Starting phenix.real_space_refine
on Wed Jan 22 05:13:23 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9bz8_45056/01_2025/9bz8_45056.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9bz8_45056/01_2025/9bz8_45056.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.0
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9bz8_45056/01_2025/9bz8_45056.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9bz8_45056/01_2025/9bz8_45056.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9bz8_45056/01_2025/9bz8_45056.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9bz8_45056/01_2025/9bz8_45056.cif"
  }
  resolution = 3.0
  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=   0.003
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      77      5.16       5
     C   12215      2.51       5
     N    2814      2.21       5
     O    3171      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 42 residue(s): 0.06s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib"
  Total number of atoms: 18277
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2611
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 322, 2611
          Classifications: {'peptide': 322}
          Link IDs: {'PTRANS': 14, 'TRANS': 307}
          Chain breaks: 3
  Restraints were copied for chains:
    C, B, E, D, G, F
  Time building chain proxies: 6.27, per 1000 atoms: 0.34
  Number of scatterers: 18277
  At special positions: 0
  Unit cell: (113.42, 113.42, 121.98, 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      77     16.00
     O    3171      8.00
     N    2814      7.00
     C   12215      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  66 " - pdb=" SG  CYS A 267 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A  84 " - pdb=" SG  CYS A 248 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 4.40
  Conformation dependent library (CDL) restraints added in 2.5 seconds
  

  4396 Ramachandran restraints generated.
    2198 Oldfield, 0 Emsley, 2198 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  4382

  Finding SS restraints...
    Secondary structure from input PDB file:
      98 helices and 7 sheets defined
      72.4% alpha, 2.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.68
  Creating SS restraints...
    Processing helix  chain 'A' and resid 2 through 11
    Processing helix  chain 'A' and resid 32 through 54
      Proline residue:  A  46  - end of helix
      removed outlier: 3.690A  pdb=" N   PHE A  54 " --> pdb=" O   ILE A  50 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 73 through 91
      removed outlier: 4.443A  pdb=" N   GLN A  89 " --> pdb=" O   TRP A  85 " (cutoff:3.500A)
      removed outlier: 4.261A  pdb=" N   GLN A  90 " --> pdb=" O   ALA A  86 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 102 through 131
      Proline residue:  A 110  - end of helix
      Proline residue:  A 123  - end of helix
    Processing helix  chain 'A' and resid 131 through 158
    Processing helix  chain 'A' and resid 197 through 207
      removed outlier: 3.795A  pdb=" N   ASN A 207 " --> pdb=" O   LYS A 203 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 209 through 240
    Processing helix  chain 'A' and resid 252 through 256
      removed outlier: 4.280A  pdb=" N   LEU A 255 " --> pdb=" O   THR A 252 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 271 through 298
      Proline residue:  A 291  - end of helix
      removed outlier: 3.687A  pdb=" N   ILE A 294 " --> pdb=" O   MET A 290 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 307 through 312
      removed outlier: 3.919A  pdb=" N   TYR A 311 " --> pdb=" O   VAL A 307 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 328 through 340
    Processing helix  chain 'A' and resid 341 through 344
    Processing helix  chain 'A' and resid 345 through 360
      removed outlier: 3.774A  pdb=" N   THR A 359 " --> pdb=" O   ASN A 355 " (cutoff:3.500A)
      removed outlier: 4.283A  pdb=" N   GLY A 360 " --> pdb=" O   ILE A 356 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 364 through 372
      removed outlier: 4.201A  pdb=" N   TYR A 368 " --> pdb=" O   ASP A 364 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 3 through 11
    Processing helix  chain 'B' and resid 32 through 54
      Proline residue:  B  46  - end of helix
      removed outlier: 3.691A  pdb=" N   PHE B  54 " --> pdb=" O   ILE B  50 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 73 through 91
      removed outlier: 4.442A  pdb=" N   GLN B  89 " --> pdb=" O   TRP B  85 " (cutoff:3.500A)
      removed outlier: 4.261A  pdb=" N   GLN B  90 " --> pdb=" O   ALA B  86 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 102 through 131
      Proline residue:  B 110  - end of helix
      Proline residue:  B 123  - end of helix
    Processing helix  chain 'B' and resid 131 through 158
    Processing helix  chain 'B' and resid 197 through 207
      removed outlier: 3.794A  pdb=" N   ASN B 207 " --> pdb=" O   LYS B 203 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 209 through 240
    Processing helix  chain 'B' and resid 252 through 256
      removed outlier: 4.280A  pdb=" N   LEU B 255 " --> pdb=" O   THR B 252 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 271 through 298
      Proline residue:  B 291  - end of helix
      removed outlier: 3.686A  pdb=" N   ILE B 294 " --> pdb=" O   MET B 290 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 307 through 312
      removed outlier: 3.920A  pdb=" N   TYR B 311 " --> pdb=" O   VAL B 307 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 328 through 340
    Processing helix  chain 'B' and resid 341 through 344
    Processing helix  chain 'B' and resid 345 through 360
      removed outlier: 3.772A  pdb=" N   THR B 359 " --> pdb=" O   ASN B 355 " (cutoff:3.500A)
      removed outlier: 4.283A  pdb=" N   GLY B 360 " --> pdb=" O   ILE B 356 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 364 through 372
      removed outlier: 4.201A  pdb=" N   TYR B 368 " --> pdb=" O   ASP B 364 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 3 through 11
    Processing helix  chain 'C' and resid 32 through 54
      Proline residue:  C  46  - end of helix
      removed outlier: 3.690A  pdb=" N   PHE C  54 " --> pdb=" O   ILE C  50 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 73 through 91
      removed outlier: 4.443A  pdb=" N   GLN C  89 " --> pdb=" O   TRP C  85 " (cutoff:3.500A)
      removed outlier: 4.262A  pdb=" N   GLN C  90 " --> pdb=" O   ALA C  86 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 102 through 131
      Proline residue:  C 110  - end of helix
      Proline residue:  C 123  - end of helix
    Processing helix  chain 'C' and resid 131 through 158
    Processing helix  chain 'C' and resid 197 through 207
      removed outlier: 3.794A  pdb=" N   ASN C 207 " --> pdb=" O   LYS C 203 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 209 through 240
    Processing helix  chain 'C' and resid 252 through 256
      removed outlier: 4.279A  pdb=" N   LEU C 255 " --> pdb=" O   THR C 252 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 271 through 298
      Proline residue:  C 291  - end of helix
      removed outlier: 3.686A  pdb=" N   ILE C 294 " --> pdb=" O   MET C 290 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 307 through 312
      removed outlier: 3.920A  pdb=" N   TYR C 311 " --> pdb=" O   VAL C 307 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 328 through 340
    Processing helix  chain 'C' and resid 341 through 344
    Processing helix  chain 'C' and resid 345 through 360
      removed outlier: 3.774A  pdb=" N   THR C 359 " --> pdb=" O   ASN C 355 " (cutoff:3.500A)
      removed outlier: 4.283A  pdb=" N   GLY C 360 " --> pdb=" O   ILE C 356 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 364 through 372
      removed outlier: 4.200A  pdb=" N   TYR C 368 " --> pdb=" O   ASP C 364 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 3 through 11
    Processing helix  chain 'D' and resid 32 through 54
      Proline residue:  D  46  - end of helix
      removed outlier: 3.690A  pdb=" N   PHE D  54 " --> pdb=" O   ILE D  50 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 73 through 91
      removed outlier: 4.442A  pdb=" N   GLN D  89 " --> pdb=" O   TRP D  85 " (cutoff:3.500A)
      removed outlier: 4.262A  pdb=" N   GLN D  90 " --> pdb=" O   ALA D  86 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 102 through 131
      Proline residue:  D 110  - end of helix
      Proline residue:  D 123  - end of helix
    Processing helix  chain 'D' and resid 131 through 158
    Processing helix  chain 'D' and resid 197 through 207
      removed outlier: 3.794A  pdb=" N   ASN D 207 " --> pdb=" O   LYS D 203 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 209 through 240
    Processing helix  chain 'D' and resid 252 through 256
      removed outlier: 4.280A  pdb=" N   LEU D 255 " --> pdb=" O   THR D 252 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 271 through 298
      Proline residue:  D 291  - end of helix
      removed outlier: 3.686A  pdb=" N   ILE D 294 " --> pdb=" O   MET D 290 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 307 through 312
      removed outlier: 3.920A  pdb=" N   TYR D 311 " --> pdb=" O   VAL D 307 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 328 through 340
    Processing helix  chain 'D' and resid 341 through 344
    Processing helix  chain 'D' and resid 345 through 360
      removed outlier: 3.773A  pdb=" N   THR D 359 " --> pdb=" O   ASN D 355 " (cutoff:3.500A)
      removed outlier: 4.283A  pdb=" N   GLY D 360 " --> pdb=" O   ILE D 356 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 364 through 372
      removed outlier: 4.201A  pdb=" N   TYR D 368 " --> pdb=" O   ASP D 364 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 3 through 11
    Processing helix  chain 'E' and resid 32 through 54
      Proline residue:  E  46  - end of helix
      removed outlier: 3.690A  pdb=" N   PHE E  54 " --> pdb=" O   ILE E  50 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 73 through 91
      removed outlier: 4.442A  pdb=" N   GLN E  89 " --> pdb=" O   TRP E  85 " (cutoff:3.500A)
      removed outlier: 4.262A  pdb=" N   GLN E  90 " --> pdb=" O   ALA E  86 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 102 through 131
      Proline residue:  E 110  - end of helix
      Proline residue:  E 123  - end of helix
    Processing helix  chain 'E' and resid 131 through 158
    Processing helix  chain 'E' and resid 197 through 207
      removed outlier: 3.795A  pdb=" N   ASN E 207 " --> pdb=" O   LYS E 203 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 209 through 240
    Processing helix  chain 'E' and resid 252 through 256
      removed outlier: 4.280A  pdb=" N   LEU E 255 " --> pdb=" O   THR E 252 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 271 through 298
      Proline residue:  E 291  - end of helix
      removed outlier: 3.687A  pdb=" N   ILE E 294 " --> pdb=" O   MET E 290 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 307 through 312
      removed outlier: 3.920A  pdb=" N   TYR E 311 " --> pdb=" O   VAL E 307 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 328 through 340
    Processing helix  chain 'E' and resid 341 through 344
    Processing helix  chain 'E' and resid 345 through 360
      removed outlier: 3.773A  pdb=" N   THR E 359 " --> pdb=" O   ASN E 355 " (cutoff:3.500A)
      removed outlier: 4.284A  pdb=" N   GLY E 360 " --> pdb=" O   ILE E 356 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 364 through 372
      removed outlier: 4.200A  pdb=" N   TYR E 368 " --> pdb=" O   ASP E 364 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 3 through 11
    Processing helix  chain 'F' and resid 32 through 54
      Proline residue:  F  46  - end of helix
      removed outlier: 3.690A  pdb=" N   PHE F  54 " --> pdb=" O   ILE F  50 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 73 through 91
      removed outlier: 4.443A  pdb=" N   GLN F  89 " --> pdb=" O   TRP F  85 " (cutoff:3.500A)
      removed outlier: 4.261A  pdb=" N   GLN F  90 " --> pdb=" O   ALA F  86 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 102 through 131
      Proline residue:  F 110  - end of helix
      Proline residue:  F 123  - end of helix
    Processing helix  chain 'F' and resid 131 through 158
    Processing helix  chain 'F' and resid 197 through 207
      removed outlier: 3.795A  pdb=" N   ASN F 207 " --> pdb=" O   LYS F 203 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 209 through 240
    Processing helix  chain 'F' and resid 252 through 256
      removed outlier: 4.280A  pdb=" N   LEU F 255 " --> pdb=" O   THR F 252 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 271 through 298
      Proline residue:  F 291  - end of helix
      removed outlier: 3.686A  pdb=" N   ILE F 294 " --> pdb=" O   MET F 290 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 307 through 312
      removed outlier: 3.920A  pdb=" N   TYR F 311 " --> pdb=" O   VAL F 307 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 328 through 340
    Processing helix  chain 'F' and resid 341 through 344
    Processing helix  chain 'F' and resid 345 through 360
      removed outlier: 3.774A  pdb=" N   THR F 359 " --> pdb=" O   ASN F 355 " (cutoff:3.500A)
      removed outlier: 4.284A  pdb=" N   GLY F 360 " --> pdb=" O   ILE F 356 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 364 through 372
      removed outlier: 4.201A  pdb=" N   TYR F 368 " --> pdb=" O   ASP F 364 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 3 through 11
    Processing helix  chain 'G' and resid 32 through 54
      Proline residue:  G  46  - end of helix
      removed outlier: 3.690A  pdb=" N   PHE G  54 " --> pdb=" O   ILE G  50 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 73 through 91
      removed outlier: 4.443A  pdb=" N   GLN G  89 " --> pdb=" O   TRP G  85 " (cutoff:3.500A)
      removed outlier: 4.262A  pdb=" N   GLN G  90 " --> pdb=" O   ALA G  86 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 102 through 131
      Proline residue:  G 110  - end of helix
      Proline residue:  G 123  - end of helix
    Processing helix  chain 'G' and resid 131 through 158
    Processing helix  chain 'G' and resid 197 through 207
      removed outlier: 3.796A  pdb=" N   ASN G 207 " --> pdb=" O   LYS G 203 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 209 through 240
    Processing helix  chain 'G' and resid 252 through 256
      removed outlier: 4.280A  pdb=" N   LEU G 255 " --> pdb=" O   THR G 252 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 271 through 298
      Proline residue:  G 291  - end of helix
      removed outlier: 3.686A  pdb=" N   ILE G 294 " --> pdb=" O   MET G 290 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 307 through 312
      removed outlier: 3.920A  pdb=" N   TYR G 311 " --> pdb=" O   VAL G 307 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 328 through 340
    Processing helix  chain 'G' and resid 341 through 344
    Processing helix  chain 'G' and resid 345 through 360
      removed outlier: 3.773A  pdb=" N   THR G 359 " --> pdb=" O   ASN G 355 " (cutoff:3.500A)
      removed outlier: 4.283A  pdb=" N   GLY G 360 " --> pdb=" O   ILE G 356 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 364 through 372
      removed outlier: 4.201A  pdb=" N   TYR G 368 " --> pdb=" O   ASP G 364 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 64 through 66
    Processing sheet with id=AA2, first strand: chain 'B' and resid 64 through 66
    Processing sheet with id=AA3, first strand: chain 'C' and resid 64 through 66
    Processing sheet with id=AA4, first strand: chain 'D' and resid 64 through 66
    Processing sheet with id=AA5, first strand: chain 'E' and resid 64 through 66
    Processing sheet with id=AA6, first strand: chain 'F' and resid 64 through 66
    Processing sheet with id=AA7, first strand: chain 'G' and resid 64 through 66

    1142 hydrogen bonds defined for protein.
    3363 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 5.47

