Starting phenix.real_space_refine
on Thu Sep 26 10:35:21 2024 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jae_6345/09_2024/3jae_6345.cif
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jae_6345/09_2024/3jae_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jae_6345/09_2024/3jae_6345.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jae_6345/09_2024/3jae_6345.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jae_6345/09_2024/3jae_6345.cif"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jae_6345/09_2024/3jae_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-5461/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: 6.19, per 1000 atoms: 0.48
  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=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 214 " - pdb=" SG  CYS A 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: 3.25
  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: 1.77
  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: 4.19

  Time building geometry restraints manager: 3.78 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: 7532
       16.88 -    33.76: 250
       33.76 -    50.63: 20
       50.63 -    67.51: 11
       67.51 -    84.39: 5
  Dihedral angle restraints: 7818
    sinusoidal: 2828
      harmonic: 4990
  Sorted by residual:
  dihedral pdb=" CB  CYS A 214 "
           pdb=" SG  CYS A 214 "
           pdb=" SG  CYS A 225 "
           pdb=" CB  CYS A 225 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -149.62   63.62     1      1.00e+01 1.00e-02 5.33e+01
  dihedral pdb=" CA  LEU B 150 "
           pdb=" C   LEU B 150 "
           pdb=" N   VAL B 151 "
           pdb=" CA  VAL B 151 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  156.59   23.41     0      5.00e+00 4.00e-02 2.19e+01
  dihedral pdb=" CA  LEU A 150 "
           pdb=" C   LEU A 150 "
           pdb=" N   VAL A 151 "
           pdb=" CA  VAL A 151 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  156.64   23.36     0      5.00e+00 4.00e-02 2.18e+01
  ... (remaining 7815 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:
        2.04 -     2.61: 119
        2.61 -     3.18: 11647
        3.18 -     3.76: 19111
        3.76 -     4.33: 26141
        4.33 -     4.90: 42158
  Nonbonded interactions: 99176
  Sorted by model distance:
  nonbonded pdb=" SG  CYS D 214 "
            pdb=" SG  CYS D 225 "
     model   vdw
     2.038 3.760
  nonbonded pdb=" SG  CYS C 214 "
            pdb=" SG  CYS C 225 "
     model   vdw
     2.039 3.760
  nonbonded pdb=" SG  CYS B 214 "
            pdb=" SG  CYS B 225 "
     model   vdw
     2.040 3.760
  nonbonded pdb=" SG  CYS E 214 "
            pdb=" SG  CYS E 225 "
     model   vdw
     2.040 3.760
  nonbonded pdb=" OG1 THR A 128 "
            pdb=" O   LEU E 114 "
     model   vdw
     2.202 3.040
  ... (remaining 99171 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'C'
  selection = chain 'D'
  selection = chain 'E'
}
ncs_group {
  reference = chain 'F'
  selection = chain 'G'
  selection = chain 'H'
  selection = chain 'I'
  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:             1.190
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.540
  Check model and map are aligned:         0.110
  Set scattering table:                    0.140
  Process input model:                     29.810
  Find NCS groups from input model:        0.390
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.890
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   35.120
-------------------------------------------------------------------------------
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  13145  Z= 0.417
  Angle     :  1.255   7.985  17975  Z= 0.839
  Chirality :  0.046   0.186   2130
  Planarity :  0.006   0.059   2245
  Dihedral  :  9.721  84.390   4575
  Min Nonbonded Distance : 2.038

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 

*********************** 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 fitting.
    rotamer outliers: 0
    poor density    : 332
  time to evaluate  : 1.486 
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: 0.2623
  time to fit residues: 121.8545
Evaluate side-chains
  167 residues out of total 1505 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 167
  time to evaluate  : 1.451 
-------------------------------------------------------------------------------
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

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7803
moved from start:          0.2991

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.065  13145  Z= 0.274
  Angle     :  0.874  10.619  17975  Z= 0.437
  Chirality :  0.048   0.241   2130
  Planarity :  0.005   0.039   2245
  Dihedral  :  7.873  59.581   2025
  Min Nonbonded Distance : 2.391

Molprobity Statistics.
  All-atom Clashscore : 18.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.84 %
    Favored  : 99.16 %
  Rotamer:
    Outliers :  2.44 %
    Allowed  : 10.16 %
    Favored  : 87.40 %
  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:  0.60 (0.21), residues: 520
  sheet:  0.54 (0.25), residues: 380
  loop : -1.33 (0.19), residues: 770

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.002   TRP C 255 
 HIS   0.001   0.001   HIS C 231 
 PHE   0.029   0.002   PHE B 115 
 TYR   0.024   0.002   TYR D 239 
 ARG   0.008   0.001   ARG A 287 

