0.116576 restraints weight = 9763.445|
|-----------------------------------------------------------------------------|
r_work (start): 0.3363 rms_B_bonded: 3.17
r_work: 0.3222 rms_B_bonded: 3.68 restraints_weight: 0.5000
r_work (final): 0.3222
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7477
moved from start:          0.1765

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.038   8276  Z= 0.151
  Angle     :  0.499   8.122  11200  Z= 0.261
  Chirality :  0.040   0.139   1281
  Planarity :  0.003   0.035   1421
  Dihedral  :  3.870  18.640   1136
  Min Nonbonded Distance : 2.470

Molprobity Statistics.
  All-atom Clashscore : 3.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.58 %
    Favored  : 98.42 %
  Rotamer:
    Outliers :  2.03 %
    Allowed  : 14.08 %
    Favored  : 83.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.37 (0.27), residues: 1011
  helix:  2.75 (0.26), residues: 396
  sheet:  0.33 (0.33), residues: 238
  loop : -0.74 (0.30), residues: 377

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP N  47 
 HIS   0.004   0.001   HIS X 357 
 PHE   0.010   0.001   PHE X 212 
 TYR   0.011   0.001   TYR A  72 
 ARG   0.002   0.000   ARG N  19 

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

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

  2022 Ramachandran restraints generated.
    1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2022 Ramachandran restraints generated.
    1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 98
  time to evaluate  : 0.824 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: N    6 GLU cc_start: 0.7939 (mp0) cc_final: 0.7475 (mp0)
REVERT: Y   59 TYR cc_start: 0.8525 (OUTLIER) cc_final: 0.7253 (m-80)
REVERT: Y  175 GLN cc_start: 0.8050 (pt0) cc_final: 0.7715 (pt0)
REVERT: Y  186 ASP cc_start: 0.7950 (m-30) cc_final: 0.7634 (m-30)
REVERT: Y  220 GLN cc_start: 0.7275 (pt0) cc_final: 0.6916 (pt0)
REVERT: Y  267 ASP cc_start: 0.7522 (m-30) cc_final: 0.7302 (m-30)
REVERT: Y  268 ASN cc_start: 0.7030 (t0) cc_final: 0.6697 (t0)
REVERT: Y  303 ASP cc_start: 0.7451 (m-30) cc_final: 0.6989 (p0)
  outliers start: 18
  outliers final: 12
  residues processed: 109
  average time/residue: 0.2193
  time to fit residues: 31.9100
Evaluate side-chains
  107 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 94
  time to evaluate  : 0.917 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   93 PHE
Chi-restraints excluded: chain A residue  161 LEU
Chi-restraints excluded: chain N residue   91 THR
Chi-restraints excluded: chain N residue  105 ARG
Chi-restraints excluded: chain X residue  209 GLU
Chi-restraints excluded: chain X residue  221 MET
Chi-restraints excluded: chain Y residue   59 TYR
Chi-restraints excluded: chain Y residue  100 VAL
Chi-restraints excluded: chain Y residue  118 ASP
Chi-restraints excluded: chain Y residue  120 ILE
Chi-restraints excluded: chain Y residue  217 MET
Chi-restraints excluded: chain Y residue  243 THR
Chi-restraints excluded: chain Z residue   17 GLU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 27 optimal weight:    0.9980
   chunk 37 optimal weight:    2.9990
   chunk 85 optimal weight:    0.1980
   chunk 72 optimal weight:    0.9990
   chunk 69 optimal weight:    3.9990
   chunk 52 optimal weight:    3.9990
   chunk 80 optimal weight:    2.9990
   chunk 86 optimal weight:    0.6980
   chunk 51 optimal weight:    0.5980
   chunk 32 optimal weight:    4.9990
   chunk 61 optimal weight:    2.9990
   overall best weight:    0.6982

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

Flipped N/Q/H residues before XYZ refinement:
X  35 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3903 r_free = 0.3903 target = 0.167308 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3417 r_free = 0.3417 target = 0.121974 restraints weight = 9592.381|
|-----------------------------------------------------------------------------|
r_work (start): 0.3395 rms_B_bonded: 3.03
r_work: 0.3253 rms_B_bonded: 3.60 restraints_weight: 0.5000
r_work (final): 0.3253
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7569
moved from start:          0.1860