  Time building geometry restraints manager: 5.21 seconds

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

  Histogram of bond lengths:
        1.23 -     1.35: 5383
        1.35 -     1.47: 4718
        1.47 -     1.58: 8519
        1.58 -     1.70: 0
        1.70 -     1.82: 98
  Bond restraints: 18718
  Sorted by residual:
  bond pdb=" CA  VAL A 101 "
       pdb=" C   VAL A 101 "
    ideal  model  delta    sigma   weight residual
    1.525  1.551 -0.026 2.10e-02 2.27e+03 1.59e+00
  bond pdb=" CA  VAL C 101 "
       pdb=" C   VAL C 101 "
    ideal  model  delta    sigma   weight residual
    1.525  1.551 -0.026 2.10e-02 2.27e+03 1.59e+00
  bond pdb=" CA  VAL G 101 "
       pdb=" C   VAL G 101 "
    ideal  model  delta    sigma   weight residual
    1.525  1.551 -0.026 2.10e-02 2.27e+03 1.56e+00
  bond pdb=" CA  VAL B 101 "
       pdb=" C   VAL B 101 "
    ideal  model  delta    sigma   weight residual
    1.525  1.550 -0.025 2.10e-02 2.27e+03 1.47e+00
  bond pdb=" CA  VAL F 101 "
       pdb=" C   VAL F 101 "
    ideal  model  delta    sigma   weight residual
    1.525  1.550 -0.025 2.10e-02 2.27e+03 1.47e+00
  ... (remaining 18713 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.32: 24846
        1.32 -     2.65: 445
        2.65 -     3.97: 84
        3.97 -     5.29: 56
        5.29 -     6.61: 14
  Bond angle restraints: 25445
  Sorted by residual:
  angle pdb=" CA  VAL B 101 "
        pdb=" C   VAL B 101 "
        pdb=" N   PRO B 102 "
      ideal   model   delta    sigma   weight residual
     116.90  120.02   -3.12 1.50e+00 4.44e-01 4.33e+00
  angle pdb=" CA  VAL F 101 "
        pdb=" C   VAL F 101 "
        pdb=" N   PRO F 102 "
      ideal   model   delta    sigma   weight residual
     116.90  120.01   -3.11 1.50e+00 4.44e-01 4.29e+00
  angle pdb=" CA  VAL C 101 "
        pdb=" C   VAL C 101 "
        pdb=" N   PRO C 102 "
      ideal   model   delta    sigma   weight residual
     116.90  119.97   -3.07 1.50e+00 4.44e-01 4.20e+00
  angle pdb=" CA  VAL D 101 "
        pdb=" C   VAL D 101 "
        pdb=" N   PRO D 102 "
      ideal   model   delta    sigma   weight residual
     116.90  119.97   -3.07 1.50e+00 4.44e-01 4.20e+00
  angle pdb=" CA  VAL E 101 "
        pdb=" C   VAL E 101 "
        pdb=" N   PRO E 102 "
      ideal   model   delta    sigma   weight residual
     116.90  119.97   -3.07 1.50e+00 4.44e-01 4.18e+00
  ... (remaining 25440 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.87: 9591
       16.87 -    33.74: 1082
       33.74 -    50.61: 378
       50.61 -    67.48: 35
       67.48 -    84.36: 22
  Dihedral angle restraints: 11108
    sinusoidal: 4367
      harmonic: 6741
  Sorted by residual:
  dihedral pdb=" CB  CYS A  84 "
           pdb=" SG  CYS A  84 "
           pdb=" SG  CYS A 248 "
           pdb=" CB  CYS A 248 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   15.39   77.61     1      1.00e+01 1.00e-02 7.54e+01
  dihedral pdb=" CA  ASP E 364 "
           pdb=" CB  ASP E 364 "
           pdb=" CG  ASP E 364 "
           pdb=" OD1 ASP E 364 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -89.73   59.73     1      2.00e+01 2.50e-03 1.19e+01
  dihedral pdb=" CA  ASP C 364 "
           pdb=" CB  ASP C 364 "
           pdb=" CG  ASP C 364 "
           pdb=" OD1 ASP C 364 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -89.71   59.71     1      2.00e+01 2.50e-03 1.19e+01
  ... (remaining 11105 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.052: 2539
       0.052 -    0.103: 475
       0.103 -    0.155: 24
       0.155 -    0.206: 0
       0.206 -    0.258: 7
  Chirality restraints: 3045
  Sorted by residual:
  chirality pdb=" CB  ILE A 217 "
            pdb=" CA  ILE A 217 "
            pdb=" CG1 ILE A 217 "
            pdb=" CG2 ILE A 217 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.39    0.26 2.00e-01 2.50e+01 1.66e+00
  chirality pdb=" CB  ILE C 217 "
            pdb=" CA  ILE C 217 "
            pdb=" CG1 ILE C 217 "
            pdb=" CG2 ILE C 217 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.39    0.26 2.00e-01 2.50e+01 1.63e+00
  chirality pdb=" CB  ILE G 217 "
            pdb=" CA  ILE G 217 "
            pdb=" CG1 ILE G 217 "
            pdb=" CG2 ILE G 217 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.39    0.26 2.00e-01 2.50e+01 1.63e+00
  ... (remaining 3042 not shown)

  Planarity restraints: 3052
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG B  29 "   -0.065 9.50e-02 1.11e+02   2.92e-02 6.65e-01
        pdb=" NE  ARG B  29 "    0.006 2.00e-02 2.50e+03
        pdb=" CZ  ARG B  29 "   -0.006 2.00e-02 2.50e+03
        pdb=" NH1 ARG B  29 "    0.003 2.00e-02 2.50e+03
        pdb=" NH2 ARG B  29 "   -0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG D  29 "    0.064 9.50e-02 1.11e+02   2.90e-02 6.64e-01
        pdb=" NE  ARG D  29 "   -0.006 2.00e-02 2.50e+03
        pdb=" CZ  ARG D  29 "    0.006 2.00e-02 2.50e+03
        pdb=" NH1 ARG D  29 "   -0.003 2.00e-02 2.50e+03
        pdb=" NH2 ARG D  29 "    0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG C  29 "    0.064 9.50e-02 1.11e+02   2.88e-02 6.61e-01
        pdb=" NE  ARG C  29 "   -0.006 2.00e-02 2.50e+03
        pdb=" CZ  ARG C  29 "    0.006 2.00e-02 2.50e+03
        pdb=" NH1 ARG C  29 "   -0.003 2.00e-02 2.50e+03
        pdb=" NH2 ARG C  29 "    0.000 2.00e-02 2.50e+03
  ... (remaining 3049 not shown)

  Histogram of nonbonded interaction distances:
        2.03 -     2.60: 121
        2.60 -     3.18: 15335
        3.18 -     3.75: 29563
        3.75 -     4.33: 37205
        4.33 -     4.90: 65176
  Nonbonded interactions: 147400
  Sorted by model distance:
  nonbonded pdb=" SG  CYS B  84 "
            pdb=" SG  CYS B 248 "
     model   vdw
     2.029 3.760
  nonbonded pdb=" SG  CYS E  84 "
            pdb=" SG  CYS E 248 "
     model   vdw
     2.029 3.760
  nonbonded pdb=" SG  CYS D  84 "
            pdb=" SG  CYS D 248 "
     model   vdw
     2.029 3.760
  nonbonded pdb=" SG  CYS C  84 "
            pdb=" SG  CYS C 248 "
     model   vdw
     2.030 3.760
  nonbonded pdb=" SG  CYS G  84 "
            pdb=" SG  CYS G 248 "
     model   vdw
     2.030 3.760
  ... (remaining 147395 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: 0.12
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'C'
  selection = chain 'B'
  selection = chain 'E'
  selection = chain 'D'
  selection = chain 'G'
  selection = chain 'F'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.720
  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:          0.650
  Check model and map are aligned:         0.130
  Set scattering table:                    0.160
  Process input model:                     35.130
  Find NCS groups from input model:        0.310
  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:             0.010
  Load rotamer database and sin/cos tables:12.820
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   49.980
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8322
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026  18718  Z= 0.140
  Angle     :  0.512   6.613  25445  Z= 0.259
  Chirality :  0.038   0.258   3045
  Planarity :  0.003   0.029   3052
  Dihedral  : 16.193  84.356   6720
  Min Nonbonded Distance : 2.029

Molprobity Statistics.
  All-atom Clashscore : 7.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.23 %
    Favored  : 97.77 %
  Rotamer:
    Outliers :  2.73 %
    Allowed  : 22.53 %
    Favored  : 74.74 %
  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:  2.18 (0.18), residues: 2198
  helix:  2.54 (0.13), residues: 1505
  sheet:  0.26 (0.47), residues: 91
  loop : -1.34 (0.26), residues: 602

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A  74 
 HIS   0.001   0.000   HIS C 106 
 PHE   0.008   0.001   PHE B  12 
 TYR   0.006   0.001   TYR A 232 
 ARG   0.007   0.001   ARG C  29 

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

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

  4396 Ramachandran restraints generated.
    2198 Oldfield, 0 Emsley, 2198 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4396 Ramachandran restraints generated.
    2198 Oldfield, 0 Emsley, 2198 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  445 residues out of total 2051 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 56
    poor density    : 389
  time to evaluate  : 2.205 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  152 ARG cc_start: 0.6923 (ptm-80) cc_final: 0.6338 (mtm110)
REVERT: A  354 GLU cc_start: 0.8961 (tp30) cc_final: 0.8484 (tp30)
REVERT: A  358 ASN cc_start: 0.8702 (t0) cc_final: 0.8397 (t0)
REVERT: B  152 ARG cc_start: 0.6669 (ptm-80) cc_final: 0.6132 (mtm110)
REVERT: B  354 GLU cc_start: 0.8884 (tp30) cc_final: 0.8602 (tp30)
REVERT: B  358 ASN cc_start: 0.8710 (t0) cc_final: 0.8374 (t0)
REVERT: C   14 ASP cc_start: 0.8010 (m-30) cc_final: 0.7777 (p0)
REVERT: C  152 ARG cc_start: 0.6764 (ptm-80) cc_final: 0.6278 (mtm110)
REVERT: C  354 GLU cc_start: 0.8941 (tp30) cc_final: 0.8694 (tp30)
REVERT: D  152 ARG cc_start: 0.6761 (ptm-80) cc_final: 0.6240 (mtm110)
REVERT: D  240 PHE cc_start: 0.7038 (OUTLIER) cc_final: 0.5983 (m-80)
REVERT: D  354 GLU cc_start: 0.8943 (tp30) cc_final: 0.8691 (tp30)
REVERT: E  152 ARG cc_start: 0.6982 (ptm-80) cc_final: 0.6399 (mtm110)
REVERT: E  354 GLU cc_start: 0.8967 (tp30) cc_final: 0.8702 (tp30)
REVERT: F  152 ARG cc_start: 0.6876 (ptm-80) cc_final: 0.6446 (mtm110)
REVERT: F  354 GLU cc_start: 0.8969 (tp30) cc_final: 0.8553 (tp30)
REVERT: F  358 ASN cc_start: 0.8695 (t0) cc_final: 0.8446 (t0)
REVERT: G  152 ARG cc_start: 0.6832 (ptm-80) cc_final: 0.6233 (mtm110)
REVERT: G  354 GLU cc_start: 0.9005 (tp30) cc_final: 0.8740 (tp30)
  outliers start: 56
  outliers final: 19
  residues processed: 416
  average time/residue: 1.4052
  time to fit residues: 649.9510
Evaluate side-chains
  270 residues out of total 2051 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 250
  time to evaluate  : 2.070 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   13 SER
Chi-restraints excluded: chain A residue  124 ASN
Chi-restraints excluded: chain B residue   13 SER
Chi-restraints excluded: chain B residue  101 VAL
Chi-restraints excluded: chain B residue  124 ASN
Chi-restraints excluded: chain C residue   13 SER
Chi-restraints excluded: chain C residue  101 VAL
Chi-restraints excluded: chain C residue  124 ASN
Chi-restraints excluded: chain D residue   13 SER
Chi-restraints excluded: chain D residue  101 VAL
Chi-restraints excluded: chain D residue  124 ASN
Chi-restraints excluded: chain D residue  240 PHE
Chi-restraints excluded: chain E residue   13 SER
Chi-restraints excluded: chain E residue  124 ASN
Chi-restraints excluded: chain E residue  255 LEU
Chi-restraints excluded: chain F residue   13 SER
Chi-restraints excluded: chain F residue  101 VAL
Chi-restraints excluded: chain F residue  124 ASN
Chi-restraints excluded: chain G residue  101 VAL
Chi-restraints excluded: chain G residue  240 PHE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 224
   random chunks:
   chunk 189 optimal weight:   10.0000
   chunk 169 optimal weight:    5.9990
   chunk 94 optimal weight:    9.9990
   chunk 57 optimal weight:   20.0000
   chunk 114 optimal weight:    6.9990
   chunk 90 optimal weight:    7.9990
   chunk 175 optimal weight:    5.9990
   chunk 67 optimal weight:    6.9990
   chunk 106 optimal weight:    2.9990
   chunk 130 optimal weight:    3.9990
   chunk 203 optimal weight:    0.8980
   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 266 GLN
A 355 ASN
B  56 GLN
B 266 GLN
B 282 ASN
B 355 ASN
C 266 GLN
C 355 ASN
D 266 GLN
D 355 ASN
E 266 GLN
E 355 ASN
F 266 GLN
F 355 ASN
G  56 GLN
G 266 GLN
G 355 ASN

Total number of N/Q/H flips: 17

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3782 r_free = 0.3782 target = 0.124592 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3113 r_free = 0.3113 target = 0.082071 restraints weight = 31089.026|
|-----------------------------------------------------------------------------|
r_work (start): 0.3059 rms_B_bonded: 2.46
r_work: 0.2917 rms_B_bonded: 3.20 restraints_weight: 0.5000
r_work (final): 0.2917
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8274
moved from start:          0.2066

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.041  18718  Z= 0.384
  Angle     :  0.654   8.069  25445  Z= 0.321
  Chirality :  0.042   0.215   3045
  Planarity :  0.004   0.033   3052
  Dihedral  :  4.527  48.643   2451
  Min Nonbonded Distance : 2.570

Molprobity Statistics.
  All-atom Clashscore : 6.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.82 %
    Favored  : 98.18 %
  Rotamer:
    Outliers :  6.58 %
    Allowed  : 23.84 %
    Favored  : 69.58 %
  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:  1.99 (0.19), residues: 2198
  helix:  2.33 (0.13), residues: 1526
  sheet:  0.05 (0.48), residues: 126
  loop : -1.41 (0.28), residues: 546

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP C 127 
 HIS   0.005   0.001   HIS B 106 
 PHE   0.017   0.002   PHE B 333 
 TYR   0.024   0.002   TYR A 232 
 ARG   0.005   0.001   ARG B 128 

