Starting phenix.real_space_refine
on Wed Jun 11 14:16:33 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/3jae_6345/06_2025/3jae_6345.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/3jae_6345/06_2025/3jae_6345.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.9
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/3jae_6345/06_2025/3jae_6345.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/3jae_6345/06_2025/3jae_6345.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/3jae_6345/06_2025/3jae_6345.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/3jae_6345/06_2025/3jae_6345.cif"
  }
  resolution = 3.9
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   1.000
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      65      5.16       5
     C    8360      2.51       5
     N    2130      2.21       5
     O    2270      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 25 residue(s): 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib"
  Total number of atoms: 12825
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 2537
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 338, 2537
          Classifications: {'peptide': 338}
          Incomplete info: {'truncation_to_alanine': 55}
          Link IDs: {'PTRANS': 15, 'TRANS': 322}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 198
          Unresolved non-hydrogen angles: 242
          Unresolved non-hydrogen dihedrals: 163
          Unresolved non-hydrogen chiralities: 12
          Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 9, 'PHE:plan': 3, 'GLU:plan': 9, 'ARG:plan': 3}
          Unresolved non-hydrogen planarities: 110
    Chain: "G"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
  Restraints were copied for chains:
    C, B, E, D, F, I, H, J
  Time building chain proxies: 5.57, per 1000 atoms: 0.43
  Number of scatterers: 12825
  At special positions: 0
  Unit cell: (96.0324, 98.4636, 127.638, 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      65     16.00
     O    2270      8.00
     N    2130      7.00
     C    8360      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=5, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 214 " - pdb=" SG  CYS A 225 " distance=2.04
    Simple disulfide: pdb=" SG  CYS C 214 " - pdb=" SG  CYS C 225 " distance=2.04
    Simple disulfide: pdb=" SG  CYS B 214 " - pdb=" SG  CYS B 225 " distance=2.04
    Simple disulfide: pdb=" SG  CYS E 214 " - pdb=" SG  CYS E 225 " distance=2.04
    Simple disulfide: pdb=" SG  CYS D 214 " - pdb=" SG  CYS D 225 " distance=2.04

  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
  Links applied
    BETA1-4
      " NAG F   1 " - " NAG F   2 "
      " NAG G   1 " - " NAG G   2 "
      " NAG H   1 " - " NAG H   2 "
      " NAG I   1 " - " NAG I   2 "
      " NAG J   1 " - " NAG J   2 "
  Time building additional restraints: 3.37
  Conformation dependent library (CDL) restraints added in 1.7 seconds
  