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.038   8276  Z= 0.161
  Angle     :  0.503   9.627  11200  Z= 0.260
  Chirality :  0.040   0.209   1281
  Planarity :  0.003   0.035   1421
  Dihedral  :  3.816  18.805   1136
  Min Nonbonded Distance : 2.468

Molprobity Statistics.
  All-atom Clashscore : 3.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.68 %
    Favored  : 98.32 %
  Rotamer:
    Outliers :  1.80 %
    Allowed  : 14.75 %
    Favored  : 83.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.43 (0.27), residues: 1011
  helix:  2.78 (0.26), residues: 396
  sheet:  0.36 (0.34), residues: 229
  loop : -0.65 (0.30), residues: 386

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP N  47 
 HIS   0.004   0.001   HIS X 357 
 PHE   0.013   0.001   PHE A 177 
 TYR   0.011   0.001   TYR A  72 
 ARG   0.002   0.000   ARG N  19 

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

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

  2022 Ramachandran restraints generated.
    1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2022 Ramachandran restraints generated.
    1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 98
  time to evaluate  : 0.874 
Fit side-chains
   revert: symmetry clash
REVERT: N    6 GLU cc_start: 0.7955 (mp0) cc_final: 0.7476 (mp0)
REVERT: Y   59 TYR cc_start: 0.8525 (OUTLIER) cc_final: 0.7331 (m-80)
REVERT: Y  175 GLN cc_start: 0.8074 (pt0) cc_final: 0.7772 (pt0)
REVERT: Y  220 GLN cc_start: 0.7362 (pt0) cc_final: 0.6977 (pt0)
REVERT: Y  268 ASN cc_start: 0.7092 (t0) cc_final: 0.6782 (t0)
REVERT: Y  303 ASP cc_start: 0.7483 (m-30) cc_final: 0.7067 (p0)
  outliers start: 16
  outliers final: 13
  residues processed: 107
  average time/residue: 0.2237
  time to fit residues: 31.9278
Evaluate side-chains
  110 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 96
  time to evaluate  : 0.817 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   93 PHE
Chi-restraints excluded: chain A residue  161 LEU
Chi-restraints excluded: chain N residue   91 THR
Chi-restraints excluded: chain N residue  105 ARG
Chi-restraints excluded: chain X residue  209 GLU
Chi-restraints excluded: chain X residue  210 THR
Chi-restraints excluded: chain X residue  221 MET
Chi-restraints excluded: chain Y residue   59 TYR
Chi-restraints excluded: chain Y residue  100 VAL
Chi-restraints excluded: chain Y residue  118 ASP
Chi-restraints excluded: chain Y residue  120 ILE
Chi-restraints excluded: chain Y residue  217 MET
Chi-restraints excluded: chain Y residue  243 THR
Chi-restraints excluded: chain Z residue   17 GLU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 36 optimal weight:    3.9990
   chunk 43 optimal weight:    0.8980
   chunk 69 optimal weight:    0.9990
   chunk 47 optimal weight:    0.9990
   chunk 20 optimal weight:    0.7980
   chunk 26 optimal weight:    1.9990
   chunk 12 optimal weight:    0.3980
   chunk 92 optimal weight:    7.9990
   chunk 90 optimal weight:    2.9990
   chunk 19 optimal weight:    1.9990
   chunk 23 optimal weight:    4.9990
   overall best weight:    0.8184

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

Flipped N/Q/H residues before XYZ refinement:
A  83 ASN
A 194 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3865 r_free = 0.3865 target = 0.165352 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3433 r_free = 0.3433 target = 0.124138 restraints weight = 9786.217|
|-----------------------------------------------------------------------------|
r_work (start): 0.3430 rms_B_bonded: 2.55
r_work: 0.3270 rms_B_bonded: 3.12 restraints_weight: 0.5000
r_work (final): 0.3270
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7184
moved from start:          0.1964

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   8276  Z= 0.170
  Angle     :  0.505   9.749  11200  Z= 0.261
  Chirality :  0.040   0.153   1281
  Planarity :  0.003   0.036   1421
  Dihedral  :  3.788  18.556   1136
  Min Nonbonded Distance : 2.446