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

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

  4396 Ramachandran restraints generated.
    2198 Oldfield, 0 Emsley, 2198 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4396 Ramachandran restraints generated.
    2198 Oldfield, 0 Emsley, 2198 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  392 residues out of total 2051 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 135
    poor density    : 257
  time to evaluate  : 2.242 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   14 ASP cc_start: 0.8461 (m-30) cc_final: 0.7980 (t0)
REVERT: A  124 ASN cc_start: 0.8186 (OUTLIER) cc_final: 0.7900 (p0)
REVERT: A  144 GLU cc_start: 0.8269 (OUTLIER) cc_final: 0.8043 (mp0)
REVERT: A  152 ARG cc_start: 0.6231 (ptm-80) cc_final: 0.5800 (mtm110)
REVERT: A  240 PHE cc_start: 0.7572 (OUTLIER) cc_final: 0.7047 (m-80)
REVERT: A  358 ASN cc_start: 0.8787 (t0) cc_final: 0.8439 (t0)
REVERT: B   14 ASP cc_start: 0.8661 (m-30) cc_final: 0.7825 (p0)
REVERT: B  144 GLU cc_start: 0.8344 (OUTLIER) cc_final: 0.8091 (mp0)
REVERT: B  152 ARG cc_start: 0.6177 (ptm-80) cc_final: 0.5756 (mtm110)
REVERT: B  240 PHE cc_start: 0.7658 (OUTLIER) cc_final: 0.7341 (m-80)
REVERT: B  358 ASN cc_start: 0.8810 (t0) cc_final: 0.8416 (t0)
REVERT: C   14 ASP cc_start: 0.8604 (m-30) cc_final: 0.7747 (p0)
REVERT: C  152 ARG cc_start: 0.6071 (ptm-80) cc_final: 0.5739 (mtm110)
REVERT: C  297 MET cc_start: 0.8132 (OUTLIER) cc_final: 0.7524 (pmm)
REVERT: D  124 ASN cc_start: 0.8204 (OUTLIER) cc_final: 0.7920 (p0)
REVERT: D  152 ARG cc_start: 0.6185 (ptm-80) cc_final: 0.5760 (mtm110)
REVERT: D  306 ASN cc_start: 0.7685 (t0) cc_final: 0.7438 (t0)
REVERT: E   14 ASP cc_start: 0.8591 (m-30) cc_final: 0.7868 (p0)
REVERT: E  144 GLU cc_start: 0.8175 (OUTLIER) cc_final: 0.7896 (mp0)
REVERT: E  152 ARG cc_start: 0.6220 (ptm-80) cc_final: 0.5770 (mtm110)
REVERT: E  200 GLN cc_start: 0.8869 (mm-40) cc_final: 0.8306 (mm-40)
REVERT: E  297 MET cc_start: 0.7861 (pmm) cc_final: 0.7592 (pmm)
REVERT: E  306 ASN cc_start: 0.7541 (t0) cc_final: 0.7060 (t0)
REVERT: F   14 ASP cc_start: 0.8552 (m-30) cc_final: 0.7899 (t70)
REVERT: F  152 ARG cc_start: 0.6236 (ptm-80) cc_final: 0.5970 (mtp-110)
REVERT: F  358 ASN cc_start: 0.8860 (t0) cc_final: 0.8580 (t0)
REVERT: G   14 ASP cc_start: 0.8603 (m-30) cc_final: 0.7869 (p0)
REVERT: G  144 GLU cc_start: 0.8171 (OUTLIER) cc_final: 0.7930 (mp0)
REVERT: G  152 ARG cc_start: 0.6131 (ptm-80) cc_final: 0.5669 (mtm110)
REVERT: G  317 PHE cc_start: 0.7912 (OUTLIER) cc_final: 0.7590 (m-80)
  outliers start: 135
  outliers final: 47
  residues processed: 363
  average time/residue: 1.2245
  time to fit residues: 502.0790
Evaluate side-chains
  302 residues out of total 2051 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 57
    poor density    : 245
  time to evaluate  : 2.123 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  124 ASN
Chi-restraints excluded: chain A residue  144 GLU
Chi-restraints excluded: chain A residue  154 ILE
Chi-restraints excluded: chain A residue  224 ILE
Chi-restraints excluded: chain A residue  240 PHE
Chi-restraints excluded: chain A residue  242 LEU
Chi-restraints excluded: chain A residue  255 LEU
Chi-restraints excluded: chain A residue  287 VAL
Chi-restraints excluded: chain A residue  313 VAL
Chi-restraints excluded: chain A residue  352 VAL
Chi-restraints excluded: chain B residue  101 VAL
Chi-restraints excluded: chain B residue  144 GLU
Chi-restraints excluded: chain B residue  224 ILE
Chi-restraints excluded: chain B residue  240 PHE
Chi-restraints excluded: chain B residue  242 LEU
Chi-restraints excluded: chain B residue  255 LEU
Chi-restraints excluded: chain B residue  352 VAL
Chi-restraints excluded: chain C residue   16 LEU
Chi-restraints excluded: chain C residue  101 VAL
Chi-restraints excluded: chain C residue  144 GLU
Chi-restraints excluded: chain C residue  224 ILE
Chi-restraints excluded: chain C residue  242 LEU
Chi-restraints excluded: chain C residue  255 LEU
Chi-restraints excluded: chain C residue  287 VAL
Chi-restraints excluded: chain C residue  297 MET
Chi-restraints excluded: chain C residue  352 VAL
Chi-restraints excluded: chain D residue   34 VAL
Chi-restraints excluded: chain D residue  101 VAL
Chi-restraints excluded: chain D residue  124 ASN
Chi-restraints excluded: chain D residue  224 ILE
Chi-restraints excluded: chain D residue  240 PHE
Chi-restraints excluded: chain D residue  242 LEU
Chi-restraints excluded: chain D residue  287 VAL
Chi-restraints excluded: chain E residue  124 ASN
Chi-restraints excluded: chain E residue  144 GLU
Chi-restraints excluded: chain E residue  202 LEU
Chi-restraints excluded: chain E residue  224 ILE
Chi-restraints excluded: chain E residue  242 LEU
Chi-restraints excluded: chain E residue  255 LEU
Chi-restraints excluded: chain E residue  287 VAL
Chi-restraints excluded: chain E residue  352 VAL
Chi-restraints excluded: chain F residue  101 VAL
Chi-restraints excluded: chain F residue  124 ASN
Chi-restraints excluded: chain F residue  224 ILE
Chi-restraints excluded: chain F residue  240 PHE
Chi-restraints excluded: chain F residue  242 LEU
Chi-restraints excluded: chain F residue  255 LEU
Chi-restraints excluded: chain F residue  287 VAL
Chi-restraints excluded: chain F residue  341 VAL
Chi-restraints excluded: chain F residue  352 VAL
Chi-restraints excluded: chain G residue  144 GLU
Chi-restraints excluded: chain G residue  224 ILE
Chi-restraints excluded: chain G residue  240 PHE
Chi-restraints excluded: chain G residue  242 LEU
Chi-restraints excluded: chain G residue  287 VAL
Chi-restraints excluded: chain G residue  317 PHE
Chi-restraints excluded: chain G residue  352 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 224
   random chunks:
   chunk 35 optimal weight:    9.9990
   chunk 55 optimal weight:    0.8980
   chunk 110 optimal weight:    9.9990
   chunk 84 optimal weight:    2.9990
   chunk 141 optimal weight:    5.9990
   chunk 39 optimal weight:    2.9990
   chunk 6 optimal weight:    3.9990
   chunk 18 optimal weight:    2.9990
   chunk 164 optimal weight:    2.9990
   chunk 210 optimal weight:    2.9990
   chunk 144 optimal weight:    0.9990
   overall best weight:    2.1788

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

Flipped N/Q/H residues before XYZ refinement:
B 355 ASN
C 266 GLN
C 355 ASN
D 355 ASN
E 355 ASN
F 355 ASN
G   5 HIS
G  56 GLN
G 355 ASN

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3781 r_free = 0.3781 target = 0.124791 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3114 r_free = 0.3114 target = 0.082228 restraints weight = 30706.831|
|-----------------------------------------------------------------------------|
r_work (start): 0.3065 rms_B_bonded: 2.46
r_work: 0.2925 rms_B_bonded: 3.19 restraints_weight: 0.5000
r_work (final): 0.2925
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8287
moved from start:          0.2252

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.049  18718  Z= 0.251
  Angle     :  0.598   8.078  25445  Z= 0.289
  Chirality :  0.040   0.182   3045
  Planarity :  0.003   0.029   3052
  Dihedral  :  4.332  51.724   2440
  Min Nonbonded Distance : 2.617

Molprobity Statistics.
  All-atom Clashscore : 5.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.87 %
    Favored  : 98.13 %
  Rotamer:
    Outliers :  6.09 %
    Allowed  : 23.26 %
    Favored  : 70.65 %
  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:  2.04 (0.19), residues: 2198
  helix:  2.36 (0.13), residues: 1526
  sheet:  0.25 (0.48), residues: 126
  loop : -1.42 (0.28), residues: 546

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP F  85 
 HIS   0.003   0.001   HIS B 106 
 PHE   0.010   0.001   PHE D 240 
 TYR   0.022   0.002   TYR E 232 
 ARG   0.005   0.001   ARG F  29 

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

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

  4396 Ramachandran restraints generated.
    2198 Oldfield, 0 Emsley, 2198 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4396 Ramachandran restraints generated.
    2198 Oldfield, 0 Emsley, 2198 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  374 residues out of total 2051 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 125
    poor density    : 249
  time to evaluate  : 1.981 
Fit side-chains
   revert: symmetry clash
REVERT: A   14 ASP cc_start: 0.8435 (m-30) cc_final: 0.7996 (t0)
REVERT: A  124 ASN cc_start: 0.8138 (OUTLIER) cc_final: 0.7853 (p0)
REVERT: A  144 GLU cc_start: 0.8286 (OUTLIER) cc_final: 0.7995 (mp0)
REVERT: A  152 ARG cc_start: 0.6295 (ptm-80) cc_final: 0.5803 (mtm110)
REVERT: A  240 PHE cc_start: 0.7702 (OUTLIER) cc_final: 0.7151 (m-80)
REVERT: A  358 ASN cc_start: 0.8802 (t0) cc_final: 0.8458 (t0)
REVERT: B   14 ASP cc_start: 0.8604 (m-30) cc_final: 0.7819 (p0)
REVERT: B  144 GLU cc_start: 0.8317 (OUTLIER) cc_final: 0.8014 (mp0)
REVERT: B  152 ARG cc_start: 0.6239 (ptm-80) cc_final: 0.5741 (mtm110)
REVERT: B  240 PHE cc_start: 0.7673 (OUTLIER) cc_final: 0.7376 (m-80)
REVERT: B  266 GLN cc_start: 0.8666 (OUTLIER) cc_final: 0.8243 (tt0)
REVERT: B  306 ASN cc_start: 0.7534 (t0) cc_final: 0.7036 (t0)
REVERT: B  309 LYS cc_start: 0.9084 (mmtt) cc_final: 0.8865 (mmtp)
REVERT: B  358 ASN cc_start: 0.8833 (t0) cc_final: 0.8449 (t0)
REVERT: C   14 ASP cc_start: 0.8462 (m-30) cc_final: 0.7701 (p0)
REVERT: C  152 ARG cc_start: 0.6123 (ptm-80) cc_final: 0.5746 (mtm110)
REVERT: D   14 ASP cc_start: 0.8290 (m-30) cc_final: 0.7593 (p0)
REVERT: D  124 ASN cc_start: 0.8254 (OUTLIER) cc_final: 0.7975 (p0)
REVERT: D  152 ARG cc_start: 0.6203 (ptm-80) cc_final: 0.5707 (mtm110)
REVERT: D  290 MET cc_start: 0.8874 (OUTLIER) cc_final: 0.8639 (mmm)
REVERT: D  306 ASN cc_start: 0.7582 (t0) cc_final: 0.7319 (t0)
REVERT: E   14 ASP cc_start: 0.8505 (m-30) cc_final: 0.7787 (p0)
REVERT: E  144 GLU cc_start: 0.8202 (OUTLIER) cc_final: 0.7920 (mp0)
REVERT: E  152 ARG cc_start: 0.6210 (ptm-80) cc_final: 0.5752 (mtm110)
REVERT: E  266 GLN cc_start: 0.8747 (OUTLIER) cc_final: 0.8438 (tt0)
REVERT: E  297 MET cc_start: 0.7957 (OUTLIER) cc_final: 0.7714 (pmm)
REVERT: E  306 ASN cc_start: 0.7553 (t0) cc_final: 0.7286 (t0)
REVERT: F   14 ASP cc_start: 0.8573 (m-30) cc_final: 0.7864 (t0)
REVERT: F  124 ASN cc_start: 0.8136 (OUTLIER) cc_final: 0.7828 (p0)
REVERT: F  152 ARG cc_start: 0.6210 (ptm-80) cc_final: 0.5861 (mtm110)
REVERT: F  358 ASN cc_start: 0.8866 (t0) cc_final: 0.8585 (t0)
REVERT: G   14 ASP cc_start: 0.8522 (m-30) cc_final: 0.7824 (p0)
REVERT: G   29 ARG cc_start: 0.8883 (mtm-85) cc_final: 0.8615 (mtt180)
REVERT: G  128 ARG cc_start: 0.8649 (tmm-80) cc_final: 0.8390 (ttt-90)
REVERT: G  144 GLU cc_start: 0.8192 (OUTLIER) cc_final: 0.7839 (mp0)
REVERT: G  152 ARG cc_start: 0.6259 (ptm-80) cc_final: 0.5728 (mtm110)
REVERT: G  266 GLN cc_start: 0.8909 (OUTLIER) cc_final: 0.8416 (tt0)
REVERT: G  317 PHE cc_start: 0.7905 (OUTLIER) cc_final: 0.7584 (m-80)
  outliers start: 125
  outliers final: 52
  residues processed: 347
  average time/residue: 1.0926
  time to fit residues: 435.8256
Evaluate side-chains
  307 residues out of total 2051 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 67
    poor density    : 240
  time to evaluate  : 1.805 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   30 LEU
Chi-restraints excluded: chain A residue  124 ASN
Chi-restraints excluded: chain A residue  144 GLU
Chi-restraints excluded: chain A residue  154 ILE
Chi-restraints excluded: chain A residue  223 LEU
Chi-restraints excluded: chain A residue  224 ILE
Chi-restraints excluded: chain A residue  240 PHE
Chi-restraints excluded: chain A residue  242 LEU
Chi-restraints excluded: chain A residue  255 LEU
Chi-restraints excluded: chain A residue  287 VAL
Chi-restraints excluded: chain A residue  352 VAL
Chi-restraints excluded: chain B residue  144 GLU
Chi-restraints excluded: chain B residue  224 ILE
Chi-restraints excluded: chain B residue  240 PHE
Chi-restraints excluded: chain B residue  242 LEU
Chi-restraints excluded: chain B residue  255 LEU
Chi-restraints excluded: chain B residue  266 GLN
Chi-restraints excluded: chain B residue  352 VAL
Chi-restraints excluded: chain C residue   30 LEU
Chi-restraints excluded: chain C residue  101 VAL
Chi-restraints excluded: chain C residue  144 GLU
Chi-restraints excluded: chain C residue  224 ILE
Chi-restraints excluded: chain C residue  240 PHE
Chi-restraints excluded: chain C residue  242 LEU
Chi-restraints excluded: chain C residue  287 VAL
Chi-restraints excluded: chain C residue  352 VAL
Chi-restraints excluded: chain D residue   30 LEU
Chi-restraints excluded: chain D residue   34 VAL
Chi-restraints excluded: chain D residue  101 VAL
Chi-restraints excluded: chain D residue  124 ASN
Chi-restraints excluded: chain D residue  224 ILE
Chi-restraints excluded: chain D residue  240 PHE
Chi-restraints excluded: chain D residue  242 LEU
Chi-restraints excluded: chain D residue  272 VAL
Chi-restraints excluded: chain D residue  276 ARG
Chi-restraints excluded: chain D residue  287 VAL
Chi-restraints excluded: chain D residue  290 MET
Chi-restraints excluded: chain D residue  352 VAL
Chi-restraints excluded: chain E residue   30 LEU
Chi-restraints excluded: chain E residue  124 ASN
Chi-restraints excluded: chain E residue  144 GLU
Chi-restraints excluded: chain E residue  224 ILE
Chi-restraints excluded: chain E residue  242 LEU
Chi-restraints excluded: chain E residue  255 LEU
Chi-restraints excluded: chain E residue  266 GLN
Chi-restraints excluded: chain E residue  287 VAL
Chi-restraints excluded: chain E residue  297 MET
Chi-restraints excluded: chain E residue  341 VAL
Chi-restraints excluded: chain E residue  352 VAL
Chi-restraints excluded: chain F residue  101 VAL
Chi-restraints excluded: chain F residue  124 ASN
Chi-restraints excluded: chain F residue  224 ILE
Chi-restraints excluded: chain F residue  240 PHE
Chi-restraints excluded: chain F residue  242 LEU
Chi-restraints excluded: chain F residue  287 VAL
Chi-restraints excluded: chain F residue  352 VAL
Chi-restraints excluded: chain G residue   30 LEU
Chi-restraints excluded: chain G residue  101 VAL
Chi-restraints excluded: chain G residue  144 GLU
Chi-restraints excluded: chain G residue  202 LEU
Chi-restraints excluded: chain G residue  224 ILE
Chi-restraints excluded: chain G residue  240 PHE
Chi-restraints excluded: chain G residue  242 LEU
Chi-restraints excluded: chain G residue  266 GLN
Chi-restraints excluded: chain G residue  287 VAL
Chi-restraints excluded: chain G residue  317 PHE
Chi-restraints excluded: chain G residue  352 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 224
   random chunks:
   chunk 163 optimal weight:   10.0000
   chunk 62 optimal weight:    0.0170
   chunk 133 optimal weight:    0.7980
   chunk 37 optimal weight:    0.9990
   chunk 12 optimal weight:    4.9990
   chunk 32 optimal weight:    2.9990
   chunk 71 optimal weight:    2.9990
   chunk 96 optimal weight:    4.9990
   chunk 91 optimal weight:   10.0000
   chunk 5 optimal weight:    1.9990
   chunk 6 optimal weight:    1.9990
   overall best weight:    1.1624

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

Flipped N/Q/H residues before XYZ refinement:
A 340 ASN
B 355 ASN
C 266 GLN
C 340 ASN
C 355 ASN
D 340 ASN
D 355 ASN
E 340 ASN
E 355 ASN
F 340 ASN
F 355 ASN
G  56 GLN
G 355 ASN

Total number of N/Q/H flips: 13

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3796 r_free = 0.3796 target = 0.125938 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3138 r_free = 0.3138 target = 0.083666 restraints weight = 30526.278|
|-----------------------------------------------------------------------------|
r_work (start): 0.3089 rms_B_bonded: 2.46
r_work: 0.2949 rms_B_bonded: 3.19 restraints_weight: 0.5000
r_work (final): 0.2949
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8253
moved from start:          0.2321

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028  18718  Z= 0.184
  Angle     :  0.593   8.748  25445  Z= 0.282
  Chirality :  0.039   0.178   3045
  Planarity :  0.003   0.028   3052
  Dihedral  :  4.341  52.944   2439
  Min Nonbonded Distance : 2.417

Molprobity Statistics.
  All-atom Clashscore : 5.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.50 %
    Favored  : 98.50 %
  Rotamer:
    Outliers :  5.12 %
    Allowed  : 24.28 %
    Favored  : 70.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.19 (0.19), residues: 2198
  helix:  2.48 (0.13), residues: 1519
  sheet:  0.26 (0.48), residues: 126
  loop : -1.30 (0.28), residues: 553

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP F  85 
 HIS   0.003   0.001   HIS B 106 
 PHE   0.010   0.001   PHE D  12 
 TYR   0.023   0.001   TYR E 232 
 ARG   0.006   0.001   ARG F  29 

