Starting phenix.real_space_refine
on Mon Jan 20 08:52:47 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8xxq_38758/01_2025/8xxq_38758.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8xxq_38758/01_2025/8xxq_38758.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.75
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8xxq_38758/01_2025/8xxq_38758.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8xxq_38758/01_2025/8xxq_38758.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8xxq_38758/01_2025/8xxq_38758.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8xxq_38758/01_2025/8xxq_38758.cif"
  }
  resolution = 2.75
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.037
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     104      5.16       5
     C    9620      2.51       5
     N    2608      2.21       5
     O    2840      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 28 residue(s): 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib"
  Total number of atoms: 15172
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 3793
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 499, 3793
          Classifications: {'peptide': 499}
          Link IDs: {'PTRANS': 29, 'TRANS': 469}
    Chain: "B"
      Number of atoms: 3793
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 499, 3793
          Classifications: {'peptide': 499}
          Link IDs: {'PTRANS': 29, 'TRANS': 469}
    Chain: "C"
      Number of atoms: 3793
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 499, 3793
          Classifications: {'peptide': 499}
          Link IDs: {'PTRANS': 29, 'TRANS': 469}
    Chain: "D"
      Number of atoms: 3793
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 499, 3793
          Classifications: {'peptide': 499}
          Link IDs: {'PTRANS': 29, 'TRANS': 469}
  Time building chain proxies: 8.88, per 1000 atoms: 0.59
  Number of scatterers: 15172
  At special positions: 0
  Unit cell: (108.712, 107, 101.864, 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     104     16.00
     O    2840      8.00
     N    2608      7.00
     C    9620      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  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: 3.66
  Conformation dependent library (CDL) restraints added in 1.9 seconds
  

  3976 Ramachandran restraints generated.
    1988 Oldfield, 0 Emsley, 1988 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3648