Molprobity Statistics.
  All-atom Clashscore : 3.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.88 %
    Favored  : 98.12 %
  Rotamer:
    Outliers :  1.80 %
    Allowed  : 15.32 %
    Favored  : 82.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.50 (0.27), residues: 1011
  helix:  2.89 (0.26), residues: 390
  sheet:  0.45 (0.33), residues: 237
  loop : -0.68 (0.30), residues: 384

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP N  47 
 HIS   0.005   0.001   HIS X 357 
 PHE   0.013   0.001   PHE X 222 
 TYR   0.012   0.001   TYR A  72 
 ARG   0.002   0.000   ARG N  19 

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

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

  2022 Ramachandran restraints generated.
    1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2022 Ramachandran restraints generated.
    1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 101
  time to evaluate  : 0.904 
Fit side-chains
   revert: symmetry clash
REVERT: N    6 GLU cc_start: 0.7954 (mp0) cc_final: 0.7393 (mp0)
REVERT: X  310 ASP cc_start: 0.6777 (m-30) cc_final: 0.6561 (m-30)
REVERT: Y   59 TYR cc_start: 0.8484 (OUTLIER) cc_final: 0.7214 (m-80)
REVERT: Y  175 GLN cc_start: 0.8010 (pt0) cc_final: 0.7652 (pt0)
REVERT: Y  186 ASP cc_start: 0.7731 (m-30) cc_final: 0.7375 (m-30)
REVERT: Y  220 GLN cc_start: 0.7044 (pt0) cc_final: 0.6545 (pt0)
REVERT: Y  268 ASN cc_start: 0.6900 (t0) cc_final: 0.6592 (t0)
REVERT: Y  303 ASP cc_start: 0.7226 (m-30) cc_final: 0.6686 (p0)
  outliers start: 16
  outliers final: 11
  residues processed: 110
  average time/residue: 0.2196
  time to fit residues: 32.8587
Evaluate side-chains
  105 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 93
  time to evaluate  : 0.866 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   93 PHE
Chi-restraints excluded: chain N residue   91 THR
Chi-restraints excluded: chain N residue  105 ARG
Chi-restraints excluded: chain X residue  210 THR
Chi-restraints excluded: chain X residue  221 MET
Chi-restraints excluded: chain Y residue   59 TYR
Chi-restraints excluded: chain Y residue  100 VAL
Chi-restraints excluded: chain Y residue  118 ASP
Chi-restraints excluded: chain Y residue  120 ILE
Chi-restraints excluded: chain Y residue  243 THR
Chi-restraints excluded: chain Z residue   17 GLU
Chi-restraints excluded: chain Z residue   54 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 71 optimal weight:    5.9990
   chunk 5 optimal weight:    3.9990
   chunk 1 optimal weight:    0.9980
   chunk 95 optimal weight:    6.9990
   chunk 84 optimal weight:    2.9990
   chunk 37 optimal weight:    0.9990
   chunk 18 optimal weight:   10.0000
   chunk 98 optimal weight:    2.9990
   chunk 14 optimal weight:    6.9990
   chunk 52 optimal weight:    4.9990
   chunk 30 optimal weight:    5.9990
   overall best weight:    2.3988

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

Flipped N/Q/H residues before XYZ refinement:
Y 340 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3786 r_free = 0.3786 target = 0.158257 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3323 r_free = 0.3323 target = 0.115477 restraints weight = 9973.583|
|-----------------------------------------------------------------------------|
r_work (start): 0.3310 rms_B_bonded: 2.83
r_work: 0.3149 rms_B_bonded: 3.29 restraints_weight: 0.5000
r_work (final): 0.3149
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7394
moved from start:          0.2341

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.042   8276  Z= 0.385
  Angle     :  0.663  10.256  11200  Z= 0.344
  Chirality :  0.046   0.145   1281
  Planarity :  0.004   0.038   1421
  Dihedral  :  4.439  18.442   1136
  Min Nonbonded Distance : 2.479

