Starting phenix.real_space_refine
on Sat Dec 28 17:59:13 2024 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7f2o_31429/12_2024/7f2o_31429.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7f2o_31429/12_2024/7f2o_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_31429/12_2024/7f2o_31429.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7f2o_31429/12_2024/7f2o_31429.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7f2o_31429/12_2024/7f2o_31429.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7f2o_31429/12_2024/7f2o_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-5532/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: 5.10, per 1000 atoms: 0.57
  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: 2.45
  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: 1.17
  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: 2.84

  Time building geometry restraints manager: 2.71 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:             0.450
  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:          0.330
  Check model and map are aligned:         0.060
  Set scattering table:                    0.080
  Process input model:                     22.700
  Find NCS groups from input model:        0.100
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:12.660
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   36.440
-------------------------------------------------------------------------------
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   9191  Z= 0.174
  Angle     :  0.574   7.394  12464  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 

*********************** 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  : 1.019 
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: 0.9972
  time to fit residues: 314.7349
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  : 1.052 
-------------------------------------------------------------------------------
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:    1.9990
   chunk 102 optimal weight:    2.9990
   overall best weight:    0.9790

-------------------------------------------------------------------------------
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

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6707
moved from start:          0.2496

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.074   9191  Z= 0.294
  Angle     :  0.635   9.122  12464  Z= 0.336
  Chirality :  0.045   0.197   1418
  Planarity :  0.005   0.043   1580
  Dihedral  :  5.695  37.653   1251
  Min Nonbonded Distance : 2.551

Molprobity Statistics.
  All-atom Clashscore : 7.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.50 %
    Favored  : 98.50 %
  Rotamer:
    Outliers :  2.85 %
    Allowed  : 12.63 %
    Favored  : 84.52 %
  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:  0.52 (0.25), residues: 1130
  helix:  1.65 (0.25), residues: 394
  sheet: -0.77 (0.30), residues: 273
  loop :  0.07 (0.31), residues: 463

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.002   TRP B 169 
 HIS   0.010   0.002   HIS S 167 
 PHE   0.017   0.002   PHE B 235 
 TYR   0.029   0.002   TYR R 322 
 ARG   0.007   0.001   ARG A 232 

*********************** 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
  316 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 288
  time to evaluate  : 0.971 
Fit side-chains
REVERT: A   10 LYS cc_start: 0.8032 (ttmm) cc_final: 0.7812 (mtpp)
REVERT: A   15 ARG cc_start: 0.8115 (ttt90) cc_final: 0.7908 (ttt90)
REVERT: A   17 LYS cc_start: 0.7978 (mttt) cc_final: 0.7766 (mttt)
REVERT: A   33 THR cc_start: 0.8743 (t) cc_final: 0.8542 (p)
REVERT: A  188 LYS cc_start: 0.8017 (mttt) cc_final: 0.7807 (mmtt)
REVERT: A  199 PHE cc_start: 0.8409 (m-80) cc_final: 0.8194 (m-80)
REVERT: A  208 ARG cc_start: 0.7899 (ptp90) cc_final: 0.7681 (ptp-110)
REVERT: A  229 ASP cc_start: 0.7080 (t0) cc_final: 0.6737 (t0)
REVERT: A  238 ASN cc_start: 0.8234 (m-40) cc_final: 0.7985 (m-40)
REVERT: A  275 ILE cc_start: 0.8219 (mp) cc_final: 0.7885 (OUTLIER)
REVERT: A  337 GLU cc_start: 0.5537 (mt-10) cc_final: 0.5256 (mt-10)
REVERT: B   76 ASP cc_start: 0.6745 (t70) cc_final: 0.6458 (t0)
REVERT: B   83 ASP cc_start: 0.8084 (t70) cc_final: 0.7780 (t0)
REVERT: B   88 ASN cc_start: 0.7800 (m-40) cc_final: 0.7499 (m110)
REVERT: B  156 GLN cc_start: 0.7745 (mt0) cc_final: 0.7349 (mt0)
REVERT: B  170 ASP cc_start: 0.7782 (m-30) cc_final: 0.7546 (m-30)
REVERT: B  188 MET cc_start: 0.7469 (mmm) cc_final: 0.6985 (mmm)
REVERT: B  189 SER cc_start: 0.8091 (p) cc_final: 0.7777 (t)
REVERT: B  201 SER cc_start: 0.8204 (m) cc_final: 0.7562 (p)
REVERT: B  207 SER cc_start: 0.8276 (t) cc_final: 0.7862 (p)
REVERT: B  212 ASP cc_start: 0.7112 (t0) cc_final: 0.6543 (t0)
REVERT: B  217 MET cc_start: 0.7085 (ptt) cc_final: 0.6669 (ptt)
REVERT: B  221 THR cc_start: 0.7061 (m) cc_final: 0.6819 (m)
REVERT: B  228 ASP cc_start: 0.7732 (p0) cc_final: 0.7285 (p0)
REVERT: B  233 CYS cc_start: 0.7452 (OUTLIER) cc_final: 0.7124 (t)
REVERT: B  237 ASN cc_start: 0.6911 (t0) cc_final: 0.6707 (t0)
REVERT: B  239 ASN cc_start: 0.7159 (m-40) cc_final: 0.6742 (m-40)
REVERT: B  251 ARG cc_start: 0.7836 (mtm-85) cc_final: 0.7628 (ttm-80)
REVERT: B  254 ASP cc_start: 0.6141 (t0) cc_final: 0.5850 (t0)
REVERT: B  262 MET cc_start: 0.6662 (ttm) cc_final: 0.6138 (ttm)
REVERT: B  264 TYR cc_start: 0.7645 (m-80) cc_final: 0.6812 (m-80)
REVERT: B  271 CYS cc_start: 0.6969 (m) cc_final: 0.6731 (m)
REVERT: B  275 SER cc_start: 0.7886 (t) cc_final: 0.7350 (m)
REVERT: B  277 SER cc_start: 0.7868 (t) cc_final: 0.7295 (p)
REVERT: B  340 ASN cc_start: 0.7286 (m-40) cc_final: 0.7038 (m110)
REVERT: R  152 SER cc_start: 0.7919 (t) cc_final: 0.7613 (m)
REVERT: R  324 ASN cc_start: 0.7487 (t0) cc_final: 0.6823 (t0)
REVERT: R  328 ASN cc_start: 0.6648 (m110) cc_final: 0.6204 (m110)
REVERT: S   18 ARG cc_start: 0.7800 (tpp80) cc_final: 0.7599 (tpp80)
REVERT: S   93 MET cc_start: 0.7299 (tpp) cc_final: 0.7090 (ttp)
REVERT: S  161 SER cc_start: 0.7953 (p) cc_final: 0.7663 (t)
REVERT: S  231 GLN cc_start: 0.8355 (pp30) cc_final: 0.8010 (pp30)
  outliers start: 28
  outliers final: 8
  residues processed: 298
  average time/residue: 0.9550
  time to fit residues: 308.2869
Evaluate side-chains
  274 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 266
  time to evaluate  : 0.969 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  187 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  233 CYS
Chi-restraints excluded: chain R residue  171 VAL
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 57 optimal weight:    2.9990
   chunk 31 optimal weight:    1.9990
   chunk 85 optimal weight:    3.9990
   chunk 69 optimal weight:    0.9990
   chunk 28 optimal weight:    4.9990
   chunk 102 optimal weight:    0.4980
   chunk 111 optimal weight:    2.9990
   chunk 91 optimal weight:    0.4980
   chunk 101 optimal weight:    1.9990
   chunk 35 optimal weight:    1.9990
   chunk 82 optimal weight:    0.9980
   overall best weight:    0.9984