  Finding SS restraints...
    Secondary structure from input PDB file:
      76 helices and 16 sheets defined
      46.0% alpha, 16.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.77
  Creating SS restraints...
    Processing helix  chain 'A' and resid 43 through 64
      Proline residue:  A  59  - end of helix
    Processing helix  chain 'A' and resid 65 through 83
    Processing helix  chain 'A' and resid 83 through 95
    Processing helix  chain 'A' and resid 98 through 117
    Processing helix  chain 'A' and resid 118 through 123
    Processing helix  chain 'A' and resid 157 through 170
      Proline residue:  A 165  - end of helix
    Processing helix  chain 'A' and resid 182 through 195
      removed outlier: 4.514A  pdb=" N   THR A 186 " --> pdb=" O   VAL A 182 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 209 through 219
      removed outlier: 3.675A  pdb=" N   VAL A 213 " --> pdb=" O   GLN A 209 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 230 through 244
      removed outlier: 3.783A  pdb=" N   HIS A 244 " --> pdb=" O   ARG A 240 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 265 through 279
    Processing helix  chain 'A' and resid 280 through 283
    Processing helix  chain 'A' and resid 296 through 299
    Processing helix  chain 'A' and resid 300 through 310
    Processing helix  chain 'A' and resid 328 through 345
    Processing helix  chain 'A' and resid 379 through 384
    Processing helix  chain 'A' and resid 398 through 409
    Processing helix  chain 'A' and resid 421 through 432
    Processing helix  chain 'A' and resid 466 through 474
    Processing helix  chain 'A' and resid 485 through 489
    Processing helix  chain 'B' and resid 43 through 64
      Proline residue:  B  59  - end of helix
    Processing helix  chain 'B' and resid 65 through 83
    Processing helix  chain 'B' and resid 83 through 95
    Processing helix  chain 'B' and resid 98 through 117
    Processing helix  chain 'B' and resid 118 through 123
    Processing helix  chain 'B' and resid 157 through 170
      Proline residue:  B 165  - end of helix
    Processing helix  chain 'B' and resid 182 through 196
      removed outlier: 4.465A  pdb=" N   THR B 186 " --> pdb=" O   VAL B 182 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 209 through 219
      removed outlier: 3.740A  pdb=" N   VAL B 213 " --> pdb=" O   GLN B 209 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 230 through 244
      removed outlier: 3.772A  pdb=" N   HIS B 244 " --> pdb=" O   ARG B 240 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 265 through 279
    Processing helix  chain 'B' and resid 280 through 283
    Processing helix  chain 'B' and resid 296 through 299
    Processing helix  chain 'B' and resid 300 through 310
    Processing helix  chain 'B' and resid 328 through 345
    Processing helix  chain 'B' and resid 379 through 384
    Processing helix  chain 'B' and resid 398 through 409
    Processing helix  chain 'B' and resid 421 through 432
    Processing helix  chain 'B' and resid 466 through 474
      removed outlier: 3.583A  pdb=" N   TYR B 474 " --> pdb=" O   GLY B 470 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 485 through 489
    Processing helix  chain 'C' and resid 43 through 64
      Proline residue:  C  59  - end of helix
    Processing helix  chain 'C' and resid 65 through 83
    Processing helix  chain 'C' and resid 83 through 95
    Processing helix  chain 'C' and resid 98 through 117
    Processing helix  chain 'C' and resid 118 through 123
    Processing helix  chain 'C' and resid 157 through 170
      Proline residue:  C 165  - end of helix
      removed outlier: 3.616A  pdb=" N   CYS C 170 " --> pdb=" O   MET C 166 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 182 through 196
      removed outlier: 4.491A  pdb=" N   THR C 186 " --> pdb=" O   VAL C 182 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 210 through 219
    Processing helix  chain 'C' and resid 230 through 244
      removed outlier: 3.679A  pdb=" N   HIS C 244 " --> pdb=" O   ARG C 240 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 265 through 279
    Processing helix  chain 'C' and resid 280 through 283
    Processing helix  chain 'C' and resid 296 through 299
    Processing helix  chain 'C' and resid 300 through 310
    Processing helix  chain 'C' and resid 328 through 345
    Processing helix  chain 'C' and resid 379 through 384
    Processing helix  chain 'C' and resid 398 through 409
    Processing helix  chain 'C' and resid 421 through 432
    Processing helix  chain 'C' and resid 466 through 474
      removed outlier: 3.547A  pdb=" N   TYR C 474 " --> pdb=" O   GLY C 470 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 485 through 489
    Processing helix  chain 'D' and resid 43 through 64
      Proline residue:  D  59  - end of helix
    Processing helix  chain 'D' and resid 65 through 83
    Processing helix  chain 'D' and resid 83 through 95
    Processing helix  chain 'D' and resid 98 through 117
    Processing helix  chain 'D' and resid 118 through 123
    Processing helix  chain 'D' and resid 157 through 170
      Proline residue:  D 165  - end of helix
    Processing helix  chain 'D' and resid 182 through 195
      removed outlier: 4.477A  pdb=" N   THR D 186 " --> pdb=" O   VAL D 182 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 210 through 219
    Processing helix  chain 'D' and resid 230 through 244
      removed outlier: 3.819A  pdb=" N   HIS D 244 " --> pdb=" O   ARG D 240 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 265 through 279
    Processing helix  chain 'D' and resid 280 through 283
    Processing helix  chain 'D' and resid 296 through 299
    Processing helix  chain 'D' and resid 300 through 310
    Processing helix  chain 'D' and resid 328 through 345
    Processing helix  chain 'D' and resid 379 through 384
    Processing helix  chain 'D' and resid 398 through 409
    Processing helix  chain 'D' and resid 421 through 432
    Processing helix  chain 'D' and resid 467 through 474
    Processing helix  chain 'D' and resid 485 through 489
    Processing sheet with id=AA1, first strand: chain 'A' and resid 10 through 12
    Processing sheet with id=AA2, first strand: chain 'A' and resid 24 through 28
    Processing sheet with id=AA3, first strand: chain 'A' and resid 126 through 132
      removed outlier: 3.851A  pdb=" N   GLU A 126 " --> pdb=" O   SER A 139 " (cutoff:3.500A)
      removed outlier: 6.691A  pdb=" N   MET A 135 " --> pdb=" O   SER A 130 " (cutoff:3.500A)
      removed outlier: 6.243A  pdb=" N   HIS B 257 " --> pdb=" O   ALA B 416 " (cutoff:3.500A)
      removed outlier: 7.768A  pdb=" N   PHE B 418 " --> pdb=" O   HIS B 257 " (cutoff:3.500A)
      removed outlier: 6.776A  pdb=" N   VAL B 259 " --> pdb=" O   PHE B 418 " (cutoff:3.500A)
      removed outlier: 6.139A  pdb=" N   GLY B 258 " --> pdb=" O   VAL B 292 " (cutoff:3.500A)
      removed outlier: 6.819A  pdb=" N   VAL B 294 " --> pdb=" O   GLY B 258 " (cutoff:3.500A)
      removed outlier: 6.435A  pdb=" N   VAL B 260 " --> pdb=" O   VAL B 294 " (cutoff:3.500A)
      removed outlier: 6.191A  pdb=" N   ALA B 291 " --> pdb=" O   LEU B 394 " (cutoff:3.500A)
      removed outlier: 7.565A  pdb=" N   THR B 396 " --> pdb=" O   ALA B 291 " (cutoff:3.500A)
      removed outlier: 6.177A  pdb=" N   LEU B 293 " --> pdb=" O   THR B 396 " (cutoff:3.500A)
      removed outlier: 6.497A  pdb=" N   ILE B 371 " --> pdb=" O   LEU B 350 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 203 through 205
      removed outlier: 6.669A  pdb=" N   CYS A 147 " --> pdb=" O   LEU A 175 " (cutoff:3.500A)
      removed outlier: 7.433A  pdb=" N   LYS A 177 " --> pdb=" O   CYS A 147 " (cutoff:3.500A)
      removed outlier: 6.046A  pdb=" N   GLY A 149 " --> pdb=" O   LYS A 177 " (cutoff:3.500A)
      removed outlier: 7.711A  pdb=" N   VAL A 146 " --> pdb=" O   LYS A 223 " (cutoff:3.500A)
      removed outlier: 6.649A  pdb=" N   ILE A 225 " --> pdb=" O   VAL A 146 " (cutoff:3.500A)
      removed outlier: 6.752A  pdb=" N   ALA A 148 " --> pdb=" O   ILE A 225 " (cutoff:3.500A)
      removed outlier: 5.977A  pdb=" N   PHE A 227 " --> pdb=" O   ALA A 148 " (cutoff:3.500A)
      removed outlier: 6.721A  pdb=" N   ILE A 150 " --> pdb=" O   PHE A 227 " (cutoff:3.500A)
      removed outlier: 6.839A  pdb=" N   LYS A 223 " --> pdb=" O   ARG A 247 " (cutoff:3.500A)
      removed outlier: 8.347A  pdb=" N   GLN A 249 " --> pdb=" O   LYS A 223 " (cutoff:3.500A)
      removed outlier: 6.573A  pdb=" N   ILE A 225 " --> pdb=" O   GLN A 249 " (cutoff:3.500A)
      removed outlier: 8.033A  pdb=" N   ASN A 251 " --> pdb=" O   ILE A 225 " (cutoff:3.500A)
      removed outlier: 6.565A  pdb=" N   PHE A 227 " --> pdb=" O   ASN A 251 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 348 through 351
      removed outlier: 6.496A  pdb=" N   ILE A 371 " --> pdb=" O   LEU A 350 " (cutoff:3.500A)
      removed outlier: 6.396A  pdb=" N   GLY A 258 " --> pdb=" O   VAL A 292 " (cutoff:3.500A)
      removed outlier: 7.024A  pdb=" N   VAL A 294 " --> pdb=" O   GLY A 258 " (cutoff:3.500A)
      removed outlier: 6.574A  pdb=" N   VAL A 260 " --> pdb=" O   VAL A 294 " (cutoff:3.500A)
      removed outlier: 6.346A  pdb=" N   HIS A 257 " --> pdb=" O   ALA A 416 " (cutoff:3.500A)
      removed outlier: 7.932A  pdb=" N   PHE A 418 " --> pdb=" O   HIS A 257 " (cutoff:3.500A)
      removed outlier: 6.723A  pdb=" N   VAL A 259 " --> pdb=" O   PHE A 418 " (cutoff:3.500A)
      removed outlier: 6.605A  pdb=" N   VAL A 437 " --> pdb=" O   THR B 481 " (cutoff:3.500A)
      removed outlier: 8.160A  pdb=" N   GLN B 483 " --> pdb=" O   VAL A 437 " (cutoff:3.500A)
      removed outlier: 6.501A  pdb=" N   VAL A 439 " --> pdb=" O   GLN B 483 " (cutoff:3.500A)
      removed outlier: 3.751A  pdb=" N   GLU B 126 " --> pdb=" O   SER B 139 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 10 through 12
    Processing sheet with id=AA7, first strand: chain 'B' and resid 24 through 28
    Processing sheet with id=AA8, first strand: chain 'B' and resid 203 through 205
      removed outlier: 6.313A  pdb=" N   PHE B 174 " --> pdb=" O   ASN B 204 " (cutoff:3.500A)
      removed outlier: 6.764A  pdb=" N   VAL B 146 " --> pdb=" O   ILE B 222 " (cutoff:3.500A)
      removed outlier: 4.066A  pdb=" N   ALA B 224 " --> pdb=" O   VAL B 146 " (cutoff:3.500A)
      removed outlier: 6.791A  pdb=" N   LYS B 223 " --> pdb=" O   ARG B 247 " (cutoff:3.500A)
      removed outlier: 8.376A  pdb=" N   GLN B 249 " --> pdb=" O   LYS B 223 " (cutoff:3.500A)
      removed outlier: 6.657A  pdb=" N   ILE B 225 " --> pdb=" O   GLN B 249 " (cutoff:3.500A)
      removed outlier: 8.014A  pdb=" N   ASN B 251 " --> pdb=" O   ILE B 225 " (cutoff:3.500A)
      removed outlier: 6.742A  pdb=" N   PHE B 227 " --> pdb=" O   ASN B 251 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'C' and resid 10 through 12
    Processing sheet with id=AB1, first strand: chain 'C' and resid 24 through 28
    Processing sheet with id=AB2, first strand: chain 'C' and resid 127 through 132
      removed outlier: 6.577A  pdb=" N   MET C 135 " --> pdb=" O   SER C 130 " (cutoff:3.500A)
      removed outlier: 6.291A  pdb=" N   HIS D 257 " --> pdb=" O   ALA D 416 " (cutoff:3.500A)
      removed outlier: 7.902A  pdb=" N   PHE D 418 " --> pdb=" O   HIS D 257 " (cutoff:3.500A)
      removed outlier: 6.736A  pdb=" N   VAL D 259 " --> pdb=" O   PHE D 418 " (cutoff:3.500A)
      removed outlier: 6.225A  pdb=" N   GLY D 258 " --> pdb=" O   VAL D 292 " (cutoff:3.500A)
      removed outlier: 6.921A  pdb=" N   VAL D 294 " --> pdb=" O   GLY D 258 " (cutoff:3.500A)
      removed outlier: 6.505A  pdb=" N   VAL D 260 " --> pdb=" O   VAL D 294 " (cutoff:3.500A)
      removed outlier: 6.248A  pdb=" N   ALA D 291 " --> pdb=" O   LEU D 394 " (cutoff:3.500A)
      removed outlier: 7.604A  pdb=" N   THR D 396 " --> pdb=" O   ALA D 291 " (cutoff:3.500A)
      removed outlier: 6.158A  pdb=" N   LEU D 293 " --> pdb=" O   THR D 396 " (cutoff:3.500A)
      removed outlier: 6.502A  pdb=" N   ILE D 371 " --> pdb=" O   LEU D 350 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'C' and resid 203 through 205
      removed outlier: 6.312A  pdb=" N   PHE C 174 " --> pdb=" O   ASN C 204 " (cutoff:3.500A)
      removed outlier: 6.659A  pdb=" N   CYS C 147 " --> pdb=" O   LEU C 175 " (cutoff:3.500A)
      removed outlier: 7.600A  pdb=" N   LYS C 177 " --> pdb=" O   CYS C 147 " (cutoff:3.500A)
      removed outlier: 6.058A  pdb=" N   GLY C 149 " --> pdb=" O   LYS C 177 " (cutoff:3.500A)
      removed outlier: 7.714A  pdb=" N   VAL C 146 " --> pdb=" O   LYS C 223 " (cutoff:3.500A)
      removed outlier: 6.587A  pdb=" N   ILE C 225 " --> pdb=" O   VAL C 146 " (cutoff:3.500A)
      removed outlier: 6.723A  pdb=" N   ALA C 148 " --> pdb=" O   ILE C 225 " (cutoff:3.500A)
      removed outlier: 5.925A  pdb=" N   PHE C 227 " --> pdb=" O   ALA C 148 " (cutoff:3.500A)
      removed outlier: 6.754A  pdb=" N   ILE C 150 " --> pdb=" O   PHE C 227 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'C' and resid 348 through 351
      removed outlier: 6.502A  pdb=" N   ILE C 371 " --> pdb=" O   LEU C 350 " (cutoff:3.500A)
      removed outlier: 6.283A  pdb=" N   ALA C 291 " --> pdb=" O   LEU C 394 " (cutoff:3.500A)
      removed outlier: 7.482A  pdb=" N   THR C 396 " --> pdb=" O   ALA C 291 " (cutoff:3.500A)
      removed outlier: 6.271A  pdb=" N   LEU C 293 " --> pdb=" O   THR C 396 " (cutoff:3.500A)
      removed outlier: 6.118A  pdb=" N   GLY C 258 " --> pdb=" O   VAL C 292 " (cutoff:3.500A)
      removed outlier: 6.881A  pdb=" N   VAL C 294 " --> pdb=" O   GLY C 258 " (cutoff:3.500A)
      removed outlier: 6.499A  pdb=" N   VAL C 260 " --> pdb=" O   VAL C 294 " (cutoff:3.500A)
      removed outlier: 6.280A  pdb=" N   HIS C 257 " --> pdb=" O   ALA C 416 " (cutoff:3.500A)
      removed outlier: 7.775A  pdb=" N   PHE C 418 " --> pdb=" O   HIS C 257 " (cutoff:3.500A)
      removed outlier: 6.805A  pdb=" N   VAL C 259 " --> pdb=" O   PHE C 418 " (cutoff:3.500A)
      removed outlier: 6.745A  pdb=" N   VAL C 437 " --> pdb=" O   THR D 481 " (cutoff:3.500A)
      removed outlier: 7.954A  pdb=" N   GLN D 483 " --> pdb=" O   VAL C 437 " (cutoff:3.500A)
      removed outlier: 6.067A  pdb=" N   VAL C 439 " --> pdb=" O   GLN D 483 " (cutoff:3.500A)
      removed outlier: 6.765A  pdb=" N   MET D 135 " --> pdb=" O   SER D 130 " (cutoff:3.500A)
      removed outlier: 3.570A  pdb=" N   LEU D 137 " --> pdb=" O   MET D 128 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'D' and resid 10 through 12
    Processing sheet with id=AB6, first strand: chain 'D' and resid 24 through 28
    Processing sheet with id=AB7, first strand: chain 'D' and resid 203 through 205
      removed outlier: 6.381A  pdb=" N   PHE D 174 " --> pdb=" O   ASN D 204 " (cutoff:3.500A)
      removed outlier: 6.668A  pdb=" N   CYS D 147 " --> pdb=" O   LEU D 175 " (cutoff:3.500A)
      removed outlier: 7.482A  pdb=" N   LYS D 177 " --> pdb=" O   CYS D 147 " (cutoff:3.500A)
      removed outlier: 6.092A  pdb=" N   GLY D 149 " --> pdb=" O   LYS D 177 " (cutoff:3.500A)
      removed outlier: 6.721A  pdb=" N   VAL D 146 " --> pdb=" O   ILE D 222 " (cutoff:3.500A)
      removed outlier: 4.014A  pdb=" N   ALA D 224 " --> pdb=" O   VAL D 146 " (cutoff:3.500A)
      removed outlier: 6.856A  pdb=" N   LYS D 223 " --> pdb=" O   ARG D 247 " (cutoff:3.500A)
      removed outlier: 8.424A  pdb=" N   GLN D 249 " --> pdb=" O   LYS D 223 " (cutoff:3.500A)
      removed outlier: 6.670A  pdb=" N   ILE D 225 " --> pdb=" O   GLN D 249 " (cutoff:3.500A)
      removed outlier: 8.025A  pdb=" N   ASN D 251 " --> pdb=" O   ILE D 225 " (cutoff:3.500A)
      removed outlier: 6.513A  pdb=" N   PHE D 227 " --> pdb=" O   ASN D 251 " (cutoff:3.500A)