Molprobity Statistics.
  All-atom Clashscore : 3.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.56 %
    Favored  : 96.44 %
  Rotamer:
    Outliers :  2.36 %
    Allowed  : 15.54 %
    Favored  : 82.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.91 (0.26), residues: 1011
  helix:  2.16 (0.26), residues: 399
  sheet:  0.18 (0.34), residues: 224
  loop : -0.78 (0.30), residues: 388

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP N  47 
 HIS   0.009   0.001   HIS X 357 
 PHE   0.018   0.002   PHE Y 151 
 TYR   0.023   0.002   TYR A  72 
 ARG   0.004   0.001   ARG X 356 

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

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

  2022 Ramachandran restraints generated.
    1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2022 Ramachandran restraints generated.
    1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 98
  time to evaluate  : 0.919 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: X  213 GLN cc_start: 0.8222 (tt0) cc_final: 0.8008 (tt0)
REVERT: X  394 LEU cc_start: 0.6659 (OUTLIER) cc_final: 0.6212 (mt)
REVERT: Y   59 TYR cc_start: 0.8526 (OUTLIER) cc_final: 0.7202 (m-80)
REVERT: Y  175 GLN cc_start: 0.8064 (pt0) cc_final: 0.7704 (pt0)
REVERT: Y  197 ARG cc_start: 0.7097 (tpt170) cc_final: 0.6821 (tpt170)
REVERT: Y  268 ASN cc_start: 0.7036 (t0) cc_final: 0.6777 (t0)
REVERT: Y  303 ASP cc_start: 0.7543 (m-30) cc_final: 0.7060 (p0)
  outliers start: 21
  outliers final: 14
  residues processed: 109
  average time/residue: 0.2363
  time to fit residues: 34.0416
Evaluate side-chains
  109 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 93
  time to evaluate  : 0.836 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   93 PHE
Chi-restraints excluded: chain N residue   64 VAL
Chi-restraints excluded: chain N residue  105 ARG
Chi-restraints excluded: chain X residue  209 GLU
Chi-restraints excluded: chain X residue  210 THR
Chi-restraints excluded: chain X residue  221 MET
Chi-restraints excluded: chain X residue  394 LEU
Chi-restraints excluded: chain Y residue   59 TYR
Chi-restraints excluded: chain Y residue  100 VAL
Chi-restraints excluded: chain Y residue  118 ASP
Chi-restraints excluded: chain Y residue  120 ILE
Chi-restraints excluded: chain Y residue  243 THR
Chi-restraints excluded: chain Y residue  258 ASP
Chi-restraints excluded: chain Y residue  323 ASP
Chi-restraints excluded: chain Z residue   17 GLU
Chi-restraints excluded: chain Z residue   54 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 31 optimal weight:    0.5980
   chunk 41 optimal weight:    0.8980
   chunk 46 optimal weight:    3.9990
   chunk 38 optimal weight:    2.9990
   chunk 0 optimal weight:   10.0000
   chunk 82 optimal weight:    1.9990
   chunk 35 optimal weight:    2.9990
   chunk 60 optimal weight:    0.9980
   chunk 26 optimal weight:    3.9990
   chunk 78 optimal weight:    4.9990
   chunk 55 optimal weight:    0.6980
   overall best weight:    1.0382

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3853 r_free = 0.3853 target = 0.163897 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3410 r_free = 0.3410 target = 0.121711 restraints weight = 9803.140|
|-----------------------------------------------------------------------------|
r_work (start): 0.3388 rms_B_bonded: 2.79
r_work: 0.3227 rms_B_bonded: 3.28 restraints_weight: 0.5000
r_work (final): 0.3227
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7332
moved from start:          0.2222

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   8276  Z= 0.201
  Angle     :  0.560  10.640  11200  Z= 0.287
  Chirality :  0.041   0.137   1281
  Planarity :  0.003   0.037   1421
  Dihedral  :  4.070  20.970   1136
  Min Nonbonded Distance : 2.398

Molprobity Statistics.
  All-atom Clashscore : 4.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.78 %
    Favored  : 98.22 %
  Rotamer:
    Outliers :  1.80 %
    Allowed  : 16.78 %
    Favored  : 81.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.19 (0.26), residues: 1011
  helix:  2.52 (0.26), residues: 396
  sheet:  0.41 (0.33), residues: 231
  loop : -0.84 (0.30), residues: 384