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

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

  4396 Ramachandran restraints generated.
    2198 Oldfield, 0 Emsley, 2198 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4396 Ramachandran restraints generated.
    2198 Oldfield, 0 Emsley, 2198 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  354 residues out of total 2051 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 105
    poor density    : 249
  time to evaluate  : 1.621 
Fit side-chains
   revert: symmetry clash
REVERT: A   14 ASP cc_start: 0.8454 (m-30) cc_final: 0.7983 (t0)
REVERT: A  124 ASN cc_start: 0.8083 (OUTLIER) cc_final: 0.7729 (p0)
REVERT: A  144 GLU cc_start: 0.8290 (OUTLIER) cc_final: 0.8035 (mp0)
REVERT: A  152 ARG cc_start: 0.6301 (ptm-80) cc_final: 0.5796 (mtm110)
REVERT: A  240 PHE cc_start: 0.7661 (OUTLIER) cc_final: 0.7129 (m-80)
REVERT: A  358 ASN cc_start: 0.8809 (t0) cc_final: 0.8464 (t0)
REVERT: B   14 ASP cc_start: 0.8576 (m-30) cc_final: 0.7821 (p0)
REVERT: B  144 GLU cc_start: 0.8318 (OUTLIER) cc_final: 0.7993 (mp0)
REVERT: B  152 ARG cc_start: 0.6191 (ptm-80) cc_final: 0.5739 (mtm110)
REVERT: B  203 LYS cc_start: 0.9195 (mmmt) cc_final: 0.8772 (mmtt)
REVERT: B  240 PHE cc_start: 0.7651 (OUTLIER) cc_final: 0.7323 (m-80)
REVERT: B  266 GLN cc_start: 0.8599 (OUTLIER) cc_final: 0.8201 (tt0)
REVERT: B  306 ASN cc_start: 0.7501 (t0) cc_final: 0.6952 (t0)
REVERT: B  309 LYS cc_start: 0.9078 (mmtt) cc_final: 0.8867 (mmtp)
REVERT: B  358 ASN cc_start: 0.8844 (t0) cc_final: 0.8443 (t0)
REVERT: C   14 ASP cc_start: 0.8468 (m-30) cc_final: 0.7709 (p0)
REVERT: C  152 ARG cc_start: 0.6126 (ptm-80) cc_final: 0.5689 (mtm110)
REVERT: C  297 MET cc_start: 0.8154 (OUTLIER) cc_final: 0.7811 (pmt)
REVERT: C  306 ASN cc_start: 0.7293 (t0) cc_final: 0.7032 (t0)
REVERT: C  352 VAL cc_start: 0.8732 (OUTLIER) cc_final: 0.8504 (t)
REVERT: D   14 ASP cc_start: 0.8286 (m-30) cc_final: 0.7582 (p0)
REVERT: D  124 ASN cc_start: 0.8285 (OUTLIER) cc_final: 0.7995 (p0)
REVERT: D  152 ARG cc_start: 0.6196 (ptm-80) cc_final: 0.5711 (mtm110)
REVERT: D  240 PHE cc_start: 0.7633 (OUTLIER) cc_final: 0.6310 (t80)
REVERT: D  266 GLN cc_start: 0.8786 (OUTLIER) cc_final: 0.8405 (tp-100)
REVERT: D  306 ASN cc_start: 0.7575 (t0) cc_final: 0.7300 (t0)
REVERT: D  317 PHE cc_start: 0.7975 (OUTLIER) cc_final: 0.7631 (m-80)
REVERT: E   14 ASP cc_start: 0.8494 (m-30) cc_final: 0.7802 (p0)
REVERT: E  144 GLU cc_start: 0.8209 (OUTLIER) cc_final: 0.7917 (mp0)
REVERT: E  152 ARG cc_start: 0.6251 (ptm-80) cc_final: 0.5804 (mtm110)
REVERT: E  203 LYS cc_start: 0.9260 (mmmt) cc_final: 0.8845 (mmtt)
REVERT: E  266 GLN cc_start: 0.8658 (OUTLIER) cc_final: 0.8387 (tt0)
REVERT: E  297 MET cc_start: 0.7935 (OUTLIER) cc_final: 0.7695 (pmm)
REVERT: E  306 ASN cc_start: 0.7556 (t0) cc_final: 0.7302 (t0)
REVERT: F   14 ASP cc_start: 0.8561 (m-30) cc_final: 0.7870 (t0)
REVERT: F  124 ASN cc_start: 0.8139 (OUTLIER) cc_final: 0.7815 (p0)
REVERT: F  152 ARG cc_start: 0.6202 (ptm-80) cc_final: 0.5820 (mtm110)
REVERT: F  203 LYS cc_start: 0.9190 (mmmt) cc_final: 0.8838 (mptt)
REVERT: F  266 GLN cc_start: 0.8789 (OUTLIER) cc_final: 0.8187 (tt0)
REVERT: F  358 ASN cc_start: 0.8877 (t0) cc_final: 0.8602 (t0)
REVERT: G   14 ASP cc_start: 0.8483 (m-30) cc_final: 0.7716 (p0)
REVERT: G   29 ARG cc_start: 0.8883 (mtm-85) cc_final: 0.8610 (mtt180)
REVERT: G  128 ARG cc_start: 0.8590 (tmm-80) cc_final: 0.8316 (ttt-90)
REVERT: G  144 GLU cc_start: 0.8182 (OUTLIER) cc_final: 0.7808 (mp0)
REVERT: G  152 ARG cc_start: 0.6254 (ptm-80) cc_final: 0.5733 (mtm110)
REVERT: G  266 GLN cc_start: 0.8893 (OUTLIER) cc_final: 0.8422 (tt0)
REVERT: G  317 PHE cc_start: 0.7888 (OUTLIER) cc_final: 0.7577 (m-80)
  outliers start: 105
  outliers final: 46
  residues processed: 326
  average time/residue: 1.1444
  time to fit residues: 424.3173
Evaluate side-chains
  307 residues out of total 2051 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 66
    poor density    : 241
  time to evaluate  : 2.248 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   90 GLN
Chi-restraints excluded: chain A residue  124 ASN
Chi-restraints excluded: chain A residue  144 GLU
Chi-restraints excluded: chain A residue  223 LEU
Chi-restraints excluded: chain A residue  224 ILE
Chi-restraints excluded: chain A residue  240 PHE
Chi-restraints excluded: chain A residue  242 LEU
Chi-restraints excluded: chain A residue  255 LEU
Chi-restraints excluded: chain A residue  352 VAL
Chi-restraints excluded: chain B residue  101 VAL
Chi-restraints excluded: chain B residue  144 GLU
Chi-restraints excluded: chain B residue  202 LEU
Chi-restraints excluded: chain B residue  224 ILE
Chi-restraints excluded: chain B residue  240 PHE
Chi-restraints excluded: chain B residue  242 LEU
Chi-restraints excluded: chain B residue  255 LEU
Chi-restraints excluded: chain B residue  266 GLN
Chi-restraints excluded: chain B residue  352 VAL
Chi-restraints excluded: chain C residue   30 LEU
Chi-restraints excluded: chain C residue   90 GLN
Chi-restraints excluded: chain C residue  144 GLU
Chi-restraints excluded: chain C residue  224 ILE
Chi-restraints excluded: chain C residue  240 PHE
Chi-restraints excluded: chain C residue  242 LEU
Chi-restraints excluded: chain C residue  297 MET
Chi-restraints excluded: chain C residue  352 VAL
Chi-restraints excluded: chain D residue   30 LEU
Chi-restraints excluded: chain D residue   34 VAL
Chi-restraints excluded: chain D residue  124 ASN
Chi-restraints excluded: chain D residue  224 ILE
Chi-restraints excluded: chain D residue  240 PHE
Chi-restraints excluded: chain D residue  242 LEU
Chi-restraints excluded: chain D residue  266 GLN
Chi-restraints excluded: chain D residue  272 VAL
Chi-restraints excluded: chain D residue  276 ARG
Chi-restraints excluded: chain D residue  290 MET
Chi-restraints excluded: chain D residue  317 PHE
Chi-restraints excluded: chain D residue  352 VAL
Chi-restraints excluded: chain E residue   30 LEU
Chi-restraints excluded: chain E residue  124 ASN
Chi-restraints excluded: chain E residue  144 GLU
Chi-restraints excluded: chain E residue  224 ILE
Chi-restraints excluded: chain E residue  240 PHE
Chi-restraints excluded: chain E residue  242 LEU
Chi-restraints excluded: chain E residue  255 LEU
Chi-restraints excluded: chain E residue  266 GLN
Chi-restraints excluded: chain E residue  297 MET
Chi-restraints excluded: chain E residue  352 VAL
Chi-restraints excluded: chain F residue   30 LEU
Chi-restraints excluded: chain F residue  101 VAL
Chi-restraints excluded: chain F residue  124 ASN
Chi-restraints excluded: chain F residue  224 ILE
Chi-restraints excluded: chain F residue  240 PHE
Chi-restraints excluded: chain F residue  242 LEU
Chi-restraints excluded: chain F residue  266 GLN
Chi-restraints excluded: chain F residue  352 VAL
Chi-restraints excluded: chain G residue   30 LEU
Chi-restraints excluded: chain G residue  101 VAL
Chi-restraints excluded: chain G residue  144 GLU
Chi-restraints excluded: chain G residue  224 ILE
Chi-restraints excluded: chain G residue  240 PHE
Chi-restraints excluded: chain G residue  242 LEU
Chi-restraints excluded: chain G residue  255 LEU
Chi-restraints excluded: chain G residue  266 GLN
Chi-restraints excluded: chain G residue  317 PHE
Chi-restraints excluded: chain G residue  352 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 224
   random chunks:
   chunk 56 optimal weight:    0.9990
   chunk 194 optimal weight:   10.0000
   chunk 96 optimal weight:    5.9990
   chunk 184 optimal weight:    0.2980
   chunk 218 optimal weight:   10.0000
   chunk 131 optimal weight:    3.9990
   chunk 106 optimal weight:    0.9990
   chunk 174 optimal weight:    9.9990
   chunk 152 optimal weight:    3.9990
   chunk 155 optimal weight:   10.0000
   chunk 98 optimal weight:    5.9990
   overall best weight:    2.0588

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

Flipped N/Q/H residues before XYZ refinement:
B  56 GLN
B 355 ASN
C 266 GLN
C 340 ASN
C 355 ASN
D 355 ASN
E 355 ASN
F 282 ASN
F 355 ASN
G  56 GLN
G 282 ASN
G 355 ASN

Total number of N/Q/H flips: 12

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3777 r_free = 0.3777 target = 0.124722 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3117 r_free = 0.3117 target = 0.082382 restraints weight = 30655.617|
|-----------------------------------------------------------------------------|
r_work (start): 0.3068 rms_B_bonded: 2.45
r_work: 0.2924 rms_B_bonded: 3.19 restraints_weight: 0.5000
r_work (final): 0.2924
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8280
moved from start:          0.2470

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031  18718  Z= 0.238
  Angle     :  0.606   8.811  25445  Z= 0.289
  Chirality :  0.040   0.189   3045
  Planarity :  0.003   0.028   3052
  Dihedral  :  4.310  53.388   2437
  Min Nonbonded Distance : 2.627

Molprobity Statistics.
  All-atom Clashscore : 5.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.64 %
    Favored  : 98.36 %
  Rotamer:
    Outliers :  6.00 %
    Allowed  : 23.70 %
    Favored  : 70.31 %
  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:  2.11 (0.19), residues: 2198
  helix:  2.38 (0.13), residues: 1519
  sheet:  0.37 (0.49), residues: 126
  loop : -1.25 (0.28), residues: 553

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP F  85 
 HIS   0.004   0.001   HIS C 106 
 PHE   0.010   0.001   PHE B 129 
 TYR   0.028   0.001   TYR F 232 
 ARG   0.006   0.000   ARG F  29 