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

Flipped N/Q/H residues before XYZ refinement:
A  22 GLN
A 216 ASN
A 259 ASN
B 132 ASN
B 220 GLN
R  57 ASN
R 119 ASN
** R 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
S 167 HIS
S 194 ASN

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6753
moved from start:          0.3258

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.055   9191  Z= 0.298
  Angle     :  0.615   7.751  12464  Z= 0.323
  Chirality :  0.045   0.187   1418
  Planarity :  0.005   0.041   1580
  Dihedral  :  5.341  34.906   1248
  Min Nonbonded Distance : 2.531

Molprobity Statistics.
  All-atom Clashscore : 9.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.86 %
    Favored  : 98.14 %
  Rotamer:
    Outliers :  3.26 %
    Allowed  : 15.38 %
    Favored  : 81.36 %
  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:  0.58 (0.25), residues: 1130
  helix:  1.88 (0.26), residues: 394
  sheet: -0.92 (0.29), residues: 273
  loop :  0.05 (0.30), residues: 463

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP B 169 
 HIS   0.008   0.002   HIS S 167 
 PHE   0.022   0.002   PHE R 195 
 TYR   0.030   0.002   TYR R 322 
 ARG   0.010   0.001   ARG A 232 

*********************** 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
  307 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 275
  time to evaluate  : 0.932 
Fit side-chains
REVERT: A   10 LYS cc_start: 0.7984 (ttmm) cc_final: 0.7779 (mtpp)
REVERT: A   14 GLU cc_start: 0.6670 (tm-30) cc_final: 0.6453 (tm-30)
REVERT: A  229 ASP cc_start: 0.6974 (t0) cc_final: 0.6662 (t0)
REVERT: A  238 ASN cc_start: 0.8227 (m-40) cc_final: 0.7956 (m-40)
REVERT: B   50 THR cc_start: 0.7782 (m) cc_final: 0.7449 (t)
REVERT: B   83 ASP cc_start: 0.7876 (t70) cc_final: 0.7638 (t0)
REVERT: B   88 ASN cc_start: 0.7863 (m-40) cc_final: 0.7633 (m110)
REVERT: B  114 CYS cc_start: 0.7296 (p) cc_final: 0.7025 (p)
REVERT: B  137 ARG cc_start: 0.7392 (ttm-80) cc_final: 0.6944 (ttm-80)
REVERT: B  150 ARG cc_start: 0.8149 (mpt180) cc_final: 0.7852 (mpt180)
REVERT: B  156 GLN cc_start: 0.7968 (mt0) cc_final: 0.7564 (mt0)
REVERT: B  170 ASP cc_start: 0.7763 (m-30) cc_final: 0.7413 (m-30)
REVERT: B  189 SER cc_start: 0.8038 (p) cc_final: 0.7714 (t)
REVERT: B  201 SER cc_start: 0.8183 (m) cc_final: 0.7599 (p)
REVERT: B  207 SER cc_start: 0.8304 (t) cc_final: 0.7946 (p)
REVERT: B  212 ASP cc_start: 0.7099 (t0) cc_final: 0.6396 (t0)
REVERT: B  217 MET cc_start: 0.7106 (ptt) cc_final: 0.6576 (ptt)
REVERT: B  221 THR cc_start: 0.7129 (m) cc_final: 0.6904 (m)
REVERT: B  230 ASN cc_start: 0.7793 (m-40) cc_final: 0.7527 (m110)
REVERT: B  237 ASN cc_start: 0.6826 (t0) cc_final: 0.6585 (t0)
REVERT: B  239 ASN cc_start: 0.7178 (m-40) cc_final: 0.6957 (m110)
REVERT: B  246 ASP cc_start: 0.7289 (t70) cc_final: 0.6861 (m-30)
REVERT: B  254 ASP cc_start: 0.6142 (t0) cc_final: 0.5707 (t0)
REVERT: B  262 MET cc_start: 0.6621 (ttm) cc_final: 0.6110 (ttm)
REVERT: B  264 TYR cc_start: 0.7691 (m-80) cc_final: 0.6857 (m-80)
REVERT: B  275 SER cc_start: 0.7804 (t) cc_final: 0.7288 (m)
REVERT: B  277 SER cc_start: 0.7886 (t) cc_final: 0.7156 (p)
REVERT: B  325 MET cc_start: 0.7104 (tpp) cc_final: 0.6619 (mpp)
REVERT: B  340 ASN cc_start: 0.7253 (t0) cc_final: 0.6952 (m110)
REVERT: R  120 ASN cc_start: 0.7587 (m-40) cc_final: 0.7317 (m-40)
REVERT: R  152 SER cc_start: 0.8048 (t) cc_final: 0.7626 (m)
REVERT: R  165 MET cc_start: 0.4987 (pp-130) cc_final: 0.4475 (pp-130)
REVERT: R  309 ILE cc_start: 0.8433 (mt) cc_final: 0.8211 (mm)
REVERT: S  161 SER cc_start: 0.8062 (p) cc_final: 0.7631 (t)
REVERT: S  231 GLN cc_start: 0.8376 (pp30) cc_final: 0.7934 (pp30)
  outliers start: 32
  outliers final: 14
  residues processed: 293
  average time/residue: 1.0291
  time to fit residues: 324.4315
Evaluate side-chains
  278 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 264
  time to evaluate  : 1.007 
-------------------------------------------------------------------------------
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  301 VAL
Chi-restraints excluded: chain B residue   98 SER
Chi-restraints excluded: chain B residue  179 THR
Chi-restraints excluded: chain R residue  234 LEU
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  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=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 101 optimal weight:    0.8980
   chunk 77 optimal weight:    0.7980
   chunk 53 optimal weight:    4.9990
   chunk 11 optimal weight:    2.9990
   chunk 49 optimal weight:    0.9990
   chunk 69 optimal weight:    1.9990
   chunk 103 optimal weight:    3.9990
   chunk 109 optimal weight:    9.9990
   chunk 97 optimal weight:    0.9980
   chunk 29 optimal weight:    0.7980
   chunk 90 optimal weight:    0.5980
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
A 216 ASN
A 231 ASN
A 259 ASN
B 110 ASN
** 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: 5

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6753
moved from start:          0.3573

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.065   9191  Z= 0.265
  Angle     :  0.592   7.816  12464  Z= 0.309
  Chirality :  0.044   0.176   1418
  Planarity :  0.005   0.045   1580
  Dihedral  :  5.110  34.574   1248
  Min Nonbonded Distance : 2.479

Molprobity Statistics.
  All-atom Clashscore : 9.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.42 %
    Favored  : 98.58 %
  Rotamer:
    Outliers :  3.77 %
    Allowed  : 16.09 %
    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:  0.58 (0.25), residues: 1130
  helix:  1.99 (0.26), residues: 394
  sheet: -1.02 (0.29), residues: 275
  loop :  0.02 (0.30), residues: 461

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP B 169 
 HIS   0.004   0.001   HIS B  91 
 PHE   0.021   0.002   PHE R 319 
 TYR   0.024   0.002   TYR R 322 
 ARG   0.007   0.000   ARG A 232 

