Starting phenix.real_space_refine
on Wed Mar  4 20:49:29 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6vd7_21150/03_2026/6vd7_21150.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6vd7_21150/03_2026/6vd7_21150.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.02
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/6vd7_21150/03_2026/6vd7_21150.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6vd7_21150/03_2026/6vd7_21150.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/6vd7_21150/03_2026/6vd7_21150.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6vd7_21150/03_2026/6vd7_21150.map"
  }
  resolution = 3.02
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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=   0.008 sd=   0.694
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   11088      2.51       5
     N    2513      2.21       5
     O    2828      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 70 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 16506
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2358
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 297, 2358
          Classifications: {'peptide': 297}
          Incomplete info: {'truncation_to_alanine': 15}
          Link IDs: {'PTRANS': 15, 'TRANS': 281}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 61
          Unresolved non-hydrogen angles: 69
          Unresolved non-hydrogen dihedrals: 53
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'ASP:plan': 1, 'GLU:plan': 3, 'ARG:plan': 2, 'GLN:plan1': 1}
          Unresolved non-hydrogen planarities: 29
  Restraints were copied for chains:
    B, C, D, E, F, G
  Time building chain proxies: 2.29, per 1000 atoms: 0.14
  Number of scatterers: 16506
  At special positions: 0
  Unit cell: (107, 109.14, 117.7, 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    2828      8.00
     N    2513      7.00
     C   11088      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=14, 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
    Simple disulfide: pdb=" SG  CYS B  66 " - pdb=" SG  CYS B 267 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C  66 " - pdb=" SG  CYS C 267 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D  66 " - pdb=" SG  CYS D 267 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E  66 " - pdb=" SG  CYS E 267 " distance=2.03
    Simple disulfide: pdb=" SG  CYS F  66 " - pdb=" SG  CYS F 267 " distance=2.03
    Simple disulfide: pdb=" SG  CYS G  66 " - pdb=" SG  CYS G 267 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  84 " - pdb=" SG  CYS B 248 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C  84 " - pdb=" SG  CYS C 248 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D  84 " - pdb=" SG  CYS D 248 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E  84 " - pdb=" SG  CYS E 248 " distance=2.03
    Simple disulfide: pdb=" SG  CYS F  84 " - pdb=" SG  CYS F 248 " distance=2.03
    Simple disulfide: pdb=" SG  CYS G  84 " - pdb=" SG  CYS G 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: 1.47
  Conformation dependent library (CDL) restraints added in 718.0 milliseconds
  

  4074 Ramachandran restraints generated.
    2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  4060

  Finding SS restraints...
    Secondary structure from input PDB file:
      91 helices and 7 sheets defined
      69.4% alpha, 3.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.41
  Creating SS restraints...
    Processing helix  chain 'A' and resid 33 through 61
      Proline residue:  A  46  - end of helix
    Processing helix  chain 'A' and resid 73 through 84
      removed outlier: 4.071A  pdb=" N   VAL A  80 " --> pdb=" O   GLN A  76 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 103 through 108
    Processing helix  chain 'A' and resid 108 through 131
      removed outlier: 3.671A  pdb=" N   LEU A 113 " --> pdb=" O   PHE A 109 " (cutoff:3.500A)
      removed outlier: 4.250A  pdb=" N   LEU A 114 " --> pdb=" O   PRO A 110 " (cutoff:3.500A)
      Proline residue:  A 123  - end of helix
    Processing helix  chain 'A' and resid 131 through 154
    Processing helix  chain 'A' and resid 196 through 205
      removed outlier: 3.621A  pdb=" N   LYS A 205 " --> pdb=" O   TYR A 201 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 209 through 241
      removed outlier: 3.628A  pdb=" N   SER A 241 " --> pdb=" O   ILE A 237 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 271 through 298
      Proline residue:  A 291  - end of helix
    Processing helix  chain 'A' and resid 299 through 302
    Processing helix  chain 'A' and resid 306 through 311
    Processing helix  chain 'A' and resid 312 through 314
      No H-bonds generated for 'chain 'A' and resid 312 through 314'
    Processing helix  chain 'A' and resid 328 through 341
      removed outlier: 3.703A  pdb=" N   LEU A 332 " --> pdb=" O   ASP A 328 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 345 through 357
      removed outlier: 4.279A  pdb=" N   PHE A 349 " --> pdb=" O   LYS A 345 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 33 through 61
      Proline residue:  B  46  - end of helix
    Processing helix  chain 'B' and resid 73 through 84
      removed outlier: 4.071A  pdb=" N   VAL B  80 " --> pdb=" O   GLN B  76 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 103 through 108
    Processing helix  chain 'B' and resid 108 through 131
      removed outlier: 3.671A  pdb=" N   LEU B 113 " --> pdb=" O   PHE B 109 " (cutoff:3.500A)
      removed outlier: 4.250A  pdb=" N   LEU B 114 " --> pdb=" O   PRO B 110 " (cutoff:3.500A)
      Proline residue:  B 123  - end of helix
    Processing helix  chain 'B' and resid 131 through 154
    Processing helix  chain 'B' and resid 196 through 205
      removed outlier: 3.622A  pdb=" N   LYS B 205 " --> pdb=" O   TYR B 201 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 209 through 241
      removed outlier: 3.628A  pdb=" N   SER B 241 " --> pdb=" O   ILE B 237 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 271 through 298
      Proline residue:  B 291  - end of helix
    Processing helix  chain 'B' and resid 299 through 302
    Processing helix  chain 'B' and resid 306 through 311
    Processing helix  chain 'B' and resid 312 through 314
      No H-bonds generated for 'chain 'B' and resid 312 through 314'
    Processing helix  chain 'B' and resid 328 through 341
      removed outlier: 3.702A  pdb=" N   LEU B 332 " --> pdb=" O   ASP B 328 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 345 through 357
      removed outlier: 4.278A  pdb=" N   PHE B 349 " --> pdb=" O   LYS B 345 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 33 through 61
      Proline residue:  C  46  - end of helix
    Processing helix  chain 'C' and resid 73 through 84
      removed outlier: 4.072A  pdb=" N   VAL C  80 " --> pdb=" O   GLN C  76 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 103 through 108
    Processing helix  chain 'C' and resid 108 through 131
      removed outlier: 3.671A  pdb=" N   LEU C 113 " --> pdb=" O   PHE C 109 " (cutoff:3.500A)
      removed outlier: 4.250A  pdb=" N   LEU C 114 " --> pdb=" O   PRO C 110 " (cutoff:3.500A)
      Proline residue:  C 123  - end of helix
    Processing helix  chain 'C' and resid 131 through 154
    Processing helix  chain 'C' and resid 196 through 205
      removed outlier: 3.621A  pdb=" N   LYS C 205 " --> pdb=" O   TYR C 201 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 209 through 241
      removed outlier: 3.628A  pdb=" N   SER C 241 " --> pdb=" O   ILE C 237 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 271 through 298
      Proline residue:  C 291  - end of helix
    Processing helix  chain 'C' and resid 299 through 302
    Processing helix  chain 'C' and resid 306 through 311
    Processing helix  chain 'C' and resid 312 through 314
      No H-bonds generated for 'chain 'C' and resid 312 through 314'
    Processing helix  chain 'C' and resid 328 through 341
      removed outlier: 3.702A  pdb=" N   LEU C 332 " --> pdb=" O   ASP C 328 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 345 through 357
      removed outlier: 4.278A  pdb=" N   PHE C 349 " --> pdb=" O   LYS C 345 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 33 through 61
      Proline residue:  D  46  - end of helix
    Processing helix  chain 'D' and resid 73 through 84
      removed outlier: 4.071A  pdb=" N   VAL D  80 " --> pdb=" O   GLN D  76 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 103 through 108
    Processing helix  chain 'D' and resid 108 through 131
      removed outlier: 3.671A  pdb=" N   LEU D 113 " --> pdb=" O   PHE D 109 " (cutoff:3.500A)
      removed outlier: 4.250A  pdb=" N   LEU D 114 " --> pdb=" O   PRO D 110 " (cutoff:3.500A)
      Proline residue:  D 123  - end of helix
    Processing helix  chain 'D' and resid 131 through 154
    Processing helix  chain 'D' and resid 196 through 205
      removed outlier: 3.621A  pdb=" N   LYS D 205 " --> pdb=" O   TYR D 201 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 209 through 241
      removed outlier: 3.628A  pdb=" N   SER D 241 " --> pdb=" O   ILE D 237 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 271 through 298
      Proline residue:  D 291  - end of helix
    Processing helix  chain 'D' and resid 299 through 302
    Processing helix  chain 'D' and resid 306 through 311
    Processing helix  chain 'D' and resid 312 through 314
      No H-bonds generated for 'chain 'D' and resid 312 through 314'
    Processing helix  chain 'D' and resid 328 through 341
      removed outlier: 3.703A  pdb=" N   LEU D 332 " --> pdb=" O   ASP D 328 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 345 through 357
      removed outlier: 4.278A  pdb=" N   PHE D 349 " --> pdb=" O   LYS D 345 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 33 through 61
      Proline residue:  E  46  - end of helix
    Processing helix  chain 'E' and resid 73 through 84
      removed outlier: 4.071A  pdb=" N   VAL E  80 " --> pdb=" O   GLN E  76 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 103 through 108
    Processing helix  chain 'E' and resid 108 through 131
      removed outlier: 3.671A  pdb=" N   LEU E 113 " --> pdb=" O   PHE E 109 " (cutoff:3.500A)
      removed outlier: 4.250A  pdb=" N   LEU E 114 " --> pdb=" O   PRO E 110 " (cutoff:3.500A)
      Proline residue:  E 123  - end of helix
    Processing helix  chain 'E' and resid 131 through 154
    Processing helix  chain 'E' and resid 196 through 205
      removed outlier: 3.621A  pdb=" N   LYS E 205 " --> pdb=" O   TYR E 201 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 209 through 241
      removed outlier: 3.627A  pdb=" N   SER E 241 " --> pdb=" O   ILE E 237 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 271 through 298
      Proline residue:  E 291  - end of helix
    Processing helix  chain 'E' and resid 299 through 302
    Processing helix  chain 'E' and resid 306 through 311
    Processing helix  chain 'E' and resid 312 through 314
      No H-bonds generated for 'chain 'E' and resid 312 through 314'
    Processing helix  chain 'E' and resid 328 through 341
      removed outlier: 3.703A  pdb=" N   LEU E 332 " --> pdb=" O   ASP E 328 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 345 through 357
      removed outlier: 4.279A  pdb=" N   PHE E 349 " --> pdb=" O   LYS E 345 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 33 through 61
      Proline residue:  F  46  - end of helix
    Processing helix  chain 'F' and resid 73 through 84
      removed outlier: 4.072A  pdb=" N   VAL F  80 " --> pdb=" O   GLN F  76 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 103 through 108
    Processing helix  chain 'F' and resid 108 through 131
      removed outlier: 3.671A  pdb=" N   LEU F 113 " --> pdb=" O   PHE F 109 " (cutoff:3.500A)
      removed outlier: 4.250A  pdb=" N   LEU F 114 " --> pdb=" O   PRO F 110 " (cutoff:3.500A)
      Proline residue:  F 123  - end of helix
    Processing helix  chain 'F' and resid 131 through 154
    Processing helix  chain 'F' and resid 196 through 205
      removed outlier: 3.621A  pdb=" N   LYS F 205 " --> pdb=" O   TYR F 201 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 209 through 241
      removed outlier: 3.628A  pdb=" N   SER F 241 " --> pdb=" O   ILE F 237 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 271 through 298
      Proline residue:  F 291  - end of helix
    Processing helix  chain 'F' and resid 299 through 302
    Processing helix  chain 'F' and resid 306 through 311
    Processing helix  chain 'F' and resid 312 through 314
      No H-bonds generated for 'chain 'F' and resid 312 through 314'
    Processing helix  chain 'F' and resid 328 through 341
      removed outlier: 3.702A  pdb=" N   LEU F 332 " --> pdb=" O   ASP F 328 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 345 through 357
      removed outlier: 4.279A  pdb=" N   PHE F 349 " --> pdb=" O   LYS F 345 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 33 through 61
      Proline residue:  G  46  - end of helix
    Processing helix  chain 'G' and resid 73 through 84
      removed outlier: 4.071A  pdb=" N   VAL G  80 " --> pdb=" O   GLN G  76 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 103 through 108
    Processing helix  chain 'G' and resid 108 through 131
      removed outlier: 3.671A  pdb=" N   LEU G 113 " --> pdb=" O   PHE G 109 " (cutoff:3.500A)
      removed outlier: 4.250A  pdb=" N   LEU G 114 " --> pdb=" O   PRO G 110 " (cutoff:3.500A)
      Proline residue:  G 123  - end of helix
    Processing helix  chain 'G' and resid 131 through 154
    Processing helix  chain 'G' and resid 196 through 205
      removed outlier: 3.622A  pdb=" N   LYS G 205 " --> pdb=" O   TYR G 201 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 209 through 241
      removed outlier: 3.628A  pdb=" N   SER G 241 " --> pdb=" O   ILE G 237 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 271 through 298
      Proline residue:  G 291  - end of helix
    Processing helix  chain 'G' and resid 299 through 302
    Processing helix  chain 'G' and resid 306 through 311
    Processing helix  chain 'G' and resid 312 through 314
      No H-bonds generated for 'chain 'G' and resid 312 through 314'
    Processing helix  chain 'G' and resid 328 through 341
      removed outlier: 3.702A  pdb=" N   LEU G 332 " --> pdb=" O   ASP G 328 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 345 through 357
      removed outlier: 4.278A  pdb=" N   PHE G 349 " --> pdb=" O   LYS G 345 " (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

