Starting phenix.real_space_refine
on Wed Jan 15 07:03:32 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8uy0_42791/01_2025/8uy0_42791.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8uy0_42791/01_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_42791/01_2025/8uy0_42791.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8uy0_42791/01_2025/8uy0_42791.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8uy0_42791/01_2025/8uy0_42791.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8uy0_42791/01_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-5571/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: 5.22, per 1000 atoms: 0.64
  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: 2.22
  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: 0.95
  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: 2.34

  Time building geometry restraints manager: 2.40 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:             1.750
  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:          0.340
  Check model and map are aligned:         0.070
  Set scattering table:                    0.080
  Process input model:                     21.750
  Find NCS groups from input model:        0.090
  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:3.000
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   27.120
-------------------------------------------------------------------------------
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  : 1.025 
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: 0.2392
  time to fit residues: 39.0290
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  : 1.156 
-------------------------------------------------------------------------------
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 = 42)----------------|
| r_work = 0.3301 r_free = 0.3301 target = 0.113671 restraints weight = 9910.505|
|-----------------------------------------------------------------------------|
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: 0.7548
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  : 0.927 
Fit side-chains
   revert: symmetry clash
REVERT: A   91 ILE cc_start: 0.8176 (tt) cc_final: 0.7949 (tt)
REVERT: A   96 CYS cc_start: 0.4848 (OUTLIER) cc_final: 0.4574 (m)
REVERT: N    6 GLU cc_start: 0.8159 (mp0) cc_final: 0.7362 (mp0)
REVERT: Y   59 TYR cc_start: 0.8510 (OUTLIER) cc_final: 0.7281 (m-10)
REVERT: Y  175 GLN cc_start: 0.8129 (pt0) cc_final: 0.7770 (pt0)
REVERT: Y  186 ASP cc_start: 0.7883 (m-30) cc_final: 0.7628 (m-30)
REVERT: Y  267 ASP cc_start: 0.7615 (m-30) cc_final: 0.7400 (m-30)
REVERT: Y  268 ASN cc_start: 0.7143 (t0) cc_final: 0.6767 (t0)
REVERT: Y  303 ASP cc_start: 0.7523 (m-30) cc_final: 0.7013 (p0)
REVERT: Z   21 MET cc_start: 0.7267 (tmm) cc_final: 0.6624 (mtp)
REVERT: Z   42 GLU cc_start: 0.7275 (mm-30) cc_final: 0.7012 (mm-30)
  outliers start: 15
  outliers final: 8
  residues processed: 105
  average time/residue: 0.2234
  time to fit residues: 31.6156
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  : 0.894 
-------------------------------------------------------------------------------
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:    0.0980
   chunk 55 optimal weight:    0.7980
   chunk 77 optimal weight:    0.0980
   chunk 40 optimal weight:    0.3980
   chunk 93 optimal weight:    3.9990
   chunk 78 optimal weight:    8.9990
   chunk 96 optimal weight:    4.9990
   chunk 83 optimal weight:    0.7980
   chunk 73 optimal weight:    0.9990
   chunk 46 optimal weight:    1.9990
   chunk 99 optimal weight:    5.9990
   overall best weight:    0.4380

-------------------------------------------------------------------------------
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 = 0.3885 r_free = 0.3885 target = 0.166572 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3388 r_free = 0.3388 target = 0.120653 restraints weight = 9932.117|
|-----------------------------------------------------------------------------|
r_work (start): 0.3414 rms_B_bonded: 3.13
r_work: 0.3272 rms_B_bonded: 3.69 restraints_weight: 0.5000
r_work (final): 0.3272
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7507
moved from start:          0.1368

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.042   8276  Z= 0.143
  Angle     :  0.490   7.612  11200  Z= 0.256
  Chirality :  0.040   0.141   1281
  Planarity :  0.003   0.033   1421
  Dihedral  :  3.797  18.400   1136
  Min Nonbonded Distance : 2.520