    741 hydrogen bonds defined for protein.
    2124 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: 5.81

  Time building geometry restraints manager: 4.24 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 5023
        1.34 -     1.46: 3064
        1.46 -     1.58: 7217
        1.58 -     1.69: 0
        1.69 -     1.81: 176
  Bond restraints: 15480
  Sorted by residual:
  bond pdb=" N   SER A   3 "
       pdb=" CA  SER A   3 "
    ideal  model  delta    sigma   weight residual
    1.458  1.491 -0.033 1.90e-02 2.77e+03 3.08e+00
  bond pdb=" N   SER B   3 "
       pdb=" CA  SER B   3 "
    ideal  model  delta    sigma   weight residual
    1.458  1.491 -0.033 1.90e-02 2.77e+03 3.08e+00
  bond pdb=" N   SER D   3 "
       pdb=" CA  SER D   3 "
    ideal  model  delta    sigma   weight residual
    1.458  1.491 -0.033 1.90e-02 2.77e+03 3.03e+00
  bond pdb=" N   SER C   3 "
       pdb=" CA  SER C   3 "
    ideal  model  delta    sigma   weight residual
    1.458  1.491 -0.033 1.90e-02 2.77e+03 2.95e+00
  bond pdb=" N   ARG D 456 "
       pdb=" CA  ARG D 456 "
    ideal  model  delta    sigma   weight residual
    1.457  1.476 -0.018 1.17e-02 7.31e+03 2.45e+00
  ... (remaining 15475 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.16: 20435
        1.16 -     2.32: 387
        2.32 -     3.47: 107
        3.47 -     4.63: 54
        4.63 -     5.79: 5
  Bond angle restraints: 20988
  Sorted by residual:
  angle pdb=" C   SER D 455 "
        pdb=" N   ARG D 456 "
        pdb=" CA  ARG D 456 "
      ideal   model   delta    sigma   weight residual
     121.19  126.53   -5.34 1.59e+00 3.96e-01 1.13e+01
  angle pdb=" C   SER B 455 "
        pdb=" N   ARG B 456 "
        pdb=" CA  ARG B 456 "
      ideal   model   delta    sigma   weight residual
     120.79  124.93   -4.14 1.39e+00 5.18e-01 8.87e+00
  angle pdb=" C   SER C 455 "
        pdb=" N   ARG C 456 "
        pdb=" CA  ARG C 456 "
      ideal   model   delta    sigma   weight residual
     120.79  124.74   -3.95 1.39e+00 5.18e-01 8.07e+00
  angle pdb=" CA  GLN B 209 "
        pdb=" C   GLN B 209 "
        pdb=" O   GLN B 209 "
      ideal   model   delta    sigma   weight residual
     121.50  118.02    3.48 1.25e+00 6.40e-01 7.74e+00
  angle pdb=" C   ARG C 456 "
        pdb=" CA  ARG C 456 "
        pdb=" CB  ARG C 456 "
      ideal   model   delta    sigma   weight residual
     110.92  115.32   -4.40 1.59e+00 3.96e-01 7.65e+00
  ... (remaining 20983 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.09: 9087
       16.09 -    32.19: 221
       32.19 -    48.28: 67
       48.28 -    64.37: 2
       64.37 -    80.46: 3
  Dihedral angle restraints: 9380
    sinusoidal: 3700
      harmonic: 5680
  Sorted by residual:
  dihedral pdb=" CA  GLY D 454 "
           pdb=" C   GLY D 454 "
           pdb=" N   SER D 455 "
           pdb=" CA  SER D 455 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -160.57  -19.43     0      5.00e+00 4.00e-02 1.51e+01
  dihedral pdb=" CA  LEU D 161 "
           pdb=" C   LEU D 161 "
           pdb=" N   TRP D 162 "
           pdb=" CA  TRP D 162 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  164.31   15.69     0      5.00e+00 4.00e-02 9.85e+00
  dihedral pdb=" N   PHE D 465 "
           pdb=" CA  PHE D 465 "
           pdb=" CB  PHE D 465 "
           pdb=" CG  PHE D 465 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00 -112.23   52.23     3      1.50e+01 4.44e-03 9.09e+00
  ... (remaining 9377 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.027: 1504
       0.027 -    0.054: 528
       0.054 -    0.081: 141
       0.081 -    0.108: 130
       0.108 -    0.135: 85
  Chirality restraints: 2388
  Sorted by residual:
  chirality pdb=" CA  VAL C   5 "
            pdb=" N   VAL C   5 "
            pdb=" C   VAL C   5 "
            pdb=" CB  VAL C   5 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.58   -0.14 2.00e-01 2.50e+01 4.57e-01
  chirality pdb=" CA  VAL D 441 "
            pdb=" N   VAL D 441 "
            pdb=" C   VAL D 441 "
            pdb=" CB  VAL D 441 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.57   -0.13 2.00e-01 2.50e+01 4.23e-01
  chirality pdb=" CA  VAL C 441 "
            pdb=" N   VAL C 441 "
            pdb=" C   VAL C 441 "
            pdb=" CB  VAL C 441 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.57   -0.13 2.00e-01 2.50e+01 4.15e-01
  ... (remaining 2385 not shown)

  Planarity restraints: 2732
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE B 159 "   -0.020 5.00e-02 4.00e+02   3.08e-02 1.52e+00
        pdb=" N   PRO B 160 "    0.053 5.00e-02 4.00e+02
        pdb=" CA  PRO B 160 "   -0.016 5.00e-02 4.00e+02
        pdb=" CD  PRO B 160 "   -0.017 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE C 159 "    0.020 5.00e-02 4.00e+02   3.08e-02 1.52e+00
        pdb=" N   PRO C 160 "   -0.053 5.00e-02 4.00e+02
        pdb=" CA  PRO C 160 "    0.016 5.00e-02 4.00e+02
        pdb=" CD  PRO C 160 "    0.017 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE D 159 "    0.019 5.00e-02 4.00e+02   2.85e-02 1.30e+00
        pdb=" N   PRO D 160 "   -0.049 5.00e-02 4.00e+02
        pdb=" CA  PRO D 160 "    0.014 5.00e-02 4.00e+02
        pdb=" CD  PRO D 160 "    0.016 5.00e-02 4.00e+02
  ... (remaining 2729 not shown)

  Histogram of nonbonded interaction distances:
        2.14 -     2.69: 286
        2.69 -     3.25: 15580
        3.25 -     3.80: 25034
        3.80 -     4.35: 34175
        4.35 -     4.90: 56264
  Nonbonded interactions: 131339
  Sorted by model distance:
  nonbonded pdb=" OD2 ASP A 462 "
            pdb=" OG1 THR B 463 "
     model   vdw
     2.142 3.040
  nonbonded pdb=" OD1 ASN C 464 "
            pdb=" NE2 GLN C 469 "
     model   vdw
     2.153 3.120
  nonbonded pdb=" ND2 ASN B  33 "
            pdb=" O   ASN B 363 "
     model   vdw
     2.154 3.120
  nonbonded pdb=" OD1 ASN B 464 "
            pdb=" NE2 GLN B 469 "
     model   vdw
     2.154 3.120
  nonbonded pdb=" OD2 ASP C 462 "
            pdb=" OG1 THR D 463 "
     model   vdw
     2.161 3.040
  ... (remaining 131334 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: 0.04
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'C'
  selection = chain 'D'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.690
  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:             0.020
  Extract box with map and model:          0.520
  Check model and map are aligned:         0.100
  Set scattering table:                    0.130
  Process input model:                     35.490
  Find NCS groups from input model:        0.540
  Set up NCS constraints:                  0.080
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:13.990
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   51.570
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8144
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      :  0.002   0.033  15480  Z= 0.127
  Angle     :  0.480   5.790  20988  Z= 0.273
  Chirality :  0.041   0.135   2388
  Planarity :  0.003   0.031   2732
  Dihedral  :  8.138  80.464   5732
  Min Nonbonded Distance : 2.142

Molprobity Statistics.
  All-atom Clashscore : 4.76
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  1.86 %
    Favored  : 98.04 %
  Rotamer:
    Outliers :  0.43 %
    Allowed  :  1.58 %
    Favored  : 97.99 %
  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: -0.18 (0.19), residues: 1988
  helix:  1.10 (0.18), residues: 812
  sheet: -0.64 (0.25), residues: 396
  loop : -1.07 (0.22), residues: 780

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.002   0.000   TRP C 484 
 HIS   0.002   0.000   HIS B 115 
 PHE   0.014   0.001   PHE D 164 
 TYR   0.006   0.001   TYR A  76 
 ARG   0.002   0.000   ARG D  75 

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

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

  3976 Ramachandran restraints generated.
    1988 Oldfield, 0 Emsley, 1988 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3976 Ramachandran restraints generated.
    1988 Oldfield, 0 Emsley, 1988 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  261 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 254
  time to evaluate  : 1.759 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  501 MET cc_start: 0.0563 (mtm) cc_final: -0.0432 (mtp)
  outliers start: 7
  outliers final: 1
  residues processed: 261
  average time/residue: 1.2248
  time to fit residues: 354.3588
Evaluate side-chains
  144 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 143
  time to evaluate  : 1.733 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  172 ASN
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 196
   random chunks:
   chunk 165 optimal weight:    0.8980
   chunk 148 optimal weight:   10.0000
   chunk 82 optimal weight:    0.9990
   chunk 50 optimal weight:   10.0000
   chunk 100 optimal weight:    7.9990
   chunk 79 optimal weight:    8.9990
   chunk 153 optimal weight:    5.9990
   chunk 59 optimal weight:    5.9990
   chunk 93 optimal weight:    0.9990
   chunk 114 optimal weight:    2.9990
   chunk 177 optimal weight:    8.9990
   overall best weight:    2.3788