    1022 hydrogen bonds defined for protein.
    3024 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.45

  Time building geometry restraints manager: 1.94 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 4815
        1.34 -     1.46: 3531
        1.46 -     1.57: 8496
        1.57 -     1.69: 0
        1.69 -     1.81: 98
  Bond restraints: 16940
  Sorted by residual:
  bond pdb=" CB  THR C  59 "
       pdb=" CG2 THR C  59 "
    ideal  model  delta    sigma   weight residual
    1.521  1.478  0.043 3.30e-02 9.18e+02 1.73e+00
  bond pdb=" CB  THR E  59 "
       pdb=" CG2 THR E  59 "
    ideal  model  delta    sigma   weight residual
    1.521  1.478  0.043 3.30e-02 9.18e+02 1.72e+00
  bond pdb=" CB  THR B  59 "
       pdb=" CG2 THR B  59 "
    ideal  model  delta    sigma   weight residual
    1.521  1.478  0.043 3.30e-02 9.18e+02 1.72e+00
  bond pdb=" CB  THR A  59 "
       pdb=" CG2 THR A  59 "
    ideal  model  delta    sigma   weight residual
    1.521  1.478  0.043 3.30e-02 9.18e+02 1.71e+00
  bond pdb=" CB  THR F  59 "
       pdb=" CG2 THR F  59 "
    ideal  model  delta    sigma   weight residual
    1.521  1.478  0.043 3.30e-02 9.18e+02 1.71e+00
  ... (remaining 16935 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.43: 21900
        1.43 -     2.86: 935
        2.86 -     4.29: 228
        4.29 -     5.72: 72
        5.72 -     7.15: 7
  Bond angle restraints: 23142
  Sorted by residual:
  angle pdb=" N   VAL A 299 "
        pdb=" CA  VAL A 299 "
        pdb=" C   VAL A 299 "
      ideal   model   delta    sigma   weight residual
     108.88  116.03   -7.15 2.16e+00 2.14e-01 1.10e+01
  angle pdb=" N   VAL D 299 "
        pdb=" CA  VAL D 299 "
        pdb=" C   VAL D 299 "
      ideal   model   delta    sigma   weight residual
     108.88  116.03   -7.15 2.16e+00 2.14e-01 1.10e+01
  angle pdb=" N   VAL B 299 "
        pdb=" CA  VAL B 299 "
        pdb=" C   VAL B 299 "
      ideal   model   delta    sigma   weight residual
     108.88  116.03   -7.15 2.16e+00 2.14e-01 1.09e+01
  angle pdb=" N   VAL G 299 "
        pdb=" CA  VAL G 299 "
        pdb=" C   VAL G 299 "
      ideal   model   delta    sigma   weight residual
     108.88  116.02   -7.14 2.16e+00 2.14e-01 1.09e+01
  angle pdb=" N   VAL C 299 "
        pdb=" CA  VAL C 299 "
        pdb=" C   VAL C 299 "
      ideal   model   delta    sigma   weight residual
     108.88  116.02   -7.14 2.16e+00 2.14e-01 1.09e+01
  ... (remaining 23137 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    12.11: 8325
       12.11 -    24.22: 1083
       24.22 -    36.32: 525
       36.32 -    48.43: 42
       48.43 -    60.54: 28
  Dihedral angle restraints: 10003
    sinusoidal: 3759
      harmonic: 6244
  Sorted by residual:
  dihedral pdb=" CA  GLU B  22 "
           pdb=" C   GLU B  22 "
           pdb=" N   SER B  23 "
           pdb=" CA  SER B  23 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  149.34   30.66     0      5.00e+00 4.00e-02 3.76e+01
  dihedral pdb=" CA  GLU E  22 "
           pdb=" C   GLU E  22 "
           pdb=" N   SER E  23 "
           pdb=" CA  SER E  23 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  149.37   30.63     0      5.00e+00 4.00e-02 3.75e+01
  dihedral pdb=" CA  GLU A  22 "
           pdb=" C   GLU A  22 "
           pdb=" N   SER A  23 "
           pdb=" CA  SER A  23 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  149.40   30.60     0      5.00e+00 4.00e-02 3.75e+01
  ... (remaining 10000 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.032: 1556
       0.032 -    0.065: 870
       0.065 -    0.097: 205
       0.097 -    0.129: 141
       0.129 -    0.161: 21
  Chirality restraints: 2793
  Sorted by residual:
  chirality pdb=" CB  THR C  59 "
            pdb=" CA  THR C  59 "
            pdb=" OG1 THR C  59 "
            pdb=" CG2 THR C  59 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.39    0.16 2.00e-01 2.50e+01 6.51e-01
  chirality pdb=" CB  THR E  59 "
            pdb=" CA  THR E  59 "
            pdb=" OG1 THR E  59 "
            pdb=" CG2 THR E  59 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.39    0.16 2.00e-01 2.50e+01 6.43e-01
  chirality pdb=" CB  THR B  59 "
            pdb=" CA  THR B  59 "
            pdb=" OG1 THR B  59 "
            pdb=" CG2 THR B  59 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.39    0.16 2.00e-01 2.50e+01 6.37e-01
  ... (remaining 2790 not shown)

  Planarity restraints: 2793
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ALA G  33 "    0.020 2.00e-02 2.50e+03   3.96e-02 1.57e+01
        pdb=" C   ALA G  33 "   -0.068 2.00e-02 2.50e+03
        pdb=" O   ALA G  33 "    0.025 2.00e-02 2.50e+03
        pdb=" N   VAL G  34 "    0.023 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ALA F  33 "   -0.020 2.00e-02 2.50e+03   3.94e-02 1.55e+01
        pdb=" C   ALA F  33 "    0.068 2.00e-02 2.50e+03
        pdb=" O   ALA F  33 "   -0.025 2.00e-02 2.50e+03
        pdb=" N   VAL F  34 "   -0.023 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ALA C  33 "    0.020 2.00e-02 2.50e+03   3.93e-02 1.54e+01
        pdb=" C   ALA C  33 "   -0.068 2.00e-02 2.50e+03
        pdb=" O   ALA C  33 "    0.025 2.00e-02 2.50e+03
        pdb=" N   VAL C  34 "    0.023 2.00e-02 2.50e+03
  ... (remaining 2790 not shown)

  Histogram of nonbonded interaction distances:
        2.28 -     2.81: 4842
        2.81 -     3.33: 15941
        3.33 -     3.85: 25709
        3.85 -     4.38: 29155
        4.38 -     4.90: 51521
  Nonbonded interactions: 127168
  Sorted by model distance:
  nonbonded pdb=" O   TYR C 201 "
            pdb=" OG1 THR C 204 "
     model   vdw
     2.284 3.040
  nonbonded pdb=" O   TYR A 201 "
            pdb=" OG1 THR A 204 "
     model   vdw
     2.284 3.040
  nonbonded pdb=" O   TYR D 201 "
            pdb=" OG1 THR D 204 "
     model   vdw
     2.284 3.040
  nonbonded pdb=" O   TYR E 201 "
            pdb=" OG1 THR E 204 "
     model   vdw
     2.284 3.040
  nonbonded pdb=" O   TYR G 201 "
            pdb=" OG1 THR G 204 "
     model   vdw
     2.284 3.040
  ... (remaining 127163 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: 0.05
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'C'
  selection = chain 'D'
  selection = chain 'E'
  selection = chain 'F'
  selection = chain 'G'
}

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:             1.400
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.230
  Check model and map are aligned:         0.040
  Set scattering table:                    0.060
  Process input model:                     13.660
  Find NCS groups from input model:        0.140
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.290
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   16.850
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8323
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      :  0.008   0.049  16954  Z= 0.323
  Angle     :  0.765   7.149  23170  Z= 0.413
  Chirality :  0.045   0.161   2793
  Planarity :  0.004   0.040   2793
  Dihedral  : 13.380  60.537   5901
  Min Nonbonded Distance : 2.284

Molprobity Statistics.
  All-atom Clashscore : 6.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.68 %
    Favored  : 88.32 %
  Rotamer:
    Outliers :  0.78 %
    Allowed  :  6.17 %
    Favored  : 93.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.36 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.54 (0.17), residues: 2037
  helix: -0.17 (0.14), residues: 1260
  sheet: -0.97 (0.48), residues: 84
  loop : -4.80 (0.18), residues: 693

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 276 
 TYR   0.018   0.002   TYR E  25 
 PHE   0.017   0.002   PHE F 240 
 TRP   0.010   0.002   TRP G  85 
 HIS   0.002   0.001   HIS F 330 

Details of bonding type rmsd
  covalent geometry    : bond        0.00768 (16940)
  covalent geometry    : angle       0.76462 (23142)
  SS BOND              : bond        0.00097 (   14)
  SS BOND              : angle       0.78977 (   28)
  hydrogen bonds       : bond        0.12483 ( 1022)
  hydrogen bonds       : angle       5.22126 ( 3024)