*********************** 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
  222 residues out of total 1505 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 30
    poor density    : 192
  time to evaluate  : 1.537 
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  120 LYS cc_start: 0.8426 (ttpt) cc_final: 0.7729 (ptmm)
REVERT: A  204 ILE cc_start: 0.8695 (pt) cc_final: 0.8370 (mm)
REVERT: B  156 MET cc_start: 0.7244 (ptp) cc_final: 0.6795 (mtm)
REVERT: B  239 TYR cc_start: 0.8221 (m-80) cc_final: 0.7952 (m-80)
REVERT: B  303 MET cc_start: 0.8768 (mmm) cc_final: 0.8419 (mmm)
REVERT: D  100 ASP cc_start: 0.7530 (m-30) cc_final: 0.7227 (t0)
REVERT: D  130 ASP cc_start: 0.6974 (t0) cc_final: 0.6746 (t0)
REVERT: D  348 LEU cc_start: 0.9172 (mt) cc_final: 0.8876 (pp)
REVERT: E  100 ASP cc_start: 0.7580 (m-30) cc_final: 0.6978 (t0)
REVERT: E  297 LYS cc_start: 0.7878 (OUTLIER) cc_final: 0.7396 (mmmm)
REVERT: E  348 LEU cc_start: 0.9180 (mt) cc_final: 0.8975 (pp)
  outliers start: 30
  outliers final: 11
  residues processed: 215
  average time/residue: 0.2981
  time to fit residues: 90.5722
Evaluate side-chains
  158 residues out of total 1505 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 12
    poor density    : 146
  time to evaluate  : 1.478 
-------------------------------------------------------------------------------
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 B residue  297 LYS
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  136 ILE
Chi-restraints excluded: chain E residue  297 LYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 165
   random chunks:
   chunk 83 optimal weight:    5.9990
   chunk 46 optimal weight:    2.9990
   chunk 124 optimal weight:    0.9990
   chunk 102 optimal weight:    0.9990
   chunk 41 optimal weight:    5.9990
   chunk 150 optimal weight:    7.9990
   chunk 162 optimal weight:   40.0000
   chunk 133 optimal weight:    9.9990
   chunk 148 optimal weight:    8.9990
   chunk 51 optimal weight:    0.9980
   chunk 120 optimal weight:   10.0000
   overall best weight:    2.3988

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

Flipped N/Q/H residues before XYZ refinement:
** A 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 217 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** 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 171 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7858
moved from start:          0.3732

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034  13145  Z= 0.249
  Angle     :  0.798  11.974  17975  Z= 0.394
  Chirality :  0.045   0.244   2130
  Planarity :  0.004   0.028   2245
  Dihedral  :  7.261  59.978   2025
  Min Nonbonded Distance : 2.453

Molprobity Statistics.
  All-atom Clashscore : 16.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.28 %
    Favored  : 97.72 %
  Rotamer:
    Outliers :  2.76 %
    Allowed  : 11.71 %
    Favored  : 85.53 %
  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:  0.01 (0.19), residues: 1670
  helix:  1.53 (0.22), residues: 515
  sheet:  0.41 (0.25), residues: 385
  loop : -1.30 (0.19), residues: 770

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.027   0.002   TRP A 255 
 HIS   0.005   0.002   HIS B 217 
 PHE   0.033   0.002   PHE D 353 
 TYR   0.024   0.002   TYR A 238 
 ARG   0.004   0.001   ARG C 229 

*********************** 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
  184 residues out of total 1505 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 34
    poor density    : 150
  time to evaluate  : 1.482 
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: A  303 MET cc_start: 0.8689 (mmm) cc_final: 0.8418 (mmt)
REVERT: B  100 ASP cc_start: 0.7612 (m-30) cc_final: 0.7036 (t0)
REVERT: B  130 ASP cc_start: 0.7521 (t0) cc_final: 0.6993 (t70)
REVERT: B  303 MET cc_start: 0.8750 (mmm) cc_final: 0.8086 (mmt)
REVERT: C   72 MET cc_start: 0.7365 (tpp) cc_final: 0.6889 (tpp)
REVERT: D  100 ASP cc_start: 0.7633 (m-30) cc_final: 0.7237 (t0)
REVERT: E  100 ASP cc_start: 0.7722 (m-30) cc_final: 0.7107 (t0)
REVERT: E  120 LYS cc_start: 0.7960 (ptmt) cc_final: 0.7620 (ptmm)
  outliers start: 34
  outliers final: 16
  residues processed: 179
  average time/residue: 0.2478
  time to fit residues: 64.2281
Evaluate side-chains
  140 residues out of total 1505 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 16
    poor density    : 124
  time to evaluate  : 1.437 
-------------------------------------------------------------------------------
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  248 LEU
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 C residue  136 ILE
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  136 ILE
Chi-restraints excluded: chain D residue  168 CYS
Chi-restraints excluded: chain D residue  315 LEU
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 148 optimal weight:    9.9990
   chunk 112 optimal weight:    0.0980
   chunk 77 optimal weight:    7.9990
   chunk 16 optimal weight:    7.9990
   chunk 71 optimal weight:    2.9990
   chunk 100 optimal weight:   10.0000
   chunk 150 optimal weight:    8.9990
   chunk 159 optimal weight:    9.9990
   chunk 78 optimal weight:    3.9990
   chunk 142 optimal weight:    0.9980
   chunk 42 optimal weight:   10.0000
   overall best weight:    3.2186

