Starting phenix.real_space_refine
on Mon May 12 04:10:50 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8flu_29287/05_2025/8flu_29287_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8flu_29287/05_2025/8flu_29287.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.76
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8flu_29287/05_2025/8flu_29287.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8flu_29287/05_2025/8flu_29287.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8flu_29287/05_2025/8flu_29287_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8flu_29287/05_2025/8flu_29287_neut.cif"
  }
  resolution = 2.76
  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=   0.078
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      54      5.16       5
     C    5577      2.51       5
     N    1518      2.21       5
     O    1576      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

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

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 8725
  Number of models: 1
  Model: ""
    Number of chains: 9
    Chain: "A"
      Number of atoms: 1793
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 228, 1793
          Classifications: {'peptide': 228}
          Incomplete info: {'truncation_to_alanine': 28}
          Link IDs: {'PTRANS': 6, 'TRANS': 221}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 94
          Unresolved non-hydrogen angles: 114
          Unresolved non-hydrogen dihedrals: 74
          Unresolved non-hydrogen chiralities: 7
          Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 6, 'ARG:plan': 2, 'ASP:plan': 3}
          Unresolved non-hydrogen planarities: 51
    Chain: "B"
      Number of atoms: 2528
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 337, 2528
          Classifications: {'peptide': 337}
          Incomplete info: {'truncation_to_alanine': 16}
          Link IDs: {'PTRANS': 5, 'TRANS': 331}
          Unresolved non-hydrogen bonds: 63
          Unresolved non-hydrogen angles: 77
          Unresolved non-hydrogen dihedrals: 49
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 1, 'ARG:plan': 4, 'ASN:plan1': 2, 'ASP:plan': 4}
          Unresolved non-hydrogen planarities: 50
    Chain: "G"
      Number of atoms: 382
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 55, 382
          Classifications: {'peptide': 55}
          Incomplete info: {'truncation_to_alanine': 12}
          Link IDs: {'PTRANS': 4, 'TRANS': 50}
          Unresolved non-hydrogen bonds: 42
          Unresolved non-hydrogen angles: 50
          Unresolved non-hydrogen dihedrals: 34
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ASN:plan1': 2, 'ARG:plan': 1, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 26
    Chain: "N"
      Number of atoms: 956
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 126, 956
          Classifications: {'peptide': 126}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 5, 'TRANS': 120}
          Unresolved non-hydrogen bonds: 5
          Unresolved non-hydrogen angles: 5
          Unresolved non-hydrogen dihedrals: 5
    Chain: "P"
      Number of atoms: 271
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 32, 271
          Classifications: {'peptide': 32}
          Link IDs: {'TRANS': 31}
    Chain: "R"
      Number of atoms: 2790
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 363, 2790
          Classifications: {'peptide': 363}
          Incomplete info: {'truncation_to_alanine': 53}
          Link IDs: {'PTRANS': 11, 'TRANS': 351}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 201
          Unresolved non-hydrogen angles: 245
          Unresolved non-hydrogen dihedrals: 164
          Unresolved non-hydrogen chiralities: 12
          Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 2, 'TYR:plan': 1, 'ASN:plan1': 4, 'HIS:plan': 2, 'GLU:plan': 7, 'ARG:plan': 11}
          Unresolved non-hydrogen planarities: 122
    Chain: "A"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Classifications: {'water': 1}
    Chain: "P"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Classifications: {'water': 1}
    Chain: "R"
      Number of atoms: 3
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 3
          Classifications: {'water': 3}
          Link IDs: {None: 2}
  Time building chain proxies: 5.57, per 1000 atoms: 0.64
  Number of scatterers: 8725
  At special positions: 0
  Unit cell: (74.62, 95.12, 168.92, 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      54     16.00
     O    1576      8.00
     N    1518      7.00
     C    5577      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=6, symmetry=0
    Simple disulfide: pdb=" SG  CYS N  22 " - pdb=" SG  CYS N  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS N  99 " - pdb=" SG  CYS N 107 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R  48 " - pdb=" SG  CYS R 117 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R 108 " - pdb=" SG  CYS R 148 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R 131 " - pdb=" SG  CYS R 170 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R 281 " - pdb=" SG  CYS R 351 " 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: 2.21
  Conformation dependent library (CDL) restraints added in 1.0 seconds
  