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

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

  4074 Ramachandran restraints generated.
    2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4074 Ramachandran restraints generated.
    2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  329 residues out of total 1904 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 315
  time to evaluate  : 0.633 
Fit side-chains
REVERT: A   54 PHE cc_start: 0.7966 (m-80) cc_final: 0.6638 (t80)
REVERT: B   54 PHE cc_start: 0.8020 (m-80) cc_final: 0.7569 (m-80)
REVERT: B  104 TRP cc_start: 0.7995 (p-90) cc_final: 0.7578 (p-90)
REVERT: B  312 GLU cc_start: 0.7944 (pt0) cc_final: 0.7721 (pt0)
REVERT: C   74 TRP cc_start: 0.7373 (t-100) cc_final: 0.7141 (t-100)
REVERT: C  104 TRP cc_start: 0.7976 (p-90) cc_final: 0.7719 (p-90)
REVERT: C  244 ASP cc_start: 0.7256 (p0) cc_final: 0.6915 (p0)
REVERT: C  245 GLU cc_start: 0.7666 (pt0) cc_final: 0.7413 (pt0)
REVERT: D  104 TRP cc_start: 0.7854 (p-90) cc_final: 0.7585 (p-90)
REVERT: D  244 ASP cc_start: 0.7010 (p0) cc_final: 0.6753 (p0)
REVERT: D  312 GLU cc_start: 0.7898 (pt0) cc_final: 0.7598 (pt0)
REVERT: E   63 GLN cc_start: 0.7936 (mm110) cc_final: 0.7683 (mm-40)
REVERT: E   74 TRP cc_start: 0.7375 (t-100) cc_final: 0.7092 (t-100)
REVERT: E  327 TYR cc_start: 0.8678 (m-80) cc_final: 0.8218 (m-80)
REVERT: F   54 PHE cc_start: 0.8068 (m-80) cc_final: 0.7839 (m-80)
REVERT: F   63 GLN cc_start: 0.8075 (mm110) cc_final: 0.7738 (mm-40)
REVERT: F  244 ASP cc_start: 0.7421 (p0) cc_final: 0.7213 (p0)
REVERT: G   54 PHE cc_start: 0.8109 (m-80) cc_final: 0.6768 (t80)
REVERT: G   63 GLN cc_start: 0.8095 (mm110) cc_final: 0.7797 (mm-40)
REVERT: G  143 MET cc_start: 0.9035 (mtp) cc_final: 0.8825 (mtt)
REVERT: G  312 GLU cc_start: 0.7959 (pt0) cc_final: 0.7542 (pt0)
  outliers start: 14
  outliers final: 1
  residues processed: 315
  average time/residue: 0.1271
  time to fit residues: 60.3050
Evaluate side-chains
  226 residues out of total 1904 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 225
  time to evaluate  : 0.565 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain G residue   59 THR
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 203
   random chunks:
   chunk 98 optimal weight:    0.8980
   chunk 194 optimal weight:    5.9990
   chunk 107 optimal weight:    0.2980
   chunk 10 optimal weight:    3.9990
   chunk 66 optimal weight:    2.9990
   chunk 130 optimal weight:    2.9990
   chunk 124 optimal weight:    0.7980
   chunk 103 optimal weight:    1.9990
   chunk 200 optimal weight:    8.9990
   chunk 77 optimal weight:    9.9990
   chunk 122 optimal weight:    9.9990
   overall best weight:    1.3984

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

Flipped N/Q/H residues before XYZ refinement:
B 151 ASN
B 266 GLN
C  63 GLN
C 151 ASN
D 266 GLN
D 282 ASN
G 266 GLN
G 282 ASN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3545 r_free = 0.3545 target = 0.121125 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3246 r_free = 0.3246 target = 0.099759 restraints weight = 27221.039|
|-----------------------------------------------------------------------------|
r_work (start): 0.3218 rms_B_bonded: 2.41
r_work: 0.3103 rms_B_bonded: 2.98 restraints_weight: 0.5000
r_work: 0.2980 rms_B_bonded: 4.95 restraints_weight: 0.2500
r_work (final): 0.2980
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8415
moved from start:          0.1131

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  16954  Z= 0.143
  Angle     :  0.635   7.503  23170  Z= 0.331
  Chirality :  0.041   0.177   2793
  Planarity :  0.004   0.026   2793
  Dihedral  :  5.397  31.515   2241
  Min Nonbonded Distance : 2.576

Molprobity Statistics.
  All-atom Clashscore : 5.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.54 %
    Favored  : 91.46 %
  Rotamer:
    Outliers :  2.22 %
    Allowed  : 12.17 %
    Favored  : 85.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.90 (0.19), residues: 2037
  helix:  1.27 (0.15), residues: 1267
  sheet:  None (None), residues: 0
  loop : -4.10 (0.19), residues: 770

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG E 219 
 TYR   0.014   0.001   TYR C  25 
 PHE   0.009   0.001   PHE G 240 
 TRP   0.013   0.001   TRP C  74 
 HIS   0.003   0.001   HIS G 106 

Details of bonding type rmsd
  covalent geometry    : bond        0.00305 (16940)
  covalent geometry    : angle       0.63478 (23142)
  SS BOND              : bond        0.00173 (   14)
  SS BOND              : angle       0.67091 (   28)
  hydrogen bonds       : bond        0.06087 ( 1022)
  hydrogen bonds       : angle       4.53903 ( 3024)

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

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

  4074 Ramachandran restraints generated.
    2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4074 Ramachandran restraints generated.
    2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  280 residues out of total 1904 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 240
  time to evaluate  : 0.684 
Fit side-chains
REVERT: A   54 PHE cc_start: 0.7926 (m-80) cc_final: 0.6365 (t80)
REVERT: A  312 GLU cc_start: 0.8094 (pt0) cc_final: 0.7887 (pt0)
REVERT: B   54 PHE cc_start: 0.8034 (m-80) cc_final: 0.7674 (m-80)
REVERT: B  104 TRP cc_start: 0.8382 (p-90) cc_final: 0.8066 (p-90)
REVERT: B  312 GLU cc_start: 0.8333 (pt0) cc_final: 0.8099 (pt0)
REVERT: C  104 TRP cc_start: 0.8394 (p-90) cc_final: 0.7916 (p-90)
REVERT: D  104 TRP cc_start: 0.8352 (p-90) cc_final: 0.8023 (p-90)
REVERT: D  312 GLU cc_start: 0.8272 (pt0) cc_final: 0.7863 (pt0)
REVERT: E   51 SER cc_start: 0.8631 (m) cc_final: 0.8404 (m)
REVERT: E  244 ASP cc_start: 0.7325 (p0) cc_final: 0.7017 (p0)
REVERT: E  327 TYR cc_start: 0.8932 (m-80) cc_final: 0.8430 (m-80)
REVERT: F   54 PHE cc_start: 0.8036 (m-80) cc_final: 0.7770 (m-80)
REVERT: F  353 LEU cc_start: 0.9397 (tp) cc_final: 0.9188 (mt)
REVERT: G   54 PHE cc_start: 0.8106 (m-80) cc_final: 0.6585 (t80)
REVERT: G   63 GLN cc_start: 0.8257 (mm110) cc_final: 0.7828 (mm-40)
REVERT: G  312 GLU cc_start: 0.8344 (pt0) cc_final: 0.7907 (pt0)
  outliers start: 40
  outliers final: 22
  residues processed: 269
  average time/residue: 0.1029
  time to fit residues: 44.8499
Evaluate side-chains
  250 residues out of total 1904 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 228
  time to evaluate  : 0.470 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  310 VAL
Chi-restraints excluded: chain A residue  314 LEU
Chi-restraints excluded: chain A residue  356 ILE
Chi-restraints excluded: chain B residue   17 LEU
Chi-restraints excluded: chain B residue  356 ILE
Chi-restraints excluded: chain C residue   17 LEU
Chi-restraints excluded: chain C residue  310 VAL
Chi-restraints excluded: chain C residue  314 LEU
Chi-restraints excluded: chain C residue  356 ILE
Chi-restraints excluded: chain D residue   17 LEU
Chi-restraints excluded: chain D residue  310 VAL
Chi-restraints excluded: chain D residue  314 LEU
Chi-restraints excluded: chain D residue  356 ILE
Chi-restraints excluded: chain E residue   17 LEU
Chi-restraints excluded: chain E residue  114 LEU
Chi-restraints excluded: chain E residue  356 ILE
Chi-restraints excluded: chain F residue  310 VAL
Chi-restraints excluded: chain F residue  314 LEU
Chi-restraints excluded: chain F residue  356 ILE
Chi-restraints excluded: chain G residue  282 ASN
Chi-restraints excluded: chain G residue  341 VAL
Chi-restraints excluded: chain G residue  356 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 203
   random chunks:
   chunk 32 optimal weight:    9.9990
   chunk 176 optimal weight:    1.9990
   chunk 191 optimal weight:    0.9990
   chunk 117 optimal weight:    6.9990
   chunk 86 optimal weight:    5.9990
   chunk 161 optimal weight:    3.9990
   chunk 47 optimal weight:   10.0000
   chunk 152 optimal weight:    2.9990
   chunk 12 optimal weight:    5.9990
   chunk 197 optimal weight:    3.9990
   chunk 9 optimal weight:    6.9990
   overall best weight:    2.7990

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

Flipped N/Q/H residues before XYZ refinement:
B  63 GLN
B 266 GLN
C 266 GLN
D 266 GLN
G 282 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3521 r_free = 0.3521 target = 0.119083 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3220 r_free = 0.3220 target = 0.097919 restraints weight = 27767.979|
|-----------------------------------------------------------------------------|
r_work (start): 0.3195 rms_B_bonded: 2.40
r_work: 0.3080 rms_B_bonded: 2.97 restraints_weight: 0.5000
r_work: 0.2958 rms_B_bonded: 4.92 restraints_weight: 0.2500
r_work (final): 0.2958
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8438
moved from start:          0.1268

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048  16954  Z= 0.185
  Angle     :  0.650   8.482  23170  Z= 0.337
  Chirality :  0.043   0.190   2793
  Planarity :  0.004   0.028   2793
  Dihedral  :  5.322  28.423   2240
  Min Nonbonded Distance : 2.575

Molprobity Statistics.
  All-atom Clashscore : 5.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.05 %
    Favored  : 91.95 %
  Rotamer:
    Outliers :  2.39 %
    Allowed  : 15.45 %
    Favored  : 82.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.39 (0.20), residues: 2037
  helix:  1.54 (0.15), residues: 1288
  sheet: -0.26 (0.53), residues: 84
  loop : -4.18 (0.22), residues: 665

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG E 219 
 TYR   0.018   0.001   TYR F 327 
 PHE   0.013   0.001   PHE D 126 
 TRP   0.013   0.002   TRP E 104 
 HIS   0.003   0.001   HIS B 106 

Details of bonding type rmsd
  covalent geometry    : bond        0.00445 (16940)
  covalent geometry    : angle       0.64963 (23142)
  SS BOND              : bond        0.00107 (   14)
  SS BOND              : angle       0.70521 (   28)
  hydrogen bonds       : bond        0.06444 ( 1022)
  hydrogen bonds       : angle       4.57327 ( 3024)