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

Flipped N/Q/H residues before XYZ refinement:
** A 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**
C 202 GLN
** D  82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 171 GLN
** E  83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7906
moved from start:          0.4249

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.052  13145  Z= 0.287
  Angle     :  0.776   9.753  17975  Z= 0.380
  Chirality :  0.044   0.242   2130
  Planarity :  0.004   0.029   2245
  Dihedral  :  7.066  59.816   2025
  Min Nonbonded Distance : 2.482

Molprobity Statistics.
  All-atom Clashscore : 16.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.16 %
    Favored  : 97.84 %
  Rotamer:
    Outliers :  2.68 %
    Allowed  : 12.76 %
    Favored  : 84.55 %
  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:  0.20 (0.20), residues: 1670
  helix:  1.78 (0.23), residues: 525
  sheet:  0.28 (0.26), residues: 365
  loop : -1.11 (0.20), residues: 780

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.002   TRP D 255 
 HIS   0.004   0.001   HIS E 231 
 PHE   0.024   0.002   PHE D 353 
 TYR   0.025   0.002   TYR C 144 
 ARG   0.006   0.001   ARG E  43 

*********************** 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
  164 residues out of total 1505 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 33
    poor density    : 131
  time to evaluate  : 1.542 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  120 LYS cc_start: 0.7591 (ptpp) cc_final: 0.7343 (ptmm)
REVERT: B  303 MET cc_start: 0.8762 (mmm) cc_final: 0.8147 (mmt)
REVERT: C  255 TRP cc_start: 0.7567 (m-10) cc_final: 0.6741 (m-10)
REVERT: D  179 MET cc_start: 0.8465 (mmm) cc_final: 0.8168 (mmm)
REVERT: E   72 MET cc_start: 0.7306 (tpp) cc_final: 0.6451 (tpp)
REVERT: E  279 MET cc_start: 0.8858 (mmm) cc_final: 0.8650 (mmm)
  outliers start: 33
  outliers final: 24
  residues processed: 162
  average time/residue: 0.2504
  time to fit residues: 58.8793
Evaluate side-chains
  141 residues out of total 1505 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 24
    poor density    : 117
  time to evaluate  : 1.518 
-------------------------------------------------------------------------------
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  256 VAL
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  225 CYS
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  181 ASP
Chi-restraints excluded: chain C residue  256 VAL
Chi-restraints excluded: chain C residue  297 LYS
Chi-restraints excluded: chain C residue  315 LEU
Chi-restraints excluded: chain D residue  113 ASP
Chi-restraints excluded: chain D residue  136 ILE
Chi-restraints excluded: chain D residue  181 ASP
Chi-restraints excluded: chain D residue  255 TRP
Chi-restraints excluded: chain E residue  106 LEU
Chi-restraints excluded: chain E residue  136 ILE
Chi-restraints excluded: chain E residue  181 ASP
Chi-restraints excluded: chain E residue  255 TRP
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 165
   random chunks:
   chunk 132 optimal weight:    0.9990
   chunk 90 optimal weight:    6.9990
   chunk 2 optimal weight:    4.9990
   chunk 118 optimal weight:    7.9990
   chunk 65 optimal weight:    3.9990
   chunk 136 optimal weight:   10.0000
   chunk 110 optimal weight:    9.9990
   chunk 0 optimal weight:    9.9990
   chunk 81 optimal weight:    9.9990
   chunk 143 optimal weight:    0.7980
   chunk 40 optimal weight:    8.9990
   overall best weight:    3.5588

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

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7940
moved from start:          0.4728