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

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

  4396 Ramachandran restraints generated.
    2198 Oldfield, 0 Emsley, 2198 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4396 Ramachandran restraints generated.
    2198 Oldfield, 0 Emsley, 2198 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  374 residues out of total 2051 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 123
    poor density    : 251
  time to evaluate  : 2.056 
Fit side-chains
REVERT: A   14 ASP cc_start: 0.8488 (m-30) cc_final: 0.7614 (p0)
REVERT: A  124 ASN cc_start: 0.8164 (OUTLIER) cc_final: 0.7760 (p0)
REVERT: A  144 GLU cc_start: 0.8281 (OUTLIER) cc_final: 0.8010 (mp0)
REVERT: A  152 ARG cc_start: 0.6306 (ptm-80) cc_final: 0.5809 (mtm110)
REVERT: A  240 PHE cc_start: 0.7715 (OUTLIER) cc_final: 0.7254 (m-80)
REVERT: A  358 ASN cc_start: 0.8821 (t0) cc_final: 0.8473 (t0)
REVERT: B   14 ASP cc_start: 0.8564 (m-30) cc_final: 0.7829 (p0)
REVERT: B  144 GLU cc_start: 0.8302 (OUTLIER) cc_final: 0.7964 (mp0)
REVERT: B  152 ARG cc_start: 0.6279 (ptm-80) cc_final: 0.5821 (mtm110)
REVERT: B  203 LYS cc_start: 0.9181 (mmmt) cc_final: 0.8774 (mmtt)
REVERT: B  240 PHE cc_start: 0.7689 (OUTLIER) cc_final: 0.7429 (m-80)
REVERT: B  266 GLN cc_start: 0.8761 (OUTLIER) cc_final: 0.8337 (tt0)
REVERT: B  306 ASN cc_start: 0.7542 (t0) cc_final: 0.6984 (t0)
REVERT: B  309 LYS cc_start: 0.9067 (mmtt) cc_final: 0.8861 (mmtp)
REVERT: B  358 ASN cc_start: 0.8873 (t0) cc_final: 0.8475 (t0)
REVERT: C   14 ASP cc_start: 0.8467 (m-30) cc_final: 0.7693 (p0)
REVERT: C  144 GLU cc_start: 0.8280 (OUTLIER) cc_final: 0.7989 (mp0)
REVERT: C  152 ARG cc_start: 0.6096 (ptm-80) cc_final: 0.5657 (mtm110)
REVERT: C  297 MET cc_start: 0.8280 (OUTLIER) cc_final: 0.7983 (pmt)
REVERT: C  306 ASN cc_start: 0.7511 (t0) cc_final: 0.7258 (t0)
REVERT: D   14 ASP cc_start: 0.8300 (m-30) cc_final: 0.7583 (p0)
REVERT: D  124 ASN cc_start: 0.8327 (OUTLIER) cc_final: 0.7977 (p0)
REVERT: D  152 ARG cc_start: 0.6278 (ptm-80) cc_final: 0.5793 (mtm110)
REVERT: D  240 PHE cc_start: 0.7747 (OUTLIER) cc_final: 0.6347 (t80)
REVERT: D  266 GLN cc_start: 0.8862 (OUTLIER) cc_final: 0.8411 (tp-100)
REVERT: D  306 ASN cc_start: 0.7615 (t0) cc_final: 0.7321 (t0)
REVERT: D  317 PHE cc_start: 0.8000 (OUTLIER) cc_final: 0.7608 (m-80)
REVERT: E   14 ASP cc_start: 0.8492 (m-30) cc_final: 0.7804 (p0)
REVERT: E  144 GLU cc_start: 0.8220 (OUTLIER) cc_final: 0.7932 (mp0)
REVERT: E  152 ARG cc_start: 0.6219 (ptm-80) cc_final: 0.5766 (mtm110)
REVERT: E  200 GLN cc_start: 0.8761 (mm-40) cc_final: 0.8560 (mm-40)
REVERT: E  203 LYS cc_start: 0.9274 (mmmt) cc_final: 0.8838 (mmtt)
REVERT: E  266 GLN cc_start: 0.8724 (OUTLIER) cc_final: 0.8444 (tt0)
REVERT: E  297 MET cc_start: 0.7788 (OUTLIER) cc_final: 0.7587 (pmm)
REVERT: E  306 ASN cc_start: 0.7595 (t0) cc_final: 0.7319 (t0)
REVERT: F   14 ASP cc_start: 0.8577 (m-30) cc_final: 0.7869 (t0)
REVERT: F  152 ARG cc_start: 0.6212 (ptm-80) cc_final: 0.5833 (mtm110)
REVERT: F  203 LYS cc_start: 0.9234 (mmmt) cc_final: 0.8880 (mptt)
REVERT: F  266 GLN cc_start: 0.8855 (OUTLIER) cc_final: 0.8241 (tt0)
REVERT: F  358 ASN cc_start: 0.8926 (t0) cc_final: 0.8655 (t0)
REVERT: G   14 ASP cc_start: 0.8478 (m-30) cc_final: 0.7711 (p0)
REVERT: G   29 ARG cc_start: 0.8840 (mtm-85) cc_final: 0.8536 (mtt180)
REVERT: G  128 ARG cc_start: 0.8659 (tmm-80) cc_final: 0.8368 (ttt180)
REVERT: G  144 GLU cc_start: 0.8209 (OUTLIER) cc_final: 0.7836 (mp0)
REVERT: G  152 ARG cc_start: 0.6254 (ptm-80) cc_final: 0.5729 (mtm110)
REVERT: G  203 LYS cc_start: 0.9255 (mmmt) cc_final: 0.8849 (mmtt)
REVERT: G  266 GLN cc_start: 0.8943 (OUTLIER) cc_final: 0.8464 (tt0)
REVERT: G  317 PHE cc_start: 0.7929 (OUTLIER) cc_final: 0.7614 (m-80)
  outliers start: 123
  outliers final: 56
  residues processed: 345
  average time/residue: 1.1184
  time to fit residues: 440.3215
Evaluate side-chains
  319 residues out of total 2051 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 75
    poor density    : 244
  time to evaluate  : 2.121 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   30 LEU
Chi-restraints excluded: chain A residue  124 ASN
Chi-restraints excluded: chain A residue  144 GLU
Chi-restraints excluded: chain A residue  154 ILE
Chi-restraints excluded: chain A residue  202 LEU
Chi-restraints excluded: chain A residue  223 LEU
Chi-restraints excluded: chain A residue  224 ILE
Chi-restraints excluded: chain A residue  240 PHE
Chi-restraints excluded: chain A residue  242 LEU
Chi-restraints excluded: chain A residue  255 LEU
Chi-restraints excluded: chain A residue  287 VAL
Chi-restraints excluded: chain A residue  352 VAL
Chi-restraints excluded: chain B residue    3 ILE
Chi-restraints excluded: chain B residue  101 VAL
Chi-restraints excluded: chain B residue  144 GLU
Chi-restraints excluded: chain B residue  202 LEU
Chi-restraints excluded: chain B residue  224 ILE
Chi-restraints excluded: chain B residue  240 PHE
Chi-restraints excluded: chain B residue  242 LEU
Chi-restraints excluded: chain B residue  255 LEU
Chi-restraints excluded: chain B residue  266 GLN
Chi-restraints excluded: chain B residue  352 VAL
Chi-restraints excluded: chain C residue   30 LEU
Chi-restraints excluded: chain C residue   90 GLN
Chi-restraints excluded: chain C residue  101 VAL
Chi-restraints excluded: chain C residue  144 GLU
Chi-restraints excluded: chain C residue  224 ILE
Chi-restraints excluded: chain C residue  240 PHE
Chi-restraints excluded: chain C residue  242 LEU
Chi-restraints excluded: chain C residue  287 VAL
Chi-restraints excluded: chain C residue  297 MET
Chi-restraints excluded: chain C residue  341 VAL
Chi-restraints excluded: chain D residue   30 LEU
Chi-restraints excluded: chain D residue  101 VAL
Chi-restraints excluded: chain D residue  124 ASN
Chi-restraints excluded: chain D residue  223 LEU
Chi-restraints excluded: chain D residue  224 ILE
Chi-restraints excluded: chain D residue  240 PHE
Chi-restraints excluded: chain D residue  242 LEU
Chi-restraints excluded: chain D residue  266 GLN
Chi-restraints excluded: chain D residue  272 VAL
Chi-restraints excluded: chain D residue  276 ARG
Chi-restraints excluded: chain D residue  287 VAL
Chi-restraints excluded: chain D residue  290 MET
Chi-restraints excluded: chain D residue  317 PHE
Chi-restraints excluded: chain D residue  352 VAL
Chi-restraints excluded: chain E residue   30 LEU
Chi-restraints excluded: chain E residue  124 ASN
Chi-restraints excluded: chain E residue  144 GLU
Chi-restraints excluded: chain E residue  202 LEU
Chi-restraints excluded: chain E residue  224 ILE
Chi-restraints excluded: chain E residue  240 PHE
Chi-restraints excluded: chain E residue  242 LEU
Chi-restraints excluded: chain E residue  266 GLN
Chi-restraints excluded: chain E residue  297 MET
Chi-restraints excluded: chain E residue  352 VAL
Chi-restraints excluded: chain F residue   30 LEU
Chi-restraints excluded: chain F residue  124 ASN
Chi-restraints excluded: chain F residue  216 LEU
Chi-restraints excluded: chain F residue  224 ILE
Chi-restraints excluded: chain F residue  240 PHE
Chi-restraints excluded: chain F residue  242 LEU
Chi-restraints excluded: chain F residue  266 GLN
Chi-restraints excluded: chain F residue  352 VAL
Chi-restraints excluded: chain G residue   30 LEU
Chi-restraints excluded: chain G residue  101 VAL
Chi-restraints excluded: chain G residue  144 GLU
Chi-restraints excluded: chain G residue  224 ILE
Chi-restraints excluded: chain G residue  240 PHE
Chi-restraints excluded: chain G residue  242 LEU
Chi-restraints excluded: chain G residue  255 LEU
Chi-restraints excluded: chain G residue  266 GLN
Chi-restraints excluded: chain G residue  287 VAL
Chi-restraints excluded: chain G residue  317 PHE
Chi-restraints excluded: chain G residue  352 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 224
   random chunks:
   chunk 163 optimal weight:    9.9990
   chunk 32 optimal weight:    1.9990
   chunk 198 optimal weight:    3.9990
   chunk 221 optimal weight:   10.0000
   chunk 11 optimal weight:    0.9980
   chunk 150 optimal weight:    3.9990
   chunk 73 optimal weight:    0.6980
   chunk 13 optimal weight:    4.9990
   chunk 155 optimal weight:    9.9990
   chunk 99 optimal weight:   10.0000
   chunk 210 optimal weight:    3.9990
   overall best weight:    2.3386

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

Flipped N/Q/H residues before XYZ refinement:
A 355 ASN
B  56 GLN
B 340 ASN
B 355 ASN
C 266 GLN
C 282 ASN
C 340 ASN
C 355 ASN
D 355 ASN
E 355 ASN
F 266 GLN
F 282 ASN
F 340 ASN
G  56 GLN
G 355 ASN

Total number of N/Q/H flips: 15

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3771 r_free = 0.3771 target = 0.124318 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3100 r_free = 0.3100 target = 0.081527 restraints weight = 30714.473|
|-----------------------------------------------------------------------------|
r_work (start): 0.3052 rms_B_bonded: 2.48
r_work: 0.2912 rms_B_bonded: 3.19 restraints_weight: 0.5000
r_work (final): 0.2912
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8292
moved from start:          0.2610

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032  18718  Z= 0.260
  Angle     :  0.621   8.375  25445  Z= 0.297
  Chirality :  0.040   0.197   3045
  Planarity :  0.003   0.030   3052
  Dihedral  :  4.266  54.051   2434
  Min Nonbonded Distance : 2.624

Molprobity Statistics.
  All-atom Clashscore : 5.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.91 %
    Favored  : 98.09 %
  Rotamer:
    Outliers :  5.75 %
    Allowed  : 23.79 %
    Favored  : 70.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.04 (0.19), residues: 2198
  helix:  2.36 (0.13), residues: 1512
  sheet:  0.34 (0.49), residues: 126
  loop : -1.33 (0.28), residues: 560

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP F  85 
 HIS   0.003   0.001   HIS A 106 
 PHE   0.010   0.001   PHE A 333 
 TYR   0.029   0.002   TYR E 232 
 ARG   0.007   0.001   ARG D  29 

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

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

  4396 Ramachandran restraints generated.
    2198 Oldfield, 0 Emsley, 2198 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4396 Ramachandran restraints generated.
    2198 Oldfield, 0 Emsley, 2198 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  368 residues out of total 2051 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 118
    poor density    : 250
  time to evaluate  : 2.180 
Fit side-chains
REVERT: A   14 ASP cc_start: 0.8470 (m-30) cc_final: 0.7609 (p0)
REVERT: A  124 ASN cc_start: 0.8267 (OUTLIER) cc_final: 0.7813 (p0)
REVERT: A  144 GLU cc_start: 0.8283 (OUTLIER) cc_final: 0.8000 (mp0)
REVERT: A  152 ARG cc_start: 0.6302 (ptm-80) cc_final: 0.5791 (mtm110)
REVERT: A  240 PHE cc_start: 0.7788 (OUTLIER) cc_final: 0.7339 (m-80)
REVERT: A  317 PHE cc_start: 0.7911 (t80) cc_final: 0.7679 (m-80)
REVERT: A  358 ASN cc_start: 0.8814 (t0) cc_final: 0.8455 (t0)
REVERT: B   14 ASP cc_start: 0.8560 (m-30) cc_final: 0.7852 (p0)
REVERT: B  144 GLU cc_start: 0.8315 (OUTLIER) cc_final: 0.7976 (mp0)
REVERT: B  152 ARG cc_start: 0.6289 (ptm-80) cc_final: 0.5825 (mtm110)
REVERT: B  203 LYS cc_start: 0.9182 (mmmt) cc_final: 0.8761 (mmtt)
REVERT: B  240 PHE cc_start: 0.7732 (OUTLIER) cc_final: 0.7475 (m-80)
REVERT: B  266 GLN cc_start: 0.8795 (OUTLIER) cc_final: 0.8364 (tt0)
REVERT: B  306 ASN cc_start: 0.7580 (t0) cc_final: 0.7022 (t0)
REVERT: B  309 LYS cc_start: 0.9074 (mmtt) cc_final: 0.8871 (mmtp)
REVERT: B  317 PHE cc_start: 0.7861 (t80) cc_final: 0.7500 (m-80)
REVERT: B  358 ASN cc_start: 0.8869 (t0) cc_final: 0.8472 (t0)
REVERT: C   14 ASP cc_start: 0.8462 (m-30) cc_final: 0.7714 (p0)
REVERT: C  144 GLU cc_start: 0.8288 (OUTLIER) cc_final: 0.7989 (mp0)
REVERT: C  152 ARG cc_start: 0.6119 (ptm-80) cc_final: 0.5659 (mtm110)
REVERT: C  200 GLN cc_start: 0.8514 (mm-40) cc_final: 0.8279 (mm-40)
REVERT: C  297 MET cc_start: 0.8279 (OUTLIER) cc_final: 0.7984 (pmt)
REVERT: C  306 ASN cc_start: 0.7607 (t0) cc_final: 0.7342 (t0)
REVERT: D   14 ASP cc_start: 0.8337 (m-30) cc_final: 0.7600 (p0)
REVERT: D  124 ASN cc_start: 0.8251 (OUTLIER) cc_final: 0.7801 (p0)
REVERT: D  152 ARG cc_start: 0.6216 (ptm-80) cc_final: 0.5745 (mtm110)
REVERT: D  266 GLN cc_start: 0.8883 (OUTLIER) cc_final: 0.8481 (tp-100)
REVERT: D  306 ASN cc_start: 0.7646 (t0) cc_final: 0.7352 (t0)
REVERT: D  317 PHE cc_start: 0.8022 (OUTLIER) cc_final: 0.7594 (m-80)
REVERT: E   14 ASP cc_start: 0.8456 (m-30) cc_final: 0.7757 (p0)
REVERT: E  144 GLU cc_start: 0.8226 (OUTLIER) cc_final: 0.7936 (mp0)
REVERT: E  152 ARG cc_start: 0.6252 (ptm-80) cc_final: 0.5761 (mtm110)
REVERT: E  203 LYS cc_start: 0.9258 (mmmt) cc_final: 0.8913 (mptt)
REVERT: E  266 GLN cc_start: 0.8746 (OUTLIER) cc_final: 0.8448 (tt0)
REVERT: E  297 MET cc_start: 0.7772 (OUTLIER) cc_final: 0.7563 (pmm)
REVERT: E  306 ASN cc_start: 0.7568 (t0) cc_final: 0.7270 (t0)
REVERT: F   14 ASP cc_start: 0.8574 (m-30) cc_final: 0.8009 (t0)
REVERT: F  144 GLU cc_start: 0.8482 (mm-30) cc_final: 0.8262 (mp0)
REVERT: F  152 ARG cc_start: 0.6239 (ptm-80) cc_final: 0.5845 (mtm110)
REVERT: F  203 LYS cc_start: 0.9240 (mmmt) cc_final: 0.8901 (mptt)
REVERT: F  280 TYR cc_start: 0.8177 (t80) cc_final: 0.7649 (m-80)
REVERT: F  297 MET cc_start: 0.8114 (pmt) cc_final: 0.7881 (pmt)
REVERT: F  358 ASN cc_start: 0.8973 (t0) cc_final: 0.8697 (t0)
REVERT: G   14 ASP cc_start: 0.8488 (m-30) cc_final: 0.7723 (p0)
REVERT: G  128 ARG cc_start: 0.8671 (tmm-80) cc_final: 0.8465 (ttt-90)
REVERT: G  144 GLU cc_start: 0.8259 (OUTLIER) cc_final: 0.7868 (mp0)
REVERT: G  152 ARG cc_start: 0.6243 (ptm-80) cc_final: 0.5746 (mtm110)
REVERT: G  203 LYS cc_start: 0.9248 (mmmt) cc_final: 0.8878 (mmtt)
REVERT: G  266 GLN cc_start: 0.8966 (OUTLIER) cc_final: 0.8474 (tt0)
REVERT: G  317 PHE cc_start: 0.7940 (OUTLIER) cc_final: 0.7634 (m-80)
  outliers start: 118
  outliers final: 60
  residues processed: 344
  average time/residue: 1.1258
  time to fit residues: 442.4567
Evaluate side-chains
  320 residues out of total 2051 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 77
    poor density    : 243
  time to evaluate  : 2.235 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   30 LEU
Chi-restraints excluded: chain A residue  124 ASN
Chi-restraints excluded: chain A residue  144 GLU
Chi-restraints excluded: chain A residue  154 ILE
Chi-restraints excluded: chain A residue  202 LEU
Chi-restraints excluded: chain A residue  223 LEU
Chi-restraints excluded: chain A residue  224 ILE
Chi-restraints excluded: chain A residue  240 PHE
Chi-restraints excluded: chain A residue  242 LEU
Chi-restraints excluded: chain A residue  255 LEU
Chi-restraints excluded: chain A residue  287 VAL
Chi-restraints excluded: chain A residue  352 VAL
Chi-restraints excluded: chain B residue  101 VAL
Chi-restraints excluded: chain B residue  144 GLU
Chi-restraints excluded: chain B residue  202 LEU
Chi-restraints excluded: chain B residue  224 ILE
Chi-restraints excluded: chain B residue  240 PHE
Chi-restraints excluded: chain B residue  242 LEU
Chi-restraints excluded: chain B residue  255 LEU
Chi-restraints excluded: chain B residue  266 GLN
Chi-restraints excluded: chain B residue  352 VAL
Chi-restraints excluded: chain C residue   30 LEU
Chi-restraints excluded: chain C residue   90 GLN
Chi-restraints excluded: chain C residue  101 VAL
Chi-restraints excluded: chain C residue  144 GLU
Chi-restraints excluded: chain C residue  224 ILE
Chi-restraints excluded: chain C residue  240 PHE
Chi-restraints excluded: chain C residue  242 LEU
Chi-restraints excluded: chain C residue  287 VAL
Chi-restraints excluded: chain C residue  297 MET
Chi-restraints excluded: chain C residue  341 VAL
Chi-restraints excluded: chain D residue   30 LEU
Chi-restraints excluded: chain D residue  101 VAL
Chi-restraints excluded: chain D residue  124 ASN
Chi-restraints excluded: chain D residue  223 LEU
Chi-restraints excluded: chain D residue  224 ILE
Chi-restraints excluded: chain D residue  240 PHE
Chi-restraints excluded: chain D residue  242 LEU
Chi-restraints excluded: chain D residue  266 GLN
Chi-restraints excluded: chain D residue  272 VAL
Chi-restraints excluded: chain D residue  276 ARG
Chi-restraints excluded: chain D residue  287 VAL
Chi-restraints excluded: chain D residue  317 PHE
Chi-restraints excluded: chain D residue  341 VAL
Chi-restraints excluded: chain D residue  352 VAL
Chi-restraints excluded: chain E residue   30 LEU
Chi-restraints excluded: chain E residue  124 ASN
Chi-restraints excluded: chain E residue  144 GLU
Chi-restraints excluded: chain E residue  202 LEU
Chi-restraints excluded: chain E residue  224 ILE
Chi-restraints excluded: chain E residue  242 LEU
Chi-restraints excluded: chain E residue  255 LEU
Chi-restraints excluded: chain E residue  266 GLN
Chi-restraints excluded: chain E residue  287 VAL
Chi-restraints excluded: chain E residue  297 MET
Chi-restraints excluded: chain E residue  352 VAL
Chi-restraints excluded: chain F residue   30 LEU
Chi-restraints excluded: chain F residue  101 VAL
Chi-restraints excluded: chain F residue  124 ASN
Chi-restraints excluded: chain F residue  216 LEU
Chi-restraints excluded: chain F residue  224 ILE
Chi-restraints excluded: chain F residue  240 PHE
Chi-restraints excluded: chain F residue  242 LEU
Chi-restraints excluded: chain F residue  287 VAL
Chi-restraints excluded: chain F residue  341 VAL
Chi-restraints excluded: chain F residue  352 VAL
Chi-restraints excluded: chain G residue   30 LEU
Chi-restraints excluded: chain G residue  101 VAL
Chi-restraints excluded: chain G residue  144 GLU
Chi-restraints excluded: chain G residue  224 ILE
Chi-restraints excluded: chain G residue  240 PHE
Chi-restraints excluded: chain G residue  242 LEU
Chi-restraints excluded: chain G residue  255 LEU
Chi-restraints excluded: chain G residue  266 GLN
Chi-restraints excluded: chain G residue  287 VAL
Chi-restraints excluded: chain G residue  317 PHE
Chi-restraints excluded: chain G residue  352 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 224
   random chunks:
   chunk 164 optimal weight:    0.9980
   chunk 30 optimal weight:   20.0000
   chunk 213 optimal weight:    0.0670
   chunk 193 optimal weight:    1.9990
   chunk 150 optimal weight:    3.9990
   chunk 88 optimal weight:    1.9990
   chunk 181 optimal weight:    0.0870
   chunk 118 optimal weight:    2.9990
   chunk 125 optimal weight:    1.9990
   chunk 48 optimal weight:    0.9990
   chunk 58 optimal weight:    7.9990
   overall best weight:    0.8300