Molprobity Statistics.
  All-atom Clashscore : 3.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.19 %
    Favored  : 98.81 %
  Rotamer:
    Outliers :  1.46 %
    Allowed  : 10.59 %
    Favored  : 87.95 %
  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:  1.38 (0.26), residues: 1011
  helix:  2.68 (0.26), residues: 392
  sheet:  0.36 (0.34), residues: 229
  loop : -0.58 (0.29), residues: 390

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP N  47 
 HIS   0.004   0.001   HIS X 357 
 PHE   0.009   0.001   PHE X 212 
 TYR   0.011   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
  110 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 97
  time to evaluate  : 0.895 
Fit side-chains
   revert: symmetry clash
REVERT: N    6 GLU cc_start: 0.8012 (mp0) cc_final: 0.7342 (mp0)
REVERT: Y   44 GLN cc_start: 0.7024 (mt0) cc_final: 0.6711 (mt0)
REVERT: Y   59 TYR cc_start: 0.8323 (OUTLIER) cc_final: 0.7201 (m-80)
REVERT: Y  175 GLN cc_start: 0.8047 (pt0) cc_final: 0.7722 (pt0)
REVERT: Y  220 GLN cc_start: 0.7184 (pt0) cc_final: 0.6907 (pt0)
REVERT: Y  268 ASN cc_start: 0.7096 (t0) cc_final: 0.6728 (t0)
  outliers start: 13
  outliers final: 7
  residues processed: 102
  average time/residue: 0.2328
  time to fit residues: 31.9102
Evaluate side-chains
  101 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 93
  time to evaluate  : 0.884 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   93 PHE
Chi-restraints excluded: chain N residue  105 ARG
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
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 37 optimal weight:    5.9990
   chunk 35 optimal weight:    0.6980
   chunk 64 optimal weight:   10.0000
   chunk 25 optimal weight:    0.0000
   chunk 13 optimal weight:    1.9990
   chunk 63 optimal weight:    3.9990
   chunk 36 optimal weight:    0.5980
   chunk 6 optimal weight:    2.9990
   chunk 98 optimal weight:    5.9990
   chunk 29 optimal weight:    0.7980
   chunk 2 optimal weight:    0.9990
   overall best weight:    0.6186

-------------------------------------------------------------------------------
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 = 0.3878 r_free = 0.3878 target = 0.165959 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3384 r_free = 0.3384 target = 0.120028 restraints weight = 9762.120|
|-----------------------------------------------------------------------------|
r_work (start): 0.3409 rms_B_bonded: 3.10
r_work: 0.3266 rms_B_bonded: 3.66 restraints_weight: 0.5000
r_work (final): 0.3266
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7510
moved from start:          0.1515

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.039   8276  Z= 0.153
  Angle     :  0.487   8.069  11200  Z= 0.253
  Chirality :  0.040   0.141   1281
  Planarity :  0.003   0.035   1421
  Dihedral  :  3.700  18.293   1136
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 3.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.68 %
    Favored  : 98.32 %
  Rotamer:
    Outliers :  1.46 %
    Allowed  : 12.05 %
    Favored  : 86.49 %
  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:  1.53 (0.27), residues: 1011
  helix:  2.90 (0.26), residues: 390
  sheet:  0.59 (0.35), residues: 218
  loop : -0.68 (0.29), residues: 403

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP N  47 
 HIS   0.004   0.001   HIS X 357 
 PHE   0.011   0.001   PHE X 222 
 TYR   0.012   0.001   TYR A  72 
 ARG   0.002   0.000   ARG Y 197 