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043  13145  Z= 0.290
  Angle     :  0.767  13.420  17975  Z= 0.374
  Chirality :  0.044   0.233   2130
  Planarity :  0.004   0.029   2245
  Dihedral  :  6.939  58.925   2025
  Min Nonbonded Distance : 2.518

Molprobity Statistics.
  All-atom Clashscore : 16.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.63 %
    Favored  : 97.37 %
  Rotamer:
    Outliers :  2.85 %
    Allowed  : 13.50 %
    Favored  : 83.66 %
  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:  1.99 (0.22), residues: 530
  sheet:  0.09 (0.26), residues: 375
  loop : -0.96 (0.21), residues: 765

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP D 255 
 HIS   0.005   0.002   HIS B 231 
 PHE   0.021   0.002   PHE D 353 
 TYR   0.020   0.002   TYR E 238 
 ARG   0.007   0.001   ARG D  43 

*********************** 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
  166 residues out of total 1505 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 35
    poor density    : 131
  time to evaluate  : 1.583 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  303 MET cc_start: 0.8746 (mmm) cc_final: 0.8100 (mmt)
REVERT: D  292 LYS cc_start: 0.8750 (OUTLIER) cc_final: 0.8289 (ttmm)
REVERT: E  100 ASP cc_start: 0.7830 (m-30) cc_final: 0.7104 (t0)
  outliers start: 35
  outliers final: 28
  residues processed: 165
  average time/residue: 0.2457
  time to fit residues: 59.2303
Evaluate side-chains
  140 residues out of total 1505 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 29
    poor density    : 111
  time to evaluate  : 1.386 
-------------------------------------------------------------------------------
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  248 LEU
Chi-restraints excluded: chain A residue  255 TRP
Chi-restraints excluded: chain A residue  256 VAL
Chi-restraints excluded: chain A residue  315 LEU
Chi-restraints excluded: chain A residue  353 PHE
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  216 LYS
Chi-restraints excluded: chain B residue  225 CYS
Chi-restraints excluded: chain B residue  262 MET
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  181 ASP
Chi-restraints excluded: chain C residue  256 VAL
Chi-restraints excluded: chain C residue  315 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  292 LYS
Chi-restraints excluded: chain D residue  315 LEU
Chi-restraints excluded: chain E residue  106 LEU
Chi-restraints excluded: chain E residue  136 ILE
Chi-restraints excluded: chain E residue  255 TRP
Chi-restraints excluded: chain E residue  256 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 165
   random chunks:
   chunk 53 optimal weight:    0.9990
   chunk 143 optimal weight:    7.9990
   chunk 31 optimal weight:    7.9990
   chunk 93 optimal weight:    9.9990
   chunk 39 optimal weight:    8.9990
   chunk 159 optimal weight:    1.9990
   chunk 132 optimal weight:    5.9990
   chunk 73 optimal weight:    0.5980
   chunk 13 optimal weight:   10.0000
   chunk 52 optimal weight:    2.9990
   chunk 83 optimal weight:    7.9990
   overall best weight:    2.5188

-------------------------------------------------------------------------------
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 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 217 HIS
** 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: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7927
moved from start:          0.4985

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046  13145  Z= 0.238
  Angle     :  0.763  10.354  17975  Z= 0.365
  Chirality :  0.044   0.238   2130
  Planarity :  0.003   0.034   2245
  Dihedral  :  6.756  59.161   2025
  Min Nonbonded Distance : 2.554

Molprobity Statistics.
  All-atom Clashscore : 15.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.57 %
    Favored  : 97.43 %
  Rotamer:
    Outliers :  2.76 %
    Allowed  : 15.20 %
    Favored  : 82.03 %
  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:  0.38 (0.20), residues: 1670
  helix:  2.13 (0.22), residues: 530
  sheet: -0.01 (0.26), residues: 375
  loop : -0.96 (0.21), residues: 765

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.001   TRP D 255 
 HIS   0.004   0.001   HIS B 231 
 PHE   0.018   0.001   PHE D 353 
 TYR   0.036   0.002   TYR A 238 
 ARG   0.003   0.001   ARG B  75 

