Starting phenix.real_space_refine
on Tue Apr 29 19:49:38 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7f2o_31429/04_2025/7f2o_31429.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7f2o_31429/04_2025/7f2o_31429.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.9
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7f2o_31429/04_2025/7f2o_31429.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7f2o_31429/04_2025/7f2o_31429.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7f2o_31429/04_2025/7f2o_31429.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7f2o_31429/04_2025/7f2o_31429.cif"
  }
  resolution = 2.9
  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=   0.002 sd=   0.029
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      63      5.16       5
     C    5721      2.51       5
     N    1544      2.21       5
     O    1676      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 42 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib"
  Total number of atoms: 9004
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 1878
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 230, 1878
          Classifications: {'peptide': 230}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 4}
          Link IDs: {'PTRANS': 5, 'TRANS': 224}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 16
          Unresolved non-hydrogen angles: 17
          Unresolved non-hydrogen dihedrals: 15
          Planarities with less than four sites: {'GLU:plan': 1}
          Unresolved non-hydrogen planarities: 4
    Chain: "B"
      Number of atoms: 2605
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 341, 2605
          Classifications: {'peptide': 341}
          Incomplete info: {'truncation_to_alanine': 3}
          Link IDs: {'PTRANS': 5, 'TRANS': 335}
          Unresolved non-hydrogen bonds: 11
          Unresolved non-hydrogen angles: 14
          Unresolved non-hydrogen dihedrals: 8
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 11
    Chain: "D"
      Number of atoms: 76
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 9, 76
          Classifications: {'peptide': 9}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 3, 'TRANS': 5}
    Chain: "R"
      Number of atoms: 2308
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 287, 2308
          Classifications: {'peptide': 287}
          Link IDs: {'PTRANS': 8, 'TRANS': 278}
          Chain breaks: 1
    Chain: "S"
      Number of atoms: 1784
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 232, 1784
          Classifications: {'peptide': 232}
          Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 221}
          Chain breaks: 1
    Chain: "Y"
      Number of atoms: 353
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 51, 353
          Classifications: {'peptide': 51}
          Incomplete info: {'truncation_to_alanine': 11}
          Link IDs: {'PTRANS': 4, 'TRANS': 46}
          Unresolved non-hydrogen bonds: 41
          Unresolved non-hydrogen angles: 48
          Unresolved non-hydrogen dihedrals: 34
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 1, 'ASN:plan1': 1}
          Unresolved non-hydrogen planarities: 20
  Time building chain proxies: 5.61, per 1000 atoms: 0.62
  Number of scatterers: 9004
  At special positions: 0
  Unit cell: (122.265, 109.725, 105.545, 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      63     16.00
     O    1676      8.00
     N    1544      7.00
     C    5721      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS R 130 " - pdb=" SG  CYS R 211 " 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: 2.43
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  2260 Ramachandran restraints generated.
    1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2158

  Finding SS restraints...
    Secondary structure from input PDB file:
      28 helices and 15 sheets defined
      39.0% alpha, 24.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.21
  Creating SS restraints...
    Processing helix  chain 'A' and resid 6 through 33
      removed outlier: 3.635A  pdb=" N   VAL A  29 " --> pdb=" O   LYS A  25 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 42 through 44
      No H-bonds generated for 'chain 'A' and resid 42 through 44'
    Processing helix  chain 'A' and resid 45 through 54
    Processing helix  chain 'A' and resid 211 through 216
    Processing helix  chain 'A' and resid 229 through 245
      removed outlier: 4.069A  pdb=" N   GLN A 234 " --> pdb=" O   TYR A 230 " (cutoff:3.500A)
      removed outlier: 4.985A  pdb=" N   GLU A 235 " --> pdb=" O   ASN A 231 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 260 through 271
    Processing helix  chain 'A' and resid 274 through 279
      removed outlier: 3.680A  pdb=" N   TYR A 278 " --> pdb=" O   LYS A 274 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 280 through 285
    Processing helix  chain 'A' and resid 298 through 318
    Processing helix  chain 'A' and resid 337 through 358
    Processing helix  chain 'B' and resid 4 through 26
    Processing helix  chain 'B' and resid 29 through 34
    Processing helix  chain 'B' and resid 35 through 37
      No H-bonds generated for 'chain 'B' and resid 35 through 37'
    Processing helix  chain 'R' and resid 56 through 85
      Proline residue:  R  61  - end of helix
    Processing helix  chain 'R' and resid 90 through 119
      Proline residue:  R 111  - end of helix
    Processing helix  chain 'R' and resid 125 through 160
      removed outlier: 4.248A  pdb=" N   LEU R 129 " --> pdb=" O   PHE R 125 " (cutoff:3.500A)
      removed outlier: 3.796A  pdb=" N   ASN R 134 " --> pdb=" O   CYS R 130 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 170 through 195
      Proline residue:  R 191  - end of helix
    Processing helix  chain 'R' and resid 217 through 233
      removed outlier: 3.843A  pdb=" N   GLU R 221 " --> pdb=" O   SER R 217 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 233 through 257
    Processing helix  chain 'R' and resid 264 through 299
      Proline residue:  R 285  - end of helix
    Processing helix  chain 'R' and resid 303 through 322
      removed outlier: 4.253A  pdb=" N   PHE R 319 " --> pdb=" O   GLN R 315 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 323 through 333
      Proline residue:  R 329  - end of helix
    Processing helix  chain 'R' and resid 336 through 345
    Processing helix  chain 'S' and resid 28 through 32
    Processing helix  chain 'S' and resid 87 through 91
    Processing helix  chain 'S' and resid 220 through 224
      removed outlier: 4.030A  pdb=" N   VAL S 224 " --> pdb=" O   ALA S 221 " (cutoff:3.500A)
    Processing helix  chain 'Y' and resid 12 through 25
    Processing helix  chain 'Y' and resid 29 through 44
    Processing sheet with id=AA1, first strand: chain 'A' and resid 184 through 191
      removed outlier: 5.940A  pdb=" N   LEU A  34 " --> pdb=" O   HIS A 197 " (cutoff:3.500A)
      removed outlier: 7.370A  pdb=" N   PHE A 199 " --> pdb=" O   LEU A  34 " (cutoff:3.500A)
      removed outlier: 6.984A  pdb=" N   LEU A  36 " --> pdb=" O   PHE A 199 " (cutoff:3.500A)
      removed outlier: 7.106A  pdb=" N   VAL A 201 " --> pdb=" O   LEU A  36 " (cutoff:3.500A)
      removed outlier: 6.911A  pdb=" N   LEU A  38 " --> pdb=" O   VAL A 201 " (cutoff:3.500A)
      removed outlier: 7.012A  pdb=" N   ARG A  35 " --> pdb=" O   ALA A 220 " (cutoff:3.500A)
      removed outlier: 7.584A  pdb=" N   ILE A 222 " --> pdb=" O   ARG A  35 " (cutoff:3.500A)
      removed outlier: 5.968A  pdb=" N   LEU A  37 " --> pdb=" O   ILE A 222 " (cutoff:3.500A)
      removed outlier: 7.155A  pdb=" N   VAL A 224 " --> pdb=" O   LEU A  37 " (cutoff:3.500A)
      removed outlier: 6.777A  pdb=" N   LEU A  39 " --> pdb=" O   VAL A 224 " (cutoff:3.500A)
      removed outlier: 8.480A  pdb=" N   ASP A 226 " --> pdb=" O   LEU A  39 " (cutoff:3.500A)
      removed outlier: 6.513A  pdb=" N   ILE A 221 " --> pdb=" O   ILE A 255 " (cutoff:3.500A)
      removed outlier: 6.906A  pdb=" N   PHE A 257 " --> pdb=" O   ILE A 221 " (cutoff:3.500A)
      removed outlier: 6.244A  pdb=" N   PHE A 223 " --> pdb=" O   PHE A 257 " (cutoff:3.500A)
      removed outlier: 6.506A  pdb=" N   ASN A 259 " --> pdb=" O   PHE A 223 " (cutoff:3.500A)
      removed outlier: 5.832A  pdb=" N   VAL A 225 " --> pdb=" O   ASN A 259 " (cutoff:3.500A)
      removed outlier: 7.334A  pdb=" N   HIS A 329 " --> pdb=" O   VAL A 254 " (cutoff:3.500A)
      removed outlier: 6.105A  pdb=" N   LEU A 256 " --> pdb=" O   HIS A 329 " (cutoff:3.500A)
      removed outlier: 6.678A  pdb=" N   THR A 331 " --> pdb=" O   LEU A 256 " (cutoff:3.500A)
      removed outlier: 5.733A  pdb=" N   LEU A 258 " --> pdb=" O   THR A 331 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51
      removed outlier: 5.321A  pdb=" N   THR B  47 " --> pdb=" O   ASN B 340 " (cutoff:3.500A)
      removed outlier: 6.523A  pdb=" N   ASN B 340 " --> pdb=" O   THR B  47 " (cutoff:3.500A)
      removed outlier: 3.732A  pdb=" N   CYS B 317 " --> pdb=" O   GLY B 330 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63
      removed outlier: 3.578A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 6.444A  pdb=" N   ASP B  83 " --> pdb=" O   LYS B  89 " (cutoff:3.500A)
      removed outlier: 5.846A  pdb=" N   LYS B  89 " --> pdb=" O   ASP B  83 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105
      removed outlier: 6.685A  pdb=" N   GLY B 115 " --> pdb=" O   MET B 101 " (cutoff:3.500A)
      removed outlier: 4.335A  pdb=" N   CYS B 103 " --> pdb=" O   ALA B 113 " (cutoff:3.500A)
      removed outlier: 6.572A  pdb=" N   ALA B 113 " --> pdb=" O   CYS B 103 " (cutoff:3.500A)
      removed outlier: 5.125A  pdb=" N   TYR B 105 " --> pdb=" O   TYR B 111 " (cutoff:3.500A)
      removed outlier: 7.385A  pdb=" N   TYR B 111 " --> pdb=" O   TYR B 105 " (cutoff:3.500A)
      removed outlier: 6.111A  pdb=" N   CYS B 121 " --> pdb=" O   GLU B 138 " (cutoff:3.500A)
      removed outlier: 4.387A  pdb=" N   GLU B 138 " --> pdb=" O   CYS B 121 " (cutoff:3.500A)
      removed outlier: 6.450A  pdb=" N   ILE B 123 " --> pdb=" O   SER B 136 " (cutoff:3.500A)
      removed outlier: 3.867A  pdb=" N   ARG B 134 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 153
      removed outlier: 3.594A  pdb=" N   CYS B 148 " --> pdb=" O   SER B 160 " (cutoff:3.500A)
      removed outlier: 6.426A  pdb=" N   GLN B 156 " --> pdb=" O   LEU B 152 " (cutoff:3.500A)
      removed outlier: 6.403A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 6.053A  pdb=" N   GLN B 176 " --> pdb=" O   ASP B 170 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192
      removed outlier: 6.659A  pdb=" N   GLY B 202 " --> pdb=" O   MET B 188 " (cutoff:3.500A)
      removed outlier: 4.403A  pdb=" N   LEU B 190 " --> pdb=" O   VAL B 200 " (cutoff:3.500A)
      removed outlier: 6.875A  pdb=" N   VAL B 200 " --> pdb=" O   LEU B 190 " (cutoff:3.500A)
      removed outlier: 5.010A  pdb=" N   LEU B 192 " --> pdb=" O   LEU B 198 " (cutoff:3.500A)
      removed outlier: 7.228A  pdb=" N   LEU B 198 " --> pdb=" O   LEU B 192 " (cutoff:3.500A)
      removed outlier: 3.670A  pdb=" N   GLN B 220 " --> pdb=" O   LEU B 210 " (cutoff:3.500A)
      removed outlier: 6.712A  pdb=" N   ASP B 212 " --> pdb=" O   CYS B 218 " (cutoff:3.500A)
      removed outlier: 6.392A  pdb=" N   CYS B 218 " --> pdb=" O   ASP B 212 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234
      removed outlier: 6.471A  pdb=" N   CYS B 250 " --> pdb=" O   THR B 263 " (cutoff:3.500A)
      removed outlier: 4.646A  pdb=" N   THR B 263 " --> pdb=" O   CYS B 250 " (cutoff:3.500A)
      removed outlier: 6.941A  pdb=" N   LEU B 252 " --> pdb=" O   LEU B 261 " (cutoff:3.500A)
      removed outlier: 3.741A  pdb=" N   GLN B 259 " --> pdb=" O   ASP B 254 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278
      removed outlier: 6.218A  pdb=" N   GLY B 288 " --> pdb=" O   THR B 274 " (cutoff:3.500A)
      removed outlier: 4.319A  pdb=" N   VAL B 276 " --> pdb=" O   LEU B 286 " (cutoff:3.500A)
      removed outlier: 6.891A  pdb=" N   LEU B 286 " --> pdb=" O   VAL B 276 " (cutoff:3.500A)
      removed outlier: 4.662A  pdb=" N   PHE B 278 " --> pdb=" O   LEU B 284 " (cutoff:3.500A)
      removed outlier: 7.000A  pdb=" N   LEU B 284 " --> pdb=" O   PHE B 278 " (cutoff:3.500A)
      removed outlier: 6.822A  pdb=" N   ASP B 298 " --> pdb=" O   ARG B 304 " (cutoff:3.500A)
      removed outlier: 6.560A  pdb=" N   ARG B 304 " --> pdb=" O   ASP B 298 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'R' and resid 196 through 201
    Processing sheet with id=AB1, first strand: chain 'S' and resid 3 through 7
      removed outlier: 3.974A  pdb=" N   VAL S   5 " --> pdb=" O   SER S  23 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'S' and resid 10 through 12
      removed outlier: 3.517A  pdb=" N   ALA S  92 " --> pdb=" O   LEU S 117 " (cutoff:3.500A)
      removed outlier: 6.793A  pdb=" N   MET S  34 " --> pdb=" O   TYR S  50 " (cutoff:3.500A)
      removed outlier: 4.494A  pdb=" N   TYR S  50 " --> pdb=" O   MET S  34 " (cutoff:3.500A)
      removed outlier: 6.602A  pdb=" N   TRP S  36 " --> pdb=" O   VAL S  48 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'S' and resid 10 through 12
      removed outlier: 3.517A  pdb=" N   ALA S  92 " --> pdb=" O   LEU S 117 " (cutoff:3.500A)
      removed outlier: 4.417A  pdb=" N   PHE S 110 " --> pdb=" O   ARG S  98 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'S' and resid 140 through 142
    Processing sheet with id=AB5, first strand: chain 'S' and resid 146 through 148
      removed outlier: 5.158A  pdb=" N   LEU S 174 " --> pdb=" O   TYR S 190 " (cutoff:3.500A)
      removed outlier: 4.301A  pdb=" N   TYR S 190 " --> pdb=" O   LEU S 174 " (cutoff:3.500A)
      removed outlier: 6.591A  pdb=" N   TRP S 176 " --> pdb=" O   LEU S 188 " (cutoff:3.500A)
      removed outlier: 4.001A  pdb=" N   ARG S 191 " --> pdb=" O   ASN S 194 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'S' and resid 146 through 148
      removed outlier: 3.561A  pdb=" N   GLN S 231 " --> pdb=" O   THR S 238 " (cutoff:3.500A)
      removed outlier: 4.377A  pdb=" N   THR S 238 " --> pdb=" O   GLN S 231 " (cutoff:3.500A)