*********************** 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
  303 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 266
  time to evaluate  : 0.989 
Fit side-chains
REVERT: A    8 GLU cc_start: 0.7388 (mt-10) cc_final: 0.7180 (mt-10)
REVERT: A   14 GLU cc_start: 0.6653 (tm-30) cc_final: 0.6416 (tm-30)
REVERT: A  210 LYS cc_start: 0.7751 (mmtp) cc_final: 0.7462 (mmtt)
REVERT: A  229 ASP cc_start: 0.6864 (t0) cc_final: 0.6591 (t0)
REVERT: A  358 TYR cc_start: 0.8035 (m-80) cc_final: 0.7761 (m-80)
REVERT: B   50 THR cc_start: 0.7831 (m) cc_final: 0.7468 (t)
REVERT: B   61 MET cc_start: 0.7580 (tmm) cc_final: 0.6997 (ppp)
REVERT: B   98 SER cc_start: 0.8091 (OUTLIER) cc_final: 0.7707 (p)
REVERT: B  114 CYS cc_start: 0.7077 (p) cc_final: 0.6826 (p)
REVERT: B  134 ARG cc_start: 0.7049 (ptt90) cc_final: 0.6803 (ptt90)
REVERT: B  137 ARG cc_start: 0.7329 (ttm-80) cc_final: 0.7075 (ttm-80)
REVERT: B  145 TYR cc_start: 0.8209 (p90) cc_final: 0.7754 (p90)
REVERT: B  150 ARG cc_start: 0.8175 (mpt180) cc_final: 0.7861 (mpt180)
REVERT: B  156 GLN cc_start: 0.7986 (mt0) cc_final: 0.7558 (mt0)
REVERT: B  170 ASP cc_start: 0.7748 (m-30) cc_final: 0.7393 (m-30)
REVERT: B  189 SER cc_start: 0.8062 (p) cc_final: 0.7763 (t)
REVERT: B  201 SER cc_start: 0.8185 (m) cc_final: 0.7710 (p)
REVERT: B  207 SER cc_start: 0.8322 (t) cc_final: 0.7966 (p)
REVERT: B  212 ASP cc_start: 0.6938 (t0) cc_final: 0.6411 (t0)
REVERT: B  217 MET cc_start: 0.6958 (ptt) cc_final: 0.6573 (ptt)
REVERT: B  221 THR cc_start: 0.7158 (m) cc_final: 0.6925 (m)
REVERT: B  228 ASP cc_start: 0.7734 (p0) cc_final: 0.6522 (p0)
REVERT: B  233 CYS cc_start: 0.7465 (t) cc_final: 0.7216 (t)
REVERT: B  237 ASN cc_start: 0.6886 (t0) cc_final: 0.6637 (t0)
REVERT: B  239 ASN cc_start: 0.7139 (m-40) cc_final: 0.6926 (m110)
REVERT: B  246 ASP cc_start: 0.7240 (t70) cc_final: 0.6869 (m-30)
REVERT: B  254 ASP cc_start: 0.6169 (t0) cc_final: 0.5658 (t0)
REVERT: B  262 MET cc_start: 0.6609 (ttm) cc_final: 0.6014 (ttm)
REVERT: B  264 TYR cc_start: 0.7703 (m-80) cc_final: 0.6834 (m-80)
REVERT: B  275 SER cc_start: 0.7753 (t) cc_final: 0.7325 (m)
REVERT: B  277 SER cc_start: 0.7808 (t) cc_final: 0.7240 (p)
REVERT: B  283 ARG cc_start: 0.7418 (tpt170) cc_final: 0.7108 (tpt170)
REVERT: B  340 ASN cc_start: 0.7247 (t0) cc_final: 0.6986 (m-40)
REVERT: R   72 THR cc_start: 0.7777 (m) cc_final: 0.7507 (m)
REVERT: R  152 SER cc_start: 0.8053 (t) cc_final: 0.7633 (m)
REVERT: R  165 MET cc_start: 0.4879 (pp-130) cc_final: 0.4375 (pp-130)
REVERT: R  309 ILE cc_start: 0.8447 (mt) cc_final: 0.8156 (mm)
REVERT: S   18 ARG cc_start: 0.7938 (tpp80) cc_final: 0.7476 (tpp80)
REVERT: S   95 TYR cc_start: 0.8270 (m-80) cc_final: 0.7959 (m-80)
REVERT: S  195 LEU cc_start: 0.8262 (OUTLIER) cc_final: 0.8058 (tp)
REVERT: S  230 MET cc_start: 0.7843 (ttp) cc_final: 0.7456 (ttp)
  outliers start: 37
  outliers final: 21
  residues processed: 288
  average time/residue: 1.0375
  time to fit residues: 321.7464
Evaluate side-chains
  272 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 249
  time to evaluate  : 0.956 
-------------------------------------------------------------------------------
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  201 VAL
Chi-restraints excluded: chain A residue  251 THR
Chi-restraints excluded: chain A residue  301 VAL
Chi-restraints excluded: chain A residue  302 THR
Chi-restraints excluded: chain B residue   40 VAL
Chi-restraints excluded: chain B residue   98 SER
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain R residue  171 VAL
Chi-restraints excluded: chain R residue  217 SER
Chi-restraints excluded: chain R residue  234 LEU
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  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
Chi-restraints excluded: chain S residue  117 LEU
Chi-restraints excluded: chain S residue  195 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 62 optimal weight:    0.7980
   chunk 1 optimal weight:    0.8980
   chunk 81 optimal weight:    7.9990
   chunk 45 optimal weight:    0.9980
   chunk 93 optimal weight:    5.9990
   chunk 75 optimal weight:    0.7980
   chunk 0 optimal weight:    1.9990
   chunk 55 optimal weight:    0.0470
   chunk 98 optimal weight:    5.9990
   chunk 27 optimal weight:    0.6980
   chunk 36 optimal weight:    0.6980
   overall best weight:    0.6078

-------------------------------------------------------------------------------
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 230 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**
S 186 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6739
moved from start:          0.3764

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.056   9191  Z= 0.223
  Angle     :  0.557   7.553  12464  Z= 0.293
  Chirality :  0.042   0.165   1418
  Planarity :  0.004   0.047   1580
  Dihedral  :  4.936  33.711   1248
  Min Nonbonded Distance : 2.449

Molprobity Statistics.
  All-atom Clashscore : 9.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.59 %
    Favored  : 98.41 %
  Rotamer:
    Outliers :  3.16 %
    Allowed  : 18.13 %
    Favored  : 78.72 %
  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:  0.63 (0.25), residues: 1130
  helix:  2.03 (0.25), residues: 394
  sheet: -0.94 (0.29), residues: 267
  loop : -0.01 (0.30), residues: 469

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   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   0.005   0.000   ARG A 232 