*********************** 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
  160 residues out of total 1505 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 34
    poor density    : 126
  time to evaluate  : 1.318 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   72 MET cc_start: 0.7121 (tpp) cc_final: 0.6147 (tpp)
REVERT: A  120 LYS cc_start: 0.7492 (OUTLIER) cc_final: 0.7125 (ptpp)
REVERT: A  292 LYS cc_start: 0.8596 (ttmm) cc_final: 0.8157 (mmtm)
REVERT: A  303 MET cc_start: 0.8823 (mmm) cc_final: 0.8220 (mmt)
REVERT: D  302 TRP cc_start: 0.7930 (t60) cc_final: 0.7593 (t60)
REVERT: D  303 MET cc_start: 0.8627 (mmp) cc_final: 0.8185 (mmm)
REVERT: E  100 ASP cc_start: 0.7863 (m-30) cc_final: 0.7180 (t0)
REVERT: E  303 MET cc_start: 0.8758 (mmm) cc_final: 0.8515 (mmt)
  outliers start: 34
  outliers final: 22
  residues processed: 156
  average time/residue: 0.2507
  time to fit residues: 56.7153
Evaluate side-chains
  139 residues out of total 1505 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 23
    poor density    : 116
  time to evaluate  : 1.441 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   73 ASP
Chi-restraints excluded: chain A residue  120 LYS
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 A residue  353 PHE
Chi-restraints excluded: chain B residue  172 LEU
Chi-restraints excluded: chain B residue  181 ASP
Chi-restraints excluded: chain B residue  216 LYS
Chi-restraints excluded: chain B residue  225 CYS
Chi-restraints excluded: chain B residue  262 MET
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 D residue  113 ASP
Chi-restraints excluded: chain D residue  255 TRP
Chi-restraints excluded: chain D residue  315 LEU
Chi-restraints excluded: chain E residue  106 LEU
Chi-restraints excluded: chain E residue  136 ILE
Chi-restraints excluded: chain E residue  181 ASP
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 153 optimal weight:    0.9990
   chunk 17 optimal weight:    9.9990
   chunk 90 optimal weight:   30.0000
   chunk 116 optimal weight:    0.0010
   chunk 134 optimal weight:    0.9990
   chunk 89 optimal weight:   10.0000
   chunk 159 optimal weight:    1.9990
   chunk 99 optimal weight:    3.9990
   chunk 96 optimal weight:   20.0000
   chunk 73 optimal weight:    4.9990
   chunk 98 optimal weight:    2.9990
   overall best weight:    1.3994

-------------------------------------------------------------------------------
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 171 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  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

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7897
moved from start:          0.5172

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  13145  Z= 0.189
  Angle     :  0.759  11.062  17975  Z= 0.362
  Chirality :  0.044   0.247   2130
  Planarity :  0.003   0.050   2245
  Dihedral  :  6.591  59.700   2025
  Min Nonbonded Distance : 2.503

Molprobity Statistics.
  All-atom Clashscore : 13.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.57 %
    Favored  : 97.43 %
  Rotamer:
    Outliers :  2.20 %
    Allowed  : 15.77 %
    Favored  : 82.03 %
  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:  2.17 (0.22), residues: 530
  sheet: -0.08 (0.25), residues: 400
  loop : -1.14 (0.21), residues: 740

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.001   TRP D 255 
 HIS   0.004   0.001   HIS B 231 
 PHE   0.015   0.001   PHE D 353 
 TYR   0.026   0.002   TYR A 238 
 ARG   0.003   0.001   ARG D  43 

*********************** 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
  162 residues out of total 1505 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 27
    poor density    : 135
  time to evaluate  : 1.434 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  130 ASP cc_start: 0.7230 (t0) cc_final: 0.6618 (t0)
REVERT: B  179 MET cc_start: 0.8584 (mmm) cc_final: 0.8375 (mmm)
REVERT: B  279 MET cc_start: 0.8847 (mmm) cc_final: 0.8570 (mmt)
REVERT: C  255 TRP cc_start: 0.7855 (m-10) cc_final: 0.7275 (m-10)
REVERT: D  202 GLN cc_start: 0.7610 (mp10) cc_final: 0.7392 (pm20)
REVERT: D  302 TRP cc_start: 0.7944 (t60) cc_final: 0.7688 (t60)
REVERT: D  303 MET cc_start: 0.8620 (mmp) cc_final: 0.8254 (mmm)
REVERT: E  100 ASP cc_start: 0.7872 (m-30) cc_final: 0.7183 (t0)
REVERT: E  303 MET cc_start: 0.8774 (mmm) cc_final: 0.8459 (mmt)
  outliers start: 27
  outliers final: 20
  residues processed: 160
  average time/residue: 0.2446
  time to fit residues: 56.7191
Evaluate side-chains
  137 residues out of total 1505 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 20
    poor density    : 117
  time to evaluate  : 1.438 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   57 CYS
Chi-restraints excluded: chain A residue  120 LYS
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  314 LEU
Chi-restraints excluded: chain A residue  315 LEU
Chi-restraints excluded: chain A residue  353 PHE
Chi-restraints excluded: chain B residue  172 LEU
Chi-restraints excluded: chain B residue  216 LYS
Chi-restraints excluded: chain B residue  225 CYS
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 D residue  113 ASP
Chi-restraints excluded: chain D residue  136 ILE
Chi-restraints excluded: chain D residue  255 TRP
Chi-restraints excluded: chain E residue  106 LEU
Chi-restraints excluded: chain E residue  255 TRP
Chi-restraints excluded: chain E residue  256 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 165
   random chunks:
   chunk 63 optimal weight:    7.9990
   chunk 94 optimal weight:    5.9990
   chunk 47 optimal weight:    8.9990
   chunk 31 optimal weight:    9.9990
   chunk 30 optimal weight:    8.9990
   chunk 101 optimal weight:    1.9990
   chunk 108 optimal weight:    9.9990
   chunk 78 optimal weight:   10.0000
   chunk 14 optimal weight:    6.9990
   chunk 125 optimal weight:    0.8980
   chunk 144 optimal weight:    3.9990
   overall best weight:    3.9788