*********************** 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
  107 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 94
  time to evaluate  : 0.964 
Fit side-chains
   revert: symmetry clash
REVERT: N    6 GLU cc_start: 0.8004 (mp0) cc_final: 0.7248 (mp0)
REVERT: Y   44 GLN cc_start: 0.6924 (mt0) cc_final: 0.6639 (mt0)
REVERT: Y   59 TYR cc_start: 0.8367 (OUTLIER) cc_final: 0.7220 (m-80)
REVERT: Y  175 GLN cc_start: 0.8047 (pt0) cc_final: 0.7737 (pt0)
REVERT: Y  220 GLN cc_start: 0.7252 (pt0) cc_final: 0.6940 (pt0)
REVERT: Y  268 ASN cc_start: 0.7052 (t0) cc_final: 0.6683 (t0)
REVERT: Z   21 MET cc_start: 0.7106 (tmm) cc_final: 0.6271 (mtp)
  outliers start: 13
  outliers final: 7
  residues processed: 101
  average time/residue: 0.2416
  time to fit residues: 32.5350
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  : 0.968 
-------------------------------------------------------------------------------
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  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  243 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 56 optimal weight:    0.0070
   chunk 62 optimal weight:    6.9990
   chunk 89 optimal weight:    0.5980
   chunk 31 optimal weight:    0.8980
   chunk 46 optimal weight:    4.9990
   chunk 24 optimal weight:    3.9990
   chunk 25 optimal weight:    0.9990
   chunk 51 optimal weight:    2.9990
   chunk 38 optimal weight:    2.9990
   chunk 14 optimal weight:    7.9990
   chunk 33 optimal weight:    0.9990
   overall best weight:    0.7002

-------------------------------------------------------------------------------
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 = 0.3908 r_free = 0.3908 target = 0.168268 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3418 r_free = 0.3418 target = 0.122489 restraints weight = 9698.331|
|-----------------------------------------------------------------------------|
r_work (start): 0.3408 rms_B_bonded: 3.08
r_work: 0.3268 rms_B_bonded: 3.61 restraints_weight: 0.5000
r_work (final): 0.3268
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7545
moved from start:          0.1638

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= 0.159
  Angle     :  0.485   6.345  11200  Z= 0.252
  Chirality :  0.040   0.138   1281
  Planarity :  0.003   0.034   1421
  Dihedral  :  3.703  18.129   1136
  Min Nonbonded Distance : 2.517

Molprobity Statistics.
  All-atom Clashscore : 3.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.78 %
    Favored  : 98.22 %
  Rotamer:
    Outliers :  1.35 %
    Allowed  : 13.85 %
    Favored  : 84.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.56 (0.27), residues: 1011
  helix:  2.93 (0.26), residues: 390
  sheet:  0.61 (0.35), residues: 224
  loop : -0.67 (0.29), residues: 397

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP N  47 
 HIS   0.005   0.001   HIS X 357 
 PHE   0.010   0.001   PHE A 177 
 TYR   0.013   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
  108 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 96
  time to evaluate  : 0.904 
Fit side-chains
   revert: symmetry clash
REVERT: Y   59 TYR cc_start: 0.8394 (OUTLIER) cc_final: 0.7305 (m-80)
REVERT: Y  175 GLN cc_start: 0.8049 (pt0) cc_final: 0.7752 (pt0)
REVERT: Y  220 GLN cc_start: 0.7314 (pt0) cc_final: 0.6984 (pt0)
REVERT: Y  268 ASN cc_start: 0.7047 (t0) cc_final: 0.6727 (t0)
  outliers start: 12
  outliers final: 9
  residues processed: 102
  average time/residue: 0.2402
  time to fit residues: 32.7578
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  : 0.928 
-------------------------------------------------------------------------------
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  243 THR
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:    0.9990
   chunk 85 optimal weight:    1.9990
   chunk 72 optimal weight:    0.8980
   chunk 69 optimal weight:    0.0370
   chunk 52 optimal weight:    2.9990
   chunk 80 optimal weight:    0.0060
   chunk 86 optimal weight:    2.9990
   chunk 51 optimal weight:    0.5980
   chunk 32 optimal weight:    4.9990
   chunk 61 optimal weight:    2.9990
   overall best weight:    0.5074