    473 hydrogen bonds defined for protein.
    1323 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: 2.51

  Time building geometry restraints manager: 2.83 seconds

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

  Histogram of bond lengths:
        1.20 -     1.32: 1498
        1.32 -     1.44: 2519
        1.44 -     1.57: 5081
        1.57 -     1.69: 0
        1.69 -     1.81: 93
  Bond restraints: 9191
  Sorted by residual:
  bond pdb=" CA  THR A 331 "
       pdb=" C   THR A 331 "
    ideal  model  delta    sigma   weight residual
    1.520  1.471  0.049 1.21e-02 6.83e+03 1.64e+01
  bond pdb=" C   SER A 333 "
       pdb=" O   SER A 333 "
    ideal  model  delta    sigma   weight residual
    1.237  1.198  0.038 1.17e-02 7.31e+03 1.08e+01
  bond pdb=" CA  CYS A 332 "
       pdb=" C   CYS A 332 "
    ideal  model  delta    sigma   weight residual
    1.526  1.484  0.042 1.37e-02 5.33e+03 9.59e+00
  bond pdb=" C   SER A 333 "
       pdb=" N   VAL A 334 "
    ideal  model  delta    sigma   weight residual
    1.336  1.309  0.027 1.17e-02 7.31e+03 5.31e+00
  bond pdb=" N   THR A 331 "
       pdb=" CA  THR A 331 "
    ideal  model  delta    sigma   weight residual
    1.457  1.430  0.026 1.24e-02 6.50e+03 4.45e+00
  ... (remaining 9186 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.48: 12139
        1.48 -     2.96: 268
        2.96 -     4.44: 42
        4.44 -     5.91: 13
        5.91 -     7.39: 2
  Bond angle restraints: 12464
  Sorted by residual:
  angle pdb=" C   ALA R 321 "
        pdb=" N   TYR R 322 "
        pdb=" CA  TYR R 322 "
      ideal   model   delta    sigma   weight residual
     122.50  115.11    7.39 1.82e+00 3.02e-01 1.65e+01
  angle pdb=" N   SER A 333 "
        pdb=" CA  SER A 333 "
        pdb=" C   SER A 333 "
      ideal   model   delta    sigma   weight residual
     111.28  115.63   -4.35 1.09e+00 8.42e-01 1.59e+01
  angle pdb=" C   VAL A 334 "
        pdb=" N   ASP A 335 "
        pdb=" CA  ASP A 335 "
      ideal   model   delta    sigma   weight residual
     121.02  126.40   -5.38 1.48e+00 4.57e-01 1.32e+01
  angle pdb=" N   VAL A 334 "
        pdb=" CA  VAL A 334 "
        pdb=" C   VAL A 334 "
      ideal   model   delta    sigma   weight residual
     113.07  117.83   -4.76 1.36e+00 5.41e-01 1.23e+01
  angle pdb=" C   THR A 331 "
        pdb=" CA  THR A 331 "
        pdb=" CB  THR A 331 "
      ideal   model   delta    sigma   weight residual
     109.70  104.84    4.86 1.81e+00 3.05e-01 7.21e+00
  ... (remaining 12459 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.68: 5037
       17.68 -    35.36: 353
       35.36 -    53.05: 42
       53.05 -    70.73: 11
       70.73 -    88.41: 8
  Dihedral angle restraints: 5451
    sinusoidal: 2115
      harmonic: 3336
  Sorted by residual:
  dihedral pdb=" CA  TYR R 322 "
           pdb=" C   TYR R 322 "
           pdb=" N   SER R 323 "
           pdb=" CA  SER R 323 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  149.03   30.97     0      5.00e+00 4.00e-02 3.84e+01
  dihedral pdb=" CA  TYR S 190 "
           pdb=" C   TYR S 190 "
           pdb=" N   ARG S 191 "
           pdb=" CA  ARG S 191 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  153.66   26.34     0      5.00e+00 4.00e-02 2.77e+01
  dihedral pdb=" CA  LYS B  78 "
           pdb=" C   LYS B  78 "
           pdb=" N   LEU B  79 "
           pdb=" CA  LEU B  79 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  153.69   26.31     0      5.00e+00 4.00e-02 2.77e+01
  ... (remaining 5448 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.034: 931
       0.034 -    0.069: 330
       0.069 -    0.103: 112
       0.103 -    0.138: 40
       0.138 -    0.172: 5
  Chirality restraints: 1418
  Sorted by residual:
  chirality pdb=" CA  SER A 333 "
            pdb=" N   SER A 333 "
            pdb=" C   SER A 333 "
            pdb=" CB  SER A 333 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.34    0.17 2.00e-01 2.50e+01 7.42e-01
  chirality pdb=" CA  PHE B 292 "
            pdb=" N   PHE B 292 "
            pdb=" C   PHE B 292 "
            pdb=" CB  PHE B 292 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.34    0.17 2.00e-01 2.50e+01 7.35e-01
  chirality pdb=" CA  TYR R 322 "
            pdb=" N   TYR R 322 "
            pdb=" C   TYR R 322 "
            pdb=" CB  TYR R 322 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.35    0.16 2.00e-01 2.50e+01 6.17e-01
  ... (remaining 1415 not shown)

  Planarity restraints: 1580
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG B 150 "   -0.066 9.50e-02 1.11e+02   3.93e-02 8.91e+00
        pdb=" NE  ARG B 150 "    0.021 2.00e-02 2.50e+03
        pdb=" CZ  ARG B 150 "   -0.049 2.00e-02 2.50e+03
        pdb=" NH1 ARG B 150 "    0.017 2.00e-02 2.50e+03
        pdb=" NH2 ARG B 150 "    0.014 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU R 228 "   -0.015 2.00e-02 2.50e+03   2.95e-02 8.72e+00
        pdb=" C   LEU R 228 "    0.051 2.00e-02 2.50e+03
        pdb=" O   LEU R 228 "   -0.019 2.00e-02 2.50e+03
        pdb=" N   ASN R 229 "   -0.017 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL R 230 "    0.014 2.00e-02 2.50e+03   2.84e-02 8.05e+00
        pdb=" C   VAL R 230 "   -0.049 2.00e-02 2.50e+03
        pdb=" O   VAL R 230 "    0.018 2.00e-02 2.50e+03
        pdb=" N   VAL R 231 "    0.017 2.00e-02 2.50e+03
  ... (remaining 1577 not shown)

  Histogram of nonbonded interaction distances:
        2.19 -     2.74: 492
        2.74 -     3.28: 9670
        3.28 -     3.82: 15606
        3.82 -     4.36: 19245
        4.36 -     4.90: 32608
  Nonbonded interactions: 77621
  Sorted by model distance:
  nonbonded pdb=" NZ  LYS A 210 "
            pdb=" OD2 ASP B 228 "
     model   vdw
     2.194 3.120
  nonbonded pdb=" NE  ARG A 205 "
            pdb=" OD1 ASP B 186 "
     model   vdw
     2.249 3.120
  nonbonded pdb=" NH2 ARG A 208 "
            pdb=" OD1 ASP A 239 "
     model   vdw
     2.264 3.120
  nonbonded pdb=" OG  SER B 245 "
            pdb=" OD1 ASP B 247 "
     model   vdw
     2.284 3.040
  nonbonded pdb=" O   ALA R 158 "
            pdb=" OG1 THR R 162 "
     model   vdw
     2.285 3.040
  ... (remaining 77616 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:             0.620
  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:          0.350
  Check model and map are aligned:         0.060
  Set scattering table:                    0.080
  Process input model:                     23.440
  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:12.260
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   36.930
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6479
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      :  0.003   0.050   9192  Z= 0.146
  Angle     :  0.575   7.394  12466  Z= 0.341
  Chirality :  0.043   0.172   1418
  Planarity :  0.006   0.081   1580
  Dihedral  : 12.794  88.412   3290
  Min Nonbonded Distance : 2.194

Molprobity Statistics.
  All-atom Clashscore : 5.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.19 %
    Favored  : 96.81 %
  Rotamer:
    Outliers :  0.41 %
    Allowed  :  2.55 %
    Favored  : 97.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