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

Flipped N/Q/H residues before XYZ refinement:
A 210 HIS
A 440 ASN
B  41 GLN
B 115 HIS
B 210 HIS
B 440 ASN
** B 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  41 GLN
C 115 HIS
** C 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 365 ASN
C 413 ASN
** C 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  41 GLN
D 115 HIS
D 409 ASN
D 440 ASN

Total number of N/Q/H flips: 14

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3473 r_free = 0.3473 target = 0.084152 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3199 r_free = 0.3199 target = 0.069777 restraints weight = 41381.051|
|-----------------------------------------------------------------------------|
r_work (start): 0.3178 rms_B_bonded: 4.08
r_work: 0.3034 rms_B_bonded: 4.63 restraints_weight: 0.5000
r_work (final): 0.3034
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8469
moved from start:          0.2152

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043  15480  Z= 0.267
  Angle     :  0.582   8.998  20988  Z= 0.293
  Chirality :  0.046   0.184   2388
  Planarity :  0.004   0.037   2732
  Dihedral  :  4.128  34.866   2102
  Min Nonbonded Distance : 2.534

Molprobity Statistics.
  All-atom Clashscore : 5.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.97 %
    Favored  : 97.03 %
  Rotamer:
    Outliers :  2.01 %
    Allowed  :  9.43 %
    Favored  : 88.56 %
  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:  0.78 (0.19), residues: 1988
  helix:  1.63 (0.18), residues: 836
  sheet: -0.19 (0.27), residues: 368
  loop : -0.25 (0.23), residues: 784

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP D 162 
 HIS   0.003   0.001   HIS C 307 
 PHE   0.020   0.002   PHE D 164 
 TYR   0.015   0.002   TYR A 466 
 ARG   0.008   0.001   ARG B 312 

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

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

  3976 Ramachandran restraints generated.
    1988 Oldfield, 0 Emsley, 1988 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3976 Ramachandran restraints generated.
    1988 Oldfield, 0 Emsley, 1988 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  166 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 133
  time to evaluate  : 1.637 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   63 ASP cc_start: 0.8672 (p0) cc_final: 0.8442 (p0)
REVERT: A  486 GLU cc_start: 0.8029 (tm-30) cc_final: 0.7613 (tm-30)
REVERT: B   63 ASP cc_start: 0.8663 (p0) cc_final: 0.8374 (p0)
REVERT: B   76 TYR cc_start: 0.9363 (t80) cc_final: 0.9138 (t80)
REVERT: B  176 MET cc_start: 0.9319 (tpp) cc_final: 0.8323 (tmm)
REVERT: B  463 THR cc_start: 0.9414 (OUTLIER) cc_final: 0.9122 (p)
REVERT: B  486 GLU cc_start: 0.8023 (tm-30) cc_final: 0.7552 (tm-30)
REVERT: B  501 MET cc_start: -0.1112 (mtm) cc_final: -0.1892 (mtp)
REVERT: C   63 ASP cc_start: 0.8590 (p0) cc_final: 0.8317 (p0)
REVERT: C   76 TYR cc_start: 0.9326 (t80) cc_final: 0.9119 (t80)
REVERT: C  110 LEU cc_start: 0.9235 (tt) cc_final: 0.8987 (tm)
REVERT: C  486 GLU cc_start: 0.8008 (tm-30) cc_final: 0.7550 (tm-30)
REVERT: D   63 ASP cc_start: 0.8720 (p0) cc_final: 0.8462 (p0)
REVERT: D  486 GLU cc_start: 0.7995 (tm-30) cc_final: 0.7570 (tm-30)
  outliers start: 33
  outliers final: 7
  residues processed: 159
  average time/residue: 1.2848
  time to fit residues: 226.8228
Evaluate side-chains
  127 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 119
  time to evaluate  : 1.818 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  432 VAL
Chi-restraints excluded: chain A residue  458 SER
Chi-restraints excluded: chain B residue  432 VAL
Chi-restraints excluded: chain B residue  463 THR
Chi-restraints excluded: chain C residue  432 VAL
Chi-restraints excluded: chain C residue  458 SER
Chi-restraints excluded: chain D residue  432 VAL
Chi-restraints excluded: chain D residue  458 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 196
   random chunks:
   chunk 125 optimal weight:    5.9990
   chunk 50 optimal weight:    0.0670
   chunk 81 optimal weight:    7.9990
   chunk 169 optimal weight:    0.9990
   chunk 55 optimal weight:    0.7980
   chunk 195 optimal weight:   10.0000
   chunk 15 optimal weight:    0.9990
   chunk 56 optimal weight:    0.9990
   chunk 162 optimal weight:    0.8980
   chunk 175 optimal weight:    9.9990
   chunk 20 optimal weight:    8.9990
   overall best weight:    0.7522

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

Flipped N/Q/H residues before XYZ refinement:
A 231 ASN
A 272 GLN
B  77 GLN
B 172 ASN
B 231 ASN
** B 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 483 GLN
** C 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 272 GLN
C 409 ASN
** C 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  77 GLN
D 464 ASN

Total number of N/Q/H flips: 10

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3507 r_free = 0.3507 target = 0.085775 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3233 r_free = 0.3233 target = 0.071198 restraints weight = 40792.016|
|-----------------------------------------------------------------------------|
r_work (start): 0.3220 rms_B_bonded: 4.18
r_work: 0.3078 rms_B_bonded: 4.70 restraints_weight: 0.5000
r_work (final): 0.3078
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8410
moved from start:          0.2433

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025  15480  Z= 0.153
  Angle     :  0.522   7.370  20988  Z= 0.260
  Chirality :  0.044   0.166   2388
  Planarity :  0.004   0.035   2732
  Dihedral  :  3.991  17.804   2100
  Min Nonbonded Distance : 2.571

Molprobity Statistics.
  All-atom Clashscore : 5.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.11 %
    Favored  : 97.89 %
  Rotamer:
    Outliers :  1.76 %
    Allowed  : 10.10 %
    Favored  : 88.14 %
  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:  1.13 (0.19), residues: 1988
  helix:  1.89 (0.18), residues: 836
  sheet:  0.11 (0.27), residues: 356
  loop : -0.09 (0.23), residues: 796

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP D 162 
 HIS   0.003   0.001   HIS A 307 
 PHE   0.019   0.001   PHE C 164 
 TYR   0.014   0.001   TYR A 138 
 ARG   0.004   0.000   ARG B  75 

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

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

  3976 Ramachandran restraints generated.
    1988 Oldfield, 0 Emsley, 1988 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3976 Ramachandran restraints generated.
    1988 Oldfield, 0 Emsley, 1988 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  177 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 148
  time to evaluate  : 1.650 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   63 ASP cc_start: 0.8647 (p0) cc_final: 0.8371 (p0)
REVERT: A   76 TYR cc_start: 0.9354 (t80) cc_final: 0.9100 (t80)
REVERT: A  128 MET cc_start: 0.8485 (tpt) cc_final: 0.7943 (tpp)
REVERT: A  486 GLU cc_start: 0.7980 (tm-30) cc_final: 0.7577 (tm-30)
REVERT: B   63 ASP cc_start: 0.8580 (p0) cc_final: 0.8314 (p0)
REVERT: B   81 LYS cc_start: 0.8893 (OUTLIER) cc_final: 0.8445 (mttm)
REVERT: B  463 THR cc_start: 0.9401 (OUTLIER) cc_final: 0.9123 (p)
REVERT: B  486 GLU cc_start: 0.8049 (tm-30) cc_final: 0.7566 (tm-30)
REVERT: B  501 MET cc_start: -0.0434 (mtm) cc_final: -0.1118 (mtp)
REVERT: C   63 ASP cc_start: 0.8550 (p0) cc_final: 0.8278 (p0)
REVERT: C   76 TYR cc_start: 0.9279 (t80) cc_final: 0.8964 (t80)
REVERT: C  252 MET cc_start: 0.8809 (OUTLIER) cc_final: 0.8495 (mpp)
REVERT: C  433 ASP cc_start: 0.8667 (t0) cc_final: 0.8177 (t0)
REVERT: C  486 GLU cc_start: 0.7971 (tm-30) cc_final: 0.7550 (tm-30)
REVERT: D   63 ASP cc_start: 0.8618 (p0) cc_final: 0.8381 (p0)
REVERT: D   76 TYR cc_start: 0.9328 (t80) cc_final: 0.9077 (t80)
REVERT: D  256 ASN cc_start: 0.8642 (m-40) cc_final: 0.8341 (m-40)
REVERT: D  486 GLU cc_start: 0.7995 (tm-30) cc_final: 0.7593 (tm-30)
  outliers start: 29
  outliers final: 4
  residues processed: 169
  average time/residue: 1.2100
  time to fit residues: 228.0421
Evaluate side-chains
  131 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 124
  time to evaluate  : 1.894 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  458 SER
Chi-restraints excluded: chain B residue   81 LYS
Chi-restraints excluded: chain B residue  463 THR
Chi-restraints excluded: chain C residue  252 MET
Chi-restraints excluded: chain C residue  458 SER
Chi-restraints excluded: chain C residue  482 SER
Chi-restraints excluded: chain D residue  458 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 196
   random chunks:
   chunk 88 optimal weight:    3.9990
   chunk 182 optimal weight:    9.9990
   chunk 139 optimal weight:   10.0000
   chunk 34 optimal weight:   10.0000
   chunk 77 optimal weight:    0.6980
   chunk 84 optimal weight:    0.0170
   chunk 17 optimal weight:    8.9990
   chunk 102 optimal weight:    9.9990
   chunk 124 optimal weight:    1.9990
   chunk 195 optimal weight:    6.9990
   chunk 122 optimal weight:    7.9990
   overall best weight:    2.7424

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

Flipped N/Q/H residues before XYZ refinement:
A  41 GLN
A 483 GLN
B  77 GLN
** B 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 440 ASN
C 469 GLN
D 483 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3438 r_free = 0.3438 target = 0.082583 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3149 r_free = 0.3149 target = 0.067877 restraints weight = 41671.423|
|-----------------------------------------------------------------------------|
r_work (start): 0.3129 rms_B_bonded: 4.13
r_work: 0.2990 rms_B_bonded: 4.61 restraints_weight: 0.5000
r_work (final): 0.2990
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8485
moved from start:          0.2851