-------------------------------------------------------------------------------
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 = 0.3936 r_free = 0.3936 target = 0.170433 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3457 r_free = 0.3457 target = 0.125290 restraints weight = 9563.179|
|-----------------------------------------------------------------------------|
r_work (start): 0.3431 rms_B_bonded: 3.04
r_work: 0.3288 rms_B_bonded: 3.62 restraints_weight: 0.5000
r_work (final): 0.3288
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7486
moved from start:          0.1737

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     :  0.469   9.129  11200  Z= 0.243
  Chirality :  0.039   0.135   1281
  Planarity :  0.003   0.035   1421
  Dihedral  :  3.589  18.349   1136
  Min Nonbonded Distance : 2.486

Molprobity Statistics.
  All-atom Clashscore : 3.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.38 %
    Favored  : 98.62 %
  Rotamer:
    Outliers :  1.80 %
    Allowed  : 13.96 %
    Favored  : 84.23 %
  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:  1.69 (0.27), residues: 1011
  helix:  3.15 (0.25), residues: 386
  sheet:  0.70 (0.35), residues: 219
  loop : -0.69 (0.29), residues: 406

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP N  47 
 HIS   0.003   0.000   HIS X 357 
 PHE   0.010   0.001   PHE X 212 
 TYR   0.010   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
  115 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 99
  time to evaluate  : 0.916 
Fit side-chains
   revert: symmetry clash
REVERT: N    6 GLU cc_start: 0.7846 (mp0) cc_final: 0.7587 (mp0)
REVERT: Y   59 TYR cc_start: 0.8322 (OUTLIER) cc_final: 0.7239 (m-80)
REVERT: Y  175 GLN cc_start: 0.8034 (pt0) cc_final: 0.7746 (pt0)
REVERT: Y  220 GLN cc_start: 0.7161 (pt0) cc_final: 0.6815 (pt0)
REVERT: Y  268 ASN cc_start: 0.7007 (t0) cc_final: 0.6691 (t0)
REVERT: Z   21 MET cc_start: 0.7199 (tmm) cc_final: 0.6188 (mtp)
  outliers start: 16
  outliers final: 11
  residues processed: 107
  average time/residue: 0.2344
  time to fit residues: 33.5043
Evaluate side-chains
  104 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 92
  time to evaluate  : 0.952 
-------------------------------------------------------------------------------
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  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  217 MET
Chi-restraints excluded: chain Y residue  243 THR
Chi-restraints excluded: chain Y residue  325 MET
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 36 optimal weight:    2.9990
   chunk 43 optimal weight:    0.0070
   chunk 69 optimal weight:    3.9990
   chunk 47 optimal weight:    0.9990
   chunk 20 optimal weight:    2.9990
   chunk 26 optimal weight:    0.6980
   chunk 12 optimal weight:    2.9990
   chunk 92 optimal weight:    2.9990
   chunk 90 optimal weight:    0.9980
   chunk 19 optimal weight:    0.6980
   chunk 23 optimal weight:    7.9990
   overall best weight:    0.6800

-------------------------------------------------------------------------------
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 = 0.3880 r_free = 0.3880 target = 0.166058 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3382 r_free = 0.3382 target = 0.119802 restraints weight = 9786.832|
|-----------------------------------------------------------------------------|
r_work (start): 0.3394 rms_B_bonded: 3.11
r_work: 0.3251 rms_B_bonded: 3.67 restraints_weight: 0.5000
r_work (final): 0.3251
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7524
moved from start:          0.1818

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= 0.156
  Angle     :  0.485   8.143  11200  Z= 0.251
  Chirality :  0.040   0.136   1281
  Planarity :  0.003   0.035   1421
  Dihedral  :  3.617  18.193   1136
  Min Nonbonded Distance : 2.442

Molprobity Statistics.
  All-atom Clashscore : 3.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.58 %
    Favored  : 98.42 %
  Rotamer:
    Outliers :  1.91 %
    Allowed  : 14.19 %
    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:  1.71 (0.27), residues: 1011
  helix:  3.06 (0.25), residues: 391
  sheet:  0.70 (0.35), residues: 224
  loop : -0.62 (0.30), residues: 396