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

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

  4074 Ramachandran restraints generated.
    2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4074 Ramachandran restraints generated.
    2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  285 residues out of total 1904 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 242
  time to evaluate  : 0.567 
Fit side-chains
REVERT: A   54 PHE cc_start: 0.7879 (m-80) cc_final: 0.6373 (t80)
REVERT: B   54 PHE cc_start: 0.8079 (m-80) cc_final: 0.7754 (m-80)
REVERT: B  104 TRP cc_start: 0.8383 (p-90) cc_final: 0.8019 (p-90)
REVERT: C  104 TRP cc_start: 0.8437 (p-90) cc_final: 0.7931 (p-90)
REVERT: C  244 ASP cc_start: 0.7369 (p0) cc_final: 0.7115 (p0)
REVERT: D  104 TRP cc_start: 0.8334 (p-90) cc_final: 0.7975 (p-90)
REVERT: D  312 GLU cc_start: 0.8300 (pt0) cc_final: 0.7916 (pt0)
REVERT: E   51 SER cc_start: 0.8664 (m) cc_final: 0.8435 (m)
REVERT: E  327 TYR cc_start: 0.8962 (m-80) cc_final: 0.8458 (m-80)
REVERT: F   54 PHE cc_start: 0.8052 (m-80) cc_final: 0.7763 (m-80)
REVERT: F   63 GLN cc_start: 0.8310 (mm110) cc_final: 0.8079 (mm-40)
REVERT: F  244 ASP cc_start: 0.7210 (p0) cc_final: 0.6951 (p0)
REVERT: F  353 LEU cc_start: 0.9414 (tp) cc_final: 0.9205 (mt)
REVERT: G   54 PHE cc_start: 0.8097 (m-80) cc_final: 0.6544 (t80)
REVERT: G  312 GLU cc_start: 0.8267 (pt0) cc_final: 0.7756 (pt0)
  outliers start: 43
  outliers final: 41
  residues processed: 273
  average time/residue: 0.0998
  time to fit residues: 44.2598
Evaluate side-chains
  270 residues out of total 1904 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 229
  time to evaluate  : 0.577 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  235 TYR
Chi-restraints excluded: chain A residue  239 LEU
Chi-restraints excluded: chain A residue  297 MET
Chi-restraints excluded: chain A residue  310 VAL
Chi-restraints excluded: chain A residue  314 LEU
Chi-restraints excluded: chain A residue  356 ILE
Chi-restraints excluded: chain B residue   17 LEU
Chi-restraints excluded: chain B residue   81 ASP
Chi-restraints excluded: chain B residue  235 TYR
Chi-restraints excluded: chain B residue  238 SER
Chi-restraints excluded: chain B residue  356 ILE
Chi-restraints excluded: chain C residue   17 LEU
Chi-restraints excluded: chain C residue  235 TYR
Chi-restraints excluded: chain C residue  310 VAL
Chi-restraints excluded: chain C residue  314 LEU
Chi-restraints excluded: chain C residue  356 ILE
Chi-restraints excluded: chain D residue   17 LEU
Chi-restraints excluded: chain D residue  235 TYR
Chi-restraints excluded: chain D residue  238 SER
Chi-restraints excluded: chain D residue  310 VAL
Chi-restraints excluded: chain D residue  314 LEU
Chi-restraints excluded: chain D residue  356 ILE
Chi-restraints excluded: chain E residue   17 LEU
Chi-restraints excluded: chain E residue  114 LEU
Chi-restraints excluded: chain E residue  235 TYR
Chi-restraints excluded: chain E residue  238 SER
Chi-restraints excluded: chain E residue  239 LEU
Chi-restraints excluded: chain E residue  356 ILE
Chi-restraints excluded: chain F residue   14 ASP
Chi-restraints excluded: chain F residue   17 LEU
Chi-restraints excluded: chain F residue   81 ASP
Chi-restraints excluded: chain F residue  235 TYR
Chi-restraints excluded: chain F residue  310 VAL
Chi-restraints excluded: chain F residue  314 LEU
Chi-restraints excluded: chain F residue  356 ILE
Chi-restraints excluded: chain G residue   17 LEU
Chi-restraints excluded: chain G residue  235 TYR
Chi-restraints excluded: chain G residue  238 SER
Chi-restraints excluded: chain G residue  264 LEU
Chi-restraints excluded: chain G residue  341 VAL
Chi-restraints excluded: chain G residue  356 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 203
   random chunks:
   chunk 40 optimal weight:    2.9990
   chunk 112 optimal weight:    0.7980
   chunk 176 optimal weight:    2.9990
   chunk 177 optimal weight:    1.9990
   chunk 101 optimal weight:    4.9990
   chunk 109 optimal weight:    1.9990
   chunk 182 optimal weight:    1.9990
   chunk 18 optimal weight:    7.9990
   chunk 133 optimal weight:    7.9990
   chunk 162 optimal weight:    5.9990
   chunk 51 optimal weight:    2.9990
   overall best weight:    1.9588

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

Flipped N/Q/H residues before XYZ refinement:
B  63 GLN
D 266 GLN
G 151 ASN
G 266 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3554 r_free = 0.3554 target = 0.121755 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3250 r_free = 0.3250 target = 0.100135 restraints weight = 27398.704|
|-----------------------------------------------------------------------------|
r_work (start): 0.3222 rms_B_bonded: 2.45
r_work: 0.3106 rms_B_bonded: 3.02 restraints_weight: 0.5000
r_work (final): 0.3106
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8325
moved from start:          0.1520

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046  16954  Z= 0.149
  Angle     :  0.614   6.764  23170  Z= 0.318
  Chirality :  0.042   0.209   2793
  Planarity :  0.004   0.027   2793
  Dihedral  :  5.128  27.041   2240
  Min Nonbonded Distance : 2.561

Molprobity Statistics.
  All-atom Clashscore : 5.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.41 %
    Favored  : 92.59 %
  Rotamer:
    Outliers :  2.78 %
    Allowed  : 17.95 %
    Favored  : 79.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.02 (0.20), residues: 2037
  helix:  1.79 (0.15), residues: 1295
  sheet: -0.27 (0.51), residues: 84
  loop : -3.97 (0.23), residues: 658

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG E 219 
 TYR   0.014   0.001   TYR G 327 
 PHE   0.011   0.001   PHE D 126 
 TRP   0.014   0.001   TRP E 104 
 HIS   0.002   0.001   HIS C 330 

Details of bonding type rmsd
  covalent geometry    : bond        0.00345 (16940)
  covalent geometry    : angle       0.61390 (23142)
  SS BOND              : bond        0.00120 (   14)
  SS BOND              : angle       0.63610 (   28)
  hydrogen bonds       : bond        0.05825 ( 1022)
  hydrogen bonds       : angle       4.45001 ( 3024)

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

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

  4074 Ramachandran restraints generated.
    2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4074 Ramachandran restraints generated.
    2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  296 residues out of total 1904 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 246
  time to evaluate  : 0.633 
Fit side-chains
REVERT: A   54 PHE cc_start: 0.7857 (m-80) cc_final: 0.6376 (t80)
REVERT: A  354 GLU cc_start: 0.8231 (pp20) cc_final: 0.7889 (pt0)
REVERT: B   54 PHE cc_start: 0.8048 (m-80) cc_final: 0.7753 (m-80)
REVERT: B  104 TRP cc_start: 0.8168 (p-90) cc_final: 0.7861 (p-90)
REVERT: C  104 TRP cc_start: 0.8217 (p-90) cc_final: 0.7770 (p-90)
REVERT: C  244 ASP cc_start: 0.7139 (OUTLIER) cc_final: 0.6843 (p0)
REVERT: D  244 ASP cc_start: 0.6910 (p0) cc_final: 0.6638 (p0)
REVERT: D  245 GLU cc_start: 0.7713 (pt0) cc_final: 0.7418 (pt0)
REVERT: D  312 GLU cc_start: 0.8108 (pt0) cc_final: 0.7744 (pt0)
REVERT: E   51 SER cc_start: 0.8613 (m) cc_final: 0.8378 (m)
REVERT: E  327 TYR cc_start: 0.8781 (m-80) cc_final: 0.8265 (m-80)
REVERT: F   54 PHE cc_start: 0.8045 (m-80) cc_final: 0.7720 (m-80)
REVERT: F  244 ASP cc_start: 0.6999 (OUTLIER) cc_final: 0.6711 (p0)
REVERT: G   54 PHE cc_start: 0.8094 (m-80) cc_final: 0.6592 (t80)
REVERT: G  104 TRP cc_start: 0.8234 (p-90) cc_final: 0.7921 (p-90)
REVERT: G  312 GLU cc_start: 0.8079 (pt0) cc_final: 0.7705 (pt0)
  outliers start: 50
  outliers final: 44
  residues processed: 282
  average time/residue: 0.1014
  time to fit residues: 46.1876
Evaluate side-chains
  279 residues out of total 1904 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 233
  time to evaluate  : 0.620 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   17 LEU
Chi-restraints excluded: chain A residue  235 TYR
Chi-restraints excluded: chain A residue  297 MET
Chi-restraints excluded: chain A residue  310 VAL
Chi-restraints excluded: chain A residue  314 LEU
Chi-restraints excluded: chain A residue  341 VAL
Chi-restraints excluded: chain A residue  356 ILE
Chi-restraints excluded: chain B residue   17 LEU
Chi-restraints excluded: chain B residue   81 ASP
Chi-restraints excluded: chain B residue  235 TYR
Chi-restraints excluded: chain B residue  238 SER
Chi-restraints excluded: chain B residue  341 VAL
Chi-restraints excluded: chain B residue  356 ILE
Chi-restraints excluded: chain C residue   17 LEU
Chi-restraints excluded: chain C residue  235 TYR
Chi-restraints excluded: chain C residue  244 ASP
Chi-restraints excluded: chain C residue  310 VAL
Chi-restraints excluded: chain C residue  314 LEU
Chi-restraints excluded: chain C residue  341 VAL
Chi-restraints excluded: chain C residue  356 ILE
Chi-restraints excluded: chain D residue   17 LEU
Chi-restraints excluded: chain D residue  235 TYR
Chi-restraints excluded: chain D residue  238 SER
Chi-restraints excluded: chain D residue  310 VAL
Chi-restraints excluded: chain D residue  314 LEU
Chi-restraints excluded: chain D residue  341 VAL
Chi-restraints excluded: chain D residue  356 ILE
Chi-restraints excluded: chain E residue   17 LEU
Chi-restraints excluded: chain E residue  114 LEU
Chi-restraints excluded: chain E residue  235 TYR
Chi-restraints excluded: chain E residue  238 SER
Chi-restraints excluded: chain E residue  264 LEU
Chi-restraints excluded: chain E residue  341 VAL
Chi-restraints excluded: chain E residue  356 ILE
Chi-restraints excluded: chain F residue   14 ASP
Chi-restraints excluded: chain F residue   17 LEU
Chi-restraints excluded: chain F residue  235 TYR
Chi-restraints excluded: chain F residue  244 ASP
Chi-restraints excluded: chain F residue  310 VAL
Chi-restraints excluded: chain F residue  314 LEU
Chi-restraints excluded: chain F residue  341 VAL
Chi-restraints excluded: chain F residue  356 ILE
Chi-restraints excluded: chain G residue  235 TYR
Chi-restraints excluded: chain G residue  238 SER
Chi-restraints excluded: chain G residue  341 VAL
Chi-restraints excluded: chain G residue  356 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 203
   random chunks:
   chunk 180 optimal weight:    6.9990
   chunk 13 optimal weight:    4.9990
   chunk 86 optimal weight:    6.9990
   chunk 72 optimal weight:    5.9990
   chunk 129 optimal weight:    0.9980
   chunk 120 optimal weight:    1.9990
   chunk 1 optimal weight:    3.9990
   chunk 5 optimal weight:    4.9990
   chunk 9 optimal weight:    0.8980
   chunk 153 optimal weight:    5.9990
   chunk 175 optimal weight:    0.4980
   overall best weight:    1.6784