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: -0.75 (0.24), residues: 1130
  helix: -0.18 (0.23), residues: 410
  sheet: -0.65 (0.31), residues: 270
  loop : -0.47 (0.30), residues: 450

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.002   TRP A 211 
 HIS   0.004   0.001   HIS A 324 
 PHE   0.016   0.001   PHE D   5 
 TYR   0.028   0.003   TYR R 322 
 ARG   0.050   0.007   ARG B 150 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.15905 (  463)
  hydrogen bonds       : angle       6.80545 ( 1323)
  SS BOND              : bond        0.00123 (    1)
  SS BOND              : angle       1.29023 (    2)
  covalent geometry    : bond        0.00257 ( 9191)
  covalent geometry    : angle       0.57440 (12464)

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

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

  2260 Ramachandran restraints generated.
    1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2260 Ramachandran restraints generated.
    1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  291 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 287
  time to evaluate  : 0.915 
Fit side-chains
REVERT: A    8 GLU cc_start: 0.6969 (mt-10) cc_final: 0.6725 (mt-10)
REVERT: A   14 GLU cc_start: 0.6542 (tm-30) cc_final: 0.6316 (tm-30)
REVERT: A   17 LYS cc_start: 0.7876 (mttt) cc_final: 0.7660 (mttt)
REVERT: A   33 THR cc_start: 0.8650 (t) cc_final: 0.8257 (p)
REVERT: A  229 ASP cc_start: 0.6913 (t0) cc_final: 0.6626 (t0)
REVERT: A  238 ASN cc_start: 0.8243 (m-40) cc_final: 0.8036 (m-40)
REVERT: A  302 THR cc_start: 0.8104 (m) cc_final: 0.7812 (m)
REVERT: B   61 MET cc_start: 0.6940 (ptp) cc_final: 0.6429 (ppp)
REVERT: B   74 SER cc_start: 0.7767 (p) cc_final: 0.7331 (t)
REVERT: B   88 ASN cc_start: 0.7601 (m-40) cc_final: 0.7359 (m110)
REVERT: B   99 TRP cc_start: 0.8152 (m100) cc_final: 0.7497 (m100)
REVERT: B  120 ILE cc_start: 0.7455 (mt) cc_final: 0.7144 (mm)
REVERT: B  179 THR cc_start: 0.8093 (t) cc_final: 0.7681 (m)
REVERT: B  189 SER cc_start: 0.7894 (p) cc_final: 0.7687 (t)
REVERT: B  190 LEU cc_start: 0.7360 (tt) cc_final: 0.7096 (tp)
REVERT: B  207 SER cc_start: 0.8041 (t) cc_final: 0.7701 (p)
REVERT: B  212 ASP cc_start: 0.6972 (t0) cc_final: 0.6350 (t0)
REVERT: B  217 MET cc_start: 0.6969 (ptt) cc_final: 0.6578 (ptt)
REVERT: B  262 MET cc_start: 0.6775 (ttm) cc_final: 0.6268 (ttm)
REVERT: B  264 TYR cc_start: 0.7499 (m-80) cc_final: 0.6122 (m-80)
REVERT: B  271 CYS cc_start: 0.6976 (m) cc_final: 0.6716 (m)
REVERT: B  277 SER cc_start: 0.7788 (t) cc_final: 0.7307 (p)
REVERT: B  325 MET cc_start: 0.7089 (tpp) cc_final: 0.6302 (tpp)
REVERT: R  125 PHE cc_start: 0.8309 (m-80) cc_final: 0.8107 (m-80)
REVERT: R  248 MET cc_start: 0.5972 (mtm) cc_final: 0.5748 (mtm)
REVERT: S   86 LEU cc_start: 0.8750 (mt) cc_final: 0.8484 (mm)
REVERT: S  219 LEU cc_start: 0.7943 (tt) cc_final: 0.7669 (tt)
  outliers start: 4
  outliers final: 2
  residues processed: 291
  average time/residue: 0.9657
  time to fit residues: 304.3959
Evaluate side-chains
  256 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 254
  time to evaluate  : 1.012 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  332 CYS
Chi-restraints excluded: chain R residue  310 ILE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 95 optimal weight:    1.9990
   chunk 85 optimal weight:    5.9990
   chunk 47 optimal weight:    5.9990
   chunk 29 optimal weight:    2.9990
   chunk 57 optimal weight:    1.9990
   chunk 45 optimal weight:    0.7980
   chunk 88 optimal weight:    0.0020
   chunk 34 optimal weight:    0.0970
   chunk 53 optimal weight:    5.9990
   chunk 65 optimal weight:    0.7980
   chunk 102 optimal weight:    2.9990
   overall best weight:    0.7388

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

Flipped N/Q/H residues before XYZ refinement:
A 259 ASN
A 338 ASN
B 125 ASN
B 237 ASN
** R 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
S  77 ASN
** S 167 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
S 186 GLN
S 194 ASN
Y  18 GLN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4014 r_free = 0.4014 target = 0.157987 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3796 r_free = 0.3796 target = 0.140306 restraints weight = 11836.272|
|-----------------------------------------------------------------------------|
r_work (start): 0.3800 rms_B_bonded: 1.86
r_work: 0.3687 rms_B_bonded: 2.42 restraints_weight: 0.5000
r_work: 0.3532 rms_B_bonded: 4.24 restraints_weight: 0.2500
r_work (final): 0.3532
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7337
moved from start:          0.2472

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.065   9192  Z= 0.170
  Angle     :  0.623   8.980  12466  Z= 0.329
  Chirality :  0.044   0.190   1418
  Planarity :  0.005   0.042   1580
  Dihedral  :  5.536  36.622   1251
  Min Nonbonded Distance : 2.569

Molprobity Statistics.
  All-atom Clashscore : 7.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.33 %
    Favored  : 98.67 %
  Rotamer:
    Outliers :  2.65 %
    Allowed  : 12.63 %
    Favored  : 84.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

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:  0.62 (0.25), residues: 1130
  helix:  1.77 (0.25), residues: 394
  sheet: -0.72 (0.30), residues: 273
  loop :  0.09 (0.31), residues: 463

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.002   TRP B 169 
 HIS   0.010   0.002   HIS S 167 
 PHE   0.017   0.002   PHE R 195 
 TYR   0.027   0.002   TYR R 322 
 ARG   0.010   0.001   ARG A 232 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04158 (  463)
  hydrogen bonds       : angle       5.10110 ( 1323)
  SS BOND              : bond        0.00622 (    1)
  SS BOND              : angle       1.59663 (    2)
  covalent geometry    : bond        0.00387 ( 9191)
  covalent geometry    : angle       0.62265 (12464)

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

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

  2260 Ramachandran restraints generated.
    1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2260 Ramachandran restraints generated.
    1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  311 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 285
  time to evaluate  : 0.888 
Fit side-chains
REVERT: A   14 GLU cc_start: 0.7617 (tm-30) cc_final: 0.7392 (tm-30)
REVERT: A   17 LYS cc_start: 0.8217 (mttt) cc_final: 0.8015 (mttt)
REVERT: A  185 PHE cc_start: 0.7020 (m-80) cc_final: 0.6696 (m-80)
REVERT: A  188 LYS cc_start: 0.8411 (mttt) cc_final: 0.8173 (mttt)
REVERT: A  199 PHE cc_start: 0.8721 (m-80) cc_final: 0.8483 (m-80)
REVERT: A  200 ASP cc_start: 0.7508 (t70) cc_final: 0.6961 (t70)
REVERT: A  229 ASP cc_start: 0.7586 (t0) cc_final: 0.7139 (t0)
REVERT: A  235 GLU cc_start: 0.7336 (tt0) cc_final: 0.7115 (tt0)
REVERT: A  238 ASN cc_start: 0.8374 (m-40) cc_final: 0.8148 (m-40)
REVERT: A  246 ASN cc_start: 0.8374 (OUTLIER) cc_final: 0.8170 (t0)
REVERT: A  281 GLU cc_start: 0.7172 (OUTLIER) cc_final: 0.6849 (mp0)
REVERT: A  335 ASP cc_start: 0.7639 (t0) cc_final: 0.7424 (t0)
REVERT: B   76 ASP cc_start: 0.7018 (t70) cc_final: 0.6766 (t0)
REVERT: B  156 GLN cc_start: 0.8306 (mt0) cc_final: 0.8082 (mt0)
REVERT: B  170 ASP cc_start: 0.8178 (m-30) cc_final: 0.7943 (m-30)
REVERT: B  188 MET cc_start: 0.7960 (mmm) cc_final: 0.7637 (mmm)
REVERT: B  189 SER cc_start: 0.8227 (p) cc_final: 0.7931 (t)
REVERT: B  201 SER cc_start: 0.8210 (m) cc_final: 0.7938 (p)
REVERT: B  212 ASP cc_start: 0.7709 (t0) cc_final: 0.7409 (t0)
REVERT: B  217 MET cc_start: 0.7789 (ptt) cc_final: 0.7523 (ptt)
REVERT: B  221 THR cc_start: 0.7649 (m) cc_final: 0.7415 (m)
REVERT: B  228 ASP cc_start: 0.7998 (p0) cc_final: 0.7597 (p0)
REVERT: B  239 ASN cc_start: 0.7965 (m-40) cc_final: 0.7655 (m-40)
REVERT: B  264 TYR cc_start: 0.7900 (m-80) cc_final: 0.7209 (m-80)
REVERT: B  275 SER cc_start: 0.7972 (t) cc_final: 0.7719 (m)
REVERT: B  277 SER cc_start: 0.8072 (t) cc_final: 0.7758 (p)
REVERT: R  152 SER cc_start: 0.8294 (t) cc_final: 0.8014 (m)
REVERT: R  324 ASN cc_start: 0.7673 (t0) cc_final: 0.6664 (t0)
REVERT: R  325 SER cc_start: 0.8680 (p) cc_final: 0.8474 (t)
REVERT: R  328 ASN cc_start: 0.6866 (m110) cc_final: 0.6235 (m110)
REVERT: S   18 ARG cc_start: 0.7939 (tpp80) cc_final: 0.7655 (tpp80)
REVERT: S  161 SER cc_start: 0.7973 (p) cc_final: 0.7676 (t)
REVERT: S  231 GLN cc_start: 0.8442 (pp30) cc_final: 0.8124 (pp30)
  outliers start: 26
  outliers final: 6
  residues processed: 294
  average time/residue: 1.0263
  time to fit residues: 325.6801
Evaluate side-chains
  268 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 260
  time to evaluate  : 1.029 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  187 THR
Chi-restraints excluded: chain A residue  191 VAL
Chi-restraints excluded: chain A residue  246 ASN
Chi-restraints excluded: chain A residue  281 GLU
Chi-restraints excluded: chain A residue  301 VAL
Chi-restraints excluded: chain A residue  360 LEU
Chi-restraints excluded: chain B residue   98 SER
Chi-restraints excluded: chain R residue  271 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 21 optimal weight:    0.6980
   chunk 64 optimal weight:    0.9980
   chunk 68 optimal weight:    0.2980
   chunk 4 optimal weight:    0.8980
   chunk 20 optimal weight:    3.9990
   chunk 102 optimal weight:    2.9990
   chunk 46 optimal weight:    0.9990
   chunk 98 optimal weight:    9.9990
   chunk 78 optimal weight:    2.9990
   chunk 86 optimal weight:    1.9990
   chunk 19 optimal weight:    0.8980
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
A 259 ASN
B 110 ASN
B 125 ASN
B 132 ASN
B 220 GLN
B 340 ASN
R  57 ASN
R 119 ASN
** R 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
S 167 HIS
S 194 ASN