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

Flipped N/Q/H residues before XYZ refinement:
A 355 ASN
B 355 ASN
C 266 GLN
C 340 ASN
C 355 ASN
D 340 ASN
D 355 ASN
E 340 ASN
E 355 ASN
F 340 ASN
G 355 ASN

Total number of N/Q/H flips: 11

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3799 r_free = 0.3799 target = 0.126382 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3149 r_free = 0.3149 target = 0.084267 restraints weight = 30419.574|
|-----------------------------------------------------------------------------|
r_work (start): 0.3101 rms_B_bonded: 2.47
r_work: 0.2964 rms_B_bonded: 3.17 restraints_weight: 0.5000
r_work (final): 0.2964
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8244
moved from start:          0.2561

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031  18718  Z= 0.168
  Angle     :  0.604  12.382  25445  Z= 0.286
  Chirality :  0.039   0.185   3045
  Planarity :  0.003   0.030   3052
  Dihedral  :  4.308  55.287   2434
  Min Nonbonded Distance : 2.625

Molprobity Statistics.
  All-atom Clashscore : 5.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.59 %
    Favored  : 98.41 %
  Rotamer:
    Outliers :  4.53 %
    Allowed  : 25.35 %
    Favored  : 70.11 %
  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:  2.20 (0.19), residues: 2198
  helix:  2.46 (0.13), residues: 1512
  sheet:  0.34 (0.49), residues: 126
  loop : -1.20 (0.28), residues: 560

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP E  74 
 HIS   0.002   0.001   HIS E 106 
 PHE   0.010   0.001   PHE D  12 
 TYR   0.027   0.001   TYR E 232 
 ARG   0.007   0.001   ARG D  29 

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

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

  4396 Ramachandran restraints generated.
    2198 Oldfield, 0 Emsley, 2198 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4396 Ramachandran restraints generated.
    2198 Oldfield, 0 Emsley, 2198 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  353 residues out of total 2051 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 93
    poor density    : 260
  time to evaluate  : 2.340 
Fit side-chains
REVERT: A   14 ASP cc_start: 0.8449 (m-30) cc_final: 0.7510 (p0)
REVERT: A  144 GLU cc_start: 0.8285 (OUTLIER) cc_final: 0.8020 (mp0)
REVERT: A  152 ARG cc_start: 0.6232 (ptm-80) cc_final: 0.5745 (mtm110)
REVERT: A  203 LYS cc_start: 0.9257 (mmmt) cc_final: 0.8869 (mptt)
REVERT: A  240 PHE cc_start: 0.7670 (OUTLIER) cc_final: 0.7143 (m-80)
REVERT: A  280 TYR cc_start: 0.8211 (t80) cc_final: 0.7611 (m-80)
REVERT: A  317 PHE cc_start: 0.7863 (t80) cc_final: 0.7655 (m-80)
REVERT: A  358 ASN cc_start: 0.8826 (t0) cc_final: 0.8472 (t0)
REVERT: B   14 ASP cc_start: 0.8492 (m-30) cc_final: 0.7811 (p0)
REVERT: B  144 GLU cc_start: 0.8321 (OUTLIER) cc_final: 0.7955 (mp0)
REVERT: B  152 ARG cc_start: 0.6194 (ptm-80) cc_final: 0.5704 (mtm110)
REVERT: B  203 LYS cc_start: 0.9147 (mmmt) cc_final: 0.8759 (mmtt)
REVERT: B  240 PHE cc_start: 0.7631 (OUTLIER) cc_final: 0.7403 (m-80)
REVERT: B  266 GLN cc_start: 0.8650 (OUTLIER) cc_final: 0.8239 (tt0)
REVERT: B  306 ASN cc_start: 0.7563 (t0) cc_final: 0.7004 (t0)
REVERT: B  358 ASN cc_start: 0.8865 (t0) cc_final: 0.8503 (t0)
REVERT: C   14 ASP cc_start: 0.8447 (m-30) cc_final: 0.7641 (p0)
REVERT: C  144 GLU cc_start: 0.8264 (OUTLIER) cc_final: 0.7968 (mp0)
REVERT: C  152 ARG cc_start: 0.6107 (ptm-80) cc_final: 0.5656 (mtm110)
REVERT: C  200 GLN cc_start: 0.8521 (mm-40) cc_final: 0.8297 (mm-40)
REVERT: C  306 ASN cc_start: 0.7647 (t0) cc_final: 0.7375 (t0)
REVERT: C  352 VAL cc_start: 0.8795 (OUTLIER) cc_final: 0.8568 (t)
REVERT: D   14 ASP cc_start: 0.8324 (m-30) cc_final: 0.7600 (p0)
REVERT: D  152 ARG cc_start: 0.6298 (ptm-80) cc_final: 0.5774 (mtm110)
REVERT: D  240 PHE cc_start: 0.7747 (OUTLIER) cc_final: 0.6375 (t80)
REVERT: D  306 ASN cc_start: 0.7633 (t0) cc_final: 0.7341 (t0)
REVERT: E   14 ASP cc_start: 0.8416 (m-30) cc_final: 0.7741 (p0)
REVERT: E  144 GLU cc_start: 0.8273 (OUTLIER) cc_final: 0.7966 (mp0)
REVERT: E  152 ARG cc_start: 0.6235 (ptm-80) cc_final: 0.5761 (mtm110)
REVERT: E  203 LYS cc_start: 0.9220 (mmmt) cc_final: 0.8910 (mptt)
REVERT: E  266 GLN cc_start: 0.8684 (OUTLIER) cc_final: 0.8421 (tt0)
REVERT: E  297 MET cc_start: 0.7797 (OUTLIER) cc_final: 0.7595 (pmm)
REVERT: E  306 ASN cc_start: 0.7555 (t0) cc_final: 0.7261 (t0)
REVERT: F   14 ASP cc_start: 0.8532 (m-30) cc_final: 0.8006 (t0)
REVERT: F   89 GLN cc_start: 0.8405 (OUTLIER) cc_final: 0.7710 (tt0)
REVERT: F  144 GLU cc_start: 0.8485 (mm-30) cc_final: 0.8255 (mp0)
REVERT: F  152 ARG cc_start: 0.6155 (ptm-80) cc_final: 0.5736 (mtm110)
REVERT: F  203 LYS cc_start: 0.9205 (mmmt) cc_final: 0.8869 (mptt)
REVERT: F  280 TYR cc_start: 0.8150 (t80) cc_final: 0.7623 (m-80)
REVERT: F  358 ASN cc_start: 0.8987 (t0) cc_final: 0.8701 (t0)
REVERT: G   14 ASP cc_start: 0.8465 (m-30) cc_final: 0.7753 (p0)
REVERT: G  128 ARG cc_start: 0.8601 (tmm-80) cc_final: 0.8383 (ttt-90)
REVERT: G  144 GLU cc_start: 0.8216 (OUTLIER) cc_final: 0.7865 (mp0)
REVERT: G  152 ARG cc_start: 0.6229 (ptm-80) cc_final: 0.5728 (mtm110)
REVERT: G  203 LYS cc_start: 0.9217 (mmmt) cc_final: 0.8869 (mmtt)
REVERT: G  266 GLN cc_start: 0.8919 (OUTLIER) cc_final: 0.8438 (tt0)
REVERT: G  317 PHE cc_start: 0.7924 (OUTLIER) cc_final: 0.7614 (m-80)
  outliers start: 93
  outliers final: 51
  residues processed: 327
  average time/residue: 1.1971
  time to fit residues: 444.6234
Evaluate side-chains
  313 residues out of total 2051 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 66
    poor density    : 247
  time to evaluate  : 2.300 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   30 LEU
Chi-restraints excluded: chain A residue  124 ASN
Chi-restraints excluded: chain A residue  144 GLU
Chi-restraints excluded: chain A residue  223 LEU
Chi-restraints excluded: chain A residue  224 ILE
Chi-restraints excluded: chain A residue  240 PHE
Chi-restraints excluded: chain A residue  242 LEU
Chi-restraints excluded: chain A residue  255 LEU
Chi-restraints excluded: chain A residue  352 VAL
Chi-restraints excluded: chain B residue  101 VAL
Chi-restraints excluded: chain B residue  144 GLU
Chi-restraints excluded: chain B residue  224 ILE
Chi-restraints excluded: chain B residue  240 PHE
Chi-restraints excluded: chain B residue  242 LEU
Chi-restraints excluded: chain B residue  255 LEU
Chi-restraints excluded: chain B residue  266 GLN
Chi-restraints excluded: chain B residue  352 VAL
Chi-restraints excluded: chain C residue   30 LEU
Chi-restraints excluded: chain C residue   90 GLN
Chi-restraints excluded: chain C residue  101 VAL
Chi-restraints excluded: chain C residue  144 GLU
Chi-restraints excluded: chain C residue  224 ILE
Chi-restraints excluded: chain C residue  240 PHE
Chi-restraints excluded: chain C residue  242 LEU
Chi-restraints excluded: chain C residue  352 VAL
Chi-restraints excluded: chain C residue  356 ILE
Chi-restraints excluded: chain D residue  101 VAL
Chi-restraints excluded: chain D residue  124 ASN
Chi-restraints excluded: chain D residue  223 LEU
Chi-restraints excluded: chain D residue  224 ILE
Chi-restraints excluded: chain D residue  240 PHE
Chi-restraints excluded: chain D residue  242 LEU
Chi-restraints excluded: chain D residue  272 VAL
Chi-restraints excluded: chain D residue  276 ARG
Chi-restraints excluded: chain D residue  352 VAL
Chi-restraints excluded: chain E residue   30 LEU
Chi-restraints excluded: chain E residue  124 ASN
Chi-restraints excluded: chain E residue  144 GLU
Chi-restraints excluded: chain E residue  224 ILE
Chi-restraints excluded: chain E residue  240 PHE
Chi-restraints excluded: chain E residue  242 LEU
Chi-restraints excluded: chain E residue  266 GLN
Chi-restraints excluded: chain E residue  297 MET
Chi-restraints excluded: chain E residue  352 VAL
Chi-restraints excluded: chain F residue   30 LEU
Chi-restraints excluded: chain F residue   89 GLN
Chi-restraints excluded: chain F residue  101 VAL
Chi-restraints excluded: chain F residue  124 ASN
Chi-restraints excluded: chain F residue  138 ASP
Chi-restraints excluded: chain F residue  202 LEU
Chi-restraints excluded: chain F residue  216 LEU
Chi-restraints excluded: chain F residue  224 ILE
Chi-restraints excluded: chain F residue  240 PHE
Chi-restraints excluded: chain F residue  242 LEU
Chi-restraints excluded: chain F residue  287 VAL
Chi-restraints excluded: chain F residue  352 VAL
Chi-restraints excluded: chain G residue   30 LEU
Chi-restraints excluded: chain G residue  101 VAL
Chi-restraints excluded: chain G residue  144 GLU
Chi-restraints excluded: chain G residue  224 ILE
Chi-restraints excluded: chain G residue  240 PHE
Chi-restraints excluded: chain G residue  242 LEU
Chi-restraints excluded: chain G residue  255 LEU
Chi-restraints excluded: chain G residue  266 GLN
Chi-restraints excluded: chain G residue  317 PHE
Chi-restraints excluded: chain G residue  352 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 224
   random chunks:
   chunk 133 optimal weight:    0.5980
   chunk 108 optimal weight:    1.9990
   chunk 185 optimal weight:    9.9990
   chunk 88 optimal weight:    3.9990
   chunk 109 optimal weight:    1.9990
   chunk 138 optimal weight:    0.8980
   chunk 111 optimal weight:    8.9990
   chunk 103 optimal weight:    5.9990
   chunk 8 optimal weight:    0.8980
   chunk 5 optimal weight:    1.9990
   chunk 114 optimal weight:    0.8980
   overall best weight:    1.0582

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

Flipped N/Q/H residues before XYZ refinement:
A 340 ASN
A 355 ASN
B  56 GLN
B 355 ASN
C 266 GLN
C 282 ASN
C 340 ASN
C 355 ASN
D 355 ASN
E 355 ASN
F 340 ASN
F 355 ASN
G  56 GLN
G 355 ASN

Total number of N/Q/H flips: 14

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3797 r_free = 0.3797 target = 0.126127 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3147 r_free = 0.3147 target = 0.084117 restraints weight = 30513.887|
|-----------------------------------------------------------------------------|
r_work (start): 0.3101 rms_B_bonded: 2.47
r_work: 0.2963 rms_B_bonded: 3.17 restraints_weight: 0.5000
r_work (final): 0.2963
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8257
moved from start:          0.2604

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  18718  Z= 0.181
  Angle     :  0.618  12.116  25445  Z= 0.292
  Chirality :  0.039   0.197   3045
  Planarity :  0.003   0.032   3052
  Dihedral  :  4.388  56.928   2434
  Min Nonbonded Distance : 2.621

Molprobity Statistics.
  All-atom Clashscore : 5.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.41 %
    Favored  : 98.59 %
  Rotamer:
    Outliers :  4.34 %
    Allowed  : 25.50 %
    Favored  : 70.16 %
  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:  2.22 (0.19), residues: 2198
  helix:  2.48 (0.14), residues: 1512
  sheet:  0.32 (0.49), residues: 126
  loop : -1.16 (0.28), residues: 560

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A 104 
 HIS   0.002   0.001   HIS G 106 
 PHE   0.010   0.001   PHE D  12 
 TYR   0.030   0.001   TYR G 232 
 ARG   0.007   0.001   ARG F  29 