-------------------------------------------------------------------------------
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 171 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 ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7972
moved from start:          0.5476

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.040  13145  Z= 0.310
  Angle     :  0.806  11.317  17975  Z= 0.387
  Chirality :  0.044   0.233   2130
  Planarity :  0.004   0.055   2245
  Dihedral  :  6.801  58.043   2025
  Min Nonbonded Distance : 2.501

Molprobity Statistics.
  All-atom Clashscore : 16.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.29 %
    Favored  : 96.71 %
  Rotamer:
    Outliers :  2.68 %
    Allowed  : 16.42 %
    Favored  : 80.89 %
  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 (0.20), residues: 1670
  helix:  2.28 (0.22), residues: 535
  sheet: -0.15 (0.26), residues: 375
  loop : -0.96 (0.21), residues: 760

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.001   TRP D 255 
 HIS   0.007   0.002   HIS B 231 
 PHE   0.021   0.002   PHE E 115 
 TYR   0.027   0.002   TYR A 238 
 ARG   0.003   0.001   ARG B 212 

*********************** 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
  155 residues out of total 1505 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 33
    poor density    : 122
  time to evaluate  : 1.534 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  120 LYS cc_start: 0.7398 (OUTLIER) cc_final: 0.6825 (ptpp)
REVERT: A  130 ASP cc_start: 0.7207 (t0) cc_final: 0.6755 (t0)
REVERT: B  156 MET cc_start: 0.6891 (mtm) cc_final: 0.6639 (ptp)
REVERT: B  303 MET cc_start: 0.8758 (mmm) cc_final: 0.8087 (mmt)
REVERT: C  255 TRP cc_start: 0.7817 (m-10) cc_final: 0.7297 (m-10)
REVERT: C  303 MET cc_start: 0.8468 (mmm) cc_final: 0.7875 (mmm)
REVERT: D  204 ILE cc_start: 0.8603 (pt) cc_final: 0.8365 (mm)
REVERT: D  302 TRP cc_start: 0.7949 (t60) cc_final: 0.7545 (t60)
REVERT: D  303 MET cc_start: 0.8692 (mmp) cc_final: 0.8087 (mmt)
REVERT: E  100 ASP cc_start: 0.7890 (m-30) cc_final: 0.7187 (t0)
REVERT: E  303 MET cc_start: 0.8761 (mmm) cc_final: 0.8488 (mmt)
  outliers start: 33
  outliers final: 25
  residues processed: 154
  average time/residue: 0.3248
  time to fit residues: 75.0196
Evaluate side-chains
  138 residues out of total 1505 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 26
    poor density    : 112
  time to evaluate  : 2.158 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  120 LYS
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  314 LEU
Chi-restraints excluded: chain A residue  315 LEU
Chi-restraints excluded: chain A residue  353 PHE
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  216 LYS
Chi-restraints excluded: chain B residue  225 CYS
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  181 ASP
Chi-restraints excluded: chain C residue  256 VAL
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  106 LEU
Chi-restraints excluded: chain E residue  136 ILE
Chi-restraints excluded: chain E residue  181 ASP
Chi-restraints excluded: chain E residue  255 TRP
Chi-restraints excluded: chain E residue  256 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 165
   random chunks:
   chunk 152 optimal weight:    0.9980
   chunk 139 optimal weight:    0.0770
   chunk 148 optimal weight:    6.9990
   chunk 89 optimal weight:    8.9990
   chunk 64 optimal weight:   20.0000
   chunk 116 optimal weight:    2.9990
   chunk 45 optimal weight:    2.9990
   chunk 133 optimal weight:    5.9990
   chunk 140 optimal weight:    4.9990
   chunk 147 optimal weight:    8.9990
   chunk 97 optimal weight:    9.9990
   overall best weight:    2.4144