Total number of N/Q/H flips: 10

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4005 r_free = 0.4005 target = 0.156766 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3783 r_free = 0.3783 target = 0.138985 restraints weight = 11900.080|
|-----------------------------------------------------------------------------|
r_work (start): 0.3740 rms_B_bonded: 1.90
r_work: 0.3627 rms_B_bonded: 2.43 restraints_weight: 0.5000
r_work: 0.3473 rms_B_bonded: 4.21 restraints_weight: 0.2500
r_work (final): 0.3473
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7358
moved from start:          0.3059

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.051   9192  Z= 0.165
  Angle     :  0.597   9.245  12466  Z= 0.313
  Chirality :  0.044   0.175   1418
  Planarity :  0.004   0.040   1580
  Dihedral  :  5.221  36.155   1248
  Min Nonbonded Distance : 2.541

Molprobity Statistics.
  All-atom Clashscore : 8.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.59 %
    Favored  : 98.41 %
  Rotamer:
    Outliers :  3.36 %
    Allowed  : 15.17 %
    Favored  : 81.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

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:  0.73 (0.25), residues: 1130
  helix:  2.08 (0.25), residues: 394
  sheet: -0.87 (0.30), residues: 272
  loop :  0.08 (0.30), residues: 464

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP B 169 
 HIS   0.009   0.002   HIS S 167 
 PHE   0.025   0.002   PHE R 195 
 TYR   0.027   0.002   TYR R 322 
 ARG   0.011   0.001   ARG A 232 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04087 (  463)
  hydrogen bonds       : angle       5.01807 ( 1323)
  SS BOND              : bond        0.00287 (    1)
  SS BOND              : angle       1.29023 (    2)
  covalent geometry    : bond        0.00373 ( 9191)
  covalent geometry    : angle       0.59660 (12464)

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

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

  2260 Ramachandran restraints generated.
    1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2260 Ramachandran restraints generated.
    1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  299 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 266
  time to evaluate  : 1.598 
Fit side-chains
REVERT: A   17 LYS cc_start: 0.8248 (mttt) cc_final: 0.8039 (mttt)
REVERT: A  185 PHE cc_start: 0.7128 (m-80) cc_final: 0.6821 (m-80)
REVERT: A  229 ASP cc_start: 0.7611 (t0) cc_final: 0.7184 (t0)
REVERT: A  238 ASN cc_start: 0.8366 (m-40) cc_final: 0.8130 (m-40)
REVERT: A  281 GLU cc_start: 0.7133 (OUTLIER) cc_final: 0.6825 (mp0)
REVERT: A  335 ASP cc_start: 0.7669 (t0) cc_final: 0.7422 (t0)
REVERT: A  358 TYR cc_start: 0.8069 (m-80) cc_final: 0.7862 (m-80)
REVERT: B   50 THR cc_start: 0.7746 (m) cc_final: 0.7505 (t)
REVERT: B   76 ASP cc_start: 0.7128 (t70) cc_final: 0.6890 (t0)
REVERT: B  137 ARG cc_start: 0.7739 (ttm-80) cc_final: 0.7488 (ttm-80)
REVERT: B  156 GLN cc_start: 0.8402 (mt0) cc_final: 0.8102 (mt0)
REVERT: B  189 SER cc_start: 0.8185 (p) cc_final: 0.7930 (t)
REVERT: B  201 SER cc_start: 0.8246 (m) cc_final: 0.8029 (p)
REVERT: B  212 ASP cc_start: 0.7674 (t0) cc_final: 0.7307 (t0)
REVERT: B  217 MET cc_start: 0.7850 (ptt) cc_final: 0.7524 (ptt)
REVERT: B  228 ASP cc_start: 0.8061 (p0) cc_final: 0.7408 (p0)
REVERT: B  230 ASN cc_start: 0.8051 (m-40) cc_final: 0.7802 (m110)
REVERT: B  246 ASP cc_start: 0.7641 (t70) cc_final: 0.7412 (m-30)
REVERT: B  264 TYR cc_start: 0.7860 (m-80) cc_final: 0.7285 (m-80)
REVERT: B  275 SER cc_start: 0.8016 (t) cc_final: 0.7789 (m)
REVERT: B  277 SER cc_start: 0.8128 (t) cc_final: 0.7777 (p)
REVERT: R   64 LEU cc_start: 0.8077 (OUTLIER) cc_final: 0.7815 (mp)
REVERT: R  152 SER cc_start: 0.8332 (t) cc_final: 0.7976 (m)
REVERT: R  165 MET cc_start: 0.5607 (pp-130) cc_final: 0.5099 (pp-130)
REVERT: R  309 ILE cc_start: 0.8554 (mt) cc_final: 0.8334 (mp)
REVERT: S   18 ARG cc_start: 0.8002 (tpp80) cc_final: 0.7759 (tpp80)
REVERT: S   67 ARG cc_start: 0.8387 (ttp80) cc_final: 0.8143 (ttp80)
REVERT: S   95 TYR cc_start: 0.8344 (m-80) cc_final: 0.8110 (m-80)
REVERT: S  161 SER cc_start: 0.8164 (p) cc_final: 0.7712 (t)
REVERT: S  172 THR cc_start: 0.8654 (m) cc_final: 0.8425 (p)
REVERT: S  231 GLN cc_start: 0.8518 (pp30) cc_final: 0.8097 (pp30)
REVERT: Y   30 VAL cc_start: 0.8021 (t) cc_final: 0.7735 (t)
  outliers start: 33
  outliers final: 11
  residues processed: 282
  average time/residue: 0.9381
  time to fit residues: 287.2730
Evaluate side-chains
  273 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 260
  time to evaluate  : 0.892 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  184 ILE
Chi-restraints excluded: chain A residue  187 THR
Chi-restraints excluded: chain A residue  191 VAL
Chi-restraints excluded: chain A residue  251 THR
Chi-restraints excluded: chain A residue  281 GLU
Chi-restraints excluded: chain A residue  301 VAL
Chi-restraints excluded: chain A residue  360 LEU
Chi-restraints excluded: chain B residue   98 SER
Chi-restraints excluded: chain R residue   64 LEU
Chi-restraints excluded: chain R residue  234 LEU
Chi-restraints excluded: chain R residue  271 LEU
Chi-restraints excluded: chain R residue  281 ILE
Chi-restraints excluded: chain S residue  230 MET
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 57 optimal weight:    1.9990
   chunk 69 optimal weight:    1.9990
   chunk 106 optimal weight:    4.9990
   chunk 94 optimal weight:    0.9980
   chunk 30 optimal weight:    0.6980
   chunk 5 optimal weight:    4.9990
   chunk 83 optimal weight:    2.9990
   chunk 9 optimal weight:    0.5980
   chunk 47 optimal weight:    1.9990
   chunk 42 optimal weight:    0.6980
   chunk 105 optimal weight:    3.9990
   overall best weight:    0.9982

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

Flipped N/Q/H residues before XYZ refinement:
A 216 ASN
B 125 ASN
B 313 ASN
R 119 ASN
** R 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
S 186 GLN
S 194 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3936 r_free = 0.3936 target = 0.151384 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3706 r_free = 0.3706 target = 0.133200 restraints weight = 11891.350|
|-----------------------------------------------------------------------------|
r_work (start): 0.3707 rms_B_bonded: 1.93
r_work: 0.3590 rms_B_bonded: 2.44 restraints_weight: 0.5000
r_work: 0.3433 rms_B_bonded: 4.23 restraints_weight: 0.2500
r_work (final): 0.3433
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7370
moved from start:          0.3588

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.059   9192  Z= 0.198
  Angle     :  0.607   8.062  12466  Z= 0.317
  Chirality :  0.044   0.176   1418
  Planarity :  0.004   0.041   1580
  Dihedral  :  5.186  38.275   1248
  Min Nonbonded Distance : 2.505

Molprobity Statistics.
  All-atom Clashscore : 10.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.50 %
    Favored  : 98.50 %
  Rotamer:
    Outliers :  3.67 %
    Allowed  : 16.19 %
    Favored  : 80.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

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:  0.59 (0.25), residues: 1130
  helix:  1.94 (0.26), residues: 394
  sheet: -0.87 (0.29), residues: 272
  loop : -0.03 (0.30), residues: 464

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP B 169 
 HIS   0.006   0.001   HIS A 329 
 PHE   0.020   0.002   PHE R 195 
 TYR   0.025   0.002   TYR R 322 
 ARG   0.007   0.000   ARG A 232 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04090 (  463)
  hydrogen bonds       : angle       5.06526 ( 1323)
  SS BOND              : bond        0.00280 (    1)
  SS BOND              : angle       1.46212 (    2)
  covalent geometry    : bond        0.00454 ( 9191)
  covalent geometry    : angle       0.60669 (12464)

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

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

  2260 Ramachandran restraints generated.
    1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2260 Ramachandran restraints generated.
    1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  310 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 274
  time to evaluate  : 0.907 
Fit side-chains
   revert: symmetry clash
REVERT: A  185 PHE cc_start: 0.7270 (m-80) cc_final: 0.6936 (m-80)
REVERT: A  229 ASP cc_start: 0.7649 (t0) cc_final: 0.7187 (t0)
REVERT: A  238 ASN cc_start: 0.8301 (m-40) cc_final: 0.8072 (m-40)
REVERT: A  263 LEU cc_start: 0.8187 (mt) cc_final: 0.7987 (mp)
REVERT: A  281 GLU cc_start: 0.7146 (OUTLIER) cc_final: 0.6836 (mp0)
REVERT: A  335 ASP cc_start: 0.7728 (t0) cc_final: 0.7476 (t0)
REVERT: B   50 THR cc_start: 0.7967 (m) cc_final: 0.7689 (t)
REVERT: B   61 MET cc_start: 0.7995 (tmm) cc_final: 0.7563 (ppp)
REVERT: B  145 TYR cc_start: 0.8482 (p90) cc_final: 0.8121 (p90)
REVERT: B  156 GLN cc_start: 0.8484 (mt0) cc_final: 0.8150 (mt0)
REVERT: B  170 ASP cc_start: 0.8230 (OUTLIER) cc_final: 0.7873 (m-30)
REVERT: B  189 SER cc_start: 0.8222 (p) cc_final: 0.7961 (t)
REVERT: B  212 ASP cc_start: 0.7643 (t0) cc_final: 0.7300 (t0)
REVERT: B  217 MET cc_start: 0.7792 (ptt) cc_final: 0.7484 (ptt)
REVERT: B  264 TYR cc_start: 0.7927 (m-80) cc_final: 0.7280 (m-80)
REVERT: B  275 SER cc_start: 0.7891 (t) cc_final: 0.7658 (m)
REVERT: B  277 SER cc_start: 0.8149 (t) cc_final: 0.7814 (p)
REVERT: R   64 LEU cc_start: 0.7990 (mt) cc_final: 0.7776 (mp)
REVERT: R   90 THR cc_start: 0.7788 (m) cc_final: 0.7533 (t)
REVERT: R  120 ASN cc_start: 0.8118 (m-40) cc_final: 0.7811 (m-40)
REVERT: R  152 SER cc_start: 0.8438 (t) cc_final: 0.7996 (m)
REVERT: R  165 MET cc_start: 0.5609 (pp-130) cc_final: 0.5078 (pp-130)
REVERT: R  224 THR cc_start: 0.6752 (m) cc_final: 0.5137 (p)
REVERT: R  273 LEU cc_start: 0.7756 (OUTLIER) cc_final: 0.7510 (mt)
REVERT: S  161 SER cc_start: 0.8159 (p) cc_final: 0.7730 (t)
REVERT: Y   30 VAL cc_start: 0.7855 (t) cc_final: 0.7609 (t)
  outliers start: 36
  outliers final: 14
  residues processed: 295
  average time/residue: 0.9621
  time to fit residues: 306.5616
Evaluate side-chains
  281 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 264
  time to evaluate  : 1.036 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  187 THR
Chi-restraints excluded: chain A residue  191 VAL
Chi-restraints excluded: chain A residue  213 GLN
Chi-restraints excluded: chain A residue  249 LEU
Chi-restraints excluded: chain A residue  251 THR
Chi-restraints excluded: chain A residue  281 GLU
Chi-restraints excluded: chain A residue  301 VAL
Chi-restraints excluded: chain A residue  360 LEU
Chi-restraints excluded: chain B residue   98 SER
Chi-restraints excluded: chain B residue  170 ASP
Chi-restraints excluded: chain R residue  110 LEU
Chi-restraints excluded: chain R residue  171 VAL
Chi-restraints excluded: chain R residue  234 LEU
Chi-restraints excluded: chain R residue  273 LEU
Chi-restraints excluded: chain R residue  281 ILE
Chi-restraints excluded: chain R residue  325 SER
Chi-restraints excluded: chain S residue   23 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 59 optimal weight:    0.9980
   chunk 76 optimal weight:    0.6980
   chunk 102 optimal weight:    1.9990
   chunk 72 optimal weight:    0.9990
   chunk 25 optimal weight:    0.0040
   chunk 45 optimal weight:    0.6980
   chunk 70 optimal weight:    0.7980
   chunk 92 optimal weight:    1.9990
   chunk 37 optimal weight:    1.9990
   chunk 56 optimal weight:    2.9990
   chunk 99 optimal weight:    0.7980
   overall best weight:    0.5992