  2238 Ramachandran restraints generated.
    1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2144

  Finding SS restraints...
    Secondary structure from input PDB file:
      32 helices and 12 sheets defined
      44.3% alpha, 19.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.94
  Creating SS restraints...
    Processing helix  chain 'A' and resid 13 through 39
      removed outlier: 3.534A  pdb=" N   GLN A  35 " --> pdb=" O   GLN A  31 " (cutoff:3.500A)
      removed outlier: 3.740A  pdb=" N   VAL A  36 " --> pdb=" O   LYS A  32 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 49 through 51
      No H-bonds generated for 'chain 'A' and resid 49 through 51'
    Processing helix  chain 'A' and resid 52 through 60
    Processing helix  chain 'A' and resid 233 through 239
      removed outlier: 3.548A  pdb=" N   ASN A 239 " --> pdb=" O   GLN A 236 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 264 through 279
    Processing helix  chain 'A' and resid 281 through 285
      removed outlier: 4.103A  pdb=" N   ASP A 284 " --> pdb=" O   TRP A 281 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 293 through 303
    Processing helix  chain 'A' and resid 307 through 312
      removed outlier: 3.810A  pdb=" N   TYR A 311 " --> pdb=" O   LYS A 307 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 313 through 317
    Processing helix  chain 'A' and resid 331 through 351
    Processing helix  chain 'A' and resid 369 through 391
      removed outlier: 4.573A  pdb=" N   ARG A 373 " --> pdb=" O   THR A 369 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 5 through 26
    Processing helix  chain 'B' and resid 29 through 34
      removed outlier: 3.578A  pdb=" N   ILE B  33 " --> pdb=" O   THR B  29 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 35 through 37
      No H-bonds generated for 'chain 'B' and resid 35 through 37'
    Processing helix  chain 'G' and resid 9 through 24
    Processing helix  chain 'G' and resid 29 through 45
    Processing helix  chain 'N' and resid 28 through 32
    Processing helix  chain 'N' and resid 62 through 65
    Processing helix  chain 'N' and resid 87 through 91
    Processing helix  chain 'P' and resid 2 through 32
      removed outlier: 3.717A  pdb=" N   ASP P  17 " --> pdb=" O   LYS P  13 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 33 through 54
    Processing helix  chain 'R' and resid 169 through 174
      removed outlier: 3.743A  pdb=" N   LYS R 172 " --> pdb=" O   GLU R 169 " (cutoff:3.500A)
      removed outlier: 4.330A  pdb=" N   PHE R 173 " --> pdb=" O   CYS R 170 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 177 through 212
      removed outlier: 3.840A  pdb=" N   ARG R 181 " --> pdb=" O   GLU R 177 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 217 through 246
      removed outlier: 3.841A  pdb=" N   SER R 246 " --> pdb=" O   ALA R 242 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 278 through 311
      removed outlier: 3.503A  pdb=" N   ALA R 284 " --> pdb=" O   GLY R 280 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 316 through 347
      removed outlier: 3.585A  pdb=" N   TYR R 320 " --> pdb=" O   SER R 316 " (cutoff:3.500A)
      removed outlier: 4.564A  pdb=" N   TRP R 322 " --> pdb=" O   LYS R 318 " (cutoff:3.500A)
      removed outlier: 4.668A  pdb=" N   GLY R 323 " --> pdb=" O   LYS R 319 " (cutoff:3.500A)
      removed outlier: 4.243A  pdb=" N   LEU R 331 " --> pdb=" O   PHE R 327 " (cutoff:3.500A)
      Proline residue:  R 332  - end of helix
    Processing helix  chain 'R' and resid 356 through 359
      removed outlier: 3.809A  pdb=" N   LYS R 359 " --> pdb=" O   SER R 356 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'R' and resid 356 through 359'
    Processing helix  chain 'R' and resid 360 through 391
      Proline residue:  R 366  - end of helix
      removed outlier: 3.531A  pdb=" N   ASN R 380 " --> pdb=" O   ILE R 376 " (cutoff:3.500A)
      removed outlier: 3.628A  pdb=" N   VAL R 384 " --> pdb=" O   ASN R 380 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 400 through 418
      Proline residue:  R 415  - end of helix
    Processing helix  chain 'R' and resid 419 through 424
    Processing helix  chain 'R' and resid 434 through 460
      removed outlier: 3.971A  pdb=" N   SER R 449 " --> pdb=" O   MET R 445 " (cutoff:3.500A)
      removed outlier: 4.253A  pdb=" N   GLY R 452 " --> pdb=" O   ASN R 448 " (cutoff:3.500A)
      removed outlier: 4.658A  pdb=" N   PHE R 453 " --> pdb=" O   SER R 449 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 463 through 478
    Processing sheet with id=AA1, first strand: chain 'A' and resid 208 through 214
      removed outlier: 6.407A  pdb=" N   HIS A  41 " --> pdb=" O   HIS A 220 " (cutoff:3.500A)
      removed outlier: 7.362A  pdb=" N   PHE A 222 " --> pdb=" O   HIS A  41 " (cutoff:3.500A)
      removed outlier: 7.208A  pdb=" N   LEU A  43 " --> pdb=" O   PHE A 222 " (cutoff:3.500A)
      removed outlier: 9.591A  pdb=" N   ALA A 243 " --> pdb=" O   THR A  40 " (cutoff:3.500A)
      removed outlier: 7.229A  pdb=" N   ARG A  42 " --> pdb=" O   ALA A 243 " (cutoff:3.500A)
      removed outlier: 8.140A  pdb=" N   ILE A 245 " --> pdb=" O   ARG A  42 " (cutoff:3.500A)
      removed outlier: 6.774A  pdb=" N   LEU A  44 " --> pdb=" O   ILE A 245 " (cutoff:3.500A)
      removed outlier: 7.636A  pdb=" N   VAL A 247 " --> pdb=" O   LEU A  44 " (cutoff:3.500A)
      removed outlier: 6.500A  pdb=" N   LEU A  46 " --> pdb=" O   VAL A 247 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51
      removed outlier: 5.388A  pdb=" N   THR B  47 " --> pdb=" O   ASN B 340 " (cutoff:3.500A)
      removed outlier: 6.281A  pdb=" N   ASN B 340 " --> pdb=" O   THR B  47 " (cutoff:3.500A)
      removed outlier: 3.550A  pdb=" N   ARG B  49 " --> pdb=" O   ILE B 338 " (cutoff:3.500A)
      removed outlier: 3.781A  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: 6.557A  pdb=" N   LEU B  79 " --> pdb=" O   ALA B  92 " (cutoff:3.500A)
      removed outlier: 4.445A  pdb=" N   ALA B  92 " --> pdb=" O   LEU B  79 " (cutoff:3.500A)
      removed outlier: 6.447A  pdb=" N   ILE B  81 " --> pdb=" O   VAL B  90 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105
      removed outlier: 6.606A  pdb=" N   ASN B 125 " --> pdb=" O   VAL B 135 " (cutoff:3.500A)
      removed outlier: 6.618A  pdb=" N   VAL B 135 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151
      removed outlier: 6.205A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 5.952A  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: 3.520A  pdb=" N   SER B 189 " --> pdb=" O   GLY B 202 " (cutoff:3.500A)
      removed outlier: 4.492A  pdb=" N   SER B 207 " --> pdb=" O   ALA B 203 " (cutoff:3.500A)
      removed outlier: 6.827A  pdb=" N   ASP B 212 " --> pdb=" O   CYS B 218 " (cutoff:3.500A)
      removed outlier: 6.385A  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: 6.556A  pdb=" N   CYS B 250 " --> pdb=" O   THR B 263 " (cutoff:3.500A)
      removed outlier: 4.474A  pdb=" N   THR B 263 " --> pdb=" O   CYS B 250 " (cutoff:3.500A)
      removed outlier: 6.493A  pdb=" N   LEU B 252 " --> pdb=" O   LEU B 261 " (cutoff:3.500A)
      removed outlier: 3.842A  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: 6.287A  pdb=" N   GLY B 288 " --> pdb=" O   THR B 274 " (cutoff:3.500A)
      removed outlier: 4.273A  pdb=" N   VAL B 276 " --> pdb=" O   LEU B 286 " (cutoff:3.500A)
      removed outlier: 6.699A  pdb=" N   LEU B 286 " --> pdb=" O   VAL B 276 " (cutoff:3.500A)
      removed outlier: 4.541A  pdb=" N   PHE B 278 " --> pdb=" O   LEU B 284 " (cutoff:3.500A)
      removed outlier: 6.953A  pdb=" N   LEU B 284 " --> pdb=" O   PHE B 278 " (cutoff:3.500A)
      removed outlier: 5.780A  pdb=" N   ASP B 298 " --> pdb=" O   ARG B 304 " (cutoff:3.500A)
      removed outlier: 6.125A  pdb=" N   ARG B 304 " --> pdb=" O   ASP B 298 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'N' and resid 3 through 7
    Processing sheet with id=AB1, first strand: chain 'N' and resid 58 through 60
      removed outlier: 6.563A  pdb=" N   TRP N  36 " --> pdb=" O   VAL N  48 " (cutoff:3.500A)
      removed outlier: 4.533A  pdb=" N   ASP N  50 " --> pdb=" O   MET N  34 " (cutoff:3.500A)
      removed outlier: 6.822A  pdb=" N   MET N  34 " --> pdb=" O   ASP N  50 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'R' and resid 111 through 112
    Processing sheet with id=AB3, first strand: chain 'R' and resid 126 through 130

    489 hydrogen bonds defined for protein.
    1380 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: 2.67

  Time building geometry restraints manager: 2.51 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2836
        1.34 -     1.46: 1836
        1.46 -     1.58: 4173
        1.58 -     1.70: 0
        1.70 -     1.81: 75
  Bond restraints: 8920
  Sorted by residual:
  bond pdb=" CA  SER B 316 "
       pdb=" CB  SER B 316 "
    ideal  model  delta    sigma   weight residual
    1.536  1.483  0.053 1.42e-02 4.96e+03 1.37e+01
  bond pdb=" CA  SER B 275 "
       pdb=" CB  SER B 275 "
    ideal  model  delta    sigma   weight residual
    1.534  1.483  0.051 1.64e-02 3.72e+03 9.57e+00
  bond pdb=" N   VAL R 432 "
       pdb=" CA  VAL R 432 "
    ideal  model  delta    sigma   weight residual
    1.459  1.496 -0.037 1.30e-02 5.92e+03 8.11e+00
  bond pdb=" N   GLN P   6 "
       pdb=" CA  GLN P   6 "
    ideal  model  delta    sigma   weight residual
    1.459  1.493 -0.033 1.19e-02 7.06e+03 7.91e+00
  bond pdb=" N   ARG B 314 "
       pdb=" CA  ARG B 314 "
    ideal  model  delta    sigma   weight residual
    1.456  1.492 -0.036 1.28e-02 6.10e+03 7.90e+00
  ... (remaining 8915 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.39: 11429
        1.39 -     2.78: 571
        2.78 -     4.17: 95
        4.17 -     5.57: 30
        5.57 -     6.96: 2
  Bond angle restraints: 12127
  Sorted by residual:
  angle pdb=" N   LYS P  13 "
        pdb=" CA  LYS P  13 "
        pdb=" C   LYS P  13 "
      ideal   model   delta    sigma   weight residual
     112.38  107.34    5.04 1.22e+00 6.72e-01 1.71e+01
  angle pdb=" CA  GLY B 272 "
        pdb=" C   GLY B 272 "
        pdb=" O   GLY B 272 "
      ideal   model   delta    sigma   weight residual
     121.64  118.03    3.61 9.20e-01 1.18e+00 1.54e+01
  angle pdb=" N   TYR B  59 "
        pdb=" CA  TYR B  59 "
        pdb=" C   TYR B  59 "
      ideal   model   delta    sigma   weight residual
     113.28  108.72    4.56 1.22e+00 6.72e-01 1.40e+01
  angle pdb=" CA  THR R 430 "
        pdb=" C   THR R 430 "
        pdb=" O   THR R 430 "
      ideal   model   delta    sigma   weight residual
     121.81  117.60    4.21 1.18e+00 7.18e-01 1.28e+01
  angle pdb=" N   THR B 274 "
        pdb=" CA  THR B 274 "
        pdb=" C   THR B 274 "
      ideal   model   delta    sigma   weight residual
     113.97  109.51    4.46 1.28e+00 6.10e-01 1.21e+01
  ... (remaining 12122 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.66: 4814
       17.66 -    35.32: 329
       35.32 -    52.98: 47
       52.98 -    70.64: 17
       70.64 -    88.30: 8
  Dihedral angle restraints: 5215
    sinusoidal: 1899
      harmonic: 3316
  Sorted by residual:
  dihedral pdb=" CA  PHE N 108 "
           pdb=" C   PHE N 108 "
           pdb=" N   ASP N 109 "
           pdb=" CA  ASP N 109 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  156.00   24.00     0      5.00e+00 4.00e-02 2.30e+01
  dihedral pdb=" CA  PHE R 314 "
           pdb=" C   PHE R 314 "
           pdb=" N   PHE R 315 "
           pdb=" CA  PHE R 315 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -159.66  -20.34     0      5.00e+00 4.00e-02 1.65e+01
  dihedral pdb=" CB  CYS R 281 "
           pdb=" SG  CYS R 281 "
           pdb=" SG  CYS R 351 "
           pdb=" CB  CYS R 351 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  127.08  -34.08     1      1.00e+01 1.00e-02 1.65e+01
  ... (remaining 5212 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.047: 1038
       0.047 -    0.094: 255
       0.094 -    0.141: 62
       0.141 -    0.188: 9
       0.188 -    0.235: 3
  Chirality restraints: 1367
  Sorted by residual:
  chirality pdb=" CA  ILE B  58 "
            pdb=" N   ILE B  58 "
            pdb=" C   ILE B  58 "
            pdb=" CB  ILE B  58 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.67   -0.24 2.00e-01 2.50e+01 1.38e+00
  chirality pdb=" CA  ILE B 273 "
            pdb=" N   ILE B 273 "
            pdb=" C   ILE B 273 "
            pdb=" CB  ILE B 273 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.66   -0.23 2.00e-01 2.50e+01 1.30e+00
  chirality pdb=" CA  LYS P  13 "
            pdb=" N   LYS P  13 "
            pdb=" C   LYS P  13 "
            pdb=" CB  LYS P  13 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.71   -0.20 2.00e-01 2.50e+01 1.00e+00
  ... (remaining 1364 not shown)