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030  15480  Z= 0.276
  Angle     :  0.579  10.000  20988  Z= 0.285
  Chirality :  0.045   0.191   2388
  Planarity :  0.004   0.038   2732
  Dihedral  :  4.193  22.743   2100
  Min Nonbonded Distance : 2.578

Molprobity Statistics.
  All-atom Clashscore : 6.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.97 %
    Favored  : 97.03 %
  Rotamer:
    Outliers :  2.37 %
    Allowed  : 10.95 %
    Favored  : 86.68 %
  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:  1.27 (0.19), residues: 1988
  helix:  1.93 (0.18), residues: 840
  sheet:  0.08 (0.27), residues: 368
  loop :  0.13 (0.23), residues: 780

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP C 300 
 HIS   0.003   0.001   HIS B 257 
 PHE   0.019   0.001   PHE D 164 
 TYR   0.018   0.002   TYR C 466 
 ARG   0.003   0.000   ARG C  75 

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

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

  3976 Ramachandran restraints generated.
    1988 Oldfield, 0 Emsley, 1988 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3976 Ramachandran restraints generated.
    1988 Oldfield, 0 Emsley, 1988 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  167 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 128
  time to evaluate  : 1.696 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   63 ASP cc_start: 0.8652 (p0) cc_final: 0.8398 (p0)
REVERT: A   76 TYR cc_start: 0.9390 (t80) cc_final: 0.9131 (t80)
REVERT: A   81 LYS cc_start: 0.9005 (OUTLIER) cc_final: 0.8586 (mttm)
REVERT: A  463 THR cc_start: 0.9435 (OUTLIER) cc_final: 0.9193 (p)
REVERT: A  486 GLU cc_start: 0.8017 (tm-30) cc_final: 0.7542 (tm-30)
REVERT: B   63 ASP cc_start: 0.8591 (p0) cc_final: 0.8328 (p0)
REVERT: B   76 TYR cc_start: 0.9376 (t80) cc_final: 0.9127 (t80)
REVERT: B   77 GLN cc_start: 0.9427 (OUTLIER) cc_final: 0.9108 (pp30)
REVERT: B   81 LYS cc_start: 0.8968 (OUTLIER) cc_final: 0.8608 (mttm)
REVERT: B  463 THR cc_start: 0.9458 (OUTLIER) cc_final: 0.9086 (p)
REVERT: B  486 GLU cc_start: 0.8136 (tm-30) cc_final: 0.7642 (tm-30)
REVERT: B  501 MET cc_start: -0.0877 (mtm) cc_final: -0.1627 (mtp)
REVERT: C   63 ASP cc_start: 0.8608 (p0) cc_final: 0.8352 (p0)
REVERT: C   76 TYR cc_start: 0.9342 (t80) cc_final: 0.9120 (t80)
REVERT: C   81 LYS cc_start: 0.9006 (OUTLIER) cc_final: 0.8670 (mttm)
REVERT: C  486 GLU cc_start: 0.8119 (tm-30) cc_final: 0.7660 (tm-30)
REVERT: D   63 ASP cc_start: 0.8578 (p0) cc_final: 0.8339 (p0)
REVERT: D   76 TYR cc_start: 0.9429 (t80) cc_final: 0.9219 (t80)
REVERT: D  411 TYR cc_start: 0.8717 (m-80) cc_final: 0.8240 (m-80)
REVERT: D  433 ASP cc_start: 0.8700 (t0) cc_final: 0.8019 (t70)
REVERT: D  486 GLU cc_start: 0.8068 (tm-30) cc_final: 0.7601 (tm-30)
  outliers start: 39
  outliers final: 16
  residues processed: 157
  average time/residue: 1.2503
  time to fit residues: 220.1790
Evaluate side-chains
  140 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 118
  time to evaluate  : 1.819 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   32 THR
Chi-restraints excluded: chain A residue   81 LYS
Chi-restraints excluded: chain A residue   91 ILE
Chi-restraints excluded: chain A residue  458 SER
Chi-restraints excluded: chain A residue  463 THR
Chi-restraints excluded: chain B residue   32 THR
Chi-restraints excluded: chain B residue   77 GLN
Chi-restraints excluded: chain B residue   81 LYS
Chi-restraints excluded: chain B residue  130 SER
Chi-restraints excluded: chain B residue  187 MET
Chi-restraints excluded: chain B residue  432 VAL
Chi-restraints excluded: chain B residue  463 THR
Chi-restraints excluded: chain C residue   32 THR
Chi-restraints excluded: chain C residue   81 LYS
Chi-restraints excluded: chain C residue  286 MET
Chi-restraints excluded: chain C residue  397 GLU
Chi-restraints excluded: chain C residue  458 SER
Chi-restraints excluded: chain C residue  482 SER
Chi-restraints excluded: chain D residue   32 THR
Chi-restraints excluded: chain D residue  455 SER
Chi-restraints excluded: chain D residue  458 SER
Chi-restraints excluded: chain D residue  465 PHE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 196
   random chunks:
   chunk 47 optimal weight:    8.9990
   chunk 141 optimal weight:    9.9990
   chunk 143 optimal weight:    1.9990
   chunk 38 optimal weight:    7.9990
   chunk 74 optimal weight:    9.9990
   chunk 155 optimal weight:   10.0000
   chunk 160 optimal weight:    2.9990
   chunk 15 optimal weight:    2.9990
   chunk 10 optimal weight:    6.9990
   chunk 144 optimal weight:    2.9990
   chunk 161 optimal weight:   20.0000
   overall best weight:    3.5990

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

Flipped N/Q/H residues before XYZ refinement:
B  77 GLN
B 172 ASN
C  77 GLN
** C 172 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 = 0.3396 r_free = 0.3396 target = 0.082324 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3097 r_free = 0.3097 target = 0.067345 restraints weight = 42385.881|
|-----------------------------------------------------------------------------|
r_work (start): 0.3073 rms_B_bonded: 4.15
r_work: 0.2938 rms_B_bonded: 4.64 restraints_weight: 0.5000
r_work (final): 0.2938
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8484
moved from start:          0.3145

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.035  15480  Z= 0.341
  Angle     :  0.607   8.464  20988  Z= 0.302
  Chirality :  0.046   0.202   2388
  Planarity :  0.004   0.038   2732
  Dihedral  :  4.377  25.464   2100
  Min Nonbonded Distance : 2.567

Molprobity Statistics.
  All-atom Clashscore : 6.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.87 %
    Favored  : 97.13 %
  Rotamer:
    Outliers :  2.68 %
    Allowed  : 11.37 %
    Favored  : 85.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.21 (0.19), residues: 1988
  helix:  1.86 (0.18), residues: 840
  sheet:  0.16 (0.27), residues: 356
  loop :  0.07 (0.23), residues: 792

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP B 484 
 HIS   0.003   0.001   HIS A 219 
 PHE   0.019   0.002   PHE D 164 
 TYR   0.021   0.002   TYR C 466 
 ARG   0.003   0.000   ARG C  75 

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

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

  3976 Ramachandran restraints generated.
    1988 Oldfield, 0 Emsley, 1988 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3976 Ramachandran restraints generated.
    1988 Oldfield, 0 Emsley, 1988 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  164 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 120
  time to evaluate  : 1.765 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   63 ASP cc_start: 0.8680 (p0) cc_final: 0.8439 (p0)
REVERT: A   76 TYR cc_start: 0.9381 (t80) cc_final: 0.9143 (t80)
REVERT: A   81 LYS cc_start: 0.8928 (OUTLIER) cc_final: 0.8569 (mttm)
REVERT: A  463 THR cc_start: 0.9431 (OUTLIER) cc_final: 0.9102 (p)
REVERT: A  486 GLU cc_start: 0.8112 (tm-30) cc_final: 0.7659 (tm-30)
REVERT: B   63 ASP cc_start: 0.8669 (p0) cc_final: 0.8413 (p0)
REVERT: B   76 TYR cc_start: 0.9323 (t80) cc_final: 0.9023 (t80)
REVERT: B   81 LYS cc_start: 0.8940 (OUTLIER) cc_final: 0.8605 (mttm)
REVERT: B  486 GLU cc_start: 0.8194 (tm-30) cc_final: 0.7694 (tm-30)
REVERT: B  501 MET cc_start: -0.0438 (mtm) cc_final: -0.1282 (mtp)
REVERT: C   63 ASP cc_start: 0.8671 (p0) cc_final: 0.8425 (p0)
REVERT: C   81 LYS cc_start: 0.8947 (OUTLIER) cc_final: 0.8490 (mttm)
REVERT: C  486 GLU cc_start: 0.8180 (tm-30) cc_final: 0.7726 (tm-30)
REVERT: D   63 ASP cc_start: 0.8624 (p0) cc_final: 0.8397 (p0)
REVERT: D  411 TYR cc_start: 0.8789 (m-80) cc_final: 0.8379 (m-80)
REVERT: D  486 GLU cc_start: 0.8134 (tm-30) cc_final: 0.7687 (tm-30)
REVERT: D  498 MET cc_start: 0.3117 (mmp) cc_final: 0.2752 (tpp)
  outliers start: 44
  outliers final: 17
  residues processed: 152
  average time/residue: 1.2607
  time to fit residues: 212.9933
Evaluate side-chains
  135 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 114
  time to evaluate  : 1.855 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   32 THR
Chi-restraints excluded: chain A residue   81 LYS
Chi-restraints excluded: chain A residue   91 ILE
Chi-restraints excluded: chain A residue  130 SER
Chi-restraints excluded: chain A residue  432 VAL
Chi-restraints excluded: chain A residue  458 SER
Chi-restraints excluded: chain A residue  463 THR
Chi-restraints excluded: chain B residue   32 THR
Chi-restraints excluded: chain B residue   81 LYS
Chi-restraints excluded: chain B residue  187 MET
Chi-restraints excluded: chain B residue  432 VAL
Chi-restraints excluded: chain B residue  463 THR
Chi-restraints excluded: chain C residue   32 THR
Chi-restraints excluded: chain C residue   81 LYS
Chi-restraints excluded: chain C residue  397 GLU
Chi-restraints excluded: chain C residue  432 VAL
Chi-restraints excluded: chain C residue  458 SER
Chi-restraints excluded: chain C residue  482 SER
Chi-restraints excluded: chain D residue   32 THR
Chi-restraints excluded: chain D residue  432 VAL
Chi-restraints excluded: chain D residue  458 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 196
   random chunks:
   chunk 28 optimal weight:    4.9990
   chunk 124 optimal weight:    6.9990
   chunk 118 optimal weight:    1.9990
   chunk 179 optimal weight:    7.9990
   chunk 167 optimal weight:    8.9990
   chunk 40 optimal weight:    0.7980
   chunk 106 optimal weight:    4.9990
   chunk 70 optimal weight:    8.9990
   chunk 93 optimal weight:    1.9990
   chunk 105 optimal weight:    0.9990
   chunk 111 optimal weight:    6.9990
   overall best weight:    2.1588