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

Flipped N/Q/H residues before XYZ refinement:
A 259 ASN
B 110 ASN
B 125 ASN
B 313 ASN
R  57 ASN
** R  75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 119 ASN
** R 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3993 r_free = 0.3993 target = 0.155746 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3775 r_free = 0.3775 target = 0.138287 restraints weight = 11762.893|
|-----------------------------------------------------------------------------|
r_work (start): 0.3734 rms_B_bonded: 1.87
r_work: 0.3616 rms_B_bonded: 2.43 restraints_weight: 0.5000
r_work: 0.3457 rms_B_bonded: 4.22 restraints_weight: 0.2500
r_work (final): 0.3457
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7374
moved from start:          0.3750

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051   9192  Z= 0.150
  Angle     :  0.563   7.735  12466  Z= 0.297
  Chirality :  0.043   0.176   1418
  Planarity :  0.004   0.042   1580
  Dihedral  :  4.977  35.295   1248
  Min Nonbonded Distance : 2.454

Molprobity Statistics.
  All-atom Clashscore : 10.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.77 %
    Favored  : 98.23 %
  Rotamer:
    Outliers :  3.77 %
    Allowed  : 17.62 %
    Favored  : 78.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

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:  0.64 (0.25), residues: 1130
  helix:  2.06 (0.25), residues: 394
  sheet: -0.95 (0.30), residues: 263
  loop : -0.04 (0.30), residues: 473

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP B 169 
 HIS   0.005   0.001   HIS A 329 
 PHE   0.015   0.002   PHE A 189 
 TYR   0.022   0.002   TYR R 322 
 ARG   0.009   0.001   ARG B 134 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03882 (  463)
  hydrogen bonds       : angle       4.92683 ( 1323)
  SS BOND              : bond        0.00237 (    1)
  SS BOND              : angle       1.38377 (    2)
  covalent geometry    : bond        0.00340 ( 9191)
  covalent geometry    : angle       0.56308 (12464)

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

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

  2260 Ramachandran restraints generated.
    1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2260 Ramachandran restraints generated.
    1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  309 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 272
  time to evaluate  : 0.931 
Fit side-chains
REVERT: A   14 GLU cc_start: 0.7676 (tm-30) cc_final: 0.7448 (tm-30)
REVERT: A   46 LYS cc_start: 0.7826 (OUTLIER) cc_final: 0.7464 (ptmt)
REVERT: A  185 PHE cc_start: 0.7200 (m-80) cc_final: 0.6939 (m-80)
REVERT: A  229 ASP cc_start: 0.7604 (t0) cc_final: 0.7223 (t0)
REVERT: A  238 ASN cc_start: 0.8389 (m-40) cc_final: 0.8161 (m-40)
REVERT: A  281 GLU cc_start: 0.7060 (OUTLIER) cc_final: 0.6777 (mp0)
REVERT: A  335 ASP cc_start: 0.7730 (t0) cc_final: 0.7509 (t0)
REVERT: A  358 TYR cc_start: 0.8097 (m-80) cc_final: 0.7882 (m-80)
REVERT: B   50 THR cc_start: 0.7878 (m) cc_final: 0.7633 (t)
REVERT: B   61 MET cc_start: 0.7979 (tmm) cc_final: 0.7625 (tmm)
REVERT: B   98 SER cc_start: 0.8371 (OUTLIER) cc_final: 0.8149 (p)
REVERT: B  137 ARG cc_start: 0.7575 (ttm-80) cc_final: 0.7331 (ttm-80)
REVERT: B  156 GLN cc_start: 0.8486 (mt0) cc_final: 0.8150 (mt0)
REVERT: B  170 ASP cc_start: 0.8138 (OUTLIER) cc_final: 0.7805 (m-30)
REVERT: B  189 SER cc_start: 0.8167 (p) cc_final: 0.7917 (t)
REVERT: B  190 LEU cc_start: 0.8050 (tt) cc_final: 0.7702 (tt)
REVERT: B  212 ASP cc_start: 0.7585 (t0) cc_final: 0.7294 (t0)
REVERT: B  217 MET cc_start: 0.7822 (ptt) cc_final: 0.7536 (ptt)
REVERT: B  228 ASP cc_start: 0.7954 (p0) cc_final: 0.7530 (p0)
REVERT: B  239 ASN cc_start: 0.7789 (m-40) cc_final: 0.7440 (m110)
REVERT: B  264 TYR cc_start: 0.7859 (m-80) cc_final: 0.7306 (m-80)
REVERT: B  277 SER cc_start: 0.8091 (t) cc_final: 0.7783 (p)
REVERT: R   64 LEU cc_start: 0.8093 (mt) cc_final: 0.7878 (mp)
REVERT: R  152 SER cc_start: 0.8416 (t) cc_final: 0.8007 (m)
REVERT: R  266 ARG cc_start: 0.7265 (mtt180) cc_final: 0.7030 (ttt180)
REVERT: R  273 LEU cc_start: 0.7756 (OUTLIER) cc_final: 0.7484 (mt)
REVERT: S   18 ARG cc_start: 0.8057 (tpp80) cc_final: 0.7431 (tpp-160)
REVERT: S   93 MET cc_start: 0.8074 (ttp) cc_final: 0.7802 (ttp)
REVERT: S   95 TYR cc_start: 0.8349 (m-80) cc_final: 0.8099 (m-80)
REVERT: S  161 SER cc_start: 0.8164 (p) cc_final: 0.7732 (t)
REVERT: Y   30 VAL cc_start: 0.8004 (t) cc_final: 0.7776 (t)
  outliers start: 37
  outliers final: 16
  residues processed: 294
  average time/residue: 0.9742
  time to fit residues: 311.2618
Evaluate side-chains
  277 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 256
  time to evaluate  : 1.551 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   46 LYS
Chi-restraints excluded: chain A residue  187 THR
Chi-restraints excluded: chain A residue  192 ASP
Chi-restraints excluded: chain A residue  249 LEU
Chi-restraints excluded: chain A residue  281 GLU
Chi-restraints excluded: chain A residue  360 LEU
Chi-restraints excluded: chain B residue   43 ILE
Chi-restraints excluded: chain B residue   87 THR
Chi-restraints excluded: chain B residue   98 SER
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  170 ASP
Chi-restraints excluded: chain B residue  177 THR
Chi-restraints excluded: chain R residue  234 LEU
Chi-restraints excluded: chain R residue  271 LEU
Chi-restraints excluded: chain R residue  273 LEU
Chi-restraints excluded: chain R residue  281 ILE
Chi-restraints excluded: chain R residue  300 ILE
Chi-restraints excluded: chain R residue  325 SER
Chi-restraints excluded: chain S residue    5 VAL
Chi-restraints excluded: chain S residue   23 SER
Chi-restraints excluded: chain S residue   52 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 90 optimal weight:    2.9990
   chunk 45 optimal weight:    1.9990
   chunk 51 optimal weight:    0.8980
   chunk 54 optimal weight:    2.9990
   chunk 72 optimal weight:    0.4980
   chunk 1 optimal weight:    1.9990
   chunk 17 optimal weight:    0.9990
   chunk 31 optimal weight:    1.9990
   chunk 32 optimal weight:    0.9980
   chunk 38 optimal weight:    5.9990
   chunk 74 optimal weight:    1.9990
   overall best weight:    1.0784

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

Flipped N/Q/H residues before XYZ refinement:
A 259 ASN
A 359 ASN
B  88 ASN
B 110 ASN
** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R  75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
S 186 GLN
S 194 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3935 r_free = 0.3935 target = 0.150568 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3714 r_free = 0.3714 target = 0.133040 restraints weight = 11989.160|
|-----------------------------------------------------------------------------|
r_work (start): 0.3708 rms_B_bonded: 1.84
r_work: 0.3588 rms_B_bonded: 2.40 restraints_weight: 0.5000
r_work: 0.3428 rms_B_bonded: 4.17 restraints_weight: 0.2500
r_work (final): 0.3428
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7414
moved from start:          0.3997

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.067   9192  Z= 0.212
  Angle     :  0.613   8.098  12466  Z= 0.321
  Chirality :  0.045   0.188   1418
  Planarity :  0.005   0.043   1580
  Dihedral  :  5.093  35.955   1248
  Min Nonbonded Distance : 2.444

Molprobity Statistics.
  All-atom Clashscore : 11.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.12 %
    Favored  : 97.88 %
  Rotamer:
    Outliers :  4.18 %
    Allowed  : 18.53 %
    Favored  : 77.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

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:  0.47 (0.25), residues: 1130
  helix:  1.86 (0.25), residues: 394
  sheet: -1.01 (0.29), residues: 269
  loop : -0.08 (0.30), residues: 467

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP B 169 
 HIS   0.005   0.001   HIS A 329 
 PHE   0.017   0.002   PHE A 189 
 TYR   0.031   0.002   TYR R 322 
 ARG   0.009   0.001   ARG B 134 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04133 (  463)
  hydrogen bonds       : angle       5.07797 ( 1323)
  SS BOND              : bond        0.00213 (    1)
  SS BOND              : angle       1.58635 (    2)
  covalent geometry    : bond        0.00489 ( 9191)
  covalent geometry    : angle       0.61285 (12464)