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP N  47 
 HIS   0.005   0.001   HIS X 357 
 PHE   0.016   0.002   PHE X 222 
 TYR   0.011   0.001   TYR Y  59 
 ARG   0.003   0.000   ARG Z  62 

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

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

  2022 Ramachandran restraints generated.
    1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2022 Ramachandran restraints generated.
    1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 98
  time to evaluate  : 0.848 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: N    6 GLU cc_start: 0.8023 (mp0) cc_final: 0.7758 (mp0)
REVERT: X  213 GLN cc_start: 0.8149 (tt0) cc_final: 0.7946 (tt0)
REVERT: Y   59 TYR cc_start: 0.8493 (OUTLIER) cc_final: 0.7171 (m-80)
REVERT: Y  175 GLN cc_start: 0.8053 (pt0) cc_final: 0.7718 (pt0)
REVERT: Y  197 ARG cc_start: 0.7005 (tpt170) cc_final: 0.6737 (tpt170)
REVERT: Y  220 GLN cc_start: 0.7218 (pt0) cc_final: 0.6737 (pt0)
REVERT: Y  268 ASN cc_start: 0.6984 (t0) cc_final: 0.6703 (t0)
REVERT: Y  303 ASP cc_start: 0.7461 (m-30) cc_final: 0.6994 (p0)
  outliers start: 16
  outliers final: 13
  residues processed: 107
  average time/residue: 0.2293
  time to fit residues: 32.9432
Evaluate side-chains
  109 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 95
  time to evaluate  : 0.921 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   93 PHE
Chi-restraints excluded: chain N residue  105 ARG
Chi-restraints excluded: chain X residue  209 GLU
Chi-restraints excluded: chain X residue  210 THR
Chi-restraints excluded: chain X residue  221 MET
Chi-restraints excluded: chain Y residue   59 TYR
Chi-restraints excluded: chain Y residue  100 VAL
Chi-restraints excluded: chain Y residue  118 ASP
Chi-restraints excluded: chain Y residue  120 ILE
Chi-restraints excluded: chain Y residue  217 MET
Chi-restraints excluded: chain Y residue  243 THR
Chi-restraints excluded: chain Z residue   17 GLU
Chi-restraints excluded: chain Z residue   38 MET
Chi-restraints excluded: chain Z residue   54 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 70 optimal weight:    4.9990
   chunk 50 optimal weight:    4.9990
   chunk 29 optimal weight:    0.9990
   chunk 23 optimal weight:    3.9990
   chunk 0 optimal weight:   10.0000
   chunk 60 optimal weight:    2.9990
   chunk 79 optimal weight:    0.8980
   chunk 62 optimal weight:    0.7980
   chunk 81 optimal weight:    0.0470
   chunk 72 optimal weight:    0.0370
   chunk 86 optimal weight:    3.9990
   overall best weight:    0.5558

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3888 r_free = 0.3888 target = 0.167172 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3465 r_free = 0.3465 target = 0.126415 restraints weight = 9666.478|
|-----------------------------------------------------------------------------|
r_work (start): 0.3526 rms_B_bonded: 2.52
r_work: 0.3365 rms_B_bonded: 3.11 restraints_weight: 0.5000
r_work (final): 0.3365
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7278
moved from start:          0.2161

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.037   8276  Z= 0.148
  Angle     :  0.524  10.635  11200  Z= 0.265
  Chirality :  0.040   0.134   1281
  Planarity :  0.003   0.036   1421
  Dihedral  :  3.741  20.832   1136
  Min Nonbonded Distance : 2.407

Molprobity Statistics.
  All-atom Clashscore : 3.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.98 %
    Favored  : 98.02 %
  Rotamer:
    Outliers :  1.69 %
    Allowed  : 17.00 %
    Favored  : 81.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.51 (0.27), residues: 1011
  helix:  2.95 (0.25), residues: 389
  sheet:  0.53 (0.33), residues: 231
  loop : -0.75 (0.30), residues: 391

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP N  47 
 HIS   0.004   0.000   HIS X 357 
 PHE   0.010   0.001   PHE X 212 
 TYR   0.012   0.001   TYR Y  59 
 ARG   0.004   0.000   ARG Z  62 