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

Flipped N/Q/H residues before XYZ refinement:
B  77 GLN
** B 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 272 GLN
C  77 GLN
** C 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 231 ASN
C 436 GLN
C 483 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3417 r_free = 0.3417 target = 0.082526 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3122 r_free = 0.3122 target = 0.067599 restraints weight = 41820.076|
|-----------------------------------------------------------------------------|
r_work (start): 0.3103 rms_B_bonded: 4.17
r_work: 0.2965 rms_B_bonded: 4.73 restraints_weight: 0.5000
r_work (final): 0.2965
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8467
moved from start:          0.3196

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027  15480  Z= 0.229
  Angle     :  0.575  10.214  20988  Z= 0.280
  Chirality :  0.045   0.186   2388
  Planarity :  0.004   0.035   2732
  Dihedral  :  4.282  24.073   2100
  Min Nonbonded Distance : 2.585

Molprobity Statistics.
  All-atom Clashscore : 6.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.07 %
    Favored  : 96.93 %
  Rotamer:
    Outliers :  2.25 %
    Allowed  : 11.68 %
    Favored  : 86.07 %
  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:  1.28 (0.19), residues: 1988
  helix:  1.92 (0.18), residues: 840
  sheet:  0.16 (0.28), residues: 356
  loop :  0.11 (0.23), residues: 792

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP C 484 
 HIS   0.003   0.001   HIS A 219 
 PHE   0.019   0.001   PHE A 164 
 TYR   0.016   0.001   TYR C 466 
 ARG   0.003   0.000   ARG B  75 

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

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

  3976 Ramachandran restraints generated.
    1988 Oldfield, 0 Emsley, 1988 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3976 Ramachandran restraints generated.
    1988 Oldfield, 0 Emsley, 1988 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  160 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 123
  time to evaluate  : 1.690 
Fit side-chains
   revert: symmetry clash
REVERT: A   63 ASP cc_start: 0.8655 (p0) cc_final: 0.8416 (p0)
REVERT: A   76 TYR cc_start: 0.9365 (t80) cc_final: 0.9137 (t80)
REVERT: A   81 LYS cc_start: 0.8891 (OUTLIER) cc_final: 0.8557 (mttm)
REVERT: A  110 LEU cc_start: 0.9244 (tt) cc_final: 0.9005 (tm)
REVERT: A  188 LEU cc_start: 0.8972 (OUTLIER) cc_final: 0.8718 (mm)
REVERT: A  463 THR cc_start: 0.9415 (OUTLIER) cc_final: 0.9140 (p)
REVERT: A  486 GLU cc_start: 0.8092 (tm-30) cc_final: 0.7454 (tm-30)
REVERT: B   63 ASP cc_start: 0.8636 (p0) cc_final: 0.8368 (p0)
REVERT: B  486 GLU cc_start: 0.8137 (tm-30) cc_final: 0.7637 (tm-30)
REVERT: B  501 MET cc_start: -0.0575 (mtm) cc_final: -0.1320 (mtp)
REVERT: C   63 ASP cc_start: 0.8666 (p0) cc_final: 0.8405 (p0)
REVERT: C   76 TYR cc_start: 0.9294 (t80) cc_final: 0.9092 (t80)
REVERT: C  486 GLU cc_start: 0.8133 (tm-30) cc_final: 0.7550 (tm-30)
REVERT: D   63 ASP cc_start: 0.8603 (p0) cc_final: 0.8376 (p0)
REVERT: D  411 TYR cc_start: 0.8756 (m-80) cc_final: 0.8241 (m-80)
REVERT: D  486 GLU cc_start: 0.8052 (tm-30) cc_final: 0.7577 (tm-30)
  outliers start: 37
  outliers final: 19
  residues processed: 155
  average time/residue: 1.2298
  time to fit residues: 212.8922
Evaluate side-chains
  138 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 116
  time to evaluate  : 1.714 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   32 THR
Chi-restraints excluded: chain A residue   81 LYS
Chi-restraints excluded: chain A residue   91 ILE
Chi-restraints excluded: chain A residue  130 SER
Chi-restraints excluded: chain A residue  188 LEU
Chi-restraints excluded: chain A residue  458 SER
Chi-restraints excluded: chain A residue  463 THR
Chi-restraints excluded: chain B residue   32 THR
Chi-restraints excluded: chain B residue  123 MET
Chi-restraints excluded: chain B residue  130 SER
Chi-restraints excluded: chain B residue  458 SER
Chi-restraints excluded: chain B residue  463 THR
Chi-restraints excluded: chain C residue   32 THR
Chi-restraints excluded: chain C residue  130 SER
Chi-restraints excluded: chain C residue  166 MET
Chi-restraints excluded: chain C residue  397 GLU
Chi-restraints excluded: chain C residue  432 VAL
Chi-restraints excluded: chain C residue  458 SER
Chi-restraints excluded: chain C residue  482 SER
Chi-restraints excluded: chain D residue   32 THR
Chi-restraints excluded: chain D residue  432 VAL
Chi-restraints excluded: chain D residue  458 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 196
   random chunks:
   chunk 70 optimal weight:    5.9990
   chunk 195 optimal weight:    6.9990
   chunk 185 optimal weight:    6.9990
   chunk 15 optimal weight:    1.9990
   chunk 3 optimal weight:    7.9990
   chunk 97 optimal weight:    8.9990
   chunk 33 optimal weight:    5.9990
   chunk 121 optimal weight:    9.9990
   chunk 72 optimal weight:    6.9990
   chunk 22 optimal weight:    0.9980
   chunk 151 optimal weight:    5.9990
   overall best weight:    4.1988

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

Flipped N/Q/H residues before XYZ refinement:
** B 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  77 GLN
** C 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 207 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3373 r_free = 0.3373 target = 0.081107 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3078 r_free = 0.3078 target = 0.066398 restraints weight = 42596.059|
|-----------------------------------------------------------------------------|
r_work (start): 0.3049 rms_B_bonded: 4.03
r_work: 0.2911 rms_B_bonded: 4.60 restraints_weight: 0.5000
r_work (final): 0.2911
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8511
moved from start:          0.3404

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.035  15480  Z= 0.393
  Angle     :  0.649  12.239  20988  Z= 0.319
  Chirality :  0.047   0.207   2388
  Planarity :  0.004   0.037   2732
  Dihedral  :  4.517  26.829   2100
  Min Nonbonded Distance : 2.578

Molprobity Statistics.
  All-atom Clashscore : 7.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.07 %
    Favored  : 96.93 %
  Rotamer:
    Outliers :  2.62 %
    Allowed  : 11.92 %
    Favored  : 85.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.19 (0.20), residues: 1988
  helix:  1.83 (0.18), residues: 840
  sheet:  0.15 (0.28), residues: 356
  loop :  0.06 (0.24), residues: 792

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP D  24 
 HIS   0.005   0.001   HIS D 257 
 PHE   0.022   0.002   PHE A 155 
 TYR   0.022   0.002   TYR A 466 
 ARG   0.004   0.000   ARG C  75 

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

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

  3976 Ramachandran restraints generated.
    1988 Oldfield, 0 Emsley, 1988 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3976 Ramachandran restraints generated.
    1988 Oldfield, 0 Emsley, 1988 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  161 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 118
  time to evaluate  : 1.765 
Fit side-chains
REVERT: A   63 ASP cc_start: 0.8691 (p0) cc_final: 0.8455 (p0)
REVERT: A   81 LYS cc_start: 0.8945 (OUTLIER) cc_final: 0.8572 (mttm)
REVERT: A  344 LYS cc_start: 0.9247 (mtpt) cc_final: 0.9018 (mtpt)
REVERT: A  463 THR cc_start: 0.9409 (OUTLIER) cc_final: 0.9023 (p)
REVERT: A  486 GLU cc_start: 0.8076 (tm-30) cc_final: 0.7719 (tm-30)
REVERT: A  488 ASP cc_start: 0.8579 (m-30) cc_final: 0.8371 (m-30)
REVERT: A  498 MET cc_start: 0.2032 (OUTLIER) cc_final: 0.1694 (mmm)
REVERT: B   63 ASP cc_start: 0.8651 (p0) cc_final: 0.8399 (p0)
REVERT: B   81 LYS cc_start: 0.8903 (OUTLIER) cc_final: 0.8507 (mttm)
REVERT: B  411 TYR cc_start: 0.8696 (m-80) cc_final: 0.8451 (m-80)
REVERT: B  486 GLU cc_start: 0.8202 (tm-30) cc_final: 0.7742 (tm-30)
REVERT: B  501 MET cc_start: -0.0914 (mtm) cc_final: -0.1942 (mtp)
REVERT: C   63 ASP cc_start: 0.8702 (p0) cc_final: 0.8462 (p0)
REVERT: C   76 TYR cc_start: 0.9354 (t80) cc_final: 0.9052 (t80)
REVERT: C  486 GLU cc_start: 0.8095 (tm-30) cc_final: 0.7749 (tm-30)
REVERT: C  488 ASP cc_start: 0.8580 (m-30) cc_final: 0.8371 (m-30)
REVERT: D   63 ASP cc_start: 0.8646 (p0) cc_final: 0.8405 (p0)
REVERT: D  433 ASP cc_start: 0.8807 (t0) cc_final: 0.8147 (t0)
REVERT: D  486 GLU cc_start: 0.8085 (tm-30) cc_final: 0.7487 (tm-30)
REVERT: D  498 MET cc_start: 0.2774 (tpp) cc_final: 0.2506 (tpp)
  outliers start: 43
  outliers final: 21
  residues processed: 154
  average time/residue: 1.1913
  time to fit residues: 206.1690
Evaluate side-chains
  137 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 112
  time to evaluate  : 1.609 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   32 THR
Chi-restraints excluded: chain A residue   81 LYS
Chi-restraints excluded: chain A residue  130 SER
Chi-restraints excluded: chain A residue  432 VAL
Chi-restraints excluded: chain A residue  458 SER
Chi-restraints excluded: chain A residue  463 THR
Chi-restraints excluded: chain A residue  498 MET
Chi-restraints excluded: chain B residue   32 THR
Chi-restraints excluded: chain B residue   81 LYS
Chi-restraints excluded: chain B residue  130 SER
Chi-restraints excluded: chain B residue  432 VAL
Chi-restraints excluded: chain B residue  458 SER
Chi-restraints excluded: chain B residue  463 THR
Chi-restraints excluded: chain C residue   32 THR
Chi-restraints excluded: chain C residue  130 SER
Chi-restraints excluded: chain C residue  187 MET
Chi-restraints excluded: chain C residue  188 LEU
Chi-restraints excluded: chain C residue  210 HIS
Chi-restraints excluded: chain C residue  397 GLU
Chi-restraints excluded: chain C residue  432 VAL
Chi-restraints excluded: chain C residue  458 SER
Chi-restraints excluded: chain C residue  482 SER
Chi-restraints excluded: chain D residue   32 THR
Chi-restraints excluded: chain D residue  432 VAL
Chi-restraints excluded: chain D residue  458 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 196
   random chunks:
   chunk 168 optimal weight:    2.9990
   chunk 67 optimal weight:    1.9990
   chunk 20 optimal weight:   10.0000
   chunk 167 optimal weight:    5.9990
   chunk 178 optimal weight:    0.6980
   chunk 63 optimal weight:    0.9990
   chunk 24 optimal weight:    3.9990
   chunk 2 optimal weight:    2.9990
   chunk 150 optimal weight:    4.9990
   chunk 98 optimal weight:   10.0000
   chunk 138 optimal weight:    6.9990
   overall best weight:    1.9388