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

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

  2260 Ramachandran restraints generated.
    1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2260 Ramachandran restraints generated.
    1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  307 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 266
  time to evaluate  : 1.032 
Fit side-chains
   revert: symmetry clash
REVERT: A   14 GLU cc_start: 0.7676 (tm-30) cc_final: 0.7405 (tm-30)
REVERT: A   46 LYS cc_start: 0.7837 (OUTLIER) cc_final: 0.7449 (ptmt)
REVERT: A  185 PHE cc_start: 0.7198 (m-80) cc_final: 0.6907 (m-80)
REVERT: A  195 ASN cc_start: 0.8052 (m-40) cc_final: 0.7790 (m110)
REVERT: A  210 LYS cc_start: 0.8047 (mmtt) cc_final: 0.7703 (mmtt)
REVERT: A  229 ASP cc_start: 0.7641 (t0) cc_final: 0.7236 (t0)
REVERT: A  238 ASN cc_start: 0.8416 (m-40) cc_final: 0.8205 (m-40)
REVERT: A  257 PHE cc_start: 0.7796 (m-10) cc_final: 0.7417 (m-80)
REVERT: A  263 LEU cc_start: 0.8253 (mt) cc_final: 0.8034 (mp)
REVERT: A  301 VAL cc_start: 0.8231 (p) cc_final: 0.7977 (m)
REVERT: A  313 VAL cc_start: 0.7486 (t) cc_final: 0.7144 (m)
REVERT: A  335 ASP cc_start: 0.7734 (t0) cc_final: 0.7508 (t0)
REVERT: A  358 TYR cc_start: 0.8178 (m-80) cc_final: 0.7961 (m-80)
REVERT: B   50 THR cc_start: 0.8078 (m) cc_final: 0.7775 (t)
REVERT: B   61 MET cc_start: 0.7965 (tmm) cc_final: 0.7520 (ppp)
REVERT: B  137 ARG cc_start: 0.7621 (ttm-80) cc_final: 0.7353 (ttm-80)
REVERT: B  145 TYR cc_start: 0.8497 (p90) cc_final: 0.8059 (p90)
REVERT: B  156 GLN cc_start: 0.8489 (mt0) cc_final: 0.8161 (mt0)
REVERT: B  170 ASP cc_start: 0.8209 (OUTLIER) cc_final: 0.7848 (m-30)
REVERT: B  212 ASP cc_start: 0.7661 (t0) cc_final: 0.7342 (t0)
REVERT: B  217 MET cc_start: 0.7847 (ptt) cc_final: 0.7550 (ptt)
REVERT: B  228 ASP cc_start: 0.8099 (p0) cc_final: 0.7474 (p0)
REVERT: B  239 ASN cc_start: 0.7777 (m-40) cc_final: 0.7409 (m110)
REVERT: B  264 TYR cc_start: 0.7896 (m-80) cc_final: 0.7368 (m-80)
REVERT: B  277 SER cc_start: 0.8274 (t) cc_final: 0.7865 (p)
REVERT: R   64 LEU cc_start: 0.8111 (OUTLIER) cc_final: 0.7900 (mp)
REVERT: R  248 MET cc_start: 0.7565 (mmm) cc_final: 0.7353 (mmm)
REVERT: R  266 ARG cc_start: 0.7248 (mtt180) cc_final: 0.7044 (ttt180)
REVERT: R  300 ILE cc_start: 0.6937 (OUTLIER) cc_final: 0.6677 (mp)
REVERT: S   18 ARG cc_start: 0.8092 (tpp80) cc_final: 0.7625 (tpp80)
REVERT: S   93 MET cc_start: 0.8181 (ttp) cc_final: 0.7882 (ttp)
REVERT: S   95 TYR cc_start: 0.8335 (m-80) cc_final: 0.8054 (m-80)
REVERT: S  172 THR cc_start: 0.8824 (p) cc_final: 0.8386 (t)
  outliers start: 41
  outliers final: 18
  residues processed: 286
  average time/residue: 0.9930
  time to fit residues: 306.8484
Evaluate side-chains
  281 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 259
  time to evaluate  : 0.872 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   46 LYS
Chi-restraints excluded: chain A residue  187 THR
Chi-restraints excluded: chain A residue  200 ASP
Chi-restraints excluded: chain A residue  201 VAL
Chi-restraints excluded: chain A residue  213 GLN
Chi-restraints excluded: chain A residue  250 ARG
Chi-restraints excluded: chain A residue  360 LEU
Chi-restraints excluded: chain B residue   87 THR
Chi-restraints excluded: chain B residue   98 SER
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  170 ASP
Chi-restraints excluded: chain B residue  177 THR
Chi-restraints excluded: chain R residue   64 LEU
Chi-restraints excluded: chain R residue  137 ILE
Chi-restraints excluded: chain R residue  234 LEU
Chi-restraints excluded: chain R residue  244 THR
Chi-restraints excluded: chain R residue  271 LEU
Chi-restraints excluded: chain R residue  281 ILE
Chi-restraints excluded: chain R residue  300 ILE
Chi-restraints excluded: chain S residue    5 VAL
Chi-restraints excluded: chain S residue   23 SER
Chi-restraints excluded: chain S residue  117 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 60 optimal weight:   10.0000
   chunk 1 optimal weight:    0.9980
   chunk 105 optimal weight:    6.9990
   chunk 84 optimal weight:    0.0870
   chunk 107 optimal weight:    3.9990
   chunk 112 optimal weight:    0.9990
   chunk 111 optimal weight:    0.7980
   chunk 52 optimal weight:    1.9990
   chunk 24 optimal weight:    9.9990
   chunk 46 optimal weight:    0.8980
   chunk 45 optimal weight:    2.9990
   overall best weight:    0.7560

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

Flipped N/Q/H residues before XYZ refinement:
** A 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 259 ASN
B  88 ASN
B 110 ASN
** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R  75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
S 186 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3974 r_free = 0.3974 target = 0.153822 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3750 r_free = 0.3750 target = 0.136119 restraints weight = 12025.708|
|-----------------------------------------------------------------------------|
r_work (start): 0.3712 rms_B_bonded: 1.88
r_work: 0.3597 rms_B_bonded: 2.41 restraints_weight: 0.5000
r_work: 0.3436 rms_B_bonded: 4.21 restraints_weight: 0.2500
r_work (final): 0.3436
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7401
moved from start:          0.4114

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.063   9192  Z= 0.170
  Angle     :  0.591   8.302  12466  Z= 0.308
  Chirality :  0.044   0.179   1418
  Planarity :  0.004   0.044   1580
  Dihedral  :  4.975  35.270   1248
  Min Nonbonded Distance : 2.426

Molprobity Statistics.
  All-atom Clashscore : 10.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.86 %
    Favored  : 98.14 %
  Rotamer:
    Outliers :  4.28 %
    Allowed  : 19.35 %
    Favored  : 76.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

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:  0.49 (0.25), residues: 1130
  helix:  1.88 (0.25), residues: 394
  sheet: -1.06 (0.30), residues: 259
  loop : -0.06 (0.29), residues: 477

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP B 169 
 HIS   0.005   0.001   HIS A 329 
 PHE   0.016   0.002   PHE A 189 
 TYR   0.026   0.002   TYR R 322 
 ARG   0.010   0.000   ARG B 134 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03973 (  463)
  hydrogen bonds       : angle       5.01285 ( 1323)
  SS BOND              : bond        0.00221 (    1)
  SS BOND              : angle       1.51197 (    2)
  covalent geometry    : bond        0.00392 ( 9191)
  covalent geometry    : angle       0.59070 (12464)

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

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

  2260 Ramachandran restraints generated.
    1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2260 Ramachandran restraints generated.
    1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  289 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 247
  time to evaluate  : 1.020 
Fit side-chains
REVERT: A   14 GLU cc_start: 0.7771 (tm-30) cc_final: 0.7441 (tm-30)
REVERT: A   46 LYS cc_start: 0.7850 (OUTLIER) cc_final: 0.7480 (ptmt)
REVERT: A  185 PHE cc_start: 0.7202 (m-80) cc_final: 0.6858 (m-80)
REVERT: A  195 ASN cc_start: 0.8055 (m-40) cc_final: 0.7802 (m110)
REVERT: A  210 LYS cc_start: 0.7974 (mmtt) cc_final: 0.7696 (mmtp)
REVERT: A  229 ASP cc_start: 0.7629 (t0) cc_final: 0.7235 (t0)
REVERT: A  238 ASN cc_start: 0.8404 (m-40) cc_final: 0.8170 (m-40)
REVERT: A  257 PHE cc_start: 0.7793 (m-10) cc_final: 0.7441 (m-80)
REVERT: A  263 LEU cc_start: 0.8270 (mt) cc_final: 0.8045 (mp)
REVERT: A  284 ARG cc_start: 0.7405 (mtm-85) cc_final: 0.7204 (mtm-85)
REVERT: A  301 VAL cc_start: 0.8196 (p) cc_final: 0.7932 (m)
REVERT: A  313 VAL cc_start: 0.7405 (t) cc_final: 0.7087 (m)
REVERT: A  335 ASP cc_start: 0.7745 (t0) cc_final: 0.7530 (t0)
REVERT: A  358 TYR cc_start: 0.8049 (m-80) cc_final: 0.7819 (m-80)
REVERT: B   50 THR cc_start: 0.7971 (m) cc_final: 0.7713 (t)
REVERT: B   59 TYR cc_start: 0.7583 (OUTLIER) cc_final: 0.7206 (m-80)
REVERT: B   61 MET cc_start: 0.7907 (tmm) cc_final: 0.7512 (ppp)
REVERT: B  145 TYR cc_start: 0.8452 (p90) cc_final: 0.8158 (p90)
REVERT: B  156 GLN cc_start: 0.8448 (mt0) cc_final: 0.8169 (mt0)
REVERT: B  170 ASP cc_start: 0.8216 (OUTLIER) cc_final: 0.7896 (m-30)
REVERT: B  189 SER cc_start: 0.8314 (p) cc_final: 0.8112 (t)
REVERT: B  212 ASP cc_start: 0.7659 (t0) cc_final: 0.7358 (t0)
REVERT: B  217 MET cc_start: 0.7802 (ptt) cc_final: 0.7531 (ptt)
REVERT: B  228 ASP cc_start: 0.8125 (p0) cc_final: 0.7588 (p0)
REVERT: B  239 ASN cc_start: 0.7830 (m-40) cc_final: 0.7497 (m110)
REVERT: B  264 TYR cc_start: 0.7901 (m-80) cc_final: 0.7374 (m-80)
REVERT: B  277 SER cc_start: 0.8249 (t) cc_final: 0.7861 (p)
REVERT: R   64 LEU cc_start: 0.8140 (OUTLIER) cc_final: 0.7940 (mp)
REVERT: R  110 LEU cc_start: 0.8694 (OUTLIER) cc_final: 0.8273 (tp)
REVERT: R  266 ARG cc_start: 0.7274 (OUTLIER) cc_final: 0.7036 (ttt180)
REVERT: R  273 LEU cc_start: 0.7977 (OUTLIER) cc_final: 0.7664 (mt)
REVERT: R  300 ILE cc_start: 0.6930 (OUTLIER) cc_final: 0.6678 (mp)
REVERT: S   18 ARG cc_start: 0.8113 (tpp80) cc_final: 0.7586 (tpp-160)
REVERT: S   93 MET cc_start: 0.8107 (ttp) cc_final: 0.7818 (ttp)
REVERT: S   95 TYR cc_start: 0.8335 (m-80) cc_final: 0.8065 (m-80)
  outliers start: 42
  outliers final: 17
  residues processed: 271
  average time/residue: 1.0146
  time to fit residues: 296.5024
Evaluate side-chains
  270 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 245
  time to evaluate  : 0.928 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   46 LYS
Chi-restraints excluded: chain A residue  187 THR
Chi-restraints excluded: chain A residue  213 GLN
Chi-restraints excluded: chain A residue  250 ARG
Chi-restraints excluded: chain A residue  360 LEU
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue   87 THR
Chi-restraints excluded: chain B residue  170 ASP
Chi-restraints excluded: chain B residue  177 THR
Chi-restraints excluded: chain B residue  312 ASP
Chi-restraints excluded: chain R residue   64 LEU
Chi-restraints excluded: chain R residue  110 LEU
Chi-restraints excluded: chain R residue  234 LEU
Chi-restraints excluded: chain R residue  244 THR
Chi-restraints excluded: chain R residue  266 ARG
Chi-restraints excluded: chain R residue  270 VAL
Chi-restraints excluded: chain R residue  273 LEU
Chi-restraints excluded: chain R residue  281 ILE
Chi-restraints excluded: chain R residue  288 ILE
Chi-restraints excluded: chain R residue  300 ILE
Chi-restraints excluded: chain R residue  303 SER
Chi-restraints excluded: chain R residue  325 SER
Chi-restraints excluded: chain S residue    5 VAL
Chi-restraints excluded: chain S residue   23 SER
Chi-restraints excluded: chain S residue  162 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 39 optimal weight:    2.9990
   chunk 102 optimal weight:    0.5980
   chunk 75 optimal weight:    0.9980
   chunk 47 optimal weight:    0.9990
   chunk 82 optimal weight:    0.7980
   chunk 24 optimal weight:    8.9990
   chunk 38 optimal weight:    0.8980
   chunk 36 optimal weight:    2.9990
   chunk 35 optimal weight:    0.5980
   chunk 69 optimal weight:    1.9990
   chunk 64 optimal weight:    0.8980
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
** A 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 259 ASN
B 110 ASN
** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R  75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
S 186 GLN
S 194 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3985 r_free = 0.3985 target = 0.154648 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3766 r_free = 0.3766 target = 0.137159 restraints weight = 12101.274|
|-----------------------------------------------------------------------------|
r_work (start): 0.3728 rms_B_bonded: 1.87
r_work: 0.3609 rms_B_bonded: 2.43 restraints_weight: 0.5000
r_work: 0.3449 rms_B_bonded: 4.23 restraints_weight: 0.2500
r_work (final): 0.3449
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7400
moved from start:          0.4201