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

Flipped N/Q/H residues before XYZ refinement:
B 266 GLN
G 151 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3558 r_free = 0.3558 target = 0.121991 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3267 r_free = 0.3267 target = 0.101066 restraints weight = 27270.278|
|-----------------------------------------------------------------------------|
r_work (start): 0.3240 rms_B_bonded: 2.38
r_work: 0.3126 rms_B_bonded: 2.96 restraints_weight: 0.5000
r_work: 0.3004 rms_B_bonded: 4.92 restraints_weight: 0.2500
r_work (final): 0.3004
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8393
moved from start:          0.1708

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050  16954  Z= 0.140
  Angle     :  0.604   8.818  23170  Z= 0.311
  Chirality :  0.041   0.213   2793
  Planarity :  0.004   0.027   2793
  Dihedral  :  4.967  26.684   2240
  Min Nonbonded Distance : 2.591

Molprobity Statistics.
  All-atom Clashscore : 5.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.81 %
    Favored  : 92.19 %
  Rotamer:
    Outliers :  2.89 %
    Allowed  : 20.29 %
    Favored  : 76.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.08 (0.20), residues: 2037
  helix:  1.97 (0.15), residues: 1295
  sheet:  None (None), residues: 0
  loop : -3.75 (0.21), residues: 742

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG F 276 
 TYR   0.015   0.001   TYR C 327 
 PHE   0.010   0.001   PHE D 126 
 TRP   0.014   0.001   TRP A 104 
 HIS   0.002   0.001   HIS C 330 

Details of bonding type rmsd
  covalent geometry    : bond        0.00320 (16940)
  covalent geometry    : angle       0.60350 (23142)
  SS BOND              : bond        0.00104 (   14)
  SS BOND              : angle       0.61280 (   28)
  hydrogen bonds       : bond        0.05577 ( 1022)
  hydrogen bonds       : angle       4.37664 ( 3024)

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

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

  4074 Ramachandran restraints generated.
    2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4074 Ramachandran restraints generated.
    2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  300 residues out of total 1904 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 52
    poor density    : 248
  time to evaluate  : 0.621 
Fit side-chains
REVERT: A   54 PHE cc_start: 0.7873 (m-80) cc_final: 0.6353 (t80)
REVERT: A  354 GLU cc_start: 0.8374 (pp20) cc_final: 0.7905 (pt0)
REVERT: B   54 PHE cc_start: 0.8026 (m-80) cc_final: 0.7717 (m-80)
REVERT: B  104 TRP cc_start: 0.8266 (p-90) cc_final: 0.7979 (p-90)
REVERT: C   54 PHE cc_start: 0.8056 (m-80) cc_final: 0.7611 (m-10)
REVERT: C  104 TRP cc_start: 0.8338 (p-90) cc_final: 0.7897 (p-90)
REVERT: C  244 ASP cc_start: 0.7176 (OUTLIER) cc_final: 0.6868 (p0)
REVERT: C  310 VAL cc_start: 0.8824 (OUTLIER) cc_final: 0.8589 (p)
REVERT: D  104 TRP cc_start: 0.8298 (p-90) cc_final: 0.7944 (p-90)
REVERT: D  244 ASP cc_start: 0.7107 (p0) cc_final: 0.6836 (p0)
REVERT: D  312 GLU cc_start: 0.8230 (pt0) cc_final: 0.7859 (pt0)
REVERT: E   51 SER cc_start: 0.8642 (m) cc_final: 0.8406 (m)
REVERT: E  143 MET cc_start: 0.9301 (mtp) cc_final: 0.9035 (mtp)
REVERT: E  327 TYR cc_start: 0.8884 (m-80) cc_final: 0.8395 (m-80)
REVERT: F   54 PHE cc_start: 0.8049 (m-80) cc_final: 0.7724 (m-80)
REVERT: F  244 ASP cc_start: 0.7037 (OUTLIER) cc_final: 0.6734 (p0)
REVERT: G   54 PHE cc_start: 0.8112 (m-80) cc_final: 0.6560 (t80)
REVERT: G  104 TRP cc_start: 0.8378 (p-90) cc_final: 0.8099 (p-90)
REVERT: G  312 GLU cc_start: 0.8210 (pt0) cc_final: 0.7840 (pt0)
  outliers start: 52
  outliers final: 46
  residues processed: 284
  average time/residue: 0.1012
  time to fit residues: 46.8489
Evaluate side-chains
  285 residues out of total 1904 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 236
  time to evaluate  : 0.553 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   17 LEU
Chi-restraints excluded: chain A residue   81 ASP
Chi-restraints excluded: chain A residue  235 TYR
Chi-restraints excluded: chain A residue  264 LEU
Chi-restraints excluded: chain A residue  297 MET
Chi-restraints excluded: chain A residue  310 VAL
Chi-restraints excluded: chain A residue  314 LEU
Chi-restraints excluded: chain A residue  341 VAL
Chi-restraints excluded: chain A residue  356 ILE
Chi-restraints excluded: chain B residue   17 LEU
Chi-restraints excluded: chain B residue   81 ASP
Chi-restraints excluded: chain B residue  235 TYR
Chi-restraints excluded: chain B residue  238 SER
Chi-restraints excluded: chain B residue  341 VAL
Chi-restraints excluded: chain B residue  356 ILE
Chi-restraints excluded: chain C residue   17 LEU
Chi-restraints excluded: chain C residue   70 THR
Chi-restraints excluded: chain C residue   80 VAL
Chi-restraints excluded: chain C residue  235 TYR
Chi-restraints excluded: chain C residue  244 ASP
Chi-restraints excluded: chain C residue  310 VAL
Chi-restraints excluded: chain C residue  314 LEU
Chi-restraints excluded: chain C residue  356 ILE
Chi-restraints excluded: chain D residue   17 LEU
Chi-restraints excluded: chain D residue  235 TYR
Chi-restraints excluded: chain D residue  238 SER
Chi-restraints excluded: chain D residue  310 VAL
Chi-restraints excluded: chain D residue  314 LEU
Chi-restraints excluded: chain D residue  341 VAL
Chi-restraints excluded: chain E residue   17 LEU
Chi-restraints excluded: chain E residue  235 TYR
Chi-restraints excluded: chain E residue  238 SER
Chi-restraints excluded: chain E residue  239 LEU
Chi-restraints excluded: chain E residue  264 LEU
Chi-restraints excluded: chain E residue  341 VAL
Chi-restraints excluded: chain E residue  356 ILE
Chi-restraints excluded: chain F residue   14 ASP
Chi-restraints excluded: chain F residue   17 LEU
Chi-restraints excluded: chain F residue  235 TYR
Chi-restraints excluded: chain F residue  244 ASP
Chi-restraints excluded: chain F residue  310 VAL
Chi-restraints excluded: chain F residue  314 LEU
Chi-restraints excluded: chain F residue  341 VAL
Chi-restraints excluded: chain F residue  356 ILE
Chi-restraints excluded: chain G residue   17 LEU
Chi-restraints excluded: chain G residue  235 TYR
Chi-restraints excluded: chain G residue  238 SER
Chi-restraints excluded: chain G residue  341 VAL
Chi-restraints excluded: chain G residue  356 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 203
   random chunks:
   chunk 121 optimal weight:   10.0000
   chunk 38 optimal weight:    8.9990
   chunk 40 optimal weight:    3.9990
   chunk 139 optimal weight:    0.6980
   chunk 71 optimal weight:    0.7980
   chunk 184 optimal weight:    2.9990
   chunk 23 optimal weight:    3.9990
   chunk 36 optimal weight:    9.9990
   chunk 173 optimal weight:    5.9990
   chunk 99 optimal weight:    6.9990
   chunk 28 optimal weight:    4.9990
   overall best weight:    2.4986

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

Flipped N/Q/H residues before XYZ refinement:
B 266 GLN
F  63 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3545 r_free = 0.3545 target = 0.120990 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3237 r_free = 0.3237 target = 0.099406 restraints weight = 27386.475|
|-----------------------------------------------------------------------------|
r_work (start): 0.3212 rms_B_bonded: 2.40
r_work: 0.3096 rms_B_bonded: 3.02 restraints_weight: 0.5000
r_work (final): 0.3096
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8340
moved from start:          0.1669

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048  16954  Z= 0.170
  Angle     :  0.630   7.848  23170  Z= 0.325
  Chirality :  0.042   0.217   2793
  Planarity :  0.004   0.031   2793
  Dihedral  :  5.008  26.503   2240
  Min Nonbonded Distance : 2.573

Molprobity Statistics.
  All-atom Clashscore : 5.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.81 %
    Favored  : 92.19 %
  Rotamer:
    Outliers :  3.95 %
    Allowed  : 19.96 %
    Favored  : 76.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.13 (0.20), residues: 2037
  helix:  1.94 (0.15), residues: 1295
  sheet:  0.40 (0.81), residues: 42
  loop : -3.81 (0.22), residues: 700

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG E 219 
 TYR   0.016   0.001   TYR B  25 
 PHE   0.013   0.001   PHE E 126 
 TRP   0.016   0.002   TRP A 104 
 HIS   0.002   0.001   HIS B 106 

Details of bonding type rmsd
  covalent geometry    : bond        0.00408 (16940)
  covalent geometry    : angle       0.62951 (23142)
  SS BOND              : bond        0.00101 (   14)
  SS BOND              : angle       0.67393 (   28)
  hydrogen bonds       : bond        0.06034 ( 1022)
  hydrogen bonds       : angle       4.45582 ( 3024)