*********************** 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
  295 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 264
  time to evaluate  : 1.046 
Fit side-chains
REVERT: A   14 GLU cc_start: 0.6635 (tm-30) cc_final: 0.6410 (tm-30)
REVERT: A  194 VAL cc_start: 0.7928 (OUTLIER) cc_final: 0.7569 (t)
REVERT: A  208 ARG cc_start: 0.8148 (ptp90) cc_final: 0.7904 (ttp-110)
REVERT: A  229 ASP cc_start: 0.6913 (t0) cc_final: 0.6617 (t0)
REVERT: A  358 TYR cc_start: 0.7944 (m-80) cc_final: 0.7711 (m-80)
REVERT: B   50 THR cc_start: 0.7823 (m) cc_final: 0.7457 (t)
REVERT: B   61 MET cc_start: 0.7570 (tmm) cc_final: 0.7058 (ppp)
REVERT: B   66 ASP cc_start: 0.7747 (p0) cc_final: 0.7400 (p0)
REVERT: B   98 SER cc_start: 0.8069 (OUTLIER) cc_final: 0.7719 (p)
REVERT: B  134 ARG cc_start: 0.7058 (ptt90) cc_final: 0.6813 (ptt90)
REVERT: B  145 TYR cc_start: 0.8211 (p90) cc_final: 0.7675 (p90)
REVERT: B  150 ARG cc_start: 0.8181 (mpt180) cc_final: 0.7844 (mpt180)
REVERT: B  156 GLN cc_start: 0.7988 (mt0) cc_final: 0.7553 (mt0)
REVERT: B  170 ASP cc_start: 0.7725 (m-30) cc_final: 0.7402 (m-30)
REVERT: B  177 THR cc_start: 0.7766 (m) cc_final: 0.7368 (m)
REVERT: B  189 SER cc_start: 0.8019 (p) cc_final: 0.7728 (t)
REVERT: B  190 LEU cc_start: 0.7780 (tt) cc_final: 0.7352 (tt)
REVERT: B  201 SER cc_start: 0.8219 (m) cc_final: 0.7713 (p)
REVERT: B  207 SER cc_start: 0.8335 (t) cc_final: 0.7971 (p)
REVERT: B  212 ASP cc_start: 0.6877 (t0) cc_final: 0.6355 (t0)
REVERT: B  217 MET cc_start: 0.6952 (ptt) cc_final: 0.6575 (ptt)
REVERT: B  221 THR cc_start: 0.7141 (m) cc_final: 0.6887 (m)
REVERT: B  228 ASP cc_start: 0.7728 (p0) cc_final: 0.7019 (p0)
REVERT: B  230 ASN cc_start: 0.7820 (m-40) cc_final: 0.7567 (m110)
REVERT: B  233 CYS cc_start: 0.7485 (t) cc_final: 0.7231 (t)
REVERT: B  237 ASN cc_start: 0.6916 (t0) cc_final: 0.6699 (t0)
REVERT: B  239 ASN cc_start: 0.7102 (m-40) cc_final: 0.6800 (m-40)
REVERT: B  262 MET cc_start: 0.6592 (ttm) cc_final: 0.6073 (ttm)
REVERT: B  264 TYR cc_start: 0.7697 (m-80) cc_final: 0.6872 (m-80)
REVERT: B  275 SER cc_start: 0.7530 (t) cc_final: 0.7119 (m)
REVERT: B  277 SER cc_start: 0.7709 (t) cc_final: 0.7185 (p)
REVERT: B  340 ASN cc_start: 0.7208 (t0) cc_final: 0.6991 (m-40)
REVERT: R  152 SER cc_start: 0.8027 (t) cc_final: 0.7630 (m)
REVERT: R  309 ILE cc_start: 0.8477 (mt) cc_final: 0.8255 (mp)
REVERT: S   18 ARG cc_start: 0.7930 (tpp80) cc_final: 0.7492 (tpp80)
REVERT: S  172 THR cc_start: 0.8486 (p) cc_final: 0.8015 (t)
REVERT: S  230 MET cc_start: 0.7794 (ttp) cc_final: 0.7378 (ttp)
  outliers start: 31
  outliers final: 14
  residues processed: 280
  average time/residue: 1.0575
  time to fit residues: 318.6315
Evaluate side-chains
  269 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 253
  time to evaluate  : 1.019 
-------------------------------------------------------------------------------
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  192 ASP
Chi-restraints excluded: chain A residue  194 VAL
Chi-restraints excluded: chain A residue  249 LEU
Chi-restraints excluded: chain A residue  302 THR
Chi-restraints excluded: chain B residue   98 SER
Chi-restraints excluded: chain B residue  146 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 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   52 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 98 optimal weight:    6.9990
   chunk 21 optimal weight:    0.5980
   chunk 64 optimal weight:    1.9990
   chunk 26 optimal weight:    0.9980
   chunk 109 optimal weight:    0.9990
   chunk 90 optimal weight:    2.9990
   chunk 50 optimal weight:    0.4980
   chunk 9 optimal weight:    0.5980
   chunk 36 optimal weight:    0.7980
   chunk 57 optimal weight:    2.9990
   chunk 105 optimal weight:    0.0060
   overall best weight:    0.4996

-------------------------------------------------------------------------------
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 110 ASN
B 125 ASN
B 313 ASN
** 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: 8

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6720
moved from start:          0.3900

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.055   9191  Z= 0.213
  Angle     :  0.556   7.879  12464  Z= 0.290
  Chirality :  0.042   0.162   1418
  Planarity :  0.004   0.042   1580
  Dihedral  :  4.818  32.901   1248
  Min Nonbonded Distance : 2.433

Molprobity Statistics.
  All-atom Clashscore : 9.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.68 %
    Favored  : 98.32 %
  Rotamer:
    Outliers :  3.26 %
    Allowed  : 18.43 %
    Favored  : 78.31 %
  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 (0.25), residues: 1130
  helix:  2.10 (0.25), residues: 394
  sheet: -0.83 (0.28), residues: 284
  loop :  0.11 (0.31), residues: 452

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B 169 
 HIS   0.006   0.001   HIS A 329 
 PHE   0.016   0.002   PHE A 189 
 TYR   0.020   0.002   TYR R 322 
 ARG   0.004   0.000   ARG B 314 