  Planarity restraints: 1544
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR A 325 "   -0.048 5.00e-02 4.00e+02   7.34e-02 8.61e+00
        pdb=" N   PRO A 326 "    0.127 5.00e-02 4.00e+02
        pdb=" CA  PRO A 326 "   -0.039 5.00e-02 4.00e+02
        pdb=" CD  PRO A 326 "   -0.040 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU B  55 "   -0.012 2.00e-02 2.50e+03   2.47e-02 6.10e+00
        pdb=" C   LEU B  55 "    0.043 2.00e-02 2.50e+03
        pdb=" O   LEU B  55 "   -0.016 2.00e-02 2.50e+03
        pdb=" N   ALA B  56 "   -0.014 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PRO R 428 "   -0.011 2.00e-02 2.50e+03   2.14e-02 4.58e+00
        pdb=" C   PRO R 428 "    0.037 2.00e-02 2.50e+03
        pdb=" O   PRO R 428 "   -0.014 2.00e-02 2.50e+03
        pdb=" N   TYR R 429 "   -0.012 2.00e-02 2.50e+03
  ... (remaining 1541 not shown)

  Histogram of nonbonded interaction distances:
        2.22 -     2.76: 1520
        2.76 -     3.29: 8941
        3.29 -     3.83: 15852
        3.83 -     4.36: 19131
        4.36 -     4.90: 31893
  Nonbonded interactions: 77337
  Sorted by model distance:
  nonbonded pdb=" OD1 ASP A 274 "
            pdb=" ND2 ASN A 278 "
     model   vdw
     2.223 3.120
  nonbonded pdb=" OE2 GLU B 260 "
            pdb=" OG1 THR B 263 "
     model   vdw
     2.236 3.040
  nonbonded pdb=" O   PHE A 315 "
            pdb=" NH2 ARG A 336 "
     model   vdw
     2.249 3.120
  nonbonded pdb=" OG  SER B 147 "
            pdb=" O   VAL B 187 "
     model   vdw
     2.249 3.040
  nonbonded pdb=" OE2 GLU P   4 "
            pdb=" OH  TYR R 195 "
     model   vdw
     2.250 3.040
  ... (remaining 77332 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=0.00 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:             2.100
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.410
  Check model and map are aligned:         0.070
  Set scattering table:                    0.100
  Process input model:                     22.550
  Find NCS groups from input model:        0.110
  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:             0.000
  Load rotamer database and sin/cos tables:12.260
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   37.650
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7112
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.053   8926  Z= 0.255
  Angle     :  0.697   6.957  12139  Z= 0.439
  Chirality :  0.045   0.235   1367
  Planarity :  0.004   0.073   1544
  Dihedral  : 13.281  88.298   3053
  Min Nonbonded Distance : 2.223

Molprobity Statistics.
  All-atom Clashscore : 12.74
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  3.04 %
    Favored  : 96.87 %
  Rotamer:
    Outliers :  0.35 %
    Allowed  :  0.46 %
    Favored  : 99.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.56 (0.25), residues: 1119
  helix:  1.61 (0.25), residues: 428
  sheet: -0.68 (0.32), residues: 209
  loop : -0.15 (0.30), residues: 482

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 234 
 HIS   0.007   0.001   HIS B 266 
 PHE   0.014   0.002   PHE R 314 
 TYR   0.014   0.001   TYR R 459 
 ARG   0.003   0.000   ARG B 197 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.14074 (  489)
  hydrogen bonds       : angle       6.51501 ( 1380)
  SS BOND              : bond        0.00211 (    6)
  SS BOND              : angle       1.13029 (   12)
  covalent geometry    : bond        0.00425 ( 8920)
  covalent geometry    : angle       0.69624 (12127)

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

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

  2238 Ramachandran restraints generated.
    1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2238 Ramachandran restraints generated.
    1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  173 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 170
  time to evaluate  : 0.987 
Fit side-chains
   revert: symmetry clash
REVERT: A   53 LYS cc_start: 0.6085 (ttpp) cc_final: 0.5495 (tttt)
REVERT: N   83 MET cc_start: 0.6321 (mtm) cc_final: 0.5300 (mtm)
REVERT: R   36 GLU cc_start: 0.6776 (OUTLIER) cc_final: 0.6298 (tm-30)
REVERT: R  221 TYR cc_start: 0.7269 (t80) cc_final: 0.6913 (t80)
  outliers start: 3
  outliers final: 1
  residues processed: 173
  average time/residue: 1.2640
  time to fit residues: 232.4719
Evaluate side-chains
  116 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 114
  time to evaluate  : 0.897 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain R residue   36 GLU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 93 optimal weight:    0.5980
   chunk 84 optimal weight:    8.9990
   chunk 46 optimal weight:    0.5980
   chunk 28 optimal weight:    1.9990
   chunk 56 optimal weight:    9.9990
   chunk 44 optimal weight:    0.9980
   chunk 87 optimal weight:    0.9990
   chunk 33 optimal weight:    0.1980
   chunk 52 optimal weight:    4.9990
   chunk 64 optimal weight:    0.4980
   chunk 100 optimal weight:    1.9990
   overall best weight:    0.5780

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

Flipped N/Q/H residues before XYZ refinement:
B  44 GLN
B 156 GLN
B 220 GLN
** N  35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
P   6 GLN
** R  37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 220 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4545 r_free = 0.4545 target = 0.214852 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 68)----------------|
| r_work = 0.4138 r_free = 0.4138 target = 0.173897 restraints weight = 9920.098|
|-----------------------------------------------------------------------------|
r_work (start): 0.4151 rms_B_bonded: 1.81
r_work: 0.4065 rms_B_bonded: 2.50 restraints_weight: 0.5000
r_work: 0.3953 rms_B_bonded: 4.09 restraints_weight: 0.2500
r_work (final): 0.3953
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7420
moved from start:          0.1644

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048   8926  Z= 0.157
  Angle     :  0.611  10.867  12139  Z= 0.329
  Chirality :  0.043   0.223   1367
  Planarity :  0.004   0.056   1544
  Dihedral  :  5.672  85.154   1236
  Min Nonbonded Distance : 2.494

Molprobity Statistics.
  All-atom Clashscore : 9.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.77 %
    Favored  : 97.23 %
  Rotamer:
    Outliers :  2.54 %
    Allowed  :  9.71 %
    Favored  : 87.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.23 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.97 (0.25), residues: 1119
  helix:  2.22 (0.25), residues: 432
  sheet: -0.80 (0.31), residues: 212
  loop : -0.06 (0.30), residues: 475

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B 211 
 HIS   0.011   0.001   HIS A 357 
 PHE   0.017   0.002   PHE R 212 
 TYR   0.033   0.002   TYR R 191 
 ARG   0.005   0.000   ARG A 373 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04505 (  489)
  hydrogen bonds       : angle       4.87403 ( 1380)
  SS BOND              : bond        0.00533 (    6)
  SS BOND              : angle       2.49332 (   12)
  covalent geometry    : bond        0.00340 ( 8920)
  covalent geometry    : angle       0.60627 (12127)