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

Flipped N/Q/H residues before XYZ refinement:
A  77 GLN
B  77 GLN
** B 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 472 GLN
C  77 GLN
** C 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 256 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3412 r_free = 0.3412 target = 0.082268 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3115 r_free = 0.3115 target = 0.067341 restraints weight = 41935.277|
|-----------------------------------------------------------------------------|
r_work (start): 0.3094 rms_B_bonded: 4.12
r_work: 0.2960 rms_B_bonded: 4.67 restraints_weight: 0.5000
r_work (final): 0.2960
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8474
moved from start:          0.3393

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028  15480  Z= 0.218
  Angle     :  0.614  14.529  20988  Z= 0.294
  Chirality :  0.045   0.189   2388
  Planarity :  0.004   0.034   2732
  Dihedral  :  4.375  24.437   2100
  Min Nonbonded Distance : 2.586

Molprobity Statistics.
  All-atom Clashscore : 7.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.02 %
    Favored  : 96.98 %
  Rotamer:
    Outliers :  2.19 %
    Allowed  : 11.92 %
    Favored  : 85.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.25 (0.19), residues: 1988
  helix:  1.93 (0.18), residues: 840
  sheet:  0.11 (0.28), residues: 356
  loop :  0.08 (0.23), residues: 792

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP A 484 
 HIS   0.003   0.001   HIS A 115 
 PHE   0.025   0.001   PHE A 155 
 TYR   0.018   0.002   TYR A  76 
 ARG   0.002   0.000   ARG B  75 

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

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

  3976 Ramachandran restraints generated.
    1988 Oldfield, 0 Emsley, 1988 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3976 Ramachandran restraints generated.
    1988 Oldfield, 0 Emsley, 1988 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  156 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 120
  time to evaluate  : 1.705 
Fit side-chains
REVERT: A   63 ASP cc_start: 0.8654 (p0) cc_final: 0.8396 (p0)
REVERT: A   76 TYR cc_start: 0.9331 (t80) cc_final: 0.9106 (t80)
REVERT: A  110 LEU cc_start: 0.9252 (tt) cc_final: 0.8999 (tm)
REVERT: A  188 LEU cc_start: 0.9050 (OUTLIER) cc_final: 0.8805 (mm)
REVERT: A  261 MET cc_start: 0.8869 (mmm) cc_final: 0.8646 (mmm)
REVERT: A  463 THR cc_start: 0.9392 (OUTLIER) cc_final: 0.9085 (p)
REVERT: A  486 GLU cc_start: 0.8062 (tm-30) cc_final: 0.7722 (tm-30)
REVERT: A  488 ASP cc_start: 0.8540 (m-30) cc_final: 0.8328 (m-30)
REVERT: B   63 ASP cc_start: 0.8648 (p0) cc_final: 0.8396 (p0)
REVERT: B  486 GLU cc_start: 0.8140 (tm-30) cc_final: 0.7698 (tm-30)
REVERT: B  501 MET cc_start: -0.0620 (mtm) cc_final: -0.1708 (mtp)
REVERT: C   63 ASP cc_start: 0.8660 (p0) cc_final: 0.8408 (p0)
REVERT: C   76 TYR cc_start: 0.9285 (t80) cc_final: 0.9070 (t80)
REVERT: C  252 MET cc_start: 0.9047 (mtp) cc_final: 0.8674 (mpp)
REVERT: C  261 MET cc_start: 0.8895 (mmm) cc_final: 0.8650 (mmm)
REVERT: C  486 GLU cc_start: 0.8062 (tm-30) cc_final: 0.7705 (tm-30)
REVERT: C  488 ASP cc_start: 0.8525 (m-30) cc_final: 0.8303 (m-30)
REVERT: C  498 MET cc_start: 0.2867 (mmm) cc_final: 0.2240 (mmm)
REVERT: D   63 ASP cc_start: 0.8624 (p0) cc_final: 0.8383 (p0)
REVERT: D  433 ASP cc_start: 0.8822 (t0) cc_final: 0.8191 (t0)
REVERT: D  486 GLU cc_start: 0.7979 (tm-30) cc_final: 0.7650 (tm-30)
REVERT: D  498 MET cc_start: 0.2615 (tpp) cc_final: 0.2250 (mmp)
  outliers start: 36
  outliers final: 17
  residues processed: 148
  average time/residue: 1.2181
  time to fit residues: 201.6258
Evaluate side-chains
  134 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 115
  time to evaluate  : 1.690 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   32 THR
Chi-restraints excluded: chain A residue  188 LEU
Chi-restraints excluded: chain A residue  432 VAL
Chi-restraints excluded: chain A residue  458 SER
Chi-restraints excluded: chain A residue  463 THR
Chi-restraints excluded: chain B residue   32 THR
Chi-restraints excluded: chain B residue  130 SER
Chi-restraints excluded: chain B residue  458 SER
Chi-restraints excluded: chain B residue  463 THR
Chi-restraints excluded: chain C residue   32 THR
Chi-restraints excluded: chain C residue  123 MET
Chi-restraints excluded: chain C residue  130 SER
Chi-restraints excluded: chain C residue  188 LEU
Chi-restraints excluded: chain C residue  397 GLU
Chi-restraints excluded: chain C residue  458 SER
Chi-restraints excluded: chain C residue  482 SER
Chi-restraints excluded: chain D residue  432 VAL
Chi-restraints excluded: chain D residue  455 SER
Chi-restraints excluded: chain D residue  458 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 196
   random chunks:
   chunk 174 optimal weight:    5.9990
   chunk 183 optimal weight:    0.3980
   chunk 167 optimal weight:    1.9990
   chunk 12 optimal weight:    5.9990
   chunk 172 optimal weight:   10.0000
   chunk 30 optimal weight:    5.9990
   chunk 13 optimal weight:    2.9990
   chunk 175 optimal weight:    8.9990
   chunk 158 optimal weight:    3.9990
   chunk 108 optimal weight:    6.9990
   chunk 153 optimal weight:    9.9990
   overall best weight:    3.0788

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

Flipped N/Q/H residues before XYZ refinement:
A  77 GLN
** B  77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 256 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3394 r_free = 0.3394 target = 0.082059 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3095 r_free = 0.3095 target = 0.067134 restraints weight = 42058.050|
|-----------------------------------------------------------------------------|
r_work (start): 0.3071 rms_B_bonded: 4.07
r_work: 0.2933 rms_B_bonded: 4.66 restraints_weight: 0.5000
r_work (final): 0.2933
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8496
moved from start:          0.3482

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.033  15480  Z= 0.305
  Angle     :  0.634  13.714  20988  Z= 0.308
  Chirality :  0.046   0.196   2388
  Planarity :  0.004   0.035   2732
  Dihedral  :  4.465  25.157   2100
  Min Nonbonded Distance : 2.585

Molprobity Statistics.
  All-atom Clashscore : 7.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.07 %
    Favored  : 96.93 %
  Rotamer:
    Outliers :  1.89 %
    Allowed  : 11.98 %
    Favored  : 86.13 %
  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:  1.21 (0.19), residues: 1988
  helix:  1.86 (0.18), residues: 840
  sheet:  0.16 (0.28), residues: 356
  loop :  0.06 (0.23), residues: 792

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP D 484 
 HIS   0.003   0.001   HIS A 219 
 PHE   0.019   0.002   PHE B 164 
 TYR   0.019   0.002   TYR A 466 
 ARG   0.002   0.000   ARG B  75 