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP N  47 
 HIS   0.004   0.001   HIS X 357 
 PHE   0.011   0.001   PHE Y 241 
 TYR   0.011   0.001   TYR A  72 
 ARG   0.002   0.000   ARG X  38 

*********************** 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
  107 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 90
  time to evaluate  : 0.941 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: Y   59 TYR cc_start: 0.8364 (OUTLIER) cc_final: 0.7261 (m-80)
REVERT: Y  175 GLN cc_start: 0.8070 (pt0) cc_final: 0.7775 (pt0)
REVERT: Y  268 ASN cc_start: 0.6998 (t0) cc_final: 0.6688 (t0)
  outliers start: 17
  outliers final: 12
  residues processed: 99
  average time/residue: 0.2241
  time to fit residues: 30.1226
Evaluate side-chains
  103 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 90
  time to evaluate  : 0.891 
-------------------------------------------------------------------------------
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 X residue  314 GLU
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=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 71 optimal weight:    0.0010
   chunk 5 optimal weight:    3.9990
   chunk 1 optimal weight:    5.9990
   chunk 95 optimal weight:    6.9990
   chunk 84 optimal weight:    3.9990
   chunk 37 optimal weight:    4.9990
   chunk 18 optimal weight:    9.9990
   chunk 98 optimal weight:    2.9990
   chunk 14 optimal weight:    7.9990
   chunk 52 optimal weight:    1.9990
   chunk 30 optimal weight:    1.9990
   overall best weight:    2.1994

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

Flipped N/Q/H residues before XYZ refinement:
A 194 ASN
Y 340 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3809 r_free = 0.3809 target = 0.159139 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3293 r_free = 0.3293 target = 0.112796 restraints weight = 9953.576|
|-----------------------------------------------------------------------------|
r_work (start): 0.3307 rms_B_bonded: 3.10
r_work: 0.3164 rms_B_bonded: 3.61 restraints_weight: 0.5000
r_work (final): 0.3164
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7661
moved from start:          0.2115

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.038   8276  Z= 0.355
  Angle     :  0.619  10.470  11200  Z= 0.322
  Chirality :  0.044   0.143   1281
  Planarity :  0.004   0.039   1421
  Dihedral  :  4.189  18.146   1136
  Min Nonbonded Distance : 2.490

Molprobity Statistics.
  All-atom Clashscore : 3.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.87 %
    Favored  : 97.13 %
  Rotamer:
    Outliers :  2.25 %
    Allowed  : 14.30 %
    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:  1.23 (0.26), residues: 1011
  helix:  2.54 (0.25), residues: 396
  sheet:  0.33 (0.34), residues: 227
  loop : -0.72 (0.30), residues: 388

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP N  47 
 HIS   0.008   0.001   HIS X 357 
 PHE   0.018   0.002   PHE Y 151 
 TYR   0.024   0.002   TYR A  72 
 ARG   0.004   0.001   ARG N 118 

*********************** 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
  115 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 95
  time to evaluate  : 0.920 
Fit side-chains
   revert: symmetry clash
REVERT: Y   59 TYR cc_start: 0.8708 (OUTLIER) cc_final: 0.7494 (m-80)
REVERT: Y  175 GLN cc_start: 0.8185 (pt0) cc_final: 0.7874 (pt0)
REVERT: Y  186 ASP cc_start: 0.7941 (m-30) cc_final: 0.7636 (m-30)
REVERT: Y  267 ASP cc_start: 0.7581 (m-30) cc_final: 0.7319 (m-30)
REVERT: Y  268 ASN cc_start: 0.7137 (t0) cc_final: 0.6885 (t0)
REVERT: Y  303 ASP cc_start: 0.7644 (m-30) cc_final: 0.7192 (p0)
  outliers start: 20
  outliers final: 12
  residues processed: 106
  average time/residue: 0.2293
  time to fit residues: 32.5172
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  : 0.913 
-------------------------------------------------------------------------------
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 X residue  223 ASP
Chi-restraints excluded: chain X residue  314 GLU
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
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:    1.9990
   chunk 41 optimal weight:    3.9990
   chunk 46 optimal weight:    3.9990
   chunk 38 optimal weight:    1.9990
   chunk 0 optimal weight:   10.0000
   chunk 82 optimal weight:    2.9990
   chunk 35 optimal weight:    2.9990
   chunk 60 optimal weight:    0.9990
   chunk 26 optimal weight:    3.9990
   chunk 78 optimal weight:    3.9990
   chunk 55 optimal weight:    0.5980
   overall best weight:    1.7188