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

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

  2238 Ramachandran restraints generated.
    1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2238 Ramachandran restraints generated.
    1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  154 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 132
  time to evaluate  : 1.005 
Fit side-chains
REVERT: A   53 LYS cc_start: 0.6327 (ttpp) cc_final: 0.5581 (ttpt)
REVERT: A  208 PHE cc_start: 0.7626 (m-80) cc_final: 0.7300 (m-10)
REVERT: A  373 ARG cc_start: 0.7365 (OUTLIER) cc_final: 0.7038 (mmm-85)
REVERT: B   44 GLN cc_start: 0.7042 (OUTLIER) cc_final: 0.5820 (mp-120)
REVERT: B  170 ASP cc_start: 0.7926 (t70) cc_final: 0.7673 (p0)
REVERT: B  175 GLN cc_start: 0.7248 (mm110) cc_final: 0.6347 (pt0)
REVERT: G   50 LEU cc_start: 0.6692 (OUTLIER) cc_final: 0.5859 (mp)
REVERT: N   83 MET cc_start: 0.6829 (mtm) cc_final: 0.6001 (mtm)
REVERT: R   36 GLU cc_start: 0.6982 (OUTLIER) cc_final: 0.5994 (tm-30)
REVERT: R  180 GLU cc_start: 0.6104 (tp30) cc_final: 0.5330 (mp0)
REVERT: R  221 TYR cc_start: 0.7299 (t80) cc_final: 0.6816 (t80)
REVERT: R  438 GLN cc_start: 0.7467 (OUTLIER) cc_final: 0.7114 (mm-40)
  outliers start: 22
  outliers final: 5
  residues processed: 143
  average time/residue: 1.2601
  time to fit residues: 191.9125
Evaluate side-chains
  129 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 119
  time to evaluate  : 0.885 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  218 ASN
Chi-restraints excluded: chain A residue  373 ARG
Chi-restraints excluded: chain B residue   44 GLN
Chi-restraints excluded: chain B residue  114 CYS
Chi-restraints excluded: chain G residue   50 LEU
Chi-restraints excluded: chain N residue   25 SER
Chi-restraints excluded: chain N residue  111 THR
Chi-restraints excluded: chain N residue  113 THR
Chi-restraints excluded: chain R residue   36 GLU
Chi-restraints excluded: chain R residue  438 GLN
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 30 optimal weight:    0.0870
   chunk 5 optimal weight:    0.8980
   chunk 60 optimal weight:    2.9990
   chunk 56 optimal weight:    8.9990
   chunk 4 optimal weight:    0.6980
   chunk 85 optimal weight:    1.9990
   chunk 63 optimal weight:    0.8980
   chunk 82 optimal weight:    3.9990
   chunk 62 optimal weight:    0.5980
   chunk 81 optimal weight:    9.9990
   chunk 0 optimal weight:   10.0000
   overall best weight:    0.6358

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

Flipped N/Q/H residues before XYZ refinement:
B 156 GLN
P  10 GLN
R  37 GLN
R 380 ASN
** R 420 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4538 r_free = 0.4538 target = 0.214194 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 67)----------------|
| r_work = 0.4126 r_free = 0.4126 target = 0.172969 restraints weight = 10056.783|
|-----------------------------------------------------------------------------|
r_work (start): 0.4141 rms_B_bonded: 1.83
r_work: 0.4056 rms_B_bonded: 2.50 restraints_weight: 0.5000
r_work: 0.3944 rms_B_bonded: 4.11 restraints_weight: 0.2500
r_work (final): 0.3944
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7428
moved from start:          0.1995

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   8926  Z= 0.148
  Angle     :  0.572  10.339  12139  Z= 0.307
  Chirality :  0.042   0.242   1367
  Planarity :  0.004   0.047   1544
  Dihedral  :  5.398  86.848   1234
  Min Nonbonded Distance : 2.510

Molprobity Statistics.
  All-atom Clashscore : 9.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.41 %
    Favored  : 97.59 %
  Rotamer:
    Outliers :  2.20 %
    Allowed  : 13.06 %
    Favored  : 84.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.23 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.99 (0.26), residues: 1119
  helix:  2.26 (0.24), residues: 437
  sheet: -0.90 (0.31), residues: 216
  loop : -0.03 (0.31), residues: 466

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP P  14 
 HIS   0.009   0.001   HIS A 357 
 PHE   0.014   0.002   PHE B 199 
 TYR   0.031   0.002   TYR R 191 
 ARG   0.005   0.000   ARG A 373 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04152 (  489)
  hydrogen bonds       : angle       4.68915 ( 1380)
  SS BOND              : bond        0.00385 (    6)
  SS BOND              : angle       2.01732 (   12)
  covalent geometry    : bond        0.00324 ( 8920)
  covalent geometry    : angle       0.56850 (12127)

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

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

  2238 Ramachandran restraints generated.
    1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2238 Ramachandran restraints generated.
    1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  151 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 132
  time to evaluate  : 1.215 
Fit side-chains
REVERT: A   27 GLU cc_start: 0.7121 (tp30) cc_final: 0.6691 (tp30)
REVERT: A   53 LYS cc_start: 0.6323 (ttpp) cc_final: 0.5688 (ttpt)
REVERT: A  208 PHE cc_start: 0.7552 (m-80) cc_final: 0.7223 (m-10)
REVERT: A  373 ARG cc_start: 0.7387 (mmt-90) cc_final: 0.7102 (mmm-85)
REVERT: A  392 GLU cc_start: 0.7651 (mm-30) cc_final: 0.7409 (mt-10)
REVERT: B   87 THR cc_start: 0.7817 (t) cc_final: 0.7473 (m)
REVERT: B  105 TYR cc_start: 0.7512 (t80) cc_final: 0.7255 (t80)
REVERT: B  170 ASP cc_start: 0.8007 (t70) cc_final: 0.7715 (p0)
REVERT: B  175 GLN cc_start: 0.7287 (mm110) cc_final: 0.6328 (pt0)
REVERT: B  197 ARG cc_start: 0.6906 (OUTLIER) cc_final: 0.6704 (mpp80)
REVERT: B  219 ARG cc_start: 0.7737 (mtp-110) cc_final: 0.7187 (mmt-90)
REVERT: B  280 LYS cc_start: 0.7988 (OUTLIER) cc_final: 0.7712 (mtpt)
REVERT: G   50 LEU cc_start: 0.6667 (OUTLIER) cc_final: 0.5777 (mp)
REVERT: N   83 MET cc_start: 0.6839 (mtm) cc_final: 0.6257 (mtm)
REVERT: R  180 GLU cc_start: 0.6127 (tp30) cc_final: 0.5325 (mp0)
REVERT: R  182 GLU cc_start: 0.7541 (tm-30) cc_final: 0.7323 (tm-30)
REVERT: R  195 TYR cc_start: 0.8277 (m-80) cc_final: 0.7820 (m-80)
REVERT: R  221 TYR cc_start: 0.7228 (t80) cc_final: 0.6794 (t80)
REVERT: R  438 GLN cc_start: 0.7474 (OUTLIER) cc_final: 0.7146 (mm-40)
  outliers start: 19
  outliers final: 7
  residues processed: 137
  average time/residue: 1.2140
  time to fit residues: 177.5838
Evaluate side-chains
  124 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 113
  time to evaluate  : 0.908 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  218 ASN
Chi-restraints excluded: chain A residue  325 THR
Chi-restraints excluded: chain B residue  114 CYS
Chi-restraints excluded: chain B residue  197 ARG
Chi-restraints excluded: chain B residue  280 LYS
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain G residue   50 LEU
Chi-restraints excluded: chain N residue   25 SER
Chi-restraints excluded: chain N residue  113 THR
Chi-restraints excluded: chain R residue  438 GLN
Chi-restraints excluded: chain R residue  463 ASN
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 33 optimal weight:    0.9980
   chunk 15 optimal weight:    5.9990
   chunk 87 optimal weight:    0.9980
   chunk 26 optimal weight:    4.9990
   chunk 107 optimal weight:    2.9990
   chunk 13 optimal weight:    7.9990
   chunk 14 optimal weight:    2.9990
   chunk 77 optimal weight:   40.0000
   chunk 61 optimal weight:    9.9990
   chunk 34 optimal weight:    2.9990
   chunk 80 optimal weight:    3.9990
   overall best weight:    2.1986

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

Flipped N/Q/H residues before XYZ refinement:
A 390 GLN
B 220 GLN
G  18 GLN
** R 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 420 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4444 r_free = 0.4444 target = 0.203900 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 66)----------------|
| r_work = 0.4001 r_free = 0.4001 target = 0.160590 restraints weight = 9993.394|
|-----------------------------------------------------------------------------|
r_work (start): 0.4028 rms_B_bonded: 1.83
r_work: 0.3936 rms_B_bonded: 2.48 restraints_weight: 0.5000
r_work: 0.3818 rms_B_bonded: 4.04 restraints_weight: 0.2500
r_work (final): 0.3818
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7630
moved from start:          0.2627

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.071   8926  Z= 0.329
  Angle     :  0.721   9.716  12139  Z= 0.386
  Chirality :  0.048   0.259   1367
  Planarity :  0.005   0.044   1544
  Dihedral  :  5.398  34.946   1231
  Min Nonbonded Distance : 2.470

Molprobity Statistics.
  All-atom Clashscore : 12.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.40 %
    Favored  : 96.60 %
  Rotamer:
    Outliers :  3.58 %
    Allowed  : 14.22 %
    Favored  : 82.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.23 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.37 (0.25), residues: 1119
  helix:  1.55 (0.24), residues: 444
  sheet: -1.13 (0.32), residues: 205
  loop : -0.25 (0.29), residues: 470