  3340 Ramachandran restraints generated.
    1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3240

  Finding SS restraints...
    Secondary structure from input PDB file:
      40 helices and 20 sheets defined
      39.7% alpha, 40.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.80
  Creating SS restraints...
    Processing helix  chain 'A' and resid 25 through 34
    Processing helix  chain 'A' and resid 36 through 40
      removed outlier: 4.132A  pdb=" N   TYR A  40 " --> pdb=" O   VAL A  37 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 104 through 108
    Processing helix  chain 'A' and resid 235 through 243
      removed outlier: 4.666A  pdb=" N   TYR A 239 " --> pdb=" O   GLN A 235 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 243 through 260
      removed outlier: 3.906A  pdb=" N   SER A 247 " --> pdb=" O   MET A 243 " (cutoff:3.500A)
      removed outlier: 3.744A  pdb=" N   VAL A 256 " --> pdb=" O   ILE A 252 " (cutoff:3.500A)
      removed outlier: 4.340A  pdb=" N   SER A 257 " --> pdb=" O   LEU A 253 " (cutoff:3.500A)
      removed outlier: 4.369A  pdb=" N   PHE A 258 " --> pdb=" O   SER A 254 " (cutoff:3.500A)
      removed outlier: 3.960A  pdb=" N   TRP A 259 " --> pdb=" O   TRP A 255 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 264 through 288
      removed outlier: 4.411A  pdb=" N   ARG A 268 " --> pdb=" O   ALA A 264 " (cutoff:3.500A)
      removed outlier: 3.717A  pdb=" N   SER A 286 " --> pdb=" O   GLN A 282 " (cutoff:3.500A)
      removed outlier: 3.816A  pdb=" N   ARG A 287 " --> pdb=" O   SER A 283 " (cutoff:3.500A)
      removed outlier: 3.948A  pdb=" N   ALA A 288 " --> pdb=" O   SER A 284 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 297 through 325
      removed outlier: 3.847A  pdb=" N   ILE A 301 " --> pdb=" O   LYS A 297 " (cutoff:3.500A)
      removed outlier: 3.868A  pdb=" N   TRP A 302 " --> pdb=" O   ALA A 298 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 330 through 363
      removed outlier: 3.751A  pdb=" N   THR A 340 " --> pdb=" O   LYS A 336 " (cutoff:3.500A)
      Proline residue:  A 347  - end of helix
      removed outlier: 3.897A  pdb=" N   ILE A 359 " --> pdb=" O   ILE A 355 " (cutoff:3.500A)
      removed outlier: 4.325A  pdb=" N   THR A 360 " --> pdb=" O   PHE A 356 " (cutoff:3.500A)
      removed outlier: 3.915A  pdb=" N   TYR A 361 " --> pdb=" O   TYR A 357 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 26 through 34
    Processing helix  chain 'B' and resid 36 through 40
      removed outlier: 4.132A  pdb=" N   TYR B  40 " --> pdb=" O   VAL B  37 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 104 through 108
    Processing helix  chain 'B' and resid 235 through 243
      removed outlier: 4.665A  pdb=" N   TYR B 239 " --> pdb=" O   GLN B 235 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 243 through 260
      removed outlier: 3.907A  pdb=" N   SER B 247 " --> pdb=" O   MET B 243 " (cutoff:3.500A)
      removed outlier: 3.744A  pdb=" N   VAL B 256 " --> pdb=" O   ILE B 252 " (cutoff:3.500A)
      removed outlier: 4.340A  pdb=" N   SER B 257 " --> pdb=" O   LEU B 253 " (cutoff:3.500A)
      removed outlier: 4.368A  pdb=" N   PHE B 258 " --> pdb=" O   SER B 254 " (cutoff:3.500A)
      removed outlier: 3.960A  pdb=" N   TRP B 259 " --> pdb=" O   TRP B 255 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 264 through 288
      removed outlier: 4.411A  pdb=" N   ARG B 268 " --> pdb=" O   ALA B 264 " (cutoff:3.500A)
      removed outlier: 3.717A  pdb=" N   SER B 286 " --> pdb=" O   GLN B 282 " (cutoff:3.500A)
      removed outlier: 3.817A  pdb=" N   ARG B 287 " --> pdb=" O   SER B 283 " (cutoff:3.500A)
      removed outlier: 3.948A  pdb=" N   ALA B 288 " --> pdb=" O   SER B 284 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 297 through 325
      removed outlier: 3.847A  pdb=" N   ILE B 301 " --> pdb=" O   LYS B 297 " (cutoff:3.500A)
      removed outlier: 3.867A  pdb=" N   TRP B 302 " --> pdb=" O   ALA B 298 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 330 through 363
      removed outlier: 3.751A  pdb=" N   THR B 340 " --> pdb=" O   LYS B 336 " (cutoff:3.500A)
      Proline residue:  B 347  - end of helix
      removed outlier: 3.897A  pdb=" N   ILE B 359 " --> pdb=" O   ILE B 355 " (cutoff:3.500A)
      removed outlier: 4.325A  pdb=" N   THR B 360 " --> pdb=" O   PHE B 356 " (cutoff:3.500A)
      removed outlier: 3.914A  pdb=" N   TYR B 361 " --> pdb=" O   TYR B 357 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 26 through 34
    Processing helix  chain 'C' and resid 36 through 40
      removed outlier: 4.133A  pdb=" N   TYR C  40 " --> pdb=" O   VAL C  37 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 104 through 108
    Processing helix  chain 'C' and resid 235 through 243
      removed outlier: 4.666A  pdb=" N   TYR C 239 " --> pdb=" O   GLN C 235 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 243 through 260
      removed outlier: 3.906A  pdb=" N   SER C 247 " --> pdb=" O   MET C 243 " (cutoff:3.500A)
      removed outlier: 3.744A  pdb=" N   VAL C 256 " --> pdb=" O   ILE C 252 " (cutoff:3.500A)
      removed outlier: 4.339A  pdb=" N   SER C 257 " --> pdb=" O   LEU C 253 " (cutoff:3.500A)
      removed outlier: 4.369A  pdb=" N   PHE C 258 " --> pdb=" O   SER C 254 " (cutoff:3.500A)
      removed outlier: 3.961A  pdb=" N   TRP C 259 " --> pdb=" O   TRP C 255 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 264 through 288
      removed outlier: 4.410A  pdb=" N   ARG C 268 " --> pdb=" O   ALA C 264 " (cutoff:3.500A)
      removed outlier: 3.717A  pdb=" N   SER C 286 " --> pdb=" O   GLN C 282 " (cutoff:3.500A)
      removed outlier: 3.816A  pdb=" N   ARG C 287 " --> pdb=" O   SER C 283 " (cutoff:3.500A)
      removed outlier: 3.948A  pdb=" N   ALA C 288 " --> pdb=" O   SER C 284 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 297 through 325
      removed outlier: 3.847A  pdb=" N   ILE C 301 " --> pdb=" O   LYS C 297 " (cutoff:3.500A)
      removed outlier: 3.868A  pdb=" N   TRP C 302 " --> pdb=" O   ALA C 298 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 330 through 363
      removed outlier: 3.752A  pdb=" N   THR C 340 " --> pdb=" O   LYS C 336 " (cutoff:3.500A)
      Proline residue:  C 347  - end of helix
      removed outlier: 3.897A  pdb=" N   ILE C 359 " --> pdb=" O   ILE C 355 " (cutoff:3.500A)
      removed outlier: 4.326A  pdb=" N   THR C 360 " --> pdb=" O   PHE C 356 " (cutoff:3.500A)
      removed outlier: 3.915A  pdb=" N   TYR C 361 " --> pdb=" O   TYR C 357 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 26 through 34
    Processing helix  chain 'D' and resid 36 through 40
      removed outlier: 4.132A  pdb=" N   TYR D  40 " --> pdb=" O   VAL D  37 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 104 through 108
    Processing helix  chain 'D' and resid 235 through 243
      removed outlier: 4.665A  pdb=" N   TYR D 239 " --> pdb=" O   GLN D 235 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 243 through 260
      removed outlier: 3.906A  pdb=" N   SER D 247 " --> pdb=" O   MET D 243 " (cutoff:3.500A)
      removed outlier: 3.743A  pdb=" N   VAL D 256 " --> pdb=" O   ILE D 252 " (cutoff:3.500A)
      removed outlier: 4.340A  pdb=" N   SER D 257 " --> pdb=" O   LEU D 253 " (cutoff:3.500A)
      removed outlier: 4.370A  pdb=" N   PHE D 258 " --> pdb=" O   SER D 254 " (cutoff:3.500A)
      removed outlier: 3.960A  pdb=" N   TRP D 259 " --> pdb=" O   TRP D 255 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 264 through 288
      removed outlier: 4.410A  pdb=" N   ARG D 268 " --> pdb=" O   ALA D 264 " (cutoff:3.500A)
      removed outlier: 3.717A  pdb=" N   SER D 286 " --> pdb=" O   GLN D 282 " (cutoff:3.500A)
      removed outlier: 3.817A  pdb=" N   ARG D 287 " --> pdb=" O   SER D 283 " (cutoff:3.500A)
      removed outlier: 3.948A  pdb=" N   ALA D 288 " --> pdb=" O   SER D 284 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 297 through 325
      removed outlier: 3.847A  pdb=" N   ILE D 301 " --> pdb=" O   LYS D 297 " (cutoff:3.500A)
      removed outlier: 3.867A  pdb=" N   TRP D 302 " --> pdb=" O   ALA D 298 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 330 through 363
      removed outlier: 3.752A  pdb=" N   THR D 340 " --> pdb=" O   LYS D 336 " (cutoff:3.500A)
      Proline residue:  D 347  - end of helix
      removed outlier: 3.897A  pdb=" N   ILE D 359 " --> pdb=" O   ILE D 355 " (cutoff:3.500A)
      removed outlier: 4.325A  pdb=" N   THR D 360 " --> pdb=" O   PHE D 356 " (cutoff:3.500A)
      removed outlier: 3.915A  pdb=" N   TYR D 361 " --> pdb=" O   TYR D 357 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 26 through 34
    Processing helix  chain 'E' and resid 36 through 40
      removed outlier: 4.132A  pdb=" N   TYR E  40 " --> pdb=" O   VAL E  37 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 104 through 108
    Processing helix  chain 'E' and resid 235 through 243
      removed outlier: 4.665A  pdb=" N   TYR E 239 " --> pdb=" O   GLN E 235 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 243 through 260
      removed outlier: 3.907A  pdb=" N   SER E 247 " --> pdb=" O   MET E 243 " (cutoff:3.500A)
      removed outlier: 3.744A  pdb=" N   VAL E 256 " --> pdb=" O   ILE E 252 " (cutoff:3.500A)
      removed outlier: 4.340A  pdb=" N   SER E 257 " --> pdb=" O   LEU E 253 " (cutoff:3.500A)
      removed outlier: 4.369A  pdb=" N   PHE E 258 " --> pdb=" O   SER E 254 " (cutoff:3.500A)
      removed outlier: 3.960A  pdb=" N   TRP E 259 " --> pdb=" O   TRP E 255 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 264 through 288
      removed outlier: 4.411A  pdb=" N   ARG E 268 " --> pdb=" O   ALA E 264 " (cutoff:3.500A)
      removed outlier: 3.717A  pdb=" N   SER E 286 " --> pdb=" O   GLN E 282 " (cutoff:3.500A)
      removed outlier: 3.816A  pdb=" N   ARG E 287 " --> pdb=" O   SER E 283 " (cutoff:3.500A)
      removed outlier: 3.948A  pdb=" N   ALA E 288 " --> pdb=" O   SER E 284 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 297 through 325
      removed outlier: 3.847A  pdb=" N   ILE E 301 " --> pdb=" O   LYS E 297 " (cutoff:3.500A)
      removed outlier: 3.868A  pdb=" N   TRP E 302 " --> pdb=" O   ALA E 298 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 330 through 363
      removed outlier: 3.751A  pdb=" N   THR E 340 " --> pdb=" O   LYS E 336 " (cutoff:3.500A)
      Proline residue:  E 347  - end of helix
      removed outlier: 3.897A  pdb=" N   ILE E 359 " --> pdb=" O   ILE E 355 " (cutoff:3.500A)
      removed outlier: 4.325A  pdb=" N   THR E 360 " --> pdb=" O   PHE E 356 " (cutoff:3.500A)
      removed outlier: 3.915A  pdb=" N   TYR E 361 " --> pdb=" O   TYR E 357 " (cutoff:3.500A)
    Processing sheet with id=A, first strand: chain 'A' and resid 98 through 100
      removed outlier: 4.090A  pdb=" N   ASN A 141 " --> pdb=" O   SER A 137 " (cutoff:3.500A)
      removed outlier: 6.931A  pdb=" N   ARG A  75 " --> pdb=" O   PHE A  64 " (cutoff:3.500A)
      removed outlier: 4.551A  pdb=" N   PHE A  64 " --> pdb=" O   ARG A  75 " (cutoff:3.500A)
      removed outlier: 6.902A  pdb=" N   ASN A  77 " --> pdb=" O   ASN A  62 " (cutoff:3.500A)
      removed outlier: 4.517A  pdb=" N   ASN A  85 " --> pdb=" O   ASN A  54 " (cutoff:3.500A)
      removed outlier: 6.187A  pdb=" N   ASN A  54 " --> pdb=" O   ASN A  85 " (cutoff:3.500A)
    Processing sheet with id=B, first strand: chain 'A' and resid 122 through 124
      removed outlier: 6.931A  pdb=" N   ARG A  75 " --> pdb=" O   PHE A  64 " (cutoff:3.500A)
      removed outlier: 4.551A  pdb=" N   PHE A  64 " --> pdb=" O   ARG A  75 " (cutoff:3.500A)
      removed outlier: 6.902A  pdb=" N   ASN A  77 " --> pdb=" O   ASN A  62 " (cutoff:3.500A)
      removed outlier: 4.517A  pdb=" N   ASN A  85 " --> pdb=" O   ASN A  54 " (cutoff:3.500A)
      removed outlier: 6.187A  pdb=" N   ASN A  54 " --> pdb=" O   ASN A  85 " (cutoff:3.500A)
    Processing sheet with id=C, first strand: chain 'A' and resid 115 through 116
      removed outlier: 3.848A  pdb=" N   MET A 170 " --> pdb=" O   ALA A 228 " (cutoff:3.500A)
    Processing sheet with id=D, first strand: chain 'A' and resid 115 through 116
      removed outlier: 3.848A  pdb=" N   MET A 170 " --> pdb=" O   ALA A 228 " (cutoff:3.500A)
    Processing sheet with id=E, first strand: chain 'B' and resid 98 through 100
      removed outlier: 4.090A  pdb=" N   ASN B 141 " --> pdb=" O   SER B 137 " (cutoff:3.500A)
      removed outlier: 6.932A  pdb=" N   ARG B  75 " --> pdb=" O   PHE B  64 " (cutoff:3.500A)
      removed outlier: 4.551A  pdb=" N   PHE B  64 " --> pdb=" O   ARG B  75 " (cutoff:3.500A)
      removed outlier: 6.903A  pdb=" N   ASN B  77 " --> pdb=" O   ASN B  62 " (cutoff:3.500A)
      removed outlier: 4.518A  pdb=" N   ASN B  85 " --> pdb=" O   ASN B  54 " (cutoff:3.500A)
      removed outlier: 6.188A  pdb=" N   ASN B  54 " --> pdb=" O   ASN B  85 " (cutoff:3.500A)
    Processing sheet with id=F, first strand: chain 'B' and resid 122 through 124
      removed outlier: 6.932A  pdb=" N   ARG B  75 " --> pdb=" O   PHE B  64 " (cutoff:3.500A)
      removed outlier: 4.551A  pdb=" N   PHE B  64 " --> pdb=" O   ARG B  75 " (cutoff:3.500A)
      removed outlier: 6.903A  pdb=" N   ASN B  77 " --> pdb=" O   ASN B  62 " (cutoff:3.500A)
      removed outlier: 4.518A  pdb=" N   ASN B  85 " --> pdb=" O   ASN B  54 " (cutoff:3.500A)
      removed outlier: 6.188A  pdb=" N   ASN B  54 " --> pdb=" O   ASN B  85 " (cutoff:3.500A)
    Processing sheet with id=G, first strand: chain 'B' and resid 115 through 116
      removed outlier: 3.848A  pdb=" N   MET B 170 " --> pdb=" O   ALA B 228 " (cutoff:3.500A)
    Processing sheet with id=H, first strand: chain 'B' and resid 115 through 116
      removed outlier: 3.848A  pdb=" N   MET B 170 " --> pdb=" O   ALA B 228 " (cutoff:3.500A)
    Processing sheet with id=I, first strand: chain 'C' and resid 98 through 100
      removed outlier: 4.090A  pdb=" N   ASN C 141 " --> pdb=" O   SER C 137 " (cutoff:3.500A)
      removed outlier: 6.932A  pdb=" N   ARG C  75 " --> pdb=" O   PHE C  64 " (cutoff:3.500A)
      removed outlier: 4.551A  pdb=" N   PHE C  64 " --> pdb=" O   ARG C  75 " (cutoff:3.500A)
      removed outlier: 6.903A  pdb=" N   ASN C  77 " --> pdb=" O   ASN C  62 " (cutoff:3.500A)
      removed outlier: 4.517A  pdb=" N   ASN C  85 " --> pdb=" O   ASN C  54 " (cutoff:3.500A)
      removed outlier: 6.188A  pdb=" N   ASN C  54 " --> pdb=" O   ASN C  85 " (cutoff:3.500A)
    Processing sheet with id=J, first strand: chain 'C' and resid 122 through 124
      removed outlier: 6.932A  pdb=" N   ARG C  75 " --> pdb=" O   PHE C  64 " (cutoff:3.500A)
      removed outlier: 4.551A  pdb=" N   PHE C  64 " --> pdb=" O   ARG C  75 " (cutoff:3.500A)
      removed outlier: 6.903A  pdb=" N   ASN C  77 " --> pdb=" O   ASN C  62 " (cutoff:3.500A)
      removed outlier: 4.517A  pdb=" N   ASN C  85 " --> pdb=" O   ASN C  54 " (cutoff:3.500A)
      removed outlier: 6.188A  pdb=" N   ASN C  54 " --> pdb=" O   ASN C  85 " (cutoff:3.500A)
    Processing sheet with id=K, first strand: chain 'C' and resid 115 through 116
      removed outlier: 3.848A  pdb=" N   MET C 170 " --> pdb=" O   ALA C 228 " (cutoff:3.500A)
    Processing sheet with id=L, first strand: chain 'C' and resid 115 through 116
      removed outlier: 3.848A  pdb=" N   MET C 170 " --> pdb=" O   ALA C 228 " (cutoff:3.500A)
    Processing sheet with id=M, first strand: chain 'D' and resid 98 through 100
      removed outlier: 4.090A  pdb=" N   ASN D 141 " --> pdb=" O   SER D 137 " (cutoff:3.500A)
      removed outlier: 6.932A  pdb=" N   ARG D  75 " --> pdb=" O   PHE D  64 " (cutoff:3.500A)
      removed outlier: 4.551A  pdb=" N   PHE D  64 " --> pdb=" O   ARG D  75 " (cutoff:3.500A)
      removed outlier: 6.902A  pdb=" N   ASN D  77 " --> pdb=" O   ASN D  62 " (cutoff:3.500A)
      removed outlier: 4.518A  pdb=" N   ASN D  85 " --> pdb=" O   ASN D  54 " (cutoff:3.500A)
      removed outlier: 6.187A  pdb=" N   ASN D  54 " --> pdb=" O   ASN D  85 " (cutoff:3.500A)
    Processing sheet with id=N, first strand: chain 'D' and resid 122 through 124
      removed outlier: 6.932A  pdb=" N   ARG D  75 " --> pdb=" O   PHE D  64 " (cutoff:3.500A)
      removed outlier: 4.551A  pdb=" N   PHE D  64 " --> pdb=" O   ARG D  75 " (cutoff:3.500A)
      removed outlier: 6.902A  pdb=" N   ASN D  77 " --> pdb=" O   ASN D  62 " (cutoff:3.500A)
      removed outlier: 4.518A  pdb=" N   ASN D  85 " --> pdb=" O   ASN D  54 " (cutoff:3.500A)
      removed outlier: 6.187A  pdb=" N   ASN D  54 " --> pdb=" O   ASN D  85 " (cutoff:3.500A)
    Processing sheet with id=O, first strand: chain 'D' and resid 115 through 116
      removed outlier: 3.848A  pdb=" N   MET D 170 " --> pdb=" O   ALA D 228 " (cutoff:3.500A)
    Processing sheet with id=P, first strand: chain 'D' and resid 115 through 116
      removed outlier: 3.848A  pdb=" N   MET D 170 " --> pdb=" O   ALA D 228 " (cutoff:3.500A)
    Processing sheet with id=Q, first strand: chain 'E' and resid 98 through 100
      removed outlier: 4.090A  pdb=" N   ASN E 141 " --> pdb=" O   SER E 137 " (cutoff:3.500A)
      removed outlier: 6.931A  pdb=" N   ARG E  75 " --> pdb=" O   PHE E  64 " (cutoff:3.500A)
      removed outlier: 4.551A  pdb=" N   PHE E  64 " --> pdb=" O   ARG E  75 " (cutoff:3.500A)
      removed outlier: 6.903A  pdb=" N   ASN E  77 " --> pdb=" O   ASN E  62 " (cutoff:3.500A)
      removed outlier: 4.517A  pdb=" N   ASN E  85 " --> pdb=" O   ASN E  54 " (cutoff:3.500A)
      removed outlier: 6.187A  pdb=" N   ASN E  54 " --> pdb=" O   ASN E  85 " (cutoff:3.500A)
    Processing sheet with id=R, first strand: chain 'E' and resid 122 through 124
      removed outlier: 6.931A  pdb=" N   ARG E  75 " --> pdb=" O   PHE E  64 " (cutoff:3.500A)
      removed outlier: 4.551A  pdb=" N   PHE E  64 " --> pdb=" O   ARG E  75 " (cutoff:3.500A)
      removed outlier: 6.903A  pdb=" N   ASN E  77 " --> pdb=" O   ASN E  62 " (cutoff:3.500A)
      removed outlier: 4.517A  pdb=" N   ASN E  85 " --> pdb=" O   ASN E  54 " (cutoff:3.500A)
      removed outlier: 6.187A  pdb=" N   ASN E  54 " --> pdb=" O   ASN E  85 " (cutoff:3.500A)
    Processing sheet with id=S, first strand: chain 'E' and resid 115 through 116
      removed outlier: 3.848A  pdb=" N   MET E 170 " --> pdb=" O   ALA E 228 " (cutoff:3.500A)
    Processing sheet with id=T, first strand: chain 'E' and resid 115 through 116
      removed outlier: 3.848A  pdb=" N   MET E 170 " --> pdb=" O   ALA E 228 " (cutoff:3.500A)

    816 hydrogen bonds defined for protein.
    2373 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: 4.10