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

Flipped N/Q/H residues before XYZ refinement:
Z  59 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3817 r_free = 0.3817 target = 0.161108 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3369 r_free = 0.3369 target = 0.119428 restraints weight = 9905.036|
|-----------------------------------------------------------------------------|
r_work (start): 0.3499 rms_B_bonded: 2.61
r_work: 0.3329 rms_B_bonded: 3.18 restraints_weight: 0.5000
r_work (final): 0.3329
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7395
moved from start:          0.2198

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   8276  Z= 0.286
  Angle     :  0.585   9.660  11200  Z= 0.304
  Chirality :  0.043   0.141   1281
  Planarity :  0.004   0.038   1421
  Dihedral  :  4.201  20.304   1136
  Min Nonbonded Distance : 2.372

Molprobity Statistics.
  All-atom Clashscore : 3.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.57 %
    Favored  : 97.43 %
  Rotamer:
    Outliers :  1.46 %
    Allowed  : 15.54 %
    Favored  : 83.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.15 (0.26), residues: 1011
  helix:  2.44 (0.25), residues: 397
  sheet:  0.39 (0.34), residues: 225
  loop : -0.79 (0.30), residues: 389

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP N  47 
 HIS   0.007   0.001   HIS X 357 
 PHE   0.016   0.002   PHE Y 241 
 TYR   0.019   0.001   TYR A  72 
 ARG   0.004   0.000   ARG Y  49 

*********************** 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
  101 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 88
  time to evaluate  : 0.922 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: Y   59 TYR cc_start: 0.8472 (OUTLIER) cc_final: 0.7120 (m-80)
REVERT: Y  175 GLN cc_start: 0.8062 (pt0) cc_final: 0.7719 (pt0)
REVERT: Y  186 ASP cc_start: 0.7855 (m-30) cc_final: 0.7496 (m-30)
REVERT: Y  267 ASP cc_start: 0.7577 (m-30) cc_final: 0.7296 (m-30)
REVERT: Y  268 ASN cc_start: 0.7073 (t0) cc_final: 0.6792 (t0)
REVERT: Y  303 ASP cc_start: 0.7521 (m-30) cc_final: 0.7062 (p0)
  outliers start: 13
  outliers final: 9
  residues processed: 94
  average time/residue: 0.2433
  time to fit residues: 30.5276
Evaluate side-chains
  97 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 87
  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  243 THR
Chi-restraints excluded: chain Z residue   17 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 70 optimal weight:    3.9990
   chunk 50 optimal weight:    4.9990
   chunk 29 optimal weight:    0.9980
   chunk 23 optimal weight:    3.9990
   chunk 0 optimal weight:   10.0000
   chunk 60 optimal weight:    0.8980
   chunk 79 optimal weight:    0.9990
   chunk 62 optimal weight:   10.0000
   chunk 81 optimal weight:    0.5980
   chunk 72 optimal weight:    0.5980
   chunk 86 optimal weight:    4.9990
   overall best weight:    0.8182

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

Flipped N/Q/H residues before XYZ refinement:
N   5 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3861 r_free = 0.3861 target = 0.164997 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3427 r_free = 0.3427 target = 0.123726 restraints weight = 9709.821|
|-----------------------------------------------------------------------------|
r_work (start): 0.3429 rms_B_bonded: 2.54
r_work: 0.3267 rms_B_bonded: 3.13 restraints_weight: 0.5000
r_work (final): 0.3267
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7214
moved from start:          0.2119