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

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

  4074 Ramachandran restraints generated.
    2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4074 Ramachandran restraints generated.
    2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  309 residues out of total 1904 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 71
    poor density    : 238
  time to evaluate  : 0.629 
Fit side-chains
REVERT: A   54 PHE cc_start: 0.7889 (m-80) cc_final: 0.6392 (t80)
REVERT: A  354 GLU cc_start: 0.8269 (pp20) cc_final: 0.7820 (pt0)
REVERT: B   54 PHE cc_start: 0.8062 (m-80) cc_final: 0.7711 (m-80)
REVERT: B  104 TRP cc_start: 0.8159 (p-90) cc_final: 0.7898 (p-90)
REVERT: C  104 TRP cc_start: 0.8236 (p-90) cc_final: 0.7822 (p-90)
REVERT: C  244 ASP cc_start: 0.6992 (OUTLIER) cc_final: 0.6651 (p0)
REVERT: D  104 TRP cc_start: 0.8150 (p-90) cc_final: 0.7812 (p-90)
REVERT: D  244 ASP cc_start: 0.6979 (p0) cc_final: 0.6673 (p0)
REVERT: D  312 GLU cc_start: 0.8135 (pt0) cc_final: 0.7792 (pt0)
REVERT: E   51 SER cc_start: 0.8655 (m) cc_final: 0.8398 (m)
REVERT: E  312 GLU cc_start: 0.7655 (pt0) cc_final: 0.7336 (pt0)
REVERT: E  327 TYR cc_start: 0.8802 (m-80) cc_final: 0.8294 (m-80)
REVERT: F   54 PHE cc_start: 0.8070 (m-80) cc_final: 0.7701 (m-80)
REVERT: F  244 ASP cc_start: 0.6990 (OUTLIER) cc_final: 0.6674 (p0)
REVERT: F  354 GLU cc_start: 0.8213 (pp20) cc_final: 0.7772 (pt0)
REVERT: G   54 PHE cc_start: 0.8140 (m-80) cc_final: 0.6622 (t80)
REVERT: G  312 GLU cc_start: 0.8049 (pt0) cc_final: 0.7613 (pt0)
  outliers start: 71
  outliers final: 56
  residues processed: 291
  average time/residue: 0.1142
  time to fit residues: 53.7847
Evaluate side-chains
  290 residues out of total 1904 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 58
    poor density    : 232
  time to evaluate  : 0.635 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   17 LEU
Chi-restraints excluded: chain A residue  235 TYR
Chi-restraints excluded: chain A residue  239 LEU
Chi-restraints excluded: chain A residue  264 LEU
Chi-restraints excluded: chain A residue  297 MET
Chi-restraints excluded: chain A residue  310 VAL
Chi-restraints excluded: chain A residue  314 LEU
Chi-restraints excluded: chain A residue  341 VAL
Chi-restraints excluded: chain A residue  356 ILE
Chi-restraints excluded: chain B residue   17 LEU
Chi-restraints excluded: chain B residue   81 ASP
Chi-restraints excluded: chain B residue  235 TYR
Chi-restraints excluded: chain B residue  238 SER
Chi-restraints excluded: chain B residue  341 VAL
Chi-restraints excluded: chain B residue  356 ILE
Chi-restraints excluded: chain C residue   17 LEU
Chi-restraints excluded: chain C residue   70 THR
Chi-restraints excluded: chain C residue   80 VAL
Chi-restraints excluded: chain C residue  235 TYR
Chi-restraints excluded: chain C residue  244 ASP
Chi-restraints excluded: chain C residue  314 LEU
Chi-restraints excluded: chain C residue  341 VAL
Chi-restraints excluded: chain C residue  356 ILE
Chi-restraints excluded: chain D residue   17 LEU
Chi-restraints excluded: chain D residue   80 VAL
Chi-restraints excluded: chain D residue  235 TYR
Chi-restraints excluded: chain D residue  238 SER
Chi-restraints excluded: chain D residue  310 VAL
Chi-restraints excluded: chain D residue  314 LEU
Chi-restraints excluded: chain D residue  341 VAL
Chi-restraints excluded: chain D residue  356 ILE
Chi-restraints excluded: chain E residue   17 LEU
Chi-restraints excluded: chain E residue   80 VAL
Chi-restraints excluded: chain E residue  235 TYR
Chi-restraints excluded: chain E residue  238 SER
Chi-restraints excluded: chain E residue  239 LEU
Chi-restraints excluded: chain E residue  264 LEU
Chi-restraints excluded: chain E residue  341 VAL
Chi-restraints excluded: chain E residue  356 ILE
Chi-restraints excluded: chain F residue   14 ASP
Chi-restraints excluded: chain F residue   17 LEU
Chi-restraints excluded: chain F residue   80 VAL
Chi-restraints excluded: chain F residue  105 LEU
Chi-restraints excluded: chain F residue  198 VAL
Chi-restraints excluded: chain F residue  235 TYR
Chi-restraints excluded: chain F residue  244 ASP
Chi-restraints excluded: chain F residue  310 VAL
Chi-restraints excluded: chain F residue  314 LEU
Chi-restraints excluded: chain F residue  341 VAL
Chi-restraints excluded: chain F residue  356 ILE
Chi-restraints excluded: chain G residue   80 VAL
Chi-restraints excluded: chain G residue  198 VAL
Chi-restraints excluded: chain G residue  235 TYR
Chi-restraints excluded: chain G residue  238 SER
Chi-restraints excluded: chain G residue  239 LEU
Chi-restraints excluded: chain G residue  264 LEU
Chi-restraints excluded: chain G residue  341 VAL
Chi-restraints excluded: chain G residue  356 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 203
   random chunks:
   chunk 30 optimal weight:    4.9990
   chunk 146 optimal weight:    7.9990
   chunk 4 optimal weight:    3.9990
   chunk 9 optimal weight:    3.9990
   chunk 159 optimal weight:    4.9990
   chunk 86 optimal weight:    5.9990
   chunk 118 optimal weight:    5.9990
   chunk 75 optimal weight:    7.9990
   chunk 25 optimal weight:    0.9980
   chunk 44 optimal weight:    0.9990
   chunk 142 optimal weight:   10.0000
   overall best weight:    2.9988

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

Flipped N/Q/H residues before XYZ refinement:
G 106 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3533 r_free = 0.3533 target = 0.120173 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3225 r_free = 0.3225 target = 0.098522 restraints weight = 27232.594|
|-----------------------------------------------------------------------------|
r_work (start): 0.3198 rms_B_bonded: 2.43
r_work: 0.3082 rms_B_bonded: 3.01 restraints_weight: 0.5000
r_work: 0.2959 rms_B_bonded: 4.98 restraints_weight: 0.2500
r_work (final): 0.2959
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8438
moved from start:          0.1665

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.057  16954  Z= 0.193
  Angle     :  0.653   7.459  23170  Z= 0.338
  Chirality :  0.043   0.223   2793
  Planarity :  0.004   0.034   2793
  Dihedral  :  5.090  27.213   2240
  Min Nonbonded Distance : 2.573

Molprobity Statistics.
  All-atom Clashscore : 5.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.85 %
    Favored  : 92.15 %
  Rotamer:
    Outliers :  3.72 %
    Allowed  : 20.23 %
    Favored  : 76.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.18 (0.20), residues: 2037
  helix:  1.97 (0.15), residues: 1288
  sheet:  0.42 (0.80), residues: 42
  loop : -3.72 (0.22), residues: 707

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG E 219 
 TYR   0.017   0.001   TYR B  25 
 PHE   0.014   0.001   PHE G 126 
 TRP   0.017   0.002   TRP A 104 
 HIS   0.002   0.001   HIS B 106 

Details of bonding type rmsd
  covalent geometry    : bond        0.00472 (16940)
  covalent geometry    : angle       0.65263 (23142)
  SS BOND              : bond        0.00078 (   14)
  SS BOND              : angle       0.72069 (   28)
  hydrogen bonds       : bond        0.06346 ( 1022)
  hydrogen bonds       : angle       4.51740 ( 3024)

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

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

  4074 Ramachandran restraints generated.
    2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4074 Ramachandran restraints generated.
    2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  305 residues out of total 1904 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 67
    poor density    : 238
  time to evaluate  : 0.727 
Fit side-chains
REVERT: A   54 PHE cc_start: 0.7897 (m-80) cc_final: 0.7552 (m-80)
REVERT: A  354 GLU cc_start: 0.8429 (pp20) cc_final: 0.7975 (pt0)
REVERT: B   54 PHE cc_start: 0.8108 (m-80) cc_final: 0.7767 (m-80)
REVERT: B  104 TRP cc_start: 0.8364 (p-90) cc_final: 0.8099 (p-90)
REVERT: C  104 TRP cc_start: 0.8376 (p-90) cc_final: 0.7938 (p-90)
REVERT: C  244 ASP cc_start: 0.7159 (OUTLIER) cc_final: 0.6772 (p0)
REVERT: D  244 ASP cc_start: 0.7193 (p0) cc_final: 0.6877 (p0)
REVERT: D  312 GLU cc_start: 0.8319 (pt0) cc_final: 0.7976 (pt0)
REVERT: E   51 SER cc_start: 0.8698 (m) cc_final: 0.8438 (m)
REVERT: E  143 MET cc_start: 0.9262 (mtp) cc_final: 0.9012 (mtp)
REVERT: E  327 TYR cc_start: 0.8938 (m-80) cc_final: 0.8429 (m-80)
REVERT: F   54 PHE cc_start: 0.8075 (m-80) cc_final: 0.7708 (m-80)
REVERT: F  244 ASP cc_start: 0.7103 (OUTLIER) cc_final: 0.6788 (p0)
REVERT: G   54 PHE cc_start: 0.8148 (m-80) cc_final: 0.6581 (t80)
REVERT: G  312 GLU cc_start: 0.8197 (pt0) cc_final: 0.7802 (pt0)
  outliers start: 67
  outliers final: 62
  residues processed: 290
  average time/residue: 0.1138
  time to fit residues: 53.5515
Evaluate side-chains
  292 residues out of total 1904 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 64
    poor density    : 228
  time to evaluate  : 0.660 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   17 LEU
Chi-restraints excluded: chain A residue  235 TYR
Chi-restraints excluded: chain A residue  239 LEU
Chi-restraints excluded: chain A residue  264 LEU
Chi-restraints excluded: chain A residue  297 MET
Chi-restraints excluded: chain A residue  310 VAL
Chi-restraints excluded: chain A residue  314 LEU
Chi-restraints excluded: chain A residue  341 VAL
Chi-restraints excluded: chain A residue  356 ILE
Chi-restraints excluded: chain B residue   17 LEU
Chi-restraints excluded: chain B residue   80 VAL
Chi-restraints excluded: chain B residue   81 ASP
Chi-restraints excluded: chain B residue  235 TYR
Chi-restraints excluded: chain B residue  238 SER
Chi-restraints excluded: chain B residue  341 VAL
Chi-restraints excluded: chain B residue  356 ILE
Chi-restraints excluded: chain C residue   17 LEU
Chi-restraints excluded: chain C residue   70 THR
Chi-restraints excluded: chain C residue   80 VAL
Chi-restraints excluded: chain C residue  235 TYR
Chi-restraints excluded: chain C residue  244 ASP
Chi-restraints excluded: chain C residue  310 VAL
Chi-restraints excluded: chain C residue  314 LEU
Chi-restraints excluded: chain C residue  341 VAL
Chi-restraints excluded: chain C residue  356 ILE
Chi-restraints excluded: chain D residue   17 LEU
Chi-restraints excluded: chain D residue   70 THR
Chi-restraints excluded: chain D residue   80 VAL
Chi-restraints excluded: chain D residue  198 VAL
Chi-restraints excluded: chain D residue  235 TYR
Chi-restraints excluded: chain D residue  238 SER
Chi-restraints excluded: chain D residue  310 VAL
Chi-restraints excluded: chain D residue  314 LEU
Chi-restraints excluded: chain D residue  341 VAL
Chi-restraints excluded: chain D residue  356 ILE
Chi-restraints excluded: chain E residue   17 LEU
Chi-restraints excluded: chain E residue   34 VAL
Chi-restraints excluded: chain E residue   70 THR
Chi-restraints excluded: chain E residue   80 VAL
Chi-restraints excluded: chain E residue  235 TYR
Chi-restraints excluded: chain E residue  238 SER
Chi-restraints excluded: chain E residue  239 LEU
Chi-restraints excluded: chain E residue  341 VAL
Chi-restraints excluded: chain E residue  356 ILE
Chi-restraints excluded: chain F residue   14 ASP
Chi-restraints excluded: chain F residue   17 LEU
Chi-restraints excluded: chain F residue   34 VAL
Chi-restraints excluded: chain F residue   80 VAL
Chi-restraints excluded: chain F residue  105 LEU
Chi-restraints excluded: chain F residue  198 VAL
Chi-restraints excluded: chain F residue  235 TYR
Chi-restraints excluded: chain F residue  244 ASP
Chi-restraints excluded: chain F residue  310 VAL
Chi-restraints excluded: chain F residue  314 LEU
Chi-restraints excluded: chain F residue  341 VAL
Chi-restraints excluded: chain F residue  356 ILE
Chi-restraints excluded: chain G residue   80 VAL
Chi-restraints excluded: chain G residue  198 VAL
Chi-restraints excluded: chain G residue  235 TYR
Chi-restraints excluded: chain G residue  238 SER
Chi-restraints excluded: chain G residue  239 LEU
Chi-restraints excluded: chain G residue  264 LEU
Chi-restraints excluded: chain G residue  341 VAL
Chi-restraints excluded: chain G residue  356 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 203
   random chunks:
   chunk 108 optimal weight:    0.9990
   chunk 202 optimal weight:    4.9990
   chunk 183 optimal weight:    2.9990
   chunk 48 optimal weight:    5.9990
   chunk 94 optimal weight:    0.7980
   chunk 31 optimal weight:    0.9990
   chunk 180 optimal weight:    0.8980
   chunk 142 optimal weight:    0.7980
   chunk 174 optimal weight:    0.0770
   chunk 58 optimal weight:   10.0000
   chunk 194 optimal weight:    0.4980
   overall best weight:    0.6138