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.061   9192  Z= 0.173
  Angle     :  0.605   8.624  12466  Z= 0.314
  Chirality :  0.044   0.192   1418
  Planarity :  0.004   0.054   1580
  Dihedral  :  4.953  35.286   1248
  Min Nonbonded Distance : 2.429

Molprobity Statistics.
  All-atom Clashscore : 11.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.57 %
    Favored  : 97.43 %
  Rotamer:
    Outliers :  3.87 %
    Allowed  : 19.86 %
    Favored  : 76.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

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:  0.48 (0.25), residues: 1130
  helix:  1.84 (0.25), residues: 394
  sheet: -1.03 (0.30), residues: 249
  loop : -0.09 (0.29), residues: 487

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP B 169 
 HIS   0.005   0.001   HIS A 329 
 PHE   0.016   0.002   PHE A 189 
 TYR   0.028   0.002   TYR R 322 
 ARG   0.009   0.000   ARG B 134 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03951 (  463)
  hydrogen bonds       : angle       5.02576 ( 1323)
  SS BOND              : bond        0.00215 (    1)
  SS BOND              : angle       1.50950 (    2)
  covalent geometry    : bond        0.00401 ( 9191)
  covalent geometry    : angle       0.60460 (12464)

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

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

  2260 Ramachandran restraints generated.
    1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2260 Ramachandran restraints generated.
    1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  285 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 247
  time to evaluate  : 0.914 
Fit side-chains
REVERT: A   46 LYS cc_start: 0.7852 (OUTLIER) cc_final: 0.7533 (ptmt)
REVERT: A  185 PHE cc_start: 0.7191 (m-80) cc_final: 0.6932 (m-80)
REVERT: A  200 ASP cc_start: 0.7687 (OUTLIER) cc_final: 0.7278 (t0)
REVERT: A  210 LYS cc_start: 0.8029 (mmtt) cc_final: 0.7790 (mmtp)
REVERT: A  229 ASP cc_start: 0.7646 (t0) cc_final: 0.7214 (t0)
REVERT: A  238 ASN cc_start: 0.8370 (m-40) cc_final: 0.8160 (m-40)
REVERT: A  257 PHE cc_start: 0.7779 (m-10) cc_final: 0.7420 (m-80)
REVERT: A  263 LEU cc_start: 0.8280 (mt) cc_final: 0.8079 (mp)
REVERT: A  266 GLU cc_start: 0.7155 (mm-30) cc_final: 0.6941 (mm-30)
REVERT: A  284 ARG cc_start: 0.7359 (mtm-85) cc_final: 0.7149 (mtm-85)
REVERT: B   50 THR cc_start: 0.8045 (m) cc_final: 0.7760 (t)
REVERT: B   59 TYR cc_start: 0.7411 (OUTLIER) cc_final: 0.7042 (m-80)
REVERT: B   61 MET cc_start: 0.7924 (tmm) cc_final: 0.7623 (tmm)
REVERT: B  145 TYR cc_start: 0.8467 (p90) cc_final: 0.8058 (p90)
REVERT: B  156 GLN cc_start: 0.8444 (mt0) cc_final: 0.8140 (mt0)
REVERT: B  170 ASP cc_start: 0.8149 (OUTLIER) cc_final: 0.7798 (m-30)
REVERT: B  212 ASP cc_start: 0.7664 (t0) cc_final: 0.7411 (t0)
REVERT: B  217 MET cc_start: 0.7812 (ptt) cc_final: 0.7603 (ptt)
REVERT: B  228 ASP cc_start: 0.8061 (p0) cc_final: 0.7512 (p0)
REVERT: B  239 ASN cc_start: 0.7801 (m-40) cc_final: 0.7449 (m110)
REVERT: B  264 TYR cc_start: 0.7869 (m-80) cc_final: 0.7368 (m-80)
REVERT: B  277 SER cc_start: 0.8253 (t) cc_final: 0.7827 (p)
REVERT: R  125 PHE cc_start: 0.8472 (m-80) cc_final: 0.8066 (m-80)
REVERT: R  328 ASN cc_start: 0.6888 (OUTLIER) cc_final: 0.6619 (m110)
REVERT: S   18 ARG cc_start: 0.8113 (tpp80) cc_final: 0.7602 (tpp-160)
REVERT: S   93 MET cc_start: 0.8150 (ttp) cc_final: 0.7847 (ttp)
REVERT: S   95 TYR cc_start: 0.8337 (m-80) cc_final: 0.8054 (m-80)
REVERT: S  172 THR cc_start: 0.8557 (p) cc_final: 0.8153 (t)
  outliers start: 38
  outliers final: 21
  residues processed: 267
  average time/residue: 0.9058
  time to fit residues: 262.5924
Evaluate side-chains
  272 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 246
  time to evaluate  : 1.002 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   46 LYS
Chi-restraints excluded: chain A residue  187 THR
Chi-restraints excluded: chain A residue  200 ASP
Chi-restraints excluded: chain A residue  201 VAL
Chi-restraints excluded: chain A residue  213 GLN
Chi-restraints excluded: chain A residue  250 ARG
Chi-restraints excluded: chain A residue  360 LEU
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue   87 THR
Chi-restraints excluded: chain B residue   93 ILE
Chi-restraints excluded: chain B residue  170 ASP
Chi-restraints excluded: chain B residue  177 THR
Chi-restraints excluded: chain B residue  296 VAL
Chi-restraints excluded: chain B residue  312 ASP
Chi-restraints excluded: chain R residue  137 ILE
Chi-restraints excluded: chain R residue  234 LEU
Chi-restraints excluded: chain R residue  244 THR
Chi-restraints excluded: chain R residue  270 VAL
Chi-restraints excluded: chain R residue  271 LEU
Chi-restraints excluded: chain R residue  281 ILE
Chi-restraints excluded: chain R residue  300 ILE
Chi-restraints excluded: chain R residue  328 ASN
Chi-restraints excluded: chain S residue    5 VAL
Chi-restraints excluded: chain S residue   23 SER
Chi-restraints excluded: chain S residue  162 SER
Chi-restraints excluded: chain S residue  215 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 7 optimal weight:    0.9980
   chunk 75 optimal weight:    0.7980
   chunk 110 optimal weight:    1.9990
   chunk 105 optimal weight:    6.9990
   chunk 95 optimal weight:    0.6980
   chunk 23 optimal weight:   20.0000
   chunk 22 optimal weight:    0.8980
   chunk 101 optimal weight:    0.6980
   chunk 84 optimal weight:    0.9990
   chunk 112 optimal weight:    0.0170
   chunk 4 optimal weight:    1.9990
   overall best weight:    0.6218

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

Flipped N/Q/H residues before XYZ refinement:
** A 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 259 ASN
A 324 HIS
** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R  75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 225 ASN
** R 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
S 186 GLN
S 194 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3982 r_free = 0.3982 target = 0.154455 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3761 r_free = 0.3761 target = 0.136929 restraints weight = 11978.535|
|-----------------------------------------------------------------------------|
r_work (start): 0.3729 rms_B_bonded: 1.85
r_work: 0.3612 rms_B_bonded: 2.40 restraints_weight: 0.5000
r_work: 0.3457 rms_B_bonded: 4.16 restraints_weight: 0.2500
r_work (final): 0.3457
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7384
moved from start:          0.4265

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.057   9192  Z= 0.157
  Angle     :  0.608   8.891  12466  Z= 0.312
  Chirality :  0.044   0.191   1418
  Planarity :  0.004   0.052   1580
  Dihedral  :  4.909  35.368   1248
  Min Nonbonded Distance : 2.416

Molprobity Statistics.
  All-atom Clashscore : 11.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.39 %
    Favored  : 97.61 %
  Rotamer:
    Outliers :  4.07 %
    Allowed  : 20.16 %
    Favored  : 75.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

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:  0.53 (0.25), residues: 1130
  helix:  1.90 (0.25), residues: 394
  sheet: -1.01 (0.30), residues: 251
  loop : -0.07 (0.29), residues: 485

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP B 169 
 HIS   0.005   0.001   HIS A 197 
 PHE   0.017   0.002   PHE A 189 
 TYR   0.029   0.002   TYR R 322 
 ARG   0.009   0.000   ARG B 134 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03912 (  463)
  hydrogen bonds       : angle       4.98814 ( 1323)
  SS BOND              : bond        0.00221 (    1)
  SS BOND              : angle       1.47266 (    2)
  covalent geometry    : bond        0.00362 ( 9191)
  covalent geometry    : angle       0.60773 (12464)