  Time building geometry restraints manager: 3.99 seconds

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

  Histogram of bond lengths:
        1.21 -     1.34: 3892
        1.34 -     1.46: 2535
        1.46 -     1.58: 6613
        1.58 -     1.70: 0
        1.70 -     1.82: 105
  Bond restraints: 13145
  Sorted by residual:
  bond pdb=" C1  NAG J   2 "
       pdb=" O5  NAG J   2 "
    ideal  model  delta    sigma   weight residual
    1.406  1.455 -0.049 2.00e-02 2.50e+03 6.01e+00
  bond pdb=" C1  NAG F   2 "
       pdb=" O5  NAG F   2 "
    ideal  model  delta    sigma   weight residual
    1.406  1.455 -0.049 2.00e-02 2.50e+03 5.96e+00
  bond pdb=" C1  NAG I   2 "
       pdb=" O5  NAG I   2 "
    ideal  model  delta    sigma   weight residual
    1.406  1.454 -0.048 2.00e-02 2.50e+03 5.86e+00
  bond pdb=" C1  NAG H   2 "
       pdb=" O5  NAG H   2 "
    ideal  model  delta    sigma   weight residual
    1.406  1.454 -0.048 2.00e-02 2.50e+03 5.83e+00
  bond pdb=" C1  NAG G   2 "
       pdb=" O5  NAG G   2 "
    ideal  model  delta    sigma   weight residual
    1.406  1.454 -0.048 2.00e-02 2.50e+03 5.79e+00
  ... (remaining 13140 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.60: 15290
        1.60 -     3.19: 2172
        3.19 -     4.79: 368
        4.79 -     6.39: 108
        6.39 -     7.98: 37
  Bond angle restraints: 17975
  Sorted by residual:
  angle pdb=" C   THR D 128 "
        pdb=" CA  THR D 128 "
        pdb=" CB  THR D 128 "
      ideal   model   delta    sigma   weight residual
     116.63  109.43    7.20 1.16e+00 7.43e-01 3.85e+01
  angle pdb=" C   THR B 128 "
        pdb=" CA  THR B 128 "
        pdb=" CB  THR B 128 "
      ideal   model   delta    sigma   weight residual
     116.63  109.43    7.20 1.16e+00 7.43e-01 3.85e+01
  angle pdb=" C   THR E 128 "
        pdb=" CA  THR E 128 "
        pdb=" CB  THR E 128 "
      ideal   model   delta    sigma   weight residual
     116.63  109.45    7.18 1.16e+00 7.43e-01 3.83e+01
  angle pdb=" C   THR A 128 "
        pdb=" CA  THR A 128 "
        pdb=" CB  THR A 128 "
      ideal   model   delta    sigma   weight residual
     116.63  109.47    7.16 1.16e+00 7.43e-01 3.81e+01
  angle pdb=" N   GLU E 119 "
        pdb=" CA  GLU E 119 "
        pdb=" C   GLU E 119 "
      ideal   model   delta    sigma   weight residual
     111.33  118.79   -7.46 1.21e+00 6.83e-01 3.80e+01
  ... (remaining 17970 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.88: 7540
       16.88 -    33.76: 250
       33.76 -    50.63: 20
       50.63 -    67.51: 15
       67.51 -    84.39: 5
  Dihedral angle restraints: 7830
    sinusoidal: 2840
      harmonic: 4990
  Sorted by residual:
  dihedral pdb=" CB  CYS C 214 "
           pdb=" SG  CYS C 214 "
           pdb=" SG  CYS C 225 "
           pdb=" CB  CYS C 225 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -149.65   63.65     1      1.00e+01 1.00e-02 5.34e+01
  dihedral pdb=" CB  CYS D 214 "
           pdb=" SG  CYS D 214 "
           pdb=" SG  CYS D 225 "
           pdb=" CB  CYS D 225 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -149.64   63.64     1      1.00e+01 1.00e-02 5.34e+01
  dihedral pdb=" CB  CYS E 214 "
           pdb=" SG  CYS E 214 "
           pdb=" SG  CYS E 225 "
           pdb=" CB  CYS E 225 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -149.62   63.62     1      1.00e+01 1.00e-02 5.33e+01
  ... (remaining 7827 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.037: 1317
       0.037 -    0.074: 602
       0.074 -    0.112: 157
       0.112 -    0.149: 49
       0.149 -    0.186: 5
  Chirality restraints: 2130
  Sorted by residual:
  chirality pdb=" C1  NAG J   2 "
            pdb=" O4  NAG J   1 "
            pdb=" C2  NAG J   2 "
            pdb=" O5  NAG J   2 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.44    0.04 2.00e-02 2.50e+03 4.18e+00
  chirality pdb=" C1  NAG H   2 "
            pdb=" O4  NAG H   1 "
            pdb=" C2  NAG H   2 "
            pdb=" O5  NAG H   2 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.44    0.04 2.00e-02 2.50e+03 3.60e+00
  chirality pdb=" C1  NAG F   2 "
            pdb=" O4  NAG F   1 "
            pdb=" C2  NAG F   2 "
            pdb=" O5  NAG F   2 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.44    0.04 2.00e-02 2.50e+03 3.45e+00
  ... (remaining 2127 not shown)

  Planarity restraints: 2245
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE C 115 "   -0.020 2.00e-02 2.50e+03   2.47e-02 1.07e+01
        pdb=" CG  PHE C 115 "    0.054 2.00e-02 2.50e+03
        pdb=" CD1 PHE C 115 "   -0.025 2.00e-02 2.50e+03
        pdb=" CD2 PHE C 115 "   -0.003 2.00e-02 2.50e+03
        pdb=" CE1 PHE C 115 "    0.006 2.00e-02 2.50e+03
        pdb=" CE2 PHE C 115 "   -0.016 2.00e-02 2.50e+03
        pdb=" CZ  PHE C 115 "    0.004 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE E 115 "    0.020 2.00e-02 2.50e+03   2.47e-02 1.07e+01
        pdb=" CG  PHE E 115 "   -0.054 2.00e-02 2.50e+03
        pdb=" CD1 PHE E 115 "    0.025 2.00e-02 2.50e+03
        pdb=" CD2 PHE E 115 "    0.003 2.00e-02 2.50e+03
        pdb=" CE1 PHE E 115 "   -0.006 2.00e-02 2.50e+03
        pdb=" CE2 PHE E 115 "    0.015 2.00e-02 2.50e+03
        pdb=" CZ  PHE E 115 "   -0.004 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE A 115 "    0.020 2.00e-02 2.50e+03   2.47e-02 1.07e+01
        pdb=" CG  PHE A 115 "   -0.054 2.00e-02 2.50e+03
        pdb=" CD1 PHE A 115 "    0.025 2.00e-02 2.50e+03
        pdb=" CD2 PHE A 115 "    0.003 2.00e-02 2.50e+03
        pdb=" CE1 PHE A 115 "   -0.006 2.00e-02 2.50e+03
        pdb=" CE2 PHE A 115 "    0.016 2.00e-02 2.50e+03
        pdb=" CZ  PHE A 115 "   -0.003 2.00e-02 2.50e+03
  ... (remaining 2242 not shown)

  Histogram of nonbonded interaction distances:
        2.20 -     2.74: 1005
        2.74 -     3.28: 13587
        3.28 -     3.82: 20380
        3.82 -     4.36: 23800
        4.36 -     4.90: 40392
  Nonbonded interactions: 99164
  Sorted by model distance:
  nonbonded pdb=" OG1 THR A 128 "
            pdb=" O   LEU E 114 "
     model   vdw
     2.202 3.040
  nonbonded pdb=" O   VAL B 251 "
            pdb=" OG  SER B 254 "
     model   vdw
     2.228 3.040
  nonbonded pdb=" O   VAL D 251 "
            pdb=" OG  SER D 254 "
     model   vdw
     2.229 3.040
  nonbonded pdb=" O   VAL E 251 "
            pdb=" OG  SER E 254 "
     model   vdw
     2.229 3.040
  nonbonded pdb=" O   VAL A 251 "
            pdb=" OG  SER A 254 "
     model   vdw
     2.229 3.040
  ... (remaining 99159 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: 0.11
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'C'
  selection = chain 'B'
  selection = chain 'E'
  selection = chain 'D'
}
ncs_group {
  reference = chain 'G'
  selection = chain 'F'
  selection = chain 'I'
  selection = chain 'H'
  selection = chain 'J'
}

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 group one per residue
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:             0.950
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.510
  Check model and map are aligned:         0.100
  Set scattering table:                    0.140
  Process input model:                     29.750
  Find NCS groups from input model:        0.270
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.730
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   34.500
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7685
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      :  0.006   0.049  13155  Z= 0.416
  Angle     :  1.255   7.985  18000  Z= 0.838
  Chirality :  0.046   0.186   2130
  Planarity :  0.006   0.059   2245
  Dihedral  :  9.721  84.390   4575
  Min Nonbonded Distance : 2.202

Molprobity Statistics.
  All-atom Clashscore : 13.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.90 %
    Favored  : 99.10 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.22 %
    Favored  : 98.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.69 (0.17), residues: 1670
  helix: -1.72 (0.19), residues: 510
  sheet:  0.50 (0.26), residues: 375
  loop : -1.46 (0.17), residues: 785

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.047   0.004   TRP A 255 
 HIS   0.004   0.002   HIS B 125 
 PHE   0.054   0.004   PHE E 115 
 TYR   0.047   0.003   TYR B  74 
 ARG   0.015   0.002   ARG C 147 

Details of bonding type rmsd
  link_BETA1-4         : bond        0.00931 (    5)
  link_BETA1-4         : angle       0.89503 (   15)
  hydrogen bonds       : bond        0.11711 (  676)
  hydrogen bonds       : angle       9.03951 ( 2373)
  SS BOND              : bond        0.00841 (    5)
  SS BOND              : angle       0.54106 (   10)
  covalent geometry    : bond        0.00635 (13145)
  covalent geometry    : angle       1.25536 (17975)

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

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

  3340 Ramachandran restraints generated.
    1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3340 Ramachandran restraints generated.
    1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  332 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 332
  time to evaluate  : 1.359 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  132 LYS cc_start: 0.8107 (mttm) cc_final: 0.7869 (mtmt)
REVERT: A  204 ILE cc_start: 0.8672 (pt) cc_final: 0.8240 (mm)
REVERT: B   73 ASP cc_start: 0.6630 (p0) cc_final: 0.6369 (p0)
REVERT: B  132 LYS cc_start: 0.8100 (mttm) cc_final: 0.7831 (mtmt)
REVERT: B  303 MET cc_start: 0.8634 (mmm) cc_final: 0.8386 (mmm)
REVERT: D  252 ILE cc_start: 0.9528 (mt) cc_final: 0.9296 (mt)
REVERT: E  252 ILE cc_start: 0.9487 (mt) cc_final: 0.9246 (mt)
  outliers start: 0
  outliers final: 0
  residues processed: 332
  average time/residue: 0.2723
  time to fit residues: 126.9965
Evaluate side-chains
  167 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 167
  time to evaluate  : 1.465 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 165
   random chunks:
   chunk 139 optimal weight:    5.9990
   chunk 125 optimal weight:    6.9990
   chunk 69 optimal weight:    7.9990
   chunk 42 optimal weight:    1.9990
   chunk 84 optimal weight:    9.9990
   chunk 66 optimal weight:    3.9990
   chunk 129 optimal weight:    0.9980
   chunk 50 optimal weight:    0.9980
   chunk 78 optimal weight:    5.9990
   chunk 96 optimal weight:    7.9990
   chunk 149 optimal weight:    1.9990
   overall best weight:    1.9986

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

Flipped N/Q/H residues before XYZ refinement:
A  54 ASN
A  83 GLN
B  54 ASN
B  83 GLN
** B 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  54 ASN
** C  83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  54 ASN
D  83 GLN
** D 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  54 ASN
** E  83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2990 r_free = 0.2990 target = 0.047815 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2672 r_free = 0.2672 target = 0.036347 restraints weight = 86853.780|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.2700 r_free = 0.2700 target = 0.037282 restraints weight = 50735.721|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.2720 r_free = 0.2720 target = 0.037924 restraints weight = 35385.814|
|-----------------------------------------------------------------------------|
r_work (final): 0.2666
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8300
moved from start:          0.2941

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.060  13155  Z= 0.192
  Angle     :  0.869  10.402  18000  Z= 0.436
  Chirality :  0.048   0.245   2130
  Planarity :  0.005   0.039   2245
  Dihedral  :  7.851  59.898   2025
  Min Nonbonded Distance : 2.398

Molprobity Statistics.
  All-atom Clashscore : 18.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.90 %
    Favored  : 99.10 %
  Rotamer:
    Outliers :  2.28 %
    Allowed  :  9.84 %
    Favored  : 87.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.42 (0.18), residues: 1670
  helix:  0.59 (0.21), residues: 525
  sheet:  0.46 (0.25), residues: 380
  loop : -1.27 (0.19), residues: 765

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.002   TRP C 255 
 HIS   0.002   0.001   HIS E 231 
 PHE   0.029   0.002   PHE B 115 
 TYR   0.024   0.002   TYR D 239 
 ARG   0.007   0.001   ARG E  43 

Details of bonding type rmsd
  link_BETA1-4         : bond        0.00240 (    5)
  link_BETA1-4         : angle       1.54184 (   15)
  hydrogen bonds       : bond        0.04632 (  676)
  hydrogen bonds       : angle       5.93662 ( 2373)
  SS BOND              : bond        0.00595 (    5)
  SS BOND              : angle       1.38837 (   10)
  covalent geometry    : bond        0.00412 (13145)
  covalent geometry    : angle       0.86831 (17975)