-------------------------------------------------------------------------------
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 171 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**
E 231 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7940
moved from start:          0.5611

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040  13145  Z= 0.232
  Angle     :  0.805  15.486  17975  Z= 0.380
  Chirality :  0.044   0.239   2130
  Planarity :  0.004   0.045   2245
  Dihedral  :  6.640  59.324   2025
  Min Nonbonded Distance : 2.542

Molprobity Statistics.
  All-atom Clashscore : 14.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.69 %
    Favored  : 97.31 %
  Rotamer:
    Outliers :  1.95 %
    Allowed  : 17.24 %
    Favored  : 80.81 %
  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:  0.40 (0.21), residues: 1670
  helix:  2.34 (0.22), residues: 535
  sheet: -0.19 (0.25), residues: 400
  loop : -1.05 (0.22), residues: 735

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.001   TRP D 255 
 HIS   0.004   0.001   HIS B 231 
 PHE   0.015   0.001   PHE D 353 
 TYR   0.026   0.002   TYR B 238 
 ARG   0.002   0.000   ARG B  75 

*********************** 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
  145 residues out of total 1505 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 24
    poor density    : 121
  time to evaluate  : 1.483 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  303 MET cc_start: 0.8787 (mmm) cc_final: 0.8241 (mmt)
REVERT: B  303 MET cc_start: 0.8757 (mmm) cc_final: 0.7983 (mmt)
REVERT: C  255 TRP cc_start: 0.7791 (m-10) cc_final: 0.7267 (m-10)
REVERT: C  303 MET cc_start: 0.8464 (mmm) cc_final: 0.7835 (mmm)
REVERT: D  204 ILE cc_start: 0.8555 (pt) cc_final: 0.8332 (mm)
REVERT: E  100 ASP cc_start: 0.7800 (m-30) cc_final: 0.7149 (t0)
REVERT: E  303 MET cc_start: 0.8708 (mmm) cc_final: 0.8432 (mmt)
  outliers start: 24
  outliers final: 20
  residues processed: 143
  average time/residue: 0.2521
  time to fit residues: 52.4940
Evaluate side-chains
  135 residues out of total 1505 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 20
    poor density    : 115
  time to evaluate  : 1.542 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  120 LYS
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  353 PHE
Chi-restraints excluded: chain B residue  172 LEU
Chi-restraints excluded: chain B residue  216 LYS
Chi-restraints excluded: chain B residue  225 CYS
Chi-restraints excluded: chain B residue  314 LEU
Chi-restraints excluded: chain C residue  256 VAL
Chi-restraints excluded: chain C residue  262 MET
Chi-restraints excluded: chain D residue  132 LYS
Chi-restraints excluded: chain D residue  255 TRP
Chi-restraints excluded: chain D residue  315 LEU
Chi-restraints excluded: chain E residue  106 LEU
Chi-restraints excluded: chain E residue  136 ILE
Chi-restraints excluded: chain E residue  181 ASP
Chi-restraints excluded: chain E residue  255 TRP
Chi-restraints excluded: chain E residue  256 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 165
   random chunks:
   chunk 156 optimal weight:    0.0670
   chunk 95 optimal weight:    0.5980
   chunk 74 optimal weight:    3.9990
   chunk 108 optimal weight:    0.0670
   chunk 164 optimal weight:    8.9990
   chunk 151 optimal weight:    0.0970
   chunk 130 optimal weight:    5.9990
   chunk 13 optimal weight:    0.9990
   chunk 101 optimal weight:    0.1980
   chunk 80 optimal weight:    5.9990
   chunk 103 optimal weight:    4.9990
   overall best weight:    0.2054

-------------------------------------------------------------------------------
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 171 GLN
** B 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 202 GLN
** D  83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7857
moved from start:          0.5794

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  13145  Z= 0.188
  Angle     :  0.819  15.924  17975  Z= 0.384
  Chirality :  0.045   0.252   2130
  Planarity :  0.003   0.047   2245
  Dihedral  :  6.339  59.898   2025
  Min Nonbonded Distance : 2.543

Molprobity Statistics.
  All-atom Clashscore : 11.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.81 %
    Favored  : 97.19 %
  Rotamer:
    Outliers :  1.54 %
    Allowed  : 17.72 %
    Favored  : 80.73 %
  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:  0.40 (0.20), residues: 1670
  helix:  2.25 (0.22), residues: 535
  sheet:  0.05 (0.25), residues: 395
  loop : -1.12 (0.21), residues: 740