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

Flipped N/Q/H residues before XYZ refinement:
E 330 HIS
G 330 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3609 r_free = 0.3609 target = 0.126174 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3324 r_free = 0.3324 target = 0.105035 restraints weight = 27200.482|
|-----------------------------------------------------------------------------|
r_work (start): 0.3307 rms_B_bonded: 2.38
r_work: 0.3194 rms_B_bonded: 3.03 restraints_weight: 0.5000
r_work (final): 0.3194
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8240
moved from start:          0.2225

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.057  16954  Z= 0.123
  Angle     :  0.586   6.451  23170  Z= 0.302
  Chirality :  0.041   0.207   2793
  Planarity :  0.004   0.033   2793
  Dihedral  :  4.683  23.091   2240
  Min Nonbonded Distance : 2.557

Molprobity Statistics.
  All-atom Clashscore : 6.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.27 %
    Favored  : 92.73 %
  Rotamer:
    Outliers :  2.11 %
    Allowed  : 21.57 %
    Favored  : 76.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.47 (0.21), residues: 2037
  helix:  2.17 (0.15), residues: 1309
  sheet:  None (None), residues: 0
  loop : -3.48 (0.22), residues: 728

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG E  75 
 TYR   0.009   0.001   TYR D  79 
 PHE   0.010   0.001   PHE C  83 
 TRP   0.029   0.001   TRP F  74 
 HIS   0.001   0.001   HIS G 106 

Details of bonding type rmsd
  covalent geometry    : bond        0.00271 (16940)
  covalent geometry    : angle       0.58588 (23142)
  SS BOND              : bond        0.00149 (   14)
  SS BOND              : angle       0.63080 (   28)
  hydrogen bonds       : bond        0.04603 ( 1022)
  hydrogen bonds       : angle       4.20387 ( 3024)

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

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

  4074 Ramachandran restraints generated.
    2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4074 Ramachandran restraints generated.
    2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  301 residues out of total 1904 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 263
  time to evaluate  : 0.637 
Fit side-chains
REVERT: A   54 PHE cc_start: 0.7883 (m-80) cc_final: 0.7469 (m-80)
REVERT: A  354 GLU cc_start: 0.8214 (pp20) cc_final: 0.7753 (pt0)
REVERT: B   54 PHE cc_start: 0.7954 (m-80) cc_final: 0.7598 (m-80)
REVERT: C   54 PHE cc_start: 0.8042 (m-80) cc_final: 0.7549 (m-10)
REVERT: C  104 TRP cc_start: 0.8133 (p-90) cc_final: 0.7769 (p-90)
REVERT: C  244 ASP cc_start: 0.6905 (OUTLIER) cc_final: 0.6522 (p0)
REVERT: C  310 VAL cc_start: 0.8629 (OUTLIER) cc_final: 0.8409 (p)
REVERT: D  104 TRP cc_start: 0.8061 (p-90) cc_final: 0.7834 (p-90)
REVERT: D  244 ASP cc_start: 0.6945 (p0) cc_final: 0.6533 (p0)
REVERT: D  312 GLU cc_start: 0.7940 (pt0) cc_final: 0.7559 (pt0)
REVERT: E  312 GLU cc_start: 0.7444 (pt0) cc_final: 0.7212 (pt0)
REVERT: F  244 ASP cc_start: 0.6721 (OUTLIER) cc_final: 0.6415 (p0)
REVERT: F  354 GLU cc_start: 0.8138 (pp20) cc_final: 0.7740 (pt0)
REVERT: G   25 TYR cc_start: 0.7533 (m-80) cc_final: 0.7300 (m-80)
REVERT: G   54 PHE cc_start: 0.8091 (m-80) cc_final: 0.6596 (t80)
REVERT: G  104 TRP cc_start: 0.8173 (p-90) cc_final: 0.7935 (p-90)
REVERT: G  312 GLU cc_start: 0.8033 (pt0) cc_final: 0.7671 (pt0)
  outliers start: 38
  outliers final: 28
  residues processed: 296
  average time/residue: 0.1188
  time to fit residues: 56.0038
Evaluate side-chains
  270 residues out of total 1904 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 239
  time to evaluate  : 0.660 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   17 LEU
Chi-restraints excluded: chain A residue  235 TYR
Chi-restraints excluded: chain A residue  297 MET
Chi-restraints excluded: chain A residue  310 VAL
Chi-restraints excluded: chain B residue   80 VAL
Chi-restraints excluded: chain B residue  235 TYR
Chi-restraints excluded: chain B residue  238 SER
Chi-restraints excluded: chain C residue   17 LEU
Chi-restraints excluded: chain C residue   70 THR
Chi-restraints excluded: chain C residue  235 TYR
Chi-restraints excluded: chain C residue  244 ASP
Chi-restraints excluded: chain C residue  310 VAL
Chi-restraints excluded: chain C residue  341 VAL
Chi-restraints excluded: chain D residue   80 VAL
Chi-restraints excluded: chain D residue  235 TYR
Chi-restraints excluded: chain D residue  238 SER
Chi-restraints excluded: chain E residue   70 THR
Chi-restraints excluded: chain E residue   80 VAL
Chi-restraints excluded: chain E residue  235 TYR
Chi-restraints excluded: chain E residue  238 SER
Chi-restraints excluded: chain F residue   17 LEU
Chi-restraints excluded: chain F residue  198 VAL
Chi-restraints excluded: chain F residue  235 TYR
Chi-restraints excluded: chain F residue  244 ASP
Chi-restraints excluded: chain F residue  341 VAL
Chi-restraints excluded: chain G residue   80 VAL
Chi-restraints excluded: chain G residue  198 VAL
Chi-restraints excluded: chain G residue  235 TYR
Chi-restraints excluded: chain G residue  238 SER
Chi-restraints excluded: chain G residue  341 VAL
Chi-restraints excluded: chain G residue  354 GLU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 203
   random chunks:
   chunk 150 optimal weight:   20.0000
   chunk 117 optimal weight:    6.9990
   chunk 177 optimal weight:    8.9990
   chunk 112 optimal weight:    0.9990
   chunk 27 optimal weight:    0.9990
   chunk 54 optimal weight:    0.9980
   chunk 113 optimal weight:    4.9990
   chunk 59 optimal weight:    8.9990
   chunk 50 optimal weight:    8.9990
   chunk 123 optimal weight:    9.9990
   chunk 74 optimal weight:    5.9990
   overall best weight:    2.7988

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

Flipped N/Q/H residues before XYZ refinement:
B 266 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3552 r_free = 0.3552 target = 0.121667 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3244 r_free = 0.3244 target = 0.099928 restraints weight = 27274.437|
|-----------------------------------------------------------------------------|
r_work (start): 0.3220 rms_B_bonded: 2.42
r_work: 0.3105 rms_B_bonded: 3.03 restraints_weight: 0.5000
r_work (final): 0.3105
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8338
moved from start:          0.2021

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.053  16954  Z= 0.189
  Angle     :  0.656   6.431  23170  Z= 0.339
  Chirality :  0.044   0.224   2793
  Planarity :  0.004   0.036   2793
  Dihedral  :  4.862  26.726   2240
  Min Nonbonded Distance : 2.543

Molprobity Statistics.
  All-atom Clashscore : 5.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.56 %
    Favored  : 92.44 %
  Rotamer:
    Outliers :  2.28 %
    Allowed  : 22.12 %
    Favored  : 75.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.40 (0.20), residues: 2037
  helix:  2.15 (0.15), residues: 1288
  sheet:  0.30 (0.73), residues: 42
  loop : -3.63 (0.22), residues: 707

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG D 152 
 TYR   0.017   0.001   TYR C 327 
 PHE   0.014   0.001   PHE G 126 
 TRP   0.022   0.002   TRP E 104 
 HIS   0.002   0.001   HIS A 106 

Details of bonding type rmsd
  covalent geometry    : bond        0.00457 (16940)
  covalent geometry    : angle       0.65621 (23142)
  SS BOND              : bond        0.00080 (   14)
  SS BOND              : angle       0.72471 (   28)
  hydrogen bonds       : bond        0.06049 ( 1022)
  hydrogen bonds       : angle       4.42516 ( 3024)