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

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

  4396 Ramachandran restraints generated.
    2198 Oldfield, 0 Emsley, 2198 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4396 Ramachandran restraints generated.
    2198 Oldfield, 0 Emsley, 2198 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  338 residues out of total 2051 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 89
    poor density    : 249
  time to evaluate  : 2.006 
Fit side-chains
REVERT: A   14 ASP cc_start: 0.8457 (m-30) cc_final: 0.7517 (p0)
REVERT: A  144 GLU cc_start: 0.8265 (OUTLIER) cc_final: 0.8005 (mp0)
REVERT: A  152 ARG cc_start: 0.6252 (ptm-80) cc_final: 0.5731 (mtm110)
REVERT: A  240 PHE cc_start: 0.7647 (OUTLIER) cc_final: 0.7074 (m-80)
REVERT: A  280 TYR cc_start: 0.8225 (t80) cc_final: 0.7628 (m-80)
REVERT: A  358 ASN cc_start: 0.8833 (t0) cc_final: 0.8475 (t0)
REVERT: B   14 ASP cc_start: 0.8483 (m-30) cc_final: 0.7825 (p0)
REVERT: B  144 GLU cc_start: 0.8329 (OUTLIER) cc_final: 0.8010 (mp0)
REVERT: B  152 ARG cc_start: 0.6295 (ptm-80) cc_final: 0.5799 (mtm110)
REVERT: B  203 LYS cc_start: 0.9172 (mmmt) cc_final: 0.8809 (mmtt)
REVERT: B  240 PHE cc_start: 0.7633 (OUTLIER) cc_final: 0.7393 (m-80)
REVERT: B  266 GLN cc_start: 0.8781 (OUTLIER) cc_final: 0.8402 (tp40)
REVERT: B  306 ASN cc_start: 0.7603 (t0) cc_final: 0.7394 (t0)
REVERT: B  358 ASN cc_start: 0.8873 (t0) cc_final: 0.8499 (t0)
REVERT: C   14 ASP cc_start: 0.8440 (m-30) cc_final: 0.7646 (p0)
REVERT: C  144 GLU cc_start: 0.8292 (OUTLIER) cc_final: 0.8022 (mp0)
REVERT: C  152 ARG cc_start: 0.6122 (ptm-80) cc_final: 0.5662 (mtm110)
REVERT: C  297 MET cc_start: 0.8215 (pmm) cc_final: 0.7994 (pmt)
REVERT: C  306 ASN cc_start: 0.7658 (t0) cc_final: 0.7411 (t0)
REVERT: D   14 ASP cc_start: 0.8334 (m-30) cc_final: 0.7612 (p0)
REVERT: D  152 ARG cc_start: 0.6323 (ptm-80) cc_final: 0.5788 (mtm110)
REVERT: D  240 PHE cc_start: 0.7725 (OUTLIER) cc_final: 0.6429 (t80)
REVERT: D  266 GLN cc_start: 0.8814 (OUTLIER) cc_final: 0.8414 (tp-100)
REVERT: D  306 ASN cc_start: 0.7658 (t0) cc_final: 0.7355 (t0)
REVERT: E   14 ASP cc_start: 0.8419 (m-30) cc_final: 0.7745 (p0)
REVERT: E  144 GLU cc_start: 0.8284 (OUTLIER) cc_final: 0.7985 (mp0)
REVERT: E  152 ARG cc_start: 0.6246 (ptm-80) cc_final: 0.5740 (mtm110)
REVERT: E  203 LYS cc_start: 0.9205 (mmmt) cc_final: 0.8900 (mptt)
REVERT: E  266 GLN cc_start: 0.8705 (OUTLIER) cc_final: 0.8433 (tt0)
REVERT: E  297 MET cc_start: 0.7732 (OUTLIER) cc_final: 0.7523 (pmm)
REVERT: E  306 ASN cc_start: 0.7560 (t0) cc_final: 0.7282 (t0)
REVERT: F   14 ASP cc_start: 0.8529 (m-30) cc_final: 0.8010 (t0)
REVERT: F   89 GLN cc_start: 0.8414 (OUTLIER) cc_final: 0.7694 (tt0)
REVERT: F  144 GLU cc_start: 0.8500 (mm-30) cc_final: 0.8247 (mp0)
REVERT: F  152 ARG cc_start: 0.6172 (ptm-80) cc_final: 0.5941 (ptm-80)
REVERT: F  203 LYS cc_start: 0.9226 (mmmt) cc_final: 0.8887 (mptt)
REVERT: F  280 TYR cc_start: 0.8163 (t80) cc_final: 0.7635 (m-80)
REVERT: F  358 ASN cc_start: 0.9001 (t0) cc_final: 0.8713 (t0)
REVERT: G   14 ASP cc_start: 0.8457 (m-30) cc_final: 0.7750 (p0)
REVERT: G  128 ARG cc_start: 0.8590 (tmm-80) cc_final: 0.8366 (ttt-90)
REVERT: G  144 GLU cc_start: 0.8225 (OUTLIER) cc_final: 0.7922 (mp0)
REVERT: G  152 ARG cc_start: 0.6237 (ptm-80) cc_final: 0.5727 (mtm110)
REVERT: G  203 LYS cc_start: 0.9285 (mmmt) cc_final: 0.8916 (mmtt)
REVERT: G  266 GLN cc_start: 0.8931 (OUTLIER) cc_final: 0.8451 (tt0)
REVERT: G  317 PHE cc_start: 0.7936 (OUTLIER) cc_final: 0.7625 (m-80)
  outliers start: 89
  outliers final: 53
  residues processed: 312
  average time/residue: 1.1850
  time to fit residues: 420.1411
Evaluate side-chains
  312 residues out of total 2051 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 68
    poor density    : 244
  time to evaluate  : 2.147 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  124 ASN
Chi-restraints excluded: chain A residue  138 ASP
Chi-restraints excluded: chain A residue  144 GLU
Chi-restraints excluded: chain A residue  223 LEU
Chi-restraints excluded: chain A residue  224 ILE
Chi-restraints excluded: chain A residue  240 PHE
Chi-restraints excluded: chain A residue  242 LEU
Chi-restraints excluded: chain A residue  255 LEU
Chi-restraints excluded: chain A residue  352 VAL
Chi-restraints excluded: chain B residue  101 VAL
Chi-restraints excluded: chain B residue  129 PHE
Chi-restraints excluded: chain B residue  144 GLU
Chi-restraints excluded: chain B residue  224 ILE
Chi-restraints excluded: chain B residue  240 PHE
Chi-restraints excluded: chain B residue  242 LEU
Chi-restraints excluded: chain B residue  255 LEU
Chi-restraints excluded: chain B residue  266 GLN
Chi-restraints excluded: chain B residue  337 LEU
Chi-restraints excluded: chain B residue  352 VAL
Chi-restraints excluded: chain C residue   30 LEU
Chi-restraints excluded: chain C residue   90 GLN
Chi-restraints excluded: chain C residue  101 VAL
Chi-restraints excluded: chain C residue  144 GLU
Chi-restraints excluded: chain C residue  224 ILE
Chi-restraints excluded: chain C residue  240 PHE
Chi-restraints excluded: chain C residue  242 LEU
Chi-restraints excluded: chain C residue  356 ILE
Chi-restraints excluded: chain D residue   30 LEU
Chi-restraints excluded: chain D residue  101 VAL
Chi-restraints excluded: chain D residue  124 ASN
Chi-restraints excluded: chain D residue  223 LEU
Chi-restraints excluded: chain D residue  224 ILE
Chi-restraints excluded: chain D residue  240 PHE
Chi-restraints excluded: chain D residue  242 LEU
Chi-restraints excluded: chain D residue  266 GLN
Chi-restraints excluded: chain D residue  272 VAL
Chi-restraints excluded: chain D residue  276 ARG
Chi-restraints excluded: chain D residue  352 VAL
Chi-restraints excluded: chain E residue   30 LEU
Chi-restraints excluded: chain E residue  124 ASN
Chi-restraints excluded: chain E residue  144 GLU
Chi-restraints excluded: chain E residue  202 LEU
Chi-restraints excluded: chain E residue  224 ILE
Chi-restraints excluded: chain E residue  242 LEU
Chi-restraints excluded: chain E residue  266 GLN
Chi-restraints excluded: chain E residue  297 MET
Chi-restraints excluded: chain E residue  352 VAL
Chi-restraints excluded: chain F residue   30 LEU
Chi-restraints excluded: chain F residue   89 GLN
Chi-restraints excluded: chain F residue  101 VAL
Chi-restraints excluded: chain F residue  124 ASN
Chi-restraints excluded: chain F residue  202 LEU
Chi-restraints excluded: chain F residue  216 LEU
Chi-restraints excluded: chain F residue  224 ILE
Chi-restraints excluded: chain F residue  240 PHE
Chi-restraints excluded: chain F residue  242 LEU
Chi-restraints excluded: chain F residue  287 VAL
Chi-restraints excluded: chain F residue  352 VAL
Chi-restraints excluded: chain G residue   30 LEU
Chi-restraints excluded: chain G residue  101 VAL
Chi-restraints excluded: chain G residue  144 GLU
Chi-restraints excluded: chain G residue  224 ILE
Chi-restraints excluded: chain G residue  240 PHE
Chi-restraints excluded: chain G residue  242 LEU
Chi-restraints excluded: chain G residue  255 LEU
Chi-restraints excluded: chain G residue  266 GLN
Chi-restraints excluded: chain G residue  317 PHE
Chi-restraints excluded: chain G residue  352 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 224
   random chunks:
   chunk 121 optimal weight:    5.9990
   chunk 223 optimal weight:    4.9990
   chunk 27 optimal weight:    9.9990
   chunk 182 optimal weight:    0.9990
   chunk 65 optimal weight:    1.9990
   chunk 118 optimal weight:    0.9980
   chunk 23 optimal weight:    4.9990
   chunk 103 optimal weight:    5.9990
   chunk 222 optimal weight:   30.0000
   chunk 48 optimal weight:    0.8980
   chunk 155 optimal weight:    9.9990
   overall best weight:    1.9786

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

Flipped N/Q/H residues before XYZ refinement:
A 355 ASN
B  56 GLN
B 355 ASN
C 266 GLN
C 340 ASN
C 355 ASN
D 355 ASN
E 355 ASN
F 340 ASN
G 355 ASN

Total number of N/Q/H flips: 10

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3782 r_free = 0.3782 target = 0.124961 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3134 r_free = 0.3134 target = 0.083180 restraints weight = 30639.308|
|-----------------------------------------------------------------------------|
r_work (start): 0.3073 rms_B_bonded: 2.45
r_work: 0.2931 rms_B_bonded: 3.18 restraints_weight: 0.5000
r_work (final): 0.2931
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8256
moved from start:          0.2658

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039  18718  Z= 0.236
  Angle     :  0.645  11.548  25445  Z= 0.305
  Chirality :  0.040   0.214   3045
  Planarity :  0.003   0.038   3052
  Dihedral  :  4.490  59.601   2434
  Min Nonbonded Distance : 2.604

Molprobity Statistics.
  All-atom Clashscore : 5.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.46 %
    Favored  : 98.54 %
  Rotamer:
    Outliers :  4.29 %
    Allowed  : 25.30 %
    Favored  : 70.40 %
  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:  2.13 (0.19), residues: 2198
  helix:  2.39 (0.14), residues: 1519
  sheet:  0.30 (0.49), residues: 126
  loop : -1.19 (0.28), residues: 553

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 127 
 HIS   0.003   0.001   HIS G 106 
 PHE   0.010   0.001   PHE D  12 
 TYR   0.029   0.001   TYR E 232 
 ARG   0.007   0.001   ARG D  29 

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

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

  4396 Ramachandran restraints generated.
    2198 Oldfield, 0 Emsley, 2198 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4396 Ramachandran restraints generated.
    2198 Oldfield, 0 Emsley, 2198 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  331 residues out of total 2051 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 88
    poor density    : 243
  time to evaluate  : 2.076 
Fit side-chains
REVERT: A   14 ASP cc_start: 0.8473 (m-30) cc_final: 0.7618 (p0)
REVERT: A  144 GLU cc_start: 0.8270 (OUTLIER) cc_final: 0.8012 (mp0)
REVERT: A  152 ARG cc_start: 0.6230 (ptm-80) cc_final: 0.5715 (mtm110)
REVERT: A  240 PHE cc_start: 0.7714 (OUTLIER) cc_final: 0.7195 (m-80)
REVERT: A  358 ASN cc_start: 0.8836 (t0) cc_final: 0.8473 (t0)
REVERT: B   14 ASP cc_start: 0.8501 (m-30) cc_final: 0.7827 (p0)
REVERT: B  144 GLU cc_start: 0.8338 (OUTLIER) cc_final: 0.8030 (mp0)
REVERT: B  152 ARG cc_start: 0.6270 (ptm-80) cc_final: 0.5787 (mtm110)
REVERT: B  203 LYS cc_start: 0.9175 (mmmt) cc_final: 0.8809 (mmtt)
REVERT: B  240 PHE cc_start: 0.7641 (OUTLIER) cc_final: 0.7380 (m-80)
REVERT: B  266 GLN cc_start: 0.8778 (OUTLIER) cc_final: 0.8333 (tt0)
REVERT: B  306 ASN cc_start: 0.7512 (t0) cc_final: 0.7263 (t0)
REVERT: B  358 ASN cc_start: 0.8890 (t0) cc_final: 0.8530 (t0)
REVERT: C   14 ASP cc_start: 0.8443 (m-30) cc_final: 0.7730 (p0)
REVERT: C  144 GLU cc_start: 0.8288 (OUTLIER) cc_final: 0.7985 (mp0)
REVERT: C  152 ARG cc_start: 0.6092 (ptm-80) cc_final: 0.5613 (mtm110)
REVERT: C  200 GLN cc_start: 0.8568 (mm-40) cc_final: 0.8350 (mm-40)
REVERT: C  297 MET cc_start: 0.8220 (pmm) cc_final: 0.7944 (pmt)
REVERT: C  306 ASN cc_start: 0.7658 (t0) cc_final: 0.7407 (t0)
REVERT: D   14 ASP cc_start: 0.8350 (m-30) cc_final: 0.7610 (p0)
REVERT: D  152 ARG cc_start: 0.6199 (ptm-80) cc_final: 0.5687 (mtm110)
REVERT: D  200 GLN cc_start: 0.8638 (mm-40) cc_final: 0.8422 (mm-40)
REVERT: D  240 PHE cc_start: 0.7749 (OUTLIER) cc_final: 0.6351 (t80)
REVERT: D  266 GLN cc_start: 0.8886 (OUTLIER) cc_final: 0.8485 (tp-100)
REVERT: D  306 ASN cc_start: 0.7660 (t0) cc_final: 0.7360 (t0)
REVERT: D  317 PHE cc_start: 0.7798 (OUTLIER) cc_final: 0.7368 (m-80)
REVERT: E   14 ASP cc_start: 0.8408 (m-30) cc_final: 0.7719 (p0)
REVERT: E  144 GLU cc_start: 0.8306 (OUTLIER) cc_final: 0.7997 (mp0)
REVERT: E  152 ARG cc_start: 0.6199 (ptm-80) cc_final: 0.5709 (mtm110)
REVERT: E  203 LYS cc_start: 0.9212 (mmmt) cc_final: 0.8895 (mptt)
REVERT: E  266 GLN cc_start: 0.8772 (OUTLIER) cc_final: 0.8472 (tt0)
REVERT: E  297 MET cc_start: 0.7731 (OUTLIER) cc_final: 0.7520 (pmm)
REVERT: E  306 ASN cc_start: 0.7575 (t0) cc_final: 0.7271 (t0)
REVERT: F   14 ASP cc_start: 0.8534 (m-30) cc_final: 0.7998 (t0)
REVERT: F  152 ARG cc_start: 0.6161 (ptm-80) cc_final: 0.5928 (ptm-80)
REVERT: F  203 LYS cc_start: 0.9231 (mmmt) cc_final: 0.8900 (mptt)
REVERT: F  266 GLN cc_start: 0.8938 (OUTLIER) cc_final: 0.8314 (tt0)
REVERT: F  280 TYR cc_start: 0.8169 (t80) cc_final: 0.7605 (m-80)
REVERT: F  358 ASN cc_start: 0.9033 (t0) cc_final: 0.8735 (t0)
REVERT: G   14 ASP cc_start: 0.8484 (m-30) cc_final: 0.7773 (p0)
REVERT: G  128 ARG cc_start: 0.8584 (tmm-80) cc_final: 0.8358 (ttt-90)
REVERT: G  144 GLU cc_start: 0.8239 (OUTLIER) cc_final: 0.7938 (mp0)
REVERT: G  152 ARG cc_start: 0.6221 (ptm-80) cc_final: 0.5716 (mtm110)
REVERT: G  203 LYS cc_start: 0.9280 (mmmt) cc_final: 0.8912 (mmtt)
REVERT: G  266 GLN cc_start: 0.8966 (OUTLIER) cc_final: 0.8464 (tt0)
REVERT: G  317 PHE cc_start: 0.7922 (OUTLIER) cc_final: 0.7604 (m-80)
  outliers start: 88
  outliers final: 52
  residues processed: 309
  average time/residue: 1.1751
  time to fit residues: 412.3182
Evaluate side-chains
  307 residues out of total 2051 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 68
    poor density    : 239
  time to evaluate  : 2.157 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  124 ASN
Chi-restraints excluded: chain A residue  144 GLU
Chi-restraints excluded: chain A residue  223 LEU
Chi-restraints excluded: chain A residue  224 ILE
Chi-restraints excluded: chain A residue  240 PHE
Chi-restraints excluded: chain A residue  242 LEU
Chi-restraints excluded: chain A residue  255 LEU
Chi-restraints excluded: chain A residue  352 VAL
Chi-restraints excluded: chain B residue  101 VAL
Chi-restraints excluded: chain B residue  129 PHE
Chi-restraints excluded: chain B residue  144 GLU
Chi-restraints excluded: chain B residue  202 LEU
Chi-restraints excluded: chain B residue  224 ILE
Chi-restraints excluded: chain B residue  240 PHE
Chi-restraints excluded: chain B residue  242 LEU
Chi-restraints excluded: chain B residue  255 LEU
Chi-restraints excluded: chain B residue  266 GLN
Chi-restraints excluded: chain B residue  352 VAL
Chi-restraints excluded: chain C residue   30 LEU
Chi-restraints excluded: chain C residue  101 VAL
Chi-restraints excluded: chain C residue  144 GLU
Chi-restraints excluded: chain C residue  224 ILE
Chi-restraints excluded: chain C residue  240 PHE
Chi-restraints excluded: chain C residue  242 LEU
Chi-restraints excluded: chain D residue   30 LEU
Chi-restraints excluded: chain D residue  101 VAL
Chi-restraints excluded: chain D residue  124 ASN
Chi-restraints excluded: chain D residue  202 LEU
Chi-restraints excluded: chain D residue  223 LEU
Chi-restraints excluded: chain D residue  224 ILE
Chi-restraints excluded: chain D residue  240 PHE
Chi-restraints excluded: chain D residue  242 LEU
Chi-restraints excluded: chain D residue  266 GLN
Chi-restraints excluded: chain D residue  272 VAL
Chi-restraints excluded: chain D residue  276 ARG
Chi-restraints excluded: chain D residue  317 PHE
Chi-restraints excluded: chain D residue  352 VAL
Chi-restraints excluded: chain E residue   30 LEU
Chi-restraints excluded: chain E residue  124 ASN
Chi-restraints excluded: chain E residue  144 GLU
Chi-restraints excluded: chain E residue  202 LEU
Chi-restraints excluded: chain E residue  224 ILE
Chi-restraints excluded: chain E residue  242 LEU
Chi-restraints excluded: chain E residue  266 GLN
Chi-restraints excluded: chain E residue  297 MET
Chi-restraints excluded: chain E residue  352 VAL
Chi-restraints excluded: chain F residue   30 LEU
Chi-restraints excluded: chain F residue  101 VAL
Chi-restraints excluded: chain F residue  124 ASN
Chi-restraints excluded: chain F residue  202 LEU
Chi-restraints excluded: chain F residue  216 LEU
Chi-restraints excluded: chain F residue  224 ILE
Chi-restraints excluded: chain F residue  240 PHE
Chi-restraints excluded: chain F residue  242 LEU
Chi-restraints excluded: chain F residue  255 LEU
Chi-restraints excluded: chain F residue  266 GLN
Chi-restraints excluded: chain F residue  287 VAL
Chi-restraints excluded: chain F residue  352 VAL
Chi-restraints excluded: chain G residue   30 LEU
Chi-restraints excluded: chain G residue  101 VAL
Chi-restraints excluded: chain G residue  144 GLU
Chi-restraints excluded: chain G residue  224 ILE
Chi-restraints excluded: chain G residue  240 PHE
Chi-restraints excluded: chain G residue  242 LEU
Chi-restraints excluded: chain G residue  255 LEU
Chi-restraints excluded: chain G residue  266 GLN
Chi-restraints excluded: chain G residue  317 PHE
Chi-restraints excluded: chain G residue  352 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 224
   random chunks:
   chunk 55 optimal weight:    4.9990
   chunk 183 optimal weight:    0.8980
   chunk 120 optimal weight:    1.9990
   chunk 107 optimal weight:    0.9990
   chunk 110 optimal weight:    2.9990
   chunk 88 optimal weight:    4.9990
   chunk 21 optimal weight:    0.0270
   chunk 80 optimal weight:    0.9990
   chunk 103 optimal weight:    4.9990
   chunk 100 optimal weight:    0.8980
   chunk 63 optimal weight:    6.9990
   overall best weight:    0.7642