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.003   TRP P  14 
 HIS   0.014   0.002   HIS A 357 
 PHE   0.023   0.003   PHE A 222 
 TYR   0.031   0.002   TYR R 191 
 ARG   0.005   0.001   ARG B 214 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04934 (  489)
  hydrogen bonds       : angle       5.34741 ( 1380)
  SS BOND              : bond        0.00135 (    6)
  SS BOND              : angle       2.85116 (   12)
  covalent geometry    : bond        0.00759 ( 8920)
  covalent geometry    : angle       0.71626 (12127)

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

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

  2238 Ramachandran restraints generated.
    1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2238 Ramachandran restraints generated.
    1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  150 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 119
  time to evaluate  : 0.963 
Fit side-chains
REVERT: A   53 LYS cc_start: 0.6578 (ttpp) cc_final: 0.5627 (ttpt)
REVERT: A  216 LYS cc_start: 0.7416 (mttp) cc_final: 0.7060 (pttm)
REVERT: A  373 ARG cc_start: 0.7431 (mmt-90) cc_final: 0.7109 (mmm-85)
REVERT: A  392 GLU cc_start: 0.7802 (mm-30) cc_final: 0.7535 (mt-10)
REVERT: B   87 THR cc_start: 0.7893 (t) cc_final: 0.7556 (m)
REVERT: B  170 ASP cc_start: 0.8103 (t70) cc_final: 0.7899 (t70)
REVERT: B  258 ASP cc_start: 0.7068 (t0) cc_final: 0.6785 (m-30)
REVERT: G   50 LEU cc_start: 0.7008 (OUTLIER) cc_final: 0.6167 (mp)
REVERT: R  180 GLU cc_start: 0.6522 (OUTLIER) cc_final: 0.5799 (mp0)
REVERT: R  182 GLU cc_start: 0.7789 (tm-30) cc_final: 0.7457 (tt0)
REVERT: R  221 TYR cc_start: 0.7377 (t80) cc_final: 0.6830 (t80)
REVERT: R  438 GLN cc_start: 0.7724 (OUTLIER) cc_final: 0.7420 (mm-40)
REVERT: R  467 GLN cc_start: 0.7717 (tp40) cc_final: 0.7131 (tm-30)
  outliers start: 31
  outliers final: 11
  residues processed: 133
  average time/residue: 1.2924
  time to fit residues: 182.6684
Evaluate side-chains
  120 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 106
  time to evaluate  : 0.892 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  325 THR
Chi-restraints excluded: chain A residue  372 ILE
Chi-restraints excluded: chain B residue   65 THR
Chi-restraints excluded: chain B residue  243 THR
Chi-restraints excluded: chain B residue  280 LYS
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain G residue   50 LEU
Chi-restraints excluded: chain N residue   25 SER
Chi-restraints excluded: chain N residue   69 THR
Chi-restraints excluded: chain N residue  111 THR
Chi-restraints excluded: chain N residue  113 THR
Chi-restraints excluded: chain R residue  180 GLU
Chi-restraints excluded: chain R residue  384 VAL
Chi-restraints excluded: chain R residue  438 GLN
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 97 optimal weight:    0.7980
   chunk 29 optimal weight:    0.6980
   chunk 82 optimal weight:    0.0970
   chunk 2 optimal weight:    3.9990
   chunk 100 optimal weight:    0.7980
   chunk 76 optimal weight:    8.9990
   chunk 49 optimal weight:    0.9990
   chunk 54 optimal weight:    0.9980
   chunk 24 optimal weight:    6.9990
   chunk 84 optimal weight:    3.9990
   chunk 103 optimal weight:    5.9990
   overall best weight:    0.6778

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

Flipped N/Q/H residues before XYZ refinement:
A  31 GLN
A 390 GLN
B  44 GLN
B 156 GLN
** R 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 420 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4515 r_free = 0.4515 target = 0.211776 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 67)----------------|
| r_work = 0.4089 r_free = 0.4089 target = 0.169595 restraints weight = 9866.887|
|-----------------------------------------------------------------------------|
r_work (start): 0.4108 rms_B_bonded: 1.85
r_work: 0.4022 rms_B_bonded: 2.51 restraints_weight: 0.5000
r_work: 0.3909 rms_B_bonded: 4.10 restraints_weight: 0.2500
r_work (final): 0.3909
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7500
moved from start:          0.2660

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   8926  Z= 0.152
  Angle     :  0.577  11.115  12139  Z= 0.310
  Chirality :  0.043   0.258   1367
  Planarity :  0.004   0.044   1544
  Dihedral  :  4.963  34.839   1231
  Min Nonbonded Distance : 2.506

Molprobity Statistics.
  All-atom Clashscore : 10.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.59 %
    Favored  : 97.41 %
  Rotamer:
    Outliers :  2.54 %
    Allowed  : 15.95 %
    Favored  : 81.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.23 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.76 (0.26), residues: 1119
  helix:  2.12 (0.24), residues: 435
  sheet: -1.00 (0.31), residues: 218
  loop : -0.20 (0.31), residues: 466

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP P  14 
 HIS   0.008   0.001   HIS A 357 
 PHE   0.020   0.002   PHE A 222 
 TYR   0.026   0.002   TYR R 191 
 ARG   0.004   0.000   ARG A 373 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04108 (  489)
  hydrogen bonds       : angle       4.84106 ( 1380)
  SS BOND              : bond        0.00214 (    6)
  SS BOND              : angle       1.72427 (   12)
  covalent geometry    : bond        0.00335 ( 8920)
  covalent geometry    : angle       0.57472 (12127)

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

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

  2238 Ramachandran restraints generated.
    1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2238 Ramachandran restraints generated.
    1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  139 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 117
  time to evaluate  : 0.940 
Fit side-chains
   revert: symmetry clash
REVERT: A   27 GLU cc_start: 0.7110 (tp30) cc_final: 0.6713 (tp30)
REVERT: A   53 LYS cc_start: 0.6477 (ttpp) cc_final: 0.5704 (ttpt)
REVERT: A  373 ARG cc_start: 0.7337 (mmt-90) cc_final: 0.7012 (mmm-85)
REVERT: A  390 GLN cc_start: 0.6275 (OUTLIER) cc_final: 0.5981 (pt0)
REVERT: B   87 THR cc_start: 0.7761 (t) cc_final: 0.7507 (m)
REVERT: B  170 ASP cc_start: 0.8015 (t70) cc_final: 0.7735 (p0)
REVERT: B  219 ARG cc_start: 0.7791 (mtp-110) cc_final: 0.7219 (mmt-90)
REVERT: G   50 LEU cc_start: 0.6691 (OUTLIER) cc_final: 0.5855 (mp)
REVERT: R  180 GLU cc_start: 0.6521 (OUTLIER) cc_final: 0.5831 (mp0)
REVERT: R  182 GLU cc_start: 0.7742 (tm-30) cc_final: 0.7351 (tm-30)
REVERT: R  438 GLN cc_start: 0.7493 (OUTLIER) cc_final: 0.7192 (mm-40)
REVERT: R  467 GLN cc_start: 0.7631 (tp40) cc_final: 0.7159 (tm-30)
  outliers start: 22
  outliers final: 8
  residues processed: 128
  average time/residue: 1.1390
  time to fit residues: 156.1957
Evaluate side-chains
  114 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 102
  time to evaluate  : 0.967 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  325 THR
Chi-restraints excluded: chain A residue  390 GLN
Chi-restraints excluded: chain B residue  114 CYS
Chi-restraints excluded: chain B residue  243 THR
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain G residue   50 LEU
Chi-restraints excluded: chain N residue   25 SER
Chi-restraints excluded: chain N residue  113 THR
Chi-restraints excluded: chain R residue  180 GLU
Chi-restraints excluded: chain R residue  370 SER
Chi-restraints excluded: chain R residue  384 VAL
Chi-restraints excluded: chain R residue  438 GLN
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 73 optimal weight:    0.6980
   chunk 68 optimal weight:    2.9990
   chunk 85 optimal weight:    0.5980
   chunk 1 optimal weight:    0.8980
   chunk 104 optimal weight:    2.9990
   chunk 43 optimal weight:    0.5980
   chunk 105 optimal weight:    0.0050
   chunk 64 optimal weight:    0.8980
   chunk 109 optimal weight:    0.7980
   chunk 26 optimal weight:    1.9990
   chunk 10 optimal weight:    0.6980
   overall best weight:    0.5194

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

Flipped N/Q/H residues before XYZ refinement:
A  31 GLN
B  44 GLN
B 176 GLN
N  77 ASN
** R 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 420 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4530 r_free = 0.4530 target = 0.213433 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.4117 r_free = 0.4117 target = 0.171948 restraints weight = 9813.379|
|-----------------------------------------------------------------------------|
r_work (start): 0.4126 rms_B_bonded: 1.82
r_work: 0.4041 rms_B_bonded: 2.47 restraints_weight: 0.5000
r_work: 0.3928 rms_B_bonded: 4.04 restraints_weight: 0.2500
r_work (final): 0.3928
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7459
moved from start:          0.2722