*********************** 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
  303 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 271
  time to evaluate  : 1.156 
Fit side-chains
REVERT: A   14 GLU cc_start: 0.6606 (tm-30) cc_final: 0.6338 (tm-30)
REVERT: A  194 VAL cc_start: 0.7928 (OUTLIER) cc_final: 0.7568 (t)
REVERT: A  208 ARG cc_start: 0.8167 (ptp90) cc_final: 0.7900 (ttp-110)
REVERT: A  210 LYS cc_start: 0.7968 (OUTLIER) cc_final: 0.7740 (mmmt)
REVERT: A  229 ASP cc_start: 0.6810 (t0) cc_final: 0.6568 (t0)
REVERT: A  238 ASN cc_start: 0.8235 (m-40) cc_final: 0.7999 (m-40)
REVERT: A  257 PHE cc_start: 0.7432 (m-80) cc_final: 0.7221 (m-10)
REVERT: B   61 MET cc_start: 0.7576 (tmm) cc_final: 0.6998 (ppp)
REVERT: B   98 SER cc_start: 0.8061 (OUTLIER) cc_final: 0.7730 (p)
REVERT: B  134 ARG cc_start: 0.7051 (ptt90) cc_final: 0.6820 (ptt90)
REVERT: B  137 ARG cc_start: 0.7063 (ttm-80) cc_final: 0.6759 (ttm-80)
REVERT: B  145 TYR cc_start: 0.8202 (p90) cc_final: 0.7778 (p90)
REVERT: B  150 ARG cc_start: 0.8234 (mpt180) cc_final: 0.7868 (mpt180)
REVERT: B  156 GLN cc_start: 0.8015 (mt0) cc_final: 0.7607 (mt0)
REVERT: B  170 ASP cc_start: 0.7597 (m-30) cc_final: 0.7361 (m-30)
REVERT: B  177 THR cc_start: 0.7690 (m) cc_final: 0.7365 (m)
REVERT: B  189 SER cc_start: 0.7881 (p) cc_final: 0.7651 (p)
REVERT: B  190 LEU cc_start: 0.7854 (tt) cc_final: 0.7542 (tt)
REVERT: B  207 SER cc_start: 0.8327 (t) cc_final: 0.8054 (p)
REVERT: B  212 ASP cc_start: 0.6806 (t0) cc_final: 0.6309 (t0)
REVERT: B  217 MET cc_start: 0.6961 (ptt) cc_final: 0.6587 (ptt)
REVERT: B  221 THR cc_start: 0.7128 (m) cc_final: 0.6880 (m)
REVERT: B  228 ASP cc_start: 0.7758 (p0) cc_final: 0.6987 (p0)
REVERT: B  230 ASN cc_start: 0.7807 (m-40) cc_final: 0.7507 (m110)
REVERT: B  233 CYS cc_start: 0.7497 (t) cc_final: 0.7256 (t)
REVERT: B  239 ASN cc_start: 0.7102 (m-40) cc_final: 0.6890 (m-40)
REVERT: B  262 MET cc_start: 0.6567 (ttm) cc_final: 0.6045 (ttm)
REVERT: B  264 TYR cc_start: 0.7690 (m-80) cc_final: 0.6896 (m-80)
REVERT: B  275 SER cc_start: 0.7359 (t) cc_final: 0.6971 (m)
REVERT: B  277 SER cc_start: 0.7624 (t) cc_final: 0.7155 (p)
REVERT: R  152 SER cc_start: 0.8007 (t) cc_final: 0.7625 (m)
REVERT: R  309 ILE cc_start: 0.8466 (mt) cc_final: 0.8205 (mp)
REVERT: S   18 ARG cc_start: 0.7927 (tpp80) cc_final: 0.7518 (tpp80)
REVERT: S   95 TYR cc_start: 0.8131 (m-80) cc_final: 0.7805 (m-80)
REVERT: S  172 THR cc_start: 0.8528 (p) cc_final: 0.8084 (t)
REVERT: S  230 MET cc_start: 0.7757 (ttp) cc_final: 0.7340 (ttp)
  outliers start: 32
  outliers final: 16
  residues processed: 291
  average time/residue: 1.0148
  time to fit residues: 319.0067
Evaluate side-chains
  275 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 256
  time to evaluate  : 1.028 
-------------------------------------------------------------------------------
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  194 VAL
Chi-restraints excluded: chain A residue  201 VAL
Chi-restraints excluded: chain A residue  210 LYS
Chi-restraints excluded: chain A residue  213 GLN
Chi-restraints excluded: chain A residue  224 VAL
Chi-restraints excluded: chain A residue  249 LEU
Chi-restraints excluded: chain B residue   98 SER
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 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
Chi-restraints excluded: chain S residue  215 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 12 optimal weight:    0.9990
   chunk 62 optimal weight:    0.5980
   chunk 79 optimal weight:    0.9990
   chunk 61 optimal weight:    0.6980
   chunk 92 optimal weight:    0.4980
   chunk 108 optimal weight:    0.9980
   chunk 68 optimal weight:    0.9980
   chunk 66 optimal weight:    0.5980
   chunk 50 optimal weight:    2.9990
   chunk 67 optimal weight:    0.5980
   chunk 43 optimal weight:    5.9990
   overall best weight:    0.5980

-------------------------------------------------------------------------------
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 ** both conformations clash, **PLEASE CHECK MANUALLY**
B 110 ASN
B 125 ASN
B 340 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: 6

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6727
moved from start:          0.4061

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051   9191  Z= 0.226
  Angle     :  0.568   8.506  12464  Z= 0.295
  Chirality :  0.043   0.169   1418
  Planarity :  0.004   0.040   1580
  Dihedral  :  4.833  33.984   1248
  Min Nonbonded Distance : 2.424

Molprobity Statistics.
  All-atom Clashscore : 10.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.12 %
    Favored  : 97.88 %
  Rotamer:
    Outliers :  3.56 %
    Allowed  : 19.04 %
    Favored  : 77.39 %
  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:  2.09 (0.25), residues: 394
  sheet: -0.80 (0.30), residues: 264
  loop : -0.00 (0.30), residues: 472

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP B 169 
 HIS   0.006   0.001   HIS A 329 
 PHE   0.015   0.002   PHE A 189 
 TYR   0.031   0.002   TYR R 322 
 ARG   0.007   0.000   ARG A 284 

*********************** 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
  287 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 252
  time to evaluate  : 1.036 
Fit side-chains
   revert: symmetry clash
REVERT: A    9 ASP cc_start: 0.7313 (m-30) cc_final: 0.7095 (m-30)
REVERT: A   14 GLU cc_start: 0.6635 (tm-30) cc_final: 0.6350 (tm-30)
REVERT: A  208 ARG cc_start: 0.8171 (ptp90) cc_final: 0.7922 (ttp-110)
REVERT: A  229 ASP cc_start: 0.6743 (t0) cc_final: 0.6429 (t0)
REVERT: A  358 TYR cc_start: 0.7957 (m-80) cc_final: 0.7743 (m-80)
REVERT: B   59 TYR cc_start: 0.7121 (OUTLIER) cc_final: 0.6511 (m-80)
REVERT: B   61 MET cc_start: 0.7558 (tmm) cc_final: 0.7012 (ppp)
REVERT: B   98 SER cc_start: 0.8086 (OUTLIER) cc_final: 0.7809 (p)
REVERT: B  110 ASN cc_start: 0.7741 (m-40) cc_final: 0.7476 (m110)
REVERT: B  134 ARG cc_start: 0.6990 (ptt90) cc_final: 0.6756 (ptt90)
REVERT: B  145 TYR cc_start: 0.8176 (p90) cc_final: 0.7359 (p90)
REVERT: B  150 ARG cc_start: 0.8199 (OUTLIER) cc_final: 0.7739 (mmt180)
REVERT: B  156 GLN cc_start: 0.8028 (mt0) cc_final: 0.7633 (mt0)
REVERT: B  170 ASP cc_start: 0.7608 (m-30) cc_final: 0.7359 (m-30)
REVERT: B  177 THR cc_start: 0.7690 (m) cc_final: 0.7383 (m)
REVERT: B  189 SER cc_start: 0.7724 (p) cc_final: 0.7486 (t)
REVERT: B  190 LEU cc_start: 0.7868 (tt) cc_final: 0.7577 (tt)
REVERT: B  212 ASP cc_start: 0.6788 (t0) cc_final: 0.6307 (t0)
REVERT: B  217 MET cc_start: 0.6968 (ptt) cc_final: 0.6607 (ptt)
REVERT: B  228 ASP cc_start: 0.7641 (p0) cc_final: 0.6876 (p0)
REVERT: B  233 CYS cc_start: 0.7506 (t) cc_final: 0.7277 (t)
REVERT: B  239 ASN cc_start: 0.6984 (m-40) cc_final: 0.6657 (m110)
REVERT: B  262 MET cc_start: 0.6580 (ttm) cc_final: 0.6024 (ttm)
REVERT: B  264 TYR cc_start: 0.7705 (m-80) cc_final: 0.6877 (m-80)
REVERT: B  275 SER cc_start: 0.7330 (t) cc_final: 0.6967 (m)
REVERT: B  277 SER cc_start: 0.7708 (t) cc_final: 0.7188 (p)
REVERT: B  283 ARG cc_start: 0.7494 (tpt170) cc_final: 0.7160 (tpt170)
REVERT: R  152 SER cc_start: 0.8012 (t) cc_final: 0.7630 (m)
REVERT: R  309 ILE cc_start: 0.8496 (mt) cc_final: 0.8260 (mp)
REVERT: R  330 LEU cc_start: 0.7947 (mt) cc_final: 0.7735 (mm)
REVERT: S   18 ARG cc_start: 0.7879 (tpp80) cc_final: 0.7510 (tpp80)
REVERT: S   95 TYR cc_start: 0.8052 (m-80) cc_final: 0.7731 (m-80)
REVERT: S  230 MET cc_start: 0.7742 (ttp) cc_final: 0.7317 (ttp)
  outliers start: 35
  outliers final: 20
  residues processed: 269
  average time/residue: 1.0343
  time to fit residues: 299.6511
Evaluate side-chains
  272 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 249
  time to evaluate  : 1.099 
-------------------------------------------------------------------------------
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  201 VAL
Chi-restraints excluded: chain A residue  213 GLN
Chi-restraints excluded: chain A residue  249 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   98 SER
Chi-restraints excluded: chain B residue  150 ARG
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  296 VAL
Chi-restraints excluded: chain B residue  312 ASP
Chi-restraints excluded: chain R residue  234 LEU
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  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
Chi-restraints excluded: chain S residue  215 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 65 optimal weight:    0.6980
   chunk 32 optimal weight:    0.9980
   chunk 21 optimal weight:    0.6980
   chunk 69 optimal weight:    1.9990
   chunk 74 optimal weight:    0.9980
   chunk 53 optimal weight:    2.9990
   chunk 10 optimal weight:    2.9990
   chunk 85 optimal weight:    4.9990
   chunk 99 optimal weight:    3.9990
   chunk 104 optimal weight:    2.9990
   chunk 95 optimal weight:    0.3980
   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 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 125 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: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6742
moved from start:          0.4162