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

Flipped N/Q/H residues before XYZ refinement:
A 355 ASN
B 355 ASN
C 266 GLN
C 340 ASN
C 355 ASN
D 355 ASN
E 355 ASN
F 340 ASN
G  56 GLN
G 355 ASN

Total number of N/Q/H flips: 10

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3806 r_free = 0.3806 target = 0.126829 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3167 r_free = 0.3167 target = 0.085213 restraints weight = 30499.112|
|-----------------------------------------------------------------------------|
r_work (start): 0.3114 rms_B_bonded: 2.46
r_work: 0.2973 rms_B_bonded: 3.19 restraints_weight: 0.5000
r_work (final): 0.2973
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8235
moved from start:          0.2662

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  18718  Z= 0.172
  Angle     :  0.641  11.381  25445  Z= 0.303
  Chirality :  0.039   0.207   3045
  Planarity :  0.003   0.031   3052
  Dihedral  :  4.412  57.189   2434
  Min Nonbonded Distance : 2.594

Molprobity Statistics.
  All-atom Clashscore : 5.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.64 %
    Favored  : 98.36 %
  Rotamer:
    Outliers :  3.51 %
    Allowed  : 26.28 %
    Favored  : 70.21 %
  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:  2.27 (0.19), residues: 2198
  helix:  2.50 (0.14), residues: 1512
  sheet:  0.25 (0.49), residues: 126
  loop : -1.09 (0.28), residues: 560

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP E  74 
 HIS   0.002   0.001   HIS A 106 
 PHE   0.010   0.001   PHE D  12 
 TYR   0.028   0.001   TYR E 232 
 ARG   0.007   0.001   ARG D  29 

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

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

  4396 Ramachandran restraints generated.
    2198 Oldfield, 0 Emsley, 2198 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4396 Ramachandran restraints generated.
    2198 Oldfield, 0 Emsley, 2198 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  324 residues out of total 2051 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 72
    poor density    : 252
  time to evaluate  : 2.306 
Fit side-chains
REVERT: A   14 ASP cc_start: 0.8459 (m-30) cc_final: 0.7527 (p0)
REVERT: A  144 GLU cc_start: 0.8297 (OUTLIER) cc_final: 0.8003 (mp0)
REVERT: A  152 ARG cc_start: 0.6234 (ptm-80) cc_final: 0.5712 (mtm110)
REVERT: A  240 PHE cc_start: 0.7571 (OUTLIER) cc_final: 0.6949 (m-80)
REVERT: A  280 TYR cc_start: 0.8207 (t80) cc_final: 0.7627 (m-80)
REVERT: A  358 ASN cc_start: 0.8847 (t0) cc_final: 0.8483 (t0)
REVERT: B   14 ASP cc_start: 0.8456 (m-30) cc_final: 0.7817 (p0)
REVERT: B  144 GLU cc_start: 0.8344 (OUTLIER) cc_final: 0.8032 (mp0)
REVERT: B  152 ARG cc_start: 0.6271 (ptm-80) cc_final: 0.5751 (mtm110)
REVERT: B  203 LYS cc_start: 0.9204 (mmmt) cc_final: 0.8845 (mmtt)
REVERT: B  240 PHE cc_start: 0.7622 (OUTLIER) cc_final: 0.7375 (m-80)
REVERT: B  306 ASN cc_start: 0.7560 (t0) cc_final: 0.7295 (t0)
REVERT: B  358 ASN cc_start: 0.8935 (t0) cc_final: 0.8537 (t0)
REVERT: C   14 ASP cc_start: 0.8430 (m-30) cc_final: 0.7635 (p0)
REVERT: C  144 GLU cc_start: 0.8325 (OUTLIER) cc_final: 0.8049 (mp0)
REVERT: C  152 ARG cc_start: 0.6098 (ptm-80) cc_final: 0.5610 (mtm110)
REVERT: C  200 GLN cc_start: 0.8552 (mm-40) cc_final: 0.8335 (mm-40)
REVERT: C  297 MET cc_start: 0.8197 (pmm) cc_final: 0.7914 (pmt)
REVERT: C  306 ASN cc_start: 0.7674 (t0) cc_final: 0.7423 (t0)
REVERT: C  352 VAL cc_start: 0.8821 (p) cc_final: 0.8607 (t)
REVERT: D   14 ASP cc_start: 0.8330 (m-30) cc_final: 0.7631 (p0)
REVERT: D  152 ARG cc_start: 0.6309 (ptm-80) cc_final: 0.5768 (mtm110)
REVERT: D  200 GLN cc_start: 0.8619 (mm-40) cc_final: 0.8397 (mm-40)
REVERT: D  240 PHE cc_start: 0.7711 (OUTLIER) cc_final: 0.6349 (t80)
REVERT: D  266 GLN cc_start: 0.8812 (OUTLIER) cc_final: 0.8407 (tp-100)
REVERT: D  306 ASN cc_start: 0.7669 (t0) cc_final: 0.7401 (t0)
REVERT: E   14 ASP cc_start: 0.8391 (m-30) cc_final: 0.7735 (p0)
REVERT: E  144 GLU cc_start: 0.8300 (OUTLIER) cc_final: 0.8003 (mp0)
REVERT: E  152 ARG cc_start: 0.6152 (ptm-80) cc_final: 0.5721 (mtm110)
REVERT: E  203 LYS cc_start: 0.9222 (mmmt) cc_final: 0.8916 (mptt)
REVERT: E  266 GLN cc_start: 0.8692 (OUTLIER) cc_final: 0.8422 (tt0)
REVERT: E  306 ASN cc_start: 0.7554 (t0) cc_final: 0.7268 (t0)
REVERT: F   14 ASP cc_start: 0.8511 (m-30) cc_final: 0.7981 (t0)
REVERT: F  152 ARG cc_start: 0.6109 (ptm-80) cc_final: 0.5858 (ptm-80)
REVERT: F  203 LYS cc_start: 0.9248 (mmmt) cc_final: 0.8908 (mptt)
REVERT: F  266 GLN cc_start: 0.8851 (OUTLIER) cc_final: 0.8238 (tt0)
REVERT: F  280 TYR cc_start: 0.8140 (t80) cc_final: 0.7600 (m-80)
REVERT: F  358 ASN cc_start: 0.9071 (t0) cc_final: 0.8791 (t0)
REVERT: G   14 ASP cc_start: 0.8457 (m-30) cc_final: 0.7752 (p0)
REVERT: G  128 ARG cc_start: 0.8588 (tmm-80) cc_final: 0.8362 (ttt-90)
REVERT: G  144 GLU cc_start: 0.8223 (OUTLIER) cc_final: 0.7894 (mp0)
REVERT: G  152 ARG cc_start: 0.6184 (ptm-80) cc_final: 0.5717 (mtm110)
REVERT: G  266 GLN cc_start: 0.8931 (OUTLIER) cc_final: 0.8458 (tt0)
REVERT: G  317 PHE cc_start: 0.7889 (OUTLIER) cc_final: 0.7576 (m-80)
  outliers start: 72
  outliers final: 51
  residues processed: 307
  average time/residue: 1.1962
  time to fit residues: 416.2946
Evaluate side-chains
  306 residues out of total 2051 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 64
    poor density    : 242
  time to evaluate  : 1.987 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  124 ASN
Chi-restraints excluded: chain A residue  144 GLU
Chi-restraints excluded: chain A residue  223 LEU
Chi-restraints excluded: chain A residue  224 ILE
Chi-restraints excluded: chain A residue  240 PHE
Chi-restraints excluded: chain A residue  242 LEU
Chi-restraints excluded: chain A residue  255 LEU
Chi-restraints excluded: chain A residue  352 VAL
Chi-restraints excluded: chain B residue  101 VAL
Chi-restraints excluded: chain B residue  129 PHE
Chi-restraints excluded: chain B residue  144 GLU
Chi-restraints excluded: chain B residue  224 ILE
Chi-restraints excluded: chain B residue  240 PHE
Chi-restraints excluded: chain B residue  242 LEU
Chi-restraints excluded: chain B residue  255 LEU
Chi-restraints excluded: chain B residue  352 VAL
Chi-restraints excluded: chain C residue   30 LEU
Chi-restraints excluded: chain C residue  101 VAL
Chi-restraints excluded: chain C residue  144 GLU
Chi-restraints excluded: chain C residue  224 ILE
Chi-restraints excluded: chain C residue  240 PHE
Chi-restraints excluded: chain C residue  242 LEU
Chi-restraints excluded: chain D residue   30 LEU
Chi-restraints excluded: chain D residue  101 VAL
Chi-restraints excluded: chain D residue  124 ASN
Chi-restraints excluded: chain D residue  202 LEU
Chi-restraints excluded: chain D residue  223 LEU
Chi-restraints excluded: chain D residue  224 ILE
Chi-restraints excluded: chain D residue  240 PHE
Chi-restraints excluded: chain D residue  242 LEU
Chi-restraints excluded: chain D residue  266 GLN
Chi-restraints excluded: chain D residue  272 VAL
Chi-restraints excluded: chain D residue  276 ARG
Chi-restraints excluded: chain D residue  352 VAL
Chi-restraints excluded: chain E residue   30 LEU
Chi-restraints excluded: chain E residue  124 ASN
Chi-restraints excluded: chain E residue  144 GLU
Chi-restraints excluded: chain E residue  202 LEU
Chi-restraints excluded: chain E residue  224 ILE
Chi-restraints excluded: chain E residue  242 LEU
Chi-restraints excluded: chain E residue  266 GLN
Chi-restraints excluded: chain E residue  352 VAL
Chi-restraints excluded: chain F residue   30 LEU
Chi-restraints excluded: chain F residue  101 VAL
Chi-restraints excluded: chain F residue  124 ASN
Chi-restraints excluded: chain F residue  202 LEU
Chi-restraints excluded: chain F residue  216 LEU
Chi-restraints excluded: chain F residue  224 ILE
Chi-restraints excluded: chain F residue  240 PHE
Chi-restraints excluded: chain F residue  242 LEU
Chi-restraints excluded: chain F residue  266 GLN
Chi-restraints excluded: chain F residue  287 VAL
Chi-restraints excluded: chain F residue  352 VAL
Chi-restraints excluded: chain G residue   30 LEU
Chi-restraints excluded: chain G residue  101 VAL
Chi-restraints excluded: chain G residue  144 GLU
Chi-restraints excluded: chain G residue  202 LEU
Chi-restraints excluded: chain G residue  224 ILE
Chi-restraints excluded: chain G residue  240 PHE
Chi-restraints excluded: chain G residue  242 LEU
Chi-restraints excluded: chain G residue  255 LEU
Chi-restraints excluded: chain G residue  266 GLN
Chi-restraints excluded: chain G residue  317 PHE
Chi-restraints excluded: chain G residue  352 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 224
   random chunks:
   chunk 78 optimal weight:    2.9990
   chunk 153 optimal weight:    5.9990
   chunk 199 optimal weight:    2.9990
   chunk 46 optimal weight:    3.9990
   chunk 23 optimal weight:    4.9990
   chunk 68 optimal weight:    0.6980
   chunk 93 optimal weight:    7.9990
   chunk 167 optimal weight:    3.9990
   chunk 217 optimal weight:    0.7980
   chunk 204 optimal weight:    1.9990
   chunk 39 optimal weight:    3.9990
   overall best weight:    1.8986

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

Flipped N/Q/H residues before XYZ refinement:
A 355 ASN
B  56 GLN
B 355 ASN
C 266 GLN
C 340 ASN
C 355 ASN
D 355 ASN
E 355 ASN
F 340 ASN
G 355 ASN

Total number of N/Q/H flips: 10

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3784 r_free = 0.3784 target = 0.125107 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 66)----------------|
| r_work = 0.3125 r_free = 0.3125 target = 0.082728 restraints weight = 30567.699|
|-----------------------------------------------------------------------------|
r_work (start): 0.3073 rms_B_bonded: 2.48
r_work: 0.2931 rms_B_bonded: 3.20 restraints_weight: 0.5000
r_work (final): 0.2931
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8263
moved from start:          0.2756

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042  18718  Z= 0.238
  Angle     :  0.675  12.354  25445  Z= 0.319
  Chirality :  0.041   0.214   3045
  Planarity :  0.003   0.032   3052
  Dihedral  :  4.317  55.066   2434
  Min Nonbonded Distance : 2.582

Molprobity Statistics.
  All-atom Clashscore : 6.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.64 %
    Favored  : 98.36 %
  Rotamer:
    Outliers :  3.80 %
    Allowed  : 25.99 %
    Favored  : 70.21 %
  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:  2.15 (0.19), residues: 2198
  helix:  2.40 (0.14), residues: 1519
  sheet:  0.25 (0.49), residues: 126
  loop : -1.15 (0.29), residues: 553

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP C 127 
 HIS   0.003   0.001   HIS B 106 
 PHE   0.012   0.001   PHE E  15 
 TYR   0.030   0.001   TYR E 232 
 ARG   0.008   0.001   ARG C  29 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 11612.82 seconds
wall clock time: 207 minutes 5.26 seconds (12425.26 seconds total)