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

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

  2022 Ramachandran restraints generated.
    1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2022 Ramachandran restraints generated.
    1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 99
  time to evaluate  : 0.897 
Fit side-chains
   revert: symmetry clash
REVERT: N    6 GLU cc_start: 0.7952 (mp0) cc_final: 0.7384 (mp0)
REVERT: Y   59 TYR cc_start: 0.8378 (OUTLIER) cc_final: 0.7134 (m-80)
REVERT: Y  172 GLU cc_start: 0.7954 (tp30) cc_final: 0.7732 (tp30)
REVERT: Y  175 GLN cc_start: 0.8025 (pt0) cc_final: 0.7751 (pt0)
REVERT: Y  186 ASP cc_start: 0.7783 (m-30) cc_final: 0.7221 (m-30)
REVERT: Y  197 ARG cc_start: 0.7017 (tpt170) cc_final: 0.6746 (tpt170)
REVERT: Y  220 GLN cc_start: 0.7112 (pt0) cc_final: 0.6637 (pt0)
REVERT: Y  268 ASN cc_start: 0.6946 (t0) cc_final: 0.6679 (t0)
REVERT: Y  303 ASP cc_start: 0.7316 (m-30) cc_final: 0.6877 (p0)
  outliers start: 15
  outliers final: 11
  residues processed: 107
  average time/residue: 0.2421
  time to fit residues: 34.7619
Evaluate side-chains
  107 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 95
  time to evaluate  : 0.901 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   93 PHE
Chi-restraints excluded: chain N residue  105 ARG
Chi-restraints excluded: chain X residue  209 GLU
Chi-restraints excluded: chain X residue  210 THR
Chi-restraints excluded: chain Y residue   59 TYR
Chi-restraints excluded: chain Y residue  100 VAL
Chi-restraints excluded: chain Y residue  118 ASP
Chi-restraints excluded: chain Y residue  120 ILE
Chi-restraints excluded: chain Y residue  217 MET
Chi-restraints excluded: chain Y residue  243 THR
Chi-restraints excluded: chain Z residue   17 GLU
Chi-restraints excluded: chain Z residue   54 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 99 optimal weight:    0.9990
   chunk 86 optimal weight:    3.9990
   chunk 24 optimal weight:    2.9990
   chunk 85 optimal weight:    2.9990
   chunk 58 optimal weight:    0.0770
   chunk 28 optimal weight:   10.0000
   chunk 11 optimal weight:    1.9990
   chunk 47 optimal weight:    2.9990
   chunk 73 optimal weight:    0.8980
   chunk 29 optimal weight:    0.0770
   chunk 88 optimal weight:    0.0670
   overall best weight:    0.4236

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4084 r_free = 0.4084 target = 0.182782 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3672 r_free = 0.3672 target = 0.143759 restraints weight = 9214.280|
|-----------------------------------------------------------------------------|
r_work (start): 0.3595 rms_B_bonded: 2.28
r_work: 0.3474 rms_B_bonded: 2.86 restraints_weight: 0.5000
r_work: 0.3315 rms_B_bonded: 4.74 restraints_weight: 0.2500
r_work (final): 0.3315
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7889
moved from start:          0.2197

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.038   8276  Z= 0.139
  Angle     :  0.514  10.486  11200  Z= 0.258
  Chirality :  0.039   0.132   1281
  Planarity :  0.003   0.035   1421
  Dihedral  :  3.580  20.370   1136
  Min Nonbonded Distance : 2.423

Molprobity Statistics.
  All-atom Clashscore : 3.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.48 %
    Favored  : 98.52 %
  Rotamer:
    Outliers :  1.46 %
    Allowed  : 17.57 %
    Favored  : 80.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.64 (0.27), residues: 1011
  helix:  3.00 (0.25), residues: 392
  sheet:  0.76 (0.34), residues: 220
  loop : -0.74 (0.30), residues: 399

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP N  47 
 HIS   0.003   0.000   HIS X 357 
 PHE   0.010   0.001   PHE X 212 
 TYR   0.009   0.001   TYR Y  59 
 ARG   0.004   0.000   ARG Z  62 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4234.24 seconds
wall clock time: 73 minutes 58.36 seconds (4438.36 seconds total)