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.060   9191  Z= 0.262
  Angle     :  0.597   8.659  12464  Z= 0.308
  Chirality :  0.044   0.174   1418
  Planarity :  0.004   0.040   1580
  Dihedral  :  4.911  35.138   1248
  Min Nonbonded Distance : 2.421

Molprobity Statistics.
  All-atom Clashscore : 10.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.30 %
    Favored  : 97.70 %
  Rotamer:
    Outliers :  3.26 %
    Allowed  : 20.06 %
    Favored  : 76.68 %
  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:  1.94 (0.25), residues: 394
  sheet: -0.82 (0.30), residues: 265
  loop :  0.00 (0.30), residues: 471

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP B 169 
 HIS   0.006   0.001   HIS A 329 
 PHE   0.015   0.002   PHE A 189 
 TYR   0.029   0.002   TYR R 322 
 ARG   0.005   0.000   ARG R 297 

*********************** 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
  280 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 248
  time to evaluate  : 1.013 
Fit side-chains
   revert: symmetry clash
REVERT: A  208 ARG cc_start: 0.8149 (ptp90) cc_final: 0.7899 (ttp-110)
REVERT: A  210 LYS cc_start: 0.8002 (mmmt) cc_final: 0.7677 (mmtt)
REVERT: A  229 ASP cc_start: 0.6742 (t0) cc_final: 0.6427 (t0)
REVERT: A  358 TYR cc_start: 0.7970 (m-80) cc_final: 0.7755 (m-80)
REVERT: B   59 TYR cc_start: 0.7056 (OUTLIER) cc_final: 0.6457 (m-80)
REVERT: B   61 MET cc_start: 0.7627 (tmm) cc_final: 0.7169 (tmm)
REVERT: B   98 SER cc_start: 0.8133 (OUTLIER) cc_final: 0.7832 (p)
REVERT: B  110 ASN cc_start: 0.7775 (m-40) cc_final: 0.7502 (m110)
REVERT: B  134 ARG cc_start: 0.7084 (ptt90) cc_final: 0.6848 (ptt90)
REVERT: B  150 ARG cc_start: 0.8190 (OUTLIER) cc_final: 0.7692 (mmt180)
REVERT: B  156 GLN cc_start: 0.8007 (mt0) cc_final: 0.7604 (mt0)
REVERT: B  170 ASP cc_start: 0.7623 (m-30) cc_final: 0.7284 (m-30)
REVERT: B  177 THR cc_start: 0.7706 (m) cc_final: 0.7239 (m)
REVERT: B  190 LEU cc_start: 0.7904 (tt) cc_final: 0.7631 (tt)
REVERT: B  201 SER cc_start: 0.8255 (OUTLIER) cc_final: 0.7867 (p)
REVERT: B  207 SER cc_start: 0.8303 (t) cc_final: 0.8052 (p)
REVERT: B  212 ASP cc_start: 0.6823 (t0) cc_final: 0.6319 (t0)
REVERT: B  217 MET cc_start: 0.6976 (ptt) cc_final: 0.6625 (ptt)
REVERT: B  233 CYS cc_start: 0.7475 (t) cc_final: 0.7213 (t)
REVERT: B  239 ASN cc_start: 0.6966 (m-40) cc_final: 0.6671 (m110)
REVERT: B  262 MET cc_start: 0.6613 (ttm) cc_final: 0.6005 (ttm)
REVERT: B  264 TYR cc_start: 0.7739 (m-80) cc_final: 0.6920 (m-80)
REVERT: B  275 SER cc_start: 0.7354 (t) cc_final: 0.7023 (m)
REVERT: B  277 SER cc_start: 0.7811 (t) cc_final: 0.7249 (p)
REVERT: B  296 VAL cc_start: 0.7972 (OUTLIER) cc_final: 0.7603 (m)
REVERT: B  303 ASP cc_start: 0.6852 (m-30) cc_final: 0.6416 (m-30)
REVERT: B  340 ASN cc_start: 0.6897 (m-40) cc_final: 0.6658 (m-40)
REVERT: R  152 SER cc_start: 0.8050 (t) cc_final: 0.7656 (m)
REVERT: R  309 ILE cc_start: 0.8459 (mt) cc_final: 0.8197 (mp)
REVERT: S   18 ARG cc_start: 0.7944 (tpp80) cc_final: 0.7611 (tpp80)
REVERT: S   95 TYR cc_start: 0.7986 (m-80) cc_final: 0.7689 (m-80)
REVERT: S  230 MET cc_start: 0.7841 (ttp) cc_final: 0.7344 (ttp)
  outliers start: 32
  outliers final: 19
  residues processed: 266
  average time/residue: 0.9679
  time to fit residues: 278.6115
Evaluate side-chains
  272 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 248
  time to evaluate  : 0.967 
-------------------------------------------------------------------------------
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  201 VAL
Chi-restraints excluded: chain A residue  256 LEU
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue   67 SER
Chi-restraints excluded: chain B residue   93 ILE
Chi-restraints excluded: chain B residue   98 SER
Chi-restraints excluded: chain B residue  150 ARG
Chi-restraints excluded: chain B residue  201 SER
Chi-restraints excluded: chain B residue  263 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  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  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
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 101 optimal weight:    2.9990
   chunk 104 optimal weight:    1.9990
   chunk 61 optimal weight:    0.4980
   chunk 44 optimal weight:    3.9990
   chunk 79 optimal weight:    0.5980
   chunk 31 optimal weight:    0.6980
   chunk 91 optimal weight:    0.5980
   chunk 95 optimal weight:    0.0170
   chunk 66 optimal weight:    0.5980
   chunk 107 optimal weight:    3.9990
   chunk 65 optimal weight:    0.7980
   overall best weight:    0.4618