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

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

  3340 Ramachandran restraints generated.
    1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3340 Ramachandran restraints generated.
    1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  219 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 191
  time to evaluate  : 1.465 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  105 MET cc_start: 0.8818 (mmp) cc_final: 0.8586 (mmm)
REVERT: A  120 LYS cc_start: 0.9032 (ttpt) cc_final: 0.8805 (ptpt)
REVERT: A  132 LYS cc_start: 0.9274 (mttm) cc_final: 0.8919 (mtmt)
REVERT: A  146 ILE cc_start: 0.9361 (pt) cc_final: 0.9102 (mm)
REVERT: A  156 MET cc_start: 0.8872 (ptp) cc_final: 0.8525 (mmm)
REVERT: A  166 GLN cc_start: 0.7897 (mm-40) cc_final: 0.7419 (mm-40)
REVERT: A  204 ILE cc_start: 0.9246 (pt) cc_final: 0.9008 (mm)
REVERT: A  216 LYS cc_start: 0.9600 (mmtp) cc_final: 0.9275 (mmtp)
REVERT: A  222 LYS cc_start: 0.9286 (pttm) cc_final: 0.8921 (pttp)
REVERT: A  353 PHE cc_start: 0.9322 (t80) cc_final: 0.9056 (t80)
REVERT: B   73 ASP cc_start: 0.8091 (p0) cc_final: 0.7797 (p0)
REVERT: B  105 MET cc_start: 0.8728 (tpp) cc_final: 0.8345 (tpp)
REVERT: B  120 LYS cc_start: 0.8975 (ttpt) cc_final: 0.8692 (ptmt)
REVERT: B  132 LYS cc_start: 0.9218 (mttm) cc_final: 0.8743 (mtmt)
REVERT: B  239 TYR cc_start: 0.9321 (m-80) cc_final: 0.8866 (m-80)
REVERT: B  303 MET cc_start: 0.9400 (mmm) cc_final: 0.9065 (mmm)
REVERT: C  105 MET cc_start: 0.8901 (mmp) cc_final: 0.8688 (mmp)
REVERT: C  179 MET cc_start: 0.9188 (tpp) cc_final: 0.8677 (mmm)
REVERT: D  100 ASP cc_start: 0.8841 (m-30) cc_final: 0.7885 (t0)
REVERT: D  105 MET cc_start: 0.8671 (tpp) cc_final: 0.8363 (tpp)
REVERT: D  130 ASP cc_start: 0.8502 (t0) cc_final: 0.8278 (t0)
REVERT: D  132 LYS cc_start: 0.9257 (mttm) cc_final: 0.8811 (mtmt)
REVERT: D  156 MET cc_start: 0.8710 (ptp) cc_final: 0.8258 (mmm)
REVERT: D  166 GLN cc_start: 0.7888 (mm-40) cc_final: 0.7446 (mm-40)
REVERT: D  292 LYS cc_start: 0.9452 (mtmm) cc_final: 0.9186 (ttmm)
REVERT: D  348 LEU cc_start: 0.9300 (mt) cc_final: 0.9083 (pp)
REVERT: E  100 ASP cc_start: 0.8823 (m-30) cc_final: 0.7795 (t0)
REVERT: E  106 LEU cc_start: 0.9396 (tt) cc_final: 0.9115 (mp)
REVERT: E  120 LYS cc_start: 0.9158 (OUTLIER) cc_final: 0.8791 (ptmt)
REVERT: E  292 LYS cc_start: 0.9478 (mttt) cc_final: 0.8990 (mmtm)
REVERT: E  302 TRP cc_start: 0.9160 (t-100) cc_final: 0.8952 (t-100)
  outliers start: 28
  outliers final: 10
  residues processed: 212
  average time/residue: 0.2698
  time to fit residues: 81.0826
Evaluate side-chains
  156 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 145
  time to evaluate  : 1.895 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  248 LEU
Chi-restraints excluded: chain A residue  315 LEU
Chi-restraints excluded: chain B residue  136 ILE
Chi-restraints excluded: chain B residue  168 CYS
Chi-restraints excluded: chain B residue  172 LEU
Chi-restraints excluded: chain C residue  168 CYS
Chi-restraints excluded: chain C residue  315 LEU
Chi-restraints excluded: chain D residue  136 ILE
Chi-restraints excluded: chain D residue  315 LEU
Chi-restraints excluded: chain E residue  120 LYS
Chi-restraints excluded: chain E residue  136 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 165
   random chunks:
   chunk 66 optimal weight:    4.9990
   chunk 20 optimal weight:   10.0000
   chunk 61 optimal weight:    4.9990
   chunk 105 optimal weight:    0.0020
   chunk 28 optimal weight:    5.9990
   chunk 97 optimal weight:    5.9990
   chunk 58 optimal weight:    5.9990
   chunk 117 optimal weight:    4.9990
   chunk 160 optimal weight:    2.9990
   chunk 130 optimal weight:   10.0000
   chunk 31 optimal weight:    4.9990
   overall best weight:    3.5996

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

Flipped N/Q/H residues before XYZ refinement:
A 166 GLN
A 217 HIS
** B 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 217 HIS
C 217 HIS
** D  82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 202 GLN ** 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 = 0.2961 r_free = 0.2961 target = 0.045994 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2632 r_free = 0.2632 target = 0.034788 restraints weight = 88845.653|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.2661 r_free = 0.2661 target = 0.035686 restraints weight = 51497.149|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.2680 r_free = 0.2680 target = 0.036331 restraints weight = 35674.816|
|-----------------------------------------------------------------------------|
r_work (final): 0.2633
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8362
moved from start:          0.3743

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.045  13155  Z= 0.222
  Angle     :  0.807  11.473  18000  Z= 0.401
  Chirality :  0.045   0.236   2130
  Planarity :  0.004   0.029   2245
  Dihedral  :  7.404  59.814   2025
  Min Nonbonded Distance : 2.407

Molprobity Statistics.
  All-atom Clashscore : 17.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.92 %
    Favored  : 98.08 %
  Rotamer:
    Outliers :  2.76 %
    Allowed  : 11.22 %
    Favored  : 86.02 %
  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:  0.02 (0.19), residues: 1670
  helix:  1.57 (0.22), residues: 510
  sheet:  0.19 (0.26), residues: 365
  loop : -1.12 (0.19), residues: 795

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP C 255 
 HIS   0.006   0.002   HIS B 217 
 PHE   0.034   0.002   PHE D 353 
 TYR   0.023   0.002   TYR D 144 
 ARG   0.005   0.001   ARG A  75 

Details of bonding type rmsd
  link_BETA1-4         : bond        0.00309 (    5)
  link_BETA1-4         : angle       1.27785 (   15)
  hydrogen bonds       : bond        0.04383 (  676)
  hydrogen bonds       : angle       5.39805 ( 2373)
  SS BOND              : bond        0.00232 (    5)
  SS BOND              : angle       1.35525 (   10)
  covalent geometry    : bond        0.00463 (13145)
  covalent geometry    : angle       0.80612 (17975)

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

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

  3340 Ramachandran restraints generated.
    1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3340 Ramachandran restraints generated.
    1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  179 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 145
  time to evaluate  : 1.563 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  130 ASP cc_start: 0.8780 (t0) cc_final: 0.8280 (t0)
REVERT: A  132 LYS cc_start: 0.9313 (mttm) cc_final: 0.9042 (mtmt)
REVERT: A  156 MET cc_start: 0.8922 (ptp) cc_final: 0.8496 (mmm)
REVERT: A  166 GLN cc_start: 0.8007 (OUTLIER) cc_final: 0.7171 (mm-40)
REVERT: A  279 MET cc_start: 0.9325 (mmm) cc_final: 0.9097 (mmm)
REVERT: A  303 MET cc_start: 0.9405 (mmm) cc_final: 0.9056 (mmt)
REVERT: B   73 ASP cc_start: 0.8123 (p0) cc_final: 0.7914 (p0)
REVERT: B  105 MET cc_start: 0.8785 (tpp) cc_final: 0.8465 (tpp)
REVERT: B  126 GLU cc_start: 0.8154 (tp30) cc_final: 0.7890 (tp30)
REVERT: B  132 LYS cc_start: 0.9282 (mttm) cc_final: 0.8945 (mtmt)
REVERT: B  232 LEU cc_start: 0.9617 (OUTLIER) cc_final: 0.9404 (mm)
REVERT: B  239 TYR cc_start: 0.9229 (m-80) cc_final: 0.8778 (m-80)
REVERT: B  303 MET cc_start: 0.9359 (mmm) cc_final: 0.8578 (mmt)
REVERT: C   72 MET cc_start: 0.8803 (tpp) cc_final: 0.8158 (tpp)
REVERT: C  130 ASP cc_start: 0.8790 (OUTLIER) cc_final: 0.8371 (t70)
REVERT: C  156 MET cc_start: 0.8548 (ptp) cc_final: 0.8161 (mpp)
REVERT: C  287 ARG cc_start: 0.9011 (mmt180) cc_final: 0.8722 (mtt-85)
REVERT: D   72 MET cc_start: 0.8989 (tpp) cc_final: 0.8787 (tpp)
REVERT: D   73 ASP cc_start: 0.8377 (OUTLIER) cc_final: 0.7761 (m-30)
REVERT: D  105 MET cc_start: 0.8760 (tpp) cc_final: 0.8491 (tpp)
REVERT: D  130 ASP cc_start: 0.8841 (t0) cc_final: 0.8459 (t0)
REVERT: D  132 LYS cc_start: 0.9300 (mttm) cc_final: 0.8918 (mtmt)
REVERT: D  156 MET cc_start: 0.8708 (ptp) cc_final: 0.8398 (mtm)
REVERT: D  292 LYS cc_start: 0.9443 (mtmm) cc_final: 0.9166 (mtmm)
REVERT: D  314 LEU cc_start: 0.8685 (OUTLIER) cc_final: 0.8460 (mm)
REVERT: E  100 ASP cc_start: 0.8798 (m-30) cc_final: 0.7815 (t0)
REVERT: E  105 MET cc_start: 0.8692 (mmp) cc_final: 0.8412 (mmp)
REVERT: E  120 LYS cc_start: 0.9144 (OUTLIER) cc_final: 0.8852 (ptmt)
REVERT: E  172 LEU cc_start: 0.9543 (mp) cc_final: 0.9254 (mp)
REVERT: E  179 MET cc_start: 0.8920 (mmm) cc_final: 0.8567 (mmm)
REVERT: E  222 LYS cc_start: 0.9309 (pttp) cc_final: 0.9044 (pttp)
REVERT: E  279 MET cc_start: 0.9244 (mmm) cc_final: 0.8989 (mmm)
REVERT: E  292 LYS cc_start: 0.9377 (mttt) cc_final: 0.9073 (mmtm)
REVERT: E  297 LYS cc_start: 0.9077 (mmmm) cc_final: 0.8832 (mmmm)
REVERT: E  303 MET cc_start: 0.9362 (mmm) cc_final: 0.8994 (mmt)
  outliers start: 34
  outliers final: 19
  residues processed: 176
  average time/residue: 0.2573
  time to fit residues: 65.3731
Evaluate side-chains
  153 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 128
  time to evaluate  : 1.346 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  136 ILE
Chi-restraints excluded: chain A residue  166 GLN
Chi-restraints excluded: chain A residue  181 ASP
Chi-restraints excluded: chain A residue  248 LEU
Chi-restraints excluded: chain A residue  255 TRP
Chi-restraints excluded: chain A residue  315 LEU
Chi-restraints excluded: chain B residue  136 ILE
Chi-restraints excluded: chain B residue  172 LEU
Chi-restraints excluded: chain B residue  181 ASP
Chi-restraints excluded: chain B residue  232 LEU
Chi-restraints excluded: chain B residue  314 LEU
Chi-restraints excluded: chain C residue  130 ASP
Chi-restraints excluded: chain C residue  136 ILE
Chi-restraints excluded: chain C residue  168 CYS
Chi-restraints excluded: chain C residue  181 ASP
Chi-restraints excluded: chain C residue  256 VAL
Chi-restraints excluded: chain C residue  315 LEU
Chi-restraints excluded: chain D residue   73 ASP
Chi-restraints excluded: chain D residue  136 ILE
Chi-restraints excluded: chain D residue  168 CYS
Chi-restraints excluded: chain D residue  181 ASP
Chi-restraints excluded: chain D residue  314 LEU
Chi-restraints excluded: chain D residue  315 LEU
Chi-restraints excluded: chain E residue  120 LYS
Chi-restraints excluded: chain E residue  136 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 165
   random chunks:
   chunk 8 optimal weight:    7.9990
   chunk 46 optimal weight:    0.0040
   chunk 72 optimal weight:   30.0000
   chunk 38 optimal weight:    1.9990
   chunk 89 optimal weight:    9.9990
   chunk 25 optimal weight:    9.9990
   chunk 137 optimal weight:    0.9980
   chunk 63 optimal weight:    3.9990
   chunk 78 optimal weight:    4.9990
   chunk 130 optimal weight:    7.9990
   chunk 85 optimal weight:    8.9990
   overall best weight:    2.3998

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

Flipped N/Q/H residues before XYZ refinement:
** B 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 166 GLN
D 171 GLN
E 171 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2964 r_free = 0.2964 target = 0.045978 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2631 r_free = 0.2631 target = 0.034729 restraints weight = 88820.668|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.2660 r_free = 0.2660 target = 0.035616 restraints weight = 51998.790|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.2678 r_free = 0.2678 target = 0.036221 restraints weight = 36306.230|
|-----------------------------------------------------------------------------|
r_work (final): 0.2636
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8366
moved from start:          0.4207

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029  13155  Z= 0.166
  Angle     :  0.740  10.367  18000  Z= 0.364
  Chirality :  0.044   0.245   2130
  Planarity :  0.004   0.027   2245
  Dihedral  :  6.927  59.998   2025
  Min Nonbonded Distance : 2.508

Molprobity Statistics.
  All-atom Clashscore : 14.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.40 %
    Favored  : 97.60 %
  Rotamer:
    Outliers :  2.28 %
    Allowed  : 12.28 %
    Favored  : 85.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.14 (0.20), residues: 1670
  helix:  1.86 (0.23), residues: 525
  sheet:  0.13 (0.25), residues: 385
  loop : -1.21 (0.20), residues: 760

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.030   0.002   TRP E 255 
 HIS   0.004   0.001   HIS B 231 
 PHE   0.022   0.001   PHE D 353 
 TYR   0.022   0.002   TYR D 144 
 ARG   0.009   0.001   ARG E  43 