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.001   TRP D 255 
 HIS   0.003   0.001   HIS A 125 
 PHE   0.013   0.001   PHE D 353 
 TYR   0.020   0.001   TYR C 144 
 ARG   0.003   0.001   ARG E 287 

********************** 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
  166 residues out of total 1505 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 19
    poor density    : 147
  time to evaluate  : 1.468 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  303 MET cc_start: 0.8756 (mmm) cc_final: 0.8260 (mmt)
REVERT: A  307 LEU cc_start: 0.9451 (mt) cc_final: 0.9069 (pp)
REVERT: B  303 MET cc_start: 0.8728 (mmm) cc_final: 0.7992 (mmt)
REVERT: C  255 TRP cc_start: 0.7746 (m-10) cc_final: 0.7189 (m-10)
REVERT: C  303 MET cc_start: 0.8375 (mmm) cc_final: 0.7799 (mmm)
REVERT: D  204 ILE cc_start: 0.8465 (pt) cc_final: 0.8257 (mm)
REVERT: D  303 MET cc_start: 0.8569 (mmp) cc_final: 0.8356 (mmm)
REVERT: D  348 LEU cc_start: 0.9112 (mt) cc_final: 0.8818 (pp)
REVERT: E  100 ASP cc_start: 0.7785 (m-30) cc_final: 0.7152 (t0)
REVERT: E  303 MET cc_start: 0.8716 (mmm) cc_final: 0.8391 (mmt)
REVERT: E  348 LEU cc_start: 0.9164 (mt) cc_final: 0.8916 (pp)
  outliers start: 19
  outliers final: 13
  residues processed: 163
  average time/residue: 0.2612
  time to fit residues: 60.9081
Evaluate side-chains
  135 residues out of total 1505 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 13
    poor density    : 122
  time to evaluate  : 1.459 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  120 LYS
Chi-restraints excluded: chain A residue  136 ILE
Chi-restraints excluded: chain A residue  248 LEU
Chi-restraints excluded: chain A residue  255 TRP
Chi-restraints excluded: chain A residue  353 PHE
Chi-restraints excluded: chain B residue  225 CYS
Chi-restraints excluded: chain C residue  256 VAL
Chi-restraints excluded: chain D residue  132 LYS
Chi-restraints excluded: chain D residue  255 TRP
Chi-restraints excluded: chain D residue  315 LEU
Chi-restraints excluded: chain E residue  136 ILE
Chi-restraints excluded: chain E residue  255 TRP
Chi-restraints excluded: chain E residue  256 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 165
   random chunks:
   chunk 139 optimal weight:    0.7980
   chunk 40 optimal weight:    0.6980
   chunk 120 optimal weight:    0.5980
   chunk 19 optimal weight:    8.9990
   chunk 36 optimal weight:    1.9990
   chunk 131 optimal weight:    4.9990
   chunk 54 optimal weight:    3.9990
   chunk 134 optimal weight:    3.9990
   chunk 16 optimal weight:    0.8980
   chunk 24 optimal weight:    1.9990
   chunk 115 optimal weight:    9.9990
   overall best weight:    0.9982

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

Flipped N/Q/H residues before XYZ refinement:
** A  83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 282 GLN
** B 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 282 GLN
** 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: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3005 r_free = 0.3005 target = 0.047033 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2688 r_free = 0.2688 target = 0.035935 restraints weight = 89381.044|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.2718 r_free = 0.2718 target = 0.036857 restraints weight = 52206.784|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.2737 r_free = 0.2737 target = 0.037482 restraints weight = 36376.534|
|-----------------------------------------------------------------------------|
r_work (final): 0.2683
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8355
moved from start:          0.5914

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043  13145  Z= 0.195
  Angle     :  0.827  14.901  17975  Z= 0.390
  Chirality :  0.045   0.253   2130
  Planarity :  0.004   0.041   2245
  Dihedral  :  6.314  59.990   2025
  Min Nonbonded Distance : 2.548

Molprobity Statistics.
  All-atom Clashscore : 12.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.63 %
    Favored  : 97.37 %
  Rotamer:
    Outliers :  1.14 %
    Allowed  : 19.11 %
    Favored  : 79.76 %
  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: 535
  sheet:  0.10 (0.26), residues: 395
  loop : -1.14 (0.21), residues: 740

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.001   TRP D 255 
 HIS   0.003   0.001   HIS B 231 
 PHE   0.014   0.001   PHE A  64 
 TYR   0.028   0.001   TYR D 238 
 ARG   0.006   0.000   ARG C  75 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2298.21 seconds
wall clock time: 42 minutes 17.09 seconds (2537.09 seconds total)