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

Flipped N/Q/H residues before XYZ refinement:
A 329 HIS
B 125 ASN
** R  75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
S 186 GLN
Y  18 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6710
moved from start:          0.4248

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   9191  Z= 0.206
  Angle     :  0.588   9.010  12464  Z= 0.300
  Chirality :  0.043   0.189   1418
  Planarity :  0.004   0.040   1580
  Dihedral  :  4.795  36.503   1248
  Min Nonbonded Distance : 2.410

Molprobity Statistics.
  All-atom Clashscore : 10.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.21 %
    Favored  : 97.79 %
  Rotamer:
    Outliers :  3.16 %
    Allowed  : 20.77 %
    Favored  : 76.07 %
  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:  1.99 (0.26), residues: 394
  sheet: -0.79 (0.30), residues: 264
  loop :  0.09 (0.29), residues: 472

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 169 
 HIS   0.006   0.001   HIS A 329 
 PHE   0.016   0.001   PHE A 189 
 TYR   0.027   0.002   TYR R 322 
 ARG   0.005   0.000   ARG R 297 

*********************** 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
  273 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 242
  time to evaluate  : 0.989 
Fit side-chains
   revert: symmetry clash
REVERT: A   15 ARG cc_start: 0.8092 (ttt90) cc_final: 0.7821 (ttt180)
REVERT: A   46 LYS cc_start: 0.7749 (OUTLIER) cc_final: 0.7257 (ptmm)
REVERT: A  208 ARG cc_start: 0.8108 (ptp90) cc_final: 0.7891 (ttp-110)
REVERT: A  210 LYS cc_start: 0.7990 (mmmt) cc_final: 0.7484 (mmtt)
REVERT: A  229 ASP cc_start: 0.6757 (t0) cc_final: 0.6469 (t0)
REVERT: B   59 TYR cc_start: 0.7005 (OUTLIER) cc_final: 0.6386 (m-80)
REVERT: B   61 MET cc_start: 0.7610 (tmm) cc_final: 0.7156 (tmm)
REVERT: B   98 SER cc_start: 0.8083 (OUTLIER) cc_final: 0.7831 (p)
REVERT: B  110 ASN cc_start: 0.7750 (m-40) cc_final: 0.7437 (m110)
REVERT: B  134 ARG cc_start: 0.7030 (ptt90) cc_final: 0.6792 (ptt90)
REVERT: B  150 ARG cc_start: 0.8164 (OUTLIER) cc_final: 0.7678 (mmt180)
REVERT: B  156 GLN cc_start: 0.7984 (mt0) cc_final: 0.7573 (mt0)
REVERT: B  170 ASP cc_start: 0.7596 (m-30) cc_final: 0.7345 (m-30)
REVERT: B  177 THR cc_start: 0.7708 (m) cc_final: 0.7421 (m)
REVERT: B  188 MET cc_start: 0.6905 (mmm) cc_final: 0.6617 (mmm)
REVERT: B  189 SER cc_start: 0.8053 (t) cc_final: 0.7559 (p)
REVERT: B  201 SER cc_start: 0.8249 (OUTLIER) cc_final: 0.7863 (p)
REVERT: B  207 SER cc_start: 0.8282 (t) cc_final: 0.8071 (p)
REVERT: B  212 ASP cc_start: 0.6753 (t0) cc_final: 0.6274 (t70)
REVERT: B  217 MET cc_start: 0.6998 (ptt) cc_final: 0.6637 (ptt)
REVERT: B  228 ASP cc_start: 0.7753 (p0) cc_final: 0.6368 (p0)
REVERT: B  233 CYS cc_start: 0.7471 (t) cc_final: 0.7237 (t)
REVERT: B  239 ASN cc_start: 0.6842 (m-40) cc_final: 0.6628 (m110)
REVERT: B  262 MET cc_start: 0.6615 (ttm) cc_final: 0.5996 (ttm)
REVERT: B  264 TYR cc_start: 0.7692 (m-80) cc_final: 0.6906 (m-80)
REVERT: B  277 SER cc_start: 0.7651 (t) cc_final: 0.7157 (p)
REVERT: B  296 VAL cc_start: 0.7957 (OUTLIER) cc_final: 0.7579 (m)
REVERT: B  303 ASP cc_start: 0.6810 (m-30) cc_final: 0.6381 (m-30)
REVERT: B  325 MET cc_start: 0.6826 (tpp) cc_final: 0.6536 (tpp)
REVERT: B  340 ASN cc_start: 0.6868 (m-40) cc_final: 0.6637 (m-40)
REVERT: R  152 SER cc_start: 0.8017 (t) cc_final: 0.7641 (m)
REVERT: R  192 MET cc_start: 0.7443 (mmt) cc_final: 0.7139 (mmm)
REVERT: R  309 ILE cc_start: 0.8492 (mt) cc_final: 0.8241 (mp)
REVERT: S   18 ARG cc_start: 0.7895 (tpp80) cc_final: 0.7602 (tpp80)
REVERT: S   52 SER cc_start: 0.7197 (OUTLIER) cc_final: 0.6971 (t)
REVERT: S   95 TYR cc_start: 0.7908 (m-80) cc_final: 0.7657 (m-80)
REVERT: S  172 THR cc_start: 0.8177 (p) cc_final: 0.7908 (t)
REVERT: S  230 MET cc_start: 0.7755 (ttp) cc_final: 0.7350 (ttp)
  outliers start: 31
  outliers final: 18
  residues processed: 253
  average time/residue: 0.9882
  time to fit residues: 270.2630
Evaluate side-chains
  257 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 232
  time to evaluate  : 0.951 
-------------------------------------------------------------------------------
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  201 VAL
Chi-restraints excluded: chain A residue  213 GLN
Chi-restraints excluded: chain B residue   43 ILE
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue   67 SER
Chi-restraints excluded: chain B residue   93 ILE
Chi-restraints excluded: chain B residue   98 SER
Chi-restraints excluded: chain B residue  150 ARG
Chi-restraints excluded: chain B residue  201 SER
Chi-restraints excluded: chain B residue  263 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  271 LEU
Chi-restraints excluded: chain R residue  281 ILE
Chi-restraints excluded: chain R residue  300 ILE
Chi-restraints excluded: chain R residue  320 MET
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
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 50 optimal weight:    0.9990
   chunk 74 optimal weight:    0.9980
   chunk 112 optimal weight:    1.9990
   chunk 103 optimal weight:    1.9990
   chunk 89 optimal weight:    0.8980
   chunk 9 optimal weight:    0.9990
   chunk 69 optimal weight:    0.9990
   chunk 54 optimal weight:    0.7980
   chunk 71 optimal weight:    0.2980
   chunk 95 optimal weight:    0.3980
   chunk 27 optimal weight:    3.9990
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
** A 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 125 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: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6727
moved from start:          0.4314