Details of bonding type rmsd
  link_BETA1-4         : bond        0.00316 (    5)
  link_BETA1-4         : angle       1.39692 (   15)
  hydrogen bonds       : bond        0.03967 (  676)
  hydrogen bonds       : angle       4.95885 ( 2373)
  SS BOND              : bond        0.00183 (    5)
  SS BOND              : angle       0.90455 (   10)
  covalent geometry    : bond        0.00346 (13145)
  covalent geometry    : angle       0.73937 (17975)

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

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

  3340 Ramachandran restraints generated.
    1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3340 Ramachandran restraints generated.
    1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  169 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 141
  time to evaluate  : 1.402 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  105 MET cc_start: 0.8812 (mmm) cc_final: 0.8601 (mmm)
REVERT: A  120 LYS cc_start: 0.9231 (ttpt) cc_final: 0.8934 (ptpt)
REVERT: A  130 ASP cc_start: 0.8627 (t0) cc_final: 0.7800 (t0)
REVERT: A  132 LYS cc_start: 0.9300 (mttm) cc_final: 0.9005 (mtpt)
REVERT: A  179 MET cc_start: 0.8929 (mmm) cc_final: 0.8644 (mmm)
REVERT: A  222 LYS cc_start: 0.9166 (pttm) cc_final: 0.8962 (pttm)
REVERT: B   73 ASP cc_start: 0.8131 (p0) cc_final: 0.7825 (p0)
REVERT: B  105 MET cc_start: 0.8820 (tpp) cc_final: 0.8492 (tpp)
REVERT: B  126 GLU cc_start: 0.8245 (tp30) cc_final: 0.7883 (tp30)
REVERT: B  130 ASP cc_start: 0.8780 (t0) cc_final: 0.8139 (t0)
REVERT: B  132 LYS cc_start: 0.9294 (mttm) cc_final: 0.8936 (mtmt)
REVERT: B  279 MET cc_start: 0.9440 (mmm) cc_final: 0.9155 (mmm)
REVERT: B  303 MET cc_start: 0.9316 (mmm) cc_final: 0.8534 (mmt)
REVERT: C   72 MET cc_start: 0.8674 (tpp) cc_final: 0.7728 (tpp)
REVERT: C  109 ILE cc_start: 0.9615 (mp) cc_final: 0.9267 (mm)
REVERT: C  156 MET cc_start: 0.8574 (ptp) cc_final: 0.8307 (mpp)
REVERT: C  255 TRP cc_start: 0.8296 (m-10) cc_final: 0.7544 (m-10)
REVERT: C  287 ARG cc_start: 0.8900 (mmt180) cc_final: 0.8646 (mtt-85)
REVERT: C  314 LEU cc_start: 0.8968 (OUTLIER) cc_final: 0.8767 (mm)
REVERT: D  105 MET cc_start: 0.8819 (tpp) cc_final: 0.8425 (tpp)
REVERT: D  130 ASP cc_start: 0.8835 (t0) cc_final: 0.7982 (t0)
REVERT: D  132 LYS cc_start: 0.9288 (mttm) cc_final: 0.8903 (mtmt)
REVERT: D  156 MET cc_start: 0.8756 (ptp) cc_final: 0.8325 (mtm)
REVERT: D  179 MET cc_start: 0.8849 (mmm) cc_final: 0.8475 (mmm)
REVERT: D  314 LEU cc_start: 0.8795 (OUTLIER) cc_final: 0.8592 (mm)
REVERT: E   72 MET cc_start: 0.8628 (tpp) cc_final: 0.7573 (tpp)
REVERT: E   73 ASP cc_start: 0.8545 (p0) cc_final: 0.8227 (p0)
REVERT: E  100 ASP cc_start: 0.8784 (m-30) cc_final: 0.7938 (t0)
REVERT: E  120 LYS cc_start: 0.9171 (OUTLIER) cc_final: 0.8896 (ptmt)
REVERT: E  126 GLU cc_start: 0.8977 (mp0) cc_final: 0.8729 (tp30)
REVERT: E  287 ARG cc_start: 0.9117 (mmt180) cc_final: 0.8810 (mtp-110)
REVERT: E  292 LYS cc_start: 0.9430 (mttt) cc_final: 0.9197 (mmtm)
REVERT: E  302 TRP cc_start: 0.9181 (t-100) cc_final: 0.8689 (t60)
  outliers start: 28
  outliers final: 17
  residues processed: 165
  average time/residue: 0.2651
  time to fit residues: 63.0053
Evaluate side-chains
  143 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 123
  time to evaluate  : 1.437 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  136 ILE
Chi-restraints excluded: chain A residue  181 ASP
Chi-restraints excluded: chain A residue  248 LEU
Chi-restraints excluded: chain A residue  255 TRP
Chi-restraints excluded: chain A residue  315 LEU
Chi-restraints excluded: chain B residue  172 LEU
Chi-restraints excluded: chain B residue  181 ASP
Chi-restraints excluded: chain B residue  232 LEU
Chi-restraints excluded: chain B residue  314 LEU
Chi-restraints excluded: chain C residue  136 ILE
Chi-restraints excluded: chain C residue  168 CYS
Chi-restraints excluded: chain C residue  256 VAL
Chi-restraints excluded: chain C residue  314 LEU
Chi-restraints excluded: chain C residue  315 LEU
Chi-restraints excluded: chain D residue  113 ASP
Chi-restraints excluded: chain D residue  255 TRP
Chi-restraints excluded: chain D residue  314 LEU
Chi-restraints excluded: chain D residue  315 LEU
Chi-restraints excluded: chain E residue  120 LYS
Chi-restraints excluded: chain E residue  136 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 165
   random chunks:
   chunk 2 optimal weight:    3.9990
   chunk 109 optimal weight:    0.9990
   chunk 9 optimal weight:   10.0000
   chunk 119 optimal weight:   10.0000
   chunk 37 optimal weight:    8.9990
   chunk 66 optimal weight:    0.0270
   chunk 20 optimal weight:    9.9990
   chunk 67 optimal weight:    0.0570
   chunk 49 optimal weight:    9.9990
   chunk 91 optimal weight:    6.9990
   chunk 57 optimal weight:   10.0000
   overall best weight:    2.4162

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

Flipped N/Q/H residues before XYZ refinement:
** A  83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 171 GLN
** B  83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 217 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2964 r_free = 0.2964 target = 0.045779 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2635 r_free = 0.2635 target = 0.034671 restraints weight = 89533.561|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.2663 r_free = 0.2663 target = 0.035569 restraints weight = 52256.563|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.2683 r_free = 0.2683 target = 0.036167 restraints weight = 36523.219|
|-----------------------------------------------------------------------------|
r_work (final): 0.2637
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8377
moved from start:          0.4566

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025  13155  Z= 0.163
  Angle     :  0.720   9.389  18000  Z= 0.352
  Chirality :  0.044   0.243   2130
  Planarity :  0.004   0.032   2245
  Dihedral  :  6.716  59.667   2025
  Min Nonbonded Distance : 2.535

Molprobity Statistics.
  All-atom Clashscore : 13.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.69 %
    Favored  : 97.31 %
  Rotamer:
    Outliers :  2.52 %
    Allowed  : 12.52 %
    Favored  : 84.96 %
  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:  0.31 (0.20), residues: 1670
  helix:  2.06 (0.22), residues: 530
  sheet: -0.02 (0.25), residues: 400
  loop : -1.05 (0.21), residues: 740

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.030   0.001   TRP E 255 
 HIS   0.003   0.001   HIS D 217 
 PHE   0.019   0.001   PHE D 353 
 TYR   0.021   0.002   TYR C 144 
 ARG   0.003   0.001   ARG A  75 

Details of bonding type rmsd
  link_BETA1-4         : bond        0.00281 (    5)
  link_BETA1-4         : angle       1.17680 (   15)
  hydrogen bonds       : bond        0.03810 (  676)
  hydrogen bonds       : angle       4.69771 ( 2373)
  SS BOND              : bond        0.00077 (    5)
  SS BOND              : angle       0.51439 (   10)
  covalent geometry    : bond        0.00343 (13145)
  covalent geometry    : angle       0.71935 (17975)

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

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

  3340 Ramachandran restraints generated.
    1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3340 Ramachandran restraints generated.
    1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  167 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 136
  time to evaluate  : 1.690 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  132 LYS cc_start: 0.9294 (mttm) cc_final: 0.9052 (mtpt)
REVERT: A  216 LYS cc_start: 0.9530 (mmtp) cc_final: 0.9221 (mmmt)
REVERT: A  279 MET cc_start: 0.9404 (mmm) cc_final: 0.9152 (mmm)
REVERT: A  303 MET cc_start: 0.9438 (mmm) cc_final: 0.8728 (mmt)
REVERT: B   72 MET cc_start: 0.8923 (tpp) cc_final: 0.8626 (tpp)
REVERT: B  105 MET cc_start: 0.8832 (tpp) cc_final: 0.8509 (tpp)
REVERT: B  120 LYS cc_start: 0.9208 (ttmt) cc_final: 0.8608 (ptmm)
REVERT: B  126 GLU cc_start: 0.8343 (tp30) cc_final: 0.7972 (tp30)
REVERT: B  216 LYS cc_start: 0.9470 (mmtp) cc_final: 0.9182 (mmtp)
REVERT: B  279 MET cc_start: 0.9455 (mmm) cc_final: 0.9185 (mmm)
REVERT: B  297 LYS cc_start: 0.9190 (mtpp) cc_final: 0.8865 (tppp)
REVERT: B  303 MET cc_start: 0.9344 (mmm) cc_final: 0.8579 (mmt)
REVERT: C   73 ASP cc_start: 0.8700 (OUTLIER) cc_final: 0.8494 (m-30)
REVERT: C  169 ILE cc_start: 0.9500 (pt) cc_final: 0.9236 (mp)
REVERT: C  287 ARG cc_start: 0.8973 (mmt180) cc_final: 0.8657 (mtt-85)
REVERT: C  314 LEU cc_start: 0.9001 (OUTLIER) cc_final: 0.8798 (mm)
REVERT: D  105 MET cc_start: 0.8809 (tpp) cc_final: 0.8435 (tpp)
REVERT: D  130 ASP cc_start: 0.8853 (t0) cc_final: 0.8237 (t0)
REVERT: D  132 LYS cc_start: 0.9296 (mttm) cc_final: 0.8923 (mtmm)
REVERT: D  156 MET cc_start: 0.8564 (ptp) cc_final: 0.8357 (mmm)
REVERT: D  166 GLN cc_start: 0.7863 (mm-40) cc_final: 0.7166 (mm-40)
REVERT: D  262 MET cc_start: 0.8478 (pmm) cc_final: 0.8094 (mtp)
REVERT: D  292 LYS cc_start: 0.9455 (mtmm) cc_final: 0.9117 (mttm)
REVERT: E   71 THR cc_start: 0.9189 (OUTLIER) cc_final: 0.8953 (p)
REVERT: E   73 ASP cc_start: 0.8554 (p0) cc_final: 0.8231 (p0)
REVERT: E  100 ASP cc_start: 0.8771 (m-30) cc_final: 0.7987 (t0)
REVERT: E  120 LYS cc_start: 0.9207 (OUTLIER) cc_final: 0.8821 (ptmt)
REVERT: E  126 GLU cc_start: 0.9038 (mp0) cc_final: 0.8710 (tp30)
REVERT: E  156 MET cc_start: 0.7939 (mpp) cc_final: 0.7710 (mpp)
REVERT: E  179 MET cc_start: 0.8910 (mmm) cc_final: 0.8274 (mmm)
REVERT: E  222 LYS cc_start: 0.9286 (pttp) cc_final: 0.9067 (pttp)
REVERT: E  279 MET cc_start: 0.9277 (mmm) cc_final: 0.9034 (mmm)
REVERT: E  287 ARG cc_start: 0.9090 (mmt180) cc_final: 0.8763 (mtp-110)
REVERT: E  292 LYS cc_start: 0.9457 (mttt) cc_final: 0.9201 (mmtm)
REVERT: E  303 MET cc_start: 0.9441 (mmm) cc_final: 0.9021 (mmt)
  outliers start: 31
  outliers final: 18
  residues processed: 165
  average time/residue: 0.2561
  time to fit residues: 61.0016
Evaluate side-chains
  147 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 125
  time to evaluate  : 1.342 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  136 ILE
Chi-restraints excluded: chain A residue  181 ASP
Chi-restraints excluded: chain A residue  248 LEU
Chi-restraints excluded: chain A residue  255 TRP
Chi-restraints excluded: chain A residue  315 LEU
Chi-restraints excluded: chain B residue  136 ILE
Chi-restraints excluded: chain B residue  172 LEU
Chi-restraints excluded: chain B residue  181 ASP
Chi-restraints excluded: chain B residue  314 LEU
Chi-restraints excluded: chain C residue   73 ASP
Chi-restraints excluded: chain C residue  136 ILE
Chi-restraints excluded: chain C residue  168 CYS
Chi-restraints excluded: chain C residue  181 ASP
Chi-restraints excluded: chain C residue  256 VAL
Chi-restraints excluded: chain C residue  314 LEU
Chi-restraints excluded: chain D residue  113 ASP
Chi-restraints excluded: chain D residue  136 ILE
Chi-restraints excluded: chain D residue  255 TRP
Chi-restraints excluded: chain D residue  315 LEU
Chi-restraints excluded: chain E residue   71 THR
Chi-restraints excluded: chain E residue  120 LYS
Chi-restraints excluded: chain E residue  136 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 165
   random chunks:
   chunk 150 optimal weight:    5.9990
   chunk 129 optimal weight:    3.9990
   chunk 126 optimal weight:    4.9990
   chunk 160 optimal weight:    1.9990
   chunk 88 optimal weight:    0.0030
   chunk 56 optimal weight:   20.0000
   chunk 38 optimal weight:    0.9980
   chunk 161 optimal weight:    2.9990
   chunk 95 optimal weight:    0.7980
   chunk 115 optimal weight:    7.9990
   chunk 57 optimal weight:    0.1980
   overall best weight:    0.7992