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

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

  2260 Ramachandran restraints generated.
    1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2260 Ramachandran restraints generated.
    1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  281 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 241
  time to evaluate  : 1.073 
Fit side-chains
   revert: symmetry clash
REVERT: A  185 PHE cc_start: 0.7169 (m-80) cc_final: 0.6845 (m-80)
REVERT: A  210 LYS cc_start: 0.8014 (mmtt) cc_final: 0.7756 (mmtp)
REVERT: A  229 ASP cc_start: 0.7614 (t0) cc_final: 0.7246 (t0)
REVERT: A  257 PHE cc_start: 0.7761 (m-10) cc_final: 0.7422 (m-80)
REVERT: A  313 VAL cc_start: 0.7448 (t) cc_final: 0.7121 (m)
REVERT: B   50 THR cc_start: 0.7937 (m) cc_final: 0.7698 (t)
REVERT: B   59 TYR cc_start: 0.7449 (OUTLIER) cc_final: 0.7154 (m-80)
REVERT: B   61 MET cc_start: 0.7920 (tmm) cc_final: 0.7650 (tmm)
REVERT: B  145 TYR cc_start: 0.8448 (p90) cc_final: 0.7318 (p90)
REVERT: B  156 GLN cc_start: 0.8426 (mt0) cc_final: 0.8149 (mt0)
REVERT: B  170 ASP cc_start: 0.8116 (OUTLIER) cc_final: 0.7814 (m-30)
REVERT: B  212 ASP cc_start: 0.7642 (t0) cc_final: 0.7364 (t0)
REVERT: B  228 ASP cc_start: 0.8051 (p0) cc_final: 0.7516 (p0)
REVERT: B  264 TYR cc_start: 0.7804 (m-80) cc_final: 0.7398 (m-80)
REVERT: B  277 SER cc_start: 0.8238 (t) cc_final: 0.7863 (p)
REVERT: R  120 ASN cc_start: 0.8072 (m-40) cc_final: 0.7764 (m-40)
REVERT: R  320 MET cc_start: 0.7786 (ppp) cc_final: 0.7493 (ttp)
REVERT: R  328 ASN cc_start: 0.6808 (OUTLIER) cc_final: 0.6542 (m110)
REVERT: S   18 ARG cc_start: 0.8098 (tpp80) cc_final: 0.7542 (tpp-160)
REVERT: S   93 MET cc_start: 0.8101 (ttp) cc_final: 0.7804 (ttp)
REVERT: S   95 TYR cc_start: 0.8327 (m-80) cc_final: 0.8060 (m-80)
REVERT: S  199 VAL cc_start: 0.8165 (t) cc_final: 0.7901 (p)
  outliers start: 40
  outliers final: 28
  residues processed: 264
  average time/residue: 0.9172
  time to fit residues: 262.5334
Evaluate side-chains
  266 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 235
  time to evaluate  : 0.905 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 LEU
Chi-restraints excluded: chain A residue  187 THR
Chi-restraints excluded: chain A residue  188 LYS
Chi-restraints excluded: chain A residue  191 VAL
Chi-restraints excluded: chain A residue  201 VAL
Chi-restraints excluded: chain A residue  213 GLN
Chi-restraints excluded: chain A residue  250 ARG
Chi-restraints excluded: chain A residue  301 VAL
Chi-restraints excluded: chain A residue  360 LEU
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue   87 THR
Chi-restraints excluded: chain B residue   93 ILE
Chi-restraints excluded: chain B residue  170 ASP
Chi-restraints excluded: chain B residue  177 THR
Chi-restraints excluded: chain B residue  296 VAL
Chi-restraints excluded: chain B residue  312 ASP
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain R residue  137 ILE
Chi-restraints excluded: chain R residue  234 LEU
Chi-restraints excluded: chain R residue  244 THR
Chi-restraints excluded: chain R residue  271 LEU
Chi-restraints excluded: chain R residue  281 ILE
Chi-restraints excluded: chain R residue  300 ILE
Chi-restraints excluded: chain R residue  303 SER
Chi-restraints excluded: chain R residue  325 SER
Chi-restraints excluded: chain R residue  328 ASN
Chi-restraints excluded: chain S residue    5 VAL
Chi-restraints excluded: chain S residue   23 SER
Chi-restraints excluded: chain S residue  162 SER
Chi-restraints excluded: chain S residue  174 LEU
Chi-restraints excluded: chain S residue  215 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 85 optimal weight:    0.0040
   chunk 22 optimal weight:    0.9980
   chunk 30 optimal weight:    0.8980
   chunk 56 optimal weight:    2.9990
   chunk 78 optimal weight:    2.9990
   chunk 37 optimal weight:    0.5980
   chunk 111 optimal weight:    0.1980
   chunk 42 optimal weight:    0.9980
   chunk 106 optimal weight:    3.9990
   chunk 73 optimal weight:    0.8980
   chunk 13 optimal weight:    1.9990
   overall best weight:    0.5192

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

Flipped N/Q/H residues before XYZ refinement:
A 213 GLN
A 259 ASN
** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 125 ASN
B 230 ASN
B 237 ASN
B 239 ASN
** R  75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
S 186 GLN
S 194 ASN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3997 r_free = 0.3997 target = 0.155706 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3778 r_free = 0.3778 target = 0.138271 restraints weight = 11931.627|
|-----------------------------------------------------------------------------|
r_work (start): 0.3782 rms_B_bonded: 1.85
r_work: 0.3670 rms_B_bonded: 2.38 restraints_weight: 0.5000
r_work: 0.3518 rms_B_bonded: 4.13 restraints_weight: 0.2500
r_work (final): 0.3518
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7362
moved from start:          0.4309

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.056   9192  Z= 0.148
  Angle     :  0.618   9.321  12466  Z= 0.316
  Chirality :  0.044   0.185   1418
  Planarity :  0.005   0.091   1580
  Dihedral  :  4.933  35.770   1248
  Min Nonbonded Distance : 2.413

Molprobity Statistics.
  All-atom Clashscore : 10.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.57 %
    Favored  : 97.43 %
  Rotamer:
    Outliers :  3.46 %
    Allowed  : 22.20 %
    Favored  : 74.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

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:  0.56 (0.25), residues: 1130
  helix:  1.90 (0.25), residues: 393
  sheet: -0.96 (0.30), residues: 261
  loop : -0.01 (0.30), residues: 476

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B 169 
 HIS   0.005   0.001   HIS A 329 
 PHE   0.017   0.002   PHE A 189 
 TYR   0.030   0.002   TYR R 322 
 ARG   0.014   0.001   ARG B 137 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03818 (  463)
  hydrogen bonds       : angle       4.98630 ( 1323)
  SS BOND              : bond        0.00216 (    1)
  SS BOND              : angle       1.45402 (    2)
  covalent geometry    : bond        0.00344 ( 9191)
  covalent geometry    : angle       0.61762 (12464)

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

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

  2260 Ramachandran restraints generated.
    1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2260 Ramachandran restraints generated.
    1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  270 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 236
  time to evaluate  : 0.884 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   17 LYS cc_start: 0.8230 (mttt) cc_final: 0.7978 (mtpp)
REVERT: A   46 LYS cc_start: 0.7878 (OUTLIER) cc_final: 0.7356 (ptmm)
REVERT: A  185 PHE cc_start: 0.7160 (m-80) cc_final: 0.6860 (m-80)
REVERT: A  229 ASP cc_start: 0.7679 (t0) cc_final: 0.7280 (t0)
REVERT: A  257 PHE cc_start: 0.7724 (m-10) cc_final: 0.7360 (m-80)
REVERT: A  281 GLU cc_start: 0.6988 (mp0) cc_final: 0.6624 (mp0)
REVERT: A  284 ARG cc_start: 0.7317 (mtm-85) cc_final: 0.7010 (mtm-85)
REVERT: B   50 THR cc_start: 0.7889 (m) cc_final: 0.7672 (t)
REVERT: B   59 TYR cc_start: 0.7434 (OUTLIER) cc_final: 0.7132 (m-80)
REVERT: B   61 MET cc_start: 0.7918 (tmm) cc_final: 0.7670 (tmm)
REVERT: B   87 THR cc_start: 0.8119 (OUTLIER) cc_final: 0.7856 (m)
REVERT: B  145 TYR cc_start: 0.8410 (p90) cc_final: 0.7267 (p90)
REVERT: B  156 GLN cc_start: 0.8418 (mt0) cc_final: 0.8151 (mt0)
REVERT: B  170 ASP cc_start: 0.8083 (OUTLIER) cc_final: 0.7794 (m-30)
REVERT: B  228 ASP cc_start: 0.8039 (p0) cc_final: 0.7412 (p0)
REVERT: B  264 TYR cc_start: 0.7768 (m-80) cc_final: 0.7357 (m-80)
REVERT: B  277 SER cc_start: 0.8236 (t) cc_final: 0.7855 (p)
REVERT: R  320 MET cc_start: 0.7808 (ppp) cc_final: 0.7454 (ttp)
REVERT: R  328 ASN cc_start: 0.6721 (OUTLIER) cc_final: 0.6407 (m110)
REVERT: R  330 LEU cc_start: 0.8213 (mt) cc_final: 0.7997 (mm)
REVERT: S   18 ARG cc_start: 0.8109 (tpp80) cc_final: 0.7602 (tpp-160)
REVERT: S   93 MET cc_start: 0.8059 (ttp) cc_final: 0.7829 (ttp)
REVERT: S   95 TYR cc_start: 0.8285 (m-80) cc_final: 0.8037 (m-80)
REVERT: S  199 VAL cc_start: 0.8166 (t) cc_final: 0.7911 (p)
REVERT: S  231 GLN cc_start: 0.8534 (pp30) cc_final: 0.8116 (pp30)
  outliers start: 34
  outliers final: 24
  residues processed: 253
  average time/residue: 0.9570
  time to fit residues: 261.7726
Evaluate side-chains
  257 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 228
  time to evaluate  : 0.978 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   46 LYS
Chi-restraints excluded: chain A residue  187 THR
Chi-restraints excluded: chain A residue  188 LYS
Chi-restraints excluded: chain A residue  191 VAL
Chi-restraints excluded: chain A residue  201 VAL
Chi-restraints excluded: chain A residue  213 GLN
Chi-restraints excluded: chain A residue  250 ARG
Chi-restraints excluded: chain A residue  301 VAL
Chi-restraints excluded: chain A residue  360 LEU
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue   67 SER
Chi-restraints excluded: chain B residue   87 THR
Chi-restraints excluded: chain B residue   93 ILE
Chi-restraints excluded: chain B residue  170 ASP
Chi-restraints excluded: chain B residue  177 THR
Chi-restraints excluded: chain B residue  312 ASP
Chi-restraints excluded: chain R residue  137 ILE
Chi-restraints excluded: chain R residue  234 LEU
Chi-restraints excluded: chain R residue  244 THR
Chi-restraints excluded: chain R residue  271 LEU
Chi-restraints excluded: chain R residue  281 ILE
Chi-restraints excluded: chain R residue  300 ILE
Chi-restraints excluded: chain R residue  303 SER
Chi-restraints excluded: chain R residue  325 SER
Chi-restraints excluded: chain R residue  328 ASN
Chi-restraints excluded: chain S residue    5 VAL
Chi-restraints excluded: chain S residue   23 SER
Chi-restraints excluded: chain S residue  162 SER
Chi-restraints excluded: chain S residue  215 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 4 optimal weight:    0.9980
   chunk 61 optimal weight:    0.9990
   chunk 104 optimal weight:    2.9990
   chunk 97 optimal weight:    0.0770
   chunk 102 optimal weight:    0.8980
   chunk 40 optimal weight:    0.0980
   chunk 48 optimal weight:    0.7980
   chunk 16 optimal weight:    0.0870
   chunk 76 optimal weight:    0.7980
   chunk 90 optimal weight:    3.9990
   chunk 85 optimal weight:    0.2980
   overall best weight:    0.2716

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

Flipped N/Q/H residues before XYZ refinement:
A 259 ASN
A 329 HIS
** B 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 239 ASN
** R  75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
S 186 GLN
S 194 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4033 r_free = 0.4033 target = 0.158882 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3819 r_free = 0.3819 target = 0.141452 restraints weight = 11956.544|
|-----------------------------------------------------------------------------|
r_work (start): 0.3784 rms_B_bonded: 1.90
r_work: 0.3670 rms_B_bonded: 2.45 restraints_weight: 0.5000
r_work: 0.3515 rms_B_bonded: 4.27 restraints_weight: 0.2500
r_work (final): 0.3515
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7311
moved from start:          0.4377

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   9192  Z= 0.123
  Angle     :  0.597   9.573  12466  Z= 0.306
  Chirality :  0.043   0.171   1418
  Planarity :  0.005   0.081   1580
  Dihedral  :  4.799  34.451   1248
  Min Nonbonded Distance : 2.408

Molprobity Statistics.
  All-atom Clashscore : 10.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.57 %
    Favored  : 97.43 %
  Rotamer:
    Outliers :  2.95 %
    Allowed  : 23.22 %
    Favored  : 73.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

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:  0.65 (0.25), residues: 1130
  helix:  1.98 (0.25), residues: 393
  sheet: -0.85 (0.29), residues: 268
  loop :  0.01 (0.30), residues: 469

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP A 211 
 HIS   0.004   0.001   HIS B  54 
 PHE   0.016   0.001   PHE A 189 
 TYR   0.027   0.001   TYR R 322 
 ARG   0.015   0.001   ARG B 137 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03718 (  463)
  hydrogen bonds       : angle       4.87323 ( 1323)
  SS BOND              : bond        0.00234 (    1)
  SS BOND              : angle       1.33664 (    2)
  covalent geometry    : bond        0.00277 ( 9191)
  covalent geometry    : angle       0.59659 (12464)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 8390.57 seconds
wall clock time: 145 minutes 50.16 seconds (8750.16 seconds total)