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= 0.176
  Angle     :  0.520   9.741  11200  Z= 0.268
  Chirality :  0.041   0.135   1281
  Planarity :  0.003   0.038   1421
  Dihedral  :  3.887  20.432   1136
  Min Nonbonded Distance : 2.398

Molprobity Statistics.
  All-atom Clashscore : 3.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.18 %
    Favored  : 97.82 %
  Rotamer:
    Outliers :  1.24 %
    Allowed  : 15.99 %
    Favored  : 82.77 %
  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:  1.41 (0.26), residues: 1011
  helix:  2.83 (0.25), residues: 391
  sheet:  0.42 (0.34), residues: 228
  loop : -0.74 (0.30), residues: 392

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP N  47 
 HIS   0.005   0.001   HIS X 357 
 PHE   0.011   0.001   PHE Y 241 
 TYR   0.012   0.001   TYR A  72 
 ARG   0.003   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
  109 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 98
  time to evaluate  : 0.899 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: X  310 ASP cc_start: 0.6877 (m-30) cc_final: 0.6667 (m-30)
REVERT: Y   59 TYR cc_start: 0.8439 (OUTLIER) cc_final: 0.7028 (m-80)
REVERT: Y  175 GLN cc_start: 0.7991 (pt0) cc_final: 0.7664 (pt0)
REVERT: Y  267 ASP cc_start: 0.7588 (m-30) cc_final: 0.7326 (m-30)
REVERT: Y  268 ASN cc_start: 0.6932 (t0) cc_final: 0.6632 (t0)
REVERT: Y  303 ASP cc_start: 0.7314 (m-30) cc_final: 0.6866 (p0)
  outliers start: 11
  outliers final: 10
  residues processed: 104
  average time/residue: 0.2295
  time to fit residues: 32.1884
Evaluate side-chains
  100 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 89
  time to evaluate  : 1.036 
-------------------------------------------------------------------------------
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  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:    0.4980
   chunk 86 optimal weight:    2.9990
   chunk 24 optimal weight:    3.9990
   chunk 85 optimal weight:    0.9980
   chunk 58 optimal weight:    3.9990
   chunk 28 optimal weight:    8.9990
   chunk 11 optimal weight:    1.9990
   chunk 47 optimal weight:    2.9990
   chunk 73 optimal weight:    0.7980
   chunk 29 optimal weight:    0.8980
   chunk 88 optimal weight:    0.7980
   overall best weight:    0.7980

-------------------------------------------------------------------------------
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 = 0.3857 r_free = 0.3857 target = 0.164838 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3443 r_free = 0.3443 target = 0.125344 restraints weight = 9850.073|
|-----------------------------------------------------------------------------|
r_work (start): 0.3442 rms_B_bonded: 2.46
r_work: 0.3266 rms_B_bonded: 3.06 restraints_weight: 0.5000
r_work: 0.3111 rms_B_bonded: 4.89 restraints_weight: 0.2500
r_work (final): 0.3111
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7259
moved from start:          0.2143

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= 0.174
  Angle     :  0.525   9.300  11200  Z= 0.270
  Chirality :  0.040   0.134   1281
  Planarity :  0.003   0.038   1421
  Dihedral  :  3.814  20.381   1136
  Min Nonbonded Distance : 2.413

Molprobity Statistics.
  All-atom Clashscore : 3.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.98 %
    Favored  : 98.02 %
  Rotamer:
    Outliers :  1.24 %
    Allowed  : 16.10 %
    Favored  : 82.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.54 (0.27), residues: 1011
  helix:  2.92 (0.25), residues: 391
  sheet:  0.46 (0.33), residues: 236
  loop : -0.66 (0.31), residues: 384

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   0.012   0.001   PHE Y 241 
 TYR   0.012   0.001   TYR A  72 
 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: 3992.55 seconds
wall clock time: 71 minutes 56.70 seconds (4316.70 seconds total)