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

Flipped N/Q/H residues before XYZ refinement:
** A  83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 171 GLN
** D  82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2982 r_free = 0.2982 target = 0.046496 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2657 r_free = 0.2657 target = 0.035166 restraints weight = 89678.472|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.2686 r_free = 0.2686 target = 0.036083 restraints weight = 51689.379|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.2706 r_free = 0.2706 target = 0.036721 restraints weight = 35675.476|
|-----------------------------------------------------------------------------|
r_work (final): 0.2658
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8347
moved from start:          0.4799

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031  13155  Z= 0.123
  Angle     :  0.720  11.472  18000  Z= 0.343
  Chirality :  0.044   0.249   2130
  Planarity :  0.003   0.033   2245
  Dihedral  :  6.440  59.938   2025
  Min Nonbonded Distance : 2.573

Molprobity Statistics.
  All-atom Clashscore : 11.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.28 %
    Favored  : 97.72 %
  Rotamer:
    Outliers :  1.71 %
    Allowed  : 13.82 %
    Favored  : 84.47 %
  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:  0.29 (0.20), residues: 1670
  helix:  2.01 (0.22), residues: 535
  sheet:  0.02 (0.25), residues: 400
  loop : -1.08 (0.21), residues: 735

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.035   0.001   TRP E 255 
 HIS   0.002   0.001   HIS B 231 
 PHE   0.015   0.001   PHE D 353 
 TYR   0.020   0.002   TYR C 144 
 ARG   0.003   0.000   ARG C  75 

Details of bonding type rmsd
  link_BETA1-4         : bond        0.00428 (    5)
  link_BETA1-4         : angle       1.24798 (   15)
  hydrogen bonds       : bond        0.03561 (  676)
  hydrogen bonds       : angle       4.50408 ( 2373)
  SS BOND              : bond        0.00084 (    5)
  SS BOND              : angle       0.48554 (   10)
  covalent geometry    : bond        0.00255 (13145)
  covalent geometry    : angle       0.71940 (17975)

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

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

  3340 Ramachandran restraints generated.
    1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3340 Ramachandran restraints generated.
    1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  168 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 147
  time to evaluate  : 1.451 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  132 LYS cc_start: 0.9310 (mttm) cc_final: 0.8991 (mtmt)
REVERT: A  179 MET cc_start: 0.8929 (mmm) cc_final: 0.8584 (mmm)
REVERT: A  216 LYS cc_start: 0.9538 (mmtp) cc_final: 0.9210 (mmmt)
REVERT: A  279 MET cc_start: 0.9414 (mmm) cc_final: 0.9130 (mmm)
REVERT: A  303 MET cc_start: 0.9428 (mmm) cc_final: 0.8695 (mmt)
REVERT: B  105 MET cc_start: 0.8849 (tpp) cc_final: 0.8520 (tpp)
REVERT: B  126 GLU cc_start: 0.8403 (tp30) cc_final: 0.8002 (tp30)
REVERT: B  179 MET cc_start: 0.8922 (mmm) cc_final: 0.8614 (mmm)
REVERT: B  282 GLN cc_start: 0.9070 (mm-40) cc_final: 0.8819 (mm-40)
REVERT: B  297 LYS cc_start: 0.9136 (mtpp) cc_final: 0.8741 (tppp)
REVERT: C  126 GLU cc_start: 0.9115 (mp0) cc_final: 0.8712 (tp30)
REVERT: C  169 ILE cc_start: 0.9506 (pt) cc_final: 0.9240 (mp)
REVERT: C  255 TRP cc_start: 0.8280 (m-10) cc_final: 0.6735 (m-10)
REVERT: C  279 MET cc_start: 0.9126 (mmp) cc_final: 0.8782 (mmp)
REVERT: C  287 ARG cc_start: 0.8902 (mmt180) cc_final: 0.8581 (mtt-85)
REVERT: C  303 MET cc_start: 0.9238 (mmm) cc_final: 0.8362 (mmm)
REVERT: D  105 MET cc_start: 0.8786 (tpp) cc_final: 0.8419 (tpp)
REVERT: D  130 ASP cc_start: 0.8940 (t0) cc_final: 0.8245 (t0)
REVERT: D  132 LYS cc_start: 0.9316 (mttm) cc_final: 0.8939 (mtmt)
REVERT: D  156 MET cc_start: 0.8619 (ptp) cc_final: 0.8413 (mmm)
REVERT: D  166 GLN cc_start: 0.8053 (mm-40) cc_final: 0.7370 (mm-40)
REVERT: D  202 GLN cc_start: 0.8595 (mp10) cc_final: 0.8348 (pm20)
REVERT: D  262 MET cc_start: 0.8218 (pmm) cc_final: 0.7854 (mtp)
REVERT: D  292 LYS cc_start: 0.9456 (mtmm) cc_final: 0.9243 (mmmm)
REVERT: D  302 TRP cc_start: 0.8867 (t60) cc_final: 0.8541 (t60)
REVERT: E   71 THR cc_start: 0.9189 (OUTLIER) cc_final: 0.8956 (p)
REVERT: E   73 ASP cc_start: 0.8458 (p0) cc_final: 0.8086 (p0)
REVERT: E  100 ASP cc_start: 0.8717 (m-30) cc_final: 0.7945 (t0)
REVERT: E  106 LEU cc_start: 0.9449 (tt) cc_final: 0.9094 (mt)
REVERT: E  120 LYS cc_start: 0.9223 (OUTLIER) cc_final: 0.8864 (ptmt)
REVERT: E  126 GLU cc_start: 0.9017 (mp0) cc_final: 0.8561 (tp30)
REVERT: E  172 LEU cc_start: 0.9549 (mp) cc_final: 0.9295 (mm)
REVERT: E  179 MET cc_start: 0.8966 (mmm) cc_final: 0.8598 (mmm)
REVERT: E  287 ARG cc_start: 0.9052 (mmt180) cc_final: 0.8676 (mtp-110)
REVERT: E  292 LYS cc_start: 0.9442 (mttt) cc_final: 0.9157 (mmtm)
REVERT: E  297 LYS cc_start: 0.9149 (mtpp) cc_final: 0.8808 (mmmm)
  outliers start: 21
  outliers final: 8
  residues processed: 166
  average time/residue: 0.2797
  time to fit residues: 65.3442
Evaluate side-chains
  141 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 131
  time to evaluate  : 1.394 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  255 TRP
Chi-restraints excluded: chain A residue  315 LEU
Chi-restraints excluded: chain B residue  172 LEU
Chi-restraints excluded: chain C residue  136 ILE
Chi-restraints excluded: chain C residue  256 VAL
Chi-restraints excluded: chain D residue  113 ASP
Chi-restraints excluded: chain D residue  255 TRP
Chi-restraints excluded: chain E residue   71 THR
Chi-restraints excluded: chain E residue  120 LYS
Chi-restraints excluded: chain E residue  255 TRP
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 165
   random chunks:
   chunk 110 optimal weight:    7.9990
   chunk 15 optimal weight:    0.9980
   chunk 32 optimal weight:    5.9990
   chunk 135 optimal weight:    0.8980
   chunk 105 optimal weight:   20.0000
   chunk 27 optimal weight:   10.0000
   chunk 134 optimal weight:    8.9990
   chunk 19 optimal weight:    0.5980
   chunk 129 optimal weight:    8.9990
   chunk 47 optimal weight:    9.9990
   chunk 38 optimal weight:    0.7980
   overall best weight:    1.8582

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

Flipped N/Q/H residues before XYZ refinement:
** A  83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 171 GLN
** D  83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 217 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2972 r_free = 0.2972 target = 0.046180 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2641 r_free = 0.2641 target = 0.034890 restraints weight = 90372.909|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 23)----------------|
| r_work = 0.2672 r_free = 0.2672 target = 0.035770 restraints weight = 52519.762|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.2691 r_free = 0.2691 target = 0.036395 restraints weight = 36597.038|
|-----------------------------------------------------------------------------|
r_work (final): 0.2641
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8370
moved from start:          0.4999

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031  13155  Z= 0.142
  Angle     :  0.735  13.845  18000  Z= 0.348
  Chirality :  0.043   0.245   2130
  Planarity :  0.003   0.037   2245
  Dihedral  :  6.426  59.989   2025
  Min Nonbonded Distance : 2.547

Molprobity Statistics.
  All-atom Clashscore : 13.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.63 %
    Favored  : 97.37 %
  Rotamer:
    Outliers :  1.71 %
    Allowed  : 14.88 %
    Favored  : 83.41 %
  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:  0.33 (0.20), residues: 1670
  helix:  2.18 (0.22), residues: 535
  sheet: -0.08 (0.25), residues: 400
  loop : -1.11 (0.21), residues: 735

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.032   0.001   TRP E 255 
 HIS   0.004   0.001   HIS B 231 
 PHE   0.015   0.001   PHE D 353 
 TYR   0.024   0.002   TYR C 144 
 ARG   0.005   0.000   ARG D  75 

Details of bonding type rmsd
  link_BETA1-4         : bond        0.00371 (    5)
  link_BETA1-4         : angle       1.19260 (   15)
  hydrogen bonds       : bond        0.03598 (  676)
  hydrogen bonds       : angle       4.41040 ( 2373)
  SS BOND              : bond        0.00061 (    5)
  SS BOND              : angle       0.42381 (   10)
  covalent geometry    : bond        0.00305 (13145)
  covalent geometry    : angle       0.73439 (17975)

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

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

  3340 Ramachandran restraints generated.
    1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3340 Ramachandran restraints generated.
    1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  159 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 138
  time to evaluate  : 1.486 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   72 MET cc_start: 0.8777 (tpp) cc_final: 0.7971 (tpp)
REVERT: A   73 ASP cc_start: 0.8415 (OUTLIER) cc_final: 0.8198 (m-30)
REVERT: A  132 LYS cc_start: 0.9317 (mttm) cc_final: 0.9007 (mtpt)
REVERT: A  156 MET cc_start: 0.8365 (mpp) cc_final: 0.7963 (mpp)
REVERT: A  216 LYS cc_start: 0.9531 (mmtp) cc_final: 0.9222 (mmmt)
REVERT: A  279 MET cc_start: 0.9461 (mmm) cc_final: 0.9253 (mmm)
REVERT: B   72 MET cc_start: 0.8917 (tpp) cc_final: 0.8677 (tpp)
REVERT: B  105 MET cc_start: 0.8837 (tpp) cc_final: 0.8516 (tpp)
REVERT: B  126 GLU cc_start: 0.8410 (tp30) cc_final: 0.8021 (tp30)
REVERT: B  216 LYS cc_start: 0.9447 (mmtp) cc_final: 0.9030 (mmtt)
REVERT: B  297 LYS cc_start: 0.9168 (mtpp) cc_final: 0.8748 (tppp)
REVERT: C  126 GLU cc_start: 0.9137 (mp0) cc_final: 0.8703 (tp30)
REVERT: C  169 ILE cc_start: 0.9507 (pt) cc_final: 0.9215 (mp)
REVERT: C  255 TRP cc_start: 0.8363 (m-10) cc_final: 0.6854 (m-10)
REVERT: C  279 MET cc_start: 0.9200 (mmp) cc_final: 0.8923 (mmp)
REVERT: C  287 ARG cc_start: 0.8927 (mmt180) cc_final: 0.8600 (mtt-85)
REVERT: C  303 MET cc_start: 0.9258 (mmm) cc_final: 0.8369 (mmm)
REVERT: C  314 LEU cc_start: 0.9022 (OUTLIER) cc_final: 0.8811 (mm)
REVERT: D  105 MET cc_start: 0.8721 (tpp) cc_final: 0.8361 (tpp)
REVERT: D  130 ASP cc_start: 0.8910 (t0) cc_final: 0.8366 (t0)
REVERT: D  132 LYS cc_start: 0.9309 (mttm) cc_final: 0.8932 (mtmm)
REVERT: D  156 MET cc_start: 0.8616 (ptp) cc_final: 0.8302 (mmm)
REVERT: D  166 GLN cc_start: 0.7971 (mm-40) cc_final: 0.7237 (mm-40)
REVERT: D  262 MET cc_start: 0.8096 (pmm) cc_final: 0.7802 (mtp)
REVERT: D  292 LYS cc_start: 0.9441 (mtmm) cc_final: 0.8966 (mmmm)
REVERT: D  302 TRP cc_start: 0.8888 (t60) cc_final: 0.8470 (t60)
REVERT: D  303 MET cc_start: 0.9278 (mmp) cc_final: 0.8742 (mmt)
REVERT: E   71 THR cc_start: 0.9188 (OUTLIER) cc_final: 0.8961 (p)
REVERT: E   73 ASP cc_start: 0.8548 (p0) cc_final: 0.8142 (p0)
REVERT: E  100 ASP cc_start: 0.8696 (m-30) cc_final: 0.7910 (t0)
REVERT: E  120 LYS cc_start: 0.9237 (OUTLIER) cc_final: 0.8851 (ptmt)
REVERT: E  172 LEU cc_start: 0.9543 (mp) cc_final: 0.9285 (mm)
REVERT: E  262 MET cc_start: 0.7431 (OUTLIER) cc_final: 0.7211 (mtp)
REVERT: E  287 ARG cc_start: 0.9037 (mmt180) cc_final: 0.8662 (mtp180)
REVERT: E  292 LYS cc_start: 0.9447 (mttt) cc_final: 0.9006 (mmtm)
REVERT: E  303 MET cc_start: 0.9464 (mmm) cc_final: 0.9147 (mmt)
  outliers start: 21
  outliers final: 13
  residues processed: 157
  average time/residue: 0.2927
  time to fit residues: 65.5912
Evaluate side-chains
  142 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 124
  time to evaluate  : 1.359 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   57 CYS
Chi-restraints excluded: chain A residue   73 ASP
Chi-restraints excluded: chain A residue  136 ILE
Chi-restraints excluded: chain A residue  255 TRP
Chi-restraints excluded: chain A residue  315 LEU
Chi-restraints excluded: chain B residue  130 ASP
Chi-restraints excluded: chain B residue  172 LEU
Chi-restraints excluded: chain B residue  314 LEU
Chi-restraints excluded: chain C residue  136 ILE
Chi-restraints excluded: chain C residue  256 VAL
Chi-restraints excluded: chain C residue  314 LEU
Chi-restraints excluded: chain D residue  136 ILE
Chi-restraints excluded: chain D residue  255 TRP
Chi-restraints excluded: chain E residue   71 THR
Chi-restraints excluded: chain E residue  120 LYS
Chi-restraints excluded: chain E residue  136 ILE
Chi-restraints excluded: chain E residue  255 TRP
Chi-restraints excluded: chain E residue  262 MET
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 165
   random chunks:
   chunk 88 optimal weight:    2.9990
   chunk 127 optimal weight:    6.9990
   chunk 123 optimal weight:   30.0000
   chunk 73 optimal weight:    0.0170
   chunk 124 optimal weight:    1.9990
   chunk 75 optimal weight:    6.9990
   chunk 20 optimal weight:    6.9990
   chunk 142 optimal weight:    0.5980
   chunk 104 optimal weight:    0.8980
   chunk 37 optimal weight:    6.9990
   chunk 144 optimal weight:    7.9990
   overall best weight:    1.3022