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   8926  Z= 0.139
  Angle     :  0.547  10.023  12139  Z= 0.297
  Chirality :  0.042   0.269   1367
  Planarity :  0.004   0.048   1544
  Dihedral  :  4.787  32.703   1231
  Min Nonbonded Distance : 2.534

Molprobity Statistics.
  All-atom Clashscore : 9.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.68 %
    Favored  : 97.32 %
  Rotamer:
    Outliers :  2.54 %
    Allowed  : 16.76 %
    Favored  : 80.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.23 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.92 (0.26), residues: 1119
  helix:  2.31 (0.25), residues: 437
  sheet: -0.97 (0.31), residues: 218
  loop : -0.16 (0.31), residues: 464

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP P  14 
 HIS   0.006   0.001   HIS A 357 
 PHE   0.026   0.002   PHE A 222 
 TYR   0.027   0.002   TYR R 191 
 ARG   0.003   0.000   ARG B 214 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03989 (  489)
  hydrogen bonds       : angle       4.75161 ( 1380)
  SS BOND              : bond        0.00658 (    6)
  SS BOND              : angle       1.68287 (   12)
  covalent geometry    : bond        0.00302 ( 8920)
  covalent geometry    : angle       0.54425 (12127)

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

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

  2238 Ramachandran restraints generated.
    1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2238 Ramachandran restraints generated.
    1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  145 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 123
  time to evaluate  : 0.871 
Fit side-chains
   revert: symmetry clash
REVERT: A   27 GLU cc_start: 0.6978 (tp30) cc_final: 0.6539 (tp30)
REVERT: A   53 LYS cc_start: 0.6313 (ttpp) cc_final: 0.5656 (ttpt)
REVERT: A  208 PHE cc_start: 0.7617 (m-80) cc_final: 0.7251 (m-10)
REVERT: B   44 GLN cc_start: 0.7123 (OUTLIER) cc_final: 0.6850 (mm110)
REVERT: B   87 THR cc_start: 0.7678 (t) cc_final: 0.7460 (m)
REVERT: B  170 ASP cc_start: 0.7997 (t70) cc_final: 0.7673 (p0)
REVERT: B  175 GLN cc_start: 0.7157 (mm110) cc_final: 0.6330 (pt0)
REVERT: B  219 ARG cc_start: 0.7741 (mtp-110) cc_final: 0.7225 (mmt-90)
REVERT: B  280 LYS cc_start: 0.7956 (OUTLIER) cc_final: 0.7701 (mtpt)
REVERT: B  325 MET cc_start: 0.7314 (OUTLIER) cc_final: 0.6818 (mmt)
REVERT: G   50 LEU cc_start: 0.6621 (OUTLIER) cc_final: 0.5725 (mp)
REVERT: R  180 GLU cc_start: 0.6460 (OUTLIER) cc_final: 0.5731 (mp0)
REVERT: R  182 GLU cc_start: 0.7710 (tm-30) cc_final: 0.7380 (tm-30)
REVERT: R  221 TYR cc_start: 0.7124 (t80) cc_final: 0.6790 (t80)
REVERT: R  467 GLN cc_start: 0.7536 (tp40) cc_final: 0.7114 (tm-30)
  outliers start: 22
  outliers final: 9
  residues processed: 132
  average time/residue: 1.1249
  time to fit residues: 159.1063
Evaluate side-chains
  125 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 111
  time to evaluate  : 0.902 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  325 THR
Chi-restraints excluded: chain B residue   44 GLN
Chi-restraints excluded: chain B residue  114 CYS
Chi-restraints excluded: chain B residue  243 THR
Chi-restraints excluded: chain B residue  280 LYS
Chi-restraints excluded: chain B residue  325 MET
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain G residue   50 LEU
Chi-restraints excluded: chain N residue   25 SER
Chi-restraints excluded: chain N residue  113 THR
Chi-restraints excluded: chain R residue  180 GLU
Chi-restraints excluded: chain R residue  370 SER
Chi-restraints excluded: chain R residue  379 ILE
Chi-restraints excluded: chain R residue  384 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 92 optimal weight:    2.9990
   chunk 105 optimal weight:    0.0170
   chunk 3 optimal weight:    2.9990
   chunk 41 optimal weight:    0.8980
   chunk 100 optimal weight:    0.0770
   chunk 73 optimal weight:    0.9980
   chunk 47 optimal weight:    0.8980
   chunk 110 optimal weight:    0.8980
   chunk 30 optimal weight:    0.9980
   chunk 2 optimal weight:    5.9990
   chunk 66 optimal weight:    0.6980
   overall best weight:    0.5176

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

Flipped N/Q/H residues before XYZ refinement:
A  31 GLN
B 156 GLN
B 176 GLN
** R 420 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4515 r_free = 0.4515 target = 0.211958 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 68)----------------|
| r_work = 0.4099 r_free = 0.4099 target = 0.170384 restraints weight = 10021.904|
|-----------------------------------------------------------------------------|
r_work (start): 0.4133 rms_B_bonded: 1.83
r_work: 0.4048 rms_B_bonded: 2.50 restraints_weight: 0.5000
r_work: 0.3936 rms_B_bonded: 4.07 restraints_weight: 0.2500
r_work (final): 0.3936
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7453
moved from start:          0.2828

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   8926  Z= 0.135
  Angle     :  0.545   9.400  12139  Z= 0.295
  Chirality :  0.042   0.281   1367
  Planarity :  0.004   0.050   1544
  Dihedral  :  4.698  31.036   1231
  Min Nonbonded Distance : 2.548

Molprobity Statistics.
  All-atom Clashscore : 9.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.95 %
    Favored  : 97.05 %
  Rotamer:
    Outliers :  2.54 %
    Allowed  : 17.11 %
    Favored  : 80.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.23 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.98 (0.26), residues: 1119
  helix:  2.37 (0.25), residues: 437
  sheet: -0.96 (0.31), residues: 220
  loop : -0.11 (0.31), residues: 462

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP P  14 
 HIS   0.010   0.001   HIS A 362 
 PHE   0.032   0.002   PHE A 222 
 TYR   0.025   0.001   TYR R 191 
 ARG   0.005   0.000   ARG R 383 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03933 (  489)
  hydrogen bonds       : angle       4.64993 ( 1380)
  SS BOND              : bond        0.00237 (    6)
  SS BOND              : angle       1.67777 (   12)
  covalent geometry    : bond        0.00293 ( 8920)
  covalent geometry    : angle       0.54316 (12127)

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

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

  2238 Ramachandran restraints generated.
    1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2238 Ramachandran restraints generated.
    1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  142 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 120
  time to evaluate  : 0.903 
Fit side-chains
   revert: symmetry clash
REVERT: A   27 GLU cc_start: 0.6926 (tp30) cc_final: 0.6511 (tp30)
REVERT: A   53 LYS cc_start: 0.6329 (ttpp) cc_final: 0.5680 (ttpt)
REVERT: A  208 PHE cc_start: 0.7587 (m-80) cc_final: 0.7235 (m-10)
REVERT: A  390 GLN cc_start: 0.6349 (mt0) cc_final: 0.5943 (pt0)
REVERT: B   87 THR cc_start: 0.7643 (t) cc_final: 0.7419 (m)
REVERT: B  170 ASP cc_start: 0.7983 (t70) cc_final: 0.7668 (p0)
REVERT: B  219 ARG cc_start: 0.7777 (mtp-110) cc_final: 0.7202 (mmt-90)
REVERT: B  280 LYS cc_start: 0.7961 (OUTLIER) cc_final: 0.7754 (ttpt)
REVERT: B  325 MET cc_start: 0.7264 (OUTLIER) cc_final: 0.6782 (mmt)
REVERT: G   50 LEU cc_start: 0.6569 (OUTLIER) cc_final: 0.5692 (mp)
REVERT: R  180 GLU cc_start: 0.6452 (OUTLIER) cc_final: 0.5697 (mp0)
REVERT: R  182 GLU cc_start: 0.7705 (OUTLIER) cc_final: 0.7255 (tt0)
REVERT: R  221 TYR cc_start: 0.7173 (t80) cc_final: 0.6828 (t80)
REVERT: R  467 GLN cc_start: 0.7491 (tp40) cc_final: 0.7112 (tm-30)
  outliers start: 22
  outliers final: 10
  residues processed: 130
  average time/residue: 1.1609
  time to fit residues: 161.6803
Evaluate side-chains
  126 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 111
  time to evaluate  : 0.958 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  325 THR
Chi-restraints excluded: chain B residue  114 CYS
Chi-restraints excluded: chain B residue  243 THR
Chi-restraints excluded: chain B residue  280 LYS
Chi-restraints excluded: chain B residue  325 MET
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain G residue   50 LEU
Chi-restraints excluded: chain N residue   25 SER
Chi-restraints excluded: chain N residue   69 THR
Chi-restraints excluded: chain N residue  113 THR
Chi-restraints excluded: chain R residue  180 GLU
Chi-restraints excluded: chain R residue  182 GLU
Chi-restraints excluded: chain R residue  370 SER
Chi-restraints excluded: chain R residue  379 ILE
Chi-restraints excluded: chain R residue  384 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 38 optimal weight:    0.6980
   chunk 56 optimal weight:    0.9990
   chunk 89 optimal weight:    1.9990
   chunk 53 optimal weight:    0.9990
   chunk 106 optimal weight:    3.9990
   chunk 42 optimal weight:    0.8980
   chunk 33 optimal weight:    0.5980
   chunk 0 optimal weight:   10.0000
   chunk 3 optimal weight:    3.9990
   chunk 105 optimal weight:    0.8980
   chunk 102 optimal weight:    0.9990
   overall best weight:    0.8182