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

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

  4074 Ramachandran restraints generated.
    2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4074 Ramachandran restraints generated.
    2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  278 residues out of total 1904 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 237
  time to evaluate  : 0.633 
Fit side-chains
REVERT: A   54 PHE cc_start: 0.7913 (m-80) cc_final: 0.7521 (m-80)
REVERT: A  354 GLU cc_start: 0.8259 (pp20) cc_final: 0.7880 (pt0)
REVERT: B   54 PHE cc_start: 0.7990 (m-80) cc_final: 0.7617 (m-80)
REVERT: C  104 TRP cc_start: 0.8195 (p-90) cc_final: 0.7804 (p-90)
REVERT: C  244 ASP cc_start: 0.6920 (OUTLIER) cc_final: 0.6524 (p0)
REVERT: C  310 VAL cc_start: 0.8773 (OUTLIER) cc_final: 0.8541 (p)
REVERT: D  104 TRP cc_start: 0.8188 (p-90) cc_final: 0.7900 (p-90)
REVERT: D  244 ASP cc_start: 0.7073 (p0) cc_final: 0.6701 (p0)
REVERT: D  312 GLU cc_start: 0.8085 (pt0) cc_final: 0.7742 (pt0)
REVERT: E  312 GLU cc_start: 0.7679 (pt0) cc_final: 0.7413 (pt0)
REVERT: E  327 TYR cc_start: 0.8646 (m-80) cc_final: 0.8157 (m-80)
REVERT: F   54 PHE cc_start: 0.8040 (m-80) cc_final: 0.7703 (m-80)
REVERT: F  244 ASP cc_start: 0.6854 (OUTLIER) cc_final: 0.6523 (p0)
REVERT: F  354 GLU cc_start: 0.8222 (pp20) cc_final: 0.7834 (pt0)
REVERT: G   54 PHE cc_start: 0.8141 (m-80) cc_final: 0.6609 (t80)
REVERT: G  104 TRP cc_start: 0.8233 (p-90) cc_final: 0.7970 (p-90)
REVERT: G  312 GLU cc_start: 0.8007 (pt0) cc_final: 0.7709 (pt0)
REVERT: G  354 GLU cc_start: 0.8016 (pp20) cc_final: 0.7787 (pt0)
  outliers start: 41
  outliers final: 35
  residues processed: 274
  average time/residue: 0.1192
  time to fit residues: 52.0439
Evaluate side-chains
  268 residues out of total 1904 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 230
  time to evaluate  : 0.635 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   17 LEU
Chi-restraints excluded: chain A residue  235 TYR
Chi-restraints excluded: chain A residue  264 LEU
Chi-restraints excluded: chain A residue  297 MET
Chi-restraints excluded: chain A residue  310 VAL
Chi-restraints excluded: chain A residue  341 VAL
Chi-restraints excluded: chain B residue   80 VAL
Chi-restraints excluded: chain B residue  235 TYR
Chi-restraints excluded: chain B residue  238 SER
Chi-restraints excluded: chain C residue   17 LEU
Chi-restraints excluded: chain C residue   70 THR
Chi-restraints excluded: chain C residue  235 TYR
Chi-restraints excluded: chain C residue  244 ASP
Chi-restraints excluded: chain C residue  310 VAL
Chi-restraints excluded: chain C residue  341 VAL
Chi-restraints excluded: chain D residue   80 VAL
Chi-restraints excluded: chain D residue  235 TYR
Chi-restraints excluded: chain D residue  238 SER
Chi-restraints excluded: chain E residue   17 LEU
Chi-restraints excluded: chain E residue   34 VAL
Chi-restraints excluded: chain E residue   70 THR
Chi-restraints excluded: chain E residue   80 VAL
Chi-restraints excluded: chain E residue  235 TYR
Chi-restraints excluded: chain E residue  238 SER
Chi-restraints excluded: chain E residue  341 VAL
Chi-restraints excluded: chain F residue   17 LEU
Chi-restraints excluded: chain F residue   31 GLU
Chi-restraints excluded: chain F residue   34 VAL
Chi-restraints excluded: chain F residue  198 VAL
Chi-restraints excluded: chain F residue  235 TYR
Chi-restraints excluded: chain F residue  244 ASP
Chi-restraints excluded: chain F residue  341 VAL
Chi-restraints excluded: chain G residue   34 VAL
Chi-restraints excluded: chain G residue   80 VAL
Chi-restraints excluded: chain G residue  198 VAL
Chi-restraints excluded: chain G residue  235 TYR
Chi-restraints excluded: chain G residue  238 SER
Chi-restraints excluded: chain G residue  341 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 203
   random chunks:
   chunk 27 optimal weight:    1.9990
   chunk 109 optimal weight:    0.7980
   chunk 41 optimal weight:    7.9990
   chunk 98 optimal weight:    0.9980
   chunk 197 optimal weight:    3.9990
   chunk 138 optimal weight:    4.9990
   chunk 137 optimal weight:    1.9990
   chunk 23 optimal weight:    0.9980
   chunk 200 optimal weight:    5.9990
   chunk 170 optimal weight:    1.9990
   chunk 196 optimal weight:    0.9990
   overall best weight:    1.1584

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

Flipped N/Q/H residues before XYZ refinement:
D  63 GLN
D 151 ASN
F 330 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3598 r_free = 0.3598 target = 0.125167 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3300 r_free = 0.3300 target = 0.103575 restraints weight = 27213.511|
|-----------------------------------------------------------------------------|
r_work (start): 0.3273 rms_B_bonded: 2.44
r_work: 0.3161 rms_B_bonded: 3.03 restraints_weight: 0.5000
r_work (final): 0.3161
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8276
moved from start:          0.2249

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.056  16954  Z= 0.132
  Angle     :  0.610   6.914  23170  Z= 0.314
  Chirality :  0.042   0.217   2793
  Planarity :  0.004   0.035   2793
  Dihedral  :  4.714  23.626   2240
  Min Nonbonded Distance : 2.561

Molprobity Statistics.
  All-atom Clashscore : 6.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.27 %
    Favored  : 92.73 %
  Rotamer:
    Outliers :  2.28 %
    Allowed  : 22.12 %
    Favored  : 75.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.45 (0.21), residues: 2037
  helix:  2.23 (0.15), residues: 1295
  sheet:  None (None), residues: 0
  loop : -3.54 (0.21), residues: 742

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 219 
 TYR   0.013   0.001   TYR D  25 
 PHE   0.009   0.001   PHE C  83 
 TRP   0.018   0.001   TRP E 104 
 HIS   0.002   0.001   HIS C 106 

Details of bonding type rmsd
  covalent geometry    : bond        0.00301 (16940)
  covalent geometry    : angle       0.60964 (23142)
  SS BOND              : bond        0.00130 (   14)
  SS BOND              : angle       0.62677 (   28)
  hydrogen bonds       : bond        0.05125 ( 1022)
  hydrogen bonds       : angle       4.27144 ( 3024)

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

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

  4074 Ramachandran restraints generated.
    2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4074 Ramachandran restraints generated.
    2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  281 residues out of total 1904 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 240
  time to evaluate  : 0.638 
Fit side-chains
REVERT: A   54 PHE cc_start: 0.7903 (m-80) cc_final: 0.6456 (t80)
REVERT: A  354 GLU cc_start: 0.8291 (pp20) cc_final: 0.7828 (pt0)
REVERT: B   54 PHE cc_start: 0.7959 (m-80) cc_final: 0.7618 (m-80)
REVERT: C   54 PHE cc_start: 0.8067 (m-80) cc_final: 0.7629 (m-10)
REVERT: C  104 TRP cc_start: 0.8167 (p-90) cc_final: 0.7861 (p-90)
REVERT: C  244 ASP cc_start: 0.6913 (OUTLIER) cc_final: 0.6545 (p0)
REVERT: C  312 GLU cc_start: 0.7972 (pt0) cc_final: 0.7340 (pt0)
REVERT: D  104 TRP cc_start: 0.8113 (p-90) cc_final: 0.7893 (p-90)
REVERT: D  151 ASN cc_start: 0.9026 (OUTLIER) cc_final: 0.8817 (t0)
REVERT: D  244 ASP cc_start: 0.7063 (p0) cc_final: 0.6694 (p0)
REVERT: D  312 GLU cc_start: 0.8012 (pt0) cc_final: 0.7689 (pt0)
REVERT: E  312 GLU cc_start: 0.7568 (pt0) cc_final: 0.7317 (pt0)
REVERT: F  244 ASP cc_start: 0.6776 (OUTLIER) cc_final: 0.6505 (p0)
REVERT: G   54 PHE cc_start: 0.8122 (m-80) cc_final: 0.6612 (t80)
REVERT: G  104 TRP cc_start: 0.8166 (p-90) cc_final: 0.7933 (p-90)
REVERT: G  312 GLU cc_start: 0.7983 (pt0) cc_final: 0.7637 (pt0)
REVERT: G  354 GLU cc_start: 0.8065 (pp20) cc_final: 0.7808 (pt0)
  outliers start: 41
  outliers final: 34
  residues processed: 277
  average time/residue: 0.1197
  time to fit residues: 52.5723
Evaluate side-chains
  270 residues out of total 1904 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 233
  time to evaluate  : 0.635 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   17 LEU
Chi-restraints excluded: chain A residue  235 TYR
Chi-restraints excluded: chain A residue  297 MET
Chi-restraints excluded: chain A residue  310 VAL
Chi-restraints excluded: chain A residue  341 VAL
Chi-restraints excluded: chain B residue   70 THR
Chi-restraints excluded: chain B residue   80 VAL
Chi-restraints excluded: chain B residue  235 TYR
Chi-restraints excluded: chain B residue  238 SER
Chi-restraints excluded: chain B residue  341 VAL
Chi-restraints excluded: chain C residue   17 LEU
Chi-restraints excluded: chain C residue   70 THR
Chi-restraints excluded: chain C residue  235 TYR
Chi-restraints excluded: chain C residue  244 ASP
Chi-restraints excluded: chain C residue  341 VAL
Chi-restraints excluded: chain D residue   80 VAL
Chi-restraints excluded: chain D residue  151 ASN
Chi-restraints excluded: chain D residue  235 TYR
Chi-restraints excluded: chain D residue  238 SER
Chi-restraints excluded: chain D residue  341 VAL
Chi-restraints excluded: chain E residue   17 LEU
Chi-restraints excluded: chain E residue   70 THR
Chi-restraints excluded: chain E residue   80 VAL
Chi-restraints excluded: chain E residue  235 TYR
Chi-restraints excluded: chain E residue  238 SER
Chi-restraints excluded: chain E residue  341 VAL
Chi-restraints excluded: chain F residue   17 LEU
Chi-restraints excluded: chain F residue   34 VAL
Chi-restraints excluded: chain F residue  198 VAL
Chi-restraints excluded: chain F residue  235 TYR
Chi-restraints excluded: chain F residue  244 ASP
Chi-restraints excluded: chain F residue  341 VAL
Chi-restraints excluded: chain G residue   80 VAL
Chi-restraints excluded: chain G residue  198 VAL
Chi-restraints excluded: chain G residue  235 TYR
Chi-restraints excluded: chain G residue  238 SER
Chi-restraints excluded: chain G residue  341 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 203
   random chunks:
   chunk 96 optimal weight:    8.9990
   chunk 2 optimal weight:    6.9990
   chunk 106 optimal weight:    7.9990
   chunk 125 optimal weight:    3.9990
   chunk 68 optimal weight:    1.9990
   chunk 179 optimal weight:    0.0000
   chunk 94 optimal weight:    8.9990
   chunk 105 optimal weight:    2.9990
   chunk 133 optimal weight:    1.9990
   chunk 197 optimal weight:    2.9990
   chunk 118 optimal weight:    5.9990
   overall best weight:    1.9992

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

Flipped N/Q/H residues before XYZ refinement:
B 266 GLN
D  63 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3584 r_free = 0.3584 target = 0.124083 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3283 r_free = 0.3283 target = 0.102435 restraints weight = 27205.570|
|-----------------------------------------------------------------------------|
r_work (start): 0.3256 rms_B_bonded: 2.45
r_work: 0.3143 rms_B_bonded: 3.03 restraints_weight: 0.5000
r_work (final): 0.3143
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8296
moved from start:          0.2200

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.055  16954  Z= 0.153
  Angle     :  0.621   7.767  23170  Z= 0.321
  Chirality :  0.042   0.217   2793
  Planarity :  0.004   0.038   2793
  Dihedral  :  4.728  24.579   2240
  Min Nonbonded Distance : 2.566

Molprobity Statistics.
  All-atom Clashscore : 5.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.71 %
    Favored  : 92.29 %
  Rotamer:
    Outliers :  2.56 %
    Allowed  : 21.79 %
    Favored  : 75.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.41 (0.20), residues: 2037
  helix:  2.19 (0.15), residues: 1295
  sheet:  None (None), residues: 0
  loop : -3.53 (0.21), residues: 742

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG D 152 
 TYR   0.016   0.001   TYR D 150 
 PHE   0.010   0.001   PHE G 126 
 TRP   0.018   0.002   TRP E 104 
 HIS   0.003   0.001   HIS F 330 

Details of bonding type rmsd
  covalent geometry    : bond        0.00366 (16940)
  covalent geometry    : angle       0.62093 (23142)
  SS BOND              : bond        0.00118 (   14)
  SS BOND              : angle       0.65094 (   28)
  hydrogen bonds       : bond        0.05413 ( 1022)
  hydrogen bonds       : angle       4.30244 ( 3024)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3662.17 seconds
wall clock time: 63 minutes 33.53 seconds (3813.53 seconds total)