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

Flipped N/Q/H residues before XYZ refinement:
** A  83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 171 GLN
** B  83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 166 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2985 r_free = 0.2985 target = 0.046432 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2662 r_free = 0.2662 target = 0.035223 restraints weight = 89606.010|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 23)----------------|
| r_work = 0.2693 r_free = 0.2693 target = 0.036100 restraints weight = 52929.713|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.2712 r_free = 0.2712 target = 0.036707 restraints weight = 37375.110|
|-----------------------------------------------------------------------------|
r_work (final): 0.2660
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8357
moved from start:          0.5193

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  13155  Z= 0.131
  Angle     :  0.736  11.930  18000  Z= 0.348
  Chirality :  0.043   0.244   2130
  Planarity :  0.003   0.034   2245
  Dihedral  :  6.344  59.879   2025
  Min Nonbonded Distance : 2.511

Molprobity Statistics.
  All-atom Clashscore : 12.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.57 %
    Favored  : 97.43 %
  Rotamer:
    Outliers :  2.20 %
    Allowed  : 14.72 %
    Favored  : 83.09 %
  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:  0.35 (0.20), residues: 1670
  helix:  2.21 (0.22), residues: 535
  sheet: -0.03 (0.25), residues: 400
  loop : -1.13 (0.21), residues: 735

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.033   0.001   TRP E 255 
 HIS   0.003   0.001   HIS B 231 
 PHE   0.014   0.001   PHE D 353 
 TYR   0.021   0.001   TYR D 238 
 ARG   0.007   0.000   ARG D  43 

Details of bonding type rmsd
  link_BETA1-4         : bond        0.00384 (    5)
  link_BETA1-4         : angle       1.19406 (   15)
  hydrogen bonds       : bond        0.03527 (  676)
  hydrogen bonds       : angle       4.35608 ( 2373)
  SS BOND              : bond        0.00035 (    5)
  SS BOND              : angle       0.39093 (   10)
  covalent geometry    : bond        0.00276 (13145)
  covalent geometry    : angle       0.73530 (17975)

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

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

  3340 Ramachandran restraints generated.
    1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3340 Ramachandran restraints generated.
    1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  159 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 132
  time to evaluate  : 1.374 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   73 ASP cc_start: 0.8399 (OUTLIER) cc_final: 0.7978 (m-30)
REVERT: A  120 LYS cc_start: 0.9107 (ptmm) cc_final: 0.8790 (ptmm)
REVERT: A  132 LYS cc_start: 0.9321 (mttm) cc_final: 0.9014 (mtpt)
REVERT: A  216 LYS cc_start: 0.9537 (mmtp) cc_final: 0.9201 (mmmt)
REVERT: A  279 MET cc_start: 0.9509 (mmm) cc_final: 0.9144 (mmm)
REVERT: A  303 MET cc_start: 0.9425 (mmm) cc_final: 0.8633 (mmt)
REVERT: B   72 MET cc_start: 0.8882 (tpp) cc_final: 0.8589 (tpp)
REVERT: B  105 MET cc_start: 0.8807 (tpp) cc_final: 0.8487 (tpp)
REVERT: B  126 GLU cc_start: 0.8487 (tp30) cc_final: 0.8066 (tp30)
REVERT: B  132 LYS cc_start: 0.9350 (mttm) cc_final: 0.8959 (mtmt)
REVERT: B  156 MET cc_start: 0.8520 (mtm) cc_final: 0.8178 (mmm)
REVERT: B  169 ILE cc_start: 0.9485 (pt) cc_final: 0.9114 (mp)
REVERT: B  216 LYS cc_start: 0.9454 (mmtp) cc_final: 0.9035 (mmtt)
REVERT: B  279 MET cc_start: 0.9266 (mmm) cc_final: 0.9004 (mmt)
REVERT: B  297 LYS cc_start: 0.9159 (mtpp) cc_final: 0.8833 (tppp)
REVERT: B  303 MET cc_start: 0.9363 (mmm) cc_final: 0.8549 (mmt)
REVERT: C  126 GLU cc_start: 0.9136 (mp0) cc_final: 0.8606 (tp30)
REVERT: C  169 ILE cc_start: 0.9498 (pt) cc_final: 0.9226 (mp)
REVERT: C  255 TRP cc_start: 0.8313 (m-10) cc_final: 0.6810 (m-10)
REVERT: C  279 MET cc_start: 0.9218 (mmp) cc_final: 0.8949 (mmp)
REVERT: C  287 ARG cc_start: 0.8913 (mmt180) cc_final: 0.8650 (mtt-85)
REVERT: C  303 MET cc_start: 0.9321 (mmm) cc_final: 0.8445 (mmm)
REVERT: C  314 LEU cc_start: 0.9025 (OUTLIER) cc_final: 0.8814 (mm)
REVERT: D  105 MET cc_start: 0.8766 (tpp) cc_final: 0.8388 (tpp)
REVERT: D  130 ASP cc_start: 0.8918 (t0) cc_final: 0.8357 (t0)
REVERT: D  132 LYS cc_start: 0.9317 (mttm) cc_final: 0.8920 (mtmm)
REVERT: D  156 MET cc_start: 0.8700 (ptp) cc_final: 0.8248 (mtm)
REVERT: D  262 MET cc_start: 0.8156 (pmm) cc_final: 0.7760 (mtp)
REVERT: D  292 LYS cc_start: 0.9406 (mtmm) cc_final: 0.9177 (mmmm)
REVERT: D  302 TRP cc_start: 0.8870 (t60) cc_final: 0.8484 (t60)
REVERT: D  303 MET cc_start: 0.9263 (mmp) cc_final: 0.9014 (mmm)
REVERT: E   71 THR cc_start: 0.9187 (OUTLIER) cc_final: 0.8940 (p)
REVERT: E   73 ASP cc_start: 0.8520 (p0) cc_final: 0.7978 (p0)
REVERT: E  100 ASP cc_start: 0.8664 (m-30) cc_final: 0.7916 (t0)
REVERT: E  120 LYS cc_start: 0.9229 (OUTLIER) cc_final: 0.9009 (ptmt)
REVERT: E  126 GLU cc_start: 0.8577 (mp0) cc_final: 0.8169 (tp30)
REVERT: E  172 LEU cc_start: 0.9534 (mp) cc_final: 0.9294 (mm)
REVERT: E  262 MET cc_start: 0.7422 (OUTLIER) cc_final: 0.7190 (mtp)
REVERT: E  303 MET cc_start: 0.9447 (mmm) cc_final: 0.9140 (mmt)
  outliers start: 27
  outliers final: 12
  residues processed: 154
  average time/residue: 0.2692
  time to fit residues: 58.8857
Evaluate side-chains
  139 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 122
  time to evaluate  : 1.353 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   57 CYS
Chi-restraints excluded: chain A residue   73 ASP
Chi-restraints excluded: chain A residue  255 TRP
Chi-restraints excluded: chain A residue  315 LEU
Chi-restraints excluded: chain B residue  130 ASP
Chi-restraints excluded: chain B residue  136 ILE
Chi-restraints excluded: chain B residue  172 LEU
Chi-restraints excluded: chain B residue  314 LEU
Chi-restraints excluded: chain C residue  256 VAL
Chi-restraints excluded: chain C residue  314 LEU
Chi-restraints excluded: chain D residue  136 ILE
Chi-restraints excluded: chain D residue  172 LEU
Chi-restraints excluded: chain D residue  255 TRP
Chi-restraints excluded: chain E residue   71 THR
Chi-restraints excluded: chain E residue  120 LYS
Chi-restraints excluded: chain E residue  255 TRP
Chi-restraints excluded: chain E residue  262 MET
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 165
   random chunks:
   chunk 19 optimal weight:    0.9980
   chunk 33 optimal weight:    0.9980
   chunk 34 optimal weight:    2.9990
   chunk 52 optimal weight:    1.9990
   chunk 157 optimal weight:    8.9990
   chunk 149 optimal weight:    4.9990
   chunk 107 optimal weight:    9.9990
   chunk 39 optimal weight:    7.9990
   chunk 6 optimal weight:   20.0000
   chunk 59 optimal weight:    0.4980
   chunk 156 optimal weight:    8.9990
   overall best weight:    1.4984

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

Flipped N/Q/H residues before XYZ refinement:
** A  83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2985 r_free = 0.2985 target = 0.046453 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2657 r_free = 0.2657 target = 0.035212 restraints weight = 89866.690|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.2689 r_free = 0.2689 target = 0.036129 restraints weight = 53019.522|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.2709 r_free = 0.2709 target = 0.036763 restraints weight = 36822.351|
|-----------------------------------------------------------------------------|
r_work (final): 0.2666
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8360
moved from start:          0.5377

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  13155  Z= 0.136
  Angle     :  0.761  11.903  18000  Z= 0.357
  Chirality :  0.043   0.245   2130
  Planarity :  0.003   0.038   2245
  Dihedral  :  6.318  59.986   2025
  Min Nonbonded Distance : 2.516

Molprobity Statistics.
  All-atom Clashscore : 12.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.69 %
    Favored  : 97.31 %
  Rotamer:
    Outliers :  1.71 %
    Allowed  : 15.77 %
    Favored  : 82.52 %
  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:  0.15 (0.20), residues: 1670
  helix:  1.97 (0.22), residues: 565
  sheet: -0.10 (0.25), residues: 400
  loop : -1.36 (0.21), residues: 705

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.033   0.001   TRP E 255 
 HIS   0.004   0.001   HIS B 231 
 PHE   0.013   0.001   PHE D 353 
 TYR   0.032   0.002   TYR A 238 
 ARG   0.004   0.000   ARG E 287 

Details of bonding type rmsd
  link_BETA1-4         : bond        0.00428 (    5)
  link_BETA1-4         : angle       1.23128 (   15)
  hydrogen bonds       : bond        0.03529 (  676)
  hydrogen bonds       : angle       4.29923 ( 2373)
  SS BOND              : bond        0.00017 (    5)
  SS BOND              : angle       0.32978 (   10)
  covalent geometry    : bond        0.00293 (13145)
  covalent geometry    : angle       0.76103 (17975)