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

Flipped N/Q/H residues before XYZ refinement:
A  31 GLN
B 155 ASN
N  77 ASN
** R 420 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4501 r_free = 0.4501 target = 0.210303 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 70)----------------|
| r_work = 0.4081 r_free = 0.4081 target = 0.168337 restraints weight = 10057.766|
|-----------------------------------------------------------------------------|
r_work (start): 0.4111 rms_B_bonded: 1.83
r_work: 0.4026 rms_B_bonded: 2.48 restraints_weight: 0.5000
r_work: 0.3913 rms_B_bonded: 4.05 restraints_weight: 0.2500
r_work (final): 0.3913
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7484
moved from start:          0.2841

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   8926  Z= 0.162
  Angle     :  0.562   8.891  12139  Z= 0.304
  Chirality :  0.043   0.290   1367
  Planarity :  0.004   0.050   1544
  Dihedral  :  4.719  30.159   1231
  Min Nonbonded Distance : 2.537

Molprobity Statistics.
  All-atom Clashscore : 9.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.86 %
    Favored  : 97.14 %
  Rotamer:
    Outliers :  1.97 %
    Allowed  : 18.96 %
    Favored  : 79.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.23 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.97 (0.26), residues: 1119
  helix:  2.36 (0.25), residues: 436
  sheet: -0.91 (0.32), residues: 218
  loop : -0.15 (0.31), residues: 465

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP P  14 
 HIS   0.008   0.001   HIS A 362 
 PHE   0.038   0.002   PHE A 222 
 TYR   0.025   0.002   TYR R 191 
 ARG   0.001   0.000   ARG N  19 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04020 (  489)
  hydrogen bonds       : angle       4.67326 ( 1380)
  SS BOND              : bond        0.00285 (    6)
  SS BOND              : angle       1.82635 (   12)
  covalent geometry    : bond        0.00362 ( 8920)
  covalent geometry    : angle       0.55897 (12127)

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

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

  2238 Ramachandran restraints generated.
    1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2238 Ramachandran restraints generated.
    1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 112
  time to evaluate  : 0.976 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   27 GLU cc_start: 0.6963 (tp30) cc_final: 0.6550 (tp30)
REVERT: A   53 LYS cc_start: 0.6292 (ttpp) cc_final: 0.5518 (ttpt)
REVERT: A  208 PHE cc_start: 0.7554 (m-80) cc_final: 0.7206 (m-10)
REVERT: A  390 GLN cc_start: 0.6335 (mt0) cc_final: 0.6063 (pt0)
REVERT: B   44 GLN cc_start: 0.7018 (mp10) cc_final: 0.6794 (mm110)
REVERT: B   87 THR cc_start: 0.7690 (t) cc_final: 0.7470 (m)
REVERT: B  170 ASP cc_start: 0.7943 (t70) cc_final: 0.7686 (p0)
REVERT: B  219 ARG cc_start: 0.7755 (mtp-110) cc_final: 0.7194 (mmt-90)
REVERT: B  280 LYS cc_start: 0.7947 (OUTLIER) cc_final: 0.7737 (ttpt)
REVERT: B  325 MET cc_start: 0.7358 (OUTLIER) cc_final: 0.6898 (mmt)
REVERT: G   50 LEU cc_start: 0.6621 (OUTLIER) cc_final: 0.5711 (mp)
REVERT: R  178 THR cc_start: 0.6764 (t) cc_final: 0.6323 (p)
REVERT: R  180 GLU cc_start: 0.6445 (OUTLIER) cc_final: 0.5702 (mp0)
REVERT: R  182 GLU cc_start: 0.7683 (OUTLIER) cc_final: 0.7278 (tt0)
REVERT: R  221 TYR cc_start: 0.7291 (t80) cc_final: 0.6902 (t80)
REVERT: R  467 GLN cc_start: 0.7470 (tp40) cc_final: 0.7100 (tm-30)
  outliers start: 17
  outliers final: 10
  residues processed: 120
  average time/residue: 1.1847
  time to fit residues: 152.5305
Evaluate side-chains
  123 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 108
  time to evaluate  : 0.920 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  325 THR
Chi-restraints excluded: chain B residue  114 CYS
Chi-restraints excluded: chain B residue  243 THR
Chi-restraints excluded: chain B residue  252 LEU
Chi-restraints excluded: chain B residue  280 LYS
Chi-restraints excluded: chain B residue  325 MET
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain G residue   50 LEU
Chi-restraints excluded: chain N residue   25 SER
Chi-restraints excluded: chain N residue  113 THR
Chi-restraints excluded: chain R residue  180 GLU
Chi-restraints excluded: chain R residue  182 GLU
Chi-restraints excluded: chain R residue  370 SER
Chi-restraints excluded: chain R residue  379 ILE
Chi-restraints excluded: chain R residue  383 ARG
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 92 optimal weight:    2.9990
   chunk 76 optimal weight:    8.9990
   chunk 29 optimal weight:    0.5980
   chunk 0 optimal weight:   10.0000
   chunk 49 optimal weight:    0.6980
   chunk 81 optimal weight:    9.9990
   chunk 84 optimal weight:    7.9990
   chunk 108 optimal weight:    2.9990
   chunk 100 optimal weight:    0.0370
   chunk 64 optimal weight:    0.9990
   chunk 24 optimal weight:    7.9990
   overall best weight:    1.0662

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

Flipped N/Q/H residues before XYZ refinement:
A  31 GLN
** R 420 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4485 r_free = 0.4485 target = 0.208509 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 63)----------------|
| r_work = 0.4058 r_free = 0.4058 target = 0.166182 restraints weight = 9948.395|
|-----------------------------------------------------------------------------|
r_work (start): 0.4097 rms_B_bonded: 1.83
r_work: 0.4011 rms_B_bonded: 2.47 restraints_weight: 0.5000
r_work: 0.3898 rms_B_bonded: 4.02 restraints_weight: 0.2500
r_work (final): 0.3898
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7518
moved from start:          0.2978

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045   8926  Z= 0.190
  Angle     :  0.589   8.260  12139  Z= 0.318
  Chirality :  0.044   0.291   1367
  Planarity :  0.004   0.050   1544
  Dihedral  :  4.836  30.486   1231
  Min Nonbonded Distance : 2.520

Molprobity Statistics.
  All-atom Clashscore : 10.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.86 %
    Favored  : 97.14 %
  Rotamer:
    Outliers :  1.85 %
    Allowed  : 19.65 %
    Favored  : 78.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.23 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.86 (0.26), residues: 1119
  helix:  2.25 (0.25), residues: 435
  sheet: -0.98 (0.32), residues: 216
  loop : -0.18 (0.31), residues: 468

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP P  14 
 HIS   0.008   0.001   HIS A 357 
 PHE   0.045   0.002   PHE A 222 
 TYR   0.027   0.002   TYR A 358 
 ARG   0.002   0.000   ARG B 214 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04142 (  489)
  hydrogen bonds       : angle       4.77691 ( 1380)
  SS BOND              : bond        0.00320 (    6)
  SS BOND              : angle       1.99846 (   12)
  covalent geometry    : bond        0.00430 ( 8920)
  covalent geometry    : angle       0.58559 (12127)