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

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

  3976 Ramachandran restraints generated.
    1988 Oldfield, 0 Emsley, 1988 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3976 Ramachandran restraints generated.
    1988 Oldfield, 0 Emsley, 1988 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  150 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 119
  time to evaluate  : 1.670 
Fit side-chains
REVERT: A   63 ASP cc_start: 0.8664 (p0) cc_final: 0.8424 (p0)
REVERT: A   76 TYR cc_start: 0.9364 (t80) cc_final: 0.9126 (t80)
REVERT: A  110 LEU cc_start: 0.9250 (tt) cc_final: 0.8993 (tm)
REVERT: A  463 THR cc_start: 0.9392 (OUTLIER) cc_final: 0.9022 (p)
REVERT: A  486 GLU cc_start: 0.8043 (tm-30) cc_final: 0.7696 (tm-30)
REVERT: A  488 ASP cc_start: 0.8604 (m-30) cc_final: 0.8394 (m-30)
REVERT: B   63 ASP cc_start: 0.8658 (p0) cc_final: 0.8413 (p0)
REVERT: B  486 GLU cc_start: 0.8180 (tm-30) cc_final: 0.7735 (tm-30)
REVERT: B  501 MET cc_start: -0.0747 (mtm) cc_final: -0.1762 (mtp)
REVERT: C   63 ASP cc_start: 0.8679 (p0) cc_final: 0.8433 (p0)
REVERT: C  252 MET cc_start: 0.9074 (mtp) cc_final: 0.8698 (mpp)
REVERT: C  486 GLU cc_start: 0.8100 (tm-30) cc_final: 0.7759 (tm-30)
REVERT: C  488 ASP cc_start: 0.8563 (m-30) cc_final: 0.8338 (m-30)
REVERT: C  498 MET cc_start: 0.2499 (mmm) cc_final: 0.1645 (mmm)
REVERT: D   63 ASP cc_start: 0.8640 (p0) cc_final: 0.8407 (p0)
REVERT: D  433 ASP cc_start: 0.8787 (t0) cc_final: 0.8124 (t0)
REVERT: D  486 GLU cc_start: 0.8061 (tm-30) cc_final: 0.7546 (tm-30)
  outliers start: 31
  outliers final: 21
  residues processed: 146
  average time/residue: 1.1291
  time to fit residues: 185.4485
Evaluate side-chains
  135 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 113
  time to evaluate  : 1.793 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   32 THR
Chi-restraints excluded: chain A residue  432 VAL
Chi-restraints excluded: chain A residue  458 SER
Chi-restraints excluded: chain A residue  463 THR
Chi-restraints excluded: chain B residue   32 THR
Chi-restraints excluded: chain B residue  130 SER
Chi-restraints excluded: chain B residue  432 VAL
Chi-restraints excluded: chain B residue  458 SER
Chi-restraints excluded: chain B residue  463 THR
Chi-restraints excluded: chain C residue   32 THR
Chi-restraints excluded: chain C residue  123 MET
Chi-restraints excluded: chain C residue  130 SER
Chi-restraints excluded: chain C residue  166 MET
Chi-restraints excluded: chain C residue  188 LEU
Chi-restraints excluded: chain C residue  397 GLU
Chi-restraints excluded: chain C residue  432 VAL
Chi-restraints excluded: chain C residue  458 SER
Chi-restraints excluded: chain C residue  482 SER
Chi-restraints excluded: chain D residue   32 THR
Chi-restraints excluded: chain D residue  166 MET
Chi-restraints excluded: chain D residue  432 VAL
Chi-restraints excluded: chain D residue  458 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 196
   random chunks:
   chunk 116 optimal weight:    4.9990
   chunk 158 optimal weight:    3.9990
   chunk 135 optimal weight:    0.8980
   chunk 73 optimal weight:    0.8980
   chunk 19 optimal weight:    2.9990
   chunk 186 optimal weight:    0.9980
   chunk 187 optimal weight:    0.5980
   chunk 38 optimal weight:    0.8980
   chunk 33 optimal weight:    1.9990
   chunk 176 optimal weight:    0.0020
   chunk 8 optimal weight:    1.9990
   overall best weight:    0.6588

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

Flipped N/Q/H residues before XYZ refinement:
A  77 GLN
** B  77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 256 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3464 r_free = 0.3464 target = 0.083170 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3186 r_free = 0.3186 target = 0.068665 restraints weight = 41427.285|
|-----------------------------------------------------------------------------|
r_work (start): 0.3165 rms_B_bonded: 4.18
r_work: 0.3017 rms_B_bonded: 4.77 restraints_weight: 0.5000
r_work (final): 0.3017
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8473
moved from start:          0.3471

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028  15480  Z= 0.152
  Angle     :  0.598  12.563  20988  Z= 0.287
  Chirality :  0.044   0.171   2388
  Planarity :  0.004   0.033   2732
  Dihedral  :  4.272  20.911   2100
  Min Nonbonded Distance : 2.594

Molprobity Statistics.
  All-atom Clashscore : 8.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.97 %
    Favored  : 97.03 %
  Rotamer:
    Outliers :  1.34 %
    Allowed  : 12.71 %
    Favored  : 85.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.29 (0.19), residues: 1988
  helix:  1.95 (0.18), residues: 840
  sheet:  0.14 (0.28), residues: 356
  loop :  0.11 (0.23), residues: 792

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP B  24 
 HIS   0.004   0.001   HIS A 115 
 PHE   0.029   0.001   PHE D 164 
 TYR   0.015   0.001   TYR D  76 
 ARG   0.002   0.000   ARG A 108 

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

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

  3976 Ramachandran restraints generated.
    1988 Oldfield, 0 Emsley, 1988 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3976 Ramachandran restraints generated.
    1988 Oldfield, 0 Emsley, 1988 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  150 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 128
  time to evaluate  : 1.792 
Fit side-chains
REVERT: A   63 ASP cc_start: 0.8616 (p0) cc_final: 0.8363 (p0)
REVERT: A   76 TYR cc_start: 0.9296 (t80) cc_final: 0.8990 (t80)
REVERT: A  106 VAL cc_start: 0.9519 (t) cc_final: 0.9279 (m)
REVERT: A  463 THR cc_start: 0.9378 (OUTLIER) cc_final: 0.9147 (p)
REVERT: A  486 GLU cc_start: 0.8010 (tm-30) cc_final: 0.7665 (tm-30)
REVERT: A  488 ASP cc_start: 0.8516 (m-30) cc_final: 0.8299 (m-30)
REVERT: B   63 ASP cc_start: 0.8607 (p0) cc_final: 0.8343 (p0)
REVERT: B  486 GLU cc_start: 0.8149 (tm-30) cc_final: 0.7715 (tm-30)
REVERT: B  501 MET cc_start: -0.0774 (mtm) cc_final: -0.1806 (mtp)
REVERT: C   63 ASP cc_start: 0.8646 (p0) cc_final: 0.8376 (p0)
REVERT: C  128 MET cc_start: 0.8374 (tpt) cc_final: 0.8052 (tpp)
REVERT: C  252 MET cc_start: 0.9008 (mtp) cc_final: 0.8756 (mpp)
REVERT: C  486 GLU cc_start: 0.8055 (tm-30) cc_final: 0.7708 (tm-30)
REVERT: C  488 ASP cc_start: 0.8473 (m-30) cc_final: 0.8257 (m-30)
REVERT: C  498 MET cc_start: 0.2365 (mmm) cc_final: 0.1870 (mmm)
REVERT: D   63 ASP cc_start: 0.8593 (p0) cc_final: 0.8342 (p0)
REVERT: D  433 ASP cc_start: 0.8799 (t0) cc_final: 0.8214 (t70)
REVERT: D  486 GLU cc_start: 0.7981 (tm-30) cc_final: 0.7646 (tm-30)
REVERT: D  488 ASP cc_start: 0.8467 (m-30) cc_final: 0.8262 (m-30)
  outliers start: 22
  outliers final: 14
  residues processed: 145
  average time/residue: 1.1930
  time to fit residues: 194.2861
Evaluate side-chains
  137 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 122
  time to evaluate  : 1.642 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   32 THR
Chi-restraints excluded: chain A residue  123 MET
Chi-restraints excluded: chain A residue  458 SER
Chi-restraints excluded: chain A residue  463 THR
Chi-restraints excluded: chain B residue   32 THR
Chi-restraints excluded: chain B residue  130 SER
Chi-restraints excluded: chain B residue  166 MET
Chi-restraints excluded: chain B residue  458 SER
Chi-restraints excluded: chain B residue  463 THR
Chi-restraints excluded: chain C residue  130 SER
Chi-restraints excluded: chain C residue  458 SER
Chi-restraints excluded: chain C residue  482 SER
Chi-restraints excluded: chain D residue   32 THR
Chi-restraints excluded: chain D residue  123 MET
Chi-restraints excluded: chain D residue  458 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 196
   random chunks:
   chunk 45 optimal weight:    8.9990
   chunk 135 optimal weight:    2.9990
   chunk 105 optimal weight:    2.9990
   chunk 80 optimal weight:    0.0170
   chunk 191 optimal weight:    0.7980
   chunk 62 optimal weight:    8.9990
   chunk 137 optimal weight:    1.9990
   chunk 174 optimal weight:    4.9990
   chunk 109 optimal weight:    0.9990
   chunk 157 optimal weight:    7.9990
   chunk 83 optimal weight:    9.9990
   overall best weight:    1.3624

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

Flipped N/Q/H residues before XYZ refinement:
A  77 GLN
A 436 GLN
** B  77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 272 GLN
** B 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  77 GLN
** C 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 231 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 = 0.3450 r_free = 0.3450 target = 0.084804 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3163 r_free = 0.3163 target = 0.069967 restraints weight = 41692.369|
|-----------------------------------------------------------------------------|
r_work (start): 0.3141 rms_B_bonded: 4.15
r_work: 0.3004 rms_B_bonded: 4.68 restraints_weight: 0.5000
r_work (final): 0.3004
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8455
moved from start:          0.3490

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031  15480  Z= 0.188
  Angle     :  0.618  12.244  20988  Z= 0.301
  Chirality :  0.045   0.176   2388
  Planarity :  0.004   0.032   2732
  Dihedral  :  4.254  20.046   2100
  Min Nonbonded Distance : 2.594

Molprobity Statistics.
  All-atom Clashscore : 8.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.87 %
    Favored  : 97.13 %
  Rotamer:
    Outliers :  1.28 %
    Allowed  : 12.71 %
    Favored  : 86.01 %
  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:  1.29 (0.19), residues: 1988
  helix:  1.91 (0.18), residues: 840
  sheet:  0.18 (0.28), residues: 356
  loop :  0.14 (0.23), residues: 792

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B 162 
 HIS   0.003   0.001   HIS D 257 
 PHE   0.020   0.001   PHE B 164 
 TYR   0.019   0.001   TYR C  76 
 ARG   0.002   0.000   ARG B  75 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 7921.04 seconds
wall clock time: 141 minutes 42.28 seconds (8502.28 seconds total)