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

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

  3340 Ramachandran restraints generated.
    1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3340 Ramachandran restraints generated.
    1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  151 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 130
  time to evaluate  : 1.337 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   72 MET cc_start: 0.8760 (tpp) cc_final: 0.8509 (tpp)
REVERT: A  120 LYS cc_start: 0.9127 (ptmm) cc_final: 0.8797 (ptmm)
REVERT: A  132 LYS cc_start: 0.9306 (mttm) cc_final: 0.9011 (mtpt)
REVERT: A  216 LYS cc_start: 0.9536 (mmtp) cc_final: 0.9207 (mmmt)
REVERT: A  279 MET cc_start: 0.9519 (mmm) cc_final: 0.9071 (mmm)
REVERT: A  303 MET cc_start: 0.9407 (mmm) cc_final: 0.8634 (mmt)
REVERT: B   72 MET cc_start: 0.8990 (tpp) cc_final: 0.8684 (tpp)
REVERT: B  105 MET cc_start: 0.8778 (tpp) cc_final: 0.8467 (tpp)
REVERT: B  126 GLU cc_start: 0.8493 (tp30) cc_final: 0.8069 (tp30)
REVERT: B  156 MET cc_start: 0.8463 (mtm) cc_final: 0.7931 (mmm)
REVERT: B  169 ILE cc_start: 0.9497 (pt) cc_final: 0.9055 (mp)
REVERT: B  297 LYS cc_start: 0.9180 (mtpp) cc_final: 0.8828 (tppp)
REVERT: B  303 MET cc_start: 0.9349 (mmm) cc_final: 0.8505 (mmt)
REVERT: C  126 GLU cc_start: 0.9104 (mp0) cc_final: 0.8622 (tp30)
REVERT: C  169 ILE cc_start: 0.9484 (pt) cc_final: 0.9225 (mp)
REVERT: C  255 TRP cc_start: 0.8259 (m-10) cc_final: 0.6735 (m-10)
REVERT: C  279 MET cc_start: 0.9233 (mmp) cc_final: 0.8976 (mmp)
REVERT: C  287 ARG cc_start: 0.8910 (mmt180) cc_final: 0.8627 (mtt-85)
REVERT: C  303 MET cc_start: 0.9317 (mmm) cc_final: 0.8422 (mmm)
REVERT: C  314 LEU cc_start: 0.9052 (OUTLIER) cc_final: 0.8841 (mm)
REVERT: D  105 MET cc_start: 0.8778 (tpp) cc_final: 0.8391 (tpp)
REVERT: D  130 ASP cc_start: 0.8852 (t0) cc_final: 0.8273 (t0)
REVERT: D  132 LYS cc_start: 0.9283 (mttm) cc_final: 0.8914 (mtmm)
REVERT: D  156 MET cc_start: 0.8750 (ptp) cc_final: 0.8481 (mtm)
REVERT: D  166 GLN cc_start: 0.7285 (tm-30) cc_final: 0.6992 (tm-30)
REVERT: D  262 MET cc_start: 0.8078 (pmm) cc_final: 0.7623 (mtp)
REVERT: D  292 LYS cc_start: 0.9396 (mtmm) cc_final: 0.9167 (mmmm)
REVERT: D  302 TRP cc_start: 0.8830 (t60) cc_final: 0.8407 (t60)
REVERT: D  303 MET cc_start: 0.9234 (mmp) cc_final: 0.8656 (mmt)
REVERT: E   71 THR cc_start: 0.9221 (OUTLIER) cc_final: 0.8980 (p)
REVERT: E   73 ASP cc_start: 0.8512 (p0) cc_final: 0.7966 (p0)
REVERT: E  100 ASP cc_start: 0.8612 (m-30) cc_final: 0.7869 (t0)
REVERT: E  120 LYS cc_start: 0.9213 (OUTLIER) cc_final: 0.8991 (ptmt)
REVERT: E  126 GLU cc_start: 0.8549 (mp0) cc_final: 0.8308 (tp30)
REVERT: E  172 LEU cc_start: 0.9531 (mp) cc_final: 0.9288 (mm)
REVERT: E  303 MET cc_start: 0.9447 (mmm) cc_final: 0.9149 (mmt)
  outliers start: 21
  outliers final: 12
  residues processed: 148
  average time/residue: 0.2498
  time to fit residues: 53.4630
Evaluate side-chains
  137 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 122
  time to evaluate  : 1.328 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   57 CYS
Chi-restraints excluded: chain A residue  255 TRP
Chi-restraints excluded: chain A residue  315 LEU
Chi-restraints excluded: chain B residue  130 ASP
Chi-restraints excluded: chain B residue  136 ILE
Chi-restraints excluded: chain B residue  314 LEU
Chi-restraints excluded: chain C residue  142 VAL
Chi-restraints excluded: chain C residue  256 VAL
Chi-restraints excluded: chain C residue  314 LEU
Chi-restraints excluded: chain D residue  255 TRP
Chi-restraints excluded: chain D residue  348 LEU
Chi-restraints excluded: chain E residue   71 THR
Chi-restraints excluded: chain E residue  120 LYS
Chi-restraints excluded: chain E residue  255 TRP
Chi-restraints excluded: chain E residue  262 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 165
   random chunks:
   chunk 68 optimal weight:    0.9990
   chunk 82 optimal weight:    4.9990
   chunk 155 optimal weight:    5.9990
   chunk 116 optimal weight:    0.9980
   chunk 10 optimal weight:    8.9990
   chunk 46 optimal weight:    0.0030
   chunk 7 optimal weight:    4.9990
   chunk 105 optimal weight:   20.0000
   chunk 149 optimal weight:    6.9990
   chunk 72 optimal weight:   20.0000
   chunk 142 optimal weight:    9.9990
   overall best weight:    2.3996

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

Flipped N/Q/H residues before XYZ refinement:
** A  83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2977 r_free = 0.2977 target = 0.045939 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.2655 r_free = 0.2655 target = 0.034980 restraints weight = 91346.920|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.2687 r_free = 0.2687 target = 0.035884 restraints weight = 53709.634|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.2707 r_free = 0.2707 target = 0.036517 restraints weight = 37312.309|
|-----------------------------------------------------------------------------|
r_work (final): 0.2661
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8384
moved from start:          0.5561

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031  13155  Z= 0.160
  Angle     :  0.770  11.892  18000  Z= 0.360
  Chirality :  0.044   0.240   2130
  Planarity :  0.004   0.040   2245
  Dihedral  :  6.364  59.178   2025
  Min Nonbonded Distance : 2.559

Molprobity Statistics.
  All-atom Clashscore : 13.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.75 %
    Favored  : 97.25 %
  Rotamer:
    Outliers :  1.63 %
    Allowed  : 15.85 %
    Favored  : 82.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.06 %

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:  0.25 (0.20), residues: 1670
  helix:  2.14 (0.22), residues: 565
  sheet: -0.14 (0.25), residues: 400
  loop : -1.32 (0.21), residues: 705

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.030   0.001   TRP E 255 
 HIS   0.004   0.001   HIS B 231 
 PHE   0.013   0.001   PHE D 353 
 TYR   0.029   0.002   TYR D 238 
 ARG   0.005   0.000   ARG E 287 

Details of bonding type rmsd
  link_BETA1-4         : bond        0.00399 (    5)
  link_BETA1-4         : angle       1.24240 (   15)
  hydrogen bonds       : bond        0.03567 (  676)
  hydrogen bonds       : angle       4.33107 ( 2373)
  SS BOND              : bond        0.00041 (    5)
  SS BOND              : angle       0.40955 (   10)
  covalent geometry    : bond        0.00344 (13145)
  covalent geometry    : angle       0.76922 (17975)

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

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

  3340 Ramachandran restraints generated.
    1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3340 Ramachandran restraints generated.
    1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  151 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 131
  time to evaluate  : 1.478 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   73 ASP cc_start: 0.8551 (OUTLIER) cc_final: 0.7763 (m-30)
REVERT: A  120 LYS cc_start: 0.9191 (ptmm) cc_final: 0.8856 (ptmm)
REVERT: A  279 MET cc_start: 0.9513 (mmm) cc_final: 0.9204 (mmm)
REVERT: A  303 MET cc_start: 0.9408 (mmm) cc_final: 0.8730 (mmt)
REVERT: B   72 MET cc_start: 0.9036 (tpp) cc_final: 0.8618 (tpp)
REVERT: B  105 MET cc_start: 0.8759 (tpp) cc_final: 0.8456 (tpp)
REVERT: B  126 GLU cc_start: 0.8505 (tp30) cc_final: 0.8072 (tp30)
REVERT: B  169 ILE cc_start: 0.9534 (pt) cc_final: 0.9219 (mp)
REVERT: B  297 LYS cc_start: 0.9140 (mtpp) cc_final: 0.8800 (tppp)
REVERT: B  303 MET cc_start: 0.9327 (mmm) cc_final: 0.8441 (mmt)
REVERT: C  126 GLU cc_start: 0.9084 (mp0) cc_final: 0.8848 (mp0)
REVERT: C  169 ILE cc_start: 0.9457 (pt) cc_final: 0.9219 (mp)
REVERT: C  255 TRP cc_start: 0.8355 (m-10) cc_final: 0.6861 (m-10)
REVERT: C  287 ARG cc_start: 0.8948 (mmt180) cc_final: 0.8640 (mtt-85)
REVERT: D  105 MET cc_start: 0.8810 (tpp) cc_final: 0.8426 (tpp)
REVERT: D  130 ASP cc_start: 0.8854 (t0) cc_final: 0.8516 (t0)
REVERT: D  132 LYS cc_start: 0.9257 (mttm) cc_final: 0.8855 (mtmt)
REVERT: D  166 GLN cc_start: 0.7265 (tm-30) cc_final: 0.7019 (tm-30)
REVERT: D  292 LYS cc_start: 0.9389 (mtmm) cc_final: 0.9151 (mmmm)
REVERT: D  302 TRP cc_start: 0.8849 (t60) cc_final: 0.8390 (t60)
REVERT: D  303 MET cc_start: 0.9251 (mmp) cc_final: 0.8594 (mmt)
REVERT: E   71 THR cc_start: 0.9216 (OUTLIER) cc_final: 0.8985 (p)
REVERT: E   73 ASP cc_start: 0.8611 (p0) cc_final: 0.8084 (p0)
REVERT: E  120 LYS cc_start: 0.9230 (OUTLIER) cc_final: 0.8920 (ptmt)
REVERT: E  292 LYS cc_start: 0.9221 (OUTLIER) cc_final: 0.8902 (tppt)
REVERT: E  297 LYS cc_start: 0.9171 (mtpp) cc_final: 0.8396 (mmtm)
REVERT: E  303 MET cc_start: 0.9452 (mmm) cc_final: 0.9167 (mmt)
REVERT: E  351 LEU cc_start: 0.9701 (tp) cc_final: 0.9495 (pp)
  outliers start: 20
  outliers final: 12
  residues processed: 148
  average time/residue: 0.2586
  time to fit residues: 55.3034
Evaluate side-chains
  140 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 124
  time to evaluate  : 1.446 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   73 ASP
Chi-restraints excluded: chain A residue  136 ILE
Chi-restraints excluded: chain A residue  181 ASP
Chi-restraints excluded: chain A residue  255 TRP
Chi-restraints excluded: chain B residue  130 ASP
Chi-restraints excluded: chain B residue  136 ILE
Chi-restraints excluded: chain B residue  314 LEU
Chi-restraints excluded: chain C residue  142 VAL
Chi-restraints excluded: chain C residue  256 VAL
Chi-restraints excluded: chain D residue  255 TRP
Chi-restraints excluded: chain D residue  348 LEU
Chi-restraints excluded: chain E residue   71 THR
Chi-restraints excluded: chain E residue  120 LYS
Chi-restraints excluded: chain E residue  142 VAL
Chi-restraints excluded: chain E residue  255 TRP
Chi-restraints excluded: chain E residue  292 LYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 165
   random chunks:
   chunk 153 optimal weight:    0.9980
   chunk 42 optimal weight:    6.9990
   chunk 120 optimal weight:    4.9990
   chunk 33 optimal weight:    0.8980
   chunk 7 optimal weight:    0.0030
   chunk 11 optimal weight:    2.9990
   chunk 77 optimal weight:   10.0000
   chunk 51 optimal weight:   10.0000
   chunk 92 optimal weight:    5.9990
   chunk 125 optimal weight:    0.7980
   chunk 66 optimal weight:    0.0870
   overall best weight:    0.5568

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

Flipped N/Q/H residues before XYZ refinement:
** A  83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3002 r_free = 0.3002 target = 0.046941 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2687 r_free = 0.2687 target = 0.035835 restraints weight = 89001.507|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.2717 r_free = 0.2717 target = 0.036774 restraints weight = 51950.358|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.2738 r_free = 0.2738 target = 0.037436 restraints weight = 35884.241|
|-----------------------------------------------------------------------------|
r_work (final): 0.2687
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8352
moved from start:          0.5694

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  13155  Z= 0.128
  Angle     :  0.820  17.628  18000  Z= 0.374
  Chirality :  0.045   0.253   2130
  Planarity :  0.004   0.043   2245
  Dihedral  :  6.221  59.988   2025
  Min Nonbonded Distance : 2.550

Molprobity Statistics.
  All-atom Clashscore : 11.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.22 %
    Favored  : 97.78 %
  Rotamer:
    Outliers :  0.98 %
    Allowed  : 16.42 %
    Favored  : 82.60 %
  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:  0.29 (0.20), residues: 1670
  helix:  2.04 (0.22), residues: 535
  sheet:  0.02 (0.26), residues: 395
  loop : -1.11 (0.21), residues: 740

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.030   0.001   TRP E 255 
 HIS   0.002   0.001   HIS B 231 
 PHE   0.013   0.001   PHE A 353 
 TYR   0.023   0.001   TYR A 144 
 ARG   0.006   0.001   ARG E 287 

Details of bonding type rmsd
  link_BETA1-4         : bond        0.00397 (    5)
  link_BETA1-4         : angle       1.22244 (   15)
  hydrogen bonds       : bond        0.03512 (  676)
  hydrogen bonds       : angle       4.26240 ( 2373)
  SS BOND              : bond        0.00093 (    5)
  SS BOND              : angle       0.37577 (   10)
  covalent geometry    : bond        0.00276 (13145)
  covalent geometry    : angle       0.81935 (17975)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3412.23 seconds
wall clock time: 60 minutes 30.01 seconds (3630.01 seconds total)