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

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

  2238 Ramachandran restraints generated.
    1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2238 Ramachandran restraints generated.
    1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 114
  time to evaluate  : 0.994 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   53 LYS cc_start: 0.6393 (ttpp) cc_final: 0.5543 (ttpt)
REVERT: A  390 GLN cc_start: 0.6310 (mt0) cc_final: 0.6063 (pt0)
REVERT: B   44 GLN cc_start: 0.7068 (mp10) cc_final: 0.6850 (mm110)
REVERT: B   87 THR cc_start: 0.7743 (t) cc_final: 0.7489 (m)
REVERT: B  170 ASP cc_start: 0.7988 (t70) cc_final: 0.7660 (p0)
REVERT: B  219 ARG cc_start: 0.7768 (mtp-110) cc_final: 0.7172 (mmt-90)
REVERT: B  280 LYS cc_start: 0.8012 (OUTLIER) cc_final: 0.7768 (mtpt)
REVERT: B  325 MET cc_start: 0.7430 (OUTLIER) cc_final: 0.6955 (mmt)
REVERT: G   50 LEU cc_start: 0.6677 (OUTLIER) cc_final: 0.5781 (mp)
REVERT: R  178 THR cc_start: 0.6806 (t) cc_final: 0.6407 (p)
REVERT: R  180 GLU cc_start: 0.6448 (OUTLIER) cc_final: 0.5753 (mp0)
REVERT: R  182 GLU cc_start: 0.7683 (tm-30) cc_final: 0.7231 (tt0)
REVERT: R  221 TYR cc_start: 0.7345 (t80) cc_final: 0.6943 (t80)
  outliers start: 16
  outliers final: 10
  residues processed: 124
  average time/residue: 1.1760
  time to fit residues: 156.0431
Evaluate side-chains
  119 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 105
  time to evaluate  : 0.905 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  325 THR
Chi-restraints excluded: chain B residue  114 CYS
Chi-restraints excluded: chain B residue  243 THR
Chi-restraints excluded: chain B residue  280 LYS
Chi-restraints excluded: chain B residue  325 MET
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain G residue   50 LEU
Chi-restraints excluded: chain N residue   25 SER
Chi-restraints excluded: chain N residue   69 THR
Chi-restraints excluded: chain N residue  113 THR
Chi-restraints excluded: chain R residue  180 GLU
Chi-restraints excluded: chain R residue  370 SER
Chi-restraints excluded: chain R residue  379 ILE
Chi-restraints excluded: chain R residue  383 ARG
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 13 optimal weight:    6.9990
   chunk 33 optimal weight:    2.9990
   chunk 23 optimal weight:    6.9990
   chunk 19 optimal weight:    0.9990
   chunk 8 optimal weight:    0.9990
   chunk 100 optimal weight:    0.0010
   chunk 102 optimal weight:    0.9990
   chunk 35 optimal weight:    1.9990
   chunk 49 optimal weight:    0.7980
   chunk 41 optimal weight:    0.9990
   chunk 56 optimal weight:    1.9990
   overall best weight:    0.7592

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

Flipped N/Q/H residues before XYZ refinement:
** R 420 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4499 r_free = 0.4499 target = 0.210070 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 70)----------------|
| r_work = 0.4079 r_free = 0.4079 target = 0.168226 restraints weight = 9992.842|
|-----------------------------------------------------------------------------|
r_work (start): 0.4114 rms_B_bonded: 1.82
r_work: 0.4030 rms_B_bonded: 2.46 restraints_weight: 0.5000
r_work: 0.3918 rms_B_bonded: 4.01 restraints_weight: 0.2500
r_work (final): 0.3918
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7483
moved from start:          0.3015

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   8926  Z= 0.158
  Angle     :  0.562   8.510  12139  Z= 0.304
  Chirality :  0.043   0.292   1367
  Planarity :  0.004   0.050   1544
  Dihedral  :  4.741  29.769   1231
  Min Nonbonded Distance : 2.532

Molprobity Statistics.
  All-atom Clashscore : 9.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.86 %
    Favored  : 97.14 %
  Rotamer:
    Outliers :  1.97 %
    Allowed  : 19.77 %
    Favored  : 78.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.94 (0.26), residues: 1119
  helix:  2.31 (0.25), residues: 436
  sheet: -0.82 (0.32), residues: 223
  loop : -0.18 (0.31), residues: 460

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP P  14 
 HIS   0.007   0.001   HIS A 362 
 PHE   0.050   0.002   PHE R 335 
 TYR   0.024   0.002   TYR R 191 
 ARG   0.003   0.000   ARG B 214 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03992 (  489)
  hydrogen bonds       : angle       4.69383 ( 1380)
  SS BOND              : bond        0.00253 (    6)
  SS BOND              : angle       1.71155 (   12)
  covalent geometry    : bond        0.00350 ( 8920)
  covalent geometry    : angle       0.55948 (12127)

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

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

  2238 Ramachandran restraints generated.
    1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2238 Ramachandran restraints generated.
    1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 110
  time to evaluate  : 0.933 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   27 GLU cc_start: 0.6928 (tp30) cc_final: 0.6469 (tp30)
REVERT: A   53 LYS cc_start: 0.6202 (ttpp) cc_final: 0.5468 (ttpt)
REVERT: A  208 PHE cc_start: 0.7563 (m-80) cc_final: 0.7223 (m-10)
REVERT: A  390 GLN cc_start: 0.6254 (mt0) cc_final: 0.6032 (pt0)
REVERT: B   44 GLN cc_start: 0.7032 (mp10) cc_final: 0.6815 (mm110)
REVERT: B   87 THR cc_start: 0.7656 (t) cc_final: 0.7445 (m)
REVERT: B  170 ASP cc_start: 0.7973 (t70) cc_final: 0.7717 (p0)
REVERT: B  219 ARG cc_start: 0.7748 (mtp-110) cc_final: 0.7193 (mmt-90)
REVERT: B  280 LYS cc_start: 0.7974 (OUTLIER) cc_final: 0.7743 (ttpt)
REVERT: B  325 MET cc_start: 0.7377 (OUTLIER) cc_final: 0.6914 (mmt)
REVERT: G   50 LEU cc_start: 0.6617 (OUTLIER) cc_final: 0.5752 (mp)
REVERT: R  180 GLU cc_start: 0.6461 (OUTLIER) cc_final: 0.5738 (mp0)
REVERT: R  182 GLU cc_start: 0.7727 (tm-30) cc_final: 0.7356 (tt0)
REVERT: R  221 TYR cc_start: 0.7285 (t80) cc_final: 0.6978 (t80)
  outliers start: 17
  outliers final: 10
  residues processed: 120
  average time/residue: 1.1903
  time to fit residues: 152.8637
Evaluate side-chains
  120 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 106
  time to evaluate  : 0.922 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  325 THR
Chi-restraints excluded: chain B residue  114 CYS
Chi-restraints excluded: chain B residue  243 THR
Chi-restraints excluded: chain B residue  280 LYS
Chi-restraints excluded: chain B residue  325 MET
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain G residue   50 LEU
Chi-restraints excluded: chain N residue   25 SER
Chi-restraints excluded: chain N residue  113 THR
Chi-restraints excluded: chain R residue  180 GLU
Chi-restraints excluded: chain R residue  370 SER
Chi-restraints excluded: chain R residue  379 ILE
Chi-restraints excluded: chain R residue  383 ARG
Chi-restraints excluded: chain R residue  384 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 106 optimal weight:    5.9990
   chunk 14 optimal weight:    0.2980
   chunk 36 optimal weight:    0.6980
   chunk 78 optimal weight:    8.9990
   chunk 90 optimal weight:    2.9990
   chunk 92 optimal weight:    0.8980
   chunk 3 optimal weight:    1.9990
   chunk 55 optimal weight:    6.9990
   chunk 105 optimal weight:    0.7980
   chunk 44 optimal weight:    0.4980
   chunk 85 optimal weight:    0.5980
   overall best weight:    0.5780

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

Flipped N/Q/H residues before XYZ refinement:
R 374 ASN
** R 420 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4511 r_free = 0.4511 target = 0.211493 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 65)----------------|
| r_work = 0.4098 r_free = 0.4098 target = 0.170064 restraints weight = 10020.215|
|-----------------------------------------------------------------------------|
r_work (start): 0.4133 rms_B_bonded: 1.81
r_work: 0.4050 rms_B_bonded: 2.45 restraints_weight: 0.5000
r_work: 0.3939 rms_B_bonded: 4.00 restraints_weight: 0.2500
r_work (final): 0.3939
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7449
moved from start:          0.3096

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   8926  Z= 0.140
  Angle     :  0.555   8.391  12139  Z= 0.301
  Chirality :  0.043   0.309   1367
  Planarity :  0.004   0.051   1544
  Dihedral  :  4.663  28.983   1231
  Min Nonbonded Distance : 2.544

Molprobity Statistics.
  All-atom Clashscore : 9.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.77 %
    Favored  : 97.23 %
  Rotamer:
    Outliers :  2.08 %
    Allowed  : 19.65 %
    Favored  : 78.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.01 (0.26), residues: 1119
  helix:  2.35 (0.25), residues: 437
  sheet: -0.81 (0.32), residues: 225
  loop : -0.12 (0.31), residues: 457

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP P  14 
 HIS   0.007   0.001   HIS A 362 
 PHE   0.052   0.002   PHE R 335 
 TYR   0.024   0.001   TYR R 191 
 ARG   0.002   0.000   ARG B 214 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03902 (  489)
  hydrogen bonds       : angle       4.59142 ( 1380)
  SS BOND              : bond        0.00221 (    6)
  SS BOND              : angle       1.54418 (   12)
  covalent geometry    : bond        0.00308 ( 8920)
  covalent geometry    : angle       0.55354 (12127)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 6847.71 seconds
wall clock time: 118 minutes 39.67 seconds (7119.67 seconds total)