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.055   9191  Z= 0.251
  Angle     :  0.619  10.679  12464  Z= 0.315
  Chirality :  0.045   0.189   1418
  Planarity :  0.004   0.040   1580
  Dihedral  :  4.864  35.389   1248
  Min Nonbonded Distance : 2.416

Molprobity Statistics.
  All-atom Clashscore : 12.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.83 %
    Favored  : 97.17 %
  Rotamer:
    Outliers :  3.16 %
    Allowed  : 22.00 %
    Favored  : 74.85 %
  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:  0.68 (0.25), residues: 1130
  helix:  1.89 (0.25), residues: 393
  sheet: -0.80 (0.30), residues: 263
  loop :  0.12 (0.30), residues: 474

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP B 169 
 HIS   0.005   0.001   HIS A 329 
 PHE   0.018   0.002   PHE R  68 
 TYR   0.028   0.002   TYR R 322 
 ARG   0.005   0.000   ARG R 297 

********************** 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
  265 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 234
  time to evaluate  : 1.173 
Fit side-chains
   revert: symmetry clash
REVERT: A   46 LYS cc_start: 0.7746 (OUTLIER) cc_final: 0.7260 (ptmm)
REVERT: A  208 ARG cc_start: 0.8077 (ptp90) cc_final: 0.7851 (ttp-110)
REVERT: A  210 LYS cc_start: 0.7970 (mmmt) cc_final: 0.7715 (mmtp)
REVERT: A  229 ASP cc_start: 0.6794 (t0) cc_final: 0.6528 (t0)
REVERT: B   59 TYR cc_start: 0.7049 (OUTLIER) cc_final: 0.6461 (m-80)
REVERT: B   61 MET cc_start: 0.7609 (tmm) cc_final: 0.7147 (tmm)
REVERT: B   98 SER cc_start: 0.8107 (OUTLIER) cc_final: 0.7813 (p)
REVERT: B  110 ASN cc_start: 0.7775 (m-40) cc_final: 0.7468 (m110)
REVERT: B  134 ARG cc_start: 0.7114 (ptt90) cc_final: 0.6868 (ptt90)
REVERT: B  150 ARG cc_start: 0.8193 (OUTLIER) cc_final: 0.7781 (mpt180)
REVERT: B  156 GLN cc_start: 0.7880 (mt0) cc_final: 0.7493 (mt0)
REVERT: B  170 ASP cc_start: 0.7659 (m-30) cc_final: 0.7408 (m-30)
REVERT: B  177 THR cc_start: 0.7699 (m) cc_final: 0.7410 (m)
REVERT: B  189 SER cc_start: 0.8004 (t) cc_final: 0.7775 (t)
REVERT: B  201 SER cc_start: 0.8228 (OUTLIER) cc_final: 0.7926 (p)
REVERT: B  212 ASP cc_start: 0.6785 (t0) cc_final: 0.6292 (t70)
REVERT: B  217 MET cc_start: 0.7086 (ptt) cc_final: 0.6728 (ptt)
REVERT: B  233 CYS cc_start: 0.7453 (t) cc_final: 0.7222 (t)
REVERT: B  262 MET cc_start: 0.6649 (ttm) cc_final: 0.6088 (ttm)
REVERT: B  264 TYR cc_start: 0.7715 (m-80) cc_final: 0.6885 (m-80)
REVERT: B  275 SER cc_start: 0.7346 (t) cc_final: 0.7001 (m)
REVERT: B  277 SER cc_start: 0.7740 (t) cc_final: 0.7193 (p)
REVERT: B  296 VAL cc_start: 0.7983 (OUTLIER) cc_final: 0.7615 (m)
REVERT: B  303 ASP cc_start: 0.6798 (m-30) cc_final: 0.6383 (m-30)
REVERT: B  325 MET cc_start: 0.6910 (tpp) cc_final: 0.6695 (tpp)
REVERT: B  340 ASN cc_start: 0.6851 (m-40) cc_final: 0.6647 (m110)
REVERT: R  152 SER cc_start: 0.8044 (t) cc_final: 0.7645 (m)
REVERT: R  309 ILE cc_start: 0.8469 (mt) cc_final: 0.8221 (mp)
REVERT: R  328 ASN cc_start: 0.6377 (OUTLIER) cc_final: 0.6099 (m110)
REVERT: S   18 ARG cc_start: 0.7919 (tpp80) cc_final: 0.7625 (tpp80)
REVERT: S   52 SER cc_start: 0.7202 (OUTLIER) cc_final: 0.6983 (t)
REVERT: S  172 THR cc_start: 0.8164 (p) cc_final: 0.7643 (t)
REVERT: S  230 MET cc_start: 0.7760 (ttp) cc_final: 0.7355 (ttp)
  outliers start: 31
  outliers final: 19
  residues processed: 247
  average time/residue: 1.0088
  time to fit residues: 270.5237
Evaluate side-chains
  254 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 227
  time to evaluate  : 0.998 
-------------------------------------------------------------------------------
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  201 VAL
Chi-restraints excluded: chain A residue  256 LEU
Chi-restraints excluded: chain B residue   43 ILE
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   98 SER
Chi-restraints excluded: chain B residue  150 ARG
Chi-restraints excluded: chain B residue  201 SER
Chi-restraints excluded: chain B residue  263 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  200 GLU
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 R residue  300 ILE
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   52 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 82 optimal weight:    0.8980
   chunk 13 optimal weight:    4.9990
   chunk 24 optimal weight:   10.0000
   chunk 89 optimal weight:    0.9990
   chunk 37 optimal weight:    0.8980
   chunk 92 optimal weight:    4.9990
   chunk 11 optimal weight:    0.2980
   chunk 16 optimal weight:    0.9980
   chunk 78 optimal weight:    1.9990
   chunk 5 optimal weight:    0.7980
   chunk 64 optimal weight:    6.9990
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
** A 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 125 ASN
R  57 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: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3978 r_free = 0.3978 target = 0.154404 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3757 r_free = 0.3757 target = 0.136712 restraints weight = 11781.113|
|-----------------------------------------------------------------------------|
r_work (start): 0.3713 rms_B_bonded: 1.87
r_work: 0.3598 rms_B_bonded: 2.41 restraints_weight: 0.5000
r_work: 0.3440 rms_B_bonded: 4.19 restraints_weight: 0.2500
r_work (final): 0.3440
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7369
moved from start:          0.4412

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.059   9191  Z= 0.272
  Angle     :  0.631  10.296  12464  Z= 0.324
  Chirality :  0.045   0.202   1418
  Planarity :  0.004   0.040   1580
  Dihedral  :  4.945  35.684   1248
  Min Nonbonded Distance : 2.413

Molprobity Statistics.
  All-atom Clashscore : 12.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.39 %
    Favored  : 97.61 %
  Rotamer:
    Outliers :  3.16 %
    Allowed  : 22.00 %
    Favored  : 74.85 %
  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:  1.76 (0.25), residues: 393
  sheet: -0.84 (0.30), residues: 263
  loop :  0.06 (0.30), residues: 474

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   0.020   0.002   PHE R  68 
 TYR   0.028   0.002   TYR R 322 
 ARG   0.005   0.000   ARG B 283 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4702.82 seconds
wall clock time: 84 minutes 32.77 seconds (5